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Zhou M, Xia J, Li C. Divergence of the freshwater sleeper, Neodontobutishainanensis (Chen, 1985) (Teleostei, Odontobutidae), in the Pearl River basin and on Hainan Island of southern China. Zookeys 2024; 1197:183-196. [PMID: 38725537 PMCID: PMC11079591 DOI: 10.3897/zookeys.1197.110314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/14/2024] [Indexed: 05/12/2024] Open
Abstract
Study of divergence of freshwater fish populations between island and adjacent mainland areas can shed light on the phylogeographical relationships of these regions. Neodontobutishainanensis is a freshwater fish species restricted to Hainan Island and in Guangdong and Guangxi provinces in the southern mainland China. We examine the phylogenetic relationship and population structure of N.hainanensis based on 3,176 nuclear loci using a gene-capture method. STRUCTURE analysis and principal coordinate analyses (PCA) indicate that populations from Guangdong, Guangxi and Hainan are each distinct, except that some individuals of the Guangdong population share minor genetic components with individuals of the Guangxi population. In the concatenated gene tree, the Hainan population is grouped with the Guangdong population, but the coalescent tree groups the Hainan population as the sister to the Guangxi population. Finally, coalescent simulations confirmed the divergence pattern supported by the coalescent tree and revealed a one-way introgression from the Guangxi population to the Guangdong population, which can explain the discordant results supported by the concatenated and coalescent phylogenetic analyses. Due to recent decline of N.hainanensis populations and the genetic patterns in this species, as revealed in this study, the populations in the three areas should be treated as separate conservation units.
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Affiliation(s)
- Mingwei Zhou
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Jianhong Xia
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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Hu J, Zhao J, Sui X, Zhu R, He D. Across the highest mountain on earth: discordant phylogeographic patterns and recent dispersal of Tibetan stone loaches (Triplophysa) in the Himalayas. JOURNAL OF FISH BIOLOGY 2024; 104:374-386. [PMID: 36571395 DOI: 10.1111/jfb.15296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Phylogeographic congruence among co-distributed taxa is regarded as an inherent inference to vicariance events. Nonetheless, incongruent patterns of contemporary lineage divergence among taxa indicated that species differ in their response to common past events. To investigate the role of past events, ecological traits and lineage diversification time in shaping the contemporary phylogeographic patterns, comparative analyses were conducted for Tibetan stone loaches in the Himalayas using three gene markers and two ecological traits (depth of caudal peduncle in their length and presence/absence of posterior chamber of the air bladder). By a thorough sampling in two flanks of the Himalayas, the authors detected that phylogenetic breaks were spatially discordant and divergences of populations were also temporally asynchronous in co-distributed loaches. Estimated divergence time using fossil-calibrated node dating indicated that the Tibetan stone loaches colonised into the south flank of the Himalayas until the Pleistocene. The demographic expansions were also disconcerted between populations in north and south flanks, or east and west Himalayas. Ongoing gene flows between populations in north and south sides implied that the Himalayas do not strictly impede dispersal of cold-adapted species. The results highlight that the quaternary climatic oscillation, in conjunction with ecological traits and lineage diversification time, shaped contemporary phylogenetic patterns of stone loaches in the Himalayas and provide new insights into the biodiversity and composition of species in the Himalayas and surrounding region.
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Affiliation(s)
- Jiaxin Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoyun Sui
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ren Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Dekui He
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Ni X, Chen Y, Deng G, Fu C. Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China. Genes (Basel) 2023; 14:2146. [PMID: 38136969 PMCID: PMC10743038 DOI: 10.3390/genes14122146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.
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Affiliation(s)
| | | | | | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.N.); (Y.C.); (G.D.)
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Shuli Z, Weitao C, Zhi W, Yuefei L, Jie L, Xinhui L, Jiping Y. Mitochondrial diversity and genetic structure of common carp (Cyprinus carpio) in Pearl River and Nandujiang River. JOURNAL OF FISH BIOLOGY 2023; 102:1109-1120. [PMID: 36744763 DOI: 10.1111/jfb.15340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 02/01/2023] [Indexed: 05/13/2023]
Abstract
Common carp (Cyprinus carpio) is an important valuable cyprinid in China and has been a popular cultured aquaculture species around the globe. Understanding the genetic diversity of wild native common carp not only provides basic data for the protection and utilisation of common carp resources but also assesses the effect of human activities on the genetic diversity of this species. In this study, genetic diversity and population structure of the common carp from 15 sampling populations in the Pearl River and Nandujiang River were determined using a coalescent mitochondrial locus (MLS), including mitochondrial cytochrome b gene (Cytb) and a control region (D-loop) segment. The haplotype diversity and nucleotide diversity were 0.962 and 0.00628 in the Pearl River and 0.808 and 0.00376 in the Nandujiang River, respectively. Phylogenetic and haplotype network analyses indicated that three sub-species (a) C. c. rubrofuscus, (b) C. c. haematopterus and (c) C. c. carpio all occur in both rivers. AMOVA revealed that the variation within populations (86.2%) was the main source of the total variation. Statistically significant genetic differentiation among different Pearl River populations of C. c. rubrofuscus (Fst = 0.05-0.25) and relatively high genetic differentiation between the Nandujiang River population and the Pearl River populations (Fst > 0.238) are apparent. Bayesian clustering analyses detected that global populations consisted of eight genetic clusters and examined that Nandujiang River population included relatively pure genetic clusters. Neutrality tests suggested that native populations experienced recent population expansion, and Extended Bayesian Skyline Plot indicated that the common carp populations likely experienced a historical expansion during 0.125-0.250 MYA. Artificial fish propagation and release, escape from fish farms and Fang Sheng may explain the invasion of non-native sub-species in many river sections, such as Laibin, Rongjiang, Huizhou, Heyuan and Zhaoqing. To conserve the native common carp populations, release station should be established to culture native common carp fry. Overall, the findings can be contributed to complementing scientific knowledge for conservation and management of the wild native common carp.
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Affiliation(s)
- Zhu Shuli
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Chen Weitao
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Wu Zhi
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Li Yuefei
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Li Jie
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Li Xinhui
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Yang Jiping
- The Laboratory of Fisheries Resources and Ecology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
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Li M, Yang X, Ni X, Fu C. The role of landscape evolution in the genetic diversification of a stream fish Sarcocheilichthys parvus from Southern China. Front Genet 2023; 13:1075617. [PMID: 36685913 PMCID: PMC9853433 DOI: 10.3389/fgene.2022.1075617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Sarcocheilichthys parvus (Cypriniformes: Gobionidae) is a stream fish which is endemic to sub-tropical coastal drainages in southern China, thus offering a valuable model for understanding how genetic divergence arises in stream-adapting freshwater fishes in this region. Using the mitochondrial Cyt b gene, integrative analyses of phylogeny, population demography, and ancestral area and paleo-drainage reconstructions are carried out to explicitly explore the role of landscape evolution in genetic diversification of S. parvus. The time-calibrated phylogeny of S. parvus indicates the splitting of two major lineages (A and B) at ∼3.66 Ma. Lineage A inhabits the Poyang Lake sub-drainage of the middle Yangtze River, Han River and Pearl River, and can be split into two sub-lineages (A-I and A-II), where sub-lineage A-II can be further sub-divided into three infra-sub-lineages (A-IIa, A-IIb and A-IIc). Except for the infra-sub-lineage A-IIc, which is restricted to the Han River and Pearl River, the other sub-lineages and infra-sub-lineages live exclusively in the Poyang Lake sub-drainage. Lineage B lives in the lower Yangtze River, Qiantang River, Jiaojiang River and Ou River, displaying close genetic relationships among the drainages. Rapid population expansion has occurred since the Late Pleistocene. Our findings indicate that the splitting of lineages A and B could be attributed to geographic isolation due to the Zhe-Min Uplift, acting as a biogeographic barrier before the late Early Pleistocene. Furthermore, the strong genetic divergence within Lineage A could be explained by the isolation role of the Nanling Mountains and Poyang Lake acting as an ecological barrier; while the lack of phylogenetic structure within Lineage B may have been the result of paleo-drainage connections or episodic freshwater connections during the eustatic low stand of sea level in the late Middle-Late Pleistocene.
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Affiliation(s)
| | | | - Xiaomin Ni
- *Correspondence: Xiaomin Ni, ; Cuizhang Fu,
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Chen IS, Jang-Liaw NH. Phylogeography of Aphyocypris normalis Nichols and Pope, 1927 at Hainan Island and adjacent areas based on mitochondrial DNA data. PLoS One 2023; 18:e0282460. [PMID: 36854024 PMCID: PMC9974131 DOI: 10.1371/journal.pone.0282460] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
We investigated the genetic structure of the freshwater fish Aphyocypris normalis, in 33 populations around Hainan Island and southern mainland China. Sequencing of the mitochondrial DNA (mtDNA) cytochrome b from 127 specimens yielded 47 haplotypes, from which we inferred a Bayesian tree. This revealed three major divergences: a principal clade of specimens with widespread geographic distribution, plus two clades with limited distribution. We estimated that these diverged between 1.05-0.16 Ma. Additionally, based on molecular data and comparing with the climate patterns of Hainan Island, eight phylogeographic ranges (populations) of A. normalis were constructed: the eastern plain (E), northeastern hills and plain (NE), northwestern hills and lowlands (NW), central mountains (C), southeastern hills and plain (SE), southern mountains and hills (S), southwestern mountains and lowlands (SW), and western lowlands (W). The patterns of geographical divergence in this species do not reflect the isolation caused by the Qiongzhou (Hainan) Strait, which would generally be experienced by terrestrial animals on isolated islands. The present results indicate that the major clades within A. normalis have diverged before the temporary land bridge existed across the strait during the Last Glacial Maximum.
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Affiliation(s)
- I-Shiung Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Nian-Hong Jang-Liaw
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, Taipei, Taiwan
- * E-mail:
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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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A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yang X, Ni X, Fu C. Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China. Life (Basel) 2022; 12:1024. [PMID: 35888112 PMCID: PMC9318155 DOI: 10.3390/life12071024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023] Open
Abstract
The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.
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Wang J, Hsu KC, Chen YH, Zhao J, Tang WQ, Liu D, Yang JQ, Lin HD. Phylogeography of Tridentiger bifasciatus (Gobiidae) in the Northwestern Pacific. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.935251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The shimofuri goby (Tridentiger bifasciatus) is native to marine, brackish, and fresh waters along the coasts of the northwest Pacific. Our study examined the population genetic structure, diversity, and demography of T. bifasciatus in the China Seas, including the Yellow Sea, East China Sea, and South China Sea, using the sequences of mitochondrial DNA [mtDNA cytochrome b (cyt b) gene and d-loop region] and nuclear DNA [nuDNA ryanodine receptor 3 (Ryr3) gene]. The mtDNA dataset revealed a significant population differentiation, but the nuDNA dataset displayed the absence of genetic differentiation. The discordance between these two datasets was accounted for by population admixture, selection, and incomplete lineage sorting. Although the mtDNA and nuDNA displayed a discordant population structure, these genetic markers revealed the same population history: (1) the populations retreated into two refugia during glaciations and (2) the populations declined recently. Our study revealed that after glaciations, the re-flooding in Taiwan Strait did not shape the migrations of the southern lineage from the South China Sea to the East China Sea, and displayed that two mtDNA lineages have diverged before they migrated southward during glaciations. These results offer important resources for the further study of conservation genetics.
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Brazier T, Cherif E, Martin JF, Gilles A, Blanchet S, Zhao Y, Combe M, McCairns RJS, Gozlan RE. The influence of native populations’ genetic history on the reconstruction of invasion routes: the case of a highly invasive aquatic species. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Wang X, Tong L, Deng J, Li L, Xiang P, Xu L, Luo Z, Yang K, Song Z. Insights into historical drainage evolution based on the phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) across the upper and middle Yalong River drainage in the Hengduan Mountains region, southwest China. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Yi MR, Hsu KC, Gu S, He XB, Luo ZS, Lin HD, Yan YR. Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex. Zookeys 2022; 1084:1-26. [PMID: 35173516 PMCID: PMC8810657 DOI: 10.3897/zookeys.1084.71576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/31/2021] [Indexed: 02/06/2023] Open
Abstract
Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.
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Affiliation(s)
- Mu-Rong Yi
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Marine Resources Big Data Center of South China Sea, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524088, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Sui Gu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiong-Bo He
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhi-Sen Luo
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan
| | - Yun-Rong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Marine Resources Big Data Center of South China Sea, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524088, China
- Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China Sea, Guangdong Ocean University, Zhanjiang 524088, China
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15
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Population Genomics of Megalobrama Provides Insights into Evolutionary History and Dietary Adaptation. BIOLOGY 2022; 11:biology11020186. [PMID: 35205053 PMCID: PMC8869164 DOI: 10.3390/biology11020186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary Megalobrama is the economically most important freshwater fish genus in China. In recent years, germplasm resources of Megalobrama have been depleting as a result of environmental degradation and artificial factors. In this study, we established the whole genome database of Megalobrama populations using the whole genome re-sequencing technology, explored population genetic structure, and inferred comprehensive evolutionary relationships using principal component analysis and population structure analysis. Furthermore, employing selective sweep analysis, we identified candidate genes related to variations in feeding habits, revealing the molecular mechanisms of environmental adaptability in Megalobrama populations. Taken together, this study describes the population history and genetic diversity of Megalobrama populations and also the molecular mechanisms likely involved their environmental adaptability. These findings will make a substantial contribution to conservation and utilization of Megalobrama germplasm resources. Abstract Megalobrama, a genus of cyprinid fish, is an economically important freshwater fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni, and M. pellegrini. Population structure indicated that geographically divergent Megalobrama populations were separated into six subgroups. A phylogenetic tree showed that M. skolkovii was more closely related to M. pellegrini than other species and M. hoffmanni was clustered apart from other Megalobrama species, showing a high nucleotide diversity in geographic groups. Treemix validated gene flow from M. amblycephala to M. skolkovii, suggesting that introgression may provide an important source of genetic variation in the M. skolkovii populations. According to the demographic history analysis, it is speculated that Megalobrama might have been originally distributed in the Pearl River with some spread to Hainan Island and northern China due to lower sea levels during the glacial period. Whole-genome selective sweeps analysis demonstrated that M. amblycephala likely developed an enhanced energy metabolism mostly through fatty acid degradation pathways whereas M. hoffmanni possibly regulate lipid absorption via the cholesterol metabolism pathway. Taken together, this study provides a valuable genomic resource for future genetic investigations aiming to improve genome-assisted breeding of Megalobrama species.
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16
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Shao WH, Cheng JL, Zhang E. Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China. Front Genet 2021; 12:713793. [PMID: 34868198 PMCID: PMC8635968 DOI: 10.3389/fgene.2021.713793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.
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Affiliation(s)
- Wei-Han Shao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Li Cheng
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - E Zhang
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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17
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Wang J, Li C, Chen J, Wang J, Jin J, Jiang S, Yan L, Lin H, Zhao J. Phylogeographic structure of the dwarf snakehead ( Channa gachua) around Gulf of Tonkin: Historical biogeography and pronounced effects of sea-level changes. Ecol Evol 2021; 11:12583-12595. [PMID: 34594522 PMCID: PMC8462176 DOI: 10.1002/ece3.8003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 11/07/2022] Open
Abstract
Geological events, landscape features, and climate fluctuations have shaped the distribution of genetic diversity and evolutionary history in freshwater fish, but little attention has been paid to that around the Gulf of Tonkin; therefore, we investigated the phylogeographic structure of the dwarf snakehead (Channa gachua) on Hainan Island and mainland China, as well as two populations in Vietnam. We attempted to elucidate the origins of freshwater fish in South Hainan by incorporating genetic data from DNA markers on both the mitochondrial cytochrome b gene (cyt b) and the nuclear recombination-activating gene 1 (RAG-1). Mitochondrial phylogenetic analysis identified two major lineages (lineages A and B), which may represent separate species. Divergence data suggested that C. gachua populations diverged between 0.516 and 2.376 myr. The divergence of the two cryptic species is congruent with sea-level rise, which subsequently isolated Hainan from the mainland. During the Pleistocene glaciations, the entire region of the Gulf of Tonkin and the Qiongzhou Strait became part of the coastal plain of the Asian continent, which might have resulted in the current distribution patterns and dispersal routes of C. gachua populations. The formation of three sublineages in lineage A indicated that the Gulf of Tonkin was a geographical barrier between Hainan Island and mainland China but not between Vietnam and Hainan Island. The results of this study may help to elucidate the origins of freshwater fish in South Hainan and the phylogeographic structure of C. gachua.
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Affiliation(s)
- Junjie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Jiaqi Chen
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Jujing Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Jinjin Jin
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Shuying Jiang
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Luobin Yan
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Hung‐Du Lin
- The Affiliated School of National Tainan First Senior High SchoolTainanTaiwan
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe AquacultureGuangdong Provincial Engineering Technology Research Center for Environmentally‐friendly AquacultureGuangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhouChina
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18
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Genetic Structure and Diversity of the Yellowbelly Threadfin Bream Nemipterus bathybius in the Northern South China Sea. DIVERSITY 2021. [DOI: 10.3390/d13070324] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The genetic structure and demography of the yellowbelly threadfin bream, Nemipterus bathybius, in the northern South China Sea were examined using the mitochondrial DNA cytochrome b gene (1141 bp). High levels of haplotype and nucleotide diversities (0.98 and 5.26 × 10−3, respectively) showed that all populations exhibited a high level of genetic diversity. Analysis of molecular variance (AMOVA), FST statistics, and haplotype networks suggested the absence of significant genetic differentiation along the coast of the northern South China Sea. Although the results suggested that the lack of differentiation within the population structure of N. bathybius was shaped by ocean currents, our results also showed that the Qiongzhou Strait limited their migration between Beibu Gulf and the northern South China Sea. Neutrality tests and mismatch distributions indicated population expansion, but the Bayesian skyline plots and approximate Bayesian computation approaches suggested that the population sizes recently contracted. The diversification of multiple stocks, which were induced by two ocean current systems, contributed to these discordant results. Although these analyses of demographic history revealed no evidence for recent population bottlenecks, the population demography needs to be evaluated further.
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19
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Genetic, Morphological, and Environmental Differentiation of an Arid-Adapted Oak with a Disjunct Distribution. FORESTS 2021. [DOI: 10.3390/f12040465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The patterns of genetic and morphological diversity of a widespread species can be influenced by environmental heterogeneity and the degree of connectivity across its geographic distribution. Here, we studied Quercus havardii Rydb., a uniquely adapted desert oak endemic to the Southwest region of the United States, using genetic, morphometric, and environmental datasets over various geographic scales to quantify differentiation and understand forces influencing population divergence. First, we quantified variation by analyzing 10 eastern and 13 western populations from the disjunct distribution of Q. havardii using 11 microsatellite loci, 17 morphological variables, and 19 bioclimatic variables. We then used regressions to examine local and regional correlations of climate with genetic variation. We found strong genetic, morphological and environmental differences corresponding with the large-scale disjunction of populations. Additionally, western populations had higher genetic diversity and lower relatedness than eastern populations. Levels of genetic variation in the eastern populations were found to be primarily associated with precipitation seasonality, while levels of genetic variation in western populations were associated with lower daily temperature fluctuations and higher winter precipitation. Finally, we found little to no observed environmental niche overlap between regions. Our results suggest that eastern and western populations likely represent two distinct taxonomic entities, each associated with a unique set of climatic variables potentially influencing local patterns of diversity.
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20
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Wang IC, Lin HD, Liang CM, Huang CC, Wang RD, Yang JQ, Wang WK. Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. Zookeys 2020; 1005:57-72. [PMID: 33390755 PMCID: PMC7765746 DOI: 10.3897/zookeys.1005.57592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/25/2020] [Indexed: 11/25/2022] Open
Abstract
The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.
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Affiliation(s)
- I-Chen Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
| | - Hung-Du Lin
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
| | - Chih-Ming Liang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
| | - Chi-Chun Huang
- Taiwan Endemic Species Research Institute, Nantou 552, TaiwanTaiwan Endemic Species Research InstituteNantouTaiwan
| | - Rong-Da Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, ChinaShanghai Ocean UniversityShanghaiChina
| | - Jin-Quan Yang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, ChinaShanghai Ocean UniversityShanghaiChina
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
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21
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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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22
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Complete mitochondrial genome of the freshwater fish Acrossocheilus longipinnis (Teleostei: Cyprinidae): genome characterization and phylogenetic analysis. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00440-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Ding XH, Hsu KC, Tang WQ, Liu D, Ju YM, Lin HD, Yang JQ. Genetic diversity and structure of the Chinese lake gudgeon ( Sarcocheilichthys sinensis). Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:228-237. [PMID: 32723222 DOI: 10.1080/24701394.2020.1779239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θ π = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (TMRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.
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Affiliation(s)
- Xin-Hua Ding
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Wen-Qiao Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yu-Min Ju
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan.,Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Hung-Du Lin
- Department of Biology, The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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24
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Zhang WJ, Wang JJ, Li C, Chen JQ, Li W, Jiang SY, Hsu KC, Zhao M, Lin HD, Zhao J. Spatial genetic structure of Opsariichthys hainanensis in South China. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:98-107. [PMID: 32186219 DOI: 10.1080/24701394.2020.1741564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly Opsariichthys hainanensis, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome b (Cyt b) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in O. hainanensis. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of O. hainanensis were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.
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Affiliation(s)
- Wen-Jun 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, China
| | - Jun-Jie 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, 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, China
| | - Jia-Qi Chen
- 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, China
| | - Wei 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, China
| | - Shu-Ying Jiang
- 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, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Meiting Zhao
- Department of Geography, South China Normal University, Guangzhou, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - 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, China
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25
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Chen W, Li C, Chen F, Li Y, Yang J, Li J, Li X. Phylogeographic analyses of a migratory freshwater fish (Megalobrama terminalis) reveal a shallow genetic structure and pronounced effects of sea-level changes. Gene 2020; 737:144478. [PMID: 32061762 DOI: 10.1016/j.gene.2020.144478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 10/25/2022]
Abstract
Different types of fish taxa generally seem to present diverse phylogeographic structures and show different responses to environmental changes. In southern China, however, a large number of phylogeographic studies have been employed for small and/or benthic fish species, while phylogeographic patterns of larger and migratory species are not well understood. In this study, we chose Megalobrama terminalis, an endemic cyprinid from Southern China with a median size and relatively high migratory potential as a candidate to explore the phylogeographic structure and to seek the relevant driving forces using a multilocus approach (two mitochondrial markers and three nuclear markers). Our results show that M. terminalis exhibits three mtDNA genetic groups, each presenting genetic structure to the local geography, but the differentiation level was much weaker than that of small and/or benthic fish species reported in earlier studies. Nuclear loci did not observe pronounced genetic group subdivision, but did examine noteworthy genetic differentiation between the Hainan Island population and the mainland populations. Divergence time estimation and demographic analyses suggest that sea-level changes associated with the Late Pleistocene glacial cycles have exerted pronounced effects on the divergence of the three groups and the expansion of M. terminalis populations. Above all, our study provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this endemic organism.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Ce Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Fangcan Chen
- Guangzhou Qianjiang Water Ecological Technology Co. LTD, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jiping Yang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China.
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Zhou H, Hu Y, Jiang H, Duan G, Ling J, Pan T, Chen X, Wang H, Zhang Y. Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights. PeerJ 2020; 8:e8415. [PMID: 31998563 PMCID: PMC6979408 DOI: 10.7717/peerj.8415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022] Open
Abstract
The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish.
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Affiliation(s)
- Huaxing Zhou
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yuting Hu
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - He Jiang
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Guoqing Duan
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Jun Ling
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tingshuang Pan
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xiaolei Chen
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Huan Wang
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ye Zhang
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
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Huang XX, Hsu KC, Kang B, Kuo PH, Tsai WH, Liang CM, Lin HD, Wang WK. Population structure of Aphyocypris normalis: phylogeography and systematics. Zookeys 2019; 872:77-90. [PMID: 31528116 PMCID: PMC6718371 DOI: 10.3897/zookeys.872.33105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Aphyocyprisnormalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A.normalis using sequences of the mitochondrial DNA control region and cytochrome b gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of A.normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices NST (0.532) and GST (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus Aphyocypris were estimated.
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Affiliation(s)
- Xiao-Xia Huang
- Key laboratory of atmospheric environment and processes in the boundary layer over the low-latitude plateau region, Yunnan University, Kunming, 650091, China Yunnan University Kunming China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China Guangdong Ocean University Zhanjiang China
| | - Bin Kang
- College of Fisheries, Ocean University of China, Qingdao 266003, China Ocean University of China Qingdao China
| | - Po-Hsun Kuo
- Department of Industrial Management, National Taiwan University of Science and Technology, Taipei 106, Taiwan National Taiwan University of Science and Technology Taipei Taiwan
| | - Wan-Hsin Tsai
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan
| | - Chih-Ming Liang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan The Affiliated School of National Tainan First Senior High School Tainan Taiwan
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan
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Xue J, Zhang H, Ning X, Bu W, Yu X. Evolutionary history of a beautiful damselfly, Matrona basilaris, revealed by phylogeographic analyses: the first study of an odonate species in mainland China. Heredity (Edinb) 2018; 122:570-581. [PMID: 30356221 DOI: 10.1038/s41437-018-0158-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/18/2018] [Indexed: 11/09/2022] Open
Abstract
Matrona basilaris Selys, 1853 is a damselfly distributed mainly in mainland China. A total of 423 individuals from 48 populations covering almost the entire range were sampled to explore the genetic diversity, phylogeographic structure, and demographic dynamics of the species using sequences of three mitochondrial genes (COI, COII, and ND1) and a nuclear (ITS1 + 5.8 S + ITS2) gene. Phylogenetic tree, median-joining network, and BAPS analyses indicated a four-group division of the entire population, and the divergence event was estimated to have occurred in the middle Pleistocene. The diverse terrain of mainland China as well as past climatic oscillations were assumed to have shaped the current phylogeographic pattern of M. basilaris. Multiple lines of evidence supported population expansion in Group 1 and Group 2 but not in Group 3 or Group 4. The expansion times corresponded to the transition phase from the LIG (∼0.14-0.12 Mya) to the LGM (∼0.021-0.018 Mya). The pre-LGM expansion model reflected a different pattern affecting the historical dynamics of the population of East Asian species caused by Pleistocene climatic changes. Interestingly, Group 2 exhibited a disjunctive distribution pattern. The possible reasons were introgression caused by female-biased dispersal or human phoresy during construction of the Forbidden City during the Ming Dynasty of China.
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Affiliation(s)
- Junli Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Haiguang Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Ning
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Yu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.
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Chen W, Schmidt BV, He S. The potential colonization histories of Opsariichthys bidens (Cyprinidae) in China using Bayesian binary MCMC analysis. Gene 2018; 676:1-8. [PMID: 29990506 DOI: 10.1016/j.gene.2018.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/13/2018] [Accepted: 07/06/2018] [Indexed: 11/19/2022]
Abstract
Vicariance and/or long-distance dispersal shape the distribution patterns of many extant taxa, and orogenesis and/or climate fluctuations are key factors that drive the events of vicariance and/or dispersal. In this study, we yielded biogeographical inferences from Bayesian binary MCMC (BBM) analysis to explore the potential colonization histories of Opsariichthys bidens in China and to identify potential factors responsible for the colonization histories. Many vicariance and dispersal events were identified. The results suggested that O. bidens seemed to have originated from the Yangtze River and/or the Pearl River and experienced a Yangtze River-Pearl River split at 7.04 million years ago (Ma). BBM analysis revealed that the Pearl River populations had undergone expansions to the Hainan drainages, the Lancangjiang River (upper Mekong) and the Nanpanjiang River (upper branch of the Pearl River) at 0.74 Ma. Meanwhile, the Yangtze River populations expanded to the northeastern drainages during the Early Pleistocene. Subsequently, the northeastern drainages dispersed to the Yellow River during the Middle Pleistocene. More recently, the northeastern drainage populations also dispersed to the Huaihe River and back to the Yangtze River. A portion of the Pearl River populations originated from the Yangtze River dispersed to the Jiulongjiang River during the Middle Pleistocene. These time scales fit well with the uplift of the Qinghai-Tibet Plateau and Pleistocene glacial cycles, indicating the two factors played vital roles in shaping the colonization histories of O. bidens.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Bjorn V Schmidt
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.
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30
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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31
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Jaisuk C, Senanan W. Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand. PeerJ 2018; 6:e4487. [PMID: 29568710 PMCID: PMC5845392 DOI: 10.7717/peerj.4487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/20/2018] [Indexed: 11/20/2022] Open
Abstract
Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (n = 30–100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P < 0.05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global FST = 0.022, P < 0.01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized FST (P < 0.05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R2 = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand.
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Affiliation(s)
- Chaowalee Jaisuk
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand.,Department of Animal Science and Fisheries, Faculty of Science and Agricultural Technology, Rajamangala University of Technology Lanna Nan Campus, Nan, Thailand
| | - Wansuk Senanan
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand
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32
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Li J, Wei S, Hu M, Luo Z, Zhao M, Wu H. Reflection of paleoclimate oscillations and tectonic events in the phylogeography of moustache toads in southern China. J Zool (1987) 2018. [DOI: 10.1111/jzo.12537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- J. Li
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - S. Wei
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - M. Hu
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - Z. Luo
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - M. Zhao
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - H. Wu
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
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33
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Chen W, Zhong Z, Dai W, Fan Q, He S. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China. BMC Evol Biol 2017; 17:216. [PMID: 28899345 PMCID: PMC5596851 DOI: 10.1186/s12862-017-1058-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. CONCLUSIONS Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zaixuan Zhong
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei Dai
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qi Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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Weigand H, Weiss M, Cai H, Li Y, Yu L, Zhang C, Leese F. Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species. Mol Ecol 2017; 26:5705-5715. [PMID: 28792677 DOI: 10.1111/mec.14292] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/20/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023]
Abstract
An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.
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Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Martina Weiss
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Huimin Cai
- BGI-Shenzhen, Shenzhen, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | | | - Lili Yu
- BGI-Shenzhen, Shenzhen, China
| | | | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
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Kotsakiozi P, Gloria-Soria A, Caccone A, Evans B, Schama R, Martins AJ, Powell JR. Tracking the return of Aedes aegypti to Brazil, the major vector of the dengue, chikungunya and Zika viruses. PLoS Negl Trop Dis 2017; 11:e0005653. [PMID: 28742801 PMCID: PMC5526527 DOI: 10.1371/journal.pntd.0005653] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/19/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Aedes aegypti, commonly known as "the yellow fever mosquito", is of great medical concern today primarily as the major vector of dengue, chikungunya and Zika viruses, although yellow fever remains a serious health concern in some regions. The history of Ae. aegypti in Brazil is of particular interest because the country was subjected to a well-documented eradication program during 1940s-1950s. After cessation of the campaign, the mosquito quickly re-established in the early 1970s with several dengue outbreaks reported during the last 30 years. Brazil can be considered the country suffering the most from the yellow fever mosquito, given the high number of dengue, chikungunya and Zika cases reported in the country, after having once been declared "free of Ae. aegypti". METHODOLOGY/PRINCIPAL FINDINGS We used 12 microsatellite markers to infer the genetic structure of Brazilian Ae. aegypti populations, genetic variability, genetic affinities with neighboring geographic areas, and the timing of their arrival and spread. This enabled us to reconstruct their recent history and evaluate whether the reappearance in Brazil was the result of re-invasion from neighboring non-eradicated areas or re-emergence from local refugia surviving the eradication program. Our results indicate a genetic break separating the northern and southern Brazilian Ae. aegypti populations, with further genetic differentiation within each cluster, especially in southern Brazil. CONCLUSIONS/SIGNIFICANCE Based on our results, re-invasions from non-eradicated regions are the most likely scenario for the reappearance of Ae. aegypti in Brazil. While populations in the northern cluster are likely to have descended from Venezuela populations as early as the 1970s, southern populations seem to have derived more recently from northern Brazilian areas. Possible entry points are also revealed within both southern and northern clusters that could inform strategies to control and monitor this important arbovirus vector.
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Affiliation(s)
- Panayiota Kotsakiozi
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Benjamin Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, IOC–Fiocruz, Rio de Janeiro, Brazil
| | - Ademir Jesus Martins
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, IOC-FIOCRUZ, Rio de Janeiro, Brazil
| | - Jeffrey R. Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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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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