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Table S1 List of samples.

Table S2 Groups sampled.

Table S3 Microsatellite primer sets.

Table S4 Primers for all 36 SNP assays.

Table S5 Summary of population structure analyses for mtDNA, microsatellites, SNPs and combined nuclear markers (nDNA), and sensitivity analyses for linked SNP loci.

Table S6 Variable sites among all known mtDNA sperm whale haplotypes globally and GenBank accession numbers.

Table S7 Allele frequencies for each microsatellite locus, by strata.

Table S8 Allele frequencies for each SNP locus, by strata.

Table S9 Pairwise divergence between strata comprised of samples from females and young.

Table S10 Pairwise divergence between Gulf of Alaska males and the three low latitude strata containing females.

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