Population structure and genetic diversity of leatherback turtles (Dermochelys coriacea) in Bird’s Head Seascape, Papua-Indonesia

Abstract

Leatherback (Dermochelys coriacea) populations are endangered globally and there is a need to better understand their genetic diversity and structure in order to inform conservation efforts. Most nesting in the western Pacific is concentrated in the Bird’s Head Seascape (BHS) region of West Papua, Indonesia. Previous genetic assessment based on limited mtDNA sequences inadequately represented the demographic complexity that is now evident for West Papua leatherbacks. In this study, we quantified the genetic diversity, connectivity and structure for leatherback populations in the BHS by integrating nuclear and mitochondrial (mt) DNA data. We compared 763-bp sequences of the mtDNA control region and data from 17 microsatellite loci at two beaches, Jeen Yessa (JY) and Jeen Syuab (JS) that represent temporally separated nesting populations. We then leveraged reduced-representation (RAD-capture) and whole genome resequencing approaches to generate genome-wide SNPs. We detected low genetic diversity for all datatypes. A total of 11 mtDNA haplotypes were identified, including two new haplotypes and three previously reported from Atlantic populations. Pairwise tests of haplotype and genotype (microsatellite) frequencies found no evidence of structure between the JY (boreal summer) and JS (boreal winter) populations. Furthermore, admixture and principal components analyses of genomic SNP datasets did not identify any clear genetic structure. These results suggest that the BH leatherbacks represent a single genetic stock based on current criteria for defining population Management Units for sea turtles. This study provides the basis for further population structure assessment that includes other nesting sites in Indonesia and the broader western Pacific.