Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

Michelle Viengkone,Vicki Sahanatien,Markus G. Dyck,Martyn E. Obbard,Evan Shaun Richardson,Nick J. Lunn,Corey S. Davis,Joshua Moses Miller,Andrew Edward Derocher,René Michael Malenfant

doi:10.1002/ece3.2563

Michelle Viengkone, Vicki Sahanatien + Show 8 more

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https://doi.org/10.1002/ece3.2563

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Abstract

Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single‐nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine‐scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine‐scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine‐scale population delineation in polar bears.

Highlights

Genetic techniques have been adopted by evolutionary, ecological, and conservation biologists to delineate subpopulations (Allendorf, Hohenlohe, & Luikart, 2010; Morin, Luikart, & Wayne, 2004)
We named the four genetic clusters identified by discriminant analysis of principal components (DAPC) and STRUCTURE as: (i) Western—including individuals sampled in Western Hudson Bay (WH), Southern Hudson Bay (SH), and southern Foxe Basin (FB); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and iv) Northeast—individuals from DS (Baffin Island)
Fine-scale structure was evident in polar bears in the Hudson Bay region, which differs from the subpopulation management designations currently used

Summary

Introduction

Genetic techniques have been adopted by evolutionary, ecological, and conservation biologists to delineate subpopulations (Allendorf, Hohenlohe, & Luikart, 2010; Morin, Luikart, & Wayne, 2004). The use of microsatellites to examine genetic structure is based on their high levels of polymorphism and information content per locus (Balloux & Lugon-Moulin, 2002; Seddon, Parker, Ostrander, & Ellegren, 2005; Vignal, Milan, SanCristobal, & Eggen, 2002). With increasing interest in the use of larger numbers of markers, biallelic single-nucleotide polymorphisms (SNPs) are an. The use of SNPs for most wildlife species has been limited due to the high costs associated with discovery and typing of large marker sets (Vignal et al, 2002). The onset of new techniques to discover and genotype large marker sets simultaneously with methods like genotyping-by-sequencing may make SNP discovery and typing more cost-effective (Davey et al, 2011; Morin et al, 2004)

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