Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species

BMC Genomics

Research Article

Inge Jonassen¹  Luis A. Pastene²  Naohisa Kanda³  Francois Besnier⁴  Rasmus Skern-Mauritzen⁴  Nils Øien⁴  Hiroko K. Solvang⁴  María Quintela⁴  Geir Dahle⁴  Bjørghild B. Seliussen⁴  Kevin A. Glover⁵  Ketil Malde⁶  Hans J. Skaug⁷  Tore Haug⁸ 

[1] Department of Informatics, University of Bergen, N-5020, Bergen, Norway;Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, 104-0055, Tokyo, Japan;Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, 104-0055, Tokyo, Japan;Japan NUS Co., Ltd, Nishi-Shinjuku Kimuraya Bldg 5F, 7-5-25, 160-0023, Nishi-Shinjuku, Japan;Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway;Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway;Department of Biology, University of Bergen, N-5020, Bergen, Norway;Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway;Department of Informatics, University of Bergen, N-5020, Bergen, Norway;Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway;Department of Mathematics, University of Bergen, N-5020, Bergen, Norway;Institute of Marine Research, PO box 6404, N-9294, Tromsø, Norway;

关键词: Simulated Hybrid;    Minke Whale;    Genome Resequencing;    International Whaling Commission;    Antarctic Minke Whale;   

DOI  :  10.1186/s12864-016-3416-5

 received in 2016-08-02, accepted in 2016-12-12,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundIn 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. An example of this can be seen in the minke whale species complex. Antarctic minke whales are genetically and morphologically distinct from the common minke found in the north Atlantic and Pacific oceans, and the two species are estimated to have been isolated from each other for 5 million years or more. Recent atypical migrations from the southern to the northern hemisphere 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.ResultsA 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.ConclusionsThis 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 interested in identifying other potential whale hybrids in the world’s oceans. 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.

【 授权许可】

CC BY   
© The Author(s). 2017