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Won H, Jeon HB, Kim DY, Suk HY. Differential patterns of diversity at neutral and adaptive loci in endangered Rhodeus pseudosericeus populations. Sci Rep 2021; 11:15953. [PMID: 34354168 PMCID: PMC8342555 DOI: 10.1038/s41598-021-95385-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Given the fact that threatened species are often composed of isolated small populations, spatial continuity or demography of the populations may be major factors that have shaped the species' genetic diversity. Thus, neutral loci have been the most commonly-used markers in conservation genetics. However, the populations under the influence of different environmental factors may have evolved in response to different selective pressures, which cannot be fully reflected in neutral genetic variation. Rhodeus pseudosericeus, a bitterling species (Acheilognathidae; Cypriniformes) endemic to the Korean Peninsula, are only found in some limited areas of three rivers, Daecheon, Han and Muhan, that flow into the west coast. Here, we genotyped 24 microsatellite loci and two loci (DAB1 and DAB3) of MHC class II peptide-binding β1 domain for 222 individuals collected from seven populations. Our microsatellite analysis revealed distinctive differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, and populations were structured into two subgroups within the Han River. Apparent positive selection signatures were found in the peptide-binding residues (PBRs) of the MHC loci. The allelic distribution of MHC showed a degree of differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, partially similar to the results obtained for microsatellites, however showed rather complex patterns among populations in the Han River. Considering the apparent differences in the distribution of supertypes obtained based on the physicochemical differences induced by the polymorphisms of these PBRs, the differentiation in DAB1 between the two regional groups may result in the differences in immune function. No differentiation between these two regions was observed in the supertyping of DAB3, probably indicating that only DAB1 was associated with the response to locally specialized antigenic peptides.
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Affiliation(s)
- Hari Won
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do South Korea ,grid.410319.e0000 0004 1936 8630Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, QC H4B 1R6 Canada
| | - Hyung-Bae Jeon
- grid.410319.e0000 0004 1936 8630Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, QC H4B 1R6 Canada
| | - Dong-Young Kim
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do South Korea
| | - Ho Young Suk
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do South Korea
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Jeon YS, Ko MH, Vasil’eva ED, Myung RY, Won YJ. Genetic patterns reveal northward range expansion and cryptic diversity in Nalbant’s spined loach, Cobitis nalbanti sensu lato (Teleostei: Cypriniformes: Cobitidae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1737842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Yeon Seon Jeon
- Division of EcoScience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Myeong-Hun Ko
- Division of EcoScience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | | | - Ra-Yeon Myung
- Division of EcoScience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
- Department of Life Science, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
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Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula. Sci Rep 2020; 10:1011. [PMID: 31974505 PMCID: PMC6978382 DOI: 10.1038/s41598-020-57625-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/03/2020] [Indexed: 12/03/2022] Open
Abstract
The modern-day distribution of freshwater fishes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven different rivers to obtain better understand historical gene flow of freshwater fish on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and first colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers flowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the first genetic attempt to confirm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning.
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Lee YJ, Cha SH, An J, Suk HY. The complete mitochondrial genome information of Phoxinus phoxinus (Cypriniformes: Cyprinidae) on the Korean Peninsula and the phylogenetic implication. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3844-3845. [PMID: 33366214 PMCID: PMC7707419 DOI: 10.1080/23802359.2019.1687021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Phoxinus phoxinus is a small Leuciscinae species predominantly found in cool and well-oxygenated streams throughout a wide area encompassing Europe, Siberia and East Asia. It is believed that the populations in Korea hold important clues to how the species has been distributed south along the Eurasian continent to the Korean Peninsula. We characterized the complete mitochondrial genomes of two individual fin-clip samples collected from the two Korean river systems. The whole sequences were 17,665 and 18,220 bp, respectively, and included 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The genome size difference was due to the considerably different sizes of the control region. The overall genome structures were identical to those observed in other Leuciscinae species.
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Affiliation(s)
- Yoon Jeong Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Sun Ho Cha
- GenoTech Corporation, Daejeon, South Korea
| | - Junghwa An
- National Institute of Biological Resources, Environmental Research Complex, Incheon, South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
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Jeon HB, Kim DY, Lee YJ, Bae HG, Suk HY. The genetic structure of Squalidus multimaculatus revealing the historical pattern of serial colonization on the tip of East Asian continent. Sci Rep 2018; 8:10629. [PMID: 30006507 PMCID: PMC6045656 DOI: 10.1038/s41598-018-28340-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 06/19/2018] [Indexed: 11/28/2022] Open
Abstract
Separated river systems could create confluences via two geological processes, estuary coalescence in response to decreasing sea levels and headwater capture, allowing primary freshwater species to disperse across rivers. Squalidus multimaculatus, is an endemic and primary freshwater species restricted to the southeast coast of the Korean Peninsula. The distribution of this species is unique, given that other congeneric species, including its closely related S. gracilis majimae, as well as other cyprind species are observed throughout the peninsula except for the east coast. Phylogeographic analyses were conducted using three mitochondrial loci to identify the origin of S. multimaculatus and the historical pathways of dispersal. A strong phylogenetic affinity between S. multimaculatus and S. g. majimae and the genetic structure among populations indicated that S. multimaculatus originated from the eastward colonization of the common ancestor between S. g. majimae and S. multimaculatus via headwater capture through fault zones within successive mountain range. Following colonization, the ancestral S. multimaculatus likely migrated towards north via estuary coalescence along a well-developed continental shelf. Our study was the first empirical attempt providing insights into how freshwater organisms dispersed to the southernmost tip of East Asia, despite the potential loss of such historical imprints with anthropogenic interference.
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Affiliation(s)
- Hyung-Bae Jeon
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Dong-Young Kim
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Yoon Jeong Lee
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Han-Gyu Bae
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 38541, South Korea.
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Lee YJ, Bae HG, Jeon HB, Kim DY, Suk HY. Human-mediated processes affecting distribution and genetic structure of Squalidus multimaculatus, a freshwater cyprinid with small spatial range. Anim Cells Syst (Seoul) 2017. [DOI: 10.1080/19768354.2017.1371074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yoon Jeong Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Han-Gyu Bae
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Hyung-Bae Jeon
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Dong-Young Kim
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
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Phylogenetic relationships and genetic diversity of badgers from the Korean Peninsula: Implications for the taxonomic status of the Korean badger. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jeon HB, An J, Kweon SM, Kim S, Yu JN, Kim BJ, Kawase S, Suk HY. Development of novel microsatellite loci and analyses of genetic diversity in the endangered Tanakia somjinensis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Jeon HB, Lee YJ, Lim HJ, Cha SH, Suk HY. Complete mitochondrial genome of endangered Rhodeus pseudosericeus and its implications for the reconstruction of phylogenetic relationship among Acheilognathinae species. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:312-314. [PMID: 33644366 PMCID: PMC7871815 DOI: 10.1080/23802359.2016.1172036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rhodeus pseudosericeus is a native bitterling to the Korean Peninsula and found in very limited areas with small census size. Here, its complete mitochondrial genome was analyzed to provide novel data for the reconstruction of phylogenetic relationship among Acheilognathinae species. The genome was a 16,574 bp long consisting of 1 putative control region, 2 rRNA genes, 22 tRNA and 13 protein-coding genes. The gene arrangement was completely identical to those observed in other Acheilognathinae species as well as in other cyprinid species. In our phylogenetic analyses, three major genera of Acheilognathinae indepedently formed monophyletic groups in the tree reconstructed based on the whole genome sequences, whereas Rhodeus was not recovered as a single monophyly when solely considering protein-coding genes, indicating that the taxonomic reevaluation is still required in this subfamily.
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Affiliation(s)
- Hyung-Bae Jeon
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Yoon Jeong Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea.,Department of Optometry and Vision Science, Kyungwoon University, Gumi, South Korea
| | | | - Sun Ho Cha
- GenoTech Corporation, Daejeon, South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
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Bae HG, Suk HY. Population genetic structure and colonization history of short ninespine sticklebacks (Pungitius kaibarae). Ecol Evol 2015; 5:3075-89. [PMID: 26356579 PMCID: PMC4559051 DOI: 10.1002/ece3.1594] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/09/2015] [Accepted: 06/14/2015] [Indexed: 01/29/2023] Open
Abstract
The contemporary distribution and genetic structure of a freshwater fish provide insight into its historical geodispersal and geographical isolation following Quaternary climate changes. The short ninespine stickleback, Pungitius kaibarae, is a small gasterosteid fish occurring in freshwater systems on the Korean Peninsula and in southeast Russia. On the Korean Peninsula, P. kaibarae populations are distributed in three geographically separated regions: the NE (northeast coast), SE (southeast coast), and a limited area in the ND (Nakdong River). In this study, we used mitochondrial loci and microsatellites to investigate the evolutionary history of P. kaibarae populations by assessing their pattern of genetic structure. Our analyses revealed a marked level of divergence among three regional populations, suggesting a long history of isolation following colonization, although ND individuals showed relatively higher genetic affinity to populations from SE than those from NE. The populations from NE showed a great degree of interpopulation differentiation, whereas populations from SE exhibited only weak genetic structuring. Upon robust phylogenetic analysis, P. kaibarae formed a monophyletic group with Russian P. sinensis and P. tymensis with strong node confidence values, indicating that P. kaibarae populations on the Korean Peninsula originated from the southward migration of its ancestral lineage around the middle Pleistocene.
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Affiliation(s)
- Han-Gyu Bae
- Department of Life Sciences, Yeungnam University 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 712-749, Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do, 712-749, Korea
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