Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing
Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish ende...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Ecology and Evolution |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fevo.2022.933632/full |
| _version_ | 1817975842430517248 |
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| author | Kunyuan Wanghe Chenguang Feng Yongtao Tang Delin Qi Shahid Ahmad Ghulam Nabi Xiaohui Li Guojie Wang Longsheng Jian Sijia Liu Kai Zhao Fei Tian |
| author_facet | Kunyuan Wanghe Chenguang Feng Yongtao Tang Delin Qi Shahid Ahmad Ghulam Nabi Xiaohui Li Guojie Wang Longsheng Jian Sijia Liu Kai Zhao Fei Tian |
| author_sort | Kunyuan Wanghe |
| collection | DOAJ |
| description | Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes. |
| first_indexed | 2024-04-13T21:54:48Z |
| format | Article |
| id | doaj.art-971e7e78641d4871a28adb82ca384ff2 |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-04-13T21:54:48Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-971e7e78641d4871a28adb82ca384ff22022-12-22T02:28:17ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2022-11-011010.3389/fevo.2022.933632933632Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencingKunyuan Wanghe0Chenguang Feng1Yongtao Tang2Delin Qi3Shahid Ahmad4Ghulam Nabi5Xiaohui Li6Guojie Wang7Longsheng Jian8Sijia Liu9Kai Zhao10Fei Tian11Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaSchool of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, ChinaCollege of Fisheries, Henan Normal University, Xinxiang, Henan, ChinaState Key Laboratory of Plateau Ecology and Agriculture, College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, ChinaSchool of Ecology and Environment, Hainan University, Haikou, Hainan, ChinaInstitute of Nature Conservation, Polish Academy of Sciences, Kraków, PolandKey Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaHighland Hydrobiology and Hydroeco-environment Laboratory of Qinghai Fishery Environmental Monitoring station, Xining, Qinghai, ChinaHighland Hydrobiology and Hydroeco-environment Laboratory of Qinghai Fishery Environmental Monitoring station, Xining, Qinghai, ChinaKey Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaKey Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaKey Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaAccurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.https://www.frontiersin.org/articles/10.3389/fevo.2022.933632/fullgenetic diversity conservationnon-monophyleticpopulation phylogeny structurespecies delimitationSLAF-seqspecies synonymy |
| spellingShingle | Kunyuan Wanghe Chenguang Feng Yongtao Tang Delin Qi Shahid Ahmad Ghulam Nabi Xiaohui Li Guojie Wang Longsheng Jian Sijia Liu Kai Zhao Fei Tian Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing Frontiers in Ecology and Evolution genetic diversity conservation non-monophyletic population phylogeny structure species delimitation SLAF-seq species synonymy |
| title | Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing |
| title_full | Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing |
| title_fullStr | Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing |
| title_full_unstemmed | Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing |
| title_short | Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing |
| title_sort | phylogenetic relationship and taxonomic status of gymnocypris eckloni schizothoracinae based on specific locus amplified fragments sequencing |
| topic | genetic diversity conservation non-monophyletic population phylogeny structure species delimitation SLAF-seq species synonymy |
| url | https://www.frontiersin.org/articles/10.3389/fevo.2022.933632/full |
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