Development and application of single nucleotide polymorphisms ( SNPs ) for bowhead whale population structure analysis

We present the preliminary results of efforts to develop new class of nuclear genetic markers, single nucleotide polymorphisms (SNPs), for bowhead whale genetic studies. We have screened over 9000 bp of random bowhead DNA sequence, identifying 67 SNPs. Nineteen SNP assays were optimized initially and used to genotype modern and historical bowhead DNA samples from St. Lawrence Island and Barrow, Alaska. We developed novel methods for genotyping multiple nuclear loci from historical and poor quality samples, demonstrating high efficiency and low estimated error rates. Preliminary population analyses with this limited set of loci show no evidence of population structure for various strata analyzed previously with mtDNA and microsatellite analysis. Future application of additional loci and samples should demonstrate the power of SNPs for population structure analysis, providing a strong alternative to microsatellite loci.