Phylogeography of the Olive Ridley Sea Turtle (Lepidochelys olivacea): Standardized Global Haplotype Nomenclature and Updated Mitochondrial Lineage Distributions in the Eastern Pacific

Lepidochelys olivacea is the most abundant sea turtle species worldwide and exhibits a circumtropical distribution across the Atlantic, Pacific, and Indian Oceans. Global phylogeographic studies have identified three major mitochondrial lineages, but comparisons among regions remain limited by inconsistent mtDNA control-region fragment lengths, incompatible haplotype nomenclatures, and uneven geographic sampling. The East Pacific Regional Management Unit (RMU), which includes major nesting populations in Mexico and Costa Rica, experienced severe demographic declines during the twentieth century, and the effects of expanded sampling on current phylogeographic patterns remain uncertain. This study analyzed 1264 mtDNA control region sequences (474-bp and 653-bp fragments) to update and standardize the global genetic dataset of L. olivacea, incorporating novel samples from previously unsampled East Pacific localities. Clear phylogeographic differentiation among RMUs was detected and remained consistent across both sequence lengths, supporting the Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) lineages. Shared haplotypes between the EP and IWP lineages likely reflect historical connectivity rather than contemporary transoceanic movements. The 653-bp dataset revealed greater haplotype diversity (78 haplotypes) than the 474-bp dataset (62 haplotypes), highlighting the improved resolution provided by the longer marker. Regional diversity patterns appeared to be influenced by sampling effort, particularly in underrepresented regions such as the West Indian Ocean. Negative neutrality indices in both Pacific RMUs suggested recent population expansion. This study establishes a standardized haplotype nomenclature for L. olivacea, provides an updated view of mitochondrial lineage distributions, and offers a robust framework for future phylogeographic and conservation studies across the species’ range.