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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3416-5) contains supplementary material, which is available to authorized users.

A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations

“…While natural hybridization has been widely acknowledged as a powerful evolutionary force 6,7 , during last decades anthropogenic hybridization considerably contributed to threat the genomic integrity and survival of a number of taxa through the introgression of alien or domestic alleles in the gene pool of natural populations 3,11,12,15,41,42,59 . In particular, though some studies documented cases of beneficial introgression of domestic mutations in wild populations of North American wolves 27 and Alpine ibexes 28 , introgressive hybridization with www.nature.com/scientificreports www.nature.com/scientificreports/ domestic forms is globally recognized as a significant risk factor for the conservation of several wild taxa 14,24,28,[60][61][62] .…”

“…The red line indicates the q-threshold identified at 0.995, value corresponding to the minimum individual q iw of both simulated and real wolf parentals (see Table 2), which, minimizing the risk of both type I and type II errors, is able to efficiently discriminate between older admixed (BC3W-BC8W) and pure individuals. of populations 40 , which might occur when sample sizes vary among analyses or when unknown samples with variable levels of admixture (namely including both pure and admixed individuals) are analysed simultaneously instead of one by one 40,69,70 , conversely to other fully (Structure, NewHybrids, Baps) or partially (GeneClass) Bayesian assignment methods commonly applied for admixture identifications 33,41,42,[71][72][73][74][75][76] . As expected, the "one-by-one" approach with Parallel Structure 55 performed reliably, with very limited fluctuations of both Q i and q i among different replicates of the same runs.…”

“…Though anthropogenic hybridization has been deeply investigated for a number of animal species, only a few studies applied reliable statistical criteria to define adequate assignment q-thresholds to correctly identify non-admixed individuals and distinguish different admixture classes [1,41,42,73,77 . Conversely, most genetic investigations about hybridization in canids were mainly based on q-thresholds selected arbitrarily or chosen among those widely used in the literature (e.g.…”

“…Furthermore, particular attention should be reserved to the choice of adequate statistical computations for the assignment procedures, in order to minimise the risk that individual assignment probabilities might be affected by the allele frequencies of other samples to be assigned. In addition, the selection of statistically supported assignment q-thresholds based on individual assignment (q i -values) extrapolated from simulated data is necessary to ensure the realistic and reliable identification of admixed individuals 5,16,[40][41][42] .…”

SimHyb: a simulation software for the study of the evolution of hybridizing populations. Application to Quercus ilex and Q. suber suggests hybridization could be underestimated

“…This approach was applied by Burgarella et al (2009) in sympatric Q. ilex -Q. suber populations, estimating a current introgression rate of <2%. Later on, this procedure has been applied in studies for many other species, including animals (Neaves et al 2010, Bogdanowicz et al 2012, Malde et al 2017.…”