Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction
Abstract Background The Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea and the Japanese sea lion internationally, was endemic to the Northwest Pacific before its extinction in the 1950s. However, its origins, speciation, and genetic diversity remain poorly understood....
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2025-08-01
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| Online Access: | https://doi.org/10.1186/s12915-025-02351-3 |
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| author | Jungeun Kim Asta Blazyte Jae-Pil Choi Changjae Kim Fedor Sharko Sungwon Jeon Eun-Mi Kim Hawsun Sohn Jong Hee Lee Hyun Woo Kim Mi Hyun Yoo Kyunglee Lee Artem Nedoluzhko Jong Bhak |
| author_facet | Jungeun Kim Asta Blazyte Jae-Pil Choi Changjae Kim Fedor Sharko Sungwon Jeon Eun-Mi Kim Hawsun Sohn Jong Hee Lee Hyun Woo Kim Mi Hyun Yoo Kyunglee Lee Artem Nedoluzhko Jong Bhak |
| author_sort | Jungeun Kim |
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| description | Abstract Background The Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea and the Japanese sea lion internationally, was endemic to the Northwest Pacific before its extinction in the 1950s. However, its origins, speciation, and genetic diversity remain poorly understood. Results To address this, we sequenced DNA from 16 Z. japonicus bone fragments, obtained from Dokdo and Ulleungdo islands in Korea. Our genome-wide SNP analyses reveal Z. japonicus as the earliest diverged species within its genus, redefining its evolutionary relationship with the California (Z. californianus) and Galapagos (Z. wollebaeki) sea lions. Our research further elucidates the phylogeny of Z. japonicus, shedding light on the complexity of the genetic isolation process within its genus that was prompted by the geographic isolation of the three populations of Zalophus ancestral stock. Conversely, the genetic signature of the Dokdo sea lion genome can be modeled as an evolutionary pathway involving gene flow from Otariidae species with shared range. In addition, we discovered that the population decline of Z. japonicus started already over 100,000 years ago; however, Z. japonicus genome maintained a relatively high heterozygosity despite nearing extinction. Conclusions Our genome-scale analysis sheds light on the phylogeny of Z. japonicus, the evolutionary pathways underlying its speciation, and its genetic diversity before extinction. Broadly, we elucidate Zalophus gene flow complexity and genetic diversities among extant species. Furthermore, this study offers retrospective genomic insights into the extinction process of a carnivorous marine mammal, information that could aid conservation efforts for extant Otariidae species. |
| format | Article |
| id | doaj-art-573a1f62852a46479ef3fae25e850a9d |
| institution | Kabale University |
| issn | 1741-7007 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj-art-573a1f62852a46479ef3fae25e850a9d2025-08-20T03:43:30ZengBMCBMC Biology1741-70072025-08-0123111310.1186/s12915-025-02351-3Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinctionJungeun Kim0Asta Blazyte1Jae-Pil Choi2Changjae Kim3Fedor Sharko4Sungwon Jeon5Eun-Mi Kim6Hawsun Sohn7Jong Hee Lee8Hyun Woo Kim9Mi Hyun Yoo10Kyunglee Lee11Artem Nedoluzhko12Jong Bhak13Personal Genomics Institute, Genome Research FoundationKorean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST)Personal Genomics Institute, Genome Research FoundationClinomics, Inc., UNISTPaleogenomics Laboratory, European University at Saint PetersburgClinomics, Inc., UNISTNational Institute of Fisheries ScienceNational Institute of Fisheries ScienceNational Institute of Fisheries ScienceNational Institute of Fisheries ScienceConservation and Health Center, Seoul ZooNational Institute of Fisheries ScienceNational Research Center “Kurchatov Institute”Personal Genomics Institute, Genome Research FoundationAbstract Background The Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea and the Japanese sea lion internationally, was endemic to the Northwest Pacific before its extinction in the 1950s. However, its origins, speciation, and genetic diversity remain poorly understood. Results To address this, we sequenced DNA from 16 Z. japonicus bone fragments, obtained from Dokdo and Ulleungdo islands in Korea. Our genome-wide SNP analyses reveal Z. japonicus as the earliest diverged species within its genus, redefining its evolutionary relationship with the California (Z. californianus) and Galapagos (Z. wollebaeki) sea lions. Our research further elucidates the phylogeny of Z. japonicus, shedding light on the complexity of the genetic isolation process within its genus that was prompted by the geographic isolation of the three populations of Zalophus ancestral stock. Conversely, the genetic signature of the Dokdo sea lion genome can be modeled as an evolutionary pathway involving gene flow from Otariidae species with shared range. In addition, we discovered that the population decline of Z. japonicus started already over 100,000 years ago; however, Z. japonicus genome maintained a relatively high heterozygosity despite nearing extinction. Conclusions Our genome-scale analysis sheds light on the phylogeny of Z. japonicus, the evolutionary pathways underlying its speciation, and its genetic diversity before extinction. Broadly, we elucidate Zalophus gene flow complexity and genetic diversities among extant species. Furthermore, this study offers retrospective genomic insights into the extinction process of a carnivorous marine mammal, information that could aid conservation efforts for extant Otariidae species.https://doi.org/10.1186/s12915-025-02351-3Zalophus japonicusDokdo sea lionJapanese sea lionOtariidaeSpeciationWhole genome sequencing |
| spellingShingle | Jungeun Kim Asta Blazyte Jae-Pil Choi Changjae Kim Fedor Sharko Sungwon Jeon Eun-Mi Kim Hawsun Sohn Jong Hee Lee Hyun Woo Kim Mi Hyun Yoo Kyunglee Lee Artem Nedoluzhko Jong Bhak Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction BMC Biology Zalophus japonicus Dokdo sea lion Japanese sea lion Otariidae Speciation Whole genome sequencing |
| title | Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction |
| title_full | Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction |
| title_fullStr | Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction |
| title_full_unstemmed | Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction |
| title_short | Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction |
| title_sort | dokdo sea lion zalophus japonicus genome reveals its evolutionary trajectory before extinction |
| topic | Zalophus japonicus Dokdo sea lion Japanese sea lion Otariidae Speciation Whole genome sequencing |
| url | https://doi.org/10.1186/s12915-025-02351-3 |
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