Large‐scale connectivity, cryptic population structure, and relatedness in Eastern Pacific Olive ridley sea turtles (Lepidochelys olivacea)

Abstract

Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial control region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST = 0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and preexisting microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST = 0.08, p < .001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST = 0.103, p < .001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p < .001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin‐wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life history, particularly in light of the natal‐homing paradigm.

Global phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation

“…The microsatellite data were screened for null alleles and genotyping errors (e.g., stuttering) using Micro-Checker (Van Oosterhout et al 2004), and linkage disequilibrium between loci was estimated using Arlequin. Although Silver-Gorges et al (2020) found three of these loci linked in populations from Costa Rica and Mexico, no consistent linkage pattern within populations was detected when analyzing the present worldwide dataset and thus all 15 loci were retained.…”

“…Here we only included longer sequences (> 700 bp) to potentially increase power to resolve population structure. In total, 283 Kemp's ridley (Duchene et al 2012;Frey et al 2014;Reid et al 2019;Frandsen et al 2020) and 340 olive ridley sequences were obtained from published studies (Duchene et al 2012;Plot et al 2012;Jensen et al 2013;Revuelta et al 2015;González-Paredes et al 2017;Campista León et al 2019;Work et al 2019;Adnyana et al 2020;Silver-Gorges et al 2020;Stelfox et al 2020). Several segments from Madagascar and India (Stelfox et al 2020) were excluded because haplotype frequencies were not available, and only publicly accessible haplotypes from Adnyana et al (2020) were included.…”

“…With a new and substantially expanded data set of geographical genetic patterns, this study revisited and updated these hypotheses on the population history, phylogeography, and distribution of ridley sea turtles, as well as their global management units. Previous research relied on geographically restricted sampling, mitochondrial sequences, and ensuing limited inference power (Bowen et al 1997;Jensen et al 2013;Campista León et al 2019;Work et al 2019;Adnyana et al 2020;Silver-Gorges et al 2020;Stelfox et al 2020). Our goals were therefore to (i) investigate current geographic patterns of genetic diversity in ridley populations around the world, (ii) determine genetic relationships between populations and oceanic regions, (iii) explore changes in temporal and spatial population distributions, (iv) infer divergence and differentiation times between populations and the two ridley species, and (v) compare ridley phylogeographical patterns to those of other sea turtle taxa.…”