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Lyu B, Liu Q, Wu Y, Nguyen TQ, Che J, Nguyen SN, Myers EA, Burbrink FT, Guo P, Wang J. Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae). Ecol Evol 2024; 14:e11278. [PMID: 38628918 PMCID: PMC11019134 DOI: 10.1002/ece3.11278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.
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Affiliation(s)
- Bing Lyu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Truong Q. Nguyen
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
- Vietnam Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Sang N. Nguyen
- Institute of Tropical BiologyVietnam Academy of Science and TechnologyHo Chi Minh CityVietnam
| | - Edward A. Myers
- Department of HerpetologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
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Tsai TS, Tsai IH, Qiu JL, Chan YY, Chiang YW. Comparative analysis of Deinagkistrodon acutus venom from Taiwan and China utilizing chromatographic, electrophoretic, and bioinformatic approaches, along with ELISA employing a monospecific antivenom. Toxicon 2024; 241:107663. [PMID: 38423218 DOI: 10.1016/j.toxicon.2024.107663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
Abstract
Deinagkistrodon acutus is a medically important pitviper inhabiting mainly South China and Taiwan. The hemorrhagic effects of its envenoming are compatible to its venom, which is abundant in metalloproteases (svMPs) and C-type lectin-like proteins. In this study, we investigated geographic variations in the venom of D. acutus collected from Taiwan and four Mainland Chinese provinces: Fujian, Jiangxi, Anhui, and Hunan. The variations were assessed through high-performance liquid chromatography, non-metric multidimensional scaling analysis, gel electrophoresis, and enzyme-linked immunosorbent assay (ELISA) with a monospecific antivenom (DaMAV) generated against the Taiwanese D. acutus venom, and discussed based on venom-protein sequences in databases and literature related to D. acutus venom. Additionally, the cross-reactivity of DaMAV against Crotalus horridus and Calloselasma rhodostoma venoms was investigated. We noted differential abundances of D. acutus venom metalloproteases, C-type lectin-like proteins, and phospholipase A2, along with point mutations and selective expression of serine protease isoforms. The ELISA results revealed that the venom from Taiwan was more reactive toward Taiwanese DaMAV than the four Mainland Chinese venoms, consistent with chromatographic profile differences, whereas C. horridus venom presented moderate cross-reactivity with DaMAV. The observed immunoreactivities of these venom with DaMAV can be attributed to the high prevalence of their PIII-svMPs, which are the dominant antigens, and the conservation of PIII-svMP epitopes.
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Affiliation(s)
- Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Pingtung, 912301, Taiwan.
| | - Inn-Ho Tsai
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106319, Taiwan
| | - Jing-Lin Qiu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Pingtung, 912301, Taiwan
| | - Yuen-Ying Chan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Pingtung, 912301, Taiwan
| | - Yu-Wei Chiang
- Department of Medical Research, Taipei Veterans General Hospital, No. 322, Sec. 2, Shipai Rd., Taipei, 112062, Taiwan; Department of Biology and Anatomy, National Defense Medical Centre, No. 161, Sec. 6, Minquan E. Rd., Taipei, 11490, Taiwan
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Tan KY, Shamsuddin NN, Tan CH. Sharp-nosed Pit Viper (Deinagkistrodon acutus) from Taiwan and China: A comparative study on venom toxicity and neutralization by two specific antivenoms across the Strait. Acta Trop 2022; 232:106495. [PMID: 35504314 DOI: 10.1016/j.actatropica.2022.106495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 11/01/2022]
Abstract
In East Asia, the Sharp-nosed Pit Viper (Deinagkistrodon acutus) is a medically important venomous snake in Taiwan and China, two geographical areas long separated by the Taiwan Strait. Yet, snake venom variation is little known between specimens found across the Strait. This study thus investigated the intra-species variation of D. acutus venoms from Taiwan (Da-Taiwan) and China (Da-China) in their profiles of gel electrophoresis, toxicity, immunoreactivity and neutralization effect by antivenom. Da-China venom exhibited higher procoagulant, hemorrhagic and lethal activities than Da-Taiwan venom, presumably attributed to the higher abundance of moderate-to-high molecular weight toxins (procoagulants and hemorrhagins) in the venom. The mono-specific antivenoms produced in Taiwan (DaMAV-Taiwan) and China (DaMAV-China) were immunoreactive toward both venoms, and were able to neutralize the venom toxicity to different extents. DaMAV-Taiwan was more efficacious in neutralizing the venom procoagulant and lethal effects, while DaMAV-China was more potent against hemorrhagic effect. The discrepancy in efficacy between the two antivenoms could be due to varying proportions of neutralizing antibodies in the respective products, influenced by techniques of antibody raising and purification. Further study is warranted to elucidate variation in the proteome and antigenicity of D. acutus venom between snakes from Taiwan and China.
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Population Genetic Structure of Chlorops oryzae (Diptera, Chloropidae) in China. INSECTS 2022; 13:insects13040327. [PMID: 35447769 PMCID: PMC9032139 DOI: 10.3390/insects13040327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023]
Abstract
Frequent outbreaks have made Chlorops oryzae one of the major pests of rice in some regions. In order to understand the ecological adaptation of C. oryzae at the molecular level, and provide a scientific basis for formulating management strategies, we used two molecular markers, COI and ITS1 sequences, to systematically analyze the genetic structure of 31 populations. The higher haplotype diversity and lower nucleotide diversity indicated that the C. oryzae populations experienced rapid expansion after a “Bottleneck effect”. The results of the mismatch distribution, neutrality test (Fu’s Fs < 0, p < 0.001), and haplotype network analysis suggested that the population has recently undergone an expansion. Although genetic differentiation among C. oryzae populations was found to have existed at low/medium levels (Fst: 0.183 for COI, 0.065 for ITS1), the frequent gene flow presented as well (Nm: 2.23 for COI, 3.60 for ITS1) was supposed to be responsible for frequent local outbreaks.
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Recombinase polymerase amplification combined with fast DNA extraction for on–spot identification of Deinagkistrodon acutus, a threatened species. ANIMAL BIODIVERSITY AND CONSERVATION 2022. [DOI: 10.32800/abc.2022.45.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study addresses the use of recombinase polymerase amplification combined with fast DNA extraction for on–spot identification of Deinagkistrodon acutus, a snake species threatened
due to over–exploitation and habitat destruction. For its conservation, an efficient species identification method is urgently neededto fight against illegal capture and trade. Fourteen individuals representing 12 snake species (including D. acutus and other snake species) were collected from mountainous regions in Southern China. Genomic DNA was extracted within five minutes by a modified alkaline lysis method. Species–specific primers for recombinase polymerase amplification (RPA) were designed based on the sequences of cytochrome C oxidase subunit I (COI) barcode region, and an optimized RPA assay system was set up. Specificity and sensitivity of the assay were checked, and the assay was validated by identifying 10 commercial Qi She crude drug samples derived from D. acutus. Under optimized RPA conditions, a distinct single band of 354 bp was amplified only for D. acutus but not for the related snake species. The entire procedure can be completed in 30 min at room temperature. Commercial Qi She crude drug identification validated effectiveness of the established assay system. Using a recombinase polymerase amplification (RPA) assay with rapid DNA extraction, we established an on–spot D. acutus identification method with good specificity and sensitivity. This method could become an efficient tool for rigorous supervision of illegal D. acutus capture and trade.
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Zhu G, Yang S, Savitzky AH, Cheng Y, Mori A, Ding L, Rao D, Wang Q. Cryptic diversity and phylogeography of the Rhabdophis nuchalis group (Squamata: Colubridae). Mol Phylogenet Evol 2021; 166:107325. [PMID: 34655748 DOI: 10.1016/j.ympev.2021.107325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022]
Abstract
Previous studies, have found that the rapid uplift of the Tibetan plateau accelerated the diversification of species. However, there are few relevant biogeographic data for the Colubridae in this region. We conducted a comprehensive study of the Rhabdophis nuchalis Group, which presently contains four nominal species, R. nuchalis, R. pentasupralabialis, R. leonardi, and R. chiwen. Building upon previous studies with specimens we have recently examined, greater interspecific and intraspecific diversity has been revealed. Here we address three questions: (1) Do the intraspecific differences represent only geographic variation within lineages, or are there cryptic species? (2) What are the interspecific relationships among members of the R. nuchalis Group? (3) What has been the biogeographic history of this species group? To resolve these questions we used four mitochondrial gene sequences and one nuclear sequence to investigate the molecular phylogenetic and geographic relationships among populations. Our molecular analysis reveals cryptic species diversity within the R. nuchalis Group, and seven clades were identified in the analysis. Ancestral area estimation suggests that the R. nuchalis Group originated in the Hengduan Mountains approximately 6.24 Mya and expanded its range northward to the Qinling-Daba Mountains. The Sichuan Basin appears to have been a barrier to migration. Species divergence seems to have been related to the rapid uplift of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Alan H Savitzky
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
| | - Yuqi Cheng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Li Ding
- Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu 610041, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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Guo K, Zhong J, Xie F, Zhu L, Qu Y, Ji X. Climate warming will increase chances of hybridization and introgression between two Takydromus lizards (Lacertidae). Ecol Evol 2021; 11:8573-8584. [PMID: 34257917 PMCID: PMC8258214 DOI: 10.1002/ece3.7671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022] Open
Abstract
Coexisting species may experience population and range changes alone or jointly in response to environmental change. Here, we used six climate variables and ten modeling algorithms to predict the distribution of two Takydromus species (T. septentrionalis and T. sexlineatus) in China. We identified the sympatric and allopatric areas by comparing projections between the two species based on habitat suitability under present and future climate scenarios. We constructed the hypervolumes of six climate variables for the two species and then evaluated overlaps between hypervolumes. From this study, we know the following. First, minimum temperature of coldest month contributes the most to the prediction of habitat suitability. Second, habitats suitable for the two species will shift northward in response to climate warming. Third, the range of T. sexlineatus will expand across the four future time intervals before 2,100, namely the 2021-2040, 2041-2060, 2061-2080, and 2081-2100 intervals, under both Shared socioeconomic pathway (SSP) 245 and SSP585 scenarios, and the range of T. septentrionalis will also expand in the future except at the 2081-2100 interval under the SSP585 scenario. Fourth, the sympatric areas will contract or expand under the SSP245 scenario and expand across the four future time intervals before 2,100 under the SSP585 scenario. Fifth, the niche hypervolumes of the two species partially overlapped, and the differences in niche centroid show some degree of niche differentiation between the two species. These results allow to conclude that climate warming will not only drive the northward drift of sympatric areas but also increase the size of these areas if nothing is done to limit the emission of greenhouse gases. Given the existence of hybridization and introgression between T. septentrionalis and T. sexlineatus in the field where they coexist, we also conclude that climate warming will increase chances of hybridization and introgression between the two species.
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Affiliation(s)
- Kun Guo
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jun Zhong
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Fan Xie
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yan‐Fu Qu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
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Zhang M, Cheng J, Sun Z, Kong H, Zhang Y, Wang S, Wang X, Zhao Y, Qu H. Protective Effects of Carbon Dots Derived from Phellodendri Chinensis Cortex Carbonisata against Deinagkistrodon acutus Venom-Induced Acute Kidney Injury. NANOSCALE RESEARCH LETTERS 2019; 14:377. [PMID: 31845094 PMCID: PMC6915193 DOI: 10.1186/s11671-019-3198-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/31/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND As an emerging nanomaterial, carbon dots (CDs) have been the focus of tremendous attention for biomedical applications. However, little information is available on their bioactivity of inhibiting acute kidney injury (AKI) induced by snake venom. METHODS This study reports the development of a green, one-step pyrolysis process to synthesize CDs using Phellodendri Chinensis Cortex (PCC) as the sole precursor, and their potential application as a protectant against Deinagkistrodon acutus (D. acutus) venom-induced AKI was investigated for the first time. The AKI model was established by injecting D. acutus venom into the abdominal cavity of mice and the potential protective effects of PCC Carbonisata-CDs (PCCC-CDs) on renal abnormalities including dysfunction, inflammatory reactions, tissue damage, and thrombocytopenia at six time points (1, 3, and 12 h, and 1, 2, and 5 days) were investigated. RESULTS These results demonstrated that PCCC-CDs significantly inhibited the kidney dysfunction (reduced serum creatinine (SCR), blood urea nitrogen (BUN), urinary total protein (UTP), and microalbuminuria (MALB) concentrations) and the production of chemoattractant (monocyte chemotactic protein 1 (MCP-1)), proinflammatory cytokines (interleukin (IL)-1β), and anti-inflammatory cytokine (IL-10) in response to intraperitoneal injection of D. acutus venom. The beneficial effect of PCCC-CDs on the envenomed mice was similar to that on the change in renal histology and thrombocytopenia. CONCLUSIONS These results demonstrated the remarkable protective effects of PCCC-CDs against AKI induced by D. acutus venom, which would not only broaden the biomedical applications of CDs but also provide a potential target for the development of new therapeutic drugs for AKI induced by D. acutus snakebite envenomation.
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Affiliation(s)
- Meiling Zhang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jinjun Cheng
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Ziwei Sun
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Hui Kong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yue Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Suna Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoke Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yan Zhao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Huihua Qu
- Center of Scientific Experiment, Beijing University of Chinese Medicine, Beijing, 100029, China
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Wang DQ, Pan LL, Yang DC, Dai LL. Complete mitochondrial genome of the sharp-snouted pitviper Deinagkistrodon acutus (Reptilia, Viperidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2900-2901. [PMID: 33365782 PMCID: PMC7706857 DOI: 10.1080/23802359.2019.1660593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The sharp-snouted pitviper, Deinagkistrodon acutus, belongs to the monotypic genus Deinagkistrodon of the family Viperidae. It is one of the important species of snakes for its commercial and medicinal value. Complete mitochondrial genome sequence of the D. acutus was sequenced by next-generation sequencing technology. The total mitochondrial genome is 17,538 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 control regions. Most of the genes of D. acutus are encoded on the H-strand, except for the ND6 subunit gene and eight tRNA genes which distribute on the L-strand. Phylogenetic reconstruction result indicated that our newly determined mitochondrial genome sequence could meet the demands. The complete mitochondrial genome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of D. acutus.
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Affiliation(s)
- De-Qing Wang
- College of Life and Environment Sciences, Huangshan University, Huangshan, P. R. China
| | - Li-Li Pan
- College of Life and Environment Sciences, Huangshan University, Huangshan, P. R. China
| | - Dian-Cheng Yang
- College of Life and Environment Sciences, Huangshan University, Huangshan, P. R. China
| | - Liang-Liang Dai
- College of Life and Environment Sciences, Huangshan University, Huangshan, P. R. China
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Dong W, Wang D, Tian H, Pu Y, Yu L, Duan X, Liu S, Chen D. Genetic structure of two sympatric gudgeon fishes ( Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin. PeerJ 2019; 7:e7393. [PMID: 31404431 PMCID: PMC6688597 DOI: 10.7717/peerj.7393] [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: 10/31/2018] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
Background Xenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions. Methods In the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including F ST and F is, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history. Results Xenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa. Discussion The genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.
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Affiliation(s)
- Weiwei Dong
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China.,Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Dengqiang Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Huiwu Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Yan Pu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China.,Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Lixiong Yu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Xinbin Duan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Shaoping Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Daqing Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
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Ratnarathorn N, Harnyuttanakorn P, Chanhome L, Evans SE, Day JJ. Geographical differentiation and cryptic diversity in the monocled cobra,
Naja kaouthia
(Elapidae), from Thailand. ZOOL SCR 2019. [DOI: 10.1111/zsc.12378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Napat Ratnarathorn
- Department of Cell and Developmental Biology University College London London UK
- Department of Biology, Faculty of Science Chulalongkorn University Bangkok Thailand
- Snake Farm Queen Saovabha Memorial Institute Bangkok Thailand
| | | | - Lawan Chanhome
- Snake Farm Queen Saovabha Memorial Institute Bangkok Thailand
| | - Susan E. Evans
- Department of Cell and Developmental Biology University College London London UK
| | - Julia J. Day
- Department of Cell and Developmental Biology University College London London UK
- Department of Genetics, Evolution and Environment University College London London WC1E 6BT UK
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Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia. Mol Phylogenet Evol 2018; 133:82-91. [PMID: 30594733 DOI: 10.1016/j.ympev.2018.12.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 12/13/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
Abstract
Understanding the influence of geographical events and climate changes on genetic diversity is essential in explaining current patterns of genetic structure and geographic distribution of organisms. We inferred phylogenetic relationships, investigated historical demography, explored the evolutionary history, and clarified intraspecific taxonomy of Protobothrops mucrosquamatus, which is one of the commonest and most wide-ranging Asian pitvipers. A total of 184 samples from 54 localities were sequenced and analyzed for two mitochondrial gene fragments and two nuclear genes. Phylogenetic reconstruction based on mtDNA sequences revealed the existence of a minimum of five geographically structured and well-supported lineages within P. mucrosquamatus. Based on the mtDNA gene tree, and the geographic relationship between populations allied by matrilineal lineages, a complex longitudinal and latitudinal diversification pattern was uncovered in P. mucrosquamatus. The estimated date of the origin of the species (about 5.3 Ma) and divergence of the intraspecific lineages match the rapid uplifting of Qinghai-Xizang Plateau, and is also consistent with those of some other co-distributed Asian pitvipers. Formation of the two island lineages (Taiwan and Hainan) was generally congruent with the first isolation of the islands, but the two lineages showed different relationships with the continental Asian populations in comparison with some other pitvipers. Population historical demographic analyses, based on three methods, showed that all lineages have experienced slight population expansion in and around the Dali Glacial. Tests of intraspecific taxonomy indicated that no cryptic taxon is present within this widely distributed snake.
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Zhang T, Wang Y, Ye P, Liu J, Cheng Y, Wang S, Rohozinski J, Zhang Y, Yu A. Three-dimensional computed tomography reconstructive diagnosis of snakebite-induced cerebral infarction. JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2018; 26:165-169. [PMID: 29480239 DOI: 10.3233/xst-17348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite common injury caused by snakebite, snakebite-induced ischemic stroke is rare. We reported on a patient who incurred a large cerebral infarction after being bitten by a Deinagkistrodon acutus, one of the most poisonous snakes in the southwestern of China. Applying 3D computed tomography (CT) of head combined with cerebral angiography examinations showed a large cerebral infarction, hernia in the right brain, developmental abnormalities of the right middle cerebral artery and cerebral artery of right brain. In conclusion, head CT imaging combined with cerebral angiography provides an efficient approach in diagnosis of stroke caused by snakebites.
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Affiliation(s)
- Tianxi Zhang
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Yan Wang
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Peng Ye
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Jiaji Liu
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Yun Cheng
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Shuhong Wang
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Jan Rohozinski
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Yuanyuan Zhang
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
| | - Anyong Yu
- Department of Emergency, The First Affiliated Hospital of Zunyi Medical College, Guizhou, China
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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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Suntrarachun S, Chanhome L, Sumontha M. Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0802.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: Snakes possess adaptive characteristics of morphology that may result in incorrect reconstruction of phylogeny. Molecular approaches have become the major source of new information for advancing our understanding of evolutionary, genetic relationships, and species identification.
Objective: We studied DNA sequences of Ophiophagus hannah in different parts of Thailand and compared them with those of O. hannah from other countries.
Materials and Methods: We studied the mitochondrial NADH dehydrogenase subunit 2 (ND2) and control region (CR) sequences of 12 individuals O. hannah from different localities across Thailand. Phylogenetic analysis of DNA sequences were compared to the published sequences of O. hannah deposited in NCBI GenBank database from other countries.
Results: O. hannah could be categorized into 2 Clades, 5 haplotypes, and 4 localities based on 43 different nucleotide positions from the 736 bp of ND2 and 673 bp of CR. Clade A was haplotype A from southern Thailand. Clade B consisted of haplotypes B, C, D, and E. Haplotype B and C came from northern Thailand. Haplotype D came from western Thailand, while haplotype E was O. hannah from central Thailand. The DNA sequences of Clade B were similar to the sequences of O. hannah in Myanmar and southern China that are already deposited in NCBI GenBank database.
Conclusion: We found a different genotype of O. hannah from southern Thailand and suggest that this may be a new species of O. hannah.
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Affiliation(s)
- Sunutcha Suntrarachun
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Lawan Chanhome
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
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Zheng X, Zhou TQ, Wan T, Perdices A, Yang JQ, Tang XS, Wang ZP, Huang LQ, Huang S, He SP. Huangshan population of Chinese Zacco platypus (Teleostei, Cyprinidae) harbors diverse matrilines and high genetic diversity. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2017; 37:103-9. [PMID: 27029868 DOI: 10.13918/j.issn.2095-8137.2016.2.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Six main mitochondrial DNA (mtDNA) lineages have been described in minnow (Zacco platypus) samples obtained from northern, western and southern China. Perdices et al. (2004) predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b (cytb) sequence variations. Combined with reported data in GenBank, we identified ten matrilines (Zacco A-J) in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus.
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Affiliation(s)
- Xin Zheng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China; College of Life and Environment Sciences, Huangshan University, Huangshan Anhui 245041, China
| | - Tian-Qi Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China; College of Life and Environment Sciences, Huangshan University, Huangshan Anhui 245041, China
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Anabel Perdices
- Museo Nacional de Ciencias Naturales, CSIC, C/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Xin-Sheng Tang
- College of Life and Environment Sciences, Huangshan University, Huangshan Anhui 245041, China
| | - Zheng-Ping Wang
- College of Foreign Languages, Huangshan University, Huangshan Anhui 245041, China
| | - Li-Qun Huang
- Landscaping Bureau of Huangshan Scenic Area, Huangshan Anhui 245000, China
| | - Song Huang
- College of Life and Environment Sciences, Huangshan University, Huangshan Anhui 245041, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
| | - Shun-Ping He
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan Hubei 430072, China.
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Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, Che J, Zhang L, Ziegler T, Nguyen TQ, Burbrink FT. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri(Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Mol Ecol 2016; 25:2920-36. [DOI: 10.1111/mec.13658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Guo
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Qin Liu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Fei Zhu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Guang H. Zhong
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Xin Chen
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Edward A. Myers
- Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Avenue New York NY 10016 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Menglun Mengla Yunnan 666303 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Thomas Ziegler
- AG Zoologischer Garten Köln; Riehler Strasse 173 D-50735 Cologne Germany
| | - Truong Q. Nguyen
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Street Hanoi Vietnam
| | - Frank T. Burbrink
- Department of Herpetology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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18
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Zhu F, Liu Q, Che J, Zhang L, Chen X, Yan F, Murphy R, Guo C, Guo P. Molecular phylogeography of white-lipped tree viper (Trimeresurus; Viperidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fei Zhu
- Sichuan Key Laboratory of Bio-resources and Eco-enviroment; Ministry of Education, College of Life Sciences; Sichuan University; Chengdu, Sichuan 610065 China
| | - Qin Liu
- Department of Life Sciences and Food Engineering; Yibin University; , 8 Jiusheng Rd, 1 4 Wuliangye Ave., Yibin, Sichuan 644007 China
| | - Jing Che
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Kunming, Yunnan 650223 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou, Guangdong 510260 China
| | - Xin Chen
- Department of Biology; The College of Staten Island; The City University of New York, Staten Island; NY 10314 USA
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Kunming, Yunnan 650223 China
| | - Robert Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Kunming, Yunnan 650223 China
| | - Cong Guo
- Sichuan Key Laboratory of Bio-resources and Eco-enviroment; Ministry of Education, College of Life Sciences; Sichuan University; Chengdu, Sichuan 610065 China
| | - Peng Guo
- Department of Life Sciences and Food Engineering; Yibin University; , 8 Jiusheng Rd, 1 4 Wuliangye Ave., Yibin, Sichuan 644007 China
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Li Y, Wu X, Zhang H, Yan P, Xue H, Wu X. Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae). PLoS One 2015; 10:e0138757. [PMID: 26394403 PMCID: PMC4578928 DOI: 10.1371/journal.pone.0138757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/03/2015] [Indexed: 11/26/2022] Open
Abstract
Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.
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Affiliation(s)
- Yongmin Li
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- School of Life Sciences, Fuyang Teachers College, Fuyang, Anhui, China
| | - Xiaoyou Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Huabin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Xue
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xiaobing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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20
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The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences. PLoS One 2014; 9:e106944. [PMID: 25184236 PMCID: PMC4153689 DOI: 10.1371/journal.pone.0106944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/12/2014] [Indexed: 11/28/2022] Open
Abstract
The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two “star” clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent.
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Lu G, Lin A, Luo J, Blondel DV, Meiklejohn KA, Sun K, Feng J. Phylogeography of the Rickett's big-footed bat, Myotis pilosus (Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China. BMC Evol Biol 2013; 13:241. [PMID: 24188176 PMCID: PMC4228257 DOI: 10.1186/1471-2148-13-241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 10/29/2013] [Indexed: 12/03/2022] Open
Abstract
Background China is characterized by complex topographic structure and dramatic palaeoclimatic changes, making species biogeography studies particularly interesting. Previous researchers have also demonstrated multiple species experienced complex population histories, meanwhile multiple shelters existed in Chinese mainland. Despite this, species phylogeography is still largely unexplored. In the present study, we used a combination of microsatellites and mitochondrial DNA (mtDNA) to investigate the phylogeography of the east Asian fish-eating bat (Myotis pilosus). Results Phylogenetic analyses showed that M. pilosus comprised three main lineages: A, B and C, which corresponded to distinct geographic populations of the Yangtze Plain (YTP), Sichuan Basin (SCB) and North and South of China (NSC), respectively. The most recent common ancestor of M. pilosus was dated as 0.25 million years before present (BP). Population expansion events were inferred for populations of Clade C, North China Plain region, Clade B and YunGui Plateau region at 38,700, 15,900, 4,520 and 4,520 years BP, respectively. Conflicting results were obtained from mtDNA and microsatellite analyses; strong population genetic structure was obtained from mtDNA data but not microsatellite data. The microsatellite data indicated that genetic subdivision fits an isolation-by-distance (IBD) model, but the mtDNA data failed to support this model. Conclusions Our results suggested that Pleistocene climatic oscillations might have had a profound influence on the demographic history of M. pilosus. Spatial genetic structures of maternal lineages that are different from those observed in other sympatric bats species may be as a result of interactions among special population history and local environmental factors. There are at least three possible refugia for M. pilosus during glacial episodes. Apparently contradictory genetic structure patterns of mtDNA and microsatellite could be explained by male-mediated gene flow among populations. This study also provides insights on the necessity of conservation of M. pilosus populations to conserve this genetic biodiversity, especially in the areas of YTP, SCB and NSC regions.
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Affiliation(s)
| | | | | | | | | | - Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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Ongoing speciation in the Tibetan plateau Gymnocypris species complex. PLoS One 2013; 8:e71331. [PMID: 23977018 PMCID: PMC3744573 DOI: 10.1371/journal.pone.0071331] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/28/2013] [Indexed: 11/30/2022] Open
Abstract
Local adaptation towards divergent ecological conditions often results in genetic differentiation and adaptive phenotypic divergence. To illuminate the ecological distinctiveness of the schizothoracine fish, we studied a Gymnocypris species complex consisting of three morphs distributed across four bodies of water (the Yellow River, Lake Qinghai, the Ganzi River and Lake Keluke) in the Northeast Tibetan Plateau. We used a combination of mitochondrial (16S rRNA and Cyt b) and nuclear (RAG-2) genetic sequences to investigate the phylogeography of these morphs based on a sample of 277 specimens. Analysis of gill rakers allowed for mapping of phenotypic trajectories along the phylogeny. The phylogenetic and morphological analyses showed that the three sparsely rakered morphs were present at two extremes of the phylogenetic tree: the Yellow River morphs were located at the basal phylogenetic split, and the Lake Keluke and Ganzi River morphs at the peak, with the densely rakered Lake Qinghai morphs located between these two extremes. Age estimation further indicated that the sparsely rakered morphs constituted the oldest and youngest lineages, whereas the densely rakered morph was assigned to an intermediate-age lineage. These results are most compatible with the process of evolutionary convergence or reversal. Disruptive natural selection due to divergent habitats and dietary preferences is likely the driving force behind the formation of new morphs, and the similarities between their phenotypes may be attributable to the similarities between their forms of niche tracking associated with food acquisition. This study provides the first genetic evidence for the occurrence of convergence or reversal in the schizothoracine fish of the Tibetan Plateau at small temporal scales.
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Blair C, Davy CM, Ngo A, Orlov NL, Shi HT, Lu SQ, Gao L, Rao DQ, Murphy RW. Genealogy and Demographic History of a Widespread Amphibian throughout Indochina. J Hered 2012; 104:72-85. [PMID: 23125408 DOI: 10.1093/jhered/ess079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND1 and cytochrome b and tested hypotheses pertaining to climate, geology, and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio-Pleistocene diversification, with the former corresponding to periods of increased aridity and the onset of monsoonal weather systems. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia, suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina and further clarified the evolutionary history of lineages within P. leucomystax.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Wu Y, Wang Y, Jiang K, Hanken J. Significance of pre-Quaternary climate change for montane species diversity: insights from Asian salamanders (Salamandridae: Pachytriton). Mol Phylogenet Evol 2012; 66:380-90. [PMID: 23110935 DOI: 10.1016/j.ympev.2012.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 01/20/2023]
Abstract
Despite extensive focus on the genetic legacy of Pleistocene glaciation, impacts of earlier climatic change on biodiversity are poorly understood. Because amphibians are highly sensitive to variations in precipitation and temperature, we use a genus of Chinese montane salamanders (Salamandridae: Pachytriton) to study paleoclimatic change in East Asia, which experienced intensification of its monsoon circulation in the late Miocene associated with subsequent Pliocene warming. Using both nuclear and mitochondrial DNA sequences, we reconstruct the species tree under a coalescent model and demonstrate that all major lineages originated before the Quaternary. Initial speciation within the genus occurred after the summer monsoon entered a stage of substantial intensification. Heavy summer precipitation established temporary water connectivity through overflows between adjacent stream systems, which may facilitate geographic range expansion by aquatic species such as Pachytriton. Species were formed in allopatry likely through vicariant isolation during or after range expansion. To evaluate the influence of Pliocene warming on these cold-adapted salamanders, we construct a novel temperature buffer-zone model, which suggests widespread physiological stress or even extinction during the warming period. A significant deceleration of species accumulation rate is consistent with Pliocene range contraction, which affected P. granulosus and P. archospotus the most because they lack large temperature buffer zones. In contrast, demographic growth occurred in species for which refugia persist. The buffer-zone model reveals the Huangshan Mountain as a potential climatic refugium, which is similar to that found for other East Asian organisms. Our approach can incorporate future climatic data to evaluate the potential impact of ongoing global warming on montane species (particularly amphibians) and to predict possible population declines.
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Affiliation(s)
- Yunke Wu
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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Testing Hypotheses of Pleistocene Population History Using Coalescent Simulations: Refugial Isolation and Secondary Contact in Pseudepidalea raddei (Amphibia: Bufonidae). ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence. PLoS One 2012; 7:e36334. [PMID: 22558439 PMCID: PMC3338645 DOI: 10.1371/journal.pone.0036334] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/03/2012] [Indexed: 11/29/2022] Open
Abstract
An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization.
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Cai Y, Yan J, Xu X, Lin Z, Ji X. Mitochondrial DNA phylogeography reveals a west–east division of the northern grass lizard (
Takydromus septentrionalis
) endemic to China. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00655.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yao Cai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
- School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing, Jiangsu
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
| | - Xue‐Feng Xu
- School of Life Sciences and Food Engineering, Chuzhou University, Chuzhou, Anhui
| | - Zhi‐Hua Lin
- School of Ecology, Lishui University, Lishui, Zhejiang, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
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Tibetan Plateau Relict Snakes of the Genus Thermophis and Their Relationship to New World Relict Snakes. ASIAN HERPETOL RES 2011. [DOI: 10.3724/sp.j.1245.2011.00161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Li T, Zhang M, Qu Y, Ren Z, Zhang J, Guo Y, Heong KL, Villareal B, Zhong Y, Ma E. Population genetic structure and phylogeographical pattern of rice grasshopper, Oxya hyla intricata, across Southeast Asia. Genetica 2011; 139:511-24. [PMID: 21505761 DOI: 10.1007/s10709-011-9573-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 04/02/2011] [Indexed: 11/28/2022]
Abstract
The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu's F (s) values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.
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Affiliation(s)
- Tao Li
- Institute of Applied Biology, Shanxi University, 030006 Taiyuan, Shanxi, China
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DING LI, GAN XIAONI, HE SHUNPING, ZHAO ERMI. A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene. Mol Ecol 2011; 20:1905-22. [DOI: 10.1111/j.1365-294x.2011.05060.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau. Mol Phylogenet Evol 2009; 53:1025-31. [DOI: 10.1016/j.ympev.2009.03.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 03/11/2009] [Indexed: 11/15/2022]
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ZHAO KAI, DUAN ZIYUAN, PENG ZUOGANG, GUO SONGCHANG, LI JUNBING, HE SHUNPING, ZHAO XINQUAN. The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake. Mol Ecol 2009; 18:3616-28. [DOI: 10.1111/j.1365-294x.2009.04274.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Song G, Qu Y, Yin Z, Li S, Liu N, Lei F. Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations. BMC Evol Biol 2009; 9:143. [PMID: 19558699 PMCID: PMC2714695 DOI: 10.1186/1471-2148-9-143] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 06/27/2009] [Indexed: 11/10/2022] Open
Abstract
Background The role of Pleistocene glacial oscillations in current biodiversity and distribution patterns varies with latitude, physical topology and population life history and has long been a topic of discussion. However, there had been little phylogeographical research in south China, where the geophysical complexity is associated with great biodiversity. A bird endemic in Southeast Asia, the Grey-cheeked Fulvetta, Alcippe morrisonia, has been reported to show deep genetic divergences among its seven subspecies. In the present study, we investigated the phylogeography of A. morrisonia to explore its population structure and evolutionary history, in order to gain insight into the effect of geological events on the speciation and diversity of birds endemic in south China. Results Mitochondrial genes cytochrome b (Cytb) and cytochrome c oxidase I (COI) were represented by 1236 nucleotide sites from 151 individuals from 29 localities. Phylogenetic analysis showed seven monophyletic clades congruent with the geographically separated groups, which were identified as major sources of molecular variance (90.92%) by AMOVA. TCS analysis revealed four disconnected networks, and that no haplotype was shared among the geographical groups. The common ancestor of these populations was dated to 11.6 Mya and several divergence events were estimated along the population evolutionary history. Isolation by distance was inferred by NCPA to be responsible for the current intra-population genetic pattern and gene flow among geographical groups was interrupted. A late Pleistocene demographic expansion was detected in the eastern geographical groups, while the expansion time (0.2–0.4 Mya) was earlier than the Last Glacial Maximum. Conclusion It is proposed that the complicated topology preserves high genetic diversity and ancient lineages for geographical groups of A. morrisonia in China mainland and its two major islands, and restricts gene exchange during climate oscillations. Isolation by distance seems to be an important factor of genetic structure formation within geographical populations. Although glacial influence to population fluctuation was observed in late Pleistocene, it seems that populations in eastern China were more susceptible to climate change, and all geographical groups were growing stably through the Last Glacial Maximum. Coalescence analysis suggested that the ancestor of A. morrisonia might be traced back to the late Miocene, and the current phylogeographical structure of A. morrisonia is more likely to be attributable to a series geological events than to Pleistocene glacial cycles.
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Affiliation(s)
- Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 PR, China.
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Walker MJ, Stockman AK, Marek PE, Bond JE. Pleistocene glacial refugia across the Appalachian Mountains and coastal plain in the millipede genus Narceus: evidence from population genetic, phylogeographic, and paleoclimatic data. BMC Evol Biol 2009; 9:25. [PMID: 19183468 PMCID: PMC2652443 DOI: 10.1186/1471-2148-9-25] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 01/30/2009] [Indexed: 11/16/2022] Open
Abstract
Background Species that are widespread throughout historically glaciated and currently non-glaciated areas provide excellent opportunities to investigate the role of Pleistocene climatic change on the distribution of North American biodiversity. Many studies indicate that northern animal populations exhibit low levels of genetic diversity over geographically widespread areas whereas southern populations exhibit relatively high levels. Recently, paleoclimatic data have been combined with niche-based distribution modeling to locate possible refugia during the Last Glacial Maximum. Using phylogeographic, population, and paleoclimatic data, we show that the distribution and mitochondrial data for the millipede genus Narceus are consistent with classical examples of Pleistocene refugia and subsequent post-glacial population expansion seen in other organismal groups. Results The phylogeographic structure of Narceus reveals a complex evolutionary history with signatures of multiple refugia in southeastern North America followed by two major northern expansions. Evidence for refugial populations were found in the southern Appalachian Mountains and in the coastal plain. The northern expansions appear to have radiated from two separate refugia, one from the Gulf Coastal Plain area and the other from the mid-Atlantic coastal region. Distributional models of Narceus during the Last Glacial Maximum show a dramatic reduction from the current distribution, with suitable ecological zones concentrated along the Gulf and Atlantic coastal plain. We found a strong correlation between these zones of ecological suitability inferred from our paleo-model with levels of genetic diversity derived from phylogenetic and population estimates of genetic structuring. Conclusion The signature of climatic change, during and after the Pleistocene, on the distribution of the millipede genus Narceus is evident in the genetic data presented. Niche-based historical distribution modeling strengthens the conclusions drawn from the genetic data and proves useful in identifying probable refugia. Such interdisciplinary biogeographic studies provide a comprehensive approach to understanding these processes that generate and maintain biodiversity as well as the framework necessary to explore questions regarding evolutionary diversification of taxa.
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Affiliation(s)
- Matt J Walker
- East Carolina University, Department of Biology, Howell Science Complex N211, Greenville, NC 27858, USA.
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