Abstract
Genetic diversity (θ), effective population size (Ne), and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP) range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in Ne (θ = 4Neμ), where μ is the mutation rate. Application of the isolation-with-migration (IM) model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1–16.7), with divergence times (t) among all populations significantly greater than zero. Using a conservative (i.e., slow) fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs) for the onset of the decline in Ne predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.
Highlights
Modern fishing practices have led to declines in numerous marine species [1,2,3], with long-lived fish and mammals susceptible to over-harvesting [4], [5]
As with previous analyses of mtDNA in the Pacific, we found low levels of diversity in the Eastern Pacific (EP): seven mtDNA control region haplotypes that differed by a maximum of two base pair changes
Results from BOTTLENECK depended on the model of microsatellite mutation: under the IAM model alone, the results showed a significant excess in gene diversity, and a recent bottleneck, for all populations (p-value for one-tail test,0.05), except Cebaco Island (CEB) and Manta (MAN)
Summary
Modern fishing practices have led to declines in numerous marine species [1,2,3], with long-lived fish and mammals susceptible to over-harvesting [4], [5]. S. lewini is a large, highly-mobile circumtropical marine predator found along continental margins and oceanic islands [21] that forms large and conspicuous aggregations, in the tropical EP [22,23,24] This shark is caught both intentionally and as by-catch throughout its range [7] and Western North Atlantic stocks alone have experienced an estimated 83% reduction between 1981 and 2005 [25]. Previous genetic work on S. lewini has yielded estimates of population structure, female effective population size (Nef) and gene flow that vary widely among different regions across the globe [17], [26], [27] Some of this variability could be real, contrasting patterns among recent studies could reflect a combination of significant differences in the spatial scale of analysis, large differences in sample sizes (of individuals), and the predominant use of only a single (mtDNA) locus
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