DOI: 10.5061/dryad.fm4mk
title: Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

description: Global climate change during the Late Pleistocene periodically encroached
 and then released habitat during the glacial cycles, causing range
 expansions and contractions in some species. These dynamics have played a
 major role in geographic radiations, diversification and speciation. We
 investigate these dynamics in the most widely distributed of marine
 mammals, the killer whale (Orcinus orca), using a global data set of over
 450 samples. This marine top predator inhabits coastal and pelagic
 ecosystems ranging from the ice edge to the tropics, often exhibiting
 ecological, behavioural and morphological variation suggestive of local
 adaptation accompanied by reproductive isolation. Results suggest a rapid
 global radiation occurred over the last 350 000 years. Based on habitat
 models, we estimated there was only a 15% global contraction of core
 suitable habitat during the last glacial maximum, and the resources
 appeared to sustain a constant global effective female population size
 throughout the Late Pleistocene. Reconstruction of the ancestral
 phylogeography highlighted the high mobility of this species, identifying
 22 strongly supported long-range dispersal events including interoceanic
 and interhemispheric movement. Despite this propensity for geographic
 dispersal, the increased sampling of this study uncovered very few
 potential examples of ancestral dispersal among ecotypes. Concordance of
 nuclear and mitochondrial data further confirms genetic cohesiveness, with
 little or no current gene flow among sympatric ecotypes. Taken as a whole,
 our data suggest that the glacial cycles influenced local populations in
 different ways, with no clear global pattern, but with secondary contact
 among lineages following long-range dispersal as a potential mechanism
 driving ecological diversification.
description: Dataset_S1_Killer_Whale_SNP_genotypesO. orca SNP genotypes for 91 SNPs, 128 samples. Alleles have been re-coded for programs that only accept numerical alleles. G = 1, A =2 , C = 3, T = 4. Missing data are represented by 0.Dataset_S1_AS7genotypes.xlsxDataset_S2_Beast_in_158mtGen_partitionedInput xml file for phylogenetic analysis in the program BEAST 1.8, containing partitioned mitochondrial sequence data and phylogenetic analysis parameters as described in the methods.Dataset_S3_Beast_out_158mtGen_partitioned_consantTree file output from BEAST v1.8 phylogenetic analysis of the data from Dataset S2.Dataset_S4_SNAPPinput_AS7_42SNP_113indivInput xml file for analysis of SNP data in the program SNAPP, within the BEAST v2.0 package.Dataset_S5_SNAPPoutput_AS7_42SNP_113indivOutput phylogenetic tree file from the program SNAPP, based on data and parameters in the input file Dataset_S4.Dataset_S6_DelphinidaeXML file of aligned Delphinidae mitochondrial genome sequences with partitions and parameters used for time-calibrated phylogenetic analysis in BEAST.Dataset_S7_DelphinidaeMaximum clade credibility tree file of Delphinidae mitochondrial phylogeny from BEAST analysis of Dataset_S6.