Data from: Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes ...

• Main Authors: Foote, Andrew D., Morin, Phillip A.
• Format: Dataset
• Language: English
• Published: Dryad 2016
• Subjects: killer whale; Orcinus orca; Pacific; Killer Whale; Orca; Killer whale
• Online Access: https://dx.doi.org/10.5061/dryad.803q8; https://datadryad.org/stash/dataset/doi:10.5061/dryad.803q8

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 >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 ... : 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 >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 ...