Aim To examine the genetic structure and global phylogeography of the endangered green sea turtle, Chelonia mydas, in light of past climatic events and current conservation needs. Location Tropical and subtropical beaches around the world. Methods We analysed 386 base pairs of the mitochondrial (mt)DNA control region of 4,878 individual nesting green turtle samples from 127 rookeries globally. We used phylogeographic analysis to assess how demographic history, dispersal and barriers to gene flow have led to the current distribution of mtDNA lineages. Results We identified 11 divergent lineages that were tied to specific biogeographical regions. The phylogenetic analyses revealed an ancient origin for the species centred in the Indo‐Pacific and more recent colonization of the Central/Eastern Pacific as well as the Atlantic Basin. Overall the phylogeographic structure was strong but with a clear pattern of regional connectivity among rookeries. A Large genetic separation was found where there were obvious barriers to dispersal such as between the Atlantic and Pacific oceans and across the Pacific Ocean, as well as less obvious barriers to dispersal. Admixture of mtDNA haplotype lineages was detected at latitudinal extremes across the Indian Ocean and western Pacific Ocean resulting in these areas being nucleotide diversity hotspots. The highest regional genetic diversity and high endemic richness was observed in the SW Pacific, NW Pacific, SW Indian and NW Indian oceans. Main conclusions Past climatic fluctuations greatly affected the distribution of genetic diversity in the highly migratory green turtle. Our data suggest that past climatic events influenced local populations in different ways and the species appears to have survived the last glaciations in multiple glacial refugia.

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Understanding the dispersal pathway and connectivity of an endangered species plays an essential role in the development of strategies for its effective conservation and management. By using mtDNA control region sequences, we identified the genetic composition and estimated the origin of the northernmost feeding aggregation of green turtles Chelonia mydas around the Sanriku coast of Japan. Significant differences in haplotype frequencies between Sanriku and southern Japanese feeding aggregations, a significant correlation between genetic distance and geographical distance in Japanese feeding aggregations, and estimated contribution to the Sanriku, mainly from the Japanese rookery of Ogasawara, indicate compositional changes from the south to the north along the Japanese Archipelago and suggest that the northern feeding aggregations were occupied by turtles born mainly in Japanese rookeries. However, haplotypes specific or similar to Hawaiian and eastern Pacific rookeries were detected, and substantial contributions from Hawaii or the eastern Pacific to the Sanriku feeding aggregation were estimated. Combined with the observation of specimens with phenotypic features of the subspecies 'black turtle' nesting in the eastern Pacific, the results indicate the long-distance dispersal of hatchlings born in Hawaii or the eastern Pacific to Japanese coastal waters, possibly through the North Equatorial Current. Although the level of contribution may be small, this study genetically supports the occurrence of the westward long-distance dispersal of green turtles in the Pacific.

Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. However, there is little evidence for higher vulnerability and extinction risk in endangered species based on genomic differences between endangered and non-endangered species. This is true even in the case of functional loci, which are more likely to relate to the fitness of species than neutral loci. Here, we compared the genome-wide genetic diversity, proportion of duplicated genes ( P D ), and accumulation of deleterious variations of endangered island endemic (EIE) plants from four genera with those of their non-endangered (NE) widespread congeners. We focused on exhaustive sequences of expressed genes obtained by RNA sequencing. Most EIE species exhibited significantly lower genetic diversity and P D than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.