Haplotypes across the Oceans: worldwide phylogeography, evolution, conservation and nomenclature standardization in the leatherback sea turtle (Dermochelys coriacea).

Abstract

Inconsistent haplotype nomenclature complicates the integration of genetic data in population genetics and phylogeographic studies of the leatherback sea turtle (Dermochelys coriacea). Previous studies using control region mitochondrial DNA (mtDNA) sequences of varying lengths (e.g., 496 bp, 711 bp, 763 bp) have led to redundant classifications and misinterpretations of population structure. In this study, we reviewed 304 control region mtDNA sequences from GenBank, representing all published haplotypes across the Atlantic, Indian, and Pacific Oceans. We proposed a standardized nomenclature based on two sequence lengths: 473 bp (short) and 681 bp (long). We identified 32 haplotypes in the long-sequence dataset and 24 in the short-sequence dataset, with 21 and 14 variable sites, respectively. Haplotype network analyses revealed strong genetic structure, with Dc1.1 (long) and Dc1 (short) as the most widely distributed haplotypes. Ancestral area reconstruction indicated a Pacific origin for the most basal D. coriacea nodes, followed by multiple transitions into the Atlantic and Indian Oceans. Divergence time estimates placed the origin of the D. coriacea contemporary clade at ~4.86 million years ago (Ma), with Dc1.1 emerging around 0.49 Ma. Atlantic colonizations occurred at ~1.75 Ma and ~1.73 Ma, and Indian Ocean colonization at ~3.00 Ma. These findings support the adoption of a unified haplotype nomenclature to clarify population genetic structure and enhance the consistency of genetic assessments for conservation applications.