DOI: 10.5061/dryad.803q8
title: Data from: Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes

description: Three ecotypes of killer whale occur in partial sympatry in the North
 Pacific. Individuals assortatively mate within the same ecotype, resulting
 in correlated ecological and genetic differentiation. A key question is
 whether this pattern of evolutionary divergence is an example of incipient
 sympatric speciation from a single panmictic ancestral population, or
 whether sympatry could have resulted from multiple colonisations of the
 North Pacific and secondary contact between ecotypes. Here, we infer
 multilocus coalescent trees from &gt;1000 nuclear single-nucleotide
 polymorphisms (SNPs) and find evidence of incomplete lineage sorting so
 that the genealogies of SNPs do not all conform to a single topology. To
 disentangle whether uncertainty in the phylogenetic inference of the
 relationships among ecotypes could also result from ancestral admixture
 events we reconstructed the relationship among the ecotypes as an
 admixture graph and estimated f4-statistics using TreeMix. The results
 were consistent with episodes of admixture between two of the North
 Pacific ecotypes and the two outgroups (populations from the Southern
 Ocean and the North Atlantic). Gene flow may have occurred via unsampled
 ‘ghost’ populations rather than directly between the populations sampled
 here. Our results indicate that because of ancestral admixture events and
 incomplete lineage sorting, a single bifurcating tree does not fully
 describe the relationship among these populations. The data are therefore
 most consistent with the genomic variation among North Pacific killer
 whale ecotypes resulting from multiple colonisation events, and secondary
 contact may have facilitated evolutionary divergence. Thus, the
 present-day populations of North Pacific killer whale ecotypes have a
 complex ancestry, confounding the tree-based inference of ancestral
 geography.
description: Repeat filtered VCF
 fileSubset of a previously
 published SNP dataset available from doi: 10.5061/dryad.qk22t. Two loci
 were removed due to being in a gene putatively evolving under selection. A
 further 1,360 SNPs were removed due to being in regions of know repetitive
 elements, excessive or low coverage, or low mappability in the killer
 whale genome. This VCF file contains the genotypes of 115 individuals at
 2,316 sites.Repeat_filtered.vcfRepeat and linkage filtered VCF fileThe repeat-filtered SNP dataset was further filtered to minimise the effect of linkage by including only SNPs that were spaced &gt;100-kb apart on a scaffold, retaining the genotypes for 115 individuals at 1,346 sites.Repeat_linkage_filtered.vcfRad_orca_subsample1SNAPP input file for subsample 1Rad_orca_subsample2SNAPP input file for subsample 2Rad_orca_subsample3SNAPP input file for subsample 3Rad_orca_subsample4SNAPP input file for subsample 4Rad_orca_subsample5_10individsSNAPP input file for subsample 5Rad_orca_subsample1 treesTrees inferred by SNAPP for subsample 1Rad_orca_subsample1.treesRad_orca_subsample2_1M treesTrees inferred by SNAPP for subsample 2Rad_orca_subsample2b_1M.treesRad_orca_subsample3_1M treesTrees inferred by SNAPP for subsample 3Rad_orca_subsample3_1M.treesRad_orca_subsample4_1Mb treesTrees inferred by SNAPP for subsample 4Rad_orca_subsample4_1Mb.treesRad_orca_subsample5_10individs_1M treesTrees inferred by SNAPP for subsample 5Rad_orca_subsample5_10individs_1M.treestreemix input fileInput file for TreeMixtreemix_input.txtSTRUCTURE input fileInput file for STRUCTURE analysesSTRUCTURE_INPUT