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

Frontiers in Marine Science

Katsufumi Sato¹  Takuya Fukuoka²  Mitsuhiko P. Sato³  Yoshihisa Suyama³  Ayumi Matsuo³  Kazunari Kameda⁴  Masakado Kawata⁵  Tomoko Hamabata⁵  Satomi Kondo⁶  Isao Kawazu⁸ 

[1] Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan;International Coastal Research Center, Atmosphere and Ocean Research Institute, The University of Tokyo, Otsuchi, Japan;Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan;Kuroshima Research Station, Sea Turtle Association of Japan, Yaeyama, Japan;Laboratory of Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan;Ogasawara Marine Center, Everlasting Nature of Asia, Ogasawara, Japan;Okinawa Churashima Research Center, Okinawa Churashima Foundation, Motobu, Japan;Okinawa Churaumi Aquarium, Okinawa Churashima Foundation, Motobu, Japan;

关键词: marine turtle;    population genomics;    field sample;    MIG-seq;    natal origin identification;   

DOI  :  10.3389/fmars.2020.00658

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown