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Wang J, Zhang W, Wu J, Li C, Ju YM, Lin HD, Zhao J. Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin. Genes (Basel) 2022; 13:genes13101908. [PMID: 36292792 PMCID: PMC9602001 DOI: 10.3390/genes13101908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
The ichthyofauna of continental islands is characterized by immigration through a land bridge due to fluctuating sea levels. Hainan Island is adjacent to the southern margin of mainland China and provides opportunities for understanding the origin and diversification of freshwater fishes. The aim of our study was to evaluate the level of genetic variation and phylogeographic structure of Opsariichthys hainanensis on Hainan Island and mainland China, using mtDNA cyt b gene (1140 bp) and D-loop (926 bp), nuclear RAG1 gene (1506 bp), and 12 microsatellite loci. Mitochondrial phylogenetic analysis identified five major lineages according to the geographical distribution from different populations. We suggested that two dispersal events occurred: the population in the Changhua River migrated to the Red River (Lineage B), and the populations in the South Hainan region moved northwards to the North Hainan region. However, populations in Northwest Hainan Island dispersed to the populations around the Gulf of Tonkin (Lineage A1) and populations in Northeast Hainan Island dispersed to the populations in mainland China (Lineage A2). Our results indicated that the populations of O. hainanensis suffered a bottleneck event followed by a recent population expansion supported by the ABC analysis. We suggest that O. hainanensis populations were found mostly in the lowlands and a lack of suitable freshwater habitat in southern mainland China and Hainan during the Last Interglacial period, and then expansion occurred during the Last Glacial Maximum.
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Affiliation(s)
- Junjie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Wenjun Zhang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jinxian Wu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung 94401, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan
- Correspondence: (H.-D.L.); (J.Z.); Tel.: +886-6-2097821 (H.-D.L.); +86-020-85211372 (J.Z.)
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
- Correspondence: (H.-D.L.); (J.Z.); Tel.: +886-6-2097821 (H.-D.L.); +86-020-85211372 (J.Z.)
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Kang B, Hsu KC, Wu JH, Chiu YW, Lin HD, Ju YM. Population genetic diversity and structure of Rhinogobius candidianus (Gobiidae) in Taiwan: Translocation and release. Ecol Evol 2022; 12:e9154. [PMID: 35979520 PMCID: PMC9366559 DOI: 10.1002/ece3.9154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 06/17/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
Rhinogobius candidianus is a freshwater goby distributed in north, northwest, west, and south Taiwan, but this species has been introduced to east Taiwan and became dominant. To investigate its native population genetic diversity and structure and evaluate the sources and diversity of translocated populations, the mitochondrial DNA control region and cytochrome b gene (1981 bp) from 220 specimens were analyzed. These results indicated that (1) the east populations originated from two sources in west Taiwan; (2) translocated populations exist in east Taiwan and south Taiwan; (3) many populations have likely been moved secondarily by human intervention; (4) the effective size of the populations had declined greatly; (5) within the native populations, the ancestral populations colonized Taiwan during the land bridge phase in the Pleistocene through north Taiwan; (6) the landform changes in Taiwan shaped the population structure; and (7) the landforms of the coastline during glaciation also shaped the native range. The low-level genetic diversity, high population differentiation, and population decline greatly suggest the need for resource management and conservation interventions. Four clades (α-δ) should be managed as four distinct evolutionarily significant units, while the translocated populations should be managed as separate management units. Moreover, the translocated populations in east Taiwan should be evaluated and monitored carefully.
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Affiliation(s)
- Bin Kang
- The Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Kui-Ching Hsu
- College of Fisheries Guangdong Ocean University Zhanjiang China
| | - Jui-Hsien Wu
- Eastern Marine Biology Research Center of Fisheries Research Institute Council of Agriculture Taitung Taiwan
| | - Yuh-Wen Chiu
- Department of Biological Resources National Chiayi University Chiayi Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School Tainan Taiwan
| | - Yu-Min Ju
- National Museum of Marine Biology and Aquarium Pingtung Taiwan.,Department of Marine Biotechnology and Resources National Sun Yat-sen University Kaohsiung Taiwan
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Ju YM, Wu JH, Hsu KC, Chiu YW, Wang WK, Chen CW, Lin HD. Genetic diversity of Rhinogobius delicatus (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 32:12-19. [PMID: 33170048 DOI: 10.1080/24701394.2020.1844678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (F ST=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.
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Affiliation(s)
- Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan.,Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Jui-Hsien Wu
- Council of Agriculture, Eastern Marine Biology Research Center of Fisheries Research Institute, Taitung, Taiwan
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Yu-Wen Chiu
- Department of Biological Resources, National Chiayi University, Chiayi, Taiwan
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
| | - Chih-Wei Chen
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
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Han CC, Hsu KC, Fang LS, Cheng IM, Lin HD. Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan. BMC Genet 2019; 20:86. [PMID: 31752677 PMCID: PMC6868699 DOI: 10.1186/s12863-019-0788-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/31/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins. RESULTS In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan. CONCLUSIONS All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.
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Affiliation(s)
- Chiao-Chuan Han
- National Museum of Marine Biology and Aquarium, Pingtung, 944 Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 944 Taiwan
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Lee-Shing Fang
- Center for Environmental Toxin and Emerging-Contaminant Research,Cheng Shiu University, Kaohsiung, 83347 Taiwan
- Department of Leisure and Sport Management, Cheng Shiu University, Kaohsiung, 83347 Taiwan
| | - I-Ming Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 80424 Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, 701 Taiwan
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Li Y, Song J, Shen X, Cai Y, Cheng H, Zhang X, Yan B, Chu KH. The first mitochondrial genome of Macrobrachium rosenbergii from China: phylogeny and gene rearrangement within Caridea. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1540262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yongqi Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, China
| | - Jun Song
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, China
| | - Yuefeng Cai
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Hanliang Cheng
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Xiaqing Zhang
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Binlun Yan
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Lee SJ, Lee MY, Lin LK, Lin YK, Li Y, Shin EH, Han SH, Min MS, Lee H, Kim KS. Phylogeography of the Asian lesser white-toothed shrew, Crocidura shantungensis, in East Asia: role of the Korean Peninsula as refugium for small mammals. Genetica 2018; 146:211-226. [DOI: 10.1007/s10709-018-0014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
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Ju YM, Hsu KC, Yang JQ, Wu JH, Li S, Wang WK, Ding F, Li J, Lin HD. Mitochondrial diversity and phylogeography of Acrossocheilus paradoxus (Teleostei: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1194-1202. [DOI: 10.1080/24701394.2018.1431227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jui-Hsien Wu
- Eastern Marine Biology Research Center of Fisheries Research Institute, Council of Agriculture, Taitung, Taiwan
| | - Shan Li
- Branch of Shanghai Science & Technology, Shanghai Natural History Museum, Shanghai, China
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
| | - Fang Ding
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jun Li
- Fisheries College, Jimei University, Xiamen, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
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Han CC, Fang LS, Chang IM, Lin HD. Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:687-694. [PMID: 28712317 DOI: 10.1080/24701394.2017.1350948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.
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Affiliation(s)
- Chiao-Chuan Han
- a National Museum of Marine Biology and Aquarium , Checheng , Pingtung , Taiwan.,b Graduate Institute of Marine Biology , National Dong Hwa University , Checheng , Pingtung , Taiwan
| | - Lee-Shing Fang
- c Department of Leisure and Sport Management , Cheng Shiu University , Kaohsiung , Taiwan
| | - I-Ming Chang
- d General Education Center, Wenzao Ursuline University of Languages , Kaohsiung , Taiwan
| | - Hung-Du Lin
- e The Affiliated School of National Tainan First Senior High School , Tainan , Taiwan
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Chen PC, Shih CH, Chu TJ, Lee YC, Tzeng TD. Phylogeography and genetic structure of the oriental river prawn Macrobrachium nipponense (Crustacea: Decapoda: Palaemonidae) in East Asia. PLoS One 2017; 12:e0173490. [PMID: 28267807 PMCID: PMC5340376 DOI: 10.1371/journal.pone.0173490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/21/2017] [Indexed: 11/25/2022] Open
Abstract
The oriental river prawn (Macrobrachium nipponense) is mainly distributed in East Asia. The phylogeography, population genetic structure and historical demography of this species in the East Asia were examined by using partial sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA in mitochondrial DNA. Ten populations that included 239 individuals were collected from Taiwan (Shihmen Reservoir, SMR, Mingte Reservoir, MTR and Chengching Lake Reservoir, CLR), mainland China (Taihu Lake, TLC, Min River, MRC, Jiulong River, JRC and Shenzhen Reservoir, SRC), Japan (Biwa Lake, BLJ and Kasumigaura Lake, KLJ) and Korea (Han River, HRK). The nucleotide diversity (π) of all individuals was 0.01134, with values ranging from 0.0089 (BLJ, Japan) to 0.01425 (MTR, Taiwan). A total of 83 haplotypes were obtained, and the haplotypes were divided into 2 main lineages: lineage A included the specimens from BLJ, KLJ, CLR, MTR, TLC, MRC and JRC, and lineage B comprised the ones from HRK, SRC, SMR, MTR, TLC, MRC and JRC. Lineage A could be further divided two sub-lineages (A1 and A2). Individuals of lineage A2 were only from TLC. Demographic expansion was observed in each lineage, starting within the second-to-latest interglacial period for lineage A and within the last glacial period for lineage B. All FST values among the ten populations were significantly different, except for the values between MRC and JRC, and SMR and SRC. The phylogeography and genetic structure of M. nipponense in East Asia might be influenced by Pleistocene glacial cycles, lake isolation and human introduction. The possible dispersal routes of M. nipponense in the East Asia were also discussed.
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Affiliation(s)
- Po-Cheng Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chun-Han Shih
- Department of Leisure Management, Tungnan University, New Taipei City, Taiwan
| | - Ta-Jen Chu
- Department of Leisure and Recreation Management, Chung Hua University, Hsin Chu, Taiwan
| | - Ying-Chou Lee
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- * E-mail: (TDT); (YCL)
| | - Tzong-Der Tzeng
- Department of Leisure, Recreation and Tourism Management, Shu-Te University, Kaohsiung, Taiwan
- * E-mail: (TDT); (YCL)
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Chiang TY, Chen YY, Lee TW, Hsu KC, Lin FJ, Wang WK, Lin HD. Comparative phylogeography of two codistributed endemic cyprinids in southeastern Taiwan. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ju YM, Wu JH, Kuo PH, Hsu KC, Wang WK, Lin FJ, Lin HD. Mitochondrial genetic diversity of Rhinogobius giurinus (Teleostei: Gobiidae) in East Asia. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Zhou TQ, Lin HD, Hsu KC, Kuo PH, Wang WK, Tang WQ, Liu D, Yang JQ. Spatial genetic structure of the cyprinid fish Onychostoma lepturum on Hainan Island. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:901-908. [DOI: 10.1080/24701394.2016.1209193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tian-Qi Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Lingang New City, Shanghai, P.R. China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kui-Ching Hsu
- Department of Industrial Management, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Po-Hsun Kuo
- Department of Industrial Management, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
| | - Wen-Qiao Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Lingang New City, Shanghai, P.R. China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Lingang New City, Shanghai, P.R. China
| | - Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Lingang New City, Shanghai, P.R. China
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Yang JQ, Hsu KC, Liu ZZ, Su LW, Kuo PH, Tang WQ, Zhou ZC, Liu D, Bao BL, Lin HD. The population history of Garra orientalis (Teleostei: Cyprinidae) using mitochondrial DNA and microsatellite data with approximate Bayesian computation. BMC Evol Biol 2016; 16:73. [PMID: 27068356 PMCID: PMC4827224 DOI: 10.1186/s12862-016-0645-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/27/2016] [Indexed: 02/07/2023] Open
Abstract
Background The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass’s phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci. Results In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China. Conclusion Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.
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Affiliation(s)
- Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Kui-Ching Hsu
- Department of Industrial Management, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei, 106, Taiwan
| | - Zhi-Zhi Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Li-Wei Su
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Po-Hsun Kuo
- Department of Industrial Management, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei, 106, Taiwan
| | - Wen-Qiao Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Zhuo-Cheng Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Bao-Long Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, 701, Taiwan.
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Chang HY, Wang WK, Chen KN, Su JK, Hsin CY, Li J, Wang YK, Lin HD. Phylogeography and genetic structure of the endemic cyprinid fish Microphysogobio brevirostris in northern Taiwan. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Chiu YW, Bor H, Kuo PH, Hsu KC, Tan MS, Wang WK, Lin HD. Origins of Semisulcospira libertina (gastropoda: semisulcospiridae) in Taiwan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:518-525. [PMID: 27159703 DOI: 10.3109/24701394.2016.1149823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The most accepted hypothesis has suggested that the fauna in Taiwan Island originated from South China, but some studies supported the Japan, Ryukyu Archipelago, and Taiwan Islands as a unique biogeographical district. This study examines whether the populations of freshwater snail Semisulcospira libertina in Taiwan are closer to those in Japan based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Our study shows the populations in North Taiwan originated from Japan and the cyclic glacial caused the migrations among islands and continent repeatedly; the populations in South Taiwan might originate from South China or South Asia. Our results will not only affect the conclusions in phylogeography of freshwater species in Taiwan but also change the sampling plans in the future studies about evolutionary of freshwater species in East Asia.
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Affiliation(s)
- Yuh-Wen Chiu
- a Department of Science Education, National Museum of Marine Biology and Aquarium , Pingtung , Taiwan.,b Graduate Institute of Marine Biodiversity and Evolutionary Biology, National Dong Hwa University , Pingtung , Taiwan
| | - Hor Bor
- c Department of Biomedical Science and Environmental Biology , Kaohsiung Medical University , Kaohsiung , Taiwan
| | - Po-Hsun Kuo
- d Department of Industrial Management , National Taiwan University of Science and Technology , Taipei , Taiwan
| | - Kui-Ching Hsu
- d Department of Industrial Management , National Taiwan University of Science and Technology , Taipei , Taiwan
| | - Mian-Shin Tan
- c Department of Biomedical Science and Environmental Biology , Kaohsiung Medical University , Kaohsiung , Taiwan
| | - Wei-Kuang Wang
- e Department of Environmental Engineering and Science , Feng Chia University , Taichung , Taiwan
| | - Hung-Du Lin
- f Department of Biology, The Affiliated School of National Tainan First Senior High School , Tainan , Taiwan
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Weng YM, Yang MM, Yeh WB. A comparative phylogeographic study reveals discordant evolutionary histories of alpine ground beetles (Coleoptera, Carabidae). Ecol Evol 2016; 6:2061-73. [PMID: 27066226 PMCID: PMC4768753 DOI: 10.1002/ece3.2006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/03/2016] [Accepted: 01/18/2016] [Indexed: 11/10/2022] Open
Abstract
Taiwan, an island with three major mountain ranges, provides an ideal topography to study mountain-island effect on organisms that would be diversified in the isolation areas. Glaciations, however, might drive these organisms to lower elevations, causing gene flow among previously isolated populations. Two hypotheses have been proposed to depict the possible refugia for alpine organisms during glaciations. Nunatak hypothesis suggests that alpine species might have stayed in situ in high mountain areas during glaciations. Massif de refuge, on the other hand, proposes that alpine species might have migrated to lower ice-free areas. By sampling five sympatric carabid species of Nebria and Leistus, and using two mitochondrial genes and two nuclear genes, we evaluated the mountain-island effect on alpine carabids and tested the two proposed hypotheses with comparative phylogeographic method. Results from the phylogenetic relationships, network analysis, lineage calibration, and genetic structure indicate that the deep divergence among populations in all L. smetanai, N. formosana, and N. niitakana was subjected to long-term isolation, a phenomenon in agreement with the nunatak hypothesis. However, genetic admixture among populations of N. uenoiana and some populations of L. nokoensis complex suggests that gene flow occurred during glaciations, as a massif de refuge depicts. The speciation event in N. niitakana is estimated to have occurred before 1.89 million years ago (Mya), while differentiation among isolated populations in N. niitakana, N. formosana, L. smetanai, and L. nokoensis complex might have taken place during 0.65-1.65 Mya. While each of the alpine carabids arriving in Taiwan during different glaciation events acquired its evolutionary history, all of them had confronted the existing mountain ranges.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology National Chung Hsing University 250 Kuo-Kuang Rd South District Taichung Taiwan 40227
| | - Man-Miao Yang
- Department of Entomology National Chung Hsing University 250 Kuo-Kuang Rd South District Taichung Taiwan 40227
| | - Wen-Bin Yeh
- Department of Entomology National Chung Hsing University 250 Kuo-Kuang Rd South District Taichung Taiwan 40227
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Chen PC, Shih CH, Chu TJ, Wang D, Lee YC, Tzeng TD. Population Structure and Historical Demography of the Oriental River Prawn (Macrobrachium nipponense) in Taiwan. PLoS One 2015; 10:e0145927. [PMID: 26716687 PMCID: PMC4696665 DOI: 10.1371/journal.pone.0145927] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 12/10/2015] [Indexed: 12/05/2022] Open
Abstract
The oriental river prawn (Macrobrachium nipponense) is a non-obligatory amphidromous prawn, and it has a wide distribution covering almost the entire Taiwan. Mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA were combined and used to elucidate the population structure and historical demography of oriental river prawn in Taiwan. A total of 202 individuals from six reservoirs and three estuaries were separately collected. Nucleotide diversity (π) of all populations was 0.01217, with values ranging from 0.00188 (Shihmen Reservoir, SMR, northern Taiwan) to 0.01425 (Mingte Reservoir, MTR, west-central Taiwan). All 76 haplotypes were divided into 2 lineages: lineage A included individuals from all sampling areas except SMR, and lineage B included specimens from all sampling locations except Chengching Lake Reservoir (CLR) and Liyu Lake Reservoir (LLR). All FST values among nine populations were significantly different except the one between Jhonggang River Estuary (JGE, west-central Taiwan) and Kaoping River Estuary (KPE, southern Taiwan). UPGMA tree of nine populations showed two main groups: the first group included the SMR and Tamsui River Estuary (TSE) (both located northern Taiwan), and the second one included the other seven populations (west-central, southern and eastern Taiwan). Demographic analyses implied a population expansion occurred during the recent history of the species. The dispersal route of this species might be from China to west-central and west-southern Taiwan, and then the part individuals belonging to lineage A and B dispersed southerly and northerly, respectively. And then part individuals in west-central Taiwan fell back to and stay at estuaries as the sea level rose about 18,000 years ago.
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Affiliation(s)
- Po-Cheng Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Chun-Han Shih
- Department of Leisure Management, Tungnan University, New Taipei City, 222, Taiwan
| | - Ta-Jen Chu
- Department of Leisure and Recreation Management, Chung Hua University, Hsin Chu, 300, Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ying-Chou Lee
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
- * E-mail: (YCL); (TDT)
| | - Tzong-Der Tzeng
- Department of Leisure, Recreation and Tourism Management, Shu-Te University, Kaohsiung, 824, Taiwan
- * E-mail: (YCL); (TDT)
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Han CC, Yen TB, Chen NC, Tseng MC. Comparative Studies of 5S rDNA Profiles and Cyt b Sequences in two Onychostoma Species (Cyprinidae). Int J Mol Sci 2015; 16:29663-72. [PMID: 26690426 PMCID: PMC4691136 DOI: 10.3390/ijms161226193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/27/2015] [Accepted: 12/01/2015] [Indexed: 11/16/2022] Open
Abstract
Onychostoma barbatulum and O. alticorpus, two primarily freshwater cyprinid fish, have similar morphological characters and partially overlapping ecological habitats. In order to explore the genetic differences between these two species, chromosomal characteristics and genetic variations were examined by fluorescence in situ hybridization (FISH) of 5S rDNA and cytochrome (Cyt) b gene analysis. Ten specimens of O. barbatulum and O. alticorpus were collected from the Nanzihsian Stream in southern Taiwan. FISH revealed that the 5S rDNA loci of O. barbatulum and O. alticorpus were found at a pericentromeric and subtelomeric position, respectively, in a pair of submetacentric chromosomes. Cyt b genes were amplified and sequenced from five individuals of each species. Intraspecific genetic distances ranged from 0.001–0.004 in O. barbatulum and from 0.001–0.006 in O. alticorpus. Genetic distances between these two species ranged from 0.132–0.142. The phylogenetic tree showed these two species are not sister species. In conclusion, FISH cytogenetic information and Cyt b gene analyses indicated that these two species have significantly different genetic characteristics; nevertheless, their morphological similarities may be due to environmental adaptation.
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Affiliation(s)
- Chiao-Chuan Han
- National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan.
- Graduate Institute of Marine Biology, National Dong Hwa University, Hualien 974, Taiwan.
| | - Tsair-Bor Yen
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Nian-Cih Chen
- Institute of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Mei-Chen Tseng
- Institute of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan.
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Elsheikh MO, Begham Mustafa F, Ibrahim Eid I, Lutas A, Bhassu S. COI gene sequence analysis for testing cyclical mating in securing genetic diversity of Macrobrachium rosenbergii. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Tseng SP, Wang CJ, Li SH, Lin SM. Within-island speciation with an exceptional case of distinct separation between two sibling lizard species divided by a narrow stream. Mol Phylogenet Evol 2015; 90:164-75. [PMID: 25982689 DOI: 10.1016/j.ympev.2015.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 02/24/2015] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
Abstract
Delimitation of genetic and geographic boundaries between species is a focus of evolutionary biology. In this study, we demonstrated fine-scale differentiation of Takydromus formosanus species complex comprising four insular endemics on Taiwan Island. Phylogeny and ancestral range reconstruction based on mitochondrial DNA sequences of 430 Takydromus lizards (405 lizards of this complex throughout their distribution range, and 25 lizards from 11 other species) indicated that the major branching process occurred within Taiwan, which represented a solid evidence of within-island speciation on this small island. We further demonstrated an exceptional case of a pair of sister species, T. viridipunctatus and T. luyeanus, that were separated by a narrow stream with a width of only 15m. This pattern might be one of the narrowest contact zones ever documented in terrestrial vertebrates. To evaluate the level of genetic introgression between these sister species, a fine-scale collection of another 382 lizards was conducted along a transect line across the stream. A total of 13 microsatellite markers and mtDNA genotyping was used to detect a low proportion of hybrids (5.7-9.9% from STRUCTURE, and 2.3% from DAPC). Our results indicated that the two clades are highly differentiated across this extremely short distance.
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Affiliation(s)
- Shu-Ping Tseng
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan; Department of Entomology, National Taiwan University, Taipei 106, Taiwan
| | - Chao-Jun Wang
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Si-Min Lin
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan.
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Jean CT, Wu CY, Tsai KC, Wang WK, Hsu YY, Chang YM, Lin HD. Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation. PLoS One 2014; 9:e93387. [PMID: 24963708 PMCID: PMC4070904 DOI: 10.1371/journal.pone.0093387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/05/2014] [Indexed: 02/01/2023] Open
Abstract
Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.
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A new phylogeographic pattern of endemic Bufo bankorensis in Taiwan Island is attributed to the genetic variation of populations. PLoS One 2014; 9:e98029. [PMID: 24853679 PMCID: PMC4031179 DOI: 10.1371/journal.pone.0098029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/28/2014] [Indexed: 11/19/2022] Open
Abstract
Aim To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China. Methodology/Principal Findings Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades. Conclusions The multiple origins (different clades) of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B. bankorensis, implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups.
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Differentiation in stag beetles, Neolucanus swinhoei complex (Coleoptera: Lucanidae): four major lineages caused by periodical Pleistocene glaciations and separation by a mountain range. Mol Phylogenet Evol 2014; 78:245-59. [PMID: 24837623 DOI: 10.1016/j.ympev.2014.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 04/24/2014] [Accepted: 05/03/2014] [Indexed: 11/20/2022]
Abstract
Taxonomic debates on Neolucanus swinhoei complex consisting of N. swinhoei, N. doro doro, N. doro horaguchii, and N. euganiae, distributed exclusively in Taiwan, have been ongoing for several decades because of their overlapping morphological characters. To clarify their taxonomic status and phylogeographical history, we analyzed nine morphological characteristics and four molecular amplicons. Phylogenetic inferences based on COI+16S rDNA+wingless showed one eastern and three western lineages, with the latter consisting of one low-hill and two montane lineages. Intermingled DNA sequences from different populations within each lineage, many low FST values, and a high variance component between lineages indicate the possibility of gene flow among populations. However, positive relationships were observed between the genetic divergences of 16S rDNA and its FST values with geographic distance. A divergence estimation based on COI+16S revealed that these beetles might have originated from Asian mainland and differentiated into western and eastern lineages ca. 1Mya, with the differentiation of the western lineages occurring approximately 0.50-0.75Mya. Isolation by mountain ranges and limited flying capability of these beetles as well as populations retreat to and expansion from refugia in response to glaciation cycles have resulted in the current distribution of N. swinhoei complex. Although most morphological characters are variable and undistinguishable, multi-dimensional scaling analysis based on measurable characteristics could recognize hill N. swinhoei as a cluster distinct from the others. However, based on the realities of genetic admixture, shared phylogeographical history and overlapping characteristics, all of these stag beetles should be regarded as Neolucanus swinhoei Bates, 1866.
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Mitochondrial DNA phylogeography of Semisulcospira libertina (Gastropoda: Cerithioidea: Pleuroceridae): implications the history of landform changes in Taiwan. Mol Biol Rep 2014; 41:3733-43. [DOI: 10.1007/s11033-014-3238-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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Chai A, Zhang J, Cui Q, Yuan C. Mitochondrial genome of Onychostoma macrolepis (Osteichthyes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:240-1. [PMID: 24548011 DOI: 10.3109/19401736.2014.883605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Onychostoma macrolepis, which belongs to the genus Onychostoma (Cypriniformes, Cyprinidae), is a benthopelagic fish that inhabits the flowing freshwaters in China. The complete mitochondrial genome sequence of O. macrolepis is 16,595 bp in length and comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The base composition of the genome is 31.29% A, 24.53% T, 27.97 % C, and 16.21% G, showing considerable bias toward an A + T preference as 55.82%. The results can provide a basic database for analyzing the phylogenetic relationship and conservation genetics in the genus Onychostoma.
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Affiliation(s)
- Aihong Chai
- a College of Marine Science & Engineering, Tianjin University of Science &Technology , Tianjin , PR China and.,b Key Laboratory of Zoological Systematics and Evolution , Institute of Zoology, Chinese Academy of Sciences , Beijing , PR China
| | - Jie Zhang
- b Key Laboratory of Zoological Systematics and Evolution , Institute of Zoology, Chinese Academy of Sciences , Beijing , PR China
| | - Qingman Cui
- a College of Marine Science & Engineering, Tianjin University of Science &Technology , Tianjin , PR China and
| | - Chunying Yuan
- a College of Marine Science & Engineering, Tianjin University of Science &Technology , Tianjin , PR China and
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Wu X, Luo J, Huang S, Chen Z, Xiao H, Zhang Y. Molecular phylogeography and evolutionary history of Poropuntius huangchuchieni (Cyprinidae) in Southwest China. PLoS One 2013; 8:e79975. [PMID: 24282516 PMCID: PMC3839932 DOI: 10.1371/journal.pone.0079975] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 10/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The evolution of the Yunnan Plateau's drainages network during the Pleistocene was dominated by the intense uplifts of the Qinghai-Tibetan Plateau. In the present study, we investigated the association between the evolutionary histories of three main drainage systems and the geographic patterns of genetic differentiation of Poropuntius huangchuchieni. METHODOLOGY/PRINCIPAL FINDINGS We sequenced the complete sequences of mitochondrial control region for 304 specimens and the sequences of Cytochrome b gene for 15 specimens of the species P. huangchuchieni and 5 specimens of Poropuntius opisthoptera. Phylogenetic analysis identified five major lineages, of which lineages MK-A and MK-B constrained to the Mekong River System, lineages RL and LX to the Red River System, and lineage SW to the Salween River System. The genetic distance and network analysis detected significant divergences among these lineages. Mismatch distribution analysis implied that the population of P. huangchuchieni underwent demographic stability and the lineage MK-B, sublineages MK-A1 and LX-1 underwent a recent population expansion. The divergence of the 5 major lineages was dated back to 0.73-1.57 MYA. CONCLUSIONS/SIGNIFICANCE Our results suggest that P. opisthoptera was a paraphyletic group of P. huangchuchieni. The phylogenetic pattern of P. huangchuchieni was mostly associated with the drainage's structures and the geomorphological history of the Southwest Yunnan Plateau. Also the differentiation of the major lineages among the three drainages systems coincides with the Kunlun-Yellow River Movement (1.10-0.60 MYA). The genetic differentiation within river basins and recent demographical expansions that occurred in some lineages and sublineages are consistent with the palaeoclimatic oscillations during the Pleistocene. Additionally, our results also suggest that the populations of P. huangchuchieni had keep long term large effective population sizes and demographic stability in the recent evolutionary history, which may be responsible for the high genetic diversity and incomplete lineages sorting of Poropuntius huangchuchieni.
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Affiliation(s)
- Xiaoyun Wu
- Laboratory for Conservation and Utilization of Bio-resource, Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing Luo
- Laboratory for Conservation and Utilization of Bio-resource, Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | | | - Ziming Chen
- Laboratory for Conservation and Utilization of Bio-resource, Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Heng Xiao
- Laboratory for Conservation and Utilization of Bio-resource, Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- * E-mail: (HX); (YZ)
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resource, Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (HX); (YZ)
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Li BJ, Cheng HL. The complete mitochondrial genome sequence of Onychostoma barbatulus (Cypriniformes, Cyprinidae). MITOCHONDRIAL DNA 2013; 25:377-8. [PMID: 23992244 DOI: 10.3109/19401736.2013.809431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Onychostoma barbatulus is a small cyprinid fish and distributed mainly in Taiwan and mainland China. The total length of O. barbatulus mitogenome is 16,597 bp, and had a gene content consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region. The determination of O. barbatulus mitogenome would play an important role both in the delineation of phylogeographic history and population genetic structure, as well as reflection of conservation efforts on the genetic diversity and population vitality.
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Affiliation(s)
- Bin-Jun Li
- School of Ocean, Yantai University , Yantai , China and
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Bonilla-Rivero A, López-Rojas H. On the origin and diversification of Venezuelan freshwater fishes: the genus Gephyrocharax (Ostariophysi: Characidae) a case study. NEOTROPICAL ICHTHYOLOGY 2013. [DOI: 10.1590/s1679-62252013000300002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We conducted a phylogeographic analysis of the genus Gephyrocharaxin Venezuela to evaluate geomorphologic evidence for the formation of the country's main watersheds and to establish a biogeographical hypothesis of possible diversification mechanisms of the Neotropical freshwater fish fauna. We assayed eight enzyme systems and general proteins to estimate genetic variability (H, P), intraspecific structuring in several Gephyrocharax valencia and G. venezuelae populations (FIS, FIT, and FST), and a phylogenetic approach for the three species of Gephyrocharax in Venezuela, using Corynopoma riisei as the external group. Fourteen presumptive lociindicate that populations of the three species of Gephyrocharaxanalyzed show a clear genetic inter-specific differentiation, determined by four loci with fixed alleles (GPI-B*,IDH*, ME-1*, and ME-2*). The resulting cladogram shows two major clades: a monophyletic group consisting of Gephyrocharax n. sp. and G. venezuelae(restricted to the northwest of the country) and a group formed exclusively by G. valencia (distributed along the largest geographic range). Speciation of the Venezuelan lineages of the genus Gephyrocharaxcould be explained by the origin and course movements of the present Orinoco River together with geomorphologic processes that have occurred in northern Venezuela since the Miocene.
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Chiang TY, Lin HD, Zhao J, Kuo PH, Lee TW, Hsu KC. Diverse processes shape deep phylogeographical divergence in Cobitis sinensis
(Teleostei: Cobitidae) in East Asia. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tzen-Yuh Chiang
- Department of Life Sciences; Cheng Kung University; Tainan Taiwan
| | - Hung-Du Lin
- Department of Life Sciences; Cheng Kung University; Tainan Taiwan
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture; Key Laboratory of Ecology and Environment Science in Guangdong Higher Education; College of Life Science; South China Normal University; Guangzhou China
| | - Po-Hsun Kuo
- Department of Industrial Management; Taiwan University of Science and Technology; Taipei Taiwan
| | - Teh-Wang Lee
- Endemic Species Research Institute; Nantou Taiwan
| | - Kui-Ching Hsu
- Department of Industrial Management; Taiwan University of Science and Technology; Taipei Taiwan
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Livi S, de Innocentiis S, Longobardi A, Cataudella S, Tancioni L, Rampacci M, Marino G. Genetic structure of Barbus spp. populations in the Marches Region of central Italy and its relevance to conservation actions. JOURNAL OF FISH BIOLOGY 2013; 82:806-826. [PMID: 23464545 DOI: 10.1111/jfb.12021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 11/08/2012] [Indexed: 06/01/2023]
Abstract
A genetic survey of Barbus spp. populations in the Marches Region (Adriatic River basins), central Italy, was carried out using mitochondrial and nuclear markers (partial D-loop, cyt b sequences and microsatellite loci) in order to ascertain their systematic position and to address their genetic structure which is key to conservation action planning. Analyses were conducted on sequences obtained from 91 individuals collected from eight sampling sites in five different rivers, from two specimens provided by the Ichthyological Centre of Rome and mitochondrial sequences of Barbus spp. retrieved from GenBank. Presumptive classification based on external morphological characters was not confirmed by genetic analysis, by means of which all specimens collected in the Marches Region were ascribed to Barbus plebejus. Genetic diversity values (h and π) of sampling groups were all different from 0 except the one sample collected from the upper reaches of the River Tenna, above a hydroelectric dam. Population connectivity and colonization patterns of the studied area were inferred from an analysis of molecular variance distribution and evolutionary relationships among haplotypes. The results point to different levels of isolation among sampling groups due to ecological and anthropogenic factors and the effect of an artificial barrier on genetic variability and conservation status of the population. Finally, this study confirms the uncertainty associated with systematic classification of Barbus spp. based on morphological characters due to the phenotypic plasticity of the species.
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Affiliation(s)
- S Livi
- ISPRA Higher Institute for Environmental Protection and Research, Via Vitaliano Brancati, 48-00144 Rome, Italy.
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Phylogeographical analysis on Squalidus argentatus recapitulates historical landscapes and drainage evolution on the island of Taiwan and mainland China. Int J Mol Sci 2012; 13:1405-1425. [PMID: 22408398 PMCID: PMC3291967 DOI: 10.3390/ijms13021405] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 11/26/2022] Open
Abstract
Phylogeographical analyses on Squalidus argentatus samples from thirteen localities within mainland China and Taiwan were conducted for biogeographic studies, as their dispersal strictly depends on geological evolution of the landmasses. A total of 95 haplotypes were genotyped for mtDNA cyt b gene in 160 specimens from nine river systems. Relatively high levels of haplotype diversity (h = 0.984) and low levels of nucleotide diversity (π = 0.020) were detected in S. argentatus. Two major phylogenetic haplotype groups, A and B, were revealed via phylogenetic analysis. The degree of intergroup divergence (3.96%) indicates that these groups diverged about 4.55 myr (million years) ago. Haplotype network and population analyses indicated significant genetic structure (FST = 0.775), largely concordant with the geographical location of the populations. According to SAMOVA analysis, we divided these populations into four units: Yangtze-Pearl, Qiantang-Minjiang, Jiulong-Beijiang and Taiwan groups. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots indicated a significant population expansion for lineage A and B, approximately dated 0.35 and 0.04 myr ago, respectively. We found strong geographical organization of the haplotype clades across different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow.
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Lin HD, Chen YR, Lin SM. Strict consistency between genetic and topographic landscapes of the brown tree frog (Buergeria robusta) in Taiwan. Mol Phylogenet Evol 2012; 62:251-62. [DOI: 10.1016/j.ympev.2011.09.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/24/2011] [Accepted: 09/28/2011] [Indexed: 11/30/2022]
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Siti-Balkhis AB, Jamsari AFJ, Hwai TS, Yasin Z, Siti-Azizah MN. Evidence of geographical structuring in the Malaysian Snakehead, Channa striata based on partial segment of the CO1 gene. Genet Mol Biol 2011; 34:520-3. [PMID: 21931528 PMCID: PMC3168196 DOI: 10.1590/s1415-47572011005000016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 03/23/2011] [Indexed: 11/25/2022] Open
Abstract
Channa striata, locally known as “haruan”, is economically important in fisheries and aquaculture industries in several Asian countries. DNA sequencing, based on a partial segment of the Cytochrome oxidase c subunit 1 (CO1) gene, was used to determine genetic variation in C. striata samples from four different populations on the west coast of Peninsular Malaysia. The highest nucleotide and haplotype diversities were observed in the Linggi population (π = 0.0067, h = 0.835), and the lowest in the Timah Tasoh population (π = 0.0008, h = 0.286). Apart from Kajang-Linggi, which was insignificant, FST values were significant (p < 0.05) in all pairwise-population comparisons. Consequently, it is inferred that genetic structuring C. striata populations in this region was largely shaped by a common origin, with secondary influences from geographical factors and isolation.
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Chiang TY, Lee TW, Hsu KC, Kuo CH, Lin DY, Lin HD. Population Structure in the Endangered Cyprinid FishPararasbora moltrechtiin Taiwan, Based on Mitochondrial and Microsatellite DNAs. Zoolog Sci 2011; 28:642-51. [DOI: 10.2108/zsj.28.642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Jang-Liaw NH, Chou WH. Phylogeography of the fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), in Taiwan. Zoolog Sci 2011; 28:254-63. [PMID: 21466342 DOI: 10.2108/zsj.28.254] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A phylogenetic analysis of Taiwanese fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), was conducted to examine its genetic diversification using sequence data from a portion of the mitochondrial DNA (mtDNA) cytochrome b sequences. We collected genetic data from 200 individuals at 23 localities in Taiwan and three localities in China. A neighbor-joining tree of 39 haplotypes revealed two clades in Taiwan and a clade in China, each showing restricted geographical distribution. The pattern of geographical divergence suggests a single invasion into Taiwan. Divergence times between clades were inferred using molecular clock tests. The population relationship of L. fujianensis between Taiwan and mainland China, and the phylogenetic relationships with its congeners, e.g., L. bannaensis, L. fragilis and L. kuhlii, were obtained and discussed.
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Affiliation(s)
- Nian-Hong Jang-Liaw
- Department of Zoology, National Museum of Natural Science, 1st Kuang-Chien Rd., Taichung 404, Taiwan
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Huang JP, Lin CP. Lineage-specific late pleistocene expansion of an endemic subtropical gossamer-wing damselfly, Euphaea formosa, in Taiwan. BMC Evol Biol 2011; 11:94. [PMID: 21486452 PMCID: PMC3094233 DOI: 10.1186/1471-2148-11-94] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 04/12/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pleistocene glacial oscillations have significantly affected the historical population dynamics of temperate taxa. However, the general effects of recent climatic changes on the evolutionary history and genetic structure of extant subtropical species remain poorly understood. In the present study, phylogeographic and historical demographic analyses based on mitochondrial and nuclear DNA sequences were used. The aim was to investigate whether Pleistocene climatic cycles, paleo-drainages or mountain vicariance of Taiwan shaped the evolutionary diversification of a subtropical gossamer-wing damselfly, Euphaea formosa. RESULTS E. formosa populations originated in the middle Pleistocene period (0.3 Mya) and consisted of two evolutionarily independent lineages. It is likely that they derived from the Pleistocene paleo-drainages of northern and southern Minjiang, or alternatively by divergence within Taiwan. The ancestral North-central lineage colonized northwestern Taiwan first and maintained a slowly growing population throughout much of the early to middle Pleistocene period. The ancestral widespread lineage reached central-southern Taiwan and experienced a spatial and demographic expansion into eastern Taiwan. This expansion began approximately 30,000 years ago in the Holocene interglacial period. The ancestral southern expansion into eastern Taiwan indicates that the central mountain range (CMR) formed a barrier to east-west expansion. However, E. formosa populations in the three major biogeographic regions (East, South, and North-Central) exhibit no significant genetic partitions, suggesting that river drainages and mountains did not form strong geographical barriers against gene flow among extant populations. CONCLUSIONS The present study implies that the antiquity of E. formosa's colonization is associated with its high dispersal ability and larval tolerance to the late Pleistocene dry grasslands. The effect of late Pleistocene climatic changes on the subtropical damselfly's historical demography is lineage-specific, depending predominantly on its colonization history and geography. It is proposed that the Riss and Würm glaciations in the late Pleistocene period had a greater impact on the evolutionary diversification of subtropical insular species than the last glacial maximum (LGM).
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Affiliation(s)
- Jen-Pan Huang
- Department of Life Science & Center for Tropical Ecology and Biodiversity, Tunghai University, Taichung, Taiwan 40704
- Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA
| | - Chung-Ping Lin
- Department of Life Science & Center for Tropical Ecology and Biodiversity, Tunghai University, Taichung, Taiwan 40704
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WANG CHENFAN, HSIEH CHIAHUNG, LEE SINCHE, WANG HURNGYI. Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses. Zool J Linn Soc 2011. [DOI: 10.1111/j.1096-3642.2010.00646.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chiang TY, Lin HD, Shao KT, Hsu KC. Multiple factors have shaped the phylogeography of Chinese spiny loach Cobitis sinensis in Taiwan as inferred from mitochondrial DNA variation. JOURNAL OF FISH BIOLOGY 2010; 76:1173-1189. [PMID: 20409169 DOI: 10.1111/j.1095-8649.2010.02589.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Mitochondrial DNA cytochrome b sequences (1140 bp) in 61 specimens of Chinese spiny loach Cobitis sinensis from 12 drainages in Taiwan were identified as two major clades, exhibiting a southern and a northern distribution, north of TzengWen and south of TzengWen (including TzengWen), respectively. The divergence time between these two phylogroups was estimated at 7.34-9.06 million years before present (B.P.), but these two phylogroups were formed c. 3.41-4.23 and 2.22-2.75 M B.P., respectively. Moreover, geological events have been recalculated that Taiwan Island emerged above sea level at an estimate of c. 4-5 M B.P., and quickly became its present shape at c. 2 M B.P. through mountain building. These results suggest that these two major clades of C. sinensis in Taiwan might originate from two different continental populations, since the island's initial isolation in the Pliocene. Within southern Taiwan, the initial colonization was hypothesized to be in KaoPing River, followed by its northward dispersal. The high divergence between KaoPing and TzengWen was influenced by glaciations and landforms. Within north Taiwan, the colonization was from the Miaoli Plateau through western Taiwan to north-eastern and northern Taiwan. This dispersal pattern is concordant with the previously proposed hypothesis. Apparently, both geological and phylogeographic evidence suggested that river capture of the upper Takia River by the LanYang River promoted range expansion in freshwater fishes and also indicated that the Central Range within Taiwan did not act as a barrier to the dispersal of C. sinensis.
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Affiliation(s)
- T-Y Chiang
- Department of Life Sciences, Cheng Kung University, Tainan, Taiwan
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Lin CJ, Lin HD, Wang JP, Chao SC, Chiang TY. Phylogeography ofHemibarbus labeo(Cyprinidae): secondary contact of ancient lineages of mtDNA. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00407.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Jang-Liaw NH, Lee TH. Intraspecific Relationships of Populations of the Brown FrogRana sauteri(Ranidae) on Taiwan, Inferred from Mitochondrial CytochromebSequences. Zoolog Sci 2009; 26:608-16. [DOI: 10.2108/zsj.26.608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Yeh WB, Lee HM, Tu WC, Tang LC, Lee PY. Molecular differentiation and diversity of Forcipomyia taiwana (Diptera: Ceratopogonidae) based on the mitochondrial cytochrome oxidase II sequence. JOURNAL OF MEDICAL ENTOMOLOGY 2009; 46:249-256. [PMID: 19351075 DOI: 10.1603/033.046.0209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Forcipomyia taiwana (Shiraki), a biting midge, is one of the most annoying blood-sucking pests in Taiwan. In this study, partial DNA sequences of cytochrome c oxidase II from 113 individuals collected from 11 locations around the island were analyzed to delineate the differentiation pattern and possible dispersal processes of F. taiwana in Taiwan. The uncorrected nucleotide divergences, composed of mostly transition substitutions, were high (up to 2.7%) among the samples. Average comparable variations (approximately equal to 0.7%) were found within and between populations. Phylogenetic analysis suggested that several distinct lineages exist and some can be found simultaneously in some populations. A relationship between sequence divergences among populations and their relative geographical distances was observed. Moreover, haplotype diversity was high in all populations, and low to middle levels (Fst = 0.004-0.288) of genetic differentiation were found among populations. Linearized calibration from sequence divergences and phylogenetic analysis showed that different ancestral lineages of F. taiwana possibly emerged as early as 0.6 million years ago. Taken together, genetic exchanges among these divergently ancestral lineages, likely caused by recent artificial events, have possibly led to the similarly diversified compositions of F. taiwana populations all around Taiwan nowadays.
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Affiliation(s)
- W B Yeh
- Department of Entomology, National Chung Hsing University, Taichung 40227, Taiwan, R.O.C
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Jang-Liaw NH, Lee TH, Chou WH. Phylogeography of Sylvirana latouchii (Anura, Ranidae) in Taiwan. Zoolog Sci 2008; 25:68-79. [PMID: 18275248 DOI: 10.2108/zsj.25.68] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 09/24/2007] [Indexed: 11/17/2022]
Abstract
Biogeographic studies are important for understanding the natural history of faunas. To comprehend the geographical patterns of genetic variation in anurans in Taiwan, we investigated the genetic structure of Sylvirana latouchii (Anura, Ranidae) from 31 populations by using mitochondrial DNA (mtDNA) cytochrome b sequences. A neighbor-joining tree of 38 haplotypes revealed three major divergences in Taiwanese S. latouchii: the northern, western, and eastern-and-southern clades. Each clade was restricted to a single geographical district and showed obvious differentiation. The patterns of geographical divergence in this species reflect common historical events experienced by other native animals distributed in Taiwan. The order of divergence times between clades was inferred using a molecular clock test. The population relationship of S. latouchii between Taiwan and mainland China is discussed. Further study employing more populations of S. latouchii from mainland China is necessary to clarify the original geographical patterns and migratory history of this species.
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Affiliation(s)
- Nian-Hong Jang-Liaw
- Department of Life Sciences, National Chung Hsing University, 250 Kuo-Kuang Rd., Taichung 402, Taiwan.
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Chen SF, Rossiter SJ, Faulkes CG, Jones G. Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros). Mol Ecol 2006; 15:1643-56. [PMID: 16629817 DOI: 10.1111/j.1365-294x.2006.02879.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east-west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour-joining tree showed that R. monoceros formed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.
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