Population Genomics Pipeline using SNPs data in VCF files from Reduced-representation sequencing (RRS), such as, Genotype-by-Sequencing (GBS) and Restriction-site Associated DNA Sequencing (RAD-Seq).

Dalapicolla, J. 2023. Guia para genômica de populações aplicada a mamíferos Neotropicais: do delineamento experimental às análises básicas com polimorfismos de nucleotídeo único (SNPs). Brazilian Journal of Mammalogy e92: 1-20.

Dalapicolla J, Prado JR, Percequillo AR, Knowles LL. 2021. Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association. Journal of Biogeography 48(12): 3196-3209.

Carvalho CS, Forester BR, Mitre SK, Alves R, Imperatriz-Fonseca VL, Ramos SJ, Resende-Moreira LC, Siqueira JO, Trevelin LC, Caldeira CF, Gastauer M, Jaffé R. 2019. Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration. Molecular Ecology Resources, 21(1): 44-58

Software used in this pipeline:

RStudio version 2022.02.3 Build 492

R version 4.3.0

Inputs: .vcf files, reference file for Dioclea dataset, and .csv files with geographical coordinates for both datasets

Filtering: R scripts for filtering neutral SNPs.

Genetic Structure: R scripts for basic genomic structure analyses PCA | sNMF | DPAC | TESS3

Genetic Diversity and Distance: R scripts for basic genomic diversity Ht | Ho | FIS | FST