Determination of the haplotype and complete mitochondrial genome of the leatherback turtle Dermochelys coriacea (Testudines: Dermochelyidae) found in the vicinity of Korea

Cho, Yuna; Kim, Hye Kwon; Lee, Kyunglee; Kim, Hyun Woo; Park, Kyum Joon; Sohn, Hawsun; Choi, Youngjoon; Park, Sung-Kyun; Jeong, Dae Gwin; Kim, Ji Hyung

doi:10.1007/s12686-017-0905-z

Cited by 6 publications

(6 citation statements)

References 12 publications

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“…The Bayesian and maximum likelihood gene trees produced similar topologies (Figure 3, Figure A1). Relationships among species were consistent with previous work (Bowen & Karl, 2007;Cho et al, 2018;Duchene et al, 2012;Evers & Benson, 2019;Naro-Maciel et al, 2008;Otálora & Hernández-Fernández, 2018). However, some withinspecies relationships differed.…”

Section: Gene Tree Analysissupporting

confidence: 90%

“…These deeply diverged lineages diversified across ocean basins, with most species broadly distributed while others ( L. kempii and N. depressus ) are limited to one basin (Bowen & Karl, 1996 ). Previous studies examined relationships among sea turtle species and ocean basins through analyses of mtDNA and nuclear markers (Baltazar‐Soares et al, 2020 ; Bowen & Karl, 2007 ; Naro‐Maciel et al, 2008 ), while more recent whole mitogenome analyses increase molecular resolution, but are limited by small sample sizes (Cho et al, 2018 ; Duchene et al, 2012 ; Otálora & Hernández‐Fernández, 2018 ; Vilaça et al, 2021 ). In each case, genetic analyses focus almost exclusively on rookery sites and data, while the mechanisms driving diversification patterns may actually be due to misdirected philopatry among post‐dispersal individuals.…”

Section: Introductionmentioning

confidence: 99%

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Genetic variation among sea turtle life stages and species suggests connectivity among ocean basins

Phillips

Martin

Stahelin

et al. 2022

Ecology and Evolution

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Regional genetic differentiation of mitochondrial lineages occurs in migratory species with natal philopatry such as sea turtles. However, early juvenile dispersal represents a key opportunity for gene flow and colonization of new regions through founder events, making it an important yet under‐studied life stage. To assess connectivity among sea turtle life stages and ocean basins, we sequenced mitochondrial DNA (mtDNA) fragments from 35 juveniles sampled in the Gulf of Mexico from the rarely observed dispersal stage across three species: green turtles ( Chelonia mydas ; n = 30), hawksbills ( Eretmochelys imbricata ; n = 3), and loggerheads ( Caretta caretta ; n = 2). We estimated green turtle rookery contributions using a many‐to‐many Bayesian mixed stock analysis that incorporated dispersal probabilities based on rookery size and transport via ocean currents. We assembled a gene tree including 709 distinct mtDNA control region haplotypes from the literature for all seven extant sea turtle species to assess gaps in life‐stage data across ocean basins, as well as contextualize the lineages we sampled from dispersing juveniles. Our results indicate a high likelihood that green turtles sampled in the Gulf of Mexico originated from rookeries along the coast of Mexico, with smaller contributions from Costa Rica and Suriname. The gene tree analysis yielded species‐level relationships consistent with those presented previously, while intra‐species relationships between lineages and ocean basins differed, particularly within loggerhead and green turtle clades. Our results highlight the lack of genetic data from juvenile sea turtles, especially the early dispersal stage, and the potential for these data to answer broader questions of connectivity and diversification across species and lineages.

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Section: Gene Tree Analysissupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Genetic variation among sea turtle life stages and species suggests connectivity among ocean basins

Phillips

Martin

Stahelin

et al. 2022

Ecology and Evolution

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“…For leatherback turtles, the genetic sequences from Jeju were identified based on both short sequences of 496 bp (Dutton et al, 1999) and long sequences of 763 bp (Yoshikawa et al, 2016;Cho et al, 2018). Haplotype compositions for specific habitats based on a sequence length of 496 bp were derived from studies conducted in the western Pacific (Dutton et al, 2007;Yoshikawa et al, 2016) and the eastern Pacific (Dutton et al, 1999) (Supplementary Table 7).…”

Section: Molecular Analysismentioning

confidence: 99%

“…To fill the gaps, comprehensive investigations are needed into their genetic features and migration patterns. As of now, mitochondrial sequences for sea turtles on the Korean Peninsula have been officially reported for only a few individuals of hawksbill, olive ridley, and leatherback turtles (Cho et al, 2018). In the northwestern Pacific region, there have been few studies on these species despite regular observations (Hamann et al, 2006;Chan et al, 2007;Nishizawa et al, 2012;Fukuoka et al, 2019;Ng and Matsuzawa, 2021).…”

Section: Introductionmentioning

confidence: 99%

Connectivity between sea turtles off Jeju Island on the Korean Peninsula, and other populations in the western Pacific

Jang,

Jo,

Jang

et al. 2024

Front. Mar. Sci.

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The northwestern Pacific region is an important habitat for sea turtles, hosting five species out of seven. There is still limited information available about the sea turtle aggregations around the Korean Peninsula, which is the northern boundary for many sea turtle species in the western Pacific area. The present study aims to investigate the migratory route of sea turtles visiting Jeju Island. Five species of sea turtles were identified from by-catch and stranding data between 2013 and 2022 on Jeju Island in Korea: green (Chelonia mydas; 24 individuals), loggerhead (Caretta caretta; 9), hawksbill (Eretmochelys imbricata; 2), olive ridley (Lepidochelys olivacea; 2), and leatherback (Dermochelys coriacea; 1). Mixed stock analysis using mitochondrial DNA haplotypes revealed that Jeju green turtles primarily originate from the rookeries of the Japanese Archipelago. This connectivity between two regions was also supported by the similar genetic composition of loggerhead turtles. Similarly, satellite tracking data showed that several green turtles originating from Jeju Island migrated to waters near the Ryukyu Archipelago in Japan. Nevertheless, about 60% of the tracked green turtles stayed near Jeju Island, with most overwintering there, indicating the long residency in Jeju Island. This study also provides the genetic sequences of other three species including new orphan haplotypes of hawksbill and olive ridley turtles. Our findings suggest that Jeju Island serves as a stable foraging habitat and provide insight into understanding the habitat range of sea turtles in the western Pacific.

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“…The need for amplification through PCR can be bypassed, and genomic DNA extractions can be sequenced directly by using sequencing-by-synthesis with the complete mitochondrial genome recovered through assembly of the resulting reads. This method is possible due to the high copy number of mitochondrial DNA contained within genomic DNA, and it has been applied successfully in a wide range of taxa including invertebrates, birds, mammals, amphibians, and reptiles (Cao, Wang, Ge, & Gong, 2019;Caparroz et al, 2018;Chen, 2018;Cho et al, 2018;Cooke, King, Johnson, Boles, & Major, 2012;Figueroa & Baco, 2014;Gao et al, 2017;Huang et al, 2014). We follow a similar procedure as these studies by preparing DNA libraries from genomic DNA extractions followed by next generation sequencing to obtain complete mitochondrial genomes of L. kempii.…”

Section: Ridleys In Texas Andmentioning

confidence: 99%

Mitochondrial genomes and genetic structure of the Kemp's ridley sea turtle (Lepidochelys kempii)

Frandsen

Figueroa

George

2019

Ecology and Evolution

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The Kemp's ridley (Lepidochelys kempii) is the world's most endangered sea turtle species and is primarily distributed in the Gulf of Mexico. In the United States, South Padre Island, Texas serves as a key nesting ground for the species. Genetic studies of the Kemp's ridley have been used to aid in conservation and management practices, with the mitochondrial control region as the most commonly used marker due to its perceived hypervariability and ease of sequencing. However, with the advent of next generation sequencing technology, targeting complete mitochondrial genomes is now feasible. Here, we describe a more complete mitochondrial genome for the Kemp's ridley than has been previously published in literature and demonstrate a cost-effective and efficient method for obtaining complete mitochondrial genomes from sea turtles. We compare the genetic diversity and taxonomic resolution obtained from whole mitochondrial genomes to that obtained from the mitochondrial control region alone. We compare current genetic diversity with previous records. Furthermore, we evaluate the genetic structure between the breeding stock in South Padre Island and that of deceased Kemp's ridleys recovered on the Northern coast of the Gulf of Mexico after the 2010 BP Deepwater Horizon oil spill, and of Kemp's ridleys stranded on the East Coast of the United States. Our results show that complete mitochondrial genomes provide greater resolution than the control region alone.They also show that the genetic diversity of the Kemp's ridley has remained stable, despite large population declines, and that the genetic makeup of deceased turtles stranded after the Deepwater Horizon oil spill is indistinguishable from the breeding stock in South Padre Island, Texas. K E Y W O R D Sconservation, control region, genetic diversity, next generation sequencing, phylogeny, phylogeography

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Determination of the haplotype and complete mitochondrial genome of the leatherback turtle Dermochelys coriacea (Testudines: Dermochelyidae) found in the vicinity of Korea

Cited by 6 publications

References 12 publications

Genetic variation among sea turtle life stages and species suggests connectivity among ocean basins

Genetic variation among sea turtle life stages and species suggests connectivity among ocean basins

Connectivity between sea turtles off Jeju Island on the Korean Peninsula, and other populations in the western Pacific

Mitochondrial genomes and genetic structure of the Kemp's ridley sea turtle (Lepidochelys kempii)

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