1
|
Cho MS, Kim Y, Kim SH, Jeon JH, Yang J, Kim SC. Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives. Sci Rep 2024; 14:16255. [PMID: 39009598 DOI: 10.1038/s41598-024-63272-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/27/2024] [Indexed: 07/17/2024] Open
Abstract
Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) 't Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) 't Hart or P. kamtschaticus (Fisch.) 't Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.
Collapse
Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yongsung Kim
- Honam National Institute of Biological Resources, Mokpo, 58762, Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Ji-Hyeon Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - JiYoung Yang
- Institute for Dok-Do and Ulleung-Do Island, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| |
Collapse
|
2
|
Ko BJ, An J, Eo SH. Korean Leopard Cat (Prionailurus bengalensis) population with low genetic diversity is distinct from Southeast Asian populations. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
3
|
İbiş O, Koepfli KP, Özcan S, Tez C. Whole mitogenomes of Turkish white-toothed shrews, genus Crocidura (Eulipotyphla: Soricidae), with new insights into the phylogenetic positions of Crocidura leucodon and the Crocidura suaveolens group. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00579-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
4
|
Li H, Mo X, Sun H, Wang J, Motokawa M, Harada M, Wu Y, Li Y. Karyotypic polymorphism of Crocidura tanakae (Eulipotyphla: Soricidae) and revision of the karyotype of C. attenuata in mainland China. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Conventional karyotypes of Crocidura tanakae and C. attenuata collected from mainland China were examined by bone marrow and cell culture methods along with identification to species using molecular data. In contrast to C. tanakae from Taiwan, populations from mainland China were karyotypically polymorphic, varying in diploid number (2n) from 24 to 40 and fundamental number (FN) from 45 to 56. Autosomes are composed of 6–20 metacentric or submetacentric chromosomes, 0–8 subtelocentric chromosomes, and 0–24 telocentric chromosomes. These polymorphic karyotypes indicate the presence of two geographically separated races. The ancestral karyotype of C. tanakae potentially is the same as currently found on Taiwan: 2n = 40 and FN = 56. In contrast to C. tanakae, C. attenuata had a uniform karyotype (2n = 40, FN = 54) in mainland China, suggesting that previously reported karyotypic polymorphism in this species was an error due to the morphological crypsis between C. tanakae and C. attenuata in mainland China. The intricate karyotypic polymorphism of C. tanakae may be indicative of this species undergoing speciation.
Collapse
Affiliation(s)
- Haotian Li
- Marine College, Shandong University (Weihai), Weihai, China
| | - Xinmin Mo
- Marine College, Shandong University (Weihai), Weihai, China
| | - Huimei Sun
- Marine College, Shandong University (Weihai), Weihai, China
| | - Jing Wang
- Marine College, Shandong University (Weihai), Weihai, China
| | | | - Masashi Harada
- Laboratory Animal Center, Osaka City University, Osaka, Japan
| | - Yi Wu
- College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yuchun Li
- Marine College, Shandong University (Weihai), Weihai, China
| |
Collapse
|
5
|
Lee SH, Kim WK, Park K, No JS, Lee GY, Kim HC, Klein TA, Min MS, Lee SJ, Hwang J, Park MS, Song JW. Genetic diversity and phylogeography of Jeju Orthohantavirus (Hantaviridae) in the Republic of Korea. Virology 2020; 543:13-19. [PMID: 32056842 DOI: 10.1016/j.virol.2020.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/26/2020] [Accepted: 01/26/2020] [Indexed: 11/16/2022]
Abstract
Orthohantaviruses are negative-sense, single-stranded RNA viruses harbored by rodents, shrews, moles, and bats. Of the shrew-borne orthohantaviruses in the Republic of Korea (ROK), Jeju orthohantavirus (Jeju virus, JJUV) was found on Jeju Island. This small-scale epidemiologic survey investigated the geographic distribution and molecular phylogeny of JJUV in the ROK. In 32 trapping sites, tissues of 84 Crocidura shantungensis were analyzed for JJUV RNA. JJUV RNA was detected in seven (8.3%) shrews captured on the Korean peninsula. The molecular epidemiologic survey demonstrated the prevalence of JJUV by geographic distribution. The RNA loads of JJUV were evaluated in various tissues. Entire coding sequences of tripartite genomes were recovered from two JJUV strains on the mainland. Phylogenetic relationships of the JJUV revealed a distinct geographic lineage of mainland strains from the strains on Jeju Island. This study sheds light on the molecular epidemiology, phylogeographic diversity, and virus-host co-divergence of JJUV, ROK.
Collapse
Affiliation(s)
- Seung-Ho Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea; Center for Medical Science Research, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jin Sun No
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Heung-Chul Kim
- 5th Medical Detachment, 168th Multifunctional Medical Battalion, 65th Medical Brigade, Unit 15247, APO AP 96205-5247, USA
| | - Terry A Klein
- Public Health Command District-Korea (Provisional), 65th Medical Brigade, Unit 15281, APO AP 96205-5281, USA
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seo-Jin Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jusun Hwang
- Wildlife Ecology & Genomics Lab, College of Forest & Environmental Science, Kangwon National University, Chuncheon, Republic of Korea; Wildlife Conservation Society-Vietnam, Wildlife Health Program, Hanoi, Viet Nam
| | - Man-Seong Park
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea.
| |
Collapse
|
6
|
Biogeography of Korea's top predator, the yellow-throated Marten: evolutionary history and population dynamics. BMC Evol Biol 2019; 19:23. [PMID: 30642240 PMCID: PMC6332909 DOI: 10.1186/s12862-019-1347-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted the first population-level study of the yellow-throated marten, Martes flavigula, from the Korean Peninsula, Russian, Taiwanese and Chinese localities in a biogeographic framework using mitochondrial (cyt-b, nd2, cr) and nuclear gene sequencing (ghr). RESULTS Bayesian analyses revealed a rather young population, with a split from the most recent common ancestor at around 125 kya. Martes flavigula likely colonized the Korean Peninsula from Mainland China through the Yellow Sea twice, ca. 60 kya and 20 kya. Korean martens diversified during the Late Pleistocene with at least two dispersal events out of Korea, towards the southwest to Taiwan (ca. 80 kya) and towards the North into Russia and eastern China; most likely after the Last Glacial Maxima (ca. 20 kya). We argue that the lack of population structure and mixed populations is possibly a consequence of the high dispersal capability of the species. The Bayesian skyline plot revealed a population decline within the last 5000 years, suggesting potential negative biotic and anthropogenic effects in the area. We find that local populations are not genetically differentiated, therefore no perceptible population structure within Korea was found. CONCLUSIONS The topography and geography of the Korean Peninsula has played a pivotal role in its colonization. Connections between the Korean Peninsula and the Mainland through sea-level drops of the Yellow Sea at times of glacial maxima and the high dispersal capability of M. flavigula adds to the lack of geographical structure in this species and the paraphyly of Korean lineages.
Collapse
|
7
|
Hwang JY, Cho GJ. Identification of novel haplotypes and interpretation of gene flow of mitochondrial DNA control region of Eurasian otter (Lutra lutra) for the effective conservation. J Vet Med Sci 2018; 80:1791-1800. [PMID: 30224573 PMCID: PMC6261830 DOI: 10.1292/jvms.17-0678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The number and distribution of Eurasian otters have declined during twentieth century due to human activity and water pollution. The global conservation status of Eurasian otter is
presently ‘Near Threatened (NT)’ and strictly protected by being listed on the international legislation and conventions. A number of studies using the mitochondrial DNA (mtDNA) control
region (CR) have been conducted in order to effectively apply conservation and reintroduction programs, especially in Europe. However, aside from Europe, there have been few studies
concerning genetic diversity and phylogeny of Eurasian otters. Therefore, in this study, we sequenced partial mtDNA CR sequences (232 bp) from five South Korean Eurasian otters and analyzed
27 otters originating from parts of northeast Asia (South Korea, China, Japan and Russia (Sakhalin)), and Europe. Out of 232 bp partial mtDNA CR sequences, 13 polymorphic sites (5.6%) were
identified and 4 novel mtDNA CR haplotypes (Lut16–19) were discovered from 12 Eurasian otters originating from northeast Asian region. In this study, a comprehensive analysis of genetic
diversity and population structure of Eurasian otter between Europe and northeast Asia continents were conducted. Of these, different past demographic histories in Pleistocene period might
have largely impacted the genetic structure of each population differently. In addition, low degree of gene flow, isolation by distance (IBD) pattern from geographically wide distanced
dataset and analysis of molecular variance (AMOVA) also represented distinct genetic characteristics of Eurasian otter between Europe and northeast Asia.
Collapse
Affiliation(s)
- Ji-Yong Hwang
- Institute of Equine Science, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Gil-Jae Cho
- Institute of Equine Science, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| |
Collapse
|
8
|
Chung MY, Son S, Suh GU, Herrando-Moraira S, Lee CH, López-Pujol J, Chung MG. The Korean Baekdudaegan Mountains: A Glacial Refugium and a Biodiversity Hotspot That Needs to Be Conserved. Front Genet 2018; 9:489. [PMID: 30405696 PMCID: PMC6206444 DOI: 10.3389/fgene.2018.00489] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mi Yoon Chung
- Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Sungwon Son
- Plant Conservation Division, Korea National Arboretum, Pocheon, South Korea
| | - Gang Uk Suh
- Plant Conservation Division, Korea National Arboretum, Pocheon, South Korea
| | | | - Cheul Ho Lee
- Plant Conservation Division, Korea National Arboretum, Pocheon, South Korea
| | | | - Myong Gi Chung
- Division of Life Science and the Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|