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Islam S, Peart C, Kehlmaier C, Sun YH, Lei F, Dahl A, Klemroth S, Alexopoulou D, Del Mar Delgado M, Laiolo P, Carlos Illera J, Dirren S, Hille S, Lkhagvasuren D, Töpfer T, Kaiser M, Gebauer A, Martens J, Paetzold C, Päckert M. Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies). Mol Phylogenet Evol 2024; 198:108135. [PMID: 38925425 DOI: 10.1016/j.ympev.2024.108135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 03/25/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.
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Affiliation(s)
- Safiqul Islam
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany; Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany; Division of Systematic Zoology, Faculty of Biology, LMU Munich, Biocenter, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Claire Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Biocenter, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Christian Kehlmaier
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andreas Dahl
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Sylvia Klemroth
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Dimitra Alexopoulou
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Maria Del Mar Delgado
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Paola Laiolo
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Juan Carlos Illera
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | | | - Sabine Hille
- University of Natural Resources and Life Sciences, Vienna, Gregor Mendel-Strasse 33, 1180 Vienna, Austria
| | - Davaa Lkhagvasuren
- Department of Biology, School of Arts and Sciences, National University of Mongolia, P.O.Box 46A-546, Ulaanbaatar 210646, Mongolia
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity Change, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee, Bonn, Germany
| | | | | | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55099 Mainz, Germany
| | - Claudia Paetzold
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Martin Päckert
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany.
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Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
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Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
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3
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Yao H, Zhang Y, Wang Z, Liu G, Ran Q, Zhang Z, Guo K, Yang A, Wang N, Wang P. Inter-glacial isolation caused divergence of cold-adapted species: the case of the snow partridge. Curr Zool 2021; 68:489-498. [PMID: 36090147 PMCID: PMC9450178 DOI: 10.1093/cz/zoab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Deciphering the role of climatic oscillations in species divergence helps us understand the mechanisms that shape global biodiversity. The cold-adapted species may have expanded their distribution with the development of glaciers during glacial period. With the retreat of glaciers, these species were discontinuously distributed in the high-altitude mountains and isolated by geographical barriers. However, the study that focuses on the speciation process of cold-adapted species is scant. To fill this gap, we combined population genetic data and ecological niche models (ENMs) to explore divergence process of snow partridge (Lerwa lerwa). Lerwa lerwa is a cold-adapted bird that is distributed from 4,000 to 5,500 m. We found 2 genetic populations within L. lerwa, and they diverged from each other at about 0.40–0.44 million years ago (inter-glacial period after Zhongliangan glaciation). The ENMs suggested that L. lerwa expanded to the low elevations of the Himalayas and Hengduan mountains during glacial period, whereas it contracted to the high elevations, southern of Himalayas, and Hengduan mountains during inter-glacial periods. Effective population size trajectory also suggested that L. lerwa expanded its population size during the glacial period. Consistent with our expectation, the results support that inter-glacial isolation contributed to the divergence of cold-adapted L. lerwa on Qinghai-Tibetan Plateau. This study deepens our understanding of how climatic oscillations have driven divergence process of cold-adapted Phasianidae species distributed on mountains.
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Affiliation(s)
- Hongyan Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanan Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Hangzhou Xi’ao Environmental Science Technique Company Limited, Zhejiang 310011, China
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Ran
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Yancheng Wetland and World Natural Heritage Conservation and Management Center, Jiangsu 224000, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Keji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, Changsha 410014, China
| | - Ailin Yang
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Phylogeography of Triplophysa stenura (Nemacheilidae): Responded to the Mid-Pleistocene Climate Transition in the Qinghai-Tibetan Plateau. Zool Stud 2021; 59:e67. [PMID: 34140984 DOI: 10.6620/zs.2020.59-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022]
Abstract
Pleistocene climatic oscillations have greatly influenced the evolutionary histories and distribution patterns of most extant species. In this study, the phylogeographic patterns and evolutionary history of Triplophysa stenura were investigated. A total of 359 individuals from 19 locations covering the species' distribution range were collected, and two mitochondrial genes (COI and Cyt b) and the recombination activating protein 1 gene (Rag1) were analyzed. Two deeply divergent lineages, corresponding geographically to the northern and southern Tanggula Mountain, were observed, and shallow divergences were found within the southern and central Qinghai-Tibetan plateau (QTP). The estimated divergence time between the northern and southern Tanggula lineages was around 1.07 Mya. Within the southern Tanggula Mountain lineages, the Nu and Subansiri rivers populations were split about 0.74 Mya, and the southwestern and central QTP populations were divided with the southeastern QTP ones approximately 0.67 Mya. The divergence times of the lineages were matched with two major glaciations in QTP (the Xixiabangma Glaciation, 1.17-0.80 Mya and Kunlun Glaciation, 0.72-0.62 Mya). Together with demographic history analyses, our results highlighted that major glacial cycles during the mid-Pleistocene played a major role in sculpting the distribution pattern of T. stenura, and led to the gene homogenization crossing the drainage populations in the southwestern and central QTP.
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Dalui S, Singh SK, Joshi BD, Ghosh A, Basu S, Khatri H, Sharma LK, Chandra K, Thakur M. Geological and Pleistocene glaciations explain the demography and disjunct distribution of red panda (A. fulgens) in eastern Himalayas. Sci Rep 2021; 11:65. [PMID: 33420314 PMCID: PMC7794540 DOI: 10.1038/s41598-020-80586-6] [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: 10/05/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Pleistocene glaciations facilitated climatic oscillations that caused for enormous heterogeneity in landscapes, and consequently affected demography and distribution patterns of the mountain endemic species. In this context, we investigated demographic history and population genetic structure of red panda, distributed along the geographical proximity in the southern edge of the Qinghai-Tibetan Plateau. Bayesian based phylogeny demonstrated that red panda diverged about 0.30 million years ago (CI 0.23-0.39) into two phylogenetic (sub) species, that correspond to the middle-late Pleistocene transition. The observed intraspecific clades with respect to Himalayan and Chinese red panda indicated restricted gene flow resulting from the Pleistocene glaciations in the eastern and southern Tibetan Plateau. We found Himalayan red panda population at least in KL-India declined abruptly in last 5-10 thousand years after being under demographic equilibrium. We suggest revisiting the ongoing conservation activities through cross border collaboration by developing multi-nationals, and multi-lateral species-oriented conservation action plans to support the red panda populations in transboundary landscapes.
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Affiliation(s)
- Supriyo Dalui
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India ,grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Sujeet Kumar Singh
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Bheem Dutt Joshi
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Avijit Ghosh
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India ,grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Shambadeb Basu
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Hiren Khatri
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Lalit Kumar Sharma
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Kailash Chandra
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Mukesh Thakur
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
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6
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Hu C, Pan T, Wu Y, Zhang C, Chen W, Chang Q. Spatial genetic structure and historical demography of East Asian wild boar. Anim Genet 2020; 51:557-567. [PMID: 32510675 DOI: 10.1111/age.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/21/2020] [Accepted: 05/01/2020] [Indexed: 11/30/2022]
Abstract
Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.
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Affiliation(s)
- C Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - T Pan
- School of Life Sciences, Anhui Normal University, Wuhu, Anhui, 230039, China
| | - Y Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - C Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, 210013, China
| | - W Chen
- College of Environment and Ecology, Jiangsu Open University (The City Vocational College of Jiangsu), Nanjing, Jiangsu, 210036, China
| | - Q Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
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Rocha-Méndez A, Sánchez-González LA, González C, Navarro-Sigüenza AG. The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico. BMC Evol Biol 2019; 19:237. [PMID: 31888449 PMCID: PMC6937948 DOI: 10.1186/s12862-019-1564-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/15/2019] [Indexed: 11/30/2022] Open
Abstract
Background Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. Results We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. Conclusions Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.
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Affiliation(s)
- Alberto Rocha-Méndez
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico. .,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico.
| | - Luis A Sánchez-González
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico
| | - Clementina González
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
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Wang Z, Meng S, Rao G. Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai-Tibetan Plateau. Ecol Evol 2019; 9:8305-8319. [PMID: 31380091 PMCID: PMC6662313 DOI: 10.1002/ece3.5406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/19/2022] Open
Abstract
There are two long-standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai-Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage-specific habitat preferences.
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Affiliation(s)
- Zi‐Meng Wang
- School of Life SciencesPeking UniversityBeijingChina
| | - Shi‐Yong Meng
- School of Life SciencesPeking UniversityBeijingChina
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Ding L, Liao J. Phylogeography of the Tibetan hamster Cricetulus kamensis in response to uplift and environmental change in the Qinghai-Tibet Plateau. Ecol Evol 2019; 9:7291-7306. [PMID: 31380051 PMCID: PMC6662396 DOI: 10.1002/ece3.5301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/28/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022] Open
Abstract
AIM The evolutionary process of an organism provides valuable data toward an understanding of the Earth evolution history. To investigate the relationship between the uplift of the Qinghai-Tibet Plateau (QTP) and mammalian evolution since the late Cenozoic, the geographic distribution of genetic variations in the Tibetan hamster Cricetulus kamensis was investigated using phylogeographical methods. In particular, population divergence, demographic history, genetic variation, and the prediction of species distribution area were investigated. LOCATION The Qinghai-Tibet Plateau. METHODS A total of 53 specimens, representing 13 geographic populations, were collected from the QTP. The phylogeographical pattern and demographic history of C. kamensis were analyzed, and the probable factors in the QTP uplift and the Quaternary glacial periods were inferred from one nuclear and four mitochondrial genes. Furthermore, the species distribution model (SDM) was used to predict changes in potentially suitable habitats since the last Interglacial. RESULTS Phylogenetic analysis demonstrated that two major genetic differentiations of the C. kamensis population occurred during the Early Pleistocene that were influenced by the Qing-Zang tectonic movement from the Middle Pliocene to the Early Pleistocene. Genetic distance between two major clades indicated low genetic divergence. Demographic history analysis showed that the C. kamensis population was affected by the Quaternary glacial period. SDM analysis indicated that C. kamensis was endemic to the QTP and the suitable habitat was affected by climate change, especially during the Last Glacial Maximum (LGM). MAIN CONCLUSION Our results indicated that the QTP uplift led to the population divergence of C. kamensis, and vicariance well accounted for the geographic distribution of genetic variation in C. kamensis as a result of genetic divergence and lack of gene flow. The genetic distance shows that C. alticola may be a subspecies of C. kamensis. Demographic history analysis suggests that the QTP was affected by the last glacial period. SDM analysis supports that almost the entire QTP is covered by a huge ice sheet during the LGM.
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Affiliation(s)
- Li Ding
- School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jicheng Liao
- School of Life SciencesLanzhou UniversityLanzhouChina
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Jiang Z, Gao B, Lei F, Qu Y. Population genomics reveals that refugial isolation and habitat change lead to incipient speciation in the Ground tit. ZOOL SCR 2019. [DOI: 10.1111/zsc.12340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
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Liu Y, Dietrich CH, Wei C. Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation? BMC Evol Biol 2019; 19:5. [PMID: 30621591 PMCID: PMC6323834 DOI: 10.1186/s12862-018-1317-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Results The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations. Conclusions Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas. Electronic supplementary material The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, 61820, USA
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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12
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Feng C, Zhou W, Tang Y, Gao Y, Chen J, Tong C, Liu S, Wanghe K, Zhao K. Molecular systematics of the Triplophysa robusta (Cobitoidea) complex: Extensive gene flow in a depauperate lineage. Mol Phylogenet Evol 2018; 132:275-283. [PMID: 30550962 DOI: 10.1016/j.ympev.2018.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022]
Abstract
Gene flow between populations assumed to be isolated frequently leads to incorrect inferences of evolutionary history. Understanding gene flow and its causes has long been a key topic in evolutionary biology. In this study, we explored the evolutionary history of the Triplophysa robusta complex, using a combination of multilocus analyses and coalescent simulation. Our multilocus approach detected conspicuous mitonuclear discordances in the T. robusta complex. Mitochondrial results showed reticular clades, whereas the nuclear results corresponded with the morphological data. Coalescent simulation indicated that gene flow was the source of these discordances. Molecular clock analysis combined with geological processes suggest that intense geological upheavals have shaped a complicated evolutionary history for the T. robusta complex since the late Miocene, causing extensive gene flow which has distorted the molecular systematics of the T. robusta complex. We suggest that frequent gene flow may restrict speciation in the T. robusta complex, leading to such a depauperate lineage. Based on this comprehensive understanding, we provide our proposals for taxonomic revision of the T. robusta complex.
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Affiliation(s)
- Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiwei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Jinmin Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China.
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13
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Teng H, Zhang Y, Shi C, Mao F, Cai W, Lu L, Zhao F, Sun Z, Zhang J. Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species. Mol Biol Evol 2017; 34:2214-2228. [PMID: 28482038 PMCID: PMC5850741 DOI: 10.1093/molbev/msx157] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation.
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Affiliation(s)
- Huajing Teng
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yaohua Zhang
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chengmin Shi
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jianxu Zhang
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Wang B, Xie F, Li J, Wang G, Li C, Jiang J. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ 2017; 5:e3770. [PMID: 28924497 PMCID: PMC5598431 DOI: 10.7717/peerj.3770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/16/2017] [Indexed: 11/22/2022] Open
Abstract
The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.
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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
| | - 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
| | - Jiannan Li
- Nanjing Institute of Environmental Sciences Under Ministry of Environmental Protection, Nanjing, Jiangsu, China
| | - Gang 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
| | - 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
| | - 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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15
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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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16
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The geography and timing of genetic divergence in the lizard Phrynocephalus theobaldi on the Qinghai-Tibetan plateau. Sci Rep 2017; 7:2281. [PMID: 28536444 PMCID: PMC5442162 DOI: 10.1038/s41598-017-02674-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/18/2017] [Indexed: 11/27/2022] Open
Abstract
The Qinghai-Tibetan Plateau (QTP) represents one of the earth’s most significant physical features and there is increasing interest in the historical generation of biodiversity within this region. We hypothesized that there should be clear geographically coherent genetic structuring within one of the world’s highest altitude lizards, Phrynocephalus theobaldi, due to considerable historical population fragmentation in this environment. This was tested using a major mitochondrial DNA (mtDNA) survey and sequencing of two nuclear markers (AME and RAG-1) from P. theobaldi, from across the southern QTP. A Bayesian method (BPEC) was used to detect four geographically structured mtDNA clusters. A Bayesian phylogenetic tree, together with associated dating analyses, supported four corresponding evolutionary lineages with a timing of 3.74–7.03 Ma for the most basal P. theobaldi split and Pliocene splits of 2.97–5.79 Ma and 2.40–5.39 Ma in the two daughter lineages. Himalayan uplift and changes in the Jilong basin may have contributed to these divergences, but uplift of the Gangdese mountains is rejected due to its timing. The nuclear markers appeared to be sorted between the four mtDNA groups, and species delimitation analyses supported the four phylogeographical groups as candidate species. The study contributes to our understanding of biodiversity on the QTP.
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17
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Wang P, Liu Y, Liu Y, Chang Y, Wang N, Zhang Z. The role of niche divergence and geographic arrangement in the speciation of Eared Pheasants (Crossoptilon, Hodgson 1938). Mol Phylogenet Evol 2017; 113:1-8. [PMID: 28487259 DOI: 10.1016/j.ympev.2017.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
Abstract
One of the most contentious theories in current ecology is the ecological niche conservatism, which is defined as conservatism among closely related species; however, the ecological niche can also be shifted, as documented in several cases. Genetic drift and ecological divergent selection may cause ecological niche divergence. The current study aims to test whether the ecological niche is conserved or divergent and to determine the main factor that drives ecological niche divergence or conservation. We analyzed the phylogenetic relationship, ecological niche model (ENM) and demographic history of Eared Pheasants in the genus Crossoptilon (Galliformes: Phasianidae) to test niche conservatism with respect to different geographically distributed patterns. The phylogenetic relationship was reconstructed using ∗BEAST with mitochondrial cytochrome b (cyt b) and 44 unlinked autosomal exonic loci, and ENMs were reconstructed in MAXENT using an average of 41 occurrence sites in each species and 22 bioclimatic variables. A background similarity test was used to detect whether the ecological niche is conserved. Demographic history was estimated using the isolation with migration (IM) model. We found that there was asymmetric gene flow between the allopatric sister species Crossoptilon mantchuricum and C. auritum and the parapatric sister species C. harmani and C. crossoptilon. We found that ecological niches were divergent, not conserved, between C. mantchuricum and C. auritum, which began to diverge at approximately 0.3 million years ago. However, the ecological niches were conserved between C. crossoptilon and C. harmani, which gradually diverged approximately half a million years ago. Ecological niches can be either conserved or divergent, and ecological divergent selection for local adaptation is probably an important factor that promotes and maintains niche divergence in the face of gene flow. This study provides a better understanding of the role that divergent selection has in the initial speciation process. The platform combined demographic processes and ecological niches to offer new insights into the mechanism of biogeography patterns.
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Affiliation(s)
- Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology and Evolution/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yinong Liu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China; Beijing National Day School, Beijing 100039, PR China
| | - Yajing Chang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Nan Wang
- School of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China.
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18
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Janecka JE, Zhang Y, Li D, Munkhtsog B, Bayaraa M, Galsandorj N, Wangchuk TR, Karmacharya D, Li J, Lu Z, Uulu KZ, Gaur A, Kumar S, Kumar K, Hussain S, Muhammad G, Jevit M, Hacker C, Burger P, Wultsch C, Janecka MJ, Helgen K, Murphy WJ, Jackson R. Range-Wide Snow Leopard Phylogeography Supports Three Subspecies. J Hered 2017; 108:597-607. [DOI: 10.1093/jhered/esx044] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
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An endemic rat species complex is evidence of moderate environmental changes in the terrestrial biodiversity centre of China through the late Quaternary. Sci Rep 2017; 7:46127. [PMID: 28393882 PMCID: PMC5385558 DOI: 10.1038/srep46127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 03/13/2017] [Indexed: 11/08/2022] Open
Abstract
The underlying mechanisms that allow the Hengduan Mountains (HDM), the terrestrial biodiversity centre of China, to harbour high levels of species diversity remain poorly understood. Here, we sought to explore the biogeographic history of the endemic rat, Niviventer andersoni species complex (NASC), and to understand the long-term persistence of high species diversity in this region. In contrast to previous studies that have proposed regional refuges in eastern or southern of the HDM and emphasized the influence of climatic oscillations on local vertebrates, we found that HDM as a whole acted as refuge for the NASC and that the historical range shifts of NASC mainly occurred in the marginal regions. Demographic analyses revealed slight recent population decline in Yunnan and south-eastern Tibet, whereas of the populations in Sichuan and of the entire NASC were stable. This pattern differs greatly from classic paradigms of temperate or alpine and holarctic species. Interestingly, the mean elevation, area and climate of potential habitats of clade a (N. excelsior), an alpine inhabitant, showed larger variations than did those of clade b (N. andersoni), a middle-high altitude inhabitant. These species represent the evolutionary history of montane small mammals in regions that were less affected by the Quaternary climatic changes.
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Li Y, Ludwig A, Peng Z. Geographical differentiation of the Euchiloglanis fish complex (Teleostei: Siluriformes) in the Hengduan Mountain Region, China: Phylogeographic evidence of altered drainage patterns. Ecol Evol 2017; 7:928-940. [PMID: 28168029 PMCID: PMC5288251 DOI: 10.1002/ece3.2715] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/15/2016] [Accepted: 12/17/2016] [Indexed: 01/24/2023] Open
Abstract
The uplift of the Tibetan Plateau caused significant ecogeographical changes that had a major impact on the exchange and isolation of regional fauna and flora. Furthermore, Pleistocene glacial oscillations were linked to temporal large‐scale landmass and drainage system reconfigurations near the Hengduan Mountain Region and might have facilitated speciation and promoted biodiversity in southwestern China. However, strong biotic evidence supporting this role is lacking. Here, we use the Euchiloglanis fish species complex as a model to demonstrate the compound effects of the Tibetan Plateau uplift and Pleistocene glacial oscillations on species formation in this region. The genetic structure and geographical differentiation of the Euchiloglanis complex in four river systems within the Hengduan Mountain Region were deduced using the cytochrome b (cyt b) gene and 10 microsatellite loci from 360 to 192 individuals, respectively. The results indicated that the populations were divided into four independently evolving lineages, in which the populations from the Qingyi River and Jinsha River formed two sub‐lineages. Phylogenetic relationships were structured by geographical isolation, especially near drainage systems. Divergence time estimation analyses showed that the Euchiloglanis complex diverged from its sister clade Pareuchiloglanis sinensis at around 1.3 Million years ago (Ma). Within the Euchiloglanis complex, the divergence time between the Dadu–Yalong and Jinsha–Qingyi River populations occurred at 1.0 Ma. This divergence time was in concordance with recent geological events, including the Kun‐Huang Movement (1.2–0.6 Ma) and the lag time (<2.0 Ma) of river incision in the Hengduan Mountain Region. Population expansion signals were detected from mismatched distribution analyses, and the expansion times were concurrent with Pleistocene glacier fluctuations. Therefore, current phylogeographic patterns of the Euchiloglanis fish complex in the Hengduan Mountain Region were influenced by the uplift event of the Tibetan Plateau and were subsequently altered by paleo‐river transitions during the late Pleistocene glacial oscillations.
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Affiliation(s)
- Yanping Li
- The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Arne Ludwig
- Department of Evolutionary Genetics Institute for Zoo and Wildlife Research Berlin Germany
| | - Zuogang Peng
- The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
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Zhou W, Jin J, Wu J, Chen H, Yang J, Murphy RW, Che J. Mountains too high and valleys too deep drive population structuring and demographics in a Qinghai-Tibetan Plateau frog Nanorana pleskei (Dicroglossidae). Ecol Evol 2016; 7:240-252. [PMID: 28070287 PMCID: PMC5214757 DOI: 10.1002/ece3.2646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 12/31/2022] Open
Abstract
Pleistocene glacial–interglacial climatic oscillations greatly shaped the current genetic structure of many species. However, geographic features may influence the impact of climatic cycling. Distinct geographic and environmental characters between northern and southern parts of the eastern Qinghai–Tibetan Plateau (EQTP) facilitate explorations into the impacts of geographic features on species. The northern parts of EQTP contain large areas of marsh, and the environment is rather homogeneous. In contrast, the southern EQTP harbors complex alpine valleys and a much more heterogeneous setting. We evaluate DNA sequence variation from both the mitochondrial and nuclear genomes in Nanorana pleskei, a species endemic to the EQTP. Hypothesis testing on the evolutionary history of N. pleskei indicates that northern populations can disperse freely, but alpine valleys isolate southern populations. Demographic histories between northern and southern populations also differ. Northern populations appear to have experienced population expansions, while southern frogs exhibit a far more stable demographic history. By combining climatic analyses and species' distribution models, our study suggests that geographic and environmental features drive the differences between the northern and southern EQTP.
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Affiliation(s)
- Weiwei Zhou
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jieqiong Jin
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences Ministry of Environmental Protection Nanjing China
| | - Hongman Chen
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Junxiao Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China; Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China; Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
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Françoso E, Zuntini AR, Carnaval AC, Arias MC. Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees. BMC Evol Biol 2016; 16:267. [PMID: 27927169 PMCID: PMC5142330 DOI: 10.1186/s12862-016-0803-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Background Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages. Results Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that the warmer conditions of the Last Interglacial contributed to population contraction, while demographic expansion happened during the Last Glacial Maximum. These results are consistent with physiological data suggesting that bumblebees are well adapted to colder conditions. Intra-specific mitochondrial genealogies are not congruent between the two species, which may be explained by their documented differences in dispersal ability. Conclusions While populations of the high-dispersal B. morio are morphologically and genetically homogeneous across the species range, B. pauloensis encompasses multiple (three) mitochondrial lineages, and show clear genetic, geographic, and morphological differences. Because the lineages of B. pauloensis are currently exposed to distinct climatic conditions (and elevations), parapatric diversification may occur within this taxon. The eastern portion of the state of São Paulo, the most urbanized area in Brazil, represents the center of genetic diversity for B. pauloensis. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0803-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elaine Françoso
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, sala 320, 05508-090, São Paulo, SP, Brazil.
| | - Alexandre Rizzo Zuntini
- Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, 13083-970, Campinas, SP, Brazil
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Maria Cristina Arias
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, sala 320, 05508-090, São Paulo, SP, Brazil
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Clewing C, Albrecht C, Wilke T. A Complex System of Glacial Sub-Refugia Drives Endemic Freshwater Biodiversity on the Tibetan Plateau. PLoS One 2016; 11:e0160286. [PMID: 27500403 PMCID: PMC4976922 DOI: 10.1371/journal.pone.0160286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/15/2016] [Indexed: 11/18/2022] Open
Abstract
Although only relatively few freshwater invertebrate families are reported from the Tibetan Plateau, the degree of endemism may be high. Many endemic lineages occur within permafrost areas, raising questions about the existence of isolated intra-plateau glacial refugia. Moreover, if such refugia existed, it might be instructive to learn whether they were associated with lakes or with more dynamic ecosystems such as ponds, wetlands, or springs. To study these hypotheses, we used pulmonate snails of the plateau-wide distributed genus Radix as model group and the Lake Donggi Cona drainage system, located in the north-eastern part of the plateau, as model site. First, we performed plateau-wide phylogenetic analyses using mtDNA data to assess the overall relationships of Radix populations inhabiting the Lake Donggi Cona system for revealing refugial lineages. We then conducted regional phylogeographical analyses applying a combination of mtDNA and nuclear AFLP markers to infer the local structure and demographic history of the most abundant endemic Radix clade for identifying location and type of (sub-)refugia within the drainage system. Our phylogenetic analysis showed a high diversity of Radix lineages in the Lake Donggi Cona system. Subsequent phylogeographical analyses of the most abundant endemic clade indicated a habitat-related clustering of genotypes and several Late Pleistocene spatial/demographic expansion events. The most parsimonious explanation for these patterns would be a scenario of an intra-plateau glacial refugium in the Lake Donggi Cona drainage system, which might have consisted of isolated sub-refugia. Though the underlying processes remain unknown, an initial separation of lake and watershed populations could have been triggered by lake-level fluctuations before and during the Last Glacial Maximum. This study inferred the first intra-plateau refugium for freshwater animals on the Tibetan Plateau. It thus sheds new light on the evolutionary history of its endemic taxa and provides important insights into the complex refugial history of a high-altitude ecosystem.
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Affiliation(s)
- Catharina Clewing
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
- * E-mail:
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Chen W, Shen Y, Gan X, Wang X, He S. Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong). Ecol Evol 2016; 6:6023-36. [PMID: 27648223 PMCID: PMC5016629 DOI: 10.1002/ece3.2319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/28/2022] Open
Abstract
The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.
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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; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Xuzhen Wang
- 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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Song S, Jiang B, Liu NF. Phylogeography of chukar partridge (Alectoris chukar) in China based on mtDNA control region. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:473-481. [PMID: 27159688 DOI: 10.3109/19401736.2015.1137901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The chukar partridge (Alectoris chukar) is distributed in north and northwest of China, in mountainous areas that were heavily affected by cyclic climate and landscape changes during the last Pleistocene glaciations. Some partridge populations have colonized and expanded their present ranges only after deglaciation and recent deforestation by human. Consequently, partridges from different areas could be genetically differentiated. In this study, a 1152-1154 bp portion of the mitochondrial DNA control region were analyzed for all 279 specimens collected from 28 populations through their distribution in China. A total number of 91 haplotypes were defined by 113 variable sites. The mean haplotype diversity and nucleotide diversity were 0.939 ± 0.008 and 0.0030 ± 0.0017, respectively, for chukar. Haplotype diversity among the 28 populations varied from 0.600 ± 0.215 (HH) to 1.000 ± 0.272 (SBC), and nucleotide diversity ranged from 0.0006 ± 0.0007 (HJ) to (0.0071 ± 0.0041) (HEG). The nucleotide diversity of chukar was descending from west to east and a possible historical scenario might be that A. chukar inhabited central Asia, and then dispersed eastward. Phylogenetic analyses indicated that there was no distinct phylogeographic structure in chukar populations in China. Haplotype network of chukar was star-like with some common haplotypes shared by different samples came from different populations as center. Both unstructured phylogeographic tree and star-like haplotype network are signatures of population expansion.
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Affiliation(s)
- Sen Song
- a School of Life Sciences, Lanzhou University , Lanzhou , P.R. China
| | - Bo Jiang
- a School of Life Sciences, Lanzhou University , Lanzhou , P.R. China
| | - Nai-Fa Liu
- a School of Life Sciences, Lanzhou University , Lanzhou , P.R. China
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He D, Chen Y, Liu C, Tao J, Ding C, Chen Y. Comparative phylogeography and evolutionary history of schizothoracine fishes in the Changtang Plateau and their implications for the lake level and Pleistocene climate fluctuations. Ecol Evol 2016; 6:656-74. [PMID: 26865956 PMCID: PMC4739559 DOI: 10.1002/ece3.1890] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/17/2015] [Accepted: 11/23/2015] [Indexed: 11/13/2022] Open
Abstract
The water level oscillation of endorheic lakes and extent change of glaciers associated with the Asian monsoon are known as prominent representatives of climatic and environmental events in the Tibetan Plateau during the Quaternary. However, details process in spatial and temporal changes are still debated. We use the schizothoracines as a palaeoclimatic proxy to test two hypotheses concerning the evolution of Quaternary glaciations and lakes of the Changtang Plateau: (1) the Tibetan glaciations generally tended to decrease since the middle Pleistocene; (2) the lakes expansion was driven by summer monsoon rainfall. Based on a wide range‐wide sampling throughout in the Changtang Plateau and its adjacent drainages, we constructed phylogeny and demographic histories of schizothoracines in the Changtang Plateau. Our results showed that the populations of the exorheic rivers and lakes in southern Tibet possessed higher genetic variability, earlier coalescent and expansion times than those of the endorheic lakes in the Changtang Plateau. Population expansions are highly consistent with phases of strong summer monsoon and high lake level during interglacial stages. The maximum growth rate intervals showed three pulses from 64.7 to 54.8, 39.6 to 31.0, and 14.9 to 2.4 kya respectively. The significant positive correlations were found between regional precipitation and genetic diversity, as well as coalescence time of populations in the endorheic lakes. We suggested that the demographic history of the schizothoracines reflects the spatial and temporal changes in climate and lake level, in particular, in regional precipitation gradients associated with changes of the South Asian monsoon, and supports the climatic hypothesis of a general diminishing tend in Tibetan glaciations in the Tibetan Plateau since the middle Pleistocene.
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Affiliation(s)
- Dekui He
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Yifeng Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Chunlong Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Juan Tao
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Chengzhi Ding
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Yiyu Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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Comparative phylogeography of Meriones meridianus, Dipus sagitta, and Allactaga sibirica: Potential indicators of the impact of the Qinghai-Tibetan Plateau uplift. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Li G, Peng Z, Zhang R, Tang Y, Tong C, Feng C, Zhang C, Zhao K. Mito-nuclear phylogeography of the cyprinid fishGymnodiptychus dybowskiiin the arid Tien Shan region of Central Asia. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12724] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Guogang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish; Reproduction and Development (Ministry of Education); Southwest University School of Life Sciences; Chongqing China
| | - Renyi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
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Liu S, Jiang N, Xue D, Cheng R, Qu Y, Li X, Lei F, Han H. Evolutionary history ofApocheima cinerarius(Lepidoptera: Geometridae), a female flightless moth in northern China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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Fahey AL, Ricklefs RE, Dewoody JA. Historical demography of bird populations from Hispaniola assessed by nuclear and mitochondrial gene sequences. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a7.2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Anna L. Fahey
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47907, U.S.A
- Missouri Southern State University, 3950 E Newman Rd, Joplin, Missouri 64801, U.S.A
| | - Robert E. Ricklefs
- Department of Biology, University of Missouri at St. Louis, St. Louis, Missouri 63121, U.S.A
| | - J. Andrew Dewoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47907, U.S.A
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, U.S.A
- Purdue University, David C. Pfendler Hall, 715 W. State Street, West Lafayette, Indiana 47907, U.S.A.
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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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Liu J, Wang C, Fu D, Hu X, Xie X, Liu P, Zhang Q, Li MH. Phylogeography of Nanorana parkeri (Anura: Ranidae) and multiple refugia on the Tibetan Plateau revealed by mitochondrial and nuclear DNA. Sci Rep 2015; 5:9857. [PMID: 25985205 PMCID: PMC4434895 DOI: 10.1038/srep09857] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/23/2015] [Indexed: 01/31/2023] Open
Abstract
Quaternary climatic changes have been recognized to influence the distribution patterns and evolutionary histories of extant organisms, but their effects on alpine species are not well understood. To investigate the Pleistocene climatic oscillations on the genetic structure of amphibians, we sequenced one mitochondrial and three nuclear DNA fragments in Nanorana parkeri, a frog endemic to the Tibetan Plateau, across its distribution range in the southern plateau. Mitochondrial cytochrome b (Cytb) and three nuclear genes (c-Myc2, Rhod, and Tyr) revealed two distinct lineages (i.e. the lineages East and West), which were strongly geographically structured. The split of the two divergent lineages was dated back earlier than the Middle Pleistocene, probably being associated with climatic and ecological factors. Species distribution modeling, together with the phylogeographic structuring, supported the hypothesis of multiple refugia for N. parkeri on the Tibetan Plateau during the Pleistocene glaciations, and suggested the Yarlung Zangbo valley and the Kyichu catchment to be the potential refugia. Our findings indicate that Pleistocene climatic changes have had a great impact on the evolution and demographic history of N. parkeri. Our study has important implications for conservation of this and other frog species in the Tibetan Plateau.
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Affiliation(s)
- Jun Liu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] Deep-Sea Research Department, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya 572000, China
| | - Cuimin Wang
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Dongli Fu
- Gansu Provincial Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaoju Hu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Xiangmo Xie
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China
| | - Pengfei Liu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Qiong Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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Wang H, Luo X, Meng S, Bei Y, Song T, Meng T, Li G, Zhang B. The Phylogeography and Population Demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive Rivers as Barriers to Gene Flow. PLoS One 2015; 10:e0125770. [PMID: 25915933 PMCID: PMC4411157 DOI: 10.1371/journal.pone.0125770] [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: 10/07/2014] [Accepted: 03/26/2015] [Indexed: 11/23/2022] Open
Abstract
Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15–17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.
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Affiliation(s)
- Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xia Luo
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Shaoquan Meng
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Yongjian Bei
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Tao Song
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Tao Meng
- Guangxi Forestry Inventory and Planning Institute, Nanning, 530011, Guangxi, China
| | - Guifen Li
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
- * E-mail: (GL); (BZ)
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- * E-mail: (GL); (BZ)
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An B, Zhang L, Liu N, Wang Y. Refugia persistence of Qinghai-Tibetan plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae). PLoS One 2015; 10:e0121118. [PMID: 25822918 PMCID: PMC4378977 DOI: 10.1371/journal.pone.0121118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/10/2015] [Indexed: 11/19/2022] Open
Abstract
Most of the temperate species are expected to have moved to lower altitudes during the glacial periods of the Quaternary. Here we tested this hypothesis in a cold-tolerant avian species Tibetan snowcock (Tetraogallus tibetanus) using two segments of mitochondrial gene (a 705bp Cytochrome-b; abbrev. Cyt-b and an 854 bp Control Region; abbrev. CR) and eight microsatellite loci by characterizing population differentiation and gene flow across its range. Combined (Cyt-b + CR) datasets detected several partially lineages with poor support. Microsatellite data, however, identified two distinct lineages congruent with the geographically separated western and central regions of Qinghai-Tibetan Plateau (QTP). The phylogeographic patterns that we observed might be explained by a combination of vicariance events that led to local isolation of T. tibetanus during warm periods and range expansions and population intermixing during cold periods. The results of this study add to our knowledge of population differentiation and connectivity in high altitude mountain ecosystems.
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Affiliation(s)
- Bei An
- School of Basic Medicine Sciences, Lanzhou University, Lanzhou, China
| | - Lixun Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou, China
- * E-mail: (LZ); (NL)
| | - Naifa Liu
- School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (LZ); (NL)
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, Shandong, China
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Wang H, Liu H, Yang M, Bao L, Ge J. Phylogeographic study of Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis Rousi) reveals two distinct haplotype groups and multiple microrefugia on the Qinghai-Tibet Plateau. Ecol Evol 2014; 4:4370-9. [PMID: 25540697 PMCID: PMC4267874 DOI: 10.1002/ece3.1295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/13/2014] [Accepted: 10/01/2014] [Indexed: 11/16/2022] Open
Abstract
Historical climate change can shape the genetic pattern of a species. Studies on this phenomenon provide great advantage in predicting the response of species to current and future global climate change. Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis) is one of the most important cultivated plants in Northwest China. However, the subspecies history and the potential genetic resources within the subspecies range remain unclear. In this study, we utilized two intergenic chloroplast regions to characterize the spatial genetic distribution of the species. We found 19 haplotypes in total, 12 of which were unique to the Chinese seabuckthorn. The populations observed on the Qinghai-Tibet Plateau (QTP) consisted of most of the haplotypes, while in the northeast of the range of the subspecies, an area not on the QTP, only four haplotypes were detected. Our study also revealed two distinct haplotype groups of the subspecies with a sharp transition region located in the south of the Zoige Basin. 89.96% of the genetic variation located between the regions. Mismatch analysis indicated old expansions of these two haplotype groups, approximately around the early stage of Pleistocene. Additional morphological proofs from existing studies and habitat differentiation supported a long independent colonization history among the two regions. Potential adaptation probably occurred but needs more genome and morphology data in future. Chinese seabuckthorn have an older population expansion compared with subspecies in Europe. The lack of large land ice sheets and the heterogeneous landscape of the QTP could have provided extensive microrefugia for Chinese seabuckthorn during the glaciation period. Multiple localities sustaining high-frequency private haplotypes support this hypothesis. Our study gives clear insight into the distribution of genetic resources and the evolutionary history of Chinese seabuckthorn.
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Affiliation(s)
- Hongfang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Han Liu
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Mingbo Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Jianping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
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Chakraborty D, Ramakrishnan U, Sinha A. Quaternary climate change and social behavior shaped the genetic differentiation of an endangered montane primate from the southern edge of the Tibetan Plateau. Am J Primatol 2014; 77:271-84. [DOI: 10.1002/ajp.22343] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Debapriyo Chakraborty
- Nature Conservation Foundation; Mysore India
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
| | - Anindya Sinha
- Nature Conservation Foundation; Mysore India
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
- National Institute of Advanced Studies; Bangalore India
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Chakraborty D, Sinha A, Ramakrishnan U. Mixed fortunes: ancient expansion and recent decline in population size of a subtropical montane primate, the Arunachal macaque Macaca munzala. PLoS One 2014; 9:e97061. [PMID: 25054863 PMCID: PMC4108313 DOI: 10.1371/journal.pone.0097061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
Quaternary glacial oscillations are known to have caused population size fluctuations in many temperate species. Species from subtropical and tropical regions are, however, considerably less studied, despite representing most of the biodiversity hotspots in the world including many highly threatened by anthropogenic activities such as hunting. These regions, consequently, pose a significant knowledge gap in terms of how their fauna have typically responded to past climatic changes. We studied an endangered primate, the Arunachal macaque Macaca munzala, from the subtropical southern edge of the Tibetan plateau, a part of the Eastern Himalaya biodiversity hotspot, also known to be highly threatened due to rampant hunting. We employed a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci to investigate the factors that have potentially shaped the demographic history of the species. Analysing the genetic data with traditional statistical methods and advance Bayesian inferential approaches, we demonstrate a limited effect of past glacial fluctuations on the demographic history of the species before the last glacial maximum, approximately 20,000 years ago. This was, however, immediately followed by a significant population expansion possibly due to warmer climatic conditions, approximately 15,000 years ago. These changes may thus represent an apparent balance between that displayed by the relatively climatically stable tropics and those of the more severe, temperate environments of the past. This study also draws attention to the possibility that a cold-tolerant species like the Arunachal macaque, which could withstand historical climate fluctuations and grow once the climate became conducive, may actually be extremely vulnerable to anthropogenic exploitation, as is perhaps indicated by its Holocene ca. 30-fold population decline, approximately 3,500 years ago. Our study thus provides a quantitative appraisal of these demographically important events, emphasising the ability to potentially infer the occurrence of two separate historical events from contemporary genetic data.
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Affiliation(s)
- Debapriyo Chakraborty
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- * E-mail:
| | - Anindya Sinha
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- National Institute of Advanced Studies, Indian Institute of Science Campus, Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
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Fahey AL, Ricklefs RE, Dewoody JA. DNA-based approaches for evaluating historical demography in terrestrial vertebrates. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12259] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L. Fahey
- Departments of Forestry and Natural Resource; Purdue University; West Lafayette Indiana 47907 USA
| | - Robert E. Ricklefs
- Department of Biology; University of Missouri at St Louis; St Louis MO 63121 USA
| | - J. Andrew Dewoody
- Departments of Forestry and Natural Resource; Purdue University; West Lafayette Indiana 47907 USA
- Biological Sciences; Purdue University; West Lafayette Indiana 47907 USA
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Liu F, Ma L, Yang C, Tu F, Xu Y, Ran J, Yue B, Zhang X. Taxonomic Status ofTetraophasis obscurusandTetraophasis szechenyii(Aves: Galliformes: Phasianidae) Based on the Complete Mitochondrial Genome. Zoolog Sci 2014; 31:160-7. [DOI: 10.2108/zsj.31.160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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40
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Intraspecific lineages of the lizard Phrynocephalus putjatia from the Qinghai-Tibetan Plateau: Impact of physical events on divergence and discordance between morphology and molecular markers. Mol Phylogenet Evol 2014; 71:288-97. [DOI: 10.1016/j.ympev.2013.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/29/2013] [Accepted: 11/03/2013] [Indexed: 11/18/2022]
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Lu B, Bi K, Fu J. A phylogeographic evaluation of the Amolops mantzorum species group: cryptic species and plateau uplift. Mol Phylogenet Evol 2014; 73:40-52. [PMID: 24462636 DOI: 10.1016/j.ympev.2014.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 11/24/2022]
Abstract
Phylogeographic analysis brings organism phylogeny, regional geological/climatic history, and population demography together, and provides insights into species history and speciation. Using DNA sequence data from a mitochondrial marker (cytochrome b) and a nuclear marker (cmyc intron 2), we examined phylogeography of the Amolops mantzorum species group. We first constructed Bayesian and maximum-likelihood gene trees and medium-joint networks for the recovered haplotypes, and estimated divergence time for each major lineage. Species boundaries were then delineated using the general mixed Yule-coalescent model (GMYC) and a Bayesian species-delimitation method (BP&P). Potential gene flow between putative species was also estimated using the isolation-with-migration model. Furthermore, species-distribution modeling was used to probe linkage between climatic changes and speciation. Lastly, extended Bayesian skyline plotting was employed to reveal historical demography for each putative species. Our analyses clearly delimit nine species in the group, including four well-recognized species and five putative species, of which three are often listed as synonyms of A. mantzorum. The nominal species A. mantzorum may in fact include two cryptic species. Divergence-time estimates align the speciation events with the recent intense uplift of the Tibetan Plateau in the last 3.6 million years. The species-distribution modeling also reveals different habitat preferences among species that are potentially linked to climatic changes associated with the uplift. Furthermore, three species sustained continuous population growth through the last glaciation, while others expanded only after the last glaciation. The eastern escarpment of Tibet is a biodiversity hotspot; its rich species diversity, unique topography, and well-established geological history provide an excellent system for evolutionary studies.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, Sichuan, China
| | - Ke Bi
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, Sichuan, China; Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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42
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Qu Y, Ericson PGP, Quan Q, Song G, Zhang R, Gao B, Lei F. Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya. Mol Ecol 2014; 23:705-20. [DOI: 10.1111/mec.12619] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Per G. P. Ericson
- Department of Vertebrate Zoology; Swedish Museum of Natural History; PO Box 50007 SE-10405 Stockholm Sweden
| | - Qing Quan
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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43
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Gu L, Liu Y, Que P, Zhang Z. Quaternary climate and environmental changes have shaped genetic differentiation in a Chinese pheasant endemic to the eastern margin of the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2013; 67:129-39. [DOI: 10.1016/j.ympev.2012.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 12/13/2012] [Accepted: 12/15/2012] [Indexed: 10/27/2022]
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44
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Yu G, Zhang M, Rao D, Yang J. Effect of Pleistocene climatic oscillations on the phylogeography and demography of red knobby newt (Tylototriton shanjing) from southwestern China. PLoS One 2013; 8:e56066. [PMID: 23424644 PMCID: PMC3570421 DOI: 10.1371/journal.pone.0056066] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022] Open
Abstract
Factors that determine the genetic structure of species in southwestern China remain largely unknown. In this study, phylogeography and demography of Tylototriton shanjing was investigated from a mitochondrial perspective to address the role of the Quaternary ice ages in shaping phylogeographic history and genetic diversity of Yunnan. A total of 146 individuals from 19 populations across the entire range of the species were collected. We detected four maternal phylogenetic lineages corresponding to four population groups, and found that major glaciation events during the Pleistocene have triggered the intra-specific divergence. Coalescent simulations indicated that the populations retreated to different refugia located in southern Yunnan, northwestern Yunnan, the border region of western Yunnan with Myanmar, and middle-western Yunnan, respectively, during previous glacial periods in the Pleistocene, and these four refugia were not retained during the Last Glacial Maximum. Population expansions occurred during the last inter-glaciation, during which ice core and pollen data indicated that the temperature and precipitation gradually increased, and declines of population sizes started after the beginning of the Last Glacial Maximum when the climate became cooler and dryer. The paleo-drainage system had no contribution to the current genetic structure and the rivers were not dispersal barriers for this salamander.
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Affiliation(s)
- Guohua Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingwang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- College of Animal Science and Technology, Sichuan Agricultural University, Ya’an, Sichuan, China
- * E-mail: (DR); (JY); (MZ)
| | - Dingqi Rao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (DR); (JY); (MZ)
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (DR); (JY); (MZ)
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45
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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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46
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Fjeldså J, Bowie RC, Rahbek C. The Role of Mountain Ranges in the Diversification of Birds. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-102710-145113] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jon Fjeldså
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;
| | - Rauri C.K. Bowie
- Museum of Vertebrate Zoology & Department of Integrative Biology, University of California, Berkeley, California 94720;
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark;
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47
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Zhou W, Yan F, Fu J, Wu S, Murphy RW, Che J, Zhang Y. River islands, refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura, Ranidae) of the Qinghai-Tibetan Plateau. Mol Ecol 2012; 22:130-42. [PMID: 23116243 DOI: 10.1111/mec.12087] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/30/2012] [Accepted: 09/04/2012] [Indexed: 11/30/2022]
Abstract
Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai-Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re-treat to south-eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG-1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north-eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.
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Affiliation(s)
- Weiwei Zhou
- 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
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48
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Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F. Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus). Mol Ecol 2012; 21:6117-33. [DOI: 10.1111/mec.12080] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 09/03/2012] [Accepted: 09/11/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Qing Quan
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Shou Hsien Li
- Department of Life Science; National Taiwan Normal University; Taibei; Taiwan
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
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49
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Yan HF, Zhang CY, Wang FY, Hu CM, Ge XJ, Hao G. Population expanding with the phalanx model and lineages split by environmental heterogeneity: a case study of Primula obconica in subtropical China. PLoS One 2012; 7:e41315. [PMID: 23028425 PMCID: PMC3446961 DOI: 10.1371/journal.pone.0041315] [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: 01/05/2012] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Current and historical events have both affected the current distribution patterns and intraspecific divergence of plants. While numerous studies have focused on the Qinghai-Tibetan Plateau (QTP), the impacts of such events on the flora of subtropical China remain poorly understood. Subtropical China is famous for its highly complex topography and the limited impact from glaciation during the Pleistocene; this may have resulted in a different genetic legacy for species in this region compared to fully glaciated areas. METHODOLOGY/PRINCIPAL FINDINGS We used plastid and nuclear DNA sequence data and distribution modeling to analyze the divergence patterns and demographic history of Primula obconica Hance, a widespread herbaceous montane species in subtropical China. The phylogenetic analysis revealed two major lineages (lineage A and lineage B), representing a west-east split into the Yunnan and Eastern groups, and the Sichuan and Central groups, respectively. The Eastern and Central groups comprised relatively new derived haplotypes. Nested Clade Analysis and Bayesian Skyline Plot analyses both indicated that P. obconica mainly experienced a gradual expansion of populations. In addition, the simulated distribution of P. obconica during the Last Glacial Maximum was slightly larger than its present-day distribution. CONCLUSION/SIGNIFICANCE Our results are the first to identify a west-east migration of P. obconica. The gradual expansion pattern and a larger potential distribution range in cold periods detected for P. obconica indicate that the population expansion of this species is consistent with the phalanx model. In addition, the current patterns of genetic differentiation have persisted as a result of the extensive environmental heterogeneity that exists in subtropical China.
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Affiliation(s)
- Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Cai-Yun Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Feng-Ying Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Chi-Ming Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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50
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Phylogeography of the Phrynocephalus vlangalii Species Complex in the Upper Reaches of the Yellow River Inferred from mtDNA ND4-tRNALEU Segments. ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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