Natal Origin Identification of Green Turtles in the North Pacific by Genome-Wide Population Analysis With Limited DNA Samples

Abstract

Although studies using genome-wide single nucleotide polymorphisms (SNPs) are growing in non-model species, it is still difficult to prepare sufficient high-quality genomic DNA (gDNA) for population genomic analyses in many wild species. In this study, we first analyzed the population structure of green turtles in the North Pacific; four regions in Japan (the Yaeyama, Okinawa, Amami, and Ogasawara Islands), the Southeast Asia, Taiwan, the Federated States of Micronesia, the Republic Marshall Islands, and the Central or Eastern Pacific (C/E Pacific) using 1 ng of gDNA from green turtle field samples-including ones from dead carcasses-and multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq). In addition, we explored whether the genome-wide SNP data narrowed down the natal origins of foraging turtles that were difficult to identify by mitochondrial DNA (mtDNA) haplotype alone. The overall nesting population structure observed from genome-wide SNPs was consistent with results from mtDNA, and the population isolation of the C/E Pacific and Ogasawara Islands from the other North Pacific populations was highlighted. However, the population boundaries among the Northwestern Pacific, other than those of the Ogasawaras, were not clear. The uniqueness of the Ogasawara population in genome-wide SNP data enabled the identification of turtles that were more likely to have been born on the Ogasawara Islands. Our results show that genome-wide SNP data are more practical in identifying the natal origins of turtles that were difficult determine by the conventional mtDNA-basis mixed stock analysis. This study also showed that MIG-seq can be expected to meet the potential demand to utilize many preserved or fragmented gDNA samples for population genomics in many marine megafaunas for which sample collections are difficult.

Origins of green turtle fishery bycatch in the central Pacific revealed by mixed genetic markers

“…For sea turtles, it is recognized that new molecular assays are needed to better describe the genetic diversity of nesting populations and organize them into precise demographic units (Komoroske et al, 2017). Some labs, including ours, are currently exploring genome-wide SNP panels for sea turtle conservation genetics (Komoroske et al, 2018;Banerjee et al, 2020;Driller et al, 2020;Hamabata et al, 2020;Horne et al 2023), but the results of the present study show that not all green turtle populations require extensive panels of molecular markers for reliable stock discrimination. Furthermore, new marker development may not be fruitful without increased baseline sampling (Komoroske et al, 2017).…”

Overview of the population genetics and connectivity of sea turtles in the East Asia Region and their conservation implications

“…However, the number of MUs in Japan may increase after more comprehensive surveys using more samples and/or more sites. Importantly, the presence of endemic haplotypes not found elsewhere characterized certain rookeries in Ogasawara Island (Clade VII with CmP127, CmP128, CmP209 in Nishizawa et al, 2013;Hamabata et al, 2020), and Xisha Islands (Clade III with CmP244.1 in Song et al, 2022;Clade VIII with CmP250.1, CmP251.1, CmP252.1, CmP253.1 and CmP254.1 in Li et al, 2023). Habitat protection for these genetically unique rookeries should be accorded with high priority to sustain the essential populations.…”

“…Analysis using microsatellites and SNPs was only reported in 7 studies in this review, but it has gained popularity recently as it offers higher resolution in genetic composition to identify the natal origin and define population structure at a finer scale. For example, Hamabata et al (2020) and Hamabata et al (2023) revealed that SNPs were useful in estimating the natal origins of green turtles from the Ogasawara Islands, whose origin was indistinguishable from the Ryukyu Islands according to mtDNA. The use of mitogenomic sequencing should also be considered to improve the resolution of population structure, particularly important in areas where nuclear gene flow along migratory corridors but fine-scale female natal homing might occur.…”

Latest and comprehensive mitochondrial DNA haplotype data on green and hawksbill turtles collected in their habitats in Japan

“…Nesting sites for green turtles within Japan span the Ryukyu Archipelago and the Ogasawara Islands, whereas their foraging grounds encompass a wide coastal expanse along Japan's shores (Figure 1). Haplotype data associated with nesting populations were collected from Yaeyama (Nishizawa et al, 2011), the central Ryukyus (Hamabata et al, 2009(Hamabata et al, , 2014, and Ogasawara Islands (Nishizawa et al, 2013;Hamabata et al, 2020). Haplotype data for the foraging aggregations were collected from Yaeyama (Nishizawa et al, 2013;Hamabata et al, 2023), Okinawajima (Nishizawa et al, 2013;Hayashi and Nishizawa, 2015;Hamabata et al, 2018), Nomaike, Muroto, Kumano-nada (Hamabata et al, 2015), Oita (Kudo et al, 2021), Kanto (Nishizawa et al, 2013), and Sanriku (Nishizawa et al, 2014).…”