Global Signatures and Dynamical Origins of the Little Ice Age and

Medieval Climate Anomaly

Michael E. Mann et al.
Science 326, 1256 (2009);
DOI: 10.1126/science.1177303

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 REPORTS
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the decadal variability to be revealed and an- 13. J. Hua, W. Dexing, W. Xiuquan, Chin. J. Oceanol. Limnol. Materials and Methods
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(2008). References
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ical importance of reanalyzing historical data Lett. 35, L03618 (2008). 10.1126/science.1177012

reconstruct global patterns of surface temperature

Global Signatures and Dynamical changes over the past 1500 years. We use a
climate field reconstruction (CFR) approach (11)

Origins of the Little Ice Age and that has been rigorously tested with synthetic
“pseudoproxy” networks generated from forced

Medieval Climate Anomaly

climate model simulations (12). We interpret the
resulting reconstructions in the context of results
from climate model simulations forced by esti-
Michael E. Mann,1* Zhihua Zhang,1 Scott Rutherford,2 Raymond S. Bradley,3 mated past changes in natural (solar and volcanic)
Malcolm K. Hughes,4 Drew Shindell,5 Caspar Ammann,6 Greg Faluvegi,5 Fenbiao Ni4 radiative forcing.
We employ the global proxy data set used
Global temperatures are known to have varied over the past 1500 years, but the spatial patterns by (13) comprising more than a thousand tree-
have remained poorly defined. We used a global climate proxy network to reconstruct surface ring, ice core, coral, sediment, and other as-
temperature patterns over this interval. The Medieval period is found to display warmth that sorted proxy records spanning the ocean and
matches or exceeds that of the past decade in some regions, but which falls well below recent levels land regions of both hemispheres over the past
globally. This period is marked by a tendency for La Niña–like conditions in the tropical Pacific. 1500 years. The surface temperature field is
The coldest temperatures of the Little Ice Age are observed over the interval 1400 to 1700 C.E., reconstructed by calibrating the proxy network
with greatest cooling over the extratropical Northern Hemisphere continents. The patterns of against the spatial information contained within
temperature change imply dynamical responses of climate to natural radiative forcing changes the instrumental annual mean surface temperature
involving El Niño and the North Atlantic Oscillation–Arctic Oscillation. field (14) over a modern period of overlap be-
tween proxy and instrumental data (1850 to 1995)

C
onsiderable progress has been made over regional-scale projections, which are paramount using the RegEM CFR procedure (12) with ad-
the past decade in using climate “proxy” in assessing future climate change impacts. ditional minor modifications. Further details of
data to reconstruct large-scale trends in Patterns of past climate change can be es-
past centuries, and in using climate models to timated through the simultaneous analysis of
1
assess the roles of natural and anthropogenic multiple spatially distributed proxy records. Such Department of Meteorology and Earth and Environmental
Systems Institute, Pennsylvania State University, University
forcing in those trends (1). Owing in part to the analyses have been performed via statistical re- Park, PA 16802, USA. 2Department of Environmental Science,
sparseness of the available proxy data, less pro- construction (2–8) and model assimilation ap- Roger Williams University, Bristol, RI 02809, USA. 3Depart-
gress has been made in identifying the underly- proaches (9), but available proxy networks have ment of Geosciences, University of Massachusetts, Amherst,
ing spatial patterns of those changes, let alone been insufficient for estimating spatially resolved MA 01003–9298, USA. 4Laboratory of Tree-Ring Research, Uni-
the causal factors behind them. Yet a better large-scale temperature reconstructions beyond versity of Arizona, Tucson, AZ 85721, USA. 5NASA Goddard
Institute for Space Studies, New York, NY 10025, USA. 6Climate
understanding of past patterns of climate change the past few centuries (2, 4, 7). Global Dynamics Division, National Center for Atmospheric
and their causes (e.g., the role of past changes in Here, we employ a diverse multiproxy net- Research, Boulder, CO 80305, USA.
the El Niño–Southern Oscillation, or ENSO) work previously used to estimate global and hem- *To whom correspondence should be addressed. E-mail:
may be even more important for validating the ispheric mean annual temperature trends (10) to mann@meteo.psu.edu

1256 27 NOVEMBER 2009 VOL 326 SCIENCE www.sciencemag.org

 REPORTS
the reconstruction procedure, associated statisti- Earlier proxy-based large-scale surface tem- ature variation in earlier centuries. By contrast,
cal validation and skill assessments, uncertainty perature reconstructions (2, 15) resolved only a the current reconstructions resolve multiple de-
estimation procedures, data used, and MATLAB single statistical degree of freedom before the grees of freedom in the surface temperature field
source codes for the analysis procedures are 15th century, precluding the possibility of in- back through the 6th century, allowing us to
provided in the Materials and Methods. vestigating spatial patterns of surface temper- meaningfully interpret spatial features in the

Fig. 1. Decadal surface temperature reconstructions. NH MEAN

A

Temperature Anomaly (°C)

instrumental all proxy
Surface temperature reconstructions have been averaged 95% uncertainty
0.5 EIV IHAD screened proxy interval
over (A) the entire Northern Hemisphere (NH), (B) North
Atlantic AMO region [sea surface temperature (SST) averaged 0
over the North Atlantic ocean as defined by (30)], (C) North
Pacific PDO (Pacific Decadal Oscillation) region (SST averaged −0.5
over the central North Pacific region 22.5°N–57.5°N,
152.5°E–132.5°W as defined by (31)], and (D) Niño3 region −1
500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000
(2.5°S–2.5°N, 92.5°W–147.5°W). Shading indicates 95%
confidence intervals, based on uncertainty estimates dis- B

Temperature Anomaly (°C)

AMO
cussed in the text. The intervals best defining the MCA and 0.5
LIA based on the NH hemispheric mean series are shown by
red and blue boxes, respectively. For comparison, results are 0
also shown for parallel (“screened”) reconstructions that are
based on a subset of the proxy data that pass screening for a −0.5
local temperature signal [see (13) for details]. The Northern
Hemisphere mean Errors in Variables (EIV) reconstruction 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000
(13) is also shown for comparison.
C
Temperature Anomaly (°C)

0.5 PDO

−0.5

−1
500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000

1 D
Temperature Anomaly (°C)

Nino3
0.5

−0.5

−1

−1.5

500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000
Year A.D.

Fig. 2. Reconstructed surface tem-

perature pattern for MCA (950 to
1250 C.E.) and LIA (1400 to 1700
C.E.). Shown are the mean surface
temperature anomaly (left) and
associated relative weightings of
various proxy records used (indi- Tree ring
MXD
cated by size of symbols) for the Ice core
Coral
low-frequency component of the Speleothem
Document
reconstruction (right). Anomalies MCA
Sediment

are defined relative to the 1961–

Composite
MCA
1990 reference period mean. Sta-
tistical skill is indicated by hatching
[regions that pass validation tests
at the P = 0.05 level with respect to
RE (CE) are denoted by / (\) hatch-
ing]. Gray mask indicates regions for
which inadequate long-term modern Tree ring
MXD
observational surface temperature Ice core
Coral
data are available for the purposes Speleothem
Document
of calibration and validation. Sediment
LIA Composite
LIA
-2.5 -.9 -.7 -.5 -.3 -.1 .1 .3 .5 .7 .9 1.4
Temperature Anomaly (°C)

www.sciencemag.org SCIENCE VOL 326 27 NOVEMBER 2009 1257

 REPORTS
reconstructions. Nonetheless, certain caveats must reconstruct temperatures for the LIA interval. The reconstructed MCA pattern is charac-
be kept in mind in interpreting the proxy-based This analysis gave a reconstruction very similar terized by warmth over a large part of the North
surface temperature reconstructions. Before 1600 to the LIA reconstruction based on the full data Atlantic, Southern Greenland, the Eurasian Arctic,
C.E., the low-frequency component of the sur- set (fig. S10). and parts of North America, which appears to
face temperature reconstructions is described as
a linear combination of just two leading pat- Fig. 3. Spatial pattern of MCA-LIA A
terns of temporal variation, so that regional fea- surface temperature difference in
tures in the temperature field are represented by reconstructions and model simula-
a spatiotemporally filtered approximation. More- tions. (A) Proxy-based temperature
over, as decadal-resolution proxy data were reconstructions, (B) GISS-ER (using
used in addition to annual-resolution data, only the same solar forcing difference
interdecadal and longer-term variations are mean- used in the NCAR simulation—
ingfully resolved; i.e., the details of individual shown is the ensemble mean; see
years and even individual decades should not the SOM for example results from
be emphasized. Thus, it is the longer-term, and one of six realizations), and (C) NCAR
larger-scale, variations resolved by the recon- CSM 1.4 simulation (using the same MCA-LIA Reconstruction
structions that are most meaningful. MCA and LIA time intervals as de-
fined above). The observational mask B
The large-scale surface temperature recon-
structions, when spatially averaged, e.g., over has been applied to both model pat-
the Northern Hemisphere, yield a long-term terns for ease of comparison. Statis-
history very similar to the hemispheric mean tical skill for (A) is indicated with the
reconstructions of (13) (Fig. 1A). However, the same conventions as in Fig. 2 (statis-
spatial reconstructions can also be averaged to tical significance here indicates that
the particular test statistic indepen-
yield other indices of interest [Fig. 1, B to E;
dently passed during both the MCA
other regional average series are shown in the
and LIA intervals).
Supporting Online Material (SOM) Text]. Though
there are relatively few distinct patterns of vari- MCA-LIA GISS
ation resolved by the reconstructions, particularly
before 1600 C.E., there are notable differences of C
behavior among the various diagnosed indices.
The Atlantic Multidecadal Oscillation (AMO)
series, for example, is marked by substantial
multidecadal variability, consistent with previous
proxy studies of North Atlantic variability [e.g.,
(16)]. The high-frequency fluctuations of the
Niño3 series are consistent with the oscillatory
nature of ENSO. The Niño3 index suggests strong
and persistent La Niña conditions around 1000
MCA-LIA NCAR
years ago, as discussed further below.
Our reconstructions span two climatologically
interesting periods, the so-called Little Ice Age
Temperature Anomaly (°C)
(LIA) and Medieval Climate Anomaly (MCA).
For the purpose of investigating the associated
spatial patterns (Fig. 2), we defined the LIA and A B
MCA in terms of distinct three-century-long in-
tervals (1400 to 1700 C.E. and 950 to 1250 C.E.,
respectively), which both correspond to relative
cold and warm hemispheric conditions, respec-
tively (Fig. 1), and are distinct with regard to the
estimated external radiative forcing of the climate
(1, 17). The observed patterns are not, however,
sensitive to the precise time intervals used to de-
fine these periods (fig. S9). The MCA pattern is
based on a smaller number of predictors than the
LIA pattern (Fig. 2) and, accordingly, on fewer
resolved spatial degrees of freedom (SOM Text).
The reconstruction skill diagnostics suggest
that the MCA and LIA reconstructions are most
reliable (Fig. 2) over the Northern Hemisphere NCAR CSM 1.4 GISS-ER
and tropics, and least reliable in the Southern
Hemisphere, particularly in the extratropics. To
assess if the larger-scale features of the earlier MCA-LIA SLP (mb) MCA-LIA SLP (mb)
MCA pattern are robust, we used only the more Fig. 4. Spatial pattern of MCA-LIA sea-level pressure difference in model simulations. (A) NCAR CSM
restricted network of proxy data available back 1.4 and (B) GISS-ER. For the NCAR model, a single run was available (23). For the GISS-ER coupled
through the beginning of the MCA interval to model, we show the ensemble mean of six realizations; see SOM section 5 for further details.

1258 27 NOVEMBER 2009 VOL 326 SCIENCE www.sciencemag.org

 REPORTS
substantially exceed that of the modern late– different coupled model simulations analyzed. LIA pattern, which strongly affects the Pacific
20th century (1961–1990) baseline and is com- On the other hand, such a pattern is reproduced basin. There is no evidence of a positive NAO-
parable to or exceeds that of the past one-to-two in simulations (19) using the low-order Cane- AO response in the NCAR simulation (Fig. 4).
decades in some regions. This finding is con- Zebiak (24) model of the tropical Pacific cou- The observed patterns of change, even when
sistent with that of a recent tree-ring–based study pled ocean-atmosphere system. The discrepancy averaged over multicentury intervals, are unlike-
of high-latitude Eurasian temperatures (18). in the model responses may arise because the ly to be entirely forced in nature, as there is also
Relative warmth in the central North Pacific tropical Pacific “thermostat” mechanism (25) is a potentially important role for purely internal,
MCA is consistent with the expected extratrop- not active in either the NCAR or GISS simu- natural variability (9). Consistent with this view,
ical signature of the strong observed La Niña– lations. In (19), this mechanism is responsible we find that individual realizations of the GISS-
like pattern in the tropical Pacific (strong cooling for the La Niña–like response to the positive ER transient response to the MCA-LIA solar
in the east and warming in the west). Certain tropical radiative forcing of the MCA that arises forcing difference yield patterns that differ mod-
regions, such as central Eurasia, northwestern from a combination of relatively high solar irra- estly in their details. For at least one realization,
North America, and (with less confidence) parts diance and inactive tropical volcanism. Although for example, the reconstructed warm anomaly
of the South Atlantic, exhibit anomalous cool- there is still a vigorous debate regarding the na- over Western Europe is reproduced. In most
ness. The LIA pattern is characterized primarily ture of the response of the tropical Pacific to cases, the basic features discussed above are
by pronounced cooling over the Northern Hemi- anthropogenic radiative forcing [e.g., (26)], paleo- nonetheless evident (SOM Text).
sphere continents, but with some regions—e.g., climate evidence examined here, as elsewhere The paleoclimate reconstructions presented
parts of the Middle East, central North Atlantic, [e.g., (19, 27)], appears to support a thermostat- here hold important implications for future cli-
Africa, and isolated parts of the United States, like response, at least for natural radiatively mate change. For example, if the tropical Pacific
tropical Eurasia, and the extratropical Pacific forced climate changes in past centuries. thermostat response suggested by our analyses
Ocean—displaying warmth comparable to that The NCAR simulation also does not re- of past changes applies to anthropogenic climate
of the present day. In some places, e.g., northern produce the enhanced warming over the Eurasian change, this holds profound implications for
Labrador, apparent LIA warmth is a product, at Arctic, high-latitude North Atlantic, and North regional climate change effects such as future
least in part, of the relatively cool nature of the American region evident in the reconstructed drought patterns. Continued refinement of paleo-
1961–1990 reference period in the region. MCA-LIA pattern. As discussed previously, this climate reconstructions through expanded proxy
For comparison with model simulation re- surface temperature pattern is consistent with a databases and refinements of CFR methodol-
sults, it is useful to eliminate the influence of relative positive (negative) NAO-AO atmospher- ogy, improved estimates of past radiative forcing,
the choice of modern reference period by ex- ic circulation anomaly during the MCA (LIA), and a better understanding of the influence of
amining the pattern of the MCA-LIA difference associated with annular bands of positive (nega- radiative forcing on large-scale climate dynam-
itself (Fig. 3). The MCA-LIA pattern highlights tive) SLP anomalies in the subtropics and mid- ics should remain priorities as we work toward
the extent to which the MCA is both more “La latitudes, and negative (positive) SLP anomalies improving the regional credibility of climate
Niña–like” [e.g., (17, 19–21)] and, with en- in the subpolar latitudes. Such a pattern has been model projections.
hanced warmth over interior North America inferred in paleoclimate studies of the past mil-
and the Eurasian Arctic, and cooling over cen- lennium (5, 17, 22, 28, 29), and the negative
tral Eurasia, suggestive of the positive phase of phase of this pattern has been produced as a References and Notes
1. E. Jansen et al., in Climate Change: The Physical Science
the North Atlantic Oscillation (NAO) and dynamical response to decreased solar radiative Basis. Contribution of Working Group I to the Fourth
closely related Arctic Oscillation (AO) sea-level forcing during the LIA using a previous version Assessment Report of the Intergovernmental Panel on
pressure (SLP) pattern (17, 22), as discussed of the NASA GISS model that incorporates the Climate Change, S. Solomon et al., Eds. (Cambridge Univ.
further below. effects of ozone photochemistry on the vertical Press, New York, 2007), pp. 433–497.
2. M. E. Mann, R. S. Bradley, M. K. Hughes, Nature 392,
We examined results for two different cou- structure of the atmosphere (28, 29). These ef- 779 (1998).
pled model simulations of the past millennium, fects are not accounted for in the NCAR sim- 3. K. R. Briffa, P. D. Jones, F. H. Schweingruber, T. J. Osborn,
driven with those factors (solar irradiance changes ulation, which is limited to 36 km in vertical Nature 393, 450 (1998).
and stratospheric aerosols from explosive volcan- extent. The GISS-ER model used here extends to 4. K. R. Briffa et al., J. Geophys Res. Atmos. 106, 2929
(2001).
ic eruptions) that can most plausibly explain the ~80 km and does incorporate these processes
5. J. Luterbacher et al., Geophys. Res. Lett. 26, 2745
climate changes of the past millennium (17): (i) and, indeed, reproduces roughly the observed pat- (1999).
the National Center for Atmospheric Research tern of enhanced North American, high-latitude 6. J. Luterbacher, D. Dietrich, E. Xoplaki, M. Grosjean,
(NCAR) Climate System Model (CSM) 1.4 cou- North Atlantic, and Arctic Eurasian warming, as H. Wanner, Science 303, 1499 (2004).
pled model driven with estimated solar plus vol- a dynamical response to the imposed radiative 7. M. N. Evans, A. Kaplan, M. A. Cane, Paleoceanography
17, 1007 (2002).
canic forcing over the past millennium [see (23) forcing. These surface temperature changes are, 8. S. Rutherford et al., J. Clim. 18, 2308 (2005).
for details]; and (ii) the Goddard Institute for in turn, associated with an annular atmospheric 9. H. Goosse, H. Renssen, A. Timmermann, R. S. Bradley,
Space Studies–ER (GISS-ER) coupled model circulation response (Fig. 4) reminiscent of the M. E. Mann, Clim. Dyn. 27, 165 (2006).
with solar (but no volcanic) forcing (SOM Text), positive phase of the NAO-AO pattern, though 10. See Dataset S1 in the Materials and Methods.
scaled for an MCA-LIA solar radiative forcing at with some differences [in particular, (i) the 11. The synthetic proxy data in these tests are constructed to
have noise characteristics similar to those estimated for
the tropopause of 0.37 W/m2 (equivalent to the high- and low-pressure regions in the North actual proxy data. The calibration process, as with
MCA-LIA solar forcing difference used in the Atlantic sector are somewhat asymmetric and real-world reconstructions, is performed over a
NCAR simulation). Both simulations give very geographically shifted relative to the conven- modern interval that is subject to anthropogenic forcing.
similar estimates of the global mean MCA-LIA tional pattern—hence, for example, the relative The ability of the method to reproduce the earlier
variations is then objectively assessed. See (12) for
temperature difference (0.16° and 0.24°C for absence of warming in western Europe; and (ii) further details.
NCAR and GISS, respectively; the latter is iden- there is a positive SLP anomaly over Northern 12. M. E. Mann, S. Rutherford, E. Wahl, C. Ammann,
tical to the proxy reconstructed mean surface tem- Greenland and part of the Eurasian Arctic Ocean J. Geophys. Res. Atmos. 112, D12109 (2007).
perature difference of 0.24°C). The spatial patterns that is absent in the conventional pattern]. Com- 13. M. E. Mann et al., Proc. Natl. Acad. Sci. U.S.A. 105,
of response for the two models (Fig. 3), however, parisons over the Pacific sector and neighboring 13252 (2008).
14. P. Brohan, J. J. Kennedy, I. Harris, S. F. B. Tett, P. D. Jones,
are quite different, as discussed further below. regions, by contrast, are of limited utility, given J. Geophys. Res. Atmos. 111, D12106 (2006).
The La Niña–like nature of the MCA-LIA the inability of the GISS-ER model to reproduce 15. M. E. Mann, R. S. Bradley, M. K. Hughes, Geophys. Res.
pattern is not reproduced in either of the two the aforementioned La Niña–like feature of MCA- Lett. 26, 759 (1999).

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(2000). Science Basis. Contribution of Working Group I to the M.K.H. and F.B.N. were supported by the National
17. P. D. Jones, M. E. Mann, Rev. Geophys. 42, RG2002 Fourth Assessment Report of the Intergovernmental Panel Oceanic and Atmospheric Administration (grant
(2004). on Climate Change, S. Solomon et al., Eds. (Cambridge NA16GP2914 from CCDD). D.T.S. and G.F. acknowledge
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J. Clim. 9, 2190 (1996). support from the Office of Science (BER), U.S. 10.1126/science.1177303

Extensive, Recent Intron Gains in sophila teisseri (22), and two intron-gain alleles
segregate with an intron-free version at a locus
in the microcrustacean Daphnia pulex (23). The
Daphnia Populations latter study, in particular, inspired us to look
more deeply for evidence of recent intron gain
Wenli Li,1* Abraham E. Tucker,1* Way Sung,2 W. Kelley Thomas,2 Michael Lynch1†
or loss in D. pulex.
By artificially removing intron sequences from
all predicted gene sequences of the annotated
Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of
D. pulex genome [clone TCO (24)] and querying
highly conserved genes sampled from phylogenetically distant taxa. We report a population-
the exon-exon boundaries (n = 110,021) against
genomic approach that detected 24 discordant intron/exon boundaries between the whole-genome
another D. pulex genome sequence (TRO), we de-
sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of
tected putative intron-free alleles. After filtering for
D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence
paralogy and false positives, such as processed
of recent gains, with parallel gains often occurring at the same locations in independent allelic
pseudogenes, we sequenced the genomic regions
lineages. More than half of the recent gains are associated with short sequence repeats, suggesting
surrounding 24 intron presence/absence posi-
an origin via repair of staggered double-strand breaks. By comparing the allele-frequency
tions across 84 natural isolates of North Amer-
spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide
ican D. pulex species as well as in eight Daphnia
evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in
outgroup species. Gene trees constructed from
population-genetic settings where random genetic drift is a relatively strong force.
flanking-exon sequence for each presence/absence
polymorphism revealed the phylogenetic relation-

I
ntrons are noncoding sequences that inter- presence of introns in homologous positions ships of the polymorphic alleles, and from these
rupt eukaryotic exons and are removed from of orthologous genes of widely divergent eu- data we inferred that 87.5% (21/24) of the intron
premature mRNAs by the spliceosomal ma- karyotes (10–12) and the likely presence of a polymorphisms reflect recent intron gains, with
chinery before translation (1–3). Intron coloni- complex spliceosome in the eukaryotic ancestor three reflecting intron losses (figs. S1 to S24).
zation affects the evolution of gene structure and (13). In this context, intron-poor lineages are Most of the gains (15/28) were exclusive to Oregon
is a factor in the emergence of genomic and or- assumed to reflect a long-term history of intron populations, a genetically isolated subclade of
ganismal complexity, as newly arisen introns are loss (14). Alternatively, moderate ancestral North American D. pulex (25, 26) with a histor-
thought to be intrinsically deleterious owing to intron density followed by lineage-specific gains ically low effective population size (27). Active
the increased mutational target that they impose (15) may have occurred, even at orthologous splicing of all polymorphic introns was confirmed
on their host genes (4, 5). The number of introns positions in divergent taxa (16). However, most with reverse transcription polymerase chain reac-
in a genome is determined by the relative rates comparative studies of introns have examined tion sequencing.
of intron gain and loss over evolutionary time, only a small subset of highly conserved genes The features of newly arisen introns in D. pulex
which differ among lineages. Across eukaryotes, between deeply divergent lineages, and although are inconsistent with most hypothesized mecha-
intron numbers range from >100,000 per verte- some studies have documented unambiguous nisms of intron origin (7). We found no support
brate genome to only two in Giardia lamblia examples of intron gain (17–19) and some sta- for intron gains resulting from tandem duplications
(6, 7). The fundamental causes of this variation re- tistical procedures allow an indirect inference of of fragments of coding DNA or insertions of trans-
main controversial (8, 9), partly because of a lack parallel gains and/or losses (20, 21), compara- posable elements. Furthermore, the polymorphic
of population-level analyses with the power to tive studies of taxa with extreme sequence diver- intron sequences identified seem to be evolution-
infer the properties of recent gain or loss alleles. gence have essentially no possibility of directly ary novelties absent from well-characterized eu-
The early eukaryotic progenitor has been inferring parallel intron gains. karyotic and prokaryotic genomes. Except for
assumed to be intron-rich on the basis of the Because they potentially retain the molecular gains at one locus (Dappu-42116_2, fig. S20),
signatures of the process of intron origin, intron Blastn searches using recently gained intron se-
1
presence or absence alleles segregating in nat- quences against the D. pulex genome assembly
Biology Department, Indiana University, Bloomington, IN ural populations provide material to infer gain or (http://wfleabase.org/blast), D. pulex genome trace
47405, USA. 2Hubbard Center for Genome Studies, University
of New Hampshire, Durham, NH 03824, USA. loss mechanisms and to estimate taxon-specific files, and the full GenBank repository did not
*These authors contributed equally to this work.
turnover rates. Such polymorphisms do exist. A retrieve any homologous sequence hits.
†To whom correspondence should be addressed. E-mail: standing intron presence/absence polymorphism We observed that short direct repeats, rang-
milynch@indiana.edu was found at a locus in natural isolates of Dro- ing in size from 5 to 12 base pairs, flank many

1260 27 NOVEMBER 2009 VOL 326 SCIENCE www.sciencemag.org