Bayesian inference of a historical bottleneck in a heavily exploited marine mammal

Abstract

Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology.

Population genetic structure at the northern range limit of the threatened eastern hog-nosed snake (Heterodon platirhinos)

“…For example, ABC analysis yielded strong support for a recent bottleneck in a heavily exploited population of Antarctic fur seals (Arctocephalus gazelle), whereas traditional bottleneck tests proved equivocal (Hoffman et al 2011). ABC is robust to assumptions regarding mutation model and allows for the simultaneous assessment of multiple hypothesized demographic models as we have done here (Beaumont et al 2002;Cornuet et al 2008).…”

“…ABC approaches in tests for recent population declines are relatively new but show promise in studies of taxa of conservation concern as signals of drastic population declines often remain undetected or ambiguous (Thornton and Andolfatto 2006;Hoffman et al 2011;McCoy et al 2014). For example, ABC analysis yielded strong support for a recent bottleneck in a heavily exploited population of Antarctic fur seals (Arctocephalus gazelle), whereas traditional bottleneck tests proved equivocal (Hoffman et al 2011).…”

“…Thus, declines in population size are of obvious conservation concern as they reduce the probability of population persistence and may impair fitness (Briskie and Mackintosh 2004) and reduce evolutionary potential in the longer term (Frankham et al 1999). Genetic studies can provide important insights for species of conservation concern including helping to (1) diagnose genetically distinct clusters (Manel et al 2004), (2) quantify and understand altered dispersal patterns (Row et al 2010), (3) detect signatures of population declines, including bottlenecks, and reduced genetically effective population sizes (N e ) in populations of rare or at-risk species (Hoffman et al 2011;Wall et al 2014), and (4) identify populations that are vulnerable to inbreeding (Clark et al 2011;Storfer et al 2014). Consequently, understanding how genetic factors contribute to extinction risk in populations of critically endangered or threatened species can facilitate decisions for prioritizing conservation and management efforts.…”

Born blonde: a recessive loss‐of‐function mutation in the melanocortin 1 receptor is associated with cream coat coloration inAntarctic fur seals

“…As a conservative measure, we therefore used our dataset of 50 microsatellite loci to test for the presence of cryptic population structure. In support of previous studies of the breeding population of fur seals at South Georgia (e.g., Hoffman et al., 2011; Stoffel et al. 2015), Bayesian cluster analysis yielded a best clustering solution of K  =   1.…”

“…These effects may have been exacerbated by a severe bottleneck experienced by this species in the late 19th century (Hoffman et al. 2011). To explore how these processes could have influenced the frequency of the causative mutation, it would be interesting to carry out a temporal analysis, ideally comparing historical prebottleneck samples with those from the current day.…”