ESR 19:129-147 (2012)  -  DOI:

Empirical comparison of single nucleotide polymorphisms and microsatellites for population and demographic analyses of bowhead whales

Phillip A. Morin1,*, Frederick I. Archer1, Victoria L. Pease1, Brittany L. Hancock-Hanser1, Kelly M. Robertson1, Ryan M. Huebinger2,5, Karen K. Martien1, John W. Bickham2,6, J. Craig George3, Lianne D. Postma4, Barbara L. Taylor1

1Protected Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, USA
2Department of Forestry and Natural Resources, Purdue University, 715 West State St., West Lafayette, Indiana 47907-2061, USA
3North Slope Borough Department of Wildlife Management, PO Box 69, Barrow, Alaska 99723, USA
4Fisheries and Oceans Canada, Central and Arctic Region, 501 University Cr., Winnipeg, Manitoba R3T 2N6, Canada
5Present address: University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9160, USA 6Present address: Battelle Memorial Institute, 10777 Westheimer, Suite 1105, Houston, Texas 77042, USA

ABSTRACT: Interest in bowhead whale stock structure has been high due to the species’ extreme historical depletion, differential rates of recovery, the potential effects of climate change, and the need to set appropriate quotas for aboriginal hunts. We present an analysis of 42 linked and unlinked single nucleotide polymorphisms (SNPs) among 3 bowhead whale stocks and within the Bering/Chukchi/Beaufort Seas (BCB) stock, and compare results with previously published results of mtDNA control region sequences and 22 microsatellites. We performed tests of population structure (FST, χ2, STRUCTURE), population assignment, and estimates of effective population size (Ne), and evaluated different numbers of loci and samples to estimate the relative statistical power of SNPs and microsatellites. Results indicate that this number of SNPs provides similar power to microsatellites to detect low levels of differentiation (FST = 0.005−0.03) between bowhead populations with sample sizes of at least 20 per population. Neither marker performed well for Bayesian analysis of population structure (STRUCTURE) for the strata that had high diversity coupled with low differentiation. This example is valuable in cautioning against use of STRUCTURE to exclude demographic independence of relatively abundant populations. Microsatellites provided greater precision for estimates of Ne and for assignment tests. All 3 genetic marker types are consistent with the BCB stock being a single population. For microsatellites, differences were found between individuals born before 1949 and those born after 1979. SNPs are continuing to prove valuable as tools for understanding structure and demography of populations, and are likely to prove beneficial for long-term monitoring of bowhead whales.

KEY WORDS: Population structure · SNP · Cetacean · Population genetics · Genetic marker · Conservation management · Balaena mysticetus

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Cite this article as: Morin PA, Archer FI, Pease VL, Hancock-Hanser BL and others (2012) Empirical comparison of single nucleotide polymorphisms and microsatellites for population and demographic analyses of bowhead whales. Endang Species Res 19:129-147.

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