DOI: 10.5061/dryad.9fg2r
title: Data from: Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic

description: Aim: The Malvinas/Falkland Islands (MFI) constitute the largest
 archipelago in the southern Atlantic, and harbour endemic lineages that
 presumably evolved after sea-level rise, associated with glacial periods,
 isolated ancestral populations. We investigate the role of the MFI in
 isolating populations from continental counterparts of two highly vagile
 species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps.
 Location: Patagonia and the Malvinas/Falkland Islands. Methods: We sampled
 C. picta and C. rubidiceps on the continent and MFI. Using a
 reduced-representation genomic approach, we quantified the genetic
 differentiation between insular and continental populations of both
 species, and used coalescent-based analyses to model their demography.
 Results: The MFI harbour independently evolving lineages of C. picta and
 C. rubidiceps, which diverged from their continental counterparts during
 the Middle-Late Pleistocene and have since experienced negligible gene
 flow. Main conclusions: The c. 450 km that separate the archipelago from
 the continent are sufficient to isolate populations of these putatively
 highly vagile species. Ancestral lineages may have reached the MFI
 refugium during glacial cycles. Without conservation measures, the drastic
 decline of the morphologically, behaviourally and ecologically distinct
 continental population of C. rubidiceps, to &lt; 1000 individuals, may
 lead to the extinction of an independently evolving taxon.
description: Compressed output folder
 from the Stacks pipelineThis file contains the
 output from stacks and can be used to export genotypes with the
 "populations" module of the pipeline.Chloephaga_stacks_output.tarChloephaga picta genotypes in .vcf formatThis is a .vcf file containing genotypes for Chloephaga picta at RAD loci. It was generated using the Stacks bioinformatics pipeline.Chloephaga_picta_genotypes.vcfChloephaga rubidiceps and Chloephaga poliocephala genotypes in .vcf formatThis is a .vcf file containing genotypes for Chloephaga rubidiceps and Chloephaga poliocephala at RAD loci. It was generated using the Stacks bioinformatics pipeline.Chloephaga_rubidiceps_Chloephaga_poliocephala_genotypes.vcfChloephaga picta genotypes in genepop formatThis file contains genotypes for Chloephaga picta at RAD loci in genepop format. It was generated using the Stacks pipeline.Chloephaga_picta_genotypes.genepopChloephaga rubidiceps and Chloephaga poliocephala genotypes in genepop formatThis file contains genotypes for Chloephaga rubidiceps and Chloephaga poliocephala at RAD loci in genepop format. It was generated using the Stacks pipeline.Chloephaga_rubidiceps_Chloephaga_poliocephala_genotypes.genepoppopulations command for C. rubidicepsThis file contains the command used to export genotypes from the Stacks output contained in the Chloephaga_stacks_output.tar file. It must be used in combination with the rubidiceps.txt population map.populations_rubidiceps.shcommand for populations used to export picta genotypesThis file contains the command used to export genotypes from the Stacks output contained in the Chloephaga_stacks_output.tar file. It must be used in combination with the picta.txt population map.populations_picta.shpopulation map for C. pictaThis file contains the individuals for which genotypes are to be exported using the populations module of the Stacks pipeline in combination with the files contained in the Chloephaga_stacks_output.tar folder.picta.txtpopulation map for C. rubidiceps and C. poliocephalaThis file contains the individuals for which genotypes are to be exported using the populations module of the Stacks pipeline in combination with the files contained in the Chloephaga_stacks_output.tar folder.rubidiceps.txt