DNA IN FORENSICS 2012

“EXPLORING THE PHYLOGENIES”

5th EMPOP Meeting

8th Y-Chromosomal User Workshop

Innsbruck, Sep 06-08 2012

Abstract book &

Conference program
 DNA in Forensics 2012, Sep 06-08 2012
5th International EMPOP Meeting 8th International Forensic Y-User Workshop

Dear friends, colleagues and guests,

The fields of mitochondrial (mt)DNA and Y chromosome analysis enjoy fruitful

development as witnessed by the growing scientific contributions in different genetic disciplines.
An important basis for guiding research and exchange of ideas are international meetings.

We welcome you to DNA in Forensics 2012 in Innsbruck. The motto of this meeting is
Exploring the Phylogenies. Haploid markers are inherited along a phylogeny and therefore left
genetic footprints in modern populations. The incisiveness of the picture depends on the history of
populations and their migration. Forensic scientists are taking advantage of the derived patterns in
their daily work, e.g. by assigning geographical landscapes to lineages or by performing quality
control of datasets. We have received very interesting contributions from the forensic, population
and medical genetic fields and look forward to their presentations and vivid discussions.

We wish all participants some beautiful days in Innsbruck!

Sincerely,

Walther Parson and Lutz Roewer

We gratefully acknowledge our Industry partners – Life Technologies / Applied Biosystems,

Promega, QIAGEN, Abbott, Qualitype - and Sponsors – Unilab Laboratory Equipment, Bartelt
GmbH, Biotype Diagnostics and Fischerlehner + Kutschera Handelsgesellschaft m.b.H.

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 DNA in Forensics 2012, Sep 06-08 2012
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AGENDA

Thursday, Sep 06
10h00 - 14h00 Registration

14h00 - 14h30 Welcome

Richard Scheithauer (Innsbruck, Austria)

Mechthild Prinz (New York, USA)

Lutz Roewer (Berlin, Germany)

Walther Parson (Innsbruck, Austria)

Session I: Forensic aspects of the mitochondrial phylogeny

Chair person: Walther Parson

14h30 - 15h00 Haplogrouping and phylogenetic analysis of mtDNA profiles

Hans-Jürgen Bandelt (Hamburg, Germany)

15h00 - 15h30 A ‘‘Copernican’’ reassessment of the human mitochondrial DNA tree

from its root
Doron M Behar, van Oven M, Rosset S Metspalu M Loogväli E-L, Silva NM,
Kivisild T, Torroni A, Villems R (Haifa, Israel)

15h30 - 15h45 PhyloTree - growing and refining the human mitochondrial DNA tree
Mannis van Oven (Rotterdam, Netherlands)

15h45 - 16h00 The EMPOP concept for reporting mtDNA haplogroups in forensic
genetics
Alexander W Röck, Dür A, Parson W (Innsbruck, Austria)

16h00 - 16h15 Improved visibility of character conflicts in quasi-median networks

Bettina Zimmermann, Hiltpolt B, Röck AW, Dür A, Parson W (Innsbruck,
Austria)

16h15 - 16h30 Evaluating mtDNA profiles: Even the smallest difference has a size
Stijn Desmyter, Parson W (Brussels, Belgium)

16h30 - 17h00 Coffee break

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Session II: Applications of mtDNA analysis

Chair person: Lourdes Prieto

17h00 - 17h15 Linguistic isolates in Portugal: insights from the mitochondrial DNA
pattern
Quim Mairal, Santos C, Prata M, Aluja M, Alvarez L (Barcelona, Spain)

17h15 -17h30 Genetic microdifferentiation patterns in the mitochondrial DNA pool of

Asturias (Northern Spain)
Antonio F. Pardinas, Garcia-Vazquez E, Roca A, Lopez B (Oviedo, Spain)

17h30 - 17h45 A detailed phylogeny of rare mitochondrial DNA haplogroups from

negrito populations of Southeast Asia
Phillip L. Endicott (Paris, France)

17h45 - 18h00 Regional sampling connects population genetics with forensics – an

example from South America
Martin Bodner, Perego UA, Huber G, Fendt L, Röck AW,Zimmermann B,
Olivieri A, Gómez-Carballa A, Lancioni H, Angerhofer N, Bobillo MC,
Corach D, Woodward S, Salas A, Achilli A, Torroni A, Bandelt H-J,
Parson W (Innsbruck, Austria)

18h00 - 18h15 Genetic discovery of early medieval human skeletal remains based on
gender and mtDNA data
Christiane M Bauer, Niederstätter H, Mayr-Eduardoff MA, Berger C,
Huber G, Stadler H, Parson (Innsbruck, Austria)

18h15 - 18h30 Forensic science applied on prehistoric remains - a nine fold burial of the
4th millennium BC raised questions about kinship, locality, and
circumstances of death
Sarah Karimnia, Schlenker B, Stecher M, Bauer CM, Niederstätter H,
Parson W, Friederich S, Meller H, Alt K (Mainz, Germany)

18h30 - 18h45 Different mutational spectra of complete mitochondrial genomes of

normal and colorectal cancer cells.
Katarzyna Skonieczna, Malyarchuk B, Jawien A, Marszalek A,
Grzybowski T (Bydgoszcz, Poland)

18h45 - 19h00 MtDNA haplogroups and sudden infant death syndrome

Stephan Köhnemann, Schumann S, GeSID group,
Pfeiffer H (Münster, Germany)

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Friday, Sep 07

Session III: Updating the Y chromosome phylogeny

Chair person: Lutz Roewer

09h00 - 09h30 Y-chromosomal insights from large-scale resequencing

Chris Tyler Smith (Cambridge, United Kingdom)

09h30 - 09h45 A calibrated human Y-chromosomal phylogeny based on resequencing

Wei Wei, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y,
Tyler-Smith C (Cambridge, United Kingdom)

09h45 - 10h00 Insight into human Y chromosome variation from low-coverage

whole-genome resequencing data
Yali Xue, Chen Y, McCarthy S, Ayub Q, Jostins L, Durbin R,
Tyler-Smith C (Cambridge, United Kingdom)

10h00 - 10h15 Determining the phylogenetic position of Y-chromosomes based on

whole genome SNP calling
Anneleen van Geystelen, Decorte R, Larmuseau MHD (Leuven, Belgium)

10h15 - 10h30 Increasing phylogenetic resolution still informative for Y-chromosomal

studies on West-European populations
Marten HD Larmuseau, Vanderheyden N, Van Oven M, Kayser M,
Decorte R (Leuven, Belgium)

10h30 - 10h45 Multiple recurrent mutations at four Y-chromosomal single nucleotide

polymorphism sites in a 37 bp sequence tract on the ARSDP1
pseudogene
Harald Niederstätter, Berger B, Erhart D, Gassner C, Schennach H,
Parson W (Innsbruck, Austria)

10h45 - 11h00 Mapping the evolving Y-SNP phylogeny for building consistent Y-SNP
databases
Sascha Willuweit, Roewer L, Niederstätter H, Geppert M (Berlin, Germany)

11h00 - 11h15 Discussion (Mod. Sascha Willuweit)

11h15 - 11h45 Coffee break

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Session IV: Applications of the Y chromosome phylogenetic approach

Chair person: Daniel Corach

11h45 - 12h00 Continent-wide decoupling of Y-chromosomal genetic variation from

language and geography in native South Americans
Michael Nothnagel, Roewer L, Gusmão L, Gomes V, González M, Corach D,
Sala A, Alechine E, Palha T, Santos N, Ribeiro-dos-Santos A, Geppert M,
Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B,
González-Andrade F, Fagundes de Carvalho E, Aparecida da Silva D,
Jose Builes J, Turbon D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U,
Borjas L, Barletta C, Ewart E, Santos S, Krawczak M (Kiel, Germany)

12h00 - 12h15 Identification of a novel Native American Y chromosome founding

lineage in Northwest South America
Lutz Roewer, Nothnagel M, Gusmão L, Gomes V, González M, Corach D,
Sala A, Alechine E, Palha T, Santos N, Ribeiro-dos-Santos A, Geppert M,
Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B,
González-Andrade F, Fagundes de Carvalho E, Aparecida da Silva D,
Jose Builes J, Turbon D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U,
Borjas L, Barletta C, Ewart E, Santos S, Krawczak M (Berlin, Germany)

12h15 - 12h30 Y-haplogrouping among ethnic minority groups in South America

Toshimichi Yamamoto, Sakuma M, Kawaguchi Y, Kano Y, Danjoh I,
Nakamura Y (Nagoya, Japan)

12h30 - 12h45 Evaluating social and ethical issues in Argentinean population by genetic
marker analysis
Daniel Corach, Alechine E, Caputo M (Buenos Aires, Argentina)

12h45 - 14h00 Break

14h00 - 14h15 Tracking the Iceman’s scent by high resolution mapping of

Y haplogroup G in Tyrol (Austria)
Burkhard Berger, Niederstätter H, Erhart D, Gassner C, Schennach H,
Parson W (Innsbruck, Austria)

14h15 -14h30 Beyond the migration: the Basque diaspora in the western USA
Laura Valverde, Rosique M, García A, Köhnemann S, Cardoso S,
Odriozola A, Pfeiffer H, M de Pancorbo M (Vitoria-Gasteiz, Spain)

14h30 - 14h45 The history of Slavs in the light of Y chromosome and mtDNA variability
Mielnik - Sikorska M, Daca P, Marcin Woźniak, Malyarchuk BA,
Derenko MV, Skonieczna K, Grzybowski T (Bydgoszcz, Poland)

14h45 - 15h00 Y-chromosomal STR analysis in Pashtun populations from Southern

Afghanistan
Niaz Muhammad Achakzai (Lahore, Pakistan)

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15h00 - 15h15 Y-chromosomal phylogeny of Porja and Savara Lineages in Andhra

Pradesh, India
Rao A. Isukapatla, Pulamaghatta NV, PBSV P, Adimoolam C (Mysore, India)

15h15 - 15h30 Migration distance rather than migration rate explains genetic diversity
in patrilocal groups
Levy H, Conrado M, Montinaro F, Cristian Capelli
(Oxford, United Kingdom)

15h30 - 16h00 Coffee break

Session V: Next generation Y-STRs

Chair person: Manfred Kayser

16h00 - 16h30 Rapidly mutating Y-chromosomal STRs

Manfred Kayser, Ballantyne K, Ralf A on behalf of the RM Y-STR Study
Group (Rotterdam, Netherlands)

16h30 - 16h45 Development criteria for a next generation Y-STR multiplex for forensic
applications
Christina Bormann Chung, Mulero J, Nguyen V, Calandro L, Hennessy L
(Foster City, USA)

16h45 - 17h00 The PowerPlex® Y23 System: a single system for casework and
database (direct amplification) Y-STR analysis
Thompson JM, Ewing MM, Fulmer PM, Rabbach DR, Sprecher CJ,
Douglas R. Storts (Madison, USA)

17h00 - 17h15 Y-Chromosome specific nested PCR pre-amplification method for

improved detection of male DNA
Erin Hanson, Solivan M, Strauss S, Di Pasquale F, Engel H, Ballantyne J
(Hilden, Germany); presented by Scherer M

17h15 - 18h15 Panel discussion with companies and researchers (Manfred Kayser, Chris
Tyler-Smith; Life Technologies, Promega, Qiagen;
Chair person: Lutz Roewer)

Social Evening
Sponsoring Life Technologies

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Saturday, Sep 08

Session VI: New technologies in haploid marker analysis

Chair person: Peter de Knijff

09h00 - 09h30 mt-GoNL: deep sequencing of 750+ complete Dutch mtDNA genomes
Peter de Knijff, Vermaat M, Li M, van Oven M, de Dunnen JT, Stoneking M,
Kayser M, Laros J (Leiden, Netherlands)

09h30 - 09h45 Applications of Personal Genome Machine (PGM™) in SNP-based

human identification
Sharon C Wootton, Langit R, Lagacé R, Hennessy L (Foster City, USA)

09h45 - 10h00 Next generation mtGenome sequencing for forensic purposes using the
Ion Torrent PGM
Strobl C, Huber G, Lagace R, Langit R, Wootton S, Hennessy L,
Walther Parson (Innsbruck, Austria)

10h00 - 10h15 The impact of PCR and DNA sequencing artifacts in 454 LifeScience
data on the interpretation of mtDNA heteroplasmy
Mitchell M Holland (State College, USA)

10h15 - 10h30 Weighing the differences: the application of mass-spectrometry for

mtDNA control region analysis
Mayra Mayr-Eduardoff, Huber G, Zimmermann B, Bayer B, Schmid D,
Anslinger K, Göbel T, Niederstätter N, Schneider PM, Röck AW, Parson W
(Innsbruck, Austria)

10h30 - 11h00 Coffee break

Session VII: Biostatistics of lineage markers

Chair person: Michael Krawczak

11h00 - 11h15 Interpretation of lineage markers

Bruce S Weir, Aalbers S (Seattle, USA)

11h15 - 11h35 Evidentiary strength of a rare haplotype match

Charles H Brenner (Oakland, USA)

11h35 - 11h55 Estimating trace-suspect match probabilities for singleton Y-STRs

haplotypes using coalescence theory
Mikkel M Andersen, Caliebe A, Jochens A, Willuweit S, Krawczak M
(Aalborg, Denmark)

11h55 - 12h30 Discussion

12h30 - 12h45 Y-STR mutations: what paternity cases can tell us about the relationship
between allele length and mutation rate
Arne Jochens, Caliebe A, Roesler U, Krawczak M (Kiel, Germany)

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12h45 - 13h00 Testing Y-chromosome STR mutation rates using deep-rooting pedigrees
Johannes C Erasmus (Pretoria, South Africa)

13h00 - 13h15 Analysis of mutation rates in purported brother pairs with 17 Y-STR loci
SM Edson, Maynard L Kerry (Dover AFB, USA)

13h15 - 13h30 Searching for dependencies between mitochondrial and Y-chromosome

DNA markers
Paulina Wolanska-Nowak (Krakow, Poland)

13h30 - 13h45 Mine, yours, ours? sharing data on human genetic variation
Giovanni Destro Bisol, Anagnostou P, Capocasa M, Congiu A, Milia N,
Montinaro F, Sanna E (Rome, Italy)

14h00 Closing of Meeting

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Posters
Poster Sessions are held during all coffee breaks

Thursday: 16h30 - 17h00

Friday: 11h15 - 11h45 and 15h30 -16h00
Saturday: 10h30 - 11h00

mtDNA Phylogeny
P1 mtDNA haplogroup F1a’c is a genetic risk factor for nasopharyngeal carcinoma in
Chaoshanese
Du J, Deng J, Yao Y, Lin K, Chen S, Hu S*

P2 Mitochondrial DNA polymorphism and matrilineal genetic composition of Chaoshan

population in China
Hu S*, Deng J, Feng G, Du J, Chen S

P3 Insights into South-American colonization through mtDNA analysis in native

Colombian populations
Xavier C, Builles J, Gomes V, Ospino JM, Amorim A, Gusmao L, Goios A*

P4 Comparative mitochondrial DNA analyses in Myanmar and the distinct genetic

position of the Karen people within this multi-ethnic population
Summerer M, Horst J, Erhart G, Horst D, Horst B, Sanguansermsri T, Manhart A,
Kronenberg F, Kloss-Brandstätter A*

P5 Multiplex mutagenically separated PCR assays for simple and rapid screening of East
Asian mtDNA haplogroups on forensic samples
Kim E, Lee H, Yoon J, Yang W, Shin K*

P6 Mitochondrial DNA data of five Philippine Negrito populations

Tabbada KA, Salvador JM, Delfin FC, De Ungria MA*

P7 An approach to Equatorial Guinea demographic genetic history through maternal

lineage analysis
Valente C*, Alvarez L, López-Parra AM, Parson W, Amorim A, Prata M, Arroyo-Pardo E,
Gusmão L

P8 Mitochondrial DNA data of Cabo Verde immigrant population living in Lisboa

Afonso Costa H*, Morais P, Amorim A, Vieira Silva C, Matos S, Marques Santos R,
Espinheira R, Costa Santos J

P9 Dissection of mitochondrial DNA haplogroup L3b and its forensic applications

Pasino S*, Del Pero M, Santovito A, Robino C

P 10 Refined characterization of Portuguese mtDNA variability for forensic purposes

Rocha A, Goios A, Amorim A, Gusmao L, Alves C*

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P 11 MtDNA haplogroup distribution in Finland

Putkonen M*, Neuvonen A, Hedman M, Palo JU

P 12 Optimization and validation of a mitochondrial DNA assay in a German population

sample and application to highly degraded DNA
Zander J, Rothe J, Roewer L, Nagy M*

P 13 MtDNA analysis of Mocoví population, southern most Guaycurú speakers in South

America
Sala A*, Martí MC, Bobillo MC, Corach D

P 14 A very high level of Native American ancestry in an Amazon, Brazil, urban

population inferred by mitochondrial DNA and indels markers analysis
Hermida RM, Manta FS, Silva DA, Carvalho-Costa FA, Monteiro M, Moraes MO,
Carvalho EF*

P 15 Mitochondrial control region sequences of the Czech Republic population and a

comparison to other populations
Vanek D*, Silerova M, Urbanova V, Saskova L, Dubska J

P 16 Insertion/delection polymorphisms in South Portugal Caucasian population: a

preliminary study
Vieira Silva C*, Matos S, Amorim A, Afonso Costa H, Morais P, Marques Santos R,
Espinheira R, Costa Santos J

Y-chromosomal Phylogeny
P 17 Internal validation of the AmpFlSTR Yfiler amplification kit and calculation of the
genetic diversity of 17 Y-short tandem repeats in the Norwegian population
Hellerud BB*, Lønning L, Heitmann I, Hansen EN

P 18 Y chromosome diversity in the South and East Kazakhstan

Tarlykov P*, Zholdybayeva E, Ramanculov E

P 19 Genetic structure of the Y chromosome does not suggest intraregional sex-biased

dispersals in the population of Asturias (Northern Spain)
Cano-Garcia C, Pardinas A, Garcia-Vazquez E, Roca A, Lopez B*

P 20 Y-STR haplotypes and the genetic structure of Pathan populations in FATA and
NWFP of Pakistan
Lee H, Sim J, Choi A, Rakha A, Yang W, Shin K*

P 21 Development of six-SNPs assay for forensic analysis in European population

Ferri G*, Ferrari F, Corradini B, Santunione A, Alù M

P 22 Genetic journey of the N1c haplogroup

Pamjav H*, Nemeth E, Feher T, Volgyi A

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P 23 Phylogeographic analysis of human Y chromosome diversity in eastern Africa

Cruciani F*, Ippoliti M, Massaia A, D'Atanasio E, Moral P, Coppa A, Trombetta B,
Sellitto D, Pascone R, Scozzari R

P 24 Y-chromosome variation in geographically and linguistically isolated populations

from oriental Alps
Coia V*, Capocasa M, Scarnicci F, Boschi I, Anagnostou P, Battaggia C, Crivellaro F,
Ferri G, Brisighelli F, Busby G, Capelli C, Destro-Bisol G

P 25 Haplotype analysis of 23 polymorphic Y-STR markers in Northwest of Argentina

López-Parra AM*, Mesa M, Brabo Ferreira Palha Td, Gusmão L, Lomaglio DB, Baeza C,
García M, Marrodán M, Pacheco JL, Bejarano IF, Dip NB, Baillet G, Arroyo-Pardo E,
Dipierri JE, dos Santos SE, Ribeiro dos Santos K

P 26 Y chromosome DNA variation monitored in Slovakian populations by SNP and STR

analysis
Carnogurska J*

P 27 Y chromosome diversity in Piedmont

Caratti S*, Di Gaetano C, Matullo G, Gino S, Inturri S, Robino C

P 28 Genetic analysis of 17 Y-STR loci in Pashtun population from Swat Valley, Pakistan
Achakzai NM*

P 29 Novel Y chromosome polymorphisms in Native American haplogroup Q1a3a1

Alechine E, Corach D*

P 30 Population data for 8 Y-chromosomal STRs (not included in Y-filer™ kit) in a

population sample of Czech Republic
Vanek D*, Saskova L, Silerova M, Dubska J

P 31 Y-STR haplotype diversity of a native population of Cabo Verde living in Lisboa

Marques Santos R*, Amorim A, Afonso Costa H, Vieira Silva C, Morais P, Matos S,
Espinheira R, Costa Santos J

P 32 Y-chromosomal STRs mutation analysis by the PowerPlex® Y23 system

Ceccardi S, Riccardi LN, Fersini F, Lanzellotto R, Falconi M, Bini C*, Pelotti S

Comparative mtDNA/Y-chromosomal Phylogeny

P 33 Determination of the Y chromosome DNA haplotype and mtDNA haplotype from 50

males from 17 countries
Takasaka T*

P 34 Forensic efficiency of combined Y/mt profiles in seven Iranian groups

Bertoncini S, Farjadian S, Taglioli L, Ghaderi A, Romeo G, Luiselli D, Tofanelli S*

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P 35 Ancestry evaluation of Rio de Janeiro population by screening the Y chromosome

and mitochondrial DNA
Oliveira AM, Hermida RM, Silva DA, Gusmao L, Carvalho EF*

P 36 Haploid markers in DNA identification process in Croatia

Furač I*, Karija Vlahović M, Mašić M, Kubat M, Strinović D

Ancient DNA

P 37 Forensic science applied on prehistoric remains - a nine fold burial of the 4th
millennium BC raised questions about kinship, locality, and circumstances of death
Friederich S*, Schlenker B, Stecher M, Bauer C, Niederstätter H, Parson W, Karimnia S,
Meller H, Alt K

P 38 Establishment of mitochondrial SNPs for the investigation of skeletal material buried

in the ground
Thiele K*, Pflugbeil A, Kohl M, Bruchhaus H, Dressler J

P 39 Huns in Bavaria? Genetic analyses of an artificially deformed skull from an early

medieval cemetery in Burgweinting (Regensburg, Germany)
Schleuder R*, Wilde S, Burger J, Grupe G, Forster P, Harbeck M

P 40 Y-chromosomal analysis of skeletal remains of a Swiss national hero from the 17th
century
Haas C*, Shved N, Rühli F, Papageorgopoulou C, Krawczak M, Willuweit S, Purps J,
Roewer L

P 41 Assessment of the origins of ancient Croatian remains through mitochondrial DNA

interpretation
Phillips LA, Fox A, Primorac D*, Holland M

P 42 Genetic relationship between modern populations and the Neolithic Tyrolean Iceman
Coia V*, Cipollini G, Maixner F, Brisighelli F, Capelli C, Battaggia C, Destro Bisol G,
Zink A

P 43 Molecular genetic analyses of skeleton excavated from Auersperg Chapel

archaeological site in Slovenia
Pajnič IZ*, Pogorelc BG, Balažic J, Horvat M

P 44 DNA analysis of lineage markers (mtDNA and Y-chromosomal STRs) on ancient or

aged bone samples
Vanek D*, Saskova L, Urbanova V, Dubska J, Silerova M, Beran M

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Short Tandem Repeat polymorphisms

P 45 Forensic genetic analysis for the AmpFlSTR Yfiler system in the Korean population
Kim S, Kim K, Han M, Kim W*

P 46 Genetic polymorphisms of 19 STR Loci in the Chaoshan Han population

Shang J, Hu S*, Chen S
P 47 Central Croatian population data of eight X-linked markers in four linkage groups
Gršković B*, Mršić G, Zidkova A, Vrdoljak A, Stenzl V, Popović M, Primorac D

Non human mtDNA

P 48 Canine mitochondrial genome sequencing to improve the genetic profiling of dog hair
Verscheure S*, Desmyter S, Backeljau T

P 49 Is the Indian Wild Boar an evolutionary significant unit? Molecular insight into
phylogeny of the Wild Boars and Domestic Pig
Gupta S*, Hussain S, Singh L

New Technologies

P 50 Investigator Plus – fast, sensitive and robust amplification of common standard set
loci
Prochnow A*, Scherer M, Steeger B, Pakulla S, Breitbach M, Cornelius S, Fischer C,
Bochmann L, Schnibbe T, Engel H

P 51 How to improve STR analysis using a novel quantification technology: more than
DNA quantification
Di Pasquale F, Cornelius S, König M, Bochmann L, Prochnow A*, Schnibbe T, Engel H

P 52 Improving DNA sensitivity and strengthen reliability with low-level DNA testing
using trace amount of metal
Honda K*, Nishi T, Iwabuchi Y

P 53 Sample lysis and DNA separation in single tube assemblies for accurate forensic
profiling
Schnerr H*

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Statistics

P 54 Estimating forensic match probabilities for Y-STRs using a new, discrete Laplace
distribution
Andersen MM*, Eriksen PS, Morling N

P 55 Evaluation of the use of software as a tool in checking mitochondrial DNA HVI and
HVII sequences analysis
Funabashi K, Godoy C, Sousa M, Iwamura E*

P 56 The effect of sample size on the estimates of mtDNA genetic diversity parameters in
isolated European populations
Anagnostou P*, Capocasa M, Montinaro F, Coia V, Destro-Bisol G

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P 57 Genes, mountains and culture: evidence for the impact of ethnicity on the structure of
human populations
Capocasa M*, Battaggia C, Anagnostou P, Montinaro F, Arena A, Boschi I, Brisighelli F,
Capelli C, Coia V, Rufo F, Crivellaro F, Destro Bisol G

P 58 Critique of the haplotype surveying method

Brenner CH*

P 59 Evaluation of haplogroup predicting softwares

Caputo M, Bobillo MC, Alechine E, Sala A, Corach D*

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Oral Presentations

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Haplogrouping and phylogenetic analysis of mtDNA profiles

Bandelt H-J1,*
1
Department of Mathematics, University of Hamburg, Hamburg, Germany

Phylogenetic principles are fundamental to genetic research and forensic case studies of mtDNA.
Web resources and analytical tools for assessing phylogenetic relationships exist in abundance,
which may seduce the user to regard this enterprise as a merely automatic procedure. In particular,
haplogrouping of mtDNA in forensics has often been treated as a black box into which
control-region data are fed and correct haplogroup assignments are returned. In reality,
haplogrouping is part of a basal phylogenetic analysis with deficient information (mtDNA control
region). Since most available programs suffer from several shortcomings, the user cannot rely on
such tools without performing additional database searches and own phylogenetic analyses. The
fine-classification of region-specific lineages not yet covered by PhyloTree can constitute a further
challenge. Then supplementary sequencing of selected entire mtDNA genomes by high-throughput
sequencing is a valuable strategy. However, the forensic field should avoid pitfalls that have
occurred in molecular anthropology with most previously published data, which were
automatically generated on Illumina platforms but without the necessary manual a posteriori
analysis. Quasi-median networks, representing the duals of data tables, play a useful role in
exploratory data analysis of mtDNA sequences. Since (full) quasi-median networks of total
mtDNA data sets are often far too lage for visualization, one usually has to resort to either
mutation-filtered data for focussing on potential sequencing artifacts or to sample-skimmed data
for focussing on problematic parts of estimated mtDNA trees. Another option will be thinning of a
quasi-median network by systematically removing highly ambiguous portions of the network,
thereby modifying an earlier concept of "pruned median network".

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A ‘‘Copernican’’ reassessment of the human mitochondrial DNA tree from its root
Behar DM1,2,*, van Oven M3, Rosset S4, Metspalu M1, Loogväli E1, Silva NM5, Kivisild T1,6, Torroni A7, Villems R1
1
Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
2
Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel
3
Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam,
Netherlands
4
Department of Statistics and Operations Research, School of Mathematical Sciences, Tel Aviv University, Tel Aviv,
Israel
5
Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
6
Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of
Cambridge, Cambridge, United Kingdom
7
Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy

The principle of nested hierarchy is fundamental in our phylogenetic interpretation of the Tree of
Life. At the gene level, this means that all polymorphisms known in any given genetic loci
contribute to its ever-evolving phylogeny as reflected by their sequential accumulation in a tangled
ancestry-descendant relations since the time of the most recent common ancestor (MRCA).
Accordingly, the reconstructed ancestral sequence - the root - of any genetic locus should also
serve as the reference point for its respective phylogeny. Hence, the use of an arbitrary chosen
reference sequence within a rooted phylogeny leads to an inevitable conceptual clash between its
nomenclature scheme and very essence. The Human mitochondrial DNA (mtDNA) phylogeny is a
molecular evolution prototype of a haploid nonrecombining genetic locus, and knowledge about its
variation has been extensively used in population genetic, medical, genealogical and forensic
studies. Yet, all mutations comprising it were traditionally identified relative to the rCRS, a
recently derived reference sequence, creating an obvious inconsistency when compared to their
actual accumulation throughout the course of evolution. Recently, we have proposed switching to a
Reconstructed Sapiens Reference Sequence (RSRS) as the only phylogenetically valid reference.
The established Human mtDNA phylogeny root and the available H. Neanderthalensis complete
mtDNA sequences allowed us to set the RSRS with confidence, avoiding frequent
misunderstandings and direct errors resulting from the highly arbitrary nature of the used hitherto
reference, thus, establishing an intellectual cohesiveness with the current consensus of shared
common ancestry of all contemporary human mitochondrial genomes. To facilitate data transition,
the website www.mtdnacommunity.org was established and is committed to the support of the
"Copernican" reassessment of the human mtDNA phylogeny and to the establishment of
computational tools meant to facilitate phylogenetic analysis and comparison of complete mtDNA
sequences. The website allow an easy transition from an rCRS to an RSRS based nomenclature,
automatically labels haplogroups, performs a phylogeny based quality check, identifies private
substitutions, and compares new sequences with previously stored mitogenomes to suggest the
labelling of additional haplogroups.

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PhyloTree - growing and refining the human mitochondrial DNA tree

van Oven M1,*
1
Forensic Molecular Biology; Erasmus MC - University Medical Center, Rotterdam, Netherlands

PhyloTree (http://www.phylotree.org) provides an up-to-date phylogeny of human mitochondrial

DNA [1], and is now widely used by the forensic, population-genetic and medical research
communities. Since its inception in August 2008, PhyloTree has been updated 13 times and the
number of labeled nodes (haplogroups) has increased from 1,194 in Build 1 to 3,372 in Build 14,
representing an almost threefold resolution gain. The tree is inferred from all available complete
mtDNA sequences from the literature (numbering 15,451 as of May 1, 2012) following the
principle of maximum parsimony. Haplogroup nomenclature follows the literature as much as
possible and is extended where needed; in a number of cases, however, haplogroup nomenclature
was revised such as in haplogroup M9 [2].One of the main applications of PhyloTree is haplogroup
assignment and several tools for automated haplogrouping have adopted PhyloTree as the
underlying classification tree (e.g. HaploGrep, mthap, HmtDB). Furthermore, the tree facilitates
the selection of suitable SNPs for multiplex genotyping tools [e.g. 3].Recently, the inferred
mtDNA root sequence, the RSRS, was proposed as an evolutionary more valid reference sequence
than the rCRS [4]. Concomitantly, in Build 14, the way of denoting mutations was adjusted to
include the ancestral and derived alleles relative to the root. As this caused some inconvenience for
those used to the 'original' mutation notation, an rCRS-oriented version of PhyloTree is still
available in parallel.

1. van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human
mitochondrial DNA variation. Hum Mutat 30(2):E386-E394.

2. van Oven M (2010) Revision of the mtDNA tree and corresponding haplogroup nomenclature.
Proc Natl Acad Sci U S A 107(11):E38-E39.

3. van Oven M, Vermeulen M, Kayser M (2011) Multiplex genotyping system for efficient
inference of matrilineal genetic ancestry with continental resolution. Investig Genet 2:6.

4. Behar DM, van Oven M, Rosset S, Metspalu M, Loogväli EL, Silva NM, Kivisild T, Torroni A,
Villems R (2012) A "Copernican" reassessment of the human mitochondrial DNA tree from its
root. Am J Hum Genet 90(4):675-684.

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The EMPOP concept for reporting mtDNA haplogroups in forensic genetics

Röck AW1, Dür A2, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Institute of Mathematics, University of Innsbruck, Innsbruck, Austria

Human mitochondrial DNA (mtDNA) has proven to be a valuable resource in forensics and
population genetics. Increased availability of mtDNA data enables a deeper understanding of the
mitochondrial phylogeny. It has been shown that the assignment of haplogroups to individual
samples may be helpful to both understand the phylogeny and aid the detection of idiosyncrasies in
mtDNA data. A curated, standardized and continuously updated phylogenetic tree is available to
the community via Phylotree.org, however, current software solutions for assigning haplogroup
information to mtDNA sequences do not specifically target forensic needs. Furthermore,
haplogrouping that is solely based on a phylogenetic tree suffers from accurateness or the absence
of highly recurrent mutations that are often neglected in the phylogenetic tree. We here present an
approach tailored to particular needs of forensic genetics. Combining the alignment-independent
search engine SAM of EMPOP with high-quality haplogrouped mtDNA sequences of the database
allows for reliable haplogroup assignment of forensic samples via EMPOP. Using EMPOP as
underlying data pool in addition to a phylogenetic tree allows for incorporating the maximum
amount of information. Software-based determination of forensically relevant haplogroups
accounts for the stability needed in forensic settings. Besides an additional quality control
instrument this facilitates a more accurate assessment of the strength of evidence by providing
haplogroup distributions as additional phylogeographic information.

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Improved visibility of character conflicts in quasi-median networks

Zimmermann B1, Hiltpolt B2, Röck AW1, Dür A2, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Institute of Mathematics, University of Innsbruck, Innsbruck, Austria

Quasi-median network construction of reduced and filtered haplotypes provides a valuable tool for
graphical representation of mitochondrial DNA data (Bandelt and Dür 2007, Parson and Dür 2007,
Schwarz and Dür 2011). Errors, artefacts and ambiguities present in the data may induce character
conflicts that increase the complexity of the network, pinpointing first approaches for quality
control of data sets (Turchi et al 2007; Prieto et al 2011). However, indecipherable reticulations
due to samplesize or errors cannot be interpreted even by the trained eye.

For that reason we enhanced the editing tool of the network layout by implementing new features
and redesigned the graphical user interface. The major improvement of the new network editor
includes the possibility to highlight the induced sub graph with concurrent dimming of its
complement using mouse-over. This enables visual emphasis on substructures within a complex
network. Via mouse click on a network node a list of the included haplotypes is generated, which
allows direct inspection of the phylogenetic background. This new feature enables immediate and
simple identification and inspection of the respective haplotypes and mutations.

The new editor is demonstrated by means of population data from West Eurasia and from
East-Asia that were submitted to EMPOP (www.empop.org) for quality control. The new network
editor is available on EMPOP for registered users.

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Evaluating mtDNA profiles: Even the smallest difference has a size

Desmyter S1,*, Parson W2
1
NICC, Brussels, Belgium
2
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

The most applied way of mtDNA profile interpretation in forensics is straight forward, and hence
easy to apply in case work. When comparing profiles, two differences do exclude and equal
profiles perform a match. The intermediate situation, with only one difference between the
profiles, is considered as inconclusive. Nevertheless its simplicity, this approache neglects
completely the mutation-specific weight and can be confusing in court room. Confronted with a
single difference between mtDNA profiles in case work, extending the HV1-HV2 sequence to the
complete control region doesn’t always result in an exclusion. Further profiling of informative
positions in the coding region is for most laboratories not an option due to analytical and/or legal
limitations. Instead of reporting an mtDNA evaluation as inconclusive the DNA commission of the
ISFG and the EDNAP group proposed, already more than ten years ago, to consider the size of the
smallest difference between the profiles involved (Carracedo et al. 2000, Tully et al. 2001). On the
basis of real case work examples we will demonstrate the influence of this consideration on the
mtDNA profile interpretation. Therefore data were retrieved from the EMPOP database in its
current state, and site-specific mutation rates were used for the calculation of the likelihood ratio.

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Linguistic isolates in Portugal: insights from the mitochondrial DNA pattern

Mairal Q1, Santos C1, Prata M2,3, Aluja M1, Alvarez L2,*
1
Unitat d’Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, Barcelona, Spain
2
IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
3
Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal

The Miranda do Douro municipality, located in the northeastern region of the Portuguese territory,
has notable characteristics not only from a geographic or naturalistic point of view, but also from a
cultural perspective. One of its remarkable cultural traits is the coexistence of two different
languages: Portuguese and Mirandês, a Leonese dialect. The current persistence of the Leonese
dialect in this population falls on the singularity of the region: relative isolation implying
difficulties to communicate with other Portuguese regions and the establishment of social and
commercial relationships with adjacent Spanish territories. The objective of this study was to
characterize this population through the analysis of its maternal lineages composition to address its
phylogenetic origin in relation to other previously analysed populations in the Iberian Peninsula.
In order to accomplish this purpose, mitochondrial DNA from 121 individuals was analyzed. A
3,348 bp mtDNA fragment was amplified and sequenced in two overlapping fragments using
mitochondrial-specific primers to obtain a clear range electropherogram of the entire control
region (16,024-576 bp, according to the rCRS). Haplogroup classification was performed
following current nomenclature. The obtained results showed a haplogroup composition typically
from a Western European population, with more than half of individuals (61.2%) classified into
the macrohaplogroup R0. We also reported several lineages ascribed to an African (L2a and L1b),
Indian (M5a1) and Jewish (N1b) origin, which together account for the 10.6% of the total
variability detected. Both genetic and nucleotide diversities presented low values (0.9328 ± 0.0172
and 0.01110 ± 0.00619, respectively) when compared to its microgeographical framework. It
should be pointed out that 48% of our samples were private lineages, which let us to hypothesize
that the diversification of some of them could have occurred in the Mirandese region. The
observed pattern of mtDNA variability matches with an isolation-related hypothesis for the
survival of the Mirandese speaker population.

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Genetic microdifferentiation patterns in the mitochondrial DNA pool of Asturias (Northern

Spain)
Pardinas AF1, Garcia-Vazquez E1, Roca A1, Lopez B1,*
1
Universidad de Oviedo, Oviedo, Spain

The mitochondrial DNA composition of the autonomous community of Asturias, in Northern

Spain, has not been extensively studied. Its convoluted history, characterised by prolonged periods
of isolation, makes it an interesting target for such a research. For this purpose, full mtDNA
control region sequences were obtained from 361 volunteers with at least two generations of
Asturian maternal ancestry. Places of birth of the maternal grandmothers of the volunteers were
recorded, and sequences were grouped according to historical regions derived from ancient feudal
lordships. A SAMOVA analysis was used to define maximally-differenced population groups
based on genetic and geographic data. Results showed a significant between-group variation of
1%, without significant within-group or within-population differentiation. Such a clear genetic
structuring is striking, and was further investigated by means of BARRIER and MIGRATE
analyses. These showed the existence of two possible barriers inside the community and several
instances of asymmetric gene flow between the SAMOVA-defined groups. All this data, combined
with historical information, suggested the existence of two different processes as the cause of the
structuring: Recent external migrations in the coastal north, probably related to increased
commercial activity during the Middle Ages; and ancient isolation in the mountainous south,
probably related to the rough terrain and cultural aspects of its population.

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A detailed phylogeny of rare mitochondrial DNA haplogroups from negrito populations of

Southeast Asia
Endicott PL1,*
1
Musée de l'Homme, Paris, France

The geographic distribution and deep branching structure of the human phylogeny retains signals
for a dispersal of humans from Africa to Australia during the late Pleistocene. The presumed route
of migration was through what is now peninsular and island Southeast Asia, but at times of
reduced sea levels would have been an almost continuous land mass separated by short sea
crossings. At the time of European contact, there existed many foraging populations throughout
the region, which share a distinct phenotype of small stature, dark complexion, and tight curly
hair. These features led to them being known collectively as negritos, from the Spanish diminutive
for black. Implicit in this name is the hypothesis that they share a common evolutionary history,
representing an early substrate of humans in Southeast Asia, who have survived in isolated or
marginal environments. Phylogenetic studies of mitochondrial DNA from negrito populations
point to different axes of influence between Southeast Asia and adjoining regions. In the Westthe
Andaman Islanders are argued to have been the subject of long-term isolation after an early
settlement from South Asia, whilst the genetic diversity of those in the Philippines in the East
contains haplogroups that appear to be be autochtonous to the region as a whole.

By sequencing whole mitochondrial genomes, we obtained detailed phylogenies of rare

mitochondrial haplogroups in the Andaman and Philippine negrito populations and placed them in
a regional phylogeographic context. The branching structure of haplogroups from the Andamans
are consistent with an origin within Southeast Asia and support inferences made from nuclear
DNA for a subsequent back-migration to adjacent parts of South Asia. The haplogroups specific to
Philippine negritos, in contrast, indicate maternal connections to a population ancestral to
present-day Melanesians and Australians. By adding 25 novel sequences to a data set of over 400
Eurasian whole mitochondrial genomes, we used a Bayesian statistical approach to estimate the
dates of key nodes in the phylogeny using multiple internal calibrations. The results from this
analysis provide evidence for internal diversification of the haplogroups within Southeast Asia ~40
ka, settlement of the Andamans at approximately half this time depth, and an upper limit for a
possible back-migration to India of ~13 ka. These findings are discussed with reference to
previous studies arguing for a settlement of the Andamans up to 65 ka, and admixture between
ancestors of Philippine negritos and another species of hominin.

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Regional sampling connects population genetics with forensics – an example from South
America
Bodner M1, Perego UA2,3, Huber G1, Fendt L1, Röck AW1, Zimmermann B1, Olivieri A3, Gómez-Carballa A4, Lancioni
H5, Angerhofer N2, Bobillo MC6, Corach D6, Woodward SR2, Salas A4, Achilli A5, Torroni A3, Bandelt H-J7, Parson
W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Sorenson Molecular Genealogy Foundation, Salt Lake City, United States
3
Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
4
Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
5
Department of Cellular and Environmental Biology, University of Perugia, Perugia, Italy
6
Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos
Aires, Argentina
7
Department of Mathematics, University of Hamburg, Hamburg, Germany

For most parts of the world, the “big picture” of human dispersal conveyed by population surveys
of mitochondrial DNA (mtDNA) variation is well understood. The smaller the scale, the more
details remain to be clarified within this framework due to the lack of extensive sampling and high
quality sequencing of utmost large segments of the mitochondrial genome. With the ever growing
number of worldwide sample contributors and the advanced technologies available, a regional
concept has become realistic. By using as an example the recent discovery of two Native American
mtDNA haplogroups (D1g and D1j) whose spatial distributions are restricted to the Southern Cone
of South America, we illustrate the possibilities of regional sampling: the detailed investigation of
a restricted area or population group and the small-scale geographic and ethnic dispersal of
lineages may open a window to the past by revealing details about timing and routes of migration;
and help to understand a native group’s history. In addition to delivering a more complete coverage
of natural variation in databases, the regional concept of sampling is of highest importance in
forensic applications of mtDNA (and other markers), as rarer lineages will not only tend to be
missing in (small) countrywide samples, but local frequencies may also differ significantly from
those in a general dataset. Therefore, major regional sampling and sequencing efforts are still
mandatory for uncovering all (even the most basal) variation in mtDNA haplogroups, for
reconstructing the details of migration processes, and for yielding correct frequency estimates, by
targeting, when possible, both the general mixed population and autochthonous groups.

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Genetic discovery of early medieval human skeletal remains based on gender and mtDNA
data
Bauer CM1, Niederstätter H1, Mayr-Eduardoff MA1, Berger C1, Huber G1, Stadler H2, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Institute of Archaeologies, Innsbruck, Austria

In 2001/02 the municipal Archaeologie in Hall accomplished by order of the Institute of

Archaeologies (University of Innsbruck) successful excavations of an early Middle Age cemetery
(dated between the 6th and 12th century CE) in Volders (Tyrol), which was a major settlement
area in the Inn Valley since pre-historic times. On the basis of radiocarbon dating and grave
situations, the majority of burials are assumed to range from the late 6th to the early 7th century.
For this region and time period only scarce historical information is available. This cemetery
represents one of the largest ancient series of human remains in Tyrol and the Alpine region in
general. Of scientific interest is the burial situation in a tight area and the orientation of the
skeletons with a prevalent restriction to East-West and only few North-South directions. Because
of their excellent preservation state the historical remains lend themselves perfectly to the
application of biomolecular methods to gain increased insight for a better interpretation of the
findings. We present first comparative results of gender estimation by morphological and genetic
methods and provide an overview of mtDNA typing results using Sanger Sequencing and mass
spectrometry.

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Forensic science applied on prehistoric remains - a nine fold burial of the 4th millennium BC
raised questions about kinship, locality, and circumstances of death
Karimnia S1,*, Schlenker B2, Stecher M1, Bauer CM3, Niederstätter H3, Parson W3, Friederich S2, Meller H2, Alt K1
1
Bioarchaeometry Group, Institute of Anthropology, Johannes Gutenberg-University of Mainz, Mainz, Germany
2
Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt mit Landesmuseum für Vorgeschichte, Halle,
Germany
3
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

A monumental earth construction of the Salzmünde culture (3400-3025 BC) with 165 burials was
discovered during excavations at the eponymous site Salzmünde in Saxony-Anhalt, Germany.
Especially a multiple burial with potsherd filling that contains four adult women and five subadults
raised questions about kinship, locality and cause of death. This exceptional ninefold burial is the
matter of a transdisciplinary and integrative project combining archaeological, anthropological,
stable isotope and palaeogenetic analyses. Our aim is to shed light on the relationships of the
individuals of the ninefold burial and the circumstances that lead to the death of these people. In
order to evaluate biological kinship DNA was extracted from bone and tooth samples of seven
individuals. Mitochondrial haplotypes and haplogroups were identified by sequencing of the
hypervariable segments I and II of the control region and by analyzing 22 diagnostic coding region
single nucleotide polymorphisms. We were able to obtain reproducible endogenous DNA from all
individuals investigated. Among these seven individuals we found three different mitochondrial
lineages ascertained to distinct haplogroups suggesting maternal kinship among the individuals in
the ninefold burial. Combining the results of every discipline of the ongoing project, it is currently
not possible to define the circumstances of death. However, several burn marks on the bones of the
individuals as well as other signs of violence seem not to be caused by a catastrophe and lend
support for a violent raid or a ritual mortuary practice. Further analyses will show, whether the
Salzmünde people have been victims of an act of war or ritual practices.

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Different mutational spectra of complete mitochondrial genomes of normal and colorectal

cancer cells
Skonieczna K1,2,*, Malyarchuk B3, Jawien A4, Marszalek A5,6, Grzybowski T1
1
Nicolaus Copernicus University, Ludwik Rydygier Collegium Medicum, Institute of Forensic Medicine, Department
of Molecular and Forensic Genetics, Bydgoszcz, Poland
2
The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
3
Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan,
Russia
4
Nicolaus Copernicus University, Ludwik Rydygier Collegium Medicum, Chair and Department of General Surgery,
Bydgoszcz, Poland
5
Nicolaus Copernicus University, Ludwik Rydygier Collegium Medicum, Department of Clinical Pathomorphology,
Bydgoszcz, Poland
6
University of Medical Sciences, Department of Clinical Pathomorphology, Poznan, Poland

Although mitochondrial DNA variability in cancer cells was widely studied by medical
researchers, the reliable spectrum of mitochondrial DNA mutations in carcinogenesis is still
unresolved. Therefore, variability of the 100 complete mitochondrial genome sequences of tumor
and matched non-tumor tissues from 50 patients diagnosed with colorectal cancer were
investigated. Comparison of the whole mitochondrial DNA sequences of tumor and non-tumor
tissues from the same patient revealed somatic mutations in 82% of patients. Most of the somatic
mutations in mitochondrial DNA of cancer cells hit evolutionary stable positions in human mtDNA
phylogeny. Moreover, the most variable positions in control region reported in non-tumour cells
were found to be the least prone to somatic substitutions in cancer cells. Slightly higher frequency
of somatic mutations was found in the most conserved tRNA and rRNA genes, while the highest
variation was found in protein coding gene region. In particular, the relatively most evolutionarily
stable nd3 gene underwent somatic mutations with the highest frequency, and a relatively highly
variable nd1 gene remained unchanged in the tumor cells. Somatic substitutions observed in tRNA
and rRNA genes were predominantly located in stem regions. Moreover, majority of the somatic
substitutions located in protein coding genes lead to amino acid changes in the polypeptide
sequence, and more than half of them had a higher pathogenicity score from that observed for
mutations associated with mitochondrial diseases. The neutrality test based on the analysis of
protein-coding genes sequence variability showed relaxation of negative selection in mitochondrial
DNA of cancer cells. Therefore, these results suggest that somatic mutations might have been
introduced into mtDNA of cancer cells due to the their independence of oxidative phosphorylation.

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MtDNA haplogroups and sudden infant death syndrome

Köhnemann S1,*, Schumann S1, Pfeiffer H1, and the GeSID groupª
1
Legal Medicine, Münster, Germany

Between the years 1998 and 2001 cases of sudden infant death syndrome (SIDS) were sampled at
the Institute of Legal Medicine in Münster. MtDNA haplogroups were investigated in 232 of these
cases using frozen tissue of medulla oblongata or FFPE tissue of lung or heart. The results were
compared to 148 saliva samples of healthy children with an age between one to five years. The
results were as well compared to 842 samples representing the common mtDNA haplogroup
distribution of the German population. This study will be discussed according to the question,
whether mtDNA haplogroups are a predisposing factor for SIDS or not.
ªInstitutes of Legal Medicine, Germany

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Y-chromosomal insights from large-scale resequencing

Tyler-Smith C1,*, Wei W1,2, Ayub Q1, Chen Y1, Jostins L1, McCarthy S1, Hou Y2, Carbone I3, Durbin R1, Xue Y1
1
The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
2
Department of Forensic Genetics, School of Basic Science and Forensic Medicine, Sichuan University, Chengdu,
China
3
Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh,
United States

Next-generation sequencing technology now makes it possible to resequence whole genomes or

targeted regions on a population scale, providing extensive sequence data from the Y chromosome.
Coverage of the Y chromosome is lower than that of autosomes, and repeated sequences
complicate mapping of reads to their correct location, but about 10 Mb of unique Y sequence is
accessible to current technologies. We have explored the insights that can be obtained from two
such datasets. Complete Genomics have released high-coverage sequences of 35 diverse males
(http://www.completegenomics.com/), which we supplemented by sequencing an additional male
belonging to haplogroup A. From these sequences, we identified about 6.6 thousand Y variants,
which showed high validation rates. These variants were used to construct a maximum parsimony
phylogenetic tree that recapitulated the known phylogeny and distinguished all individuals. Using
a measured SNP mutation rate of 1x10-9 per bp per year, the ages of nodes of interest could be
estimated. The TMRCA of the entire tree was ~115 KYA (thousand years ago), and of the lineages
outside Africa ~60 KYA, both as expected. Additional insights included a rapid expansion of hg F
~40 KYA, and of R1b in Europe ~5-10 KYA. The archaeological counterpart of the former is
unclear, but the latter is likely to represent a Neolithic expansion of this lineage. The second
dataset consisted of low-coverage (~2x) sequence of 525 diverse males from the 1000 Genomes
Project (http://www.1000genomes.org/). About 18.7 thousand Y-SNPs were called, >98% of which
validated, but the callset missed ~17% of SNPs because of the low coverage. A maximum
likelihood tree was constructed that again recapitulated and refined the known phylogeny and
distinguished all individuals. The expansions noted above were also seen, although estimating
times was more complex because of the missing variants. These explorations of large-scale Y
resequencing illustrate the power and limitations of current technologies and also the need for the
community to develop efficient ways to use such large datasets, including a nomenclature
compatible with complete lineage resolution.

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 DNA in Forensics 2012, Sep 06-08 2012
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5 International EMPOP Meeting 8th International Forensic Y-User Workshop

A calibrated human Y-chromosomal phylogeny based on resequencing

Wei W1,2, Ayub Q1, Chen Y1, McCarthy S1, Hou Y2, Carbone I3, Xue Y1, Tyler-Smith C1,*
1
The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
2
Department of Forensic Genetics, School of Basic Science and Forensic Medicine, Sichuan University, Chengdu,
China
3
Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh,
United States

We have analysed a dataset of 36 complete Y-chromosomal sequences, 35 released by Complete

Genomics (http://www.completegenomics.com/) and an additional sequence from a haplogroup
A3b individual, in order to explore how effectively complete sequence data from the Y
chromosome can be used to construct and calibrate a phylogeny. We identified unique-sequence
regions of the chromosome where we expected variant identification from next-generation
sequence data to be reliable, and developed additional filtering steps for the data. Validation rates
of the resulting filtered genotype calls were >99%. In total, we identified 5,865 SNPs, 741 indels
and 56 MNPs. 4,861 of the variants are new and 262 of them are recurrent even in this small
sample. We constructed parsimony-based phylogenetic trees using PHYLIP incorporating all or
different subsets of the variants, and estimated times for the entire tree and different clades of
interest using GENETREE or the rho measure. The tree structure was consistent with literature
data. The GENETREE TMRCA for the complete set of chromosomes examined was 105-125
KYA; times for the out-of-Africa movement were 62-79 KYA, a Paleolithic expansion 37-48
KYA, and the expansion of R1b in Europe 7-10 KYA; rho times were broadly similar. Our study
identifies vast numbers of new variants, and explores the methodological steps necessary to obtain
reliable biological insights from current next-generation sequence data. It also poses challenges
such as how to develop a nomenclature system that can accommodate such extensive sequence
information, or how to identify the archaeological counterparts of the male expansions detected.

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 DNA in Forensics 2012, Sep 06-08 2012
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Insight into human Y chromosome variation from low-coverage whole-genome resequencing

data
Xue Y1, Chen Y1, McCarthy S1, Ayub Q1, Jostins L1, Durbin R1, Tyler-Smith C1,*
1
The Welcome Trust Sanger Institute, Cambridge, United Kingdom

Phase 1 of the 1000 Genomes Project has generated low-coverage whole-genome sequence data
from 1,094 individuals from worldwide populations, including 528 males. SNP calls on the Y
chromosome were made using SAMtools. In low coverage data, there are errors and uncertainty in
the genotype calls. We developed a filtering strategy to reduce these, including restricting the
analysis to 8.9 Mb of Y unique regions. We called a total of 18,692 Y-SNPs, 16,679 with the
ancestral allele known. The false negative rate and false positive variant site identification rates
were measured at 14% and 1.72% respectively by comparison with Complete Genomics calls on an
overlapping subset of samples. The genotype accuracy was 97.4% compared with HapMap3 chip
genotypes and 96.6% compared with Complete Genomics sequences. Using known literature
variants, we assigned each sample to a haplogroup and these samples covered most of the major
lineages except F, K, L, and M. A phylogenetic tree was constructed based on all the sites with
known ancestral states using the RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic
Analysis. The tree was consistent with the established structure. It confirmed Hg E (Bantu), O
(China) and R1b (Europe) expansions associated with the Neolithic transitions in different parts of
the world, and revealed that the expansion in Europe was the most extreme. One novel finding was
a striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement,
suggesting a previously unknown event of importance to male demography at this time.

References:

http://www.1000genomes.org/

http://www.completegenomics.com/

Li H., et al. (2009). The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics
25, 2078-9.

Stamatakis, A. et al. (2006) RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses

with Thousands of Taxa and Mixed Models. Bioinformatics 22, 2688–90.

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 DNA in Forensics 2012, Sep 06-08 2012
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5 International EMPOP Meeting 8th International Forensic Y-User Workshop

Determining the phylogenetic position of Y chromosomes based on whole genome SNP calling
Van Geystelen A1,2,*, Decorte R1,3, Larmuseau MH1,3,4
1
UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
2
KU Leuven, Department of Biology, Laboratory of Socioecology and Social Evolution, Leuven, Belgium
3
KU Leuven, Department of Imaging & Pathology, Forensic Medicine, Leuven, Belgium
4
KU Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Leuven, Belgium

Due to the rapid progress of next generation sequencing (NGS) facilities, an explosion of human
whole genome data will become available in the coming years. These data can be used to optimize
the phylogenetic Y-chromosomal tree and to find new genetic lineages. Moreover, the exponential
growth of known Y-chromosomal lineages will require an automatical determination of the
phylogenetical position of a sequenced Y-chromosome based on whole genome SNP calling data
and an up-to-date Y-chromosomal tree. Here, we will present a new software package, AMY-tree,
which is able to determine the phylogenetical position of a Y-chromosome using a whole genome
SNP profile. Moreover, it indicates ambiguities within the current phylogenetic Y-chromosomal
tree based on several whole genome SNP profiles. This software program also points out new
Y-SNPs which may be phylogenetically relevant in the future. AMY-tree works with SNPs which
are called from whole genome sequencing data and it makes use of several complementary
algorithms to determine the phylogenetical position of Y-chromosomes taking mistakes in the SNP
calling and the (provisional) lack of good indel calling for full genome data into account. The
AMY-tree software and all its capabilities were already tested in detail based on 36 male full
genomes with different origins and the results will be presented during this talk.

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 DNA in Forensics 2012, Sep 06-08 2012
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Increasing phylogenetic resolution still informative for Y-chromosomal studies on

West-European populations
Larmuseau MH1,2,3,*, Vanderheyden N1, Van Oven M4, Kayser M4, Decorte R5,2
1
UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
2
KU Leuven, Department of Imaging & Pathology, Forensic Medicine, Leuven, Belgium
3
KU Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Leuven, Belgium
4
Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam,
Netherlands
5
Katholieke Universiteit Leuven; Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium

An increasing number of Y-chromosomal SNPs are becoming available besides the set of SNPs
which were used to achieve the latest published phylogenetic tree of the human Y chromosome by
the Y Chromosome Consortium (YCC) in 2008. Many Y-chromosomal lineages which are defined
in this tree were mostly distributed in (Western) Europe due to the fact that most research projects
are focusing on this area. Therefore the question arises if newly discovered polymorphisms on the
Y-chromosome will still be interesting for Western Europeans on a population genetic level.

To answer this research question, the West-European region of Flanders (Belgium) was selected as
study area since its Y-chromosomal variation and distribution are well known in detail. In this
region, more than 1000 Y chromosomes which were genotyped at the highest resolution of the
YCC-tree were coupled to the in-depth genealogical data of the autochthonous DNA donors. Based
on these data the temporal changes of the population genetic pattern within Flanders are well
studied for the last centuries, and the effects of several past gene flow events were identified.

Now, a set of recently published and newly developed Y-SNPs were optimized to characterize all
Flemish Y-chromosomes belonging to haplogroups G, R1b and T. Based on this set, it was
possible for the first time to observe a significant East-West gradient in the frequency of certain
R1b Y-chromosomal lineages in addition to a previously announced North-South gradient. In this
talk we will discuss therefore the informative value of recently discovered Y-SNPs for population
genetic studies within Western Europe. The results suggest that an update of the Y-chromosomal
tree based on new polymorphisms will give the opportunity to study population genetic patterns in
more detail, even in an already well-studied region such as Western Europe.

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 DNA in Forensics 2012, Sep 06-08 2012
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Multiple recurrent mutations at four Y-chromosomal single nucleotide polymorphism sites in

a 37 bp sequence tract on the ARSDP1 pseudogene
Niederstätter H1, Berger B1, Erhart D1, Gassner C2,3, Schennach H2, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Central Institute for Blood Transfusion & Immunological Department, Innsbruck, Austria
3
Blood Transfusion Service Zürich, SRC, Schlieren, Switzerland

The male-specific region of the human Y chromosome (MSY) escapes meiotic recombination and
is passed down clonally from father to son. Mutation is the single driving force behind
Y-chromosomal diversification. The slowly mutating binary Y-chromosomal single nucleotide
polymorphisms (Y-SNPs) are considered the result of unique single base substitutions (unique
event polymorphisms, UEPs) during human evolution. Sets of these binary MSY markers form
stable paternal lineages that can be arranged to robust compound haplogroups. This enables the
reconstruction of the Y chromosome’s evolution by deducing a maximum parsimony haplogroup
tree from the present-day MSY variation. The geographical distribution of MSY variation is
non-random. Hence, Y-SNPs are of forensic interest, as they can be utilized e.g. for deducing the
bio-geographical origin of biological material. This extra information can complement STR data in
criminal investigations. For forensic applications, however, any targeted marker has to be
unequivocally interpretable. Here we report findings from a population study comprising ~3,700
samples from Tyrolean men (Austria), indicating apparent homoplastic mutations for haplogroup
R-M412, R-U152, and L-M20 Y chromosomes. The affected Y-SNPs P41, P37, L202, and L203
mapped to a 37 bp region on Yq11.21. Observing in multiple phylogenetic contexts up to four
homoplastic mutations within such a short sequence tract hardly results from a series of parallel
mutations. We rather propose heritable X-to-Y gene conversion as a more likely scenario. The four
affected Y-SNPs should be considered gametologous sequence variants (GSVs) rather than UEPs.
We also extracted information contained in the current ISOGG 2012 Y-SNP list and the human
reference genome assembly to identify additional potential inter-chromatid gene conversion
hotspots.

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 DNA in Forensics 2012, Sep 06-08 2012
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5 International EMPOP Meeting 8th International Forensic Y-User Workshop

Mapping the evolving Y-SNP phylogeny for building consistent Y-SNP databases
Willuweit S1,*, Roewer L1, Niederstätter H2, Geppert M1
1
Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin,
Berlin, Germany
2
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

The increased awareness of the practical forensic use of Y-SNPs is accompanied by a lack of
standardization of phylogenetic Y chromosome analyses. Since the last publication of the Y
Chromosome Consortium (YCC, Karafet et al. 2008) plenty of new markers, branch names and
corrections have been published in the academic literature. There is an electronic repository driven
by International Society of Genetic Genealogy (ISOGG) that tries to combine results/information
from the field of “genetic-ancestry testing” and of academic literature. Because forensic reporting
crucially depends on the scientific acceptance, standardization and reproducibility of the applied
methodology, this resource is not applicable as a reference here. Since 2008 the Y Chromosome
Haplotype Reference Database (YHRD 3.0) includes Y chromosome reference samples typed for
Y-SNPs and presents inferred haplogroups. To conform with the forensic standards it is necessary
to guarantee a correct and up-to date nomenclature as well as scrutiny to eliminate incorrect typing
results and to harmonize nomenclature. We take a case of an obvious homoplasy of the P37
mutation to propose necessary steps for the forensic validation of Y-SNPs a) Discussion and
publication of guidelines on mandatory validation requirements for new Y-SNP markers published
after 2008,b) Set-up of a central scientifically curated repository of validity states of Y-SNP
markers, c) Proposal for a revised, unequivocal nomenclature which accounts for the current Y
haplogroup phylogeny with synonymous markers and large numbers of branches (e.g. R-U152
instead of R1b1b2a1a2d).

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 DNA in Forensics 2012, Sep 06-08 2012
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Continent-wide decoupling of Y-chromosomal genetic variation from language and

geography in native South Americans
Nothnagel M1, Roewer L2,*, Gusmão L3,4, Gomes V3, González M3, Corach D5, Sala A5, Alechine E5, Palha T4, Santos
N4, Ribeiro-dos-Santos A4, Geppert M2, Willuweit S2, Nagy M2, Zweynert S2, Baeta M6, Núñez C6, Martínez-Jarreta
B6, González-Andrade F7, Fagundes de Carvalho E8, Aparecida da Silva D8, Jose Builes J9, Turbon D10, Lopez Parra
AM11, Arroyo-Pardo E11, Toscanini U12, Borjas L13, Barletta C14, Ewart E15, Santos S4, Krawczak M1
1
Christian-Albrechts University, Kiel, Germany
2
Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin,
Berlin, Germany
3
University of Porto, Porto, Portugal
4
Universidade Federal do Pará, Belém, Brazil
5
Universidad de Buenos Aires, Buenos Aires, Argentina
6
University of Zaragoza, Zaragoza, Spain
7
Ministry of Public Health, Quito, Ecuador
8
Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
9
GENES Ltda., Medellin, Colombia
10
Universitat de Barcelona, Barcelona, Spain
11
Universidad Complutense de Madrid, Madrid, Spain
12
PRICAI-Fundación Favaloro, Buenos Aires, Argentina
13
Universidad del Zulia, Maracaibo, Venezuela
14
UNMSM-Universidad, Nacional Mayor de San Marcos, Lima, Peru
15
University of Oxford, Oxford, United Kingdom

The way of initial habitation creates a primordial spatial pattern of human genetic variation that is
subsequently modified by demographic processes. Under the assumption that most such changes
follow trajectories set by climate as well as geographic and cultural conditions, some correlation
between the genetic structure on the one hand, and the linguistic and geographical structure on the
other, is to be expected in extant human populations even a long time after an initial colonization
event and has been documented in numerous studies on European and Asian populations. In
contrast, there is a notable absence of such descriptions for South America. Here, we examined
Y-chromosomal genetic diversity and its relation to geographic location and linguistic
classification on a continental scale in the so far largest study on South American natives,
involving up to 17 microsatellite markers genotyped in a total sample of 1011 individuals
representing 50 tribal populations from 81 settlements as well as single-nucleotide polymorphisms
defining the founding native American phylogenetic lineages Q and C and its sub lineages. We
observed a large decoupling of Y-chromosomal genetic diversity from geographical habitats and in
parts from language groups on a continental scale, which is consistent with a rapid peopling of the
continent and subsequent long periods of isolation of relatively small-sized tribal groups. Our
results highlight the fact that a pronounced correlation between genetic and geographic/cultural
structure can be expected only under very specific conditions, most of which are likely not to have
been met by native South Americans.

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 DNA in Forensics 2012, Sep 06-08 2012
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Identification of a novel Native American Y chromosome founding lineage in Northwest

South America
Roewer L1,*, Nothnagel M2, Gusmão L3,4, Gomes V3, González M3, Corach D5, Sala A5, Alechine E5, Palha T4, Santos
N4, Ribeiro-dos-Santos A4, Geppert M1, Willuweit S1, Nagy M1, Zweynert S1, Baeta M6, Núñez C6, Martínez-Jarreta
B6, González-Andrade F7, Fagundes de Carvalho E8, Aparecida da Silva D8, Jose Builes J9,10, Turbon D11, Lopez Parra
AM12, Arroyo-Pardo E12, Toscanini U13, Borjas L14, Barletta C15, Ewart E16, Santos S4, Krawczak M2
1
Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin,
Berlin, Germany
2
Christian-Albrechts University, Kiel, Germany
3
University of Porto, Porto, Portugal
4
Universidade Federal do Pará, Belém, Brazil
5
Universidad de Buenos Aires, Buenos Aires, Argentina
6
University of Zaragoza, Zaragoza, Spain
7
Ministry of Public Health, Quito, Ecuador
8
Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
9
GENES Ltda., Medellín, Colombia
10
Universidad de Antioquia, Medellín, Colombia
11
Universitat de Barcelona, Barcelona, Spain
12
Universidad Complutense de Madrid, Madrid, Spain
13
PRICAI-Fundación Favaloro, Buenos Aires, Argentina
14
Universidad del Zulia, Maracaibo, Venezuela
15
UNMSM-Universidad, Lima, Peru
16
University of Oxford, Oxford, United Kingdom

For the first time, we could identify a novel Native American founding lineage C-M217 (C3*)
within a restricted area of North-west South America. This finding is intriguing in view of the high
prevalence of the same haplogroup in Central, East and North East Asia, and its concurrent
absence from North America. Possible scenarios include (i) later migratory waves that quickly
passed the existing populations in North America, and (ii) long-distance trade or contact with East
Asia. Fifty years after Estrada, Meggers and Evans (1962) suggested trans-Pacific connections
between the middle Jōmon culture of Kyushu (Japan) and the littoral Valdivia culture in Ecuador
(6400-5300 YBP), based upon cultural similarity, it is indeed tempting to speculate that C-M217
(C3*) was introduced into South America from Eastern Asia by sea, either along the American
West coast or across the Pacific (with some help by major currents). The striking differences
observed between the Y-STR haplotypes of Ecuadorian and Asian C-M217 (C3*) carriers would
be explicable in terms of a long divergence time after the arrival (although a more recent
introduction cannot be excluded).

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 DNA in Forensics 2012, Sep 06-08 2012
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Y-haplogrouping among ethnic minority groups in South America

Yamamoto T1,*, Sakuma M1, Kawaguchi Y1, Kano Y1, Danjoh I2, Nakamura Y2
1
Nagoya University, Nagoya, Japan
2
RIKEN BioResource Center, Tsukuba, Japan

RIKEN BRC preserves a valuable cell collection called “the Sonoda-Tajima Cell Collection”
where cell samples collected from a variety of ethnic minority groups across the world, especially
from South America. A part of the samples were immortalized, and the B-lymphoblastoid cell lines
(B-LCLs) were established. Alternatively, it is important to investigate the genetic relationship and
structure among the present ethnic groups in South America to obtain the information about the
peopling of the Latin Americas. In the present study, we analyzed Y-haplogroups (Y-HGs) to
investigate the origin, the genetic relationship, and the degree of admixture of male-linage.

We extracted DNA from the 204 B-LCLs originated from males among ethnic minority groups (23
groups in 8 countries, and missing) in South America. These DNA samples were analyzed for
Y-HGs mainly by a method using a SNaPshot multiplex kit (Geppert, FSI genet.5:100, 2011), and
additionally by an allele-specific PCR method by ourselves.

We observed 6 patterns of electrophrogram from all of the 204 DNA samples, 162, 18, 11, 10 and
3 of Y-HG-Q, -R, -E, -FtoJ and –K-toT, respectively by the major haplogrouping. One hundred
and sixty-two samples of HG-Q were also divided into 2 sub-HG-Qs, 136 of Y-HG-Q1a3a* and 26
of Y-HG-Q1a3 by the Q-specific haplogrouping. Furthemore, by an allele-specific PCR method, 3,
1, 5 and 1 of Y-HG- G, -I, -J and –O, respectively were observed among 10 of Y-HG-FtoJ and 3 of
Y-HG-K-toT. Consequently, all of 14 samples from Sanuma tribe in Venezuela were haplogrouped
as Y-HG-Q1a3. I was indicated that this tribe is extremely isolated by 21 autosomal STRs.
Alternatively, all of 7 samples from Saraguro tribe and about half of Canar tribe in Ecuador were
not haplogrouped as Y-HG-Q. Therefore, it was suggested some ethnic minority groups in Ecuador
are more mixed with European and/or African.

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 DNA in Forensics 2012, Sep 06-08 2012
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5 International EMPOP Meeting 8th International Forensic Y-User Workshop

Evaluating social and ethical issues in Argentinean population by genetic marker analysis
Corach D1,*, Alechine E1, Caputo M1
1
Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires and
CONICET, Buenos Aires, Argentina

American continent countries are characterized by heterogeneous populations resulting from

complex admixture events in which Native American, European and Occidental Sub-Saharan
African contributors participated. The proportion of each continental contribution highly varies
between the different American countries. The foreign, European conquerors and their African
slaves -brought to the continent as working forces- determined an initial displacement of the
aboriginals since the beginning of 15th century. After almost four centuries of interethnic
interactions, during the second half of 19th and early 20th century a massive immigration, mostly
from Europe, took place, impacting drastically on the already admixed local population. Aiming to
analyze if any discrimination is operating in Argentina we investigated the frequency of Native
American maternal and paternal lineages in two different scenarios: a-Paternity testing and
b-Criminal identification. We analyzed 1024 samples donors by means of Y chromosome Q1a3a,
R1b1b2 and I haplogroups and mtDNA hg A2, B2, C and D1. Concerning matrilineage alone,
Native American-specific mt-hg proportions were significantly different between both groups
(Paternity=72.9%, Forensic=79.8%, P=0.03). In addition, Y-hg analysis did also showed a
significant difference in Native American hg Q1a3a proportion between forensic and paternity
cases (Paternity=8.6%, Forensic=18% ;P=0.0009). As expected, when considering both maternal
and paternal Native American lineages together, the difference between the groups under analysis
was also statistically significant (Paternity=6.8%, Forensic=18%; p=0.0003).Our results clearly
point that aboriginal population and their admixed descendants might have had less opportunities
in their social and economical development leading the individuals with Native American ancestry
to be marginalized and stigmatized being prone to criminal activities. Our results represent the first
objective demonstration of nowadays discrimination in Argentina and might contribute to redefine
this unacceptable social condition since all human beings inhabiting any piece of land deserve the
same rights, the Human Rights.

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 DNA in Forensics 2012, Sep 06-08 2012
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Tracking the Iceman’s scent by high resolution mapping of Y haplogroup G in Tyrol

(Austria)
Berger B1, Niederstätter H1, Erhart D1, Gassner C2,3, Schennach H3, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Blood Transfusion Service Zürich, SRC, Schlieren, Switzerland
3
Central Institute for Blood Transfusion & Immunological Department, Innsbruck, Austria

The analysis of human Y chromosome variation is a well established tool for investigating human
history on the basis of present-day genetic diversity. Most recently, progress in ancient DNA
analysis makes direct comparisons with genetic data from archeological remains increasingly
possible. For example, there is evidence from ancient genetic data for a high frequency of Y
chromosomal haplogroup G (Hg) in prehistoric populations of Central Europe, whilst nowadays
the density distribution of these Y chromosomes reaches its peak in the Caucasus. The most recent
and most prominent example for these findings is the “Tyrolean Iceman”. The 5,300 years old
mummy was found in the Ötztal Alps near the border between Italy and Tyrol (Austria). Y
chromosomal single nucleotide polymorphisms (Y-SNP) analysis assigned the Iceman to a
sub-branch of G2a, which is defined by the SNP L91. This particular Hg is very rare in
present-day populations of Europe (< 1%).

In this work we set out to test for elevated levels of G2a and in particular of G-L91 in present-day
paternal lineages in the remote mountain regions near to the site where the Iceman was found. A
population sample comprising 3,713 specimens from men living in Tyrol was genotyped for 19
Y-SNPs by single-nucleotide primer extension. This set included the G2a defining marker P15.
Preliminary results indicated that app. 11% of the Y chromosomes belonged to G2a. The spatial
distribution of this Hg featured unexpectedly high densities within or near the Ötztal Alps. L91
and additional SNPs such as L32, L487, and L645 are increasing the resolution within G2a and
will refine this pattern.

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 DNA in Forensics 2012, Sep 06-08 2012
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Beyond the migration: the Basque Diaspora in the Western USA

Valverde L1,2, Rosique M2, García A2, Köhnemann S1, Cardoso S2, Odriozola A2, Pfeiffer H1, M de Pancorbo M2,*
1
Institute of Legal Medicine, University Clinic of Münster UKM, Münster, Germany
2
BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain

The population of the Basque Country has remained isolated from the arrival of new individuals
until the second half of 20th century. However, it has been the source of several emigrant waves
looking for new opportunities even in other continents. The Western USA received a large number
of individuals, principally males, of Basque origin during the second half of the 19th century, who
settled in Basque communities that nowadays still try to maintain their ethnic identity. The settling
of a diaspora implies several phenomenons which can influence the genetic structure of the
immigrant population. For one hand, the typical consequences of a migration, which are
principally the founder effects, the interruption of the gene flow from the source population and
the admixture with the receptor population. On the other hand, the consequences of the migration
of this Basque population with strongly isolated ethnicity, which could facilitate the loss of
panmixia. With the aim of studying the effects of this migration on the genetic structure of the
paternal lineages in the Basque Diaspora in the Western USA, we have analysed 17 Y-STRs and
18 Y-SNPs in a sample set of individuals from this Diaspora and in a sample set of autochthonous
individuals from the Basque source population. The results show that the Basque Diaspora in the
Western USA largely conserves the Y-chromosome genetic legacy of the autochthonous European
Basques, with no genetic substructure, no loss of diversity and a very small amount of new
American Y-chromosomes incorporated to its gene pool.

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The history of slavs in the light of Y chromosome and mtDNA variability

Mielnik - Sikorska M1, Daca P2, Woźniak M1,*, Malyarchuk BA3, Derenko MV3, Skonieczna K1,4, Grzybowski T1
1
Nicolaus Copernicus University, Ludwik Rydygier Collegium Medicum, Institute of Forensic Medicine, Department
of Molecular and Forensic Genetics, Bydgoszcz, Poland
2
Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
3
Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
4
The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland

To explore the origin of Eastern Europeans we investigated Y chromosome and mitochondrial H5

haplogroup diversity in population samples from Ukraine and other Eastern European countries. Y
chromosome diversity was analyzed using a panel of 11 SNP polymorphisms (including M458 – so
called “Western Slavic marker”) and 17 Y-STRs on 154 DNA samples from Ukrainians. These
results were compared to previously published data from Slavic and non-Slavic populations.
Mitochondrial DNA control-region sequences of about 2700 samples obtained from Eastern
(Russians and Ukrainians) and Western Slavs (Czechs, Poles and Slovaks) were used to select 51
samples representing mitochondrial H5 haplogroup. For these mtDNAs the entire genome
sequences were determined. Together with published data we have collected 210 complete mtDNA
sequences belonging to the H5 haplogroup. Thus, improvement of the resolution of H5 haplogroup
phylogeny and evolutionary age estimation of H5 subhaplogroups were possible. We were able to
identify a number of new subhaplogroups (i.e. H5a1a1, H5a1r, H5a1s and others) as well as to
show that the founder H5 clade (12-15 ky old) is mainly represented by individuals from southern
Europe. We also showed some subclusters (H5a1a, H5a1f, H5e1a, H5a2 and H5u), which are
mainly represented by residents of central and eastern Europe. The evolutionary age of these
subhaplogorups was dated between 2-5 ky. The overall picture of Y chromosome and mtDNA
diversity in Central Europe corresponds well with origin and later expansion of Corded Ware
European culture. Thus, we suggest that genetic continuity existed in Central Europe between
Bronze Age and Middle Ages when the earliest Slavic tribes were described.

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 DNA in Forensics 2012, Sep 06-08 2012
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Y-chromosomal STR analysis in the Pashtun population of Southern Afghanistan

Achakzai NM1,*
1
CEMB, Lahore, Pakistan

Afghanistan is a landlocked country in the heart of Asia and since the dawn of humankind
Afghanistan has faced centuries of turmoil, strife, conflict, warfare, distress, social unrest, difficult
climate, harsh terrain and due to its unique geostrategic position in Eurasia which has historically
attracted commerce and conflict. It is an important stop along the Silk Road, connecting the far
eastern civilizations to the western world. A 5000-year history of constant invasion. Afghanistan
has been repeatedly invaded andconquered by rulers and super powers, neighboring interference in
this conflict-tattered land for centuries yet rarely leading to the conquest of this rugged and
challenging terrain nation. Afghans are not only shepherds, farmers and nomads but also intense
fighters and fierce warriors. Currently very limited genetic studies have been performed in Afghan
populations. 17 Y chromosomal short tandem repeats (Y-STRs) were analyzed in 125 unrelated
Pashtun (in hindi:Pathan) males residing in the Kandahar region of Southern Afghanistan. A total
of 92 unique haplotypes were observed. The predominant haplotype reached a frequency of 9.6%.
The haplotype diversity was 0.987 and the discrimination capacity 73.6%. Analysis of molecular
variance (AMOVA) reveals a considerable regional stratification within the country as well as
between different Pashtun (Pathan) groups from Afghanistan, Pakistan and India.

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Y-chromosomal phylogeny of Porja and Savara lineages in Andhra Pradesh, India

Isukapatla RA1, Pulamaghatta VN1, PBSV P1, Adimoolam C1,*
1
Anthropological Survey of India, Mysore, India

DNA Polymorphisms reveals a population’s genetic structure, migration and admixture in the past,
susceptibility to illness and genetic causes of diseases. Human Genome, DNA sequencing offers an
evidentiary alternative fossil based prehistoric reconstructions about origin and evolution of
human beings. The uniparental inherited non-recombining haploid mtDNA and Y chromosome
became an extremely powerful tool in phylogenetic studies. Studies on mtDNA, Y chromosome
and many autosomal regions supports that modern humans originated in Africa between 166,000
and 249,000 years ago then expanded throughout Africa and into rest of the world with little or no
interbreeding between modern humans and archaic populations lived elsewhere in the old-world,
including the Neanderthals in Europe and Homoerectus in Asia. In the absence of selection,
genetic drift and founder effects have played a major role in shaping haplotype frequencies, giving
rise to haplogroups and sub haplogroups that are often restricted to specific geographic areas
and/or population groups. Y chromosome haplogroups can trace back paternal lineages into the
past. Genetic data on Indian populations reveals that Indian caste and tribal populations share a
common ancestry in India. Indian Y-chromosomal data consistently suggest a largely South Asian
origin for Indian caste communities and therefore argue against any major influx, from regions
north and west of India. Hence present paper is mainly focusing on genotyping for human
Y-chromosome to investigate paternal lineages among two primitive tribal populations in Andhra
Pradesh, India. We have analyzed Y-Chromosome SNPs of the two primitive tribal groups of the
Austro-Asiatic linguistic families, Savara from Vizianagaram district and the Porja from
Visakhapatnam district of Andhra Pradesh, India and compared the data with other relevant data of
Indian tribal populations. The results reveals the occurrence of the O2a* haplogroup 68% and 61%
in Savara and Porja population respectively. Further we found H1a*, H*, C*, R1a1*, R2, P*,
O2a*, O3a3C*, and F* haplogroups in smaller frequency. From the MDS plot we found both
Savara and Porja are closely associated with Asur, Korku, Birja, Bhumji, Pando and Khasi tribal
populations of India. The results suggests that the Savara and the Porja, Austro-Asiatic language
speaking tribes of Andhra Pradesh, represent a genetic continuity between the populations of North
East India and South East Asia, thereby advocating that East India could have been a major
corridor for the movement of Austro-Asiatic populations.

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 DNA in Forensics 2012, Sep 06-08 2012
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Migration distance rather than migration rate explains genetic diversity in patrilocal groups
Levy H1, Conrado M1, Montinaro F2, Capelli C1,*
1
Departement of Zoology, University of Oxford, Oxford, United Kingdom
2
istituto Medicina Legale , Universita' Cattolica del Sacro Cuore, Rome, Italy

In patrilocal groups females preferentially move to join their mate’s paternal relatives. The
gender-biased gene flow generated by this cultural practice is expected to affect genetic diversity
across human populations. Greater female than male migration is predicted to result in a larger
decrease in between group differentiation for mitochondrial DNA (mtDNA) than for the
non-recombining part of the Y chromosome (NRY). We address the question of how patrilocality
affects the distribution of genetic variation in human populations controlling for confounding
factors such as ethno-linguistic heterogeneity and geographic distance which possibly explain the
contradictory results observed in previous studies. By combining genetic and bio-demographic
data from Lesotho (Southern Africa) and Spain (Europe), we show that preferential female
migration over short distances in patrilocal communities appears to minimize the impact of a
general higher female than male migration rate, suggesting patrilocality might influence genetic
variation only at short ranges.

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 DNA in Forensics 2012, Sep 06-08 2012
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Rapidly mutating Y-chromosomal STRs

Kayser M1,*, Ballantyne K1,2, Ralf A1, on behalf of the RM Y-STR Study Groupª
1
Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam,
Netherlands
2
Forensic Services Departement, Victoria Police, Macleod, Victoria, Australia

Y-chromosomal STRs (Y-STRs) currently applied in forensic analysis provide high but not
maximal resolution in male lineage differentiation and their power to separate male relatives is
low. Consequently, using current marker sets, conclusions from Y-STR analysis usually cannot be
made on the individual level as anticipated in the forensic arena, which represents a major draw
back. However, it would be desirable to combine the advantage of Y-chromosome analysis in
separating male from female DNA components in mixed stain analysis, such as it is essential for
solving cases of sexual assault, with the advantage of autosomal STR analysis in individual
identification, which often is not informative in mixed stain analysis. In order to find rapidly
mutating Y-STRs for differentiating male relatives, we previously performed a large mutation rate
study analyzing 186 Y-STRs in ~2000 father-son pairs and identified a set of 13 markers that
mutate considerably faster than all other loci tested. We recently showed that this set of rapidly
mutating (RM) Y-STRs can differentiate male relatives in a large number of cases (i.e., 67% of
relatives separated by 1-20 generations whereas Yfiler only did 15%). Furthermore, we showed
that RM Y-STRs increase male lineage differentiation considerably (i.e., by 8% from 90.4% with
Yfiler to 98.3% with RM Y-STRs in the worldwide HGDP-CEPH samples). To provide further
prerequisites for forensic applications of RM Y-STRs, and to make the data finally available for
haplotype search in future forensic case work, we now carried out a multicenter study involving 70
institutions from around the world. We collected quality-controlled data for the 13 previously
identified RM Y-STRs from over 10,000 unrelated male individuals; for about 7000 of them
conventional Y-STR data (Yfiler) are available to us for comparative analysis. Furthermore, we
collected RM Y-STR data on >1000 father-son pairs for additional male relative differentiation
testing. In this plenary talk I will summarize the benefits of using RM Y-STRs in forensic analyses
and will provide the first results and conclusions from this multicenter study on behalf of the RM
Y-STR Study Groupª.
ªRM Y-STR Study Group: Ballantyne K, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub
Q, Balažic J, Ballantyne J, Ballard DJ, Barbarii L, Berger B, Bobillo C, Bouabdellah M, Burri H,
Butler J, Capal T, Caratti S, Carracedo A, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble
MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, de Ungria M, Decorte R, Dixon
R, Dobosz T, Dupuy BM, Elmrghni S, Gan LSH, Gliwinski M, Gomes SC, Grol L, Haas C,
Hanson E, Henke J, Henke L, Hill CR, Holmlund G, Honda K, Immel U, Inokuchi S, Jobling MA,
Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovacevic LL, Kovatsi L, Krajewski
P, Kravchenko S, Kvitkova D, Larmuseau M, Lee EY, Lee SH, Lessig R, Livshits LA, Marjanovic
DD, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Nagaraju J, Neuhuber F, Nie S,
Oh HH, Olofsson J, Onofri V, Palo J, Pamjav H, Parson W, Payet C, Petlach M, Phillips C, Ploski
R, Prasad SPR, Primorac D, Purnomo GA, Purps J, Rangel H, Rebala K, Rerkamnuaychoke B,
Robino C, Rodríguez F, Roewer L, Rosa A, Sajantila A, Sala A, Salvador J, Sanz P, Savov A,
Schmitt C, Sharma AK, Shin KJ, Shotivaranon J, Sijen T, Silva DA, Sirker M, Siváková D, Skaro
V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A,
Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward
D, Willemse P, Winkler C, Yong RYY, Zaharova B, Zupanic Pajnic I, and Kayser M

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 DNA in Forensics 2012, Sep 06-08 2012
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Development criteria for a next generation Y-STR multiplex for forensic applications
Bormann Chung C1,*, Mulero J1, Nguyen V1, Calandro L1, Hennessy L1
1
Life Technologies, Foster City, United States

The downstream application of a forensic Y-STR multiplex defines the criteria used for developing
a kit that is fit for purpose. If the objective is to exclude close patrilineal relatives of the suspect
then markers with a high mutation rate might prove beneficial. On the other hand, in kinship
analysis markers with high mutation rates might prove problematic. The inclusion of currently
used Y-STR markers in the next generation multiplex should be considered given that the existing
Y-STR databases are already populated with profiles containing this information. New markers
could be added to enhance the capabilities of already existing Y-STR multiplexes. These
enhancements could combine features such as (1) mini-STRs, (2) the inclusion of highly
discriminating markers which could allow for better differentiation of paternal lineages in
populations with low Y-chromosome diversity and (3) rapidly mutating markers. A next generation
kit should also improve the overall balance, resistance to inhibitors of the PCR and provide shorter
time to results. This presentation will discuss a strategy for the development of an enhanced
Y-STR multiplex that combines well-known loci as well as recently characterized, highly
discriminating Y-STRs into one single reaction. This multiplex will enable higher discrimination
in paternal lineages, combined with unprecedented capabilities in terms of robustness, sensitivity
and male specificity to recover information from forensic samples.

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The PowerPlex® Y23 System: a single system for casework and database (direct
amplification) Y-STR analysis
Thompson JM1, Ewing MM1, Fulmer PM1, Rabbach DR1, Sprecher CJ1, Storts DR1,*
1
Promega Corporation, Madison, United States

Y-STR testing is an established tool in the forensic casework, paternity testing and genealogy
communities. The PowerPlex® Y23 System combines the seventeen Y-STR loci in current
commercially available Y-STR kits (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391,
DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635,
Y-GATA-H4) with six new highly discriminating Y-STR loci (DYS481, DYS533, DYS549,
DYS570, DYS576, DYS643). The additional loci and increased gene diversity increases scientists’
ability to distinguish individuals from different paternal lines from one another, enabling more
meaningful analyses. The PowerPlex® Y23 system is a robust multiplex highly tolerant of many
amplification inhibitors, including hematin, humic acid, and tannic acid. The system has proven
sensitivity, detecting minimal amounts of male DNA in the presence of excessive amounts of
female DNA. Complete Y-STR profiles are detected with 62pg of male DNA in the presence of
400ng female DNA (6450-fold excess). This Y-STR system is an excellent tool for testing in
sexual assault cases in which sperm was not detected from intimate swabs collected from female
victims. The PowerPlex® Y23 system also supports direct amplification from a variety of
substrates, including blood and buccal samples on FTA® paper (GE Healthcare/Whatman) and
other commonly used paper substrates. This system produces reliable Y-STR profiles from swabs
when processed with Promega’s SwabSolution™ Kit. Additionally, Y-STR amplification with this
system provides significant time savings due to a reduced cycling time of 90 minutes--less than
half the time required for other available Y-STR kits. By offering superior inhibitor tolerance,
proven sensitivity, and protocols for both casework and databasing, the PowerPlex® Y23 System
sets a new standard for Y-STR analysis.

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 DNA in Forensics 2012, Sep 06-08 2012
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Y chromosome specific nested PCR pre-amplification method for improved detection of male
DNA
Hanson E1,*, Solivan M1, Strauss S2, Di Pasquale F2, Engel H2, Ballantyne J1,3, presented by Scherer M
1
National Center for Forensic Science, Orlando, United States
2
QIAGEN GmbH, QIAGEN Str.1, Hilden, Germany
3
University of Central Florida, Department of Chemistry, Orlando, United States

Male DNA-containing samples collected from sexual assault or homicide victimscan contain very
low levels of cellular male DNA admixed with a large number of femaleepithelial cells. This often
results in failure to obtain an autosomal STR typing from themale DNA donor. Y-STR analysis
can be used to overcome this problem. However thereare still many instances where such an
approach does not work. This is particularly sowhen an intimate sample is collected many days
after the incident, usually as a result ofdelayed reporting by a rape victim or when there is a
significant time interval betweendeath and recovery of a rape/homicide victim’s body or when the
samples manifestsome degree of degradation. Recent technological advances in the area of DNA
profilingoffer the opportunity to improve the number of specimens that can be
successfullyanalyzed. Therefore it may be possible to develop strategies to overcome the
problemsassociated with low levels of male DNA in a background of female DNA. We
havedeveloped such a method using a selective amplification of Y chromosomal genomicDNA
prior to standard Y- STR analysis. This ‘genomic partitioning’ appears to be aneffective strategy to
further increase the signal to noise ratio of the Y chromosomal DNAcompared with the epithelial
DNA and hence allow clear unambiguous male profiles tobe obtained. Additionally, such an
approach could also be used to improve the analysisof touch or contact DNA samples which often
contain small amounts of male DNA.In this work, we have developed a 17-locus Y chromosome
specific nested PCRpre-amplification multiplex and have performed an initial validation to
demonstrate itspotential suitability for use with forensic samples. The pre-amplification takes less
than2 hours to perform and can be used in conjunction with commercially available
Y-STRamplification kits. The use of the nested PCR pre-amplification prior to Y-STR
analysisallows for the recovery of Y-STR profiles from as little as 5 pg of male DNA (~ 1
diploidcell) from various body fluids and tissue (blood, semen, saliva and skin). No
interferencefrom female DNA was observed even in the presence of female DNA in
100,000-foldexcess. We have demonstrated the method’s ability to recover Y-STR profiles
fromtouch and contact DNA samples as well as extended interval post coital samples (> 5days
after intercourse).

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Mt-GoNL: deep sequencing of 750+ complete Dutch mtDNA genomes

de Knijff P1,*, Vermaat M1, Li M2, van Oven M3, de Dunnen JT1, Stoneking M2, Kayser M3, Laros J1
1
Leiden University Medical Center, Leiden, Netherlands
2
Max Plack Insitute for Evolutionary Anthopology, Leipzig, Germany
3
Erasmus University Medical Center, Rotterdam, Netherlands

The Genome of the Netherlands (GoNL) is a national collaboration aimed at establishing a map of
Dutch genetic variation by whole genome sequencing of 250 Dutch trio families. This trio-based
setup and the high mtDNA coverage (on average 1100 times) in each sample give us the unique
opportunity to study both population-wide and intra-human variation on the mitochondrial
genome. We developed a number of techniques in which mtDNA can assist in quality control of
whole genome sequencing experiments. The high coverage facilitates simple detection of
contamination with a low percentage of foreign DNA. One such case is present in our data set and
its contamination has been confirmed by autosome analysis. Analysing violations of the
inheritance patterns allowed identification of sample swaps. One of the goals of our mtDNA study
is to define the Dutch mtDNA phylogenetic tree. Preliminary results show that the data set
contains more than 165 different mtDNA haplogroups, where H and its subclades are most
abundant, representing about 40% of individuals. This is in concordance with previous studies on
the distribution of haplogroup H in Europe. 127 haplogroups are observed in at least 2 individuals
and 68 mtDNA haplogroups are present among 4 or more individuals. In some of our samples we
noted a disagreement with respect to the defining polymorphisms for some haplogroups, indicating
opportunities for refinement of the mtDNA phylogenetic tree. Finally, indepth analyses, ongoing at
time of abstract submission, are carried out to search for previously not recognized mtDNA
variants including those defining new mtDNA haplogroups. This abstract is submitted on behalf of
the Genome of the Netherlands (GoNL) Consortium (http://www.nlgenome.com).

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 DNA in Forensics 2012, Sep 06-08 2012
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Applications of Personal Genome Machine (PGM™) in SNP-based human identification

Wootton SC1,*, Langit R1, Lagacé R1, Hennessy L1
1
Life Technologies, Foster City, United States

Genomic degradation and deconvolution of complex mixtures are among the many challenges
present in DNA-based human identification. Single nucleotide polymorphisms (SNPs) have
attributes that make them valuable identifiers for human forensics, providing a extensive pool of
possible markers and a platform for small amplicon PCR-based detection. Although SNPs are for
the most part bi-allelic, it has been estimated that approximately fifty polymorphic SNPs are
necessary to complement the discriminatory power of the 13 core STR loci [1]. High-throughput
technologies for SNP genotyping such as microarrays and next-generation sequencing have yielded
a wealth of population data, and subsets of these markers have been isolated for identification [1,
2, 3]. The PGM™ 314 chip was used to sequence a panel of fifty unlinked SNPs with high
heterozygosity and low fixation indices (Fst) curated by the SNP for ID consortium [1]. Genomic
DNA was extracted from five control individuals. Polymorphic loci were amplified using the
50-plex primer pool, barcoded, pooled, and sequenced on a single chip. SNP genotypes were called
upon mapping reads to a reference genome. Larger SNP panels targeting known and
well-characterized polymorphic regions have also been constructed using the Ampliseq Designer, a
tool for creating custom primer pools for non-conflicting multiplex PCR, used to yield the
template for PGM™ library prep. Future directions include panels of phenotypic SNPs for forensic
applications. 1. Sanchez et al. A multiplex assay with 52 single nucleotide polymorphisms for
human identification. Electrophoresis (2006) vol. 27 pp. 1713-1724 2. Pakstis et al. SNPs for a
universal individual identification panel. Human Genetics (2010) vol. 127 pp. 315-324 3. Kidd et
al. Developing a SNP panel for forensic identification of individuals. Forensic Science
International (2006) vol. 164 pp. 20-32 © 2012 Life Technologies Corporation. All rights
reserved. The trademarks mentioned herein are the property of Life Technologies Corporation
and/or its affiliate(s).

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Next Generation MtGenome Sequencing for forensic purposes using the Ion Torrent PGM
Strobl C1, Huber G1, Lagacé R2, Langit R2, Wootton S2, Hennessy L2, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Life Technologies, Foster City, United States

Sequencing mitochondrial genomes (mtGenomes) provides valuable information in population,

medical and forensic genetics. The emergence of next generation sequencing (NGS) technologies
has greatly increased sample through-put compared to traditional Sanger-type sequencing but most
platforms are cost-intensive and require long hands-on times. Also, the scientific community has
witnessed increased error rates in first attempts, which is a sensitive issue in forensics.We have
evaluated the Ion Torrent Personal Genome Sequencer (PGM, Life Technologies, Carlsbad, CA,
USA) for the generation of mtGenomes for a couple of reasons: a) it is easy-to-use compared to
other NGS instruments, b) the level of automation is relatively high, c) the costs of the instruments
and chemistry required are comparatively cheap and d) the application of barcodes allows the
simultaneous sequence analysis of mtDNA (or other loci) of multiple individuals. We are currently
testing the performance of the PGM by sequencing mtGenomes of samples that were already typed
using conventional Sanger-type sequencing. This allows direct comparison of data derived from
both technologies and evaluation of the PGM for forensic purposes.

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 DNA in Forensics 2012, Sep 06-08 2012
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The impact of PCR and DNA sequencing artifacts in 454 LifeSciences data on the
interpretation of mtDNA heteroplasmy
Holland M1,*
1
Penn State University, University Park, PA, United States

The use of second generation DNA sequencing approaches to interpret mtDNA heteroplasmy and
mixtures is of great interest to the forensic community. While successful approaches have been
developed using different platforms and covering different portions of the mtDNA genome, the
impact of PCR and sequencing-based artifacts on the interpretation process is significant, and the
extent of the impact is still relatively unknown. Until the community has a better understanding of
the impact, and the issues are addressed appropriately, the full use of this technology will be
limited. Our laboratory has focused on amplicon-based sequencing of the mtDNA control region.
For example, the HV1 segment was previously analyzed using the 454 GS Junior instrument from
Roche, and mock mixtures were generated to evaluate the system’s ability to reliably detect low
level heteroplasmy (Holland et al, Croatian Medical Journal, 52:299, 2011). Mock heteroplasmic
variants were detected routinely down to a component ratio of 1:250 (20 minor variant copies with
a coverage rate of 5,000 sequences), and were readily detected down to 1:1000 (0.1%) with
expanded coverage. The analysis of 30 individuals, representing 25 different mtDNA haplotypes,
revealed a rate of reportable heteroplasmy that was ~10 times that of conventional Sanger
sequencing; 44% versus 4%. However, considerable PCR and sequencing-based artifacts
(including errors) were also detected in the data, and in almost all cases, chimeric sequences were
observed. Interpretation of heteroplasmy is not impacted to a great extent by the presence of these
artifacts, while the deconvolution of mtDNA mixtures is greatly impacted given the increased
number of nucleotide differences between the two (or more) components. We will present our
analysis of the PCR and sequencing-based artifacts observed in 454 data, collected from hundreds
of thousands of data points, and how these artifacts impact the interpretation of mtDNA
heteroplasmy and mixtures.

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Weighing the differences: the application of Mass-Spectrometry for mtDNA control region
analysis
Mayr-Eduardoff M1, Huber G1, Zimmermann B1, Bayer B2, Schmid D2, Anslinger K2, Göbel T3, Niederstätter H1,
Schneider PM3, Röck AW1, Parson W1,*
1
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2
Institute of Legal Medicine, University of Munich, Munich, Germany
3
Institute of Legal Medicine, University of Cologne, Cologne, Germany

The first applications of mass spectrometry (MS) techniques for DNA analysis were developed in
the late 1990s. Soft electrospray ionisation allows the analysis of relatively large molecules, such
as DNA fragments in the size range of 150 base pairs. One distinctive feature of DNA typing by
mass spectrometry is that analysing PCR fragments yields so-called base composition profiles
(BCPs), which enumerate the base counts for each of the four nucleotides, but do not contain any
base-specific positional information. Consequently, BCPs are somewhat less informative than
conventionally sequenced mtDNA haplotypes, which, in turn, results in a loss of discrimination
power in the forensic context. However, two important advantages compensate for this limitation.
First, mtDNA analyses has never found broad application in the forensic field, as Sanger-type
sequencing is laborious, prone to error and the laboratory handling involves numerous steps that
harbour the inherent risk of sample mix-up and contamination. The here presented MS-approach
with the PLEX-ID instrument (Abbott) is highly automated by support of integrated liquid
handling, sample integrity is achieved by barcode-assisted processes and BCPs are generated and
interpretable by dedicated user-friendly software that opens the field of forensic mtDNA analysis
also to non-expert laboratories. Second, sample through-put is generally low for sequencing
approaches, especially when degraded mtDNA is under investigation as many individual fragments
need to be amplified, sequenced and interpreted. With PLEX-ID this complexity is greatly reduced
and analyses times are decreased from days to hours, which would allow a laboratory to answer
court requests in a timely fashion.

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 DNA in Forensics 2012, Sep 06-08 2012
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Interpretation of lineage markers

Weir BS1,*, Aalbers S2
1
Department of Biostatistics, University of Washington, Seattle, United States
2
Institute of Applied Mathematics, University of Technology Delft, Delft, Netherlands

The interpretation of Y-STR and mtDNA forensic profiles continues to be challenged by the
dependencies among profile elements, because of a lack of recombination, and by relatively small
databases. We can address the database size issue to some extent by using tagging SNPs in large
publicly-available datasets, and we also use these datasets to demonstrate the independence of
autosomal, Y-STR and mtDNA profiles. The dependencies among lineage profile elements
suggests concentrating on the profile as a unit, and invoking the population genetic arguments of
Ewens whereby increasing numbers of profile elements, and consequent increasing mutation rates,
leads to decreasing match probabilities. The somewhat different approaches of Brenner (2010) and
Buckleton, Krawzcak and Weir (2011) are examined with reference to actual and simulated data.

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Evidentiary strength of a rare haplotype match

Brenner CH1,*
1
UC Berkeley & DNA•VIEW, Oakland, United States

When a rare haplotype is shared between suspect and crime scene, how strong is the evidence
linking the two? The relevant number is the conditional probability of an innocent person to match
the crime scene profile, given available data including the crime scene profile, population data,
and scientific knowledge.

The traditional methods of evaluating the strength of DNA evidence include several institutional
misconceptions. First and most fundamental is to confuse probability (a summary of available
data) with population frequency (which is not available). Next, the normal statistical assumption
that sample frequency reasonably estimates population frequency ignores among other things
scientific knowledge and fails badly for rare traits. Third is forgetting to condition on the crime
scene observation. Hence the traditional paradigm in forensic practice is to confuse sample
frequency with population frequency and in turn confuse that with probability. The consequence is
very roundabout and unsound reasoning.

More direct methods are not difficult. One simple and validated idea is based on the proportion
singletons – of haplotypes that occur just once – in a sample, which I call κ (kappa). For
present-day Y-STR typing, the most common situation by far is that the crime scene haplotype is
previously unseen in a sample of size n-1. In that case the matching probability for an innocent
suspect is (1-κ)/n. Even simpler is to count the rate of pairwise matches in a reference database.
This empirical matching probability is appropriate on average hence slightly conservative for
previously unseen types.

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Estimating trace-suspect match probabilities for singleton Y-STRs haplotypes using

coalescence theory
Andersen MM1,*, Caliebe A2, Jochens A2, Willuweit S3, Krawczak M2
1
Aalborg University, Aalborg, Denmark
2
Christian-Albrechts University, Kiel, Germany
3
Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin,
Berlin, Germany

An important task of statistical forensic genetics is to evaluate the evidential weight provided by
some genetic data of interest, and the most consistent (and therefore generally recommended) way
of doing so is by means of the likelihood ratio. One particularly important match probability in this
context is the probability that a certain individual (the ”suspect” in a crime case) has the same
DNA profile as another individual drawn at random from the same population (the donor of a trace
found at the crime scene). Methods to estimate this trace-suspect match probability are well
established for autosomal STRs, with most of them assuming statistical independence between the
markers included in the profile.

Use of lineage markers, such as Y-chromosomal short tandem repeats (Y-STRs) or mtDNA
polymorphisms, has several advantages over autosomal markers in forensic practise, for example,
when solving cases of sexual assault. However, due to the lack of recombination, and therefore
statistical independence between loci, the calculation of match probabilities is more challenging
for lineage than for autosomal markers. In particular, when considering Y-STR haplotypes usually
comprising 7 to 17 loci, the proportion of singletons (i.e. haplotypes observed only once) in a
reference database may become so large that traditional count estimates of the corresponding
match probabilities are rendered unsatisfactory.

In this talk we present how to estimate trace-suspect match probabilities using coalescence theory
and demonstrate that it performs well in comparison with other estimators (such as the ”haplotype
surveying” method and Brenner's kappa method) based on a simulation study.

Because the coalescent-based estimator is rather computational-intensive, we shortly discuss the

practical applicability of this method.

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Y-STR mutations: what paternity cases can tell us about the relationship between allele
length and mutation rate
Jochens A1,*, Caliebe A1, Roesler U1, Krawczak M1
1
Christian-Albrechts University, Kiel, Germany

Forensic applications of Y-STR markers often require estimates of the respective mutation rates.
This is especially true for phylogenetic analyses, where mutation rates must be estimated to
calibrate the molecular clock. Usually the locus-specific fraction of observed mutations in a
sample is used for these purposes. However, it is well known that the rate of STR mutation not
only varies across loci, but does also depend on the allele length for any given locus, although the
exact nature of this dependency is still unclear. We describe some simple STR mutation models,
including a novel logistic one, incorporating allele length as a factor [1]. To fit and compare these
models, data on the inheritance of Y-STRs in father-son duos, accumulated from the forensic
literature, were used. For each locus and each model, we employed a maximum likelihood
approach to estimate the model parameters. For most loci considered, a certain version of the
logistic mutation model was found to provide the best fit according to Akaike's Information
Criterion. This implies that the mutation probability at these loci increases non-linearly with allele
length at a rate that differs between upward and downward mutations. [1] Jochens A, Caliebe A,
Roesler U, Krawczak M. Genetics 189(4): 1403-1411, 2011.

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Testing Y chromosome STR mutation rates using deep-rooting pedigrees

Erasmus JC1,*
1
University of Pretoria, Pretoria, South Africa

Y-chromosome STR mutation rates play an important role in forensic sciences, especially for
determining the paternity probability during paternity testing. Mutation rate estimates for
genealogical approaches (like father-son pair typing) normally give a higher mutation rate estimate
than population based studies with a known recent population history. The Afrikaner population
serves as a good system to test the y-chromosome STR mutation rate with a deep-rooting pedigree
approach. Deep-rooting pedigree studies are also useful for estimating the non-paternity rate of a
population. South African founding fathers from Europe often introduced unique surnames into the
Afrikaner population from the mid 1600s to 1700s. South Africa has an active genealogical
research society and records often permit researching an individuals’ pedigree that stretch back to
the founding father. Y-chromosome STR mutation and non-paternity rates were estimated from 20
deep-rooting pedigrees with 6545 meiotic transfers. Subjects that are genealogically connected to
the founding fathers were typed for 17 y-chromosome STR loci with the AmpliflSTR® Yfiler® kit
(Applied Biosystems). A recent surname (Greeff) based study estimated an average STR mutation
rate of 4.85 x 10-3 based on a single old South African family. We estimated an average STR
mutation rate of 3.1 x 10-3 and when we combined our data with the Greeff study, we obtained an
average STR mutation rate of 3.5 x 10-3 . Our mutation rate estimate is higher than the father-son
pair approach (2.8 x 10-3 ), but still falls within the confidence interval limits we obtained. We
estimated a non-paternity rate of 0.51% for the Afrikaner population, which is even lower than the
recent estimate of 0.78% for the Afrikaner population.

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Analysis of mutation rates in purported brother pairs with 17 Y-STR loci

Edson SM1,*, Maynard KL1
1
Armed Forces DNA Identification Laboratory, Dover AFB, United States

Y-STR mutation rates have most commonly been computed between father and son pairings. For
missing persons casework and examination of skeletonized human remains, reference materials
may not be available from the father or son of the decedent. While mitochondrial DNA (mtDNA)
analysis is frequently used, in cases of commingled remains where one or more individuals share a
mitotype, additional genetic means of identification need to be utilized. The Armed Forces DNA
Identification Laboratory (AFDIL) has been examining the use of Y-STR analysis as an addition to
the toolkit of genetic analysis. In the course of validating the use of the AmpFLSTR® Yfiler®
PCR Amplification Kit (Life Technologies) with skeletonized human remains, the need to examine
mutation rates in the presence of increased generational steps was identified. Four hundred
seventy-six individuals were analyzed to determine the mutation rates at 17 Y-STR loci. The
individuals selected were self-reported brothers to missing individuals and also had at least one
other brother available for comparison. Reference materials were obtained in the course of family
reference collections for mtDNA analysis. Sibling indices (both full and half) were determined
using the AmpFLSTR® Identifiler® Kit (Life Technologies) for each pair. Of the 194 alleged
sibling pairs successfully amplified, the majority of individuals were found to be consistent with
their purported brother. However, twenty of these pairs varied from each other by one or two loci,
each by a single repeat. Of note is the finding of thirteen cases of questionable genetic
relationship, including possible non-paternity and non-sibship.

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Searching for dependencies between mitochondrial and Y chromosome DNA markers

Wolanska-Nowak P1,*
1
Institute of Forensic Research, Krakow, Poland

Combining and updating evidences when conducting reasoning with uncertainty is a key topic in
forensic evidence interpretation. When dealing with identification of human remains or paternity
investigation there is a great need to use different kinds of genetic markers. Attempts to evaluate
the combined effect of separate items of evidence may be complicated without the knowledge
about possible dependency between the evidences. Autosomal DNA profile proportion in the
population is formed by the product rule and the mtDNA and Y-chromosome haplotypes estimates
are the counts in a database. Hence multiplying them is the first estimate of the joint probability on
the hypothesis on identity. However, possible dependencies may occur between the patterns of
population distribution among genetic markers with different modes of inheritance. The aim of the
study was searching for the presence of pairwise linkage disequilibrium between mtDNA and
Y-chromosome haplogroups distribution due to possible South Poland population admixture. Both
mtDNA and Y-chromosome haplogroups were assigned for 305 reference unrelated male samples.
There were observed 31 different mitochondrial and 17 Y-chromosome haplogroups, respectively,
and 88 combined haplotypes (average gene diversity over two markers = 0.708412). Performed
exact test using Markov chain of pairwise linkage disequilibrium indicated that there were no
linkage in heritability between these markers (exact p-value = 0.903564). Previously performed
population study of autosomal STR loci, showed that the FST value for South Poland population
was negligible. Hence, the real structure of South Poland population, as checked by frequencies of
particular autosomal, mitochondrial and Y-chromosome markers, respectively, demonstrates high
degree of differentiation without of significant disturbing population processes. The results
provide acceptable arguments for multiplying the likelihood ratios obtained from different kinds of
genetic markers without any further assumptions. This conclusion is very important for routine
forensic casework when assessing the combined value of genetic evidence is necessary.

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Mine, yours, ours? Sharing data on human genetic variation

Destro Bisol G1,2,*, Anagnostou P1, Capocasa M1, Congiu A3, Milia N3, Montinaro F2, Sanna E3
1
University of Rome La Sapienza, Rome, Italy
2
Istituto Italiano di Antropologia, Rome, Italy
3
University of Cagliari, Cagliari, Italy

The achievement of a robust, effective and responsible form of data sharing is currently regarded
as a priority for biological and bio-medical research. However, it has been argued that its possible
advantages in terms of better exploitation of data and optimized use of resources may be
counteracted by the time and economic costs required, by underlying ethical concerns, and
conflicts of interest with patenting discoveries. In this contrasting scenario, empirical evaluations
of data sharing may be regarded as an indispensable first step in the identification of critical
aspects and the development of strategies aimed at increasing availability of research data for the
scientific community as a whole. Research concerning human genetic variation represents a
potential forerunner in the establishment of widespread sharing of primary datasets. However, no
specific analysis has been conducted to date in order to ascertain whether the sharing of primary
datasets is common-practice in this research field. To this aim, we analyzed a total of 543
mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database
from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld,
while neither strong editorial policies nor high impact factor proved to be effective in increasing
the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we
could observe a substantially lower sharing in medical than evolutionary and forensic genetics,
more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to
e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing
should be regarded as a prerequisite for final paper acceptance, while making authors deposit their
results in open online databases which provide data quality control seems to provide the
best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to
generate withheld datasets, implying that an important portion of research funding does not
produce shared knowledge. By making the scientific community and the public aware of this
important aspect, we may help popularize a more effective culture of data sharing.

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Posters

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mtDNA haplogroup F1a’c is a genetic risk factor for nasopharyngeal carcinoma in

Chaoshanese
Du J1, Deng J1, Yao Y2, Lin K3, Chen S1, Hu S1,*
1
Molecular Biology Laboratory, Shantou University Medical College, Shantou, China
2
Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming, China
3
Department of Public Health, Shantou University Medical College, Shantou, China

Mitochondrial DNA (mtDNA) is susceptible to oxidative damage and harbours a high rate of
mutation. It is clear that mitochondial play a role in cancer development. We conducted a
case-control study to investigate the possible association between mtDNA haplogroups and
nasopharyngeal carcinoma (NPC) in 201 NPC patients and 201 normal controls from Chaoshan
population. Binary logistic regression analysis with adjustment for gender and age showed that
mtDNA haplogroup F1a’c was associated with a significant risk of NPC (P = 0.040, OR = 2.589,
95% CI: 1.045 - 6.412). A separate comparison of gender or age further confirmed that F1a’c was a
risk factor to NPC in males or in patients with age ≥ 40 years old (P = 0.009, OR = 6.697, 95% CI:
1.619-27.706; P = 0.015, OR = 4.099, 95% CI: 1.323-12.703, respectively). However, no such
significant correlations were found in females or in subjects younger than 40 years old. The
analysis stratified by gender and age further revealed that the frequency of F1a’c was significantly
higher in NPC patients than in controls for men ≥ 40 years (P = 0.015, OR=8.250, 95% CI:
1.498-45.429). In summary, our study showed that mtDNA haplogroup F1a’c tended to have an
increased risk for NPC in Chaoshanese.

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Mitochondrial DNA polymorphism and matrilineal genetic composition of Chaoshan

population in China
Hu S1,*, Deng J1, Feng G1, Du J1, Chen S1
1
Molecular Biology Laboratory, Shantou University Medical College, Shantou, China

Chaoshanese, a Chinese population residing in Chaoshan region in southern China, is an admixture

population whose gene pool is derived from the Central China Han and southern aboriginal
natives, as determined by our previous autosomal short tandem repeat (STR) study. To determine
the matrilineal genetic composition of this population, we investigated the mitochondrial DNA
(mtDNA) of various Chinese populations and analyzed the genetic relationship between
Chaoshanese and other Chinese populations from the perspective of maternal inheritance. mtDNA
polymorphisms in the hypervariable segment regions (HVS-I and HVS-II) and the COII/tRNALys
intergenic region were typed in 201 Chaoshan individuals. The mtDNA HVS-I sequence and
haplogroup frequency data of other Chinese populations were collected and used for population
comparison. Population relationships were examined by principal component, multidimensional
scaling and median-joining network analyses. In addition, admixture analysis was performed to
estimate relative contribution of northern Hans and southern natives to the Chaoshan population.
Our results showed that the Chaoshanese, along with other southern Hans, is well separated from
the northern Hans and occupies an intermediate position between northern Hans and southern
natives. In matrilineal gene pool of the Chaoshan population, genetic composition of southern
natives and northern Hans accounts for about 50%, respectively, indicating that the matrilineal
genetic composition of Chaoshan population consists of both northern Han and southern native
origin.

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Insights into South-American colonization through mtDNA analysis in native Colombian

populations
Xavier C1,2, Builles J3,4, Gomes V1, Ospino JM3, Amorim A1,2, Gusmao L1, Goios A1,*
1
IPATIMUP, Institute of Pathology and Molecular Immunology of the University of Porto, Porto, Portugal
2
Faculty of Sciences, University of Porto, Porto, Portugal
3
Laboratorio Genes Ltda, Medellin, Colombia
4
Instituto de Biologia, Universidad de Antioquia, Medellin, Colombia

Aiming to add some clues on the colonization of the American continent, more precisely the
entrance points and dispersion routes taken, studies with lineage DNA markers such as
mitochondrial DNA (mtDNA) and Y chromosome have been performed, which allow tracing back
the history of populations because they are transmitted without recombination to the descendants.

In the present study we determined the matrilineal ancestry of samples from two regions in
Colombia through mtDNA analysis. Based on the observation of Native American haplogroups in
both populations, we also intended to perceive if there are differences that could indicate different
migrations towards the South of the continent.

The complete mtDNA control region was sequenced for 98 samples from the two groups (38
Emberá from Antioquia and 60 samples from various ethnic groups from Cauca) and compared
with the revised Cambridge Reference Sequence. Haplogroup frequencies were calculated and
phylogenetic analyses were performed.

The vast majority of haplogroups found in both Colombian populations are typically Native
American. Our results show that while in the Antioquia region, the Emberá population presents a
very reduced number of haplotypes, all belonging to haplogroups A, B and D, the Cauca region is
more diverse and has a significant percentage of C haplogroup lineages. When dividing the Cauca
group into smaller speaking groups it is visible that they are obviously distinct and behave as small
populations that have suffered evolutionary forces along time such as genetic drift and bottlenecks.
When comparing with other populations from literature, there is a notable proximity between
Chibchan speaking groups, whereas non-Chibchan remain differentiated. Regarding a geographic
separation, there is no visible substructure. Instead, distinct patterns are visible both in northern
and southern populations within Colombia which may result from distinct ancient routes.

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Comparative mitochondrial DNA analyses in Myanmar and the distinct genetic position of
the Karen people within this multi-ethnic population
Summerer M1, Horst J2, Erhart G1, Horst D3, Horst B4, Sanguansermsri T5, Manhart A1, Kronenberg F1,
Kloss-Brandstätter A1,*
1
Sektion für Genetische Epidemiologie, Medizinische Universität Innsbruck, Innsbruck, Austria
2
Institut für Humangenetik, Universität Münster, Münster, Germany
3
Pathologisches Institut, Ludwig-Maximilians-Universität, München, Germany
4
Department of Dermatology, Columbia University, New York, United States
5
Department of Pediatrics, Chiang Mai University, Chiang Mai, Thailand

Background: Myanmar (Burma) is the largest country in Southeast Asia, with a population of 56
million people subdivided into more than 100 ethnic groups. The Bamar represent the largest
group (68%) amongst them. Ruled by changing kingdoms and dynasties and lying on the trade
route between India and China, Burma was influenced by a variety of cultures. Since Burma’s
independence after the British occupation, minorities suffer from government’s repression and
especially the Karen people (7%) struggle against the domination of the Bamar culture. We
analyzed the mtDNA control region of 327 unrelated donors from Myanmar according to highest
quality standards. To refine haplogroup information, 44 selected lineages were subjected to
complete mitochondrial genome sequencing.Mitochondrial data from Myanmar were compared
with other Southeast and East Asian populations.

Results: The distribution of the macro-haplogroups M and N and the geographic assignment of the
haplogroups were typical for Southeast Asia, however, the frequency of individual haplotypes was
very specific in Myanmar.In general, the Myanmar sample exhibited pronounced mtDNA
diversity, with the ethnic group of the Bamar being the most diverse. The haplotype composition
of the Karen people, in contrast, was significantly more homogenous than other ethnic groups. We
found 10 new mtDNA lineages, represented by 15 haplotypes, mostly within macro-haplogroup M.
No traces of European contribution to the gene pool were detected.

Conclusions:The multi-ethnic population and the complex history of Myanmar are well reflected
in its distinct mtDNA heterogeneity, nevertheless genetic diversity cannot exclusively be attributed
to variation due to ethnicity. In this region with its long history of human settlement, plenty of
mitochondrial haplogroups, especially in the complex haplogroup M, await to be newly described.

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Multiplex mutagenically separated PCR assays for simple and rapid screening of East Asian
mtDNA haplogroups on forensic samples
Kim E1, Lee H1,2, Yoon J1, Yang W1, Shin K1,2,*
1
Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of
Medicine, Seoul, South Korea
2
Human Identification Research Center, Yonsei University, Seoul, South Korea

Nucleotide polymorphisms in human mitochondria DNA (mtDNA) have been one of the main
issues in population genetics, clinical medicine, and forensic science. Especially, determination of
human mtDNA haplogroup has become a useful tool to study human evolutionary history and to
infer the matrilineal bio-geographic ancestry. In forensic field, the screening of mtDNA
haplogroups by genotyping of mtDNA single nucleotide polymorphisms (SNPs) can help
guarantee the quality of mtDNA sequence data as well as can reduce the need to sequence samples
that do not match. Here, a multiplex mutagenically separated (MS) PCR system was developed for
simultaneous rapid detection of 14 coding region SNPs and one deletion motif representing
common mtDNA haplogroups of East Asia; mtDNA haplogroups M, G, D, D4, D5, M7, M8, M9,
M10, N, A, N9, R, F, and B. As the D4 haplotypes occur most frequently (> 25% in Koreans),
additional multiplex MS PCR system was also developed for the determination of four coding
region SNPs to further define D4 subhaplogroups D4a, D4b, D4e, and D4j. The multiplex MS PCR
system we developed has the advantage of being a one step procedure that requires only a single
PCR amplification with allele-specific primers and allowing straightforward designation of
haplogroups along the branches of the phylogenetic tree. Therefore, it would be a simple, rapid,
and reliable detection method useful for large-scale screening of mtDNA variations to determine
East Asian mtDNA haplogroups.

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Mitochondrial DNA data of five Philippine Negrito populations

Tabbada KA1, Salvador JM1, Delfin FC1, De Ungria MA1,*
1
DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Quezon City,
Philippines

Understanding human history, ancestry and human origins is a source of identity and pride for a
country and its people. A multicenter population genetic study involving 73 Asian populations
(which includes five Philippine “Negrito” groups) and 54,794 autosomal single nucleotide
polymorphisms (aSNPs) showed that Austronesian language speaking Filipinos are genetically
associated with other Austronesian groups in Asia and that ancestors of Filipino “Negrito” groups
were part of the first wave of modern humans that populated the Asia-Pacific region (HUGO
Pan-Asian SNP Consortium 2009). This new discovery underscores the importance of
characterizing lineage genetic markers found on the mitochondrial DNA and Y-chromosome in
order to provide a greater understanding of the genetic variations that appear to be specific for
some Philippine groups. This study therefore aimed at investigating the patterns of mtDNA
variation in the five Philippine “Negrito” groups included in the multicenter study and comparing
these with previously generated mtDNA sequence of Filipinos in Philippine regional centers
(National Capital Region, Cebu City and Zamboanga City) (Tabbada et. al., 2009) and other Asian
countries in order to evaluate existing theories of prehistoric migration and peopling of the
Asia-Pacific region. Archived samples consisting of FTA®-bound buccal DNA from sixty (n=60)
unrelated individuals belonging to five Philippine “Negrito” groups namely, Aetas of Zambales,
Aetas of Bataan, Agtas of Bicol, Irayas of Mindoro and Atis of Panay Island, were amplified at
mtDNA HVRI and HVRII and sequenced using Big Dye® Terminator chemistry (Applied
Biosystems). Mitochondrial DNA haplogroup affiliation of each sample was determined using
mtDNA tree Build 10 (http://www.phylotree.org). If needed, the haplogroup identity of some
samples was confirmed using PCR-RFLP reaction. Classification of Philippine “Negrito” mtDNA
sequences and a comparison with existing Philippine and Asian populations’ mtDNA data will be
presented.

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An approach to Equatorial Guinea demographic genetic history through maternal lineage

analysis
Valente C1,2,*, Alvarez L1, López-Parra AM3, Parson W4, Amorim A1,2, Prata M1,2, Arroyo-Pardo E3, Gusmão L1
1
IPATIMUP, Porto, Portugal
2
Faculty of Sciences, University of Porto, Porto, Portugal
3
Departamento de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid,
Madrid, Spain
4
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

Equatorial Guinea is located in the Central-West African coast, limited by Cameroon on the North
and Gabon on the South. The country is composed by continental and an insular portion, this one
formed by several islands, among which highlight Bioko where the capital Malabo is located. Due
to its geographical situation, just behind to the start point of the Bantu expansion, the majority of
the country populations belongs to this group, been the Fang tribe the most representative,
encompassing 80% of the total inhabitants. The main goal of this work was to assess the pattern of
diversity in maternal lineages from Equatorial Guinea population. For this propose sequences of
the complete control region of mitochondrial DNA (16024-576bp) in 50 unrelated individuals were
obtained, through the analysis of a 3.5 Kpb mitochondrial segment resulting from the amplification
of two shorter overlapping fragments. The majority of the haplogroups detected are characteristic
of Sub-saharan populations. In this sense, haplogroups L0, L1, L2 and L3 represent 92% of the
total maternal lineages, whereas previous Y-chromosome results showed a lower proportion of
male lineages of sub-Sahara African ancestry, due to the presence of European lineages that
explained around 14% of the total variability. Gene diversity level found (0.9984 ± 0.0044)was in
the same range of the value revealed analysing the Y-chromosome polymorphisms (0.9994 ±
0.0019). The number of different mtDNA haplotypes detected, 48 out of 50, which bring to light
the great diversity hallmark of African populations. Nevertheless, the diversity in Equatorial
Guinea appears too high for a population strongly influenced by the Bantu expansion. This kind of
studies are crucial to get a full understanding of the origin and history of human populations,
although more analyses are still ongoing, such as comparisons with surrounding populations
located also in the Western African coast.

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Mitochondrial DNA data of Cabo Verde immigrant population living in Lisboa

Afonso Costa H1,2,*, Morais P1,3, Amorim A1,2,4, Vieira Silva C1,2, Matos S1,3, Marques Santos R1,2, Espinheira R1,2,
Costa Santos J5,2,6
1
Servico de Genetica e Biologia Forense, Delegacao do Sul do Instituto Nacional de Medicina Legal e Ciencias
Forenses, I.P., Lisboa, Portugal
2
CENCIFOR - Centro de Ciencias Forenses, Coimbra, Portugal
3
Biologia Molecular em Saude, Escola Superior de Saude Egas Moniz, Almada, Portugal
4
Antropologia Forense, Faculdade de Ciencias e Tecnologia da Universidade de Coimbra, Coimbra, Portugal
5
Servico de Clinica Forense, Delegacao do Sul do Instituto Nacional de Medicina Legal e Ciencias Forenses, I.P.,
Lisboa, Portugal
6
Medicina Legal e Ciencias Forenses, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal

Mitochondrial DNA (mtDNA) analysis found an important role in forensic genetics, especially
when nuclear DNA analysis does not give a conclusive response. It is a powerful tool to exclude
samples as originating from the same matriline. Features that increase the vested interest of
mtDNA are the high copy number per cell, maternal inheritance, absence of recombination, and
high mutation rate. Due to higher overall mutation rate, control region is comparatively enriched in
sequence variation and therefore its analysis is important to establish haplotypes and haplogroups.
Haplogroup assignment became noteworthy to clarify the history and demographic past of a
population. As well as occurs all over Europe, in Portugal, and particularly in Lisboa, immigrant
populations are increasing. The Instituto Nacional de Medicina Legal e Ciências Forenses is
carrying out a comprehensive genetic study with the aim of portray the genetic diversity of the
immigrants who live in Lisboa. Within that objective the present study intends to: obtain the
mtDNA variability of Cabo Verde Immigrant Population Living in Lisboa and classify haplotypes
into haplogroups. MtDNA control region was amplified using two pairs of primers L15997/ H016
and L16555/ H599. The cycle sequencing was performed using the ABI Prism® BigDye®
Terminator v.3.1 Cycle Sequence Kit (Applied Biosystems, Foster City, CA) and BetterBuffer
(Microzone Limited, Sussek, UK). Analysis was done with ABI DNA Sequencing Analysis V5.2
and SeqScape v2.5. The obtained haplotypes were compared with the Cambridge Reference
Sequence (CRS) and typed following the nomenclature of the International Union of Pure and
Applied Chemistry (IUPAC). Haplogroups were determined on the mtDNAmanager. Preliminary
results showed great variability, with high frequency of unique haplotypes and significant values
of nucleotide and sequence diversity. The majority of mtDNA sequences were included into
specific African mtDNA haplogroups and a minority of mtDNA lineages belongs to West Eurasian
haplogroups.

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Dissection of mitochondrial DNA haplogroup L3b and its forensic applications

Pasino S1,*, Del Pero M2, Santovito A2, Robino C1
1
Department of Anatomy, Pharmacology and Legal Medicine, University of Turin, Turin, Italy
2
Department of Animal and Human Biology, University of Turin, Turin, Italy

In a study of the variability of mitochondrial DNA (mtDNA) control regions HVI/II in a

population sample (n=100) from Ivory Coast (North West Africa), a random match probability
(RMP) of 1.56% was observed. When mtDNA haplotypes were affiliated to haplogroups, based on
patterns of shared haplogroup-associated polymorphisms, it could be seen that the most common
haplotype, observed with a frequency of 6%, could be assigned to haplogroup L3b. In general,
haplogroup L3b (representing 16% of all mtDNA lineages) showed a low haplotype diversity
(RMP=20.31%) in the Ivorian population sample.

Here we describe the combination of two multiplex single base extension assays, interrogating a
total of 13 mtDNA coding region single nucleotide polymorphisms (SNPs), for the dissection of
mtDNA haplogroup L3b. By multiplex SNP typing, the assignement of putative L3b mtDNA
sequences was confirmed on a molecular basis, and further discrimination among samples sharing
identical HVI/II haplotypes was possible. Individuals carrying the most common haplotype could
be subdivided in L3b2 (n=4) and L3b1a (n=2) and, on the whole, the RMP was reduced to 1.38%.

The described assays can therefore increase the forensic informativeness of mtDNA analysis in
investigations involving subjects of West African descent, allowing rapid screening of samples in
high volume casework and exclusion of multiple suspects.

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Refined characterization of Portuguese mtDNA variability for forensic purposes

Rocha A1, Goios A1, Amorim A1,2, Gusmao L1, Alves C1,*
1
IPATIMUP, Institute of Pathology and Molecular Immunology of the University of Porto, Porto, Portugal
2
Faculty of Sciences, University of Porto, Porto, Portugal

The analysis of mtDNA polymorphisms has become a useful tool in fields such as forensic science,
human population genetics and molecular evolution studies. The amount of data accumulated from
different populations all over the world is massive. Still, the Portuguese population is poorly
characterized for the mtDNA complete control region and lacks a comprehensive database of good
quality sequences.

For this reason we have sequenced the mtDNA complete control region of 298 unrelated
individuals equally distributed through North, Center and South of Portugal and undertaken
haplogroup classification. Specific coding region single nucleotide polymorphisms (SNPs) were
further genotyped by single base extension multiplex reactions in individuals classified within
haplogroup H, which encompasses over 40% of the total mtDNA variation in Western Europe.

A total of 106 studied individuals (35.6%) were classified within haplogroup H. The southern
region showed a slightly lower percentage of individuals classified in haplogroup H (32%) in
comparison with the other two regions (37%). The remaining sequences were classified into the
following major haplogroups: R* (incl. B, J, T - 20.1%), U (incl. K - 19.5%), N* (incl. I, W, X –
10.1%), R0 (except H – 7.0%), L (except L3 – 5.4%) and M (incl. D - 0,7%) (Nomenclature
according to PhyloTree.org - mtDNA tree Build 14, 5 Apr 2012).

With this study, we provide a better characterization of the mtDNA variability in the Portuguese
population by collaborating and contributing to the enrichment of the EMPOP database
(www.empop.org). Finally, by comparing the three regions, North, Center and South, we will
understand whether the Portuguese sample should be considered as a whole, when applied to
routine forensic genetic casework.

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MtDNA haplogroup distribution in Finland

Putkonen M1,*, Neuvonen A1, Hedman M1, Palo JU1
1
Laboratory of Forensic Biology, Department of Forensic Medicine, Hjelt Insititute, University of Helsinki, Helsinki,
Finland

According to earlier studies the diversity of mtDNA haplotypes within Finnish population is
comparable to other European populations and, geographically relatively uniformly distributed.
This is in stark contrast with Y-chromosomal haplotypes showing considerable differences
between East and West Finland.

To complement the previous haplotype-level analyses, we have in the present study investigated
the Finnish mtDNA diversity on subhaplogroup levels. In order to gain more in-depth view on the
Finnish population history we explored differences in regional distribution and diversity of
haplogroups and subhaplogroups. The haplogroup information was inferred from control region
HV1 and HV2 data using mtDNA tree Build 14 (PhyloTree.org, 5 Apr 2012). The sample
consisted of 384 haplotypes (303 when rapidly mutating sites 309.1C(C), 315.1C, 16182C, 16183C
and 16193.1C(C) were omitted) from 832 randomly chosen individuals geographically assigned to
different regions of Finland based on donors’ place of residence.

Despite the mtDNA diversity in Finland is, compared to Y-chromosomal variation, high and
relatively uniformly distributed, the haplogroup data showed some statistically significant
geographical differences within Finland. By contrasting these haplogroup diversity patterns with
other markers, data inferred for different ancestral source populations and possible past
colonization routes, a more detailed picture of the Finnish past can be achieved.

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Optimization and validation of a mitochondrial DNA assay in a German population sample

and application to highly degraded DNA
Zander J1, Rothe J1, Roewer L1, Nagy M1,*
1
Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin,
Berlin, Germany

Mitochondrial DNA is a powerful tool in forensic casework. The high copy number of
mitochondrial genomes permits a successful amplification even then if nuclear DNA is widely
degraded or limited. Due to the maternal inheritance mitochondrial DNA analysis make it possible
to reconstruct relationships and to trace back branches of haplogroups and their subgroups to
conclude chronological and geographical details of migration. Recently, Parson and colleagues
developed and evaluated three different mitochondrial DNA genotyping assays for the analysis of
the whole mitochondrial DNA control region, dependent on the quality of the DNA (Parson &
Bandelt, 2007: mitochondrial standard assay; Berger & Parson, 2009: Midi-Mito assay; Eichmann
& Parson, 2008: Mini-Mito assay). In our study we present a German population study of about
200 individuals aiming to optimize the handling of the assay. Sequencing and evaluation were
performed according to EMPOP quality studies. Our study presents a summary of our experiences
and difficulties which we obtained during the establishment and validation of the two published
mitochondrial analysis methods (standard assay and Midi-Mito assay) in our routine work. Besides
the application of the mitochondrial DNA method to population genetics we also show the
applicability of this assay in our practical casework. We used the optimized Midi-Mito assay to
determine the haplotypes and their associated haplogroups of skeletons for which no or only few
STR genotyping information was available. Because of the high sensitivity of the mtDNA assay
profiles could be generated from picograms of DNA and highly degraded DNA.

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MtDNA analysis of Mocoví population, southern most Guaycurú speakers in South America
Sala A1,*, Martí MC2, Bobillo MC1, Corach D1
1
1- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires and
CONICET, Buenos Aires, Argentina
2
2- Centro Científico Tecnológico, CONICET, Santa Fe, Argentina

Mocoví is the south most ethnicity, linguistically associated to Pilagá, Toba and Wichi tribes,
representing the Mataco-Guaycurú speakers group. Mocoví inhabit Chaco and Santa Fe provinces
and amounts over 15.000 people. Aiming to increase the knowledge of Guaycurú speakers, Mocoví
individuals (N= 27) and additional Tobas (N= 47) from Santa Fe province were analyzed by means
mitochondrial DNA Control Region sequencing under EMPOP guidelines. The results were
compared with previously obtained sequence data of three ethnic groups that inhabit the area of
Argentinean Gran Chaco: Pilagá (N=55, from Formosa province), Toba (N=64), from Formosa and
Chaco provinces and Wichi (N= 48) from Formosa. The entire mtDNA Control Region (16024 to
576) was sequenced in a total of 241 unrelated individuals. Sequencing strategy included the use
of at least six primers for each sample in order to obtain unambiguous sequences. The four Native
American haplogroups (Hgs) were present in these groups, with diverse frequencies. Hgs B2 and D
(subhaplogroups D1 and D4g) are well represented in Pilagá, Toba and Wichi. Mocoví showed
high frequency in HgA (52%) meanwhile the frequency of HgD is very low (7%). Haplogroup C is
absent in Tobas and Wichi, whereas is present in Pilagá and Mocoví with a frequency around of
17%. The haplotype diversity in Mocoví sample was higher than the rest of the groups and highest
genetic distances were observed when this group was compared with Toba, Pilagá and Wichi.
Genetic distances were all significant, except between Toba´s groups. This work allowed us to
analyze the spread of mitochondrial lineages from Mataco-Guaycurú speakers and to find the
relationship between the individuals that inhabit nowadays the Argentinean Gran Chaco.

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A very high level of Native American ancestry in an Amazon, Brazil, urban population
inferred by mitochondrial DNA and indels markers analysis
Hermida RM1, Manta FS1, Silva DA1, Carvalho-Costa FA2, Monteiro M2, Moraes MO2, Carvalho EF1,*
1
State University of Rio de Janeiro, Rio de Janeiro, Brazil
2
Oswaldo Cruz Institute, Rio de Janeiro, Brazil

The Brazilian population is highly heterogeneous as a result of five centuries of interethnic mating
between Native Americans, European colonizers and Africans brought to the country during 3
centuries of slavery. This study aimed to assess the proportions of interethnic admixture in the
urban population of Santa Izabel do Rio Negro, Amazonas, Brazil, whose inhabitants are known as
descendants from Tukano Oriental and Aruak groups, using mitochondrial DNA (mtDNA) and
autosomal Ancestry Informative Markers (AIMs). A total of 100 individuals were characterized by
sequencing analysis of the full mtDNA control region.The haplogroups A, B, C and D that
characterize the mitochondrial amerindian lineages were present in very high frequencies as about
of 39%, 21%, 28% and 11%, respectively, while only one sample showed european ancestry. The
same population sample had been genotyped for 46 AIM-Indels markers and the ancestry estimates
were then assessed using HGDP-CEPH samples as ancestral reference. The global admixture
estimates showed a predominantly Native American ancestry (83,5 %) followed by European (12,0
%) and African (4,6 %) contributions.. The interethnic admixture scenery captured by autosomal
AIM-Indels and mtDNA genetic information at Santa Izabel do Rio Negro are in agreement with
historical records.

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Mitochondrial control region sequences of the Czech Republic population and a comparison
to other populations
Vanek D1,2,*, Silerova M1, Urbanova V1, Saskova L1, Dubska J1
1
Forensic DNA Service, Prague 8, Czech Republic
2
2nd Faculty of Medicine,Charles University in Prague, Prague, Czech Republic

The correct use of mitochondrial DNA (mtDNA) testing in the forensic context requires
appropriate population databases to determine the relative rarity of the haplotype of the tested
sample. The aim of this study was to evaluate the results of full HVRI and HVRII mtDNA
sequences of more than 250 unrelated individuals and to compare the data to the previously
published Czech population data obtained using PCR-RFLP. The Genetic diversity (GD) and
Random match probability (RMP) of the Czech mtDNA population data were also compared to the
other European populations. The results indicate that the full control region sequencing can bring
more precise population information that is useful for the comparison with other data sets and also
for the forensic identification purposes.

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Insertion/delection polymorphisms in South Portugal Caucasian population: a preliminary

study
Vieira Silva C1,2,*, Matos S3,1, Amorim A1,2,4, Afonso Costa H1,2, Morais P1,3, Marques Santos R1,2, Espinheira R1,2,
Costa Santos J5,2,6
1
Servico de Genetica e Biologia Forense, Delegacao do Sul do Instituto Nacional de Medicina Legal e Ciencias
Forenses, I.P., Lisboa, Portugal
2
CENCIFOR - Centro de Ciencias Forenses, Coimbra, Portugal
3
Biologia Molecular em Saude, Escola Superior de Saude Egas Moniz, Almada, Portugal
4
Antropologia Forense, Faculdade de Ciencias e Tecnologia da Universidade de Coimbra, Coimbra, Portugal
5
Servico de Clinica Forense, Delegacao do Sul do Instituto Nacional de Medicina Legal e Ciencias Forenses, I.P.,
Lisboa, Portugal
6
Medicina Legal e Ciencias Forenses, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal

Human genetic identification is usually based on the study of STR markers. Recent advances in
forensic genetics have focused on the development of genotyping assays using shorter amplicons
in order to improve the successful amplification of degraded samples. Single Nucleotide
Polymorphisms (SNP) and Insertion/Deletion polymorphisms (INDEL) have in this kind of
forensic samples, considerable potential in the field of identification, since they can combine
desirable characteristics of both, STR and SNP. In this study, a set of 30 biallelic
Delection/Insertion polymorphisms (DIP or INDEL) distributed over 19 autosomes plus
Amelogenin in a single multiplex PCR reaction was applied to 100 healthy and unrelated caucasian
individuals (50 males and 50 females) selected from our laboratory casework samples. DNA was
isolated from blood stain cells by chelex method and DNA concentrations were estimated by Real
Time PCR using the Quantifiler™ Human DNA quantification kit on an ABI Prism 7500 (Applied
Biosystems). INDEL’s amplification was performed with Investigator DIPplex® kit (Qiagen) in an
ABI Prism 3130xl, according to manufacturer’s instructions. Allele distribution, Observed (OH)
and Expected Heterozigoty (EH), and Hardy Weinberg (HWE) departure were estimated by
Arlequin 3.5.1.2. Preliminary results reveal that at the population level the overall loci meet HWE
(p<0.05) and so, in the near future, these markers will be an important tool in our routine genetic
identification.

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Internal validation of the AmpFlSTR Yfiler amplification kit and calculation of the genetic
diversity of 17 Y-short tandem repeats in the Norwegian population
Hellerud BB1,*, Lønning L1, Heitmann I1, Hansen EN1
1
Norwegian Institute of Public Health, Criminal Forensic Genetics, Oslo, Norway

A total of 290 haplotypes were identified using seventeen short tandem repeats included in the
AmpFlSTR Yfiler amplification kit. 264 (91%) of the haplotypes were unique and the overall
haplotype diversity was 0.997. Average locus diversity was 0.63. As a part of the internal
validation the stutter, N-banding and pull ups were calculated and were found to correspond to
Mulero et al. (2006). After implementation of the kit, the interlocus balance (rfu values) has been
found to be greater for the stains than reference samples.

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Y chromosome diversity in the South and East Kazakhstan

Tarlykov P1,2,*, Zholdybayeva E1, Ramanculov E1
1
National Center for Biotechnology, Astana, Kazakhstan
2
L.N. Gumilyov Eurasian National University, Astana, Kazakhstan

In the past, the territory of Kazakhstan has been inhabited by different nomadic tribes. Since then,
its territory has always been a keystone on the geopolitical map of the Central Asia. 17 Y-specific
STR loci have been analyzed in a total of 166 unrelated males from two different regions in
Kazakhstan in order to understand the genetic structure of the present day Kazakh population
represented in a current study by South Kazakhstan region (n=99) and East Kazakhstan region
(n=67). A questionnaire was filled by participants to confirm their ancestry up to the last three
generations. Sample collection, questionnaire and informed consent used in this study were
approved by an appropriate ethical committee. Multiplex PCR amplification of 17 loci was
performed using AmpFℓSTR® Yfiler™ kit (Applied Biosystems). The genotyping data have been
deposited to the Y-Chromosome Haplotype Reference Database (accession numbers YA003700,
YA003729, www.yhrd.com). A total of 92 different Y-STR haplotypes were observed in the
studied Kazakh population sample. Statistical analysis of data was carried out using Arlequin ver.
3.5.1.2 Overall haplotype diversity was 0.930 and discrimination capacity was 0.076. The
commonest haplotype 15-12-29-23-10-13-12-13,18-10-12-15-19-15-17-19-12 (DYS19, DYS389I,
DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS438, DYS439, DYS437,
DYS448, DYS456, DYS458, DYS635, GATA H4) was shared by 41 individuals from East
Kazakhstan region. The second most prevalent haplotype
16-13-29-25-10-11-13-12,13-10-10-14-22-15-17-21-11 was shared by 13 individuals from South
Kazakhstan region. Not a single haplotype was found to be common between South and East
Kazakhstan providing evidence for population substructuring. Absence of recent common
ancestors in these two subpopulations is also supported by a specific historical source of
information common for a few Central Asian countries, called “Shezhire”, which is a verbal and
sometimes written genealogical data kept in the families and passed down from father to son.

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Genetic structure of the Y chromosome does not suggest intraregional sex-biased dispersals
in the population of Asturias (Northern Spain)
Cano-Garcia C1, Pardinas A1, Garcia-Vazquez E1, Roca A1, Lopez B1,*
1
University of Oviedo, Oviedo, Spain

Traditional cultural and anthropological studies of the autochtonous population of Asturias have
indicated a deep-rooted custom of matrilocality, dated at least to the pre-Roman “Astur” tribes.
This custom is deemed to have important influences in the present-day distribution of social and
linguistic features inside this Spanish autonomous community. A previous survey found a
significant genetic structure for the mitochondrial DNA control region between different regions
of Asturias, indirectly supporting this theory. In this study, we performed Y-Chromosome
genotyping in 184 males with at least two generations of Asturian paternal ancestry, using 14 SNP
markers and 13 STRs. Haplotype data and place of birth of the paternal grandfathers of all the
volunteers were used in a SAMOVA analysis, which created maximally-differenced population
groups. Final between-group variation was significant and almost reached 5%, with a group
composition that was similar (but not equal) to that found for the mitochondrial DNA. BARRIER
and MIGRATE analyses were also performed to obtain male gene-flow tendencies between these
groups. This structure and its associated features are discussed in the light of historical and genetic
data, finding that sex-biased social customs cannot be invoked as important driving forces behind
the present day patterns of the Asturian gene pool.

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Y-STR haplotypes and the genetic structure of Pathan populations in FATA and NWFP of
Pakistan
Lee H1, Sim J1, Choi A1, Rakha A2, Yang W1, Shin K1,*
1
Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
2
Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan

The Pathans represent the tribes who speak Pashto and inhabit mainly the North West Frontier
Province (N.W.F.P.), adjoining tribal areas of Pakistan, and southern and eastern parts of
Afghanistan. Pathans are the second-largest ethnic group in Pakistan, and have reigned as the
dominant ethnic group in Afghanistan for over 300 years. Here, 22 Y-STRs were analyzed in 270
unrelated Pathans from N.W.F.P. and Federally Administered Tribal Areas (FATA) of Pakistan;
234 are from N.W.F.P. and 36 are from FATA. In haplotype analysis, 200 different haplotypes
were observed with haplotype diversity of 0.9957 in Pathans from N.W.F.P. and 32 different
haplotypes were observed with haplotype diversity of 0.9889 in Pathans from FATA. In analysis of
molecular variance between the neighboring Pathan populations inhabiting Afghanistan, Pakistan
and India, the Pathan population from N.W.F.P. did not show significant difference from Pathans
of North Afghanistan and Yousafzai Pathans of Khyber Pakhtunkhwa, Pakistan. Interestingly, the
Pathan population from FATA did not show significant difference from Afridi Pathans in India.
Considering that the Afridi Pathans of Pakistan mainly inhabit rough hilly area covering most of
the Khyber Agency, FR Peshawar and FR Kohat in FATA, the close genetic distance between
Afridi Pathans in India and the Pathan population from FATA of the present study and their large
genetic distance from other Pathan populations reveal a considerable regional stratification
between different Pathan population groups from Afghanistan, Pakistan and India but high
homogeneity between Pathan populations sharing the history of inhabiting the same region.

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Development of six-SNPs assay for forensic analysis in European population

Ferri G1,*, Ferrari F1, Corradini B1, Santunione A1, Alù M1
1
Department of Legal Medicine, University of Modena e Reggio Emilia, Modena, Italy

Y-chromosomal SNPs analysis show regional specificity useful in forensic investigation for
inferring the male genetic background of individuals and population and to predict biogeographical
origin of the donor of a crime scene sample. Due to its exclusively paternal inheritance, the
Y-chromosome has been extensively used in evolutionary and forensic genetics to investigate the
phylogeny and the history of population and their migration. A large scale parsimonious
phylogenetic tree representing worldwide Y-chromosome variation has been constructed and
comprises major haplogroups. The aim of this study was to set-up six multiplex assays based on
SNaPshot kit to identify markers inside major clades of European population. Specifically, we
design PCR and minisequencing primers targeting a total of 33 Y-mutations downstream R1*, I*,
J2*, G* and E1b1b1* haplogroups. The PCR fragments were chosen to get the shortest product
possible in order to improve the performance in degraded samples (amplicons principally ranging
from 56 bp to 140 bp). This assay based on a 6-multiplex PCR reaction is a suitable tool for
detecting the main European haplogroups in forensic casework and population study.

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Genetic journey of the N1c haplogroup

Pamjav H1,*, Nemeth E1, Feher T1, Volgyi A1
1
Institute of Forensic Medicine, Budapest, Hungary

Binary and Y-STR polymorphisms associated with the NRY region of the human Y chromosome
preserve the paternal genetic legacy that has persisted to the present, permitting inference of
human evolution, population migration and demographic history.The NRY region of the Y
chromosome acts much like mtDNA to reveal the structure among human populations and possibly
to infer the order and timing of their descents. In the present study, we have investigated the origin
of haplogroup N1c-Tat phylogeographic structure and the genetic relationship of Eurasian
populations by examining STR variation in a large number of individuals. We have identified 54
samples as the haplogroup N1c-Tat from 5 population groups (N=632). To place the results into a
wider geographic context, we included 209 samples from published sources and 296 samples from
the FTDNA public database into the phylogenetic analysis. According to previous studies
haplogroup N-M231 is of East Asian ancestry. Our results suggest that N1c-Tat mutation probably
originated in South Siberia 8-9 thousand years ago and had spread through the Urals into the
European part of present-day Russia. Its distribution is not fully correlated with the spread of
Uralic languages. Turkic-speaking ethnic groups in South Siberia have high N1c-Tat presence and
STR variance, while the N1c-L550 subgroup largely occurs among non-Uralic-speaking European
populations. Only the European N1c-Tat (xL550) subgroup can be linked to the spread of
Finno-Ugric languages from the Kama-Urals area ~6,000 years ago. The subgroup N1c-L550
cannot be considered Finno-Ugric origin and its carriers might have been assimilated by
Indo-European groups, resulting in their spread across Europe in historical times with Vikings and
Balto-Slavs. Based on the present study Buryats were dominated by a young, about 800-years old
N1c-Tat cluster, which suggest that this ethnic group could be a relatively recent admixture of
Mongolian conquerors with a Paleo-Siberian population groups.

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Phylogeographic analysis of human Y chromosome diversity in eastern Africa

Cruciani F1,*, Ippoliti M1, Massaia A1, D'Atanasio E1, Moral P2, Coppa A3, Trombetta B1, Sellitto D4, Pascone R5,
Scozzari R1
1
Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
2
Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
3
Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
4
Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
5
Dipartimento di Pediatria e Neuropsichiatria Infantile, Sapienza Università di Roma, Rome, Italy

Encompassing an area characterized by enormous geographic variety, as well as ethnic, linguistic

and cultural diversity, eastern Africa has seen remarkable levels of human migration and
interaction over a very long period of time. Despite its importance for the evolutionary history of
our species, this region has nonetheless seen less evolutionary genetic research than other regions
in the African continent. In a study of 750 males from 25 eastern African populations, we have
analyzed 107 Y-specific biallelic polymorphic markers, many of which here described for the first
time. We observed 44 different Y chromosome haplogroups, some of which - haplogroups
A-M13/V3, J-M267/V44, E-M215 and E-M329 - showed peculiar and interesting geographic
distributions in the region. Phylogeographic analysis of the data showed that the gene pool of
eastern Africa has been shaped by different processes associated with the physical geography of
the area, social structure of some populations, demic diffusions and important cultural innovations.

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Y-chromosome variation in geographically and linguistically isolated populations from

oriental Alps
Coia V1,2,*, Capocasa M3, Scarnicci F4, Boschi I4, Anagnostou P5, Battaggia C5, Crivellaro F6, Ferri G7, Brisighelli F8,5,
Busby G9, Capelli C9, Destro-Bisol G5,10
1
European Academy of Bolzano (EURAC-reserch), Institute for Mummies and the Iceman, Bolzano, Italy
2
Università degli Studi di Trento, Dipartimento di Filosofia, Storia e Beni Culturali, Trento, Italy
3
Università La Sapienza, Dipartimento Biologia e Biotecnologie “Charles Darwin”, Roma, Italy
4
Università Cattolica di Roma, Istituto di Medicina Legale e delle Assicurazioni, Roma, Italy
5
Università La Sapienza, Dipartimento Biologia Ambientale, Roma, Italy
6
Leverhulme Centre for Human Evolutionary Studies, Cambridge, United Kingdom
7
Università di Modena e Reggio Emilia, Dipartimento integrato di servizi diagnostici e di laboratorio e di medicina
legale, Modena, Italy
8
Universidade de Santiago de Compostela, Unidade de Xenética, Facultade de Medicina, Instituto de Ciencias
Forenses, Santiago de Compostela, Spain
9
University of Oxford, Department of Zoology, Oxford, United Kingdom
10
Istituto Italiano di Antropologia, Roma, Italy

As a result of ancient and complex peopling processes and the presence of physical barriers, the
Alpine area provides unique opportunities for anthropological and genetic studies of linguistic and
geographical isolation. In this study, we have investigated the genetic structure of thirteen
populations (for a total of 533 individuals) from the Eastern Italian Alps. These include six
linguistically isolated groups - five German-speaking communities (among which Cimbrians from
Luserna and Giazza, and the communities from Sappada, Sauris and Timau) and one
Ladin-speaking group from Trentino. All samples were typed for 17 microsatellites (Y-filer
profile) and 57 Single Nucleotide Polymorphisms in order to get an exhaustive overview of their Y
chromosome variation and haplogroups composition. Such results were compared with genetic
data available for European populations, with the aim of investigating the effect of linguistic and
geographic isolating factors on the genetic structure of the populations under study. Finally, we
carried out a comparative analysis between Y-chromosomal and mitochondrial data on the same
Alpine populations in order to test sex biased genetic patterns possibly related to cultural factors.

The research is supported by the “Provincia Autonoma di Trento” (Post-doc project “ BIOSTRE”
to V.C). and Ministero dell'Istruzione, dell'Università e della Ricerca (200975T9EW_004), La
Sapienza Università di Roma (C26A117JKC).

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Haplotype analysis of 23 polymorphic Y-STR markers in Northwest of Argentina

López-Parra AM1,*, Mesa M2, Brabo Ferreira Palha Td3,4, Gusmão L5, Lomaglio DB6, Baeza C1, García M2, Marrodán
M2, Pacheco JL7, Bejarano IF8, Dip NB6, Baillet G9, Arroyo-Pardo E1, Dipierri JE10, dos Santos SE3, Ribeiro dos
Santos K3
1
Laboratory of Forensic and Population Genetics. Dept. Toxicology and Health Legislation, Faculty of Medicine,
Complutense University of Madrid, Madrid, Spain
2
Departamento de Zoología y Antropología Física. Facultad de Biología. Universidad Complutense de Madrid.
Madrid, España., Madrid, Spain
3
Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém,
Para, Brazil
4
Centro de Perícias Científicas Renato Chaves, Belém, Para, Brazil
5
IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
6
Centro de Estudios de Antropología Biológica. Facultad de Ciencias Exactas y Naturales. Universidad Nacional de
Catamarca, Argentina, Catamarca, Argentina
7
Departamento de Enfermería. Escuela Universitaria de Enfermería, Fisioterapia y Podología. Complutense
University of Madrid, Madrid, Spain
8
Unidad de Investigación en Antropología Biológica. Facultad de Humanidades y Ciencias Sociales. Universidad
Nacional de Jujuy. San Salvador de Jujuy, Argentina, San Salvador de Jujuy, Spain
9
Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-
CONICET, La Plata, Argentina
10
Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina

Catamarca and Jujuy are two provinces of Argentina, placed in the extreme Northwest of the
country, close to the borders with Chile, and Bolivia. Both of them are included in NOA
(Northwest Argentina), one of the six historical-geographical regions that divide Argentina.
Different studies on South American populations have proposed that actual population is
composed by Native American maternal lineages and European paternal lineages with different
proportions of them among regions. 23 Y-STRs were studied in samples from autochthonous
individuals from Jujuy (n=59) and Catamarca (n=27), using PCR primers and conditions described
previously. To assign the most probable haplogroup of each individual, we used Haplogroup
Predictor program that assigns the most probable haplogroup from the Y-STR profiles. All samples
of the 2 populations show different haplotypes for 23 Y-STRs, except two males from Jujuy. The
total haplotype diversity was estimated at 0.9915 in Catamarca and 0.9959 in Jujuy according to
minimal haplotype. Results about inferred haplogroups showed that the population sample from
Jujuy was mainly composed by Native American haplogroup Q (49.15%), while the population
sample from Catamarca was mainly composed by European haplogroups (77.78%), mostly R1b.
Haplogroups distribution in Jujuy province, as some other populations from NOA, was different
from most of the populations outside NW of Argentina. The rest of provinces of Argentina show
higher frequencies in non Native American lineages, such as R1b or E, than in Native American
lineage, varying from one locality to another. Jujuy province shows a composition of haplogroups
of closer proximity to neighboring countries, such as Bolivia, which could suggest a common
origin or/and a continued gene flow.

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Y chromosome DNA variation monitored in Slovakian populations by SNP and STR analysis
Carnogurska J1,*
1
University of Presov, Presov, Slovakia

In the Slovak Republic live approximately 400.000 Romanies. The highest concentration of the
Romany population lives in Eastern Slovakia. Slovakian Romany population represents relatively
isolated ethnic group providing a unique opportunity for genetic study. This study provides
additional population genetic data of the three different East Slovakian populations. Many
Y-chromosomal single nucleotide polymorphisms (SNPs) are now available. The haplogroups
which they define are highly non-randomly distributed among populations. 49 Y-chromosomal
single nucleotide polymorphisms (SNPs) and 17 Y-chromosomal STR loci were tested in 525
unrelated male individuals from East Slovakia: Slovak population (n=243) and two Romany
populations: Romany group from region Spiš (n=125) and Romanies from region Prešov (n=157).
DNA was isolated from the buccal swabs using JetQuick kit according to the manufacturer's
protocol. Samples of DNA were amplified with the AmpFlSTR Y filer PCR Amplification Kit and
analyzed with Genetic Analyzer 3500 (Applied Biosystems,USA).The Y-SNP loci were tested with
the amplification of 10–12 ng genomic DNA, performed in ABI 7500 systems using TaqMan
probes. Haplogroup diversity values were calculated and the populations were compared with
G-test. The Slovakian Y chromosomal haplogroups were R1a1-M198, R1b1-P25. In the Romany
population from Prešov it was haplogroup H1a-M82 and R1a1-M198. In Romany group from Spiš
the most frequent haplogroup was J2a2-M67. The H1a-M82 haplogroup was the most frequent in
both Romany groups with the frequency as high as 50%. The Romany populations were
significantly different in comparison with Slovakian population. This work is the result of the
implementation of the project ITMS 26220120041. Keywords:Y-chromosome; SNPs; STR,
Romanies, Slovakia

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Y chromosome diversity in Piedmont

Caratti S1,*, Di Gaetano C2,3, Matullo G2,3, Gino S1, Inturri S1, Robino C1
1
Department of Anatomy, Pharmacology and Legal Medicine, University of Turin, Turin, Italy
2
Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy
3
HuGeF, Human Genetics Foundation, Turin, Italy

Y-chromosomal variability of 17 short tandem repeat (STR) and 18 single nucleotide

polymorphisms (SNP) loci was evaluated in three different population samples from Piedmont
(North West Italy): Biella (Northern Piedmont, n=80); Trino (Central Piedmont, n=46); Cuneo
(Southern Piedmont, n=90). Participating individuals were carefully selected based on their
genealogical ancestry: Biella and Cuneo samples included adult males with at least three
generations of residence (thus predating the industrial immigration from Southern Italy that took
place in the 1950s); the Trino sample consisted of subjects belonging to an association dating back
to the Middle-Ages, which limits membership to families who have been settled in the village
since the 13th century.

AMOVA analysis of Y-SNP haplogroups indicated a variation among individuals within and
among sampling areas of 99.97 and 0.03% (p=0.378±0.013), respectively. Trino showed reduced
values of Y-STR haplotype diversity (h=0.983), compared to Cuneo (h=0.999) and Biella
(h=0.998). Absence of significant variation among sampling areas (0.10%, p=0.350±0.004) was
confirmed by AMOVA at haplotype level, andno significant differences were observed when
pairwise genetic distances (RST) between the three samples were calculated. On the contrary,
multiple significant RST values were obtained when Piedmont samples were compared with
available population data from North East, Central and South Italy.

The obtained results confirm that, although the Y-chromosomal landscape of Piedmont seems
fairly homogeneous, genetic heterogeneity is present in Italy at the inter regional level.

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Genetic analysis of 17 Y-STR loci in Pashtun population from Swat Valley, Pakistan
Achakzai NM1,*
1
CEMB, Lahore, Pakistan

17 Y-Chromosomal short tandem repeats (Y-STRs) included in the AmpFlSTR Yfiler

amplification kit (Applied Biosystems, Foster City, USA) DYS19, DYS389I, DYS389II, DYS390,
DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456,
DYS458, DYS635 and Y-GATA-H4 were analyzed in 71 unrelated Pashtun (Pathan) males
residing in the Swat Valley of Khyber Pakhtunkhwa province, Pakistan. A total of 43 unique
haplotypes were observed. The predominant haplotype reached a frequency of 23.94%. The
haplotype diversity was 0.860465 and the discrimination capacity 60.56%. Analysis of molecular
variance (AMOVA) reveals a considerable regional stratification within the country as well as
between different Pashtun (Pathan) groups living in Pakistan.

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Novel Y chromosome polymorphisms in Native American haplogroup Q1a3a1

Alechine E1, Corach D1,*
1
Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires and
CONICET, Buenos Aires, Argentina

Since 1996, when DYS199 marker was first described on the Y chromosome (Underhill et al),
Native American populations have been characterized by DYS199/M3 polymorphism. The high
frequency of its derived state, attaining 77% in Native American males (Bortolini et al. 2003),
might be explained by: (a) an extremely reduced number of colonists carrying this marker or (b)
increased reproductive fitness. Y-chromosome characteristics related to male fertility may
influence the high prevalence of haplogroup Q1a3a1 within Native Americans. Therefore, the aim
of this work was to analyze STS markers on the Y chromosome linked to fertility in samples from
confirmed fathers belonging to haplogroup (hg) Q1a3a1 and reference hg R1b1a2. Unrelated male
samples from routine paternity casework have been analyzed including those belonging either to
hg Q1a3a1 or R1b1a2. Paternity was assessed by PowerPlex®16 and Y-chromosome haplogroups
by Real Time PCR followed by HRM. Afterwards, sY1261, sY1191, sY1291, sY1206 and sY1201
STS markers located in AZFb/c regions have been amplified and analyzed by capillary
electrophoresis. A novel SNP variant was found on the distal copy of the sY1206 marker showing
a G>T variation exclusively in haplogroup Q1a3a1. Moreover, marker sY1291 showed a 21bp size
difference between haplogroup Q1a3a1 (517pb) and R1b1a2 (538pb) due to a homopolymeric T
track. This last finding is in concordance with previously published results (Lin et al. 2006), where
a length difference was first characterized for this marker but not linked to any haplogroup or
population. Nevertheless, no differential deletions of the Y-STSs markers analyzed were found
between haplogroup Q1a3a1 and R1b1a2, conversely to what has been previously described
(Repping et al. 2004, 2006). These results were consistent within all the analyzed samples. The
present results describe two novel Y chromosome polymorphisms and disprove the presence of the
b2/b3 deletion as a characteristic of hg Q1a3a1.

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Population data for 8 Y-chromosomal STRs (not included in Y-filer™ kit) in a population
sample of Czech Republic
Vanek D1,2,*, Saskova L1, Silerova M1, Dubska J1,1
1
Forensic DNA Service, Prague 8, Czech Republic
2
2nd Faculty of Medicine,Charles University in Prague, Prague, Czech Republic

The newly designed Y-chromosome miniSTR pentaplexes I and II include 8 “non-core“ Y-STR
loci DYS388, DYS426, DYS444, DYS446, DYS447, DYS449, DYS459, DYS481 plus additional
2 Y-STR loci DYS392 and DYS438 that overlap with the of Y-filer™ kit. The amplicon sizes
were designed as “miniSTRs” so the pentaplexes can be also used for degraded and ancient DNA
typing. The Y-pentaplexes I and II were used to obtain the allele frequencies and gene diversities
for the population sample of more than 140 unrelated individuals from the Czech Republic.The
data show that the additional Y-STR loci (on top of Y-filer) are extremely useful not only in the
complex genealogical studies but also as a research tool for the Y-chromosome and surname
correlation studies.

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Y-STR haplotype diversity of a native population of Cabo Verde living in Lisboa

Marques Santos R1,2,*, Amorim A1,2,3, Afonso Costa H1,2, Vieira Silva C1,2, Morais P1,4, Matos S1,4, Espinheira R1,2,
Costa Santos J5,2,6
1
Servico de Genetica e Biologia Forense, Delegacao do Sul do Instituto Nacional de Medicina Legal e Ciencias
Forenses, I.P., Lisboa, Portugal
2
CENCIFOR - Centro de Ciencias Forenses, Coimbra, Portugal
3
Antropologia Forense, Faculdade de Ciencias e Tecnologia da Universidade de Coimbra, Coimbra, Portugal
4
Biologia Molecular em Saude, Escola Superior de Saude Egas Moniz, Almada, Portugal
5
Servico de Clinica Forense, Delegacao do Sul do Instituto Nacional de Medicina Legal e Ciencias Forenses, I.P.,
Lisboa, Portugal
6
Medicina Legal e Ciencias Forenses, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal

Cabo Verde is an African archipelago located in the West African coast of the Atlantic Ocean.
Historically, native population of Cabo Verde is the result of an admixture of Caucasian European
colonizers and African slaves. As well as it occurs all over Europe, in Portugal and particularly in
Lisboa, immigrant populations are clearly increasing. According to Portuguese Foreign Affair
Services, in 2010 the number of immigrants from Cabo Verde living in Lisbon was up to 34234.
The Y-chromosome, male specific and constitutively haploid, is one of the smallest human
chromosomes with an average size of 60 million base pairs that largely escapes to meiotic
recombination. The combinations of allelic variants of markers along the chromosome, defined as
haplotypes, pass intact from generation to generation. They change only by mutation and so
preserve a record of their history. This unique biology has led to the widespread use of genetic
markers in determining patrilineal relationships and haplogroups within and between populations,
with application in population studies and provides a powerful discrimination tool for routine
forensic applications. The main goal of this study is to complement our previous studies with
autosomal STR, X-chromosome and mitochondrial DNA of genetic structure of Cabo Verde
immigrants, with patrilineal/Y-haplotype characterization. We studied a sample of 50 unrelated
and healthy male individual’s natives of Cabo Verde, actually living in Lisboa and undergoing
forensic investigations in Portuguese Instituto Nacional de Medicina Legal e Ciências Forenses.
We analysed the markers included in the European Minimal Haplotype (EMH): DYS19,
DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393, recommended by
the International Y-STR User Group for Identity Testing, plus the DYS437, DYS438 and DYS439,
recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and also
DYS448, DYS456, DYS458, DYS635 e GATA H4, to increase haplotype and gene diversity.

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Y-chromosomal STRs mutation analysis by the PowerPlex® Y23 system

Ceccardi S1, Riccardi LN1, Fersini F1, Lanzellotto R1, Falconi M2, Bini C1,*, Pelotti S1
1
Department of Medicine and Public Health, Section of Legal Medicine, University of Bologna, Bologna, Italy
2
Department of Anatomical Sciences, University of Bologna, Bologna, Italy

Y-STRs analysis is a useful tool in forensic casework especially for kinship testing as well as in
genealogical research for inference on population history and evolution. The new commercial kit
PowerPlex® Y23 system (Promega) allows for the detection of seventeen commonly used Y-STR
loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438,
DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA-H4) plus six new highly discriminating
Y-STR loci (DYS481, DYS533, DYS549, DYS570, DYS576, DYS643) increasing the ability to
distinguish individuals from different male lineages and providing more meaningful analyses. In
this study, we analyzed the 23 Y-STR markers of the PowerPlex® Y23 system in a particular
deficiency paternity case, previously typed with a different commercial kit, which showed single
repeat mutations at DYS439 and DYS385. In addition, we investigated a total of 60 male germline
transmissions of confirmed paternity cases (probability > 99.9%) reporting preliminary data about
mutation rates of the six new Y-STR loci. Knowledge about mutation rates and the mutational
process of Y-chromosomal STRs is crucial for the correct interpretation of resulting genetic
profiles and for improving forensic probability calculations. This study increases Y-chromosome
haplotypes data and provide a contribution to the Y-STR mutation databases as requested by the
forensic community.

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Determination of the Y chromosome DNA haplotype and mtDNA haplotype from 50 males
from 17 countries
Takasaka T1,*
1
Kyoto Prefectural University of Medicine, Kyoto, Japan

To obtain reference DNA necessary to identify the ethnicity of males, we compared the detection
rate of haplotype Y chromosome DNA of 50 men from 17 countries. Additionally, mtDNA
haplotypes were determined and they were considered as the reference for maternal ethnic
identification. In low diversity Y-STR loci (DYS389 I, DYS391, DYS439, DYS392, H4, DYS437)
weak differences in allele patterns were present among the three ethnic groupings. However, the
DYS385ab locus displayed high diversity of allele types and allele pattern differences varied with
ethnicity. Within locus DYS390 allele 21 was absent from European, rare in Asian and
predominate in African samples. Utilizing ISOGG classifications it was possible to determine
Y-haplogroup from pre-determined Y-SNP ratios. In the future, urban crime, large natural
disasters and accidents have the possibility of increasing as globalization progresses. In such
ethnically mixed urban areas it will be increasingly necessary to determine the ethnic origin of
individuals. In these cases it is necessary to perform quick individual identification through DNA
typing. For this to take place, in addition to the establishing of a methodology, further collection of
DNA polymorphism information from each ethnic group is necessary.

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Forensic efficiency of combined Y/mt profiles in seven Iranian groups

Bertoncini S1, Farjadian S2, Taglioli L1, Ghaderi A2, Romeo G3, Luiselli D3, Tofanelli S1,*
1
University of Pisa, Pisa, Italy
2
Shiraz University of Medical Sciences, Shiraz, Iran
3
University of Bologna, Bologna, Italy

Despite cultural and geographic barriers, the genetic landscape of Iran as defined by Y-STR and
mt-HVSI markers is considered fairly homogeneous. Hence, low LR values for both, individual
and ethnic assignment of the DNA evidence, may be obtained. In the present research, haplotypes
at Y-filer and HVSI panels of loci were analyzed in 130 healthy unrelated males from seven
Iranian native groups. A separate analysis of the haplotype profiles failed to detect a population
sub-structure whereas the outlying position of three ethnic groups (Balochs, Qashqaee and
Zoroastrians) as well as maximum levels of genetic diversity and discrimination capacity (H,
DC=1) were obtained in every group by combining the two profiles.It can be argued that, when
combined, the forensic efficiency of routinely used panels of loci can be largely sufficient to
resolve cases of human identification even in genetically homogeneous populations.

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Ancestry evaluation of Rio de Janeiro population by screening the Y chromosome and

mitochondrial DNA
Oliveira AM1, Hermida RM1, Silva DA1, Gusmao L2, Carvalho EF1,*
1
State University of Rio de Janeiro, Rio de Janeiro, Brazil
2
IPATIMUP, Porto, Portugal

The Brazilian population is derived from an admixture between Native Americans, Europeans,
mainly Portuguese, and Africans, which are mainly bantu speakers that had been brought to the
country as slaves between the XVI and XIX centuries. The historical records lack information
concerning the regions of Africa from where the slaves had been taken to America. The analysis of
17 Y-STR loci in 152 healthy self declared afro-descendants revealed 151 different haplotypes
with eleven of them showing typical bantu founder profiles. The haplotypic diversity was very
high (0.9988/+-0.0003), revealing no strong founder effects. Additionally, 43 Y-SNP markers were
typed in the same samples allowing the discrimination of 15 haplogroups. A significant proportion
of European lineages (71%) were detected, followed by African (26%) and Amerindian (3%)
lineages. African chromosomes were mostly represented by E1b1a-M2 and E1b1a7-M191
chromosomes that are the most frequent ones in all Bantu groups, including those in Central
Africa. The haplotypes from samples carrying typical African haplogroups were compared with
those found in several bantu populations. Pairwise FST showed no significant genetic distance
among the self declared African descendants from Rio de Janeiro and Angola populations (FST =
0.06131 , p= 0.00069 ± 0.0003). Out of 152 samples, 70 were sequenced for the entire mtDNA
control region in order to provide maternal ancestry information. The mtDNA data showed a very
important African contribution (81%), represented mainly by the L0, L1, L2 and L3 haplogroups,
followed by Amerindian (14%), represented by the haplogroups A and C, and a lower number of
European lineages (4%). In summary, concerning the Rio de Janeiro population, the
Y-chromosome lineages of self declared afrodescendants, show a major contribution of Europeans,
followed by Africans and, to a lesser extent Amerindians, as we have already described for the
general population. On the other hand, data from mtDNA revealed to be the African, followed by
the Amerindian, the mainly maternal inheritance sources contributing to both samples from general
population and self declared afro-descendants from Rio de Janeiro population, while a poor
European lineages contribution has been observed.

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Haploid markers in DNA identification process in Croatia

Furač I1,*, Karija Vlahović M1, Mašić M1, Kubat M1, Strinović D1
1
School of Medicine, Zagreb, Croatia

Identification process in Croatia involves DNA based identification since the method was
recognized as the precise and straightforward way to answer the question of identity. The majority
of identification cases are those of war victims’ remains. As the time goes by, DNA analysis is
taking over the most important role in the identification process because bodies exhumed twenty
years after the death could hardly be identified by any other method. For many reasons, such as
cost effectiveness and informative results, typing of nuclear STR markers using different multiplex
kits is the first choice. It has been almost 15 years since we introduced haploid DNA markers as a
method of choice for typing samples to help identification of skeletal remains. In some cases, even
when genomic DNA was successfully amplified, the additional information was still needed for
final conclusion. Y chromosome STR multiplex kits are especially useful in cases when only male
relatives are available for testing. When the genomic DNA is present in a low copy number, it is
severely degraded or only distant relatives are available, we sequence two hypervariable segments
(HV1 and HV2) within the mitochondrial non-coding region. Here we will present several
identification cases where haploid typing results were very helpful in establishing the identity of
the human remains.

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Forensic science applied on prehistoric remains - a nine fold burial of the 4th millennium BC
raised questions about kinship, locality, and circumstances of death
Friederich S1,*, Schlenker B1, Stecher M2, Bauer CM3, Niederstätter H3, Parson W3, Karimnia S2, Meller H1, Alt K2
1
Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt mit Landesmuseum für Vorgeschichte, Halle,
Germany
2
Bioarchaeometry Group, Institute of Anthropology, Johannes Gutenberg-University of Mainz, Mainz, Germany
3
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

A monumental earth construction of the Salzmünde culture (3400-3025 BC) with 165 burials was
discovered during excavations at the eponymous site Salzmünde in Saxony-Anhalt, Germany.
Especially a multiple burial with potsherd filling that contains four adult women and five subadults
raised questions about kinship, locality and cause of death. This exceptional ninefold burial is the
matter of a transdisciplinary and integrative project combining archaeological, anthropological,
stable isotope and palaeogenetic analyses. Our aim is to shed light on the relationships of the
individuals of the ninefold burial and the circumstances that lead to the death of these people. In
order to evaluate biological kinship DNA was extracted from bone and tooth samples of seven
individuals. Mitochondrial haplotypes and haplogroups were identified by sequencing of the
hypervariable segments I and II of the control region and by analyzing 22 diagnostic coding region
single nucleotide polymorphisms. We were able to obtain reproducible endogenous DNA from all
individuals investigated. Among these seven individuals we found three different mitochondrial
lineages ascertained to distinct haplogroups suggesting maternal kinship among the individuals in
the ninefold burial.Combining the results of every discipline of the ongoing project, it is currently
not possible to define the circumstances of death. However, several burn marks on the bones of the
individuals as well as other signs of violence seem not to be caused by a catastrophe and lend
support for a violent raid or a ritual mortuary practice. Further analyses will show, whether the
Salzmünde people have been victims of an act of war or ritual practices.

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Establishment of mitochondrial SNPs for the investigation of skeletal material buried in the
ground
Thiele K1,*, Pflugbeil A1, Kohl M1, Bruchhaus H1, Dressler J1
1
Institute of Legal Medicine, University of Leipzig, Leipzig, Germany

In forensic and anthropological work on cases of degraded skeletal materials, the analysis of
mitochondrial SNPs is of vital importance; this will be shown in a spectacular skeleton find on the
premises of the prison in Chemnitz, found in 2002 through excavation works. For each individual,
the investigations were carried out at cranial and postcranial parts of skeletons, which had been
buried in the ground for about 60 years, and the respective teeth, as far as available. Following the
appropriate mechanical cleaning and crushing, DNA isolation was carried out by a combination of
the All-tissue DNA kit of the enterprise GENIAL and a DNA cleaning by phenol chloroform. The
quantities of bone and tooth manure included in the DNA isolation ranged from 0,8 g and 2,5 g.
After inquiry in the literature (Brandstätter et al., Vallone et al.) 24 SNPs were chosen from the
coded and non-coded region of the mtDNA. For single base extension, SNaPshot Multiplex Kit
(Applied Biosystems) was used. The analysis of the samples was carried out with the ABI
PRISMTM 310 Genetic Sequenzer. With this applied DNA separation method it was possible to
typify mitochondrial SNPs of skeletal material, which even with STR-analysis is difficult to
investigate. This established method is the basis of ancestry investigations with medieval skeleton
finds.

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Huns in Bavaria? Genetic analyses of an artificially deformed skull from an early medieval
cemetery in Burgweinting (Regensburg, Germany)
Schleuder R1,*, Wilde S1,2, Burger J2, Grupe G1, Forster P3, Harbeck M4
1
Department Biology I, Ludwig-Maximilians-University, Munich, Germany
2
Department of Anthropology, Johannes Gutenberg-University, Mainz, Germany
3
Institute of Forensic Genetics, Münster, Germany
4
State Collection of Anthropology and Palaeoanatomy, Munich, Germany

The morphological examination of an early medieval burial site in Burgweinting, which is dated to
the end of the 5th century, revealed one female with an artificially, circularly deformed skull, a
practice that is thought to be associated with the arrival of Nomads of the Eurasian steppe,
particularly the Huns.

Individuals with such artificial cranial deformations also can be found in other Late Roman and
Early Medieval cemeteries in Europe mostly in the Carpathian basin but only as few isolated cases
in Western Europe, where mostly women show such deformations.

Regarding the artificial cranial deformations it is unclear whether a foreign custom was taken over
by Germanic tribes or whether the individuals were members or descendants of Eurasian nomads.

With the help of the find of Burgweinting, we exemplarily investigated this question.To identify
the possible foreign origin of this female with alleged “Asian” skull deformation we sequenced the
HVRI and HVRII region of the mitochondrial DNA.

Our results show that the ancestry of a woman with artificially deformed skull can be linked to an
at least partly Asian origin. So this indicates that at least some of the few individuals with skull
deformation had not adopted the costume but can be seen as former members or descendants of the
hunnish tribal community.

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Assessment of the origins of ancient Croatian remains through mitochondrial DNA

interpretation
Phillips LA1, Fox A1, Primorac D2,*, Holland M1
1
Penn State University, State College, United States
2
University of Split, Split, Croatia

Croatia as a modern country is relatively new, stemming from the disbanding of Yugoslavia, but
the roots of its people span back for thousands of years. In the course of that time varied
populations of people have passed through the area, each leaving their mark on the mitochondrial
DNA (mtDNA) of the region. While the population of the country is primarily Croat now, there are
various other groups such as Serbs residing on the land as well. A look at the mtDNA of past
residents will portray the influence of the nomadic Slavic groups of the region, as well as that of
previous Germanic and Frankish rule. Mass graves found in the early 1980s have been unearthed
as the country led itself into a more modern future, yet the questions of the origins of these
remains are still largely unanswered. This joint project between the Pennsylvania State University
and the University of Split in Croatia will assess mtDNA profiles from remains of a Croatian
gravesite in Šopot-Benkovac. While 10 samples have been analyzed so far, extracted by
demineralization and targetting the HV1 and HV2 regions of the mitochondrial genome, inhibition
was observed in preliminary testing. This is a common occurrence in ancient bone, along with
DNA degradation, so to combat the inhibition we have conducted extractions with the Prepfiler
BTA DNA Extraction Kit from Applied Biosystems. Initial results from the use of this kit have
indicated a promising reduction in the inhibition, wiwith sufficient DNA yields for analysis.
Haplogroups observed thus far are H1 and U. The ancestral route of the Croat people has not been
completely elucidated, and so much can still be learned from these uncovered bones and teeth.

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Genetic relationship between modern populations and the Neolithic Tyrolean Iceman
Coia V1,*, Cipollini G1, Maixner F1, Brisighelli F2,3, Capelli C4, Battaggia C3, Destro Bisol G3,5, Zink A1
1
European Academy of Bolzano (EURAC-research), Institute for Mummies and the Iceman, Bolzano, Italy
2
Universidade de Santiago de Compostela, Unidade de Xenética, Facultade de Medicina, Instituto de Ciencias
Forenses, Santiago de Compostela, Spain
3
Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
4
Department of Zoology, University of Oxford, Oxford, United Kingdom
5
Istituto Italiano di Antropologia, Roma, Italy

After its discovery in the Italian part of the Ötztal Alps in early 90s, numerous archaeological,
biochemical and genetic studies have been concerned with the mummified body of the Tyrolean
Iceman, an individual who lived in the south ridge of the Alpine area during the Copper Age
(about 5,300 y.a). However, some important questions remain unresolved. The key aspect regards
the genetic relationships between the Iceman and modern populations. In fact, recent study on the
complete genome of the mitochondrial DNA showed that the Iceman belonged to a branch of
haplogroup K1 (named K1f or K1Ö defined by two specific mutations, the 3513T and 8137T),
that has not yet been found in extant populations. These results suggests that this lineage could be
now extinct or very rare. However, this study was limited by the scarcity of data from modern
European populations, especially from the Alpine region of interest. In the framework of the
ongoing project “Reconstruction of the peopling of Eastern Alps by analyzing the genetic
variability of modern populations and comparison with ancient DNA data” we are analyzing the
complete mtdna genome of K lineages (at least 50) from different areas of oriental alps and
collecting all complete K mtdna data available from literature. The genetic data will be analyzed in
order to get an updated phylogenetic tree of haplogroup K in Europe and to test the presence of
lineage related to the Iceman.

(The project is supported by the “Provincia Autonoma di Bolzano – Alto Adige, Ripartizione
Diritto allo studio, università e ricerca scientifica, Postdoctoral Research Fellow to V. C).

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Molecular genetic analyses of skeleton excavated from Auersperg Chapel archaeological site
in Slovenia
Pajnič IZ1,*, Pogorelc BG1, Balažic J1, Horvat M2
1
Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
2
City museum of Ljubljana, Ljubljana, Slovenia

In 2009 the archaeologists excavated five skeletons from the 17th century archaeological site in
Ljubljana. They were found in the side chapel of the church in the Franciscans monastery which
was the Auersperg tomb. Beside the skeletons the bronze bowl with the heart was found and the
name of Ferdinand II and the year of death (1655 - 1706) engraved. The Auersperg (Turjaški) were
the most influential aristocrat family on Slovenian territory and one of the richest in Hapsburg
empire. In 2011 we have been asked for identification of five skeletons excavated from the
Auersperg chapel. Skeletons were badly remained and bones degraded to small peaces. Fragments
of femurs and teeth were preserved only for two skeletons and for the rest of three skeletons the
fragments of cranium were used for molecular genetic analyses. We cleaned the bones and teeth,
removed surface contamination, and ground them into powder using liquid nitrogen. Prior to DNA
isolation bone or tooth powder was decalcified. The nuclear DNA of the samples was quantified
using real-time polymerase chain reaction. We extracted up to 10,7 ng DNA/g of bone and tooth
powder from Auersperg chapel archaeological site skeletal remains. We obtained complete genetic
profile of autosomal DNA, Y-STR haplotype, and mtDNA haplotype for HVI and HVII region
from one skeleton. For traceability in the event of contamination, we created an elimination
database including genetic profiles of the nuclear and mtDNA of all persons that had been in
contact with the skeletal remains and no match was found. We are waiting for the family reference
samples for comparison with genetic profiles obtained and for identification of the skeleton
excavated from Auersperg chapel archaeological site. This is the first archaeogenetic research in
Slovenia.

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DNA analysis of lineage markers (mtDNA and Y-chromosomal STRs) on ancient or aged
bone samples
Vanek D1,2,*, Saskova L1, Urbanova V1, Dubska J1, Silerova M1, Beran M2
1
Forensic DNA Service, Prague 8, Czech Republic
2
2nd Faculty of Medicine,Charles University in Prague, Prague, Czech Republic

Bone samples belong to the group of the most challenging samples we can face during our forensic
practise. Criminal cases involving up to 20-years old skeletons are not rare and having a robust
and reliable DNA extraction and STR typing method is a must. Work with the ostheological
specimen that is several hundred years old is even more challenging and the chance of false
negative or false positive identification results is increasing with the longer post-mortem interval
and bad storage conditions. The authors of this talk will demonstrate how can be the DNA
analysis of lineage markers (mtDNA and Y-chromosomal STRs) utilized during the process of
DNA based identification of ancient or aged bone samples.

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Forensic genetic analysis for the AmpFlSTR Yfiler system in the Korean population
Kim S1, Kim K2, Han M3, Kim W2,*
1
Eastern District Office, National Forensic Service, Wonju, South Korea
2
Dankook University, Cheonan, South Korea
3
Forensic DNA Center, National Forensic Service, Seoul, South Korea

Y chromosome short tandem repeats (STRs) are a powerful tool for forensic purposes and
evolutionary studies. We have analyzed variation of 17 Y-STR loci contained in the AmpFlSTR
Yfiler PCR amplification kit in a sample of 105 unrelated individuals for the same samples
recently typed for a set of rapidly-mutating Y-STRs (RM Y-STRs) from Korea. Allele frequencies
and forensic parameters have been used to evaluate suitability and robustness of the kit for
forensic genetic analyses. A total of 103 haplotypes were identified, 101 of which were unique.
Total haplotype diversity was greater than 99.96% for the Korean population. The lowest gene
diversity studied was 0.333 for DYS391 and the highest 0.968 for DYS385a/b. Discrimination
capacity was 98.10%. Multidimensional scaling (MDS) plot of genetic distances (4̅D) calculated
from allele frequencies of the 17 STR loci with published data showed that the Koreans appeared
to have the most genetic affinity with the Vietnamese, followed by Japanese and Mongolian
Khalkh of the East Asians but tend to be different from the Europeans. Our data, therefore, can be
used to extend the results obtained with other STRs, as well as provide valuable information for
forensic and population genetic studies in the Korean population.

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Genetic polymorphisms of 19 STR Loci in the Chaoshan Han population

Shang J1, Hu S1,*, Chen S1
1
Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China

[Objective] To investigate the genetic polymorphism of the 19 short tandem repeat(STR) loci
D8S1179, D21S11, CSF1PO, D3S1358, D7S820, TH01, D13S317, D2S1338, D18S51, D16S539,
TPOX, vWA, D19S433, D5S818, FGA, PentaD, PendaE, D12S391, D6S1043 in Chaoshan Han
population, and to compare the forensic application of the three different kits: PowerPlex
16、Identifiler and Sinofiler. [Methods] Allele frequencies for 19 STR loci were determined in a
sample of 1004 unrelated Chinese individuals from Chaoshan area of Guangdong Province, a
littoral located in the southeast of the Mainland China. The allele frequencies and statistical
analysis were performed using the Modified-powerstate program. [Results] A total of 227 alleles
and 872 genotypes were detected. The allele frequencies vary between 0.001 and 0.570, the
genotype frequencies between 0.001 and 0.347, the observed heterozygosity (Ho) between 0.588
and 0.884, and the polymorphic information content (PIC) between 0.51 and 0.90. No deviations
of the observed allele frequency from Hardy-Weinberg equilibrium expection were found for
Chi-square test (P>0.05) except D2S1338 loci. Total discrimination power (TDP) of 19 STR loci is
0.999999999999999999999316072. The TDP of PowerPlex 16, Identifiler, and Sinofiler are
0.99999999999999999454124,0.9999999999999999887466,0.99999999999999999952528,
respectively. The cumulative probability of paternity exclusion (CPE) for triplet cases with 19
STR loci is 0.9999999868343, and the CPE of PowerPlex 16, Identifiler, and Sinofiler are
0.99999870529, 0.99999823985, 0.999999682455, respectively. [Conclusion] All 19 STR loci
showed highly polymorphic in Chaoshan Han population. The three kits are all suitable for
forensic work for the Chaoshan Han population, among which Sinofiler is the most powerful
system. The allele frequencies reported in this study would serve as a reference database for
personal identification and paternity testing.

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Central Croatian population data of eight X-linked markers in four linkage groups
Gršković B1,2,*, Mršić G1,2, Zidkova A3,4, Vrdoljak A1,2, Stenzl V5, Popović M2,6, Primorac D7,8,9,10
1
Forensic Science Centre “Ivan Vučetić”, General Police Directorate, Ministry of Interior, Zagreb, Croatia
2
University Center for Forensic Sciences, University of Split, Split, Croatia
3
First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
4
Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
5
Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
6
Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
7
University of Split, Medical School, Split, Croatia
8
University of Osijek, Medical School, Osijek, Croatia
9
Eberly College of Science, Penn State University, Pennsylvania State, United States
10
University of New Haven, New Haven, Connecticut, United States

The analysis of short tandem repeats (STRs) located on X chromosome shown to be particularly
powerful in solving complex kinship cases. The aim of this study was to analyze 8 X-STRs in
central Croatian population. We carried out a statistical analysis of the data from previously
performed genetic analyses collected during routine forensic work by the Forensic Science Centre
‘‘Ivan Vučetić’’. A total of 99 unrelated healthy women and 78 men from central Croatia were
typed using Mentype Argus X-8 PCR amplification kit. The allele and haplotype frequencies were
determined by counting. Haplotype frequencies were calculated only in male samples. Arlequin
3.5 software was used to assess Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD),
observed and expected heterozygosity. For HWE and LD tests Bonferroni correction was used.
Power of discrimination (PD) for males and females was calculated according to Desmarais.
Polymorphism information content (PIC) was determined using online database ChrX-STR.org
that calculates population-genetic data. In female samples deviations from HWE (p>0.00625) for
each locus were not found. LD test performed on female and male samples, revealed no significant
association between markers (p>0.00178). In 78 men, 37, 30, 35 and 30 haplotypes were found for
linkage groups 1-4. Locus DXS10135 was the most polymorphic (PIC=0.9306). DXS7423 and
DXS8378 loci showed the lowest values (0.6316 and 0.6447). PIC for whole marker set was
0.999998. PD varied from 0.6922 to 0.9345 in male and from 0.8447 to 0.9918 in female samples.
Combined PD reached 99.9999% in males and 99.99999999% in females. Further analyses that
will include more X-STR loci are needed to increase discrimination power for kinship and
paternity testing as well as population genetics studies. Nevertheless, Mentype Argus X-8 kit can
be used as an additional marker panel for forensic identification and complex kinship cases in
central Croatian population.

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Canine mitochondrial genome sequencing to improve the genetic profiling of dog hair
Verscheure S1,*, Desmyter S1, Backeljau T2,3
1
National Institute of Criminalistics and Criminology, Brussels, Belgium
2
Royal Belgian Institute of Natural Sciences, Brussels, Belgium
3
University of Antwerp, Antwerp, Belgium

Genetic identification of traces of non-human origin is becoming increasingly important in

forensic casework. Dog hairs are frequently discovered on crime scenes and on the clothing of
victims or suspects. Given that nuclear DNA analysis is impracticable for hair shafts, the profiling
has to focus on mitochondrial DNA (mtDNA).

Previously, the control region of the canine mitochondrial genome (mtGenome) was explored at
the NICC. A Belgian population database was assembled and showed sufficient diversity for
application of control region analysis of dog hairs in forensic casework. Nonetheless, its
discriminative power is smaller compared to the human control region. Moreover, the frequent
occurrence of a number of haplotypes in the population is disadvantageous for the evidential value
of the analysis, an observation made in several other studies worldwide.

The objective of the current project is to improve the discriminative power of the mtDNA profiling
of canine trace material by exploiting the genetic information in the coding region of the
mitochondrial genome. A method was established to sequence the entire canine mtGenome
according to QA standards, based on only 2 overlapping amplicons of about 9 kb each and double
strand sequence coverage that determines each position at least twice independently.

The mtGenome sequences of about 125 dogs selected from the previous population study were
assembled. These sequences improve the resolution of the phylogeny of the canine population.
Applying a phylogenetic approach, the informative positions of the mtGenome that contribute
most to the improvement of the discriminative power of canine mtDNA analysis can be
determined.

The whole mtGenome structure should enable us to develop an improved sequencing strategy for
mtDNA profiling of dog hair. Since whole mtGenome sequencing is unfeasible for trace material,
alternative approaches will need to be used such as SNP-multiplexes that focus only on identifying
a number of informative sites.

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Is the Indian Wild Boar an evolutionary significant unit? Molecular insight into phylogeny of
the Wild Boars and Domestic Pig
Gupta S1,*, Hussain S1, Ajit K1, Singh L2,3
1
Wildlife Institute of India, Dehra Dun, India
2
Centre for Cellular and Molecular Biology, Hyderabad, India
3
Banaras Hindu University, Varanasi, India

We examined genetic variations among wild pigs from India and compared their molecular
phylogeny with those of domestic pigs and wild pigs of non-Indian races by analysing the
sequence of the mitochondrial cytochrome-b gene. Our study revealed unambiguous genetic
variations between the Indian wild pig and the domestic pig. Our study also differentiates the
Indian Wild pigs from the wild pig races of the world. It is evident that the Indian wild boar is a
unique species or at least an incipient species that exhibits a high degree (more than 3%) of genetic
variation within the evolutionarily conserved cytochrome-b gene compared with other wild boar
races. The phylogenetic tree indicates that domestic pigs in India are not originated from Indian
wild pigs. We conclude that the 3% nucleotide difference between the Indian wild pigs and
domestic pig is helpful in differentiating between them as well as differentiating them from other
wild pig races. This strategy is helpful in identification of the confiscated biological sample of
these two subspecies for unambiguous differentiation of the wild and domestic pigs for solving the
wildlife forensic cases.

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Investigator Plus – fast, sensitive and robust amplification of common standard set loci
Prochnow A1,*, Scherer M1, Steeger B1, Pakulla S1, Breitbach M1, Cornelius S1, Fischer C1, Bochmann L1, Schnibbe
T1, Engel H1
1
QIAGEN GmbH, Hilden, Germany

Forensic DNA laboratories are challenged by the requirement to provide results on the identity of
genetic evidence within a very short time. Thus, in addition to crucial quality parameters like
sensitivity and robustness, speed becomes an increasingly important feature of STR PCR assays.
We have developed a set of next generation Investigator Plus kits that combine all critical features
necessary for fast and reliable analysis of demanding forensic samples: ESSplex (European
Standard Set), ESSplex SE (including SE33), and IDplex (CODIS). Based on our fast-cycling PCR
technology, we have introduced a novel reaction mix that allows completing a standard 30 cycle
amplification in as little as 90 minutes. Using this protocol, well balanced full profiles can reliably
be obtained with 100pg of DNA template. All Plus assays are very robust towards potential PCR
inhibitors and can tolerate concentrations up to 200ng/μl humic acid, or up to 750μM hematin.
They provide a clean baseline without any dye artifacts. We furthermore will show results on
direct amplification from FTA paper and buccal swabs. The combination of all features mentioned
above helps to reduce the number of samples that have to undergo reanalysis, which further
contributes to more streamlined and efficient laboratory workflows.

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How to improve STR analysis using a novel quantification technology: more than DNA
quantification
Di Pasquale F1, Cornelius S1, König M1, Bochmann L1, Prochnow A1,*, Schnibbe T1, Engel H1
1
QIAGEN GmbH, Hilden, Germany

Quantification in forensic casework analysis is typically the only pre-STR analysis step and could
be seen as a quality control step rather than just a quantification of the DNA concentration.

Thus, we present data from our novel human DNA quantification assay product line, called
Investigator® Quantiplex Kits, that is available as human (Quantiplex Kit) and human/male
(Quantiplex HYres Kit) configuration. Both provide fast and accurate quantification of DNA in
forensic database and casework samples with a very high sensitivity and accuracy due to the
trusted and validated autosomal multi-copy target 4NS1C and the validated multi-copy target on
the Y-chromosome. Detection of inhibitors is ensured by a balanced internal amplification control,
without significantly affecting the DNA quantification results. This novel technique of high
quality control standards provides a highly accurate assay for DNA quantification in forensics. The
assay ensures an improved correlation to the STR results in comparison to other standard real-time
PCR methods.

The Investigator Quantiplex product line utilizes a novel PCR fast-cycling technology as well as
Scorpion primers that enable rapid results. Using the Rotor-Gene Q system, quantification can be
performed in around 50 minutes.

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Improving DNA sensitivity and strengthen reliability with low-level DNA testing using trace
amount of metal
Honda K1,*, Nishi T1, Iwabuchi Y1
1
University of Tsukuba, Tsukuba, Japan

The amount of DNA recovered from a crime scene may often not be enough to obtain a full profile
using conventional multiplex kit. Improved sensitivity in a detection technique is a usually a
valuable cue to enable results to be obtained from limited biological evidence. Without the
increasing the ability to make copies of DNA, many forensic samples would be impossible to
analyze. However, DNA from crime scenes is often limited in both quantity and quality and
including contamination. So, we presented new efforts for improving low-level DNA testing.
Materials and method We used commercially available 9948 male control DNA (Promega) as the
PCR template (50pg). In addition, trace amount of various biological samples were tested.
Amplification were done by the addition of various trace elements with the AmpFLSTR™ Y
filer and PowerPlex™ Y System according to the manufacturer’s instructions,using the AmpliTaq
Gold. In order to evaluate the assay sensitivity, appropriate concentrations of metal (As, Cd,
Cu,Hg, Pb, Mn, Tl, Ga, Se, V, Zn, etc.) were added to the buffer in a dilution series from 0.01-1.0
µg/ml. The effect of metal to enhance the PCR reaction was quantified according to the
manufacturer’s protocol on an Applied Biosystems 7500 Real-Time PCR system (Applied
Biosystems). Results We found that some metals (Cu, As, Zn etc.)remarkably enhance PCR. The
enhancement effect is found at a range of concentrations, from 0.01 µg/ml to 1.0 µg/ml in the
reaction mixture. The most effective concentration is0.2µg/ml (200ppb) in reaction mixture. We
will present the detailed data in the meeting.

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Sample lysis and DNA separation in single tube assemblies for accurate forensic profiling
Schnerr H1,*
1
Biotype Diagnostic GmbH, Dresden, Germany

The importance to improve the quantity and quality of DNA isolated from forensic samples is
without controversy. Extraction of genomic DNA forms the first step of DNA profiling and its
quality is most critical for all subsequent steps to increase the potential to obtain maximum
information from downstream Short Tandem Repeat (STR) analysis. It starts with the disruption of
the cellular structure to create a lysate and the separation of the soluble DNA from cell debris and
other insoluble material to prepare a DNA lysate for further purification. Overall efficiency will be
improved, and the yield of isolated DNA will be optimised by carrying out the lysis directly in a
single tube assembly with subsequent quantitative recovery of the lysis buffer from both routine
and challenging samples.A novel kind of extraction systems was developed that allows simple and
fast separation of substrate from lysate in an all-in-one system. This approach eliminates the
manual lysate and substrate transfer steps, saving time and minimizing cross contamination and
sample transposition events significantly. Flexibility of the systems in terms of lysis conditions
and required reagents was demonstrated using a variety of lysis protocols. Small evaporation rates
in vapor tightness tests confirmed that these systems are ideally suited for incubations at higher
temperatures and over longer periods too. The SQ version rationalizes the lysis portion of DNA
extraction method and overcomes obvious difficulties with commonly used methods. The
performed study proved their suitability for effective DNA preparations even from low sample
inputs providing particle-free DNA lysates of highest quality and maximized yield. Significant
time savings and improved reproducibility were demonstrated too. Gradual DNA extraction in a
single tube assembly represents the unique characteristic of the DL version for differential lysis of
mixed specimens. Differential lysis was shown under mild conditions to separate the female DNA
and harsher lysis conditions that break the spermatozoa within the same filter column and without
necessity of sample carriage. The DNA lysates were further purified and used to generate
autosomal STR profiles of both the victim and the perpetrator. Due to high yield of DNA, the
chance of a successful DNA-profile by downstream analysis was significantly increased. Thereby,
simple handling allows timesavings and higher throughput in a manual process to allow reliable
improvement of crimesolution rates and showed its qualification to speed up analysis of
backlogged crime samples.In summary, universal DNA extraction systems were developed to
provide particle-free DNA lysates of highest quality using a diversity of specimens including
forensic sample material. Improvements of overall efficiency, in particular maximizing the
performance of the early steps of the extraction method was shown to achieve better genotyping
results.Furthermore, the DL version demonstrated the potential as an improved methodology
toovercome the often claimed difficulties in differential extraction, thus, has the potential towork
off backlogs of rape kits.

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Estimating forensic match probabilities for Y-STRs using a new, discrete Laplace
distribution
Andersen MM1,*, Eriksen PS1, Morling N2
1
Aalborg University, Aalborg, Denmark
2
University of Copenhagen, Copenhagen, Denmark

The evidential weight of Y-STR investigations in crime cases may be expressed as the likelihood
ratio Pr(Y-STR-profile | H0)/Pr(Y-STR-profile | H1), where Y-STR-profile is the profile of the
stain found at the scene of crime and Pr(Y-STR-profile | H1) is the probability of the
Y-STR-profile among random individuals. Even with a limited number of STR loci investigated,
the majority of Y-STR-profiles in small database samples are only found once. This indicates that,
if the Y-STR-profile has not been observed before, a naïve estimate of the probability of the
Y-STR-profile, like 1/n or 1/(n+1), where n is the total number of individuals in the database
sample, most likely is overestimated. We present a new method that is inspired by Fisher-Wright
theory and an assumption of discrete Laplace, ‘wandering’ distribution of the Y-STR-profiles.

A simulation study of populations created according to the Fisher-Wright model with fixed
expected end population sizes, two initial population sizes, two mutation rates, two different
numbers of generations was performed. This was repeated five times in total for each combination.
Fifty databases with 500, 1,000 and 5,000 Y-STR-profiles, respectively, were randomly sampled
from each population. The total number of data sets was 6,000.

In the simulated data, the average deviation of the estimated probabilities of the Y-STR-profiles
from the true population frequencies using the discrete Laplace method was smaller than those
calculated with the naïve estimate method and Brenner’s kappa method.

The simulation method is implemented in R and public available

on http://cran.r-project.org/web/packages/fwsim/index.html and the discree Laplace estimation
method on http://cran.r-project.org/web/packages/disclapmix/index.html.

Thus, under the assumption that the Y-STR-profiles are distributed according to the Fisher-Wright
model, the discrete Laplace estimation method for estimation of Y-STR-allele probabilities seems
to give the best estimates when compared to other suggested estimation methods.

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Evaluation of the use of software as a tool in checking mitochondrial DNA HVI and HVII
sequences analysis
Funabashi K1, Godoy C1, Sousa M1,2, Iwamura E1,*
1
Escola Paulista de Medicina -UNIFESP, São Paulo, Brazil
2
São Paulo Criminalistic Institute – DNA Laboratory, São Paulo, Brazil

The work presented here discusses the use of the Mitotyper TM software (presented by Elling &
Den Hartog in 24th World congress of ISFG 2011) to check the sequences analyses in order to
avoid potential problems, such as errors describing the sequence difference-from –reference
polymorphisms.

We analyzed the HVI and HVII regions in a sample of 124 not related individuals from São Paulo,
Brazil. The first analyses were performed by two independent analysts as previously described
Godoy et al (Forensic Science International Genetics Supplement Series e149-150, 2011). We
re-analyzed these samples with the Mitotyper TM software reviewing and comparing the
polymorphisms found. The program detected polymorphisms in four samples that had not been
observed in the previous two manual analyses. In one additional sample, a more accurate
description of the polymorphism, in the software analysis, allowed the haplogroup to be more
specifically classified. The divergent manual results found- 5 of 124 (4%)- were due to the
interpretation and experience of the third analyst in manipulating the raw electropherogram data.

We conclude that Mitotyper has all the rules for the sequence analyses and is a good tool to help to
check and validate the results. The software is useful for efficiently checking the sample analysis
in routine research and casework, allowing the users to double check the analyses, saving time for
the manual and laborious analysis in divergent samples. However, good quality eletropherograms
are still essential for correct sequence analysis. (FAPESP 2010/19127-2, CNPq, Capes)

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The effect of sample size on the estimates of mtDNA genetic diversity parameters in isolated
European populations
Anagnostou P1,2,*, Capocasa M3, Montinaro F4, Coia V5, Destro-Bisol G1,2
1
Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Roma, Italy
2
Istituto Italiano di Antropologia, Roma, Italy
3
Dipartimento Biologia e Biotecnologie “Charles Darwin”, Università di Roma "La Sapienza", Roma, Italy
4
Facoltà di Medicina, Istituto di Medicina Legale, Università Cattolica, Roma, Italy
5
European Academy of Bolzano (EURAC-research), Institute for Mummies and the Iceman, Bolzano, Italy

The study of human genetic Isolates provides an opportunity to analyze the effects of
geographical and cultural factors on the genetic structure of human populations. Numerous studies
have investigated genetic Isolation in Europe, focusing on fluctuations of measures of genetic
diversity . Unfortunately, some of the features often associated to isolation (small census sizes
and high degree of endogamy) may also limit the number of unrelated individuals which is
possible to collect. Thus, it becomes difficult to disentangle the effect of genetic isolation from
those created by inadequate sample size. In the present study we evaluate how sample size may
affect estimates of diversity measures through a reanalysis of the current mitochondrial data on
European genetic isolates. We retrieved genetic data of 24 populations characterized by
geographic and/or cultural isolation and compared them with open European populations for
several intra and inter population diversity parameters (HD, MNPD, Fst, Fu’s Fs) using a random
resampling approach. Our results shows that these measures may differ in robustness and
informativity. Reviewing published studies in the light of our approach, we suggest that care
should be taken when drawing inferences of genetic isolation using small sample sizes.

This research is supported by Ministero dell'Istruzione, dell'Università e della Ricerca

(200975T9EW_004), La Sapienza Università di Roma (C26A117JKC) and Istituto Italiano di
Antropologia

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 DNA in Forensics 2012, Sep 06-08 2012
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5 International EMPOP Meeting 8th International Forensic Y-User Workshop

Genes, mountains and culture: evidence for the impact of ethnicity on the structure of human
populations
Capocasa M1,2,*, Battaggia C3, Anagnostou P3,2, Montinaro F4, Arena A2, Boschi I4, Brisighelli F3,5, Capelli C6, Coia
V7,8, Rufo F1,2, Crivellaro F9, Destro Bisol G3,2
1
Dipartimento Biologia e Biotecnologie “Charles Darwin”, Università La Sapienza, Rome, Italy
2
Istituto Italiano di Antropologia, Rome, Italy
3
Dipartimento di Biologia Ambientale, Università La Sapienza, Rome, Italy
4
Facolta di Medicina, Istituto di Medicina Legale, Università Cattolica, Rome, Italy
5
Unidade de Xenética, Facultade de Medicina, Instituto de Ciencias Forenses, Universidade de Santiago de
Compostela, Santiago de Compostela, Spain
6
Department of Zoology, University of Oxford, Oxford, United Kingdom
7
Universita degli studi di Trento, Dipartimento di Filosofia, Storia e Beni culturali, Trento, Italy
8
European Academy of Bolzano (EURAC-research), Institute for Mummies and the Iceman, Bolzano, Italy
9
Department of Biological Anthropology, Leverhulme Centre for Human Evolutionary Studies, Cambridge, United
Kingdom

In the current anthropological approaches, ethnicity is a symbolic construction produced by

specific historical, social and political circumstances. Individuals belonging to a given ethnic
group tend to self-attribute a reciprocal similarity, both biological and cultural, and a diversity
compared to neighbors. In the long term, this may lead to a reduction of intra-group genetic
variability associated with endogamy and genetic drift. In this study we assess the impact of ethnic
boundaries on genetic structures in European populations, using mitochondrial control region data.
First, we investigated the degree of genetic differentiation between three german-speaking
neighboring populations of the north-eastern Italian Alps: Sappada, Sauris and Timau. These
populations share many cultural aspects, but their components do not self-identify as belonging to
the same community. Thereafter, we compared the results obtained with those of other well
defined ethnic groups, Cimbrians and Ladins from north Italy and Aromuns from Albania and
Macedonia. We observed in all groups a reduced genetic diversity and a high differentiation with
respect to other neighbouring and European populations. These analyses highlighted a higher
diversity among the german-speaking populations of the north-eastern Italian Alps than Cimbrians,
Ladins and Aromuns, pointing to the importance of ethnicity as a factor shaping genetic structure
in human populations.

This research is supported by Ministero dell'Istruzione, dell'Università e della Ricerca

(200975T9EW_004), La Sapienza Università di Roma (C26A117JKC) and the Istituto Italiano di
Antropologia.

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 DNA in Forensics 2012, Sep 06-08 2012
th
5 International EMPOP Meeting 8th International Forensic Y-User Workshop

Critique of the haplotype surveying method

Brenner CH1,*
1
UC Berkeley & DNA•VIEW, Oakland, United States

A method called “haplotype surveying” has been proposed to assess the rarity of a Y-haplotype
and is often taken to be a valid calculation for forensic evidence connecting suspect to crime
scene. I am skeptical of the method for several reasons.

One – Wrong statement of the problem, and no explicit model.

Haplotype surveying is presented as a method to estimate frequencies, but that is not the same as
the normally relevant evidential question of a conditional (upon having observed the crime scene
type) match probability of an innocent suspect. Careless definitions can have real and detrimental
consequences. For example, the first published version of haplotype surveying forgot to consider
the crime scene type.

The “survey” idea that the popularity of a haplotype is related to that of its neighbors hints at a
model involving mutation, but nothing is explicit and there is no indication of the nature of the
process relating incidences of neighboring types. Consequently it is perhaps not surprising that, as
Veldman noted

Two – The implied model not correctly implemented.

The weighting formula presented in the model treats a distance of two mutations between a pair of
haplotypes almost the same as a distance of three and not much differently than a distance of one. I
do not see what model would give rise to the formula.

Three – Drift, not considered, likely overwhelms the neighbor correlation concept.

An explicit statement of the intended model would be helpful, but the method seems to assume
some kind of mutational equilibrium as might exist in an infinite population. Possibly neighboring
haplotypes are envisioned as replenishing one another over generations via mutation. But computer
simulations suggest that such an effect would be very minor compared to random drift.

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 DNA in Forensics 2012, Sep 06-08 2012
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5 International EMPOP Meeting 8th International Forensic Y-User Workshop

Evaluation of haplogroup predicting softwares

Caputo M1, Bobillo MC1, Alechine E1, Sala A1, Corach D1,*
1
Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, and
Consejo Nacional de Investigaciones Científicas. (CONICET), Caba, Argentina

In population genetics studies, huge collections of Y-STR haplotypes have been published;
unfortunately most of them lack information concerning the haplogroups to which the haplotype
belong. Inferring haplogroups from haplotype data is an attractive alternative, however a robust
informatic approach should be used. Based on the most theoretical criticism rised by some authors,
we decided to empirically test the Athey’s Haplogroup Predictor with samples previously typed for
haplogroup defining SNPs. One hundred and one unrelated male samples were haplotyped by
AmpFLSTR Y-Filer (Applied Biosystem) and haplogrouped by SNP detection performed by
different approaches, namely Real Time PCR followed by High Resolution Melting, amplicon
sequencing, SnapShot mini-sequencing and/or primer specific PCR. The analyzed SNPs were M3
for Q1a3a, M269 for R1b1b2 and U179 for I Haplogroups. Thirty one samples were assigned as
“not determined” and 70 samples were haplogrouped as I, Q1a3a or R1b1b2. The prediction of
Y-Chromosome haplogroups from these samples was performed by Athey’s Haplogroup Predictor
considering “equal priors”. All the haplogroups predicted by the online program matched the
assignment by SNP genotyping. An average probability of 99.7%, 96.9% and 99.99% was obtained
for Q, I, R1b haplogroup assignment, respectively, using Y-Filer STR panel. An adequate
correlation between the haplogroups predicted by the software and SNP haplogroup typing was
obtained. The use of Athey’s Haplogroup Predictor by means of 17 markers (Y-Filer Panel)
showed a reliable accuracy to predict at least I, Q1a3a and R1b haplogroups. Its use might offer an
opportunity for retrieving valuable information from published haplotypes. Increasing the number
of reference samples from which haplogroup have been precisely defined by SNP analysis will
highly improve the software accuracy. Meanwhile, this approach represents an acceptable
screening criteria that may allow analyzing previously published results.

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