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Chen S, Du Z, Zhao P, Wang X, Wu Y, Li H, Cai W. Phylogeographic Pattern of the Assassin Bug Sycanus bifidus Inferred from Mitochondrial Genomes and Nuclear Genes. BIOLOGY 2024; 13:305. [PMID: 38785787 PMCID: PMC11118239 DOI: 10.3390/biology13050305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
The assassin bug Sycanus bifidus has a wide distribution across southern China. This study explored its distribution and evolution by analyzing mitochondrial and nuclear ribosomal RNA genes, revealing how Pleistocene climate and geological changes shaped its phylogeography. We identified two main clades, A and B, that diverged in the Middle Pleistocene. Hainan Island's populations form a unique group within Clade A, suggesting that the Qiongzhou Strait served as a dispersal corridor during glaciation. Rising sea levels likely separated the Hainan population afterward. Ecological niche modeling showed that both populations have been viable since the last interglacial period, with demographic analyses indicating possible expansions during the Middle and Late Pleistocene, driven by favorable climates. This study highlights the significant effects of Pleistocene sea-level and climatic changes on the distribution and evolution of S. bifidus in China.
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Affiliation(s)
- Suyi Chen
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Zhenyong Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Ping Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Ministry of Education) and Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China;
- Department of Plant Protection, Kaili University, Kaili 556000, China
| | - Xuan Wang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yunfei Wu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China;
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
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2
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Moon Y, Kim C, Yoon S, Kang W. Identification of Risk Areas for Gloydius Snakebites in South Korea. Animals (Basel) 2023; 13:1959. [PMID: 37370469 DOI: 10.3390/ani13121959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Snakebites can pose a significant threat to human health as the destruction of natural habitats and increased human intrusion into ecosystems result in more frequent encounters with snakes. Mitigation measures for snakebites are particularly crucial for hiking trails where transportation of snakebite victims to medical facilities is challenging due to limited emergency resources and difficult access. This study employed a random forest-based species distribution model approach to investigate the potential habitats of Gloydius spp., specifically Gloydius saxatilis, Gloydius brevicaudus, and Gloydius ussuriensis, in South Korea and to assess the snakebite risk in national parks. Potential habitats of Gloydius spp. were identified and visualized by overlaying binary maps derived from species distribution models (SDMs) of each Gloydius spp. that corresponded to high-risk snakebite areas. In addition, hiking trails with high snakebite risk in the national parks were identified after demonstrating the statistical correlation between the potential habitat distribution of Gloydius spp. and the actual snakebite incidents in major regions of South Korea. The primary environmental variables determining Gloydius spp. habitat were the topographic position index, slope, and the annual average of the maximum and minimum temperatures. The potential habitat of G. saxatilis generally appeared in high-altitude mountainous areas, mostly in the eastern part of the study area. Favorable habitats for G. brevicaudus and G. ussuriensis were predominantly located in mountainous areas throughout the study area, with the exception of some high-altitude mountainous terrain in the east. The number of snakebite incidents per 10,000 people was significantly correlated with the area ratio of Gloydius spp. potential habitat (Spearman's rho = 0.638, p < 0.01). The proportion of snakebite risk areas among national parks in South Korea ranged from 18% to 57%. This study can support practical solutions to prevent injuries and fatalities among hikers due to snakebites by identifying areas with a high risk of snakebite accidents at the hiking-trail level.
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Affiliation(s)
- Youngjoo Moon
- Department of Forest Resources, Graduate School, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 02707, Republic of Korea
| | - Chaewan Kim
- Department of Forest Resources, Graduate School, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 02707, Republic of Korea
| | - Sungsoo Yoon
- Ecological Information Team, National Institute of Ecology, 1210 Geumgang-ro, Seocheon-gun 33657, Republic of Korea
| | - Wanmo Kang
- Department of Forest Environment and Systems, College of Science and Technology, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 02707, Republic of Korea
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3
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Jiang Y, Yan S, Luo T, Xiao N, Deng H, Zhou J. Large mountains make small barriers: Species composition and spatial dynamics history of the
Odorrana schmackeri
complex in the karst area of Guizhou, China. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Yu Jiang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences Xiamen University Xiamen China
- School of Life Sciences Guizhou Normal University Guiyang China
| | - Shasha Yan
- School of Karst Sciences Guizhou Normal University Guiyang China
| | - Tao Luo
- School of Life Sciences Guizhou Normal University Guiyang China
| | - Ning Xiao
- Guiyang Healthcare Vocational University Guiyang China
| | - Huaiqing Deng
- School of Life Sciences Guizhou Normal University Guiyang China
| | - Jiang Zhou
- School of Karst Sciences Guizhou Normal University Guiyang China
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4
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Lee YS, Do MS, Kim W, Jeon HS, Lee SC, Jung JH, An J. Phylogenetic relationships between three Korean pit viper Gloydius (Serpentes: Crotalinae) species using mitochondrial DNA genes. Genes Genomics 2022; 44:517-526. [PMID: 35195889 DOI: 10.1007/s13258-022-01222-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/20/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Molecular phylogenetic studies of the Asian pit viper genus Gloydius have been widely published in Asia, but Korea population have not been conducted till date. OBJECTIVE This study aimed to analyze the phylogenetic relationships of three Gloydius species (G. saxatilis, G. brevicaudus, and G. ussuriensis) from Korea with other Gloydius species, based on Cytochrome b and ND4. METHODS We compared 160 samples representing the three species with those of 17 reference species and their phylogenetic status and genetic diversity were analyzed with concatenated sequences of two mitochondrial DNA. RESULTS Korean G. brevicaudus and G. saxatilis showed high haplotype diversity and relatively low and moderate nucleotide diversity, respectively. Although G. ussuriensis showed high genetic diversity, it was low in the Baengnyeong Island population. The phylogenetic tree represented two major lineages. One major lineage comprised G. ussuriensis, G. tsushimaensis, G. blomhoffii, and G. brevicaudus. The Chinese G. ussuriensis belonged to the same clade as the Korean G. ussuriensis and was closely related to the Baengnyeong Island population. Moreover, G. tsushimaensis was closely related to G. ussuriensis from southwestern Korean and Jeju Island populations. The other major lineage comprised the remaining 12 species and G. saxatilis. Korean G. saxatilis was closely related to G. saxatilis, G. shedanoensis, and G. intermedius from China. CONCLUSION The phylogenetic status of the Korean Gloydius species in comparison with the other Gloydius species was identified. We suggesting the conservation management unit for the Baengnyeong Island population, while the current conservation status of Korean G. saxatilis is suggested to be revised to a higher level.
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Affiliation(s)
- Yun Sun Lee
- National Migratory Birds Center, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Min Seock Do
- Animal Resources Division, National Institute of Biological Resources, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Wanggyu Kim
- Animal Resources Division, National Institute of Biological Resources, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Hye Sook Jeon
- Animal Resources Division, National Institute of Biological Resources, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Sang-Cheol Lee
- Department of Biology, Incheon National University, Incheon, Republic of Korea
| | - Ji-Hwa Jung
- Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea.
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5
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Hu Y, Li S, Liu H, Kim ST, Kurenshchikov DK, Hou Z. Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia. Mol Ecol 2021; 31:343-355. [PMID: 34657344 DOI: 10.1111/mec.16223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 01/12/2023]
Abstract
Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27 Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.
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Affiliation(s)
- Yueyao Hu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongguang Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Seung-Tae Kim
- Life and Environment Research Institute, Konkuk University, Seoul, Republic of Korea
| | - Dmitry K Kurenshchikov
- Laboratory of the Animal Ecology, Institute of Water and Ecology Problems, Far East Branch of the Russian Academy of Sciences, Khabarovsk, Russia
| | - Zhonge Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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6
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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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7
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Borzée A, Litvinchuk SN, Ri K, Andersen D, Nam TY, Jon GH, Man HS, Choe JS, Kwon S, Othman SN, Messenger K, Bae Y, Shin Y, Kim A, Maslova I, Luedtke J, Hobin L, Moores N, Seliger B, Glenk F, Jang Y. Update on Distribution and Conservation Status of Amphibians in the Democratic People's Republic of Korea: Conclusions Based on Field Surveys, Environmental Modelling, Molecular Analyses and Call Properties. Animals (Basel) 2021; 11:2057. [PMID: 34359183 PMCID: PMC8300379 DOI: 10.3390/ani11072057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Determining the range, status, ecology and behaviour of species from areas where surveys and samplings are uncommon or difficult to conduct is a challenge, such as in the Democratic People's Republic of Korea (DPR Korea). Here, we used genetic samples, field surveys, call recordings, photographic identification and a literature review to estimate the presence, range and status of amphibians in the DPR Korea. From our combined results and based on the IUCN Red List categories and criteria, we were able to estimate the national threat levels for most species. Our results demonstrated the presence of 18 native species and the suspected presence of Karsenia koreana and two Onychodactylus species. We reported the first record for Rana uenoi in the vicinity of Pyongyang using molecular tools and similarly confirmed the presence of Dryophytes japonicus at the same location. Based on distribution and modelling, we can expect the contact zone between species within the Rana and Onychodactylus genera to be located along the Changbai Massif, a mountain range that marks a shift in ecoregions and acts as a barrier to dispersion. The species richness was higher in the lowlands and at lower latitudes, with such areas populated by up to 11 species, while more northern regions were characterised by species richness of about half of that value. The combination of ecological models and known threats resulted in the recommendation of ten species as threatened at the national level following the IUCN Red List categories and criteria. This high number of threatened species was anticipated based on the high threat level to amphibians in bordering nations and globally. While the ecology of species in the DPR Korea is still understudied, we argue that species relying on agricultural wetlands such as rice paddies are not under imminent threat due to the enduring presence of extensive agricultural landscapes with low rates of chemical use and mechanisation. The maintenance of such landscapes is a clear benefit to amphibian species, in contrast to more industrialised agricultural landscapes in neighbouring nations. In comparison, the status of species dependent on forested habitats is unclear and threat levels are likely to be higher because of deforestation, as in neighbouring nations.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
| | - Spartak N. Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 St. Petersburg, Russia;
- Department of Zoology and Physiology, Dagestan State University, Gadzhiyev str. 43-a, Makhachkala, 3367000 Dagestan, Russia
| | - Kyongsim Ri
- Department of International Economic Cooperation, Ministry of Land and Environment Protection, Pyongyang, Democratic People’s Republic of Korea
| | - Desiree Andersen
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Tu Yong Nam
- Institute of Zoology, State Academy of Science, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Gwang Hyok Jon
- Department of Ecology, State Academy of Science, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Ho Song Man
- Department of Ecology, Life Science College, Kim Il Sung University, Ryongnam-dong, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Jong Sik Choe
- Department of Ecology, Life Science College, Kim Il Sung University, Ryongnam-dong, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Sera Kwon
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Siti N. Othman
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Kevin Messenger
- Herpetology and Applied Conservation Lab, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China;
| | - Yoonhyuk Bae
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Yucheol Shin
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
| | - Ajoung Kim
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Irina Maslova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Jennifer Luedtke
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
- Re:wild, Austin, TX 78746, USA
| | - Louise Hobin
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
| | - Nial Moores
- Birds Korea, 101-1902, Hyundai I Park, Busan 48559, Korea;
| | | | - Felix Glenk
- Hanns Seidel Foundation, Seoul 04419, Korea; (B.S.); (F.G.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea;
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Yu L, Zhao S, Meng F, Shi Y, Xu C. Dispersal and mating patterns determine the fate of naturally dispersed populations: evidence from Bombina orientalis. BMC Ecol Evol 2021; 21:111. [PMID: 34098874 PMCID: PMC8182911 DOI: 10.1186/s12862-021-01844-3] [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: 05/05/2020] [Accepted: 06/02/2021] [Indexed: 12/05/2022] Open
Abstract
Background In contrast to the explosive increase of a population following biological invasion, natural dispersal, i.e., when a population disperses from its original range into a new range, is a passive process that is affected by resources, the environment, and other factors. Natural dispersal is also negatively impacted by genetic drift and the founder effect. Although the fates of naturally dispersed populations are unknown, they can adapt evolutionarily over time to the new environment. Can naturally dispersed populations evolve beneficial adaptive strategies to offset these negative effects to maintain their population in a stable state? Results The current study addressed this question by focusing on the toad Bombina orientalis, the population of which underwent natural dispersal following the Last Glacial Maximum in Northeast Asia. Population genetic approaches were used to determine the genetic structure, dispersal pattern, and mating system of the population of B. orientalis in northeast China (Northern population). The results showed that this northern population of B. orientalis is a typical naturally dispersed population, in which the stable genetic structure and high level of genetic diversity of the population have been maintained through the long-distance biased dispersal behavior of males and the pattern of promiscuity within the population. Conclusions Our findings suggest that naturally dispersed populations can evolve effective adaptive strategies to maintain a stable population. Different species may have different strategies. The relevance of these maintenance mechanisms for naturally dispersed populations provide a new perspective for further understanding the processes of speciation and evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01844-3.
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Affiliation(s)
- Liqun Yu
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Shuai Zhao
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Fanbing Meng
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Yanshuang Shi
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Chunzhu Xu
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China.
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9
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Yu L, Zhao S, Shi Y, Meng F, Xu C. Evolutionary history of the oriental fire-bellied toad ( Bombina orientalis) in Northeast China. Ecol Evol 2021; 11:4232-4242. [PMID: 33976806 PMCID: PMC8093726 DOI: 10.1002/ece3.7318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan-Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire-bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan-Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire-bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.
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Affiliation(s)
- Liqun Yu
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Shuai Zhao
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Yanshuang Shi
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Fanbing Meng
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Chunzhu Xu
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
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10
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Othman SN, Putri ET, Messenger KR, Bae Y, Yang Y, Bova T, Reed T, Amin H, Chuang MF, Jang Y, Borzée A. Impact of the Miocene orogenesis on Kaloula spp. radiation and implication of local refugia on genetic diversification. Integr Zool 2021; 17:261-284. [PMID: 33734569 DOI: 10.1111/1749-4877.12538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phylogeography of the Kaloula genus in East Asia is still poorly understood. One of the difficulties is the absence of fossils to corroborate molecular dating estimates. Here, we examined the mitochondrial structure of Kaloula spp. in East Asia and focused on the impact of glaciations on the northernmost species: Kaloula borealis. We determined the phylogenetic relationships, molecular dating, and genetic connectivity assessments within the genus from 1211 bp of concatenated mitochondrial 12S and 16S. The relaxed clock analyses reveal the emergence of Kaloula spp. common ancestor in East and Southeast Asia between the Eocene and Oligocene, c. 38.47 Ma (24.69-53.65). The genetic diversification of lineages then increased on the East Asian Mainland during the Lower Miocene, c. 20.10 (8.73-30.65), most likely originating from the vicariance and radiation triggered by the orogeny of the Qinghai-Tibetan Plateau. Later, the dispersal towards the North East Asian Mainland during the Upper Miocene drove the population diversification of K. borealis c. 9.01 Ma (3.66-15.29). Finally, the central mainland population became isolated following orogenesis events and diverged into K. rugifera during the Pliocene, c. 3.06 Ma (0.02-10.90). The combination of population genetic and barrier analyses revealed a significant genetic isolation between populations of Kaloula spp. matching with the massive Qinling-Daba Mountain chain located in south-central China. Finally, we highlight a young divergence within the Eastern Mainland population of K. borealis, possibly attributed to refugia in south eastern China from which populations later expanded.
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Affiliation(s)
- Siti N Othman
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Eggy Triana Putri
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea.,Department of Biology, Faculty of Mathematics and Natural Science, Andalas University, Indonesia
| | - Kevin R Messenger
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yoonhyuk Bae
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yi Yang
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Timothy Bova
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Thomas Reed
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hina Amin
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ming-Feng Chuang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
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11
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Promnun P, Tandavanitj N, Kongrit C, Kongsatree K, Kongpraphan P, Dongkumfu W, Kumsuan D, Khudamrongsawat J. Phylogeography and ecological niche modeling reveal evolutionary history of Leiolepis ocellata (Squamata, Leiolepidae). Ecol Evol 2021; 11:2221-2233. [PMID: 33717450 PMCID: PMC7920770 DOI: 10.1002/ece3.7186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/22/2020] [Indexed: 12/03/2022] Open
Abstract
Leiolepis ocellata is a lizard species distributing in topographically diverse habitats in northern Thailand. To explore its evolutionary history, 113 samples of L. ocellata were collected from 11 localities covering its distributional range in northern Thailand, and sequenced for mtDNA fragments (Cyt b and ND2). Pairwise comparisons across sampling localities yielded significant genetic differentiation (F ST and Jost's D) but no clear pattern of isolation by distance could be demonstrated based on the Mantel test. Phylogenetic and network analyses highlighted six haplogroups. Their divergence times were estimated to occur during the Pleistocene, much more recent than major orogenic events affecting northern Thailand. Instead, the results suggested that lineage divergences, of particularly eastern and western haplogroups of the region, coincided with the major rivers in the region (Yom river and Ping river, respectively), indicating vicariance in response to riverine barriers. Furthermore, ecological niche modeling suggested an expansion of suitable habitats of L. ocellata, when LGM-liked conditions. This expansion potentially facilitated their dispersal among adjacent localities leading to lineage diversification and genetic admixture, after the riverine divergence.
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Affiliation(s)
- Pattarapon Promnun
- Animal Systematics and Molecular Ecology LaboratoryDepartment of BiologyFaculty of ScienceMahidol UniversityRatchathewi, BangkokThailand
| | - Nontivich Tandavanitj
- Department of BiologyFaculty of ScienceChulalongkorn UniversityPathumwan, BangkokThailand
| | - Chalita Kongrit
- Animal Systematics and Molecular Ecology LaboratoryDepartment of BiologyFaculty of ScienceMahidol UniversityRatchathewi, BangkokThailand
| | - Kritsayam Kongsatree
- Doi Suthep‐Pui National ParkSuthep, Mueang Chiang Mai District, Chiang MaiThailand
| | | | | | | | - Jenjit Khudamrongsawat
- Animal Systematics and Molecular Ecology LaboratoryDepartment of BiologyFaculty of ScienceMahidol UniversityRatchathewi, BangkokThailand
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12
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Kazemi E, Nazarizadeh M, Fatemizadeh F, Khani A, Kaboli M. The phylogeny, phylogeography, and diversification history of the westernmost Asian cobra (Serpentes: Elapidae: Naja oxiana) in the Trans-Caspian region. Ecol Evol 2021; 11:2024-2039. [PMID: 33717439 PMCID: PMC7920780 DOI: 10.1002/ece3.7144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 11/21/2022] Open
Abstract
We conducted a comprehensive analysis of the phylogenetic, phylogeographic, and demographic relationships of Caspian cobra (Naja oxiana; Eichwald, 1831) populations based on a concatenated dataset of two mtDNA genes (cyt b and ND4) across the species' range in Iran, Afghanistan, and Turkmenistan, along with other members of Asian cobras (i.e., subgenus Naja Laurenti, 1768). Our results robustly supported that the Asiatic Naja are monophyletic, as previously suggested by other studies. Furthermore, N. kaouthia and N. sagittifera were recovered as sister taxa to each other, and in turn sister clades to N. oxiana. Our results also highlighted the existence of a single major evolutionary lineage for populations of N. oxiana in the Trans-Caspian region, suggesting a rapid expansion of this cobra from eastern to western Asia, coupled with a rapid range expansion from east of Iran toward the northeast. However, across the Iranian range of N. oxiana, subdivision of populations was not supported, and thus, a single evolutionary significant unit is proposed for inclusion in future conservation plans in this region.
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Affiliation(s)
- Elmira Kazemi
- Department of EnvironmentFaculty of Natural Resources and EnvironmentScience and Research BranchIslamic Azad UniversityTehranIran
| | - Masoud Nazarizadeh
- Department of ParasitologyFaculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Institute of ParasitologyBiology Centre CAS, v.v.i.České BudějoviceCzech Republic
| | - Faezeh Fatemizadeh
- Department of Environmental ScienceFaculty of Natural ResourcesUniversity of TehranKarajIran
| | - Ali Khani
- Department of EnvironmentKhorasan RazaviMashhadIran
| | - Mohammad Kaboli
- Department of Environmental ScienceFaculty of Natural ResourcesUniversity of TehranKarajIran
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13
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Hao M, Jin Q, Meng G, Yang C, Yang S, Shi Z, Tang M, Liu S, Li Y, Zhang D, Su X, Shih C, Sun Y, Zhou X, Zhang AB. Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group. Mol Ecol 2020; 29:2492-2510. [PMID: 32163643 DOI: 10.1111/mec.15412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/04/2020] [Accepted: 03/03/2020] [Indexed: 11/30/2022]
Abstract
Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.
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Affiliation(s)
- Mengdi Hao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Qian Jin
- College of Life Sciences, Capital Normal University, Beijing, China.,Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, China
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Caiqing Yang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shenzhou Yang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiyong Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yinan Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Dan Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xu Su
- Guizhou Provincial Center for Disease Control and Prevention, Guizhou, China
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, Beijing, China.,Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Yiran Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
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14
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Fong JJ, Yang BT, Li PP, Waldman B, Min MS. Phylogenetic Systematics of the Water Toad (Bufo stejnegeri) Elucidates the Evolution of Semi-aquatic Toad Ecology and Pleistocene Glacial Refugia. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Pan T, Wang H, Duan S, Ali I, Yan P, Cai R, Wang M, Zhang J, Zhang H, Zhang B, Wu X. Historical population decline and habitat loss in a critically endangered species, the Chinese alligator (Alligator sinensis). Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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16
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Pan T, Zhou K, Zhang S, Shu Y, Zhang J, Li E, Wang M, Yan P, Wu H. Effects of dispersal barriers and geographic distance on the genetic structure of a narrowly distributed frog in a spatially structured landscape. J Zool (1987) 2019. [DOI: 10.1111/jzo.12730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Pan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - K. Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - S.‐L. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - Y.‐L. Shu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - J.‐H. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - E. Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - M.‐S. Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - P. Yan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - H.‐L. Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
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17
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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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18
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Wang L, Zhuang H, Zhang Y, Wei W. Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS). BMC Evol Biol 2019; 19:145. [PMID: 31311504 PMCID: PMC6635994 DOI: 10.1186/s12862-019-1474-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time. RESULTS Two main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau. CONCLUSIONS This study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).
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Affiliation(s)
- Liufu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Hang Zhuang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Wenzhi Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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19
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Du Z, Ishikawa T, Liu H, Kamitani S, Tadauchi O, Cai W, Li H. Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences. Int J Mol Sci 2019; 20:ijms20051234. [PMID: 30870981 PMCID: PMC6429140 DOI: 10.3390/ijms20051234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022] Open
Abstract
The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and one nuclear gene to investigate the phylogeographic pattern of the assassin bug based on comprehensive sampling in China, Japan, South Korea, Vietnam, and Laos. High levels of genetic differentiation were detected among the geographic populations classified into the northern and southern groups. A significant correlation was detected between genetic and geographical distances. The East China Sea land bridge served as a “dispersal corridor” during Pleistocene glaciation. The estimated divergence time indicated that the northern group may have separated from the eastern Chinese populations when the sea level rapidly rose during the “Ryukyu Coral Sea Stage” and the East China Sea land bridge was completely submerged. Demographic history and ecological niche modeling suggested that appropriate climatic conditions may have accounted for the rapid spread across the Korean Peninsula and Japan during the late Pleistocene. Our study underscores the pivotal roles of the Pleistocene sea level changes and climatic fluctuations in determining the distribution patterns of East Asian reduviids.
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Affiliation(s)
- Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Tadashi Ishikawa
- Laboratory of Entomology, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan.
| | - Hui Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan.
| | - Satoshi Kamitani
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan.
| | - Osamu Tadauchi
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan.
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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20
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Asadi A, Montgelard C, Nazarizadeh M, Moghaddasi A, Fatemizadeh F, Simonov E, Kami HG, Kaboli M. Evolutionary history and postglacial colonization of an Asian pit viper (Gloydius halys caucasicus) into Transcaucasia revealed by phylogenetic and phylogeographic analyses. Sci Rep 2019; 9:1224. [PMID: 30718614 PMCID: PMC6362119 DOI: 10.1038/s41598-018-37558-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/10/2018] [Indexed: 11/17/2022] Open
Abstract
It has been generally acknowledged that glacial climates at the time of the Pleistocene altered the patterns of species distributions, prompting latitudinal and altitudinal distribution shifts in several species, including poikilothermic species commonly known for their thermal sensitivity. However, the historical phylogeographic patterns of such species have remained largely unknown. Here, we present the historical biogeographic, phylogenetic, and phylogeographic relationships of the Caucasian pit viper, G. h. caucasicus, based on two mtDNA (cyt b and ND4) and one nDNA (c-mos) genes. This pit viper represents the westernmost member of the Crotalinae subfamily in the Palearctic and occurs in a variety of habitats, from 30 m to 3,000 m above sea level. In Iran, it is distributed on the northern and southern slopes of the Alborz Mountains, rendering it a target for phylogenetic and phylogeographic studies of a terrestrial poikilothermic animal. Our study identified four Iranian lineages of G. h. caucasicus along the northeastern to northwestern slopes of the Alborz Mountains and southern Azerbaijan (Talysh Mountains). Diversification of the Iranian lineages highlights population expansion and subsequent isolation into four plausible refugial areas during the Quaternary paleo-climatic oscillations, confirmed by our molecular dating and historical biogeographic analyses. The results of coalescence-based simulations support the incursion of the species from northeastern Iran to the western end of the Alborz, and then toward Transcaucasia via two directions: northern and southern slopes of the Alborz Mountains. Furthermore, our results clearly implied that G. h. caucasicus should be elevated to species rank and further referred to as G. caucasicus (Nikolsky, 1916).
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Affiliation(s)
- Atefeh Asadi
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, University Montpellier, Univ Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Claudine Montgelard
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, University Montpellier, Univ Paul Valéry Montpellier 3, IRD, Montpellier, France
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Masoud Nazarizadeh
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Akram Moghaddasi
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Faezeh Fatemizadeh
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Evgeniy Simonov
- Laboratory of Forest Genomics Siberian Federal University, 660036, Akademgorodok 50a/2, rasnoyarsk, Russia
| | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, Iran
| | - Mohammad Kaboli
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran.
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21
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Pan T, Wang H, Orozcoterwengel P, Hu CC, Wu GY, Qian LF, Sun ZL, Shi WB, Yan P, Wu XB, Zhang BW. Long-term sky islands generate highly divergent lineages of a narrowly distributed stream salamander (Pachyhynobius shangchengensis) in mid-latitude mountains of East Asia. BMC Evol Biol 2019; 19:1. [PMID: 30606099 PMCID: PMC6318985 DOI: 10.1186/s12862-018-1333-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/17/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Climate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands. RESULTS The Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. In the present study, we used mtDNA genes (Cyt b and ND2) of 193 individuals and 12 nuclear microsatellite loci genotyped on 370 individuals, representing 6 populations (JTX, KHJ, MW, TTZ, BYM and KJY) across the taxon's distribution area, to investigate their genetic variation and evolutionary history of P. shangchengensis. Most populations showed unusually high levels of genetic diversity. Phylogenetic analyses revealed five monophyletic clades with divergence times ranging from 3.96 to 1.4 Mya. Accordingly, significant genetic differentiation was present between these populations. Bayesian skyline plot analyses provided that all populations underwent long-term population expansions since the last inter-glacial (0.13 Mya ~ 0.12 Mya). Msvar analyses found recent signals of population decline for two northern populations (JTX and KHJ) reflecting a strong bottleneck (approximately 15-fold decrease) during the mid-Holocene (about 6000 years ago). Ecological niche modelling has shown a discontinuity in suitable habitats for P. shangchengensis under different historical climatic conditions. CONCLUSIONS Our results suggest that the niche conservatism of P. shangchengensis and sky island effects may have led to long-term isolation between populations. In sky island refuges, the mid-latitude Dabie Mountains have provided a long-term stable environment for P. shangchengensis, which has led to the accumulation of genetic diversity and has promoted genetic divergence.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- School of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China
| | - Hui Wang
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | | | - Chao-Chao Hu
- Analytical and Testing Center, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Gui-You Wu
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Li-Fu Qian
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Zhong-Lou Sun
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Wen-Bo Shi
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Peng Yan
- School of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China
| | - Xiao-Bing Wu
- School of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China
| | - Bao-Wei Zhang
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- School of Biosciences, Cardiff University, Cardiff, 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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Song W, Cao LJ, Li BY, Gong YJ, Hoffmann AA, Wei SJ. Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest. BMC Evol Biol 2018; 18:152. [PMID: 30314450 PMCID: PMC6186135 DOI: 10.1186/s12862-018-1269-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Refugial populations in Quaternary glaciations are critical to understanding the evolutionary history and climatic interactions of many extant species. Compared with the well-studied areas of Europe and Northern America, refugia of species in eastern Asia remain largely unknown. Here, we investigated the phylogeographic history of a globally important insect pest, the oriental fruit moth Grapholita molesta, in its native range of China. RESULTS Genetic structure analyses unveiled three distinct groups and a set of populations with admixture. Approximate Bayesian Computation (ABC) analyses support range expansion of this moth from southwest groups of Yunnan and Sichuan to northern and eastern China. A set of admixed populations was found around these two ancestral groups. This pattern of genetic structure points to two refugia located in the Yunnan region and Sichuan Basin. The split of the two refugia was dated to 329.2 thousand years ago in the penultimate glacial period. One of the lineages was exclusively found around the Sichuan Basin, indicating the formation of endemic populations in this refugium. Ecological niche model analysis suggested a shrinking distribution from the LIG period to the MID period in the Sichuan lineage but a wide and stable distribution in the other lineage. CONCLUSIONS Our results for the first time suggest that Yunnan and Sichuan jointly served as two large-scale refugia in eastern Asia in Quaternary glaciations, helping to maintain genetic diversity overall.
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Affiliation(s)
- Wei Song
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
- College of Forestry, Beijing Forestry University, Beijing, 100083 China
| | - Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
| | - Ya-Jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
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24
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Wang B, Nishikawa K, Matsui M, Nguyen TQ, Xie F, Li C, Khatiwada JR, Zhang B, Gong D, Mo Y, Wei G, Chen X, Shen Y, Yang D, Xiong R, Jiang J. Phylogenetic surveys on the newt genus Tylototriton sensu lato (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts. PeerJ 2018; 6:e4384. [PMID: 29576937 PMCID: PMC5853667 DOI: 10.7717/peerj.4384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato, distributed across the mountain ranges of southeastern Asia. Gene-tree and species-tree analyses of two mitochondrial genes and two nuclear genes revealed five major clades in the genus, and suggested several cryptic species. Dating estimates suggested that the genus originated in the early-to-middle Miocene. Under different species delimitating scenarios, diversification analyses with birth-death likelihood tests indicated that the genus held a higher diversification rate in the late Miocene-to-Pliocene era than that in the Pleistocene. Ancestral area reconstructions indicated that the genus originated from the northern Indochina Peninsula. Accordingly, we hypothesized that the Miocene Climatic Transition triggered the diversification of the genus, and the reinforcement of East Asian monsoons associated with the stepwise uplifts of the Tibetan Plateau promoted the radiation of the genus in southeastern Asia during the Miocene-to-Pliocene period. Quaternary glacial cycles likely had limited effects on speciation events in the genus, but mainly had contributions on their intraspecific differentiations.
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Affiliation(s)
- Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Janak Raj Khatiwada
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Baowei Zhang
- College of Life Science, Anhui University, Hefei, China
| | - Dajie Gong
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Yunming Mo
- Natural History Museum of Guangxi, Nanning, China
| | - Gang Wei
- Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
| | - Xiaohong Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Youhui Shen
- College of Life Science, Hunan Normal University, Changsha, China
| | - Daode Yang
- Institute of Wildlife Conservation, Central South University of Forestry & Technology, Changsha, China
| | - Rongchuan Xiong
- Department of Life Science, Liupanshui Normal University, Liupanshui, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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25
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Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot. Mol Phylogenet Evol 2017; 116:157-171. [DOI: 10.1016/j.ympev.2017.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 11/21/2022]
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26
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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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Yang BT, Zhou Y, Min MS, Matsui M, Dong BJ, Li PP, Fong JJ. Diversity and phylogeography of Northeast Asian brown frogs allied to Rana dybowskii (Anura, Ranidae). Mol Phylogenet Evol 2017; 112:148-157. [DOI: 10.1016/j.ympev.2017.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 04/29/2017] [Indexed: 11/27/2022]
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28
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Yang H, Lin CP, Liang AP. Phylogeography of the Rice Spittle Bug (Callitettix versicolor) Implies Two Long-Term Mountain Barriers in South China. Zoolog Sci 2017; 33:592-602. [PMID: 27927096 DOI: 10.2108/zs160042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
South China is a region of remarkable topographic complexity. However, the impact of climate fluctuations in the Pleistocene on the local fauna and especially insects has not been extensively studied. We integrated mitochondrial DNA (mtDNA) and microsatellite data of the rice spittle bug, Callitettix versicolor, to determine the genetic structure, potential biogeographic barriers, and historical demography of this species. The mtDNA data revealed two distinct lineages (Western and Eastern) congruent with the geographically separated western and eastern sub-regions of the Hengduan Mountains. The Eastern lineage was subdivided into two sub-lineages, E1 and E2, congruent with the geographically separated northern and southern sub-regions of the Dabie Mountains. E2 was further subdivided into two sub-groups, E2-1 and E2-2, with a hybrid zone (Guizhou and Hunan Provinces) in which their areas were contiguous. The genetic structures constructed using mtDNA were corroborated by four clusters (G1-G4) of microsatellite data. The populations of each cluster were nearly consistent with a sub-lineage of the mtDNA gene tree (G1-G4 corresponded to the Western, E1, E2-2 and E2-1 lineages, respectively). The divergence time estimated between the Western and Eastern lineages was 1.17 (0.50-2.37) to 0.89 (0.39-1.78) Mya, indicating that the lineages diversified on both geographic and temporal scales. The historical demography of the Eastern lineage showed continuous population growth after the Last Interglacial (LIG) and a stable population during the Last Glacial Maximum (LGM) period. However, the Western lineage remained largely unchanged during the LIG and LGM periods. This suggests that the historical demography of C. versicolor is probably related not only to the paleoclimate of South China, but also to the geological restriction and specific habitat preferences of species.
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Affiliation(s)
- Han Yang
- 1 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chung-Ping Lin
- 2 Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ai-Ping Liang
- 1 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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29
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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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30
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Fong JJ, Li PP, Yang BT, Zhou ZY, Leaché AD, Min MS, Waldman B. Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis). Mol Phylogenet Evol 2015; 97:69-75. [PMID: 26748269 DOI: 10.1016/j.ympev.2015.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 12/18/2015] [Accepted: 12/24/2015] [Indexed: 11/18/2022]
Abstract
The Oriental fire-bellied toad (Bombina orientalis) is a commonly used study organism, but knowledge of its evolutionary history is incomplete. We analyze sequence data from four genetic markers (mtDNA genes encoding cytochrome c oxidase subunit I, cytochrome b, and 12S-16S rRNA; nuDNA gene encoding recombination activating gene 2) from 188 individuals across its range in Northeast Asia to elucidate phylogeographic patterns and to identify the historic events that shaped its evolutionary history. Although morphologically similar across its range, B. orientalis exhibits phylogeographic structure, which we infer was shaped by geologic, climatic, and anthropogenic events. Phylogenetic and divergence-dating analyses recover four genetically distinct groups of B. orientalis: Lineage 1-Shandong Province and Beijing (China); Lineage 2-Bukhan Mountain (Korea); Lineage 3-Russia, Northeast China, and northern South Korea; and Lineage 4-South Korea. Lineage 2 was previously unknown. Additionally, we discover an area of secondary contact on the Korean Peninsula, and infer a single dispersal event as the origin of the insular Jeju population. Skyline plots estimate different population histories for the four lineages: Lineages 1 and 2 experienced population decreases, Lineage 3 remained stable, while Lineage 4 experienced a sharp increase during the Holocene. The timing of the population expansion of Lineage 4 coincides with the advent of rice cultivation, which may have facilitated the increase in population size by providing additional breeding habitat.
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Affiliation(s)
- Jonathan J Fong
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea; Science Unit, Lingnan University, Tuen Mun, New Territories, Hong Kong
| | - Pi-Peng Li
- Center for Chinese Endemic Herp-breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China.
| | - Bao-Tian Yang
- Center for Chinese Endemic Herp-breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Zheng-Yan Zhou
- Center for Chinese Endemic Herp-breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
| | - Mi-Sook Min
- College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea.
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea.
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Song G, Zhang R, DuBay SG, Qu Y, Dong L, Wang W, Zhang Y, Lambert DM, Lei F. East Asian allopatry and north Eurasian sympatry in Long-tailed Tit lineages despite similar population dynamics during the late Pleistocene. ZOOL SCR 2015. [DOI: 10.1111/zsc.12148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Center for Developmental Biology; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Shane G. DuBay
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Life Sciences Section; Integrative Research Center; Field Museum of Natural History; Chicago IL 60605 USA
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Wenjuan Wang
- Center for Watershed Ecology; Institute of Life Science; Nanchang University; Nanchang 330031 China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - David M. Lambert
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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32
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YE J, XIAO Z, LI C, WANG F, LIAO J, FU J, ZHANG Z. Past climate change and recent anthropogenic activities affect genetic structure and population demography of the greater long-tailed hamster in northern China. Integr Zool 2015. [DOI: 10.1111/1749-4877.12150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junbin YE
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Zhenlong XIAO
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Chuanhai LI
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Fusheng WANG
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Jicheng LIAO
- School of Life Sciences; Lanzhou University; Lanzhou China
| | - Jinzhong FU
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada
| | - Zhibin ZHANG
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing 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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34
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Low Genetic Diversity and Moderate Inbreeding Risk of an Insular Endemic Pit Viper (Gloydius shedaoensis): Implication for Conservation. J HERPETOL 2015. [DOI: 10.1670/13-185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Tian S, Lei SQ, Hu W, Deng LL, Li B, Meng QL, Soltis DE, Soltis PS, Fan DM, Zhang ZY. Repeated range expansions and inter-/postglacial recolonization routes of Sargentodoxa cuneata (Oliv.) Rehd. et Wils. (Lardizabalaceae) in subtropical China revealed by chloroplast phylogeography. Mol Phylogenet Evol 2015; 85:238-46. [DOI: 10.1016/j.ympev.2015.02.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/15/2015] [Accepted: 02/18/2015] [Indexed: 11/24/2022]
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36
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You CW, Poyarkov NA, Lin SM. Diversity of the snail-eating snakesPareas(Serpentes, Pareatidae) from Taiwan. ZOOL SCR 2015. [DOI: 10.1111/zsc.12111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chung-Wei You
- Department of Life Science; National Taiwan Normal University; Taipei Taiwan
| | - Nikolay A. Poyarkov
- Department of Vertebrate Zoology; Biological Faculty; Lomonosov Moscow State University; Leninskiye Gory, GSP-1 Moscow 119991 Russia
- Joint Russian-Vietnamese Tropical Research and Technological Center; South Branch, 3, Street 3/2, 10 District Ho Chi Minh City Vietnam
| | - Si-Min Lin
- Department of Life Science; National Taiwan Normal University; Taipei Taiwan
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Xu W, Yin W, Chen A, Li J, Lei G, Fu C. Phylogeographical analysis of a cold-temperate freshwater fish, the Amur sleeper (Perccottus glenii) in the Amur and Liaohe River basins of Northeast Asia. Zoolog Sci 2014; 31:671-9. [PMID: 25284386 DOI: 10.2108/zs130046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii, among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early-early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle-early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii.
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Affiliation(s)
- Wang Xu
- 1 Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University, Shanghai 200433, China
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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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Gao JF, Wang J, He Y, Qu YF, Lin LH, Ma XM, Ji X. Proteomic and biochemical analyses of short-tailed pit viper (Gloydius brevicaudus) venom: age-related variation and composition-activity correlation. J Proteomics 2014; 105:307-22. [PMID: 24487038 DOI: 10.1016/j.jprot.2014.01.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/11/2014] [Accepted: 01/15/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED We conducted an in-depth analysis of the proteomic and biochemical profiles of the venom of neonate and adult short-tailed pit vipers (Gloydius brevicaudus). Identified proteins were assigned to a few main toxin families. Disintegrin, phospholipase A2 (PLA2), serine proteinase, cysteine-rich secretory protein, C-type lectin-like protein, l-amino acid oxidase and snake venom metalloproteinase (SVMP) were detected in both venoms, while 5'-nucleotidase was detected only in the adult venom. SVMP was the predominant protein family in both venoms (neonate: 65.7%; adult: 64.4%), followed by PLA2 (neonate: 13.4%; adult: 25.0%). Antivenomic analysis revealed that commercial G. brevicaudus antivenom almost neutralized the chromatographic peaks with medium and high molecular masses in both venoms, but did not completely recognize peaks with low molecular mass. Toxicological and enzymatic activities show remarkable age-related variation in G. brevicaudus venom, probably resulting from variation in venom composition. Our data demonstrate age-related variation across venomics, antivenomics and biochemical profiles of G. brevicaudus venom, and have implications for the management of G. brevicaudus bites, including improving antivenom preparation by combining both venoms. BIOLOGICAL SIGNIFICANCE This study investigates the composition and biochemical activity of neonate and adult Gloydius brevicaudus venoms. We found remarkable age-related variation in venom biological activity, likely the result of variation in venom composition. Antivenomics analysis was used to explore difference in neonate and adult G. brevicaudus venoms. Our findings have implications for the diagnosis and clinical management of G. brevicaudus bites, and the design of venom mixtures that will increase the efficacy of commercial antivenom. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Jian-Fang Gao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, School of Life Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Jin Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China
| | - Ying He
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, School of Life Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, School of Life Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Xiao-Mei Ma
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, School of Life Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China.
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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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Neonate-to-adult transition of snake venomics in the short-tailed pit viper, Gloydius brevicaudus. J Proteomics 2013; 84:148-57. [DOI: 10.1016/j.jprot.2013.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/04/2013] [Accepted: 04/04/2013] [Indexed: 11/20/2022]
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Dong L, Heckel G, Liang W, Zhang Y. Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers. Mol Ecol 2013; 22:3376-90. [PMID: 23692215 DOI: 10.1111/mec.12315] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 11/27/2022]
Abstract
The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.
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Affiliation(s)
- Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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Wang B, Jiang J, Xie F, Li C. Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains. J Mol Evol 2013; 76:112-28. [PMID: 23381112 DOI: 10.1007/s00239-013-9544-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Accepted: 01/19/2013] [Indexed: 11/24/2022]
Abstract
Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F(ct) = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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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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Zhang R, Song G, Qu Y, Alström P, Ramos R, Xing X, Ericson PG, Fjeldså J, Wang H, Yang X, Kristin A, Shestopalov AM, Choe JC, Lei F. Comparative phylogeography of two widespread magpies: Importance of habitat preference and breeding behavior on genetic structure in China. Mol Phylogenet Evol 2012; 65:562-72. [DOI: 10.1016/j.ympev.2012.07.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 07/11/2012] [Accepted: 07/14/2012] [Indexed: 01/11/2023]
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46
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Lukoschek V, Osterhage JL, Karns DR, Murphy JC, Voris HK. Phylogeography of the Mekong mud snake (Enhydris subtaeniata): the biogeographic importance of dynamic river drainages and fluctuating sea levels for semiaquatic taxa in Indochina. Ecol Evol 2012; 1:330-42. [PMID: 22393504 PMCID: PMC3287308 DOI: 10.1002/ece3.29] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/05/2011] [Accepted: 08/08/2011] [Indexed: 11/11/2022] Open
Abstract
During the Cenozoic, Southeast Asia was profoundly affected by plate tectonic events, dynamic river systems, fluctuating sea levels, shifting coastlines, and climatic variation, which have influenced the ecological and evolutionary trajectories of the Southeast Asian flora and fauna. We examined the role of these paleogeographic factors on shaping phylogeographic patterns focusing on a species of semiaquatic snake, Enhydris subtaeniata (Serpentes: Homalopsidae) using sequence data from three mitochondrial fragments (cytochrome b, ND4, and ATPase-2785 bp). We sampled E. subtaeniata from seven locations in three river drainage basins that encompassed most of this species' range. Genetic diversities were typically low within locations but high across locations. Moreover, each location had a unique suite of haplotypes not shared among locations, and pairwise φ(ST) values (0.713-0.998) were highly significant between all location pairs. Relationships among phylogroups were well resolved and analysis of molecular variance (AMOVA) revealed strong geographical partitioning of genetic variance among the three river drainage basins surveyed. The genetic differences observed among the populations of E. subtaeniata were likely shaped by the Quaternary landscapes of Indochina and the Sunda Shelf. Historically, the middle and lower Mekong consisted of strongly dissected river valleys separated by low mountain ranges and much of the Sunda Shelf consisted of lowland river valleys that served to connect faunas associated with major regional rivers. It is thus likely that the contemporary genetic patterns observed among populations of E. subtaeniata are the result of their histories in a complex terrain that created abundant opportunities for genetic isolation and divergence yet also provided lowland connections across now drowned river valleys.
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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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Yan XU, Qin LIU, Edward AMYERS, Lian WANG, Song HUANG, Yun HE, Peihao PENG, Peng GUO. Molecular Phylogeny of the Genus Gloydius (Serpentes: Crotalinae). ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wang B, Jiang J, Xie F, Li C. Postglacial colonization of the Qinling Mountains: phylogeography of the swelled vent frog (Feirana quadranus). PLoS One 2012; 7:e41579. [PMID: 22848532 PMCID: PMC3405020 DOI: 10.1371/journal.pone.0041579] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/22/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling-Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia). METHODOLOGY/PRINCIPAL FINDINGS We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang-Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling-Micang-Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang-Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline. CONCLUSIONS/SIGNIFICANCE The Qinling-Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang-Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Feng Xie
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Cheng Li
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
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