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

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 (F ST , χ 2 , STRUCTURE), population assignment, and estimates of effective population size (N e ), 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 (F ST = 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 N e 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 Resale or republication not permitted without written consent of the publisherEndang Species Res 19: 129-147, 2012 tide polymorphism (SNP) genotyping is slowly growing in popularity for population genetics and molecular ecology (Brumfield et al. 2003, Morin et al. 2004, Seddon et al. 2005, Seeb et al. 2011, but it remains to be seen how appropriate SNPs are for some applications. Despite some significant benefits to using SNPs (e.g. large number of SNPs in most genomes, ease and efficiency of genotyping, simple and low mutation rate; reviewed in Morin et al. 2004, Helyar et al. 2011, there are questions about whether they provide sufficient statistical power to detect low levels of population structure (e.g. for demographically independent populations with N e m ≥ 1, where N e is the effective population size and m is the migration rate per generation; Wright 1931) without using hundreds or thousands of SNPs. Additionally, their appropriateness for estimating demographic parameters has not been fully evaluated.We previously evaluated the statistical power for detecting population structure based on simulated data (Morin ...

Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

“…SNPs often prove to be equivalent or better than microsatellites for population genetic and phylogenetic analyses, especially when larger numbers of SNPs can be genotyped (Morin et al . , ; Willing et al . ).…”

Comparing estimates of number of breeders Nb based on microsatellites and single nucleotide polymorphism of three groups of brown trout (Salmo trutta L.)

“…The relationships between MS‐ and SNP‐based estimates of N b differed from the N e estimates of bowhead whales ( Balaena mysticetus L.), which did not show a consequent relationship between MS‐ and SNP‐based estimates, including 42 SNPs (Morin et al . ). This could be due to the number of SNPs, as N b based on one SNP per BTLG group (40 SNPs) in the present study also gave a divergent high N b estimate for the W/1+ group.…”

“…; Morin et al . ; Weinman et al . ), and the heterozygote excess in all samples is expected in small populations (Robertson ; Rasmussen ), as the background of the HeE method for N b estimation.…”

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“…For instance, Morin et al . () found that nearly six times as many SNP loci than microsatellite loci were needed in order to accurately assign samples from two geographically disjunct populations of bowhead whales. Assignment tests can also be applied to AFLP data.…”