Data from: Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species
Dussex, Nicolas, University of Otago
Taylor, Helen R., University of Otago
Stovall, Willam R., University of Otago
Rutherford, Kim, University of Otago
Dodds, Ken G., AgResearch (New Zealand)
Clarke, Shannon M., University of Otago
Gemmell, Neil J., University of Otago
Published Aug 10, 2019 on Dryad.
Cite this dataset
Dussex, Nicolas et al. (2019). Data from: Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species [Dataset]. Dryad. https://doi.org/10.5061/dryad.63nm407
Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation‐by‐distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10‐fold and 250‐fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next‐generation markers and methods are powerful tools for resolving fine‐scale structure and informing conservation and management efforts.
Stacks and Plink Commands
GBS pipeline commands for SNP discrovery including Stacks and post-filtering with populations and Plink