Fine-scale genetic population structure of loggerhead turtles in the Northwest Pacific

Abstract

Effective conservation of globally distributed marine species relies on identification of demographically independent populations to ensure that management actions are directed at the appropriate scale. This identification is particularly challenging for species with complex life histories when local breeding populations have not been adequately sampled. We used mtDNA to analyze the population structure of loggerhead turtles from a total of 555 samples collected from 12 nesting sites in Japan in the Northwest Pacific, including previously unsampled rookeries in the Ryukyu Archipelago, for a comprehensive coverage of the nesting distribution. We identified a total of 9 haplotypes based on 820 bp of the mtDNA control region, including 5 variants of a single previously described 380 bp haplotype. We discovered that 1 haplotype (CcP1.1) previously rare in the North Pacific is common in the Ryukyu Archipelago. Based on analysis of haplotype frequencies, we found significant differentiation among regionally grouped nesting populations (analysis of molecular variance p < 0.0001, df = 8; pairwise F ST ranging from 0.033 to 0.145). Our results provide evidence to support the recognition of 3 management units (MU) within the NW Pacific Regional Management Unit (RMU). These include (1) the Ryukyu MU that includes Okinawa, Okinoerabu and Amami, (2) Yakushima Island MU and (3) a Mainland MU that includes Bousou, Enshu-nada, Shikoku, Kii and Eastern Kyushu. These new data from Japan will provide important baseline data for global genetic stock assessments and contribute to our understanding of the population structure, ecology and life history of this migratory marine species in the northern Pacific.

Intrapopulation variability in the timing of ontogenetic habitat shifts in sea turtles revealed using δ15N values from bone growth rings

“…Given new population structure analysis (Matsuzawa et al . ), genetically linked behavioural differences may drive these patterns, yet this remains to be explored. Periodic environmental, oceanographic and/or climate fluxes may also facilitate movement of juvenile turtles between habitats.…”

Are we working towards global research priorities for management and conservation of sea turtles?

“…Gaos et al 2016, Vargas et al 2016 loggerhead (e.g. Nishizawa et al 2014a, Shamblin et al 2014, Matsuzawa et al 2016, and olive ridley turtles (Jensen et al 2013). Globally, significant advances have been made integrating male-and female-mediated gene flow by incorporating both mitochondrial and nuclear DNA (Dutton et al 2013) for delineating demographically independent populations.…”

Mitochondrial DNA short tandem repeats unveil hidden population structuring and migration routes of an endangered marine turtle

“…Among those, genetics has been the preferred method to evaluate population structure. The levels of connectivity among populations can be inferred through the degree of genetic differentiation retained as a result of isolation (Matsuzawa et al, ; Roden et al, ), and can also reflect the historical processes that shaped the actual distributions (Clusa et al, ). Contemporary movements of individuals can also be tracked using tag–recapture techniques (Rees et al, ), satellite telemetry (Stokes et al, ), or stable isotopes (Hobson, ), thus linking reproductive areas with developmental and foraging areas.…”