  Background: In the marine environment, where there are few absolute physical
barriers, contemporary contact between previously isolated species can occur
across great distances, and in some cases, may be inter-oceanic. [..] in the
minke whale species complex [...] migrations [..] have been documented and
fertile hybrids and back-crossed individuals between both species have also
been identified. However, it is not known whether this represents a
contemporary event, potentially driven by ecosystem changes in the Antarctic,
or a sporadic occurrence happening over an evolutionary time-scale. We
successfully used whole genome resequencing to identify a panel of diagnostic
SNPs which now enable us address this evolutionary question.
  Results: A large number of SNPs displaying fixed or nearly fixed allele
frequency differences among the minke whale species were identified from the
sequence data. Five panels of putatively diagnostic markers were established on
a genotyping platform for validation of allele frequencies; two panels (26 and
24 SNPs) separating the two species of minke whale, and three panels (22, 23,
and 24 SNPs) differentiating the three subspecies of common minke whale. The
panels were validated against a set of reference samples, demonstrating the
ability to accurately identify back-crossed whales up to three generations.
  Conclusions: This work has resulted in the development of a panel of novel
diagnostic genetic markers to address inter-oceanic and global contact among
the genetically isolated minke whale species and sub-species. These markers,
including a globally relevant genetic reference data set for this species
complex, are now openly available for researchers [..]. The approach used here,
combining whole genome resequencing and high-throughput genotyping, represents
a universal approach to develop similar tools for other species and population
complexes.
