Genetic signature of a recent metapopulation bottleneck in the olive ridley turtle (Lepidochelys olivacea) after intensive commercial exploitation in Mexico

•First genetic signal linked to recent, human-driven bottlenecks in sea turtles.•Genetic erosion detected in the entire metapopulation.•Genetic assessments of bottlenecks in a marine vertebrate improved with large sampling.•We inform on the relationship between nesting colony and metapopulation dynamics.•The results are useful in the development of management plans and population monitoring.

Information on the demographic and genetic consequences of overexploitation of large marine vertebrates is often difficult to demonstrate on ecological time scales. We investigate the genetic impacts of recent commercial activities along Mexico’s Pacific coast on the nesting colonies of a long-lived vertebrate of conservation concern, the olive ridley turtle (Lepidochelys olivacea). This species was severely impacted by a commercial fishery between 1960 and 1990 (e.g. >350,000 individuals were caught in a single year), depleting important nesting areas within few decades. Microsatellite DNA variation of 334 samples representing 18 nesting sites revealed a clear signature of recent bottlenecks associated with changes in allelic diversity. Consistent with theoretical expectations and other empirical studies, we found no evidence for bottlenecks based on measures of heterozygosity. The bottleneck signal was strong across the highly connected metapopulation and also apparent in six nesting sites in a pattern consistent with the history of demographic disequilibria produced by their overexploitation. In addition, we clarify population structure across Mexico and show that Mismaloya, a key colony where human harvest led to a dramatic change in the species’ reproduction mode, has not been supplemented by gene flow after the bottleneck and has diverged genetically from other demes. This is perhaps the first study to detect recent signatures of anthropogenic-driven population declines in sea turtles using genetics. This enables managers to consider information about genetic signatures of contemporary demographic changes during the development of conservation management plans and during population monitoring.