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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] [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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2
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She H, Jiang Z, Song G, Ericson PGP, Luo X, Shao S, Lei F, Qu Y. Quantifying adaptive divergence of the snowfinches in a common landscape. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Huishang She
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science University of Chinese Academy of Sciences Beijing China
| | - Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science University of Chinese Academy of Sciences Beijing China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Xu Luo
- Faculty of Biodiversity and Conservation Southwest Forestry University Kunming China
| | - Shimiao Shao
- 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
- College of Life Science University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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3
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Cheng R, Han H, Xue D, Zhu C, Jiang N. Shennongjia-Wushan Mountains-One cryptic glacial refugium introduced by the phylogeographical study of the Geometridae moth Ourapteryx szechuana Wehrli. Ecol Evol 2021; 11:10066-10076. [PMID: 34367559 PMCID: PMC8328460 DOI: 10.1002/ece3.7794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/10/2021] [Accepted: 05/28/2021] [Indexed: 12/03/2022] Open
Abstract
The origin and evolution of biodiversity in the Shennongjia and Wushan Mountains, located in central China, are little known. In this study, we used Ourapteryx szechuana, which is widely distributed in China and northern Nepal, to explore whether these mountains acted as glacial refugia during climate oscillations of the Quaternary. In total, 192 samples of O. szechuana were collected throughout much of the distribution range. Phylogenetic analysis, molecular dating, demographic history reconstructions, and MAXENT were used to investigate the evolutionary history and differentiation mechanisms and predict the potential species distributions during four different periods. The phylogenetic tree and the star-like median-joining network strongly supported two reciprocally monophyletic and allopatric lineages. Lineage I was restricted to the Shennongjia and Wushan Mountains. The divergence time of O. szechuana from its sister species O. thibetaria was approximately 1.94 Ma. The differentiation processes of the two intraspecific lineages occurred at approximately 0.47 Ma. The demographic history reconstruction and the ecological niche model suggested that Lineage II experienced an expansion after the LGM (Last Glacial Maximum), whereas Lineage I did not experience any expansion. Our results suggested the Naynayxungla glaciation promoted the divergence of the two lineages by restricting them to different refugia. The valleys of the Shennongjia-Wushan Mountains may have kept stable and warm (thus ice-free) environments during Quaternary glaciations, allowing this region to act as a glacial refugia. Our studies show that the Shennongjia and Wushan Mountains are likely to be important but little studied glacial refugia for the insect and thus worthy of more attention.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Nan Jiang
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
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4
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Qu Y, Chen C, Chen X, Hao Y, She H, Wang M, Ericson PGP, Lin H, Cai T, Song G, Jia C, Chen C, Zhang H, Li J, Liang L, Wu T, Zhao J, Gao Q, Zhang G, Zhai W, Zhang C, Zhang YE, Lei F. The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau. Proc Natl Acad Sci U S A 2021; 118:e2012398118. [PMID: 33753478 PMCID: PMC8020664 DOI: 10.1073/pnas.2012398118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.
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Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Xiumin Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Mengxia Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Haiyan Lin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Jiang Li
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Tianyu Wu
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Jinyang Zhao
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Guojie Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China;
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
- Chinese Institute for Brain Research, 102206 Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
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5
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Li D, Davis JE, Sun Y, Wang G, Nabi G, Wingfield JC, Lei F. Coping with extremes: convergences of habitat use, territoriality, and diet in summer but divergences in winter between two sympatric snow finches on the Qinghai-Tibet Plateau. Integr Zool 2020; 15:533-543. [PMID: 32627943 DOI: 10.1111/1749-4877.12462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the Qinghai-Tibet Plateau, extreme environmental conditions have imposed intense selective pressure on the evolution of phenotypic traits of wild animals. To date, limited information is available on behavioral and ecological traits concerning niche differentiation among sympatric animals on the Qinghai-Tibet Plateau, especially during winter when the environments are most severe. Here, we studied the seasonal variations in habitat occurrence, territorial behavior, and diet in two sympatric snow finches (the white-rumped snow finch, Onychostruthus taczanowskii, WRSF; and the rufous-necked snow finch, Pyrgilauda ruficollis, RNSF) to determine convergence and divergence of ecological traits in such severe climatic conditions. Our results showed that: (i) WRSF occupied rural areas as a dominant species throughout the annual cycle while RNSF occupied the rural areas in summer and then shifted to human-occupied areas in winter and spring; (ii) WRSFs exhibited robust aggressive behavior and territoriality during winter relative to RNSFs; (iii) the diets of both species varied with the season but did not vary between species except that WRSF ate significantly more seeds but RNSF consumed more starchy material derived from human food waste during winter. Therefore, the separations in the spatial niche and territoriality between WRSF and RNSF, especially in winter, may contribute to alleviating the pressure of interspecific competition, and promoting the coexistence of the two sympatric snow finches in the extreme environments on the Qinghai-Tibet Plateau.
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Affiliation(s)
- Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei Province, China.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, USA
| | - Jason E Davis
- Department of Biology, Radford University, Radford, Virginia, USA
| | - Yanfeng Sun
- Ocean College, Hebei Agricultural University, Qinhuangdao, Hebei Province, China
| | - Gang Wang
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, USA
| | - Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei Province, China
| | - John C Wingfield
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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6
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Li D, Davis JE, Wang G, Nabi G, Bishop VR, Sun Y, Meddle SL, Wingfield JC, Lei F. Coping with extremes: Remarkably blunt adrenocortical responses to acute stress in two sympatric snow finches on the Qinghai-Tibet Plateau during winter relative to other seasons. Gen Comp Endocrinol 2020; 291:113434. [PMID: 32057911 DOI: 10.1016/j.ygcen.2020.113434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/02/2020] [Accepted: 02/09/2020] [Indexed: 11/24/2022]
Abstract
The extreme climatic conditions (ECCs) of the Qinghai-Tibet Plateau impose strong selective pressures on the evolution of phenotypic traits in free-living animals. It is not well understood how animals on the Qinghai-Tibet Plateau modify their adrenocortical functions in response to both predictable and unpredictable events of ECCs, especially when the available resources are lowest during the wintering life-history stage. To uncover potential physiological mechanisms, we studied the life history stage dependent features of morphology, the plasma corticosterone response to acute stress and brain glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) mRNA expression in two sympatric snow finches: the white-rumped snow finch (Onychostruthus taczanowskii, WRSF); and the rufous-necked snow finch, Pyrgilauda ruficollis, RNSF) in Qinghai Province, China. Our results showed that (a) baseline corticosterone and stressor-induced corticosterone levels significantly varied with life history stage, but not between the species; (b) in WRSF, GR mRNA expression in the paraventricular nucleus was higher in the wintering stage compared to the pre-basic molt stage. There were no differences in hippocampus MR mRNA expression between stages in either species; (c) in the wintering stage, the suppression of corticosterone secretion in both species was an unexpected strategy in free-living animals. Both convergent and divergent phenotypic traits of adrenocortical responses to acute stress in two sympatric snow finches contribute to our understanding of the coping mechanisms of closely related species in the severe winter on the Qinghai-Tibet Plateau.
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Affiliation(s)
- Dongming Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China; Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USA
| | - Jason E Davis
- Department of Biology, Radford University, Radford, VA, USA
| | - Gang Wang
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USA
| | - Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Valerie R Bishop
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
| | - Yanfeng Sun
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Simone L Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
| | - John C Wingfield
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USA.
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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7
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Schweizer M, Liu Y, Olsson U, Shirihai H, Huang Q, Leader PJ, Copete JL, Kirwan GM, Chen G, Svensson L. Contrasting patterns of diversification in two sister species of martins (Aves: Hirundinidae): The Sand Martin Riparia riparia and the Pale Martin R. diluta. Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.02.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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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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9
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Zhang H, Li W, Hu Y, Zhang Y. Opposite companion effect on flight initiation distance in sympatric species: plateau pika ( Ochotona curzoniae) and White-rumped Snowfinch ( Onychostruthus taczanowskii). CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There are many factors influencing prey’s risk perception and escape decision during predator–prey encounters. The distance at which animals move away from perceived danger (often quantified as flight initiation distance or FID) has been used by behavioral ecologists to understand the economics of antipredator behavior. Using general linear models, we investigated escape decision-making processes in plateau pika (Ochotona curzoniae (Hodgson, 1858)) and White-rumped Snowfinch (Onychostruthus taczanowskii (Prjevalsky, 1876), formerly known as Montifringilla taczanowskii Przewalski, 1876) together and we found that (i) there are significant positive correlations between starting distance and FID in both species; (ii) pika escapes at a longer distance from an approaching intruder when it is far from its burrow; (iii) foraging animals tolerate closer distances than watching ones, both in pikas and in Snowfinches; (iv) conspecifics seem to have no effect on pikas’ escaping behavior, while the appearance of Snowfinches dramatically decreases the FID of pikas. On the contrary, conspecifics significantly decrease the FID of Snowfinches, while the presence of pikas has no effects. These findings provide new evidence, which are consistent with optimal escape theory. These novel results in multispecies interactions prompt us to pay attention to the potential relationship between pikas and Snowfinches, as well as the “bird–pika in one hole” phenomenon.
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Affiliation(s)
- He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yanping Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
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10
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Ma Y, Wang X, Huang Y, Lei F. Complete mitochondrial genome of the Onychostruthus taczanowskii (Aves, Passeridae) and its phylogenetic analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2984-5. [DOI: 10.3109/19401736.2015.1060473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yonggui Ma
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi’an, China,
- Ministry of Education Key Laboratory of Qinghai-Tibet Plateau Resources and Environment, Qinghai Normal University, Xining, China, and
| | - Xiaoyang Wang
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi’an, China,
| | - Yuan Huang
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi’an, China,
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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11
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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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12
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Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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13
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Pitfalls in comparisons of genetic distances: a case study of the avian family Acrocephalidae. Mol Phylogenet Evol 2011; 62:319-28. [PMID: 22023826 DOI: 10.1016/j.ympev.2011.10.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 08/09/2011] [Accepted: 10/03/2011] [Indexed: 11/22/2022]
Abstract
Genetic distances are increasingly being used for identification and species delimitation, especially since the introduction of "barcoding". While for phylogenetic inferences great care is generally taken to choose the best-fit evolutionary model, this is usually neglected in calculating genetic distances. Moreover, distances obtained from others than best-fit models, different lengths of sequences, and even different loci are often freely compared. We examined the influence of different methods on calculating genetic distances using mitochondrial cytochrome b sequences for the passerine family Acrocephalidae. We found substantial differences between: (1) corrected distances based on the best-fit model (TrN+Γ) vs. uncorrected p-distances; (2) distances calculated based on different parts of the same gene; and (3) distances calculated using the methods of "complete deletion" vs. "pairwise deletion" for sequences that included uncertain nucleotides. All these methodological differences affected comparisons between species and potential taxonomical conclusions. We suggest that (1) different loci are incomparable. (2) Only perfectly homologous regions (same length, same part of locus) should be compared. (3) In the case of sequences with some uncertain nucleotides, only distances calculated by the method of "complete deletion" are fully comparable. (4) Only distances based on the optimal substitution model should be used. (5) Even within the same locus, corrected genetic distances are unique to the study in which they are calculated, as they are conditional on the particular dataset and model selected for that dataset.
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14
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Phylogeography of Phrynocephalus erythrurus from the Qiangtang Plateau of the Tibetan Plateau. Mol Phylogenet Evol 2009; 54:933-40. [PMID: 19900565 DOI: 10.1016/j.ympev.2009.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 10/16/2009] [Accepted: 11/01/2009] [Indexed: 11/18/2022]
Abstract
Phrynocephalus erythrurus of the Qiangtang Plateau occupies the highest regions of any reptile on earth. Here, we report mitochondrial DNA haplotypes sampled throughout the distribution of P. erythrurus and analyze patterns of genetic divergence among populations. The species diverged into two major lineages/subspecies at 3.67mya corresponding to the Northern and Southern Qiangtang Plateau. The Northern Qiangtang lineage diverged into two subpopulations at 2.76mya separated by the Beilu River Region and Wulanwula Mountains. Haplotypes from the southern Qiangtang lineage diverged 0.98mya as a star-shaped pattern. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruptions to gene flow. There was no evidence of sudden recent range expansions within any of the clades/lineages. NCPA infers allopatric fragmentation and restricted gene flow as the most likely mechanisms of population differentiation. Our results also indicate the presence of at least three refugia since the Hongya glaciation. Mountain movement and glaciations since mid-Pliocene are considered to have shaped phylogenetic patterns of P. erythrurus. P. erythrurus parva is suggested as a valid subspecies of P. erythrurus. Using four calibration points, we estimate an evolutionary rate of 0.762% divergence per lineage per million years for a mitochondrial genomic segment comprising the genes encoding ND2, tRNA(Trp) and tRNA(Ala).
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Liu Z, Ren B, Wu R, Zhao L, Hao Y, Wang B, Wei F, Long Y, Li M. The effect of landscape features on population genetic structure in Yunnan snub-nosed monkeys (Rhinopithecus bieti) implies an anthropogenic genetic discontinuity. Mol Ecol 2009; 18:3831-46. [PMID: 19732331 DOI: 10.1111/j.1365-294x.2009.04330.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub-nosed monkey (Rhinopithecus bieti), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% (r = 0.51, P = 0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti. Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.
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Affiliation(s)
- Zhijin Liu
- Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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16
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Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume’s ground tit (Pseudopodoces humilis). Mol Phylogenet Evol 2009; 51:312-26. [DOI: 10.1016/j.ympev.2009.01.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Interspecific dominance and asymmetric competition with respect to nesting habitats between two snowfinch species in a high-altitude extreme environment. Ecol Res 2008. [DOI: 10.1007/s11284-008-0530-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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A molecular phylogeny of the Sylvia cantillans complex: cryptic species within the Mediterranean basin. Mol Phylogenet Evol 2008; 48:461-72. [PMID: 18590968 DOI: 10.1016/j.ympev.2008.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 05/07/2008] [Accepted: 05/08/2008] [Indexed: 11/20/2022]
Abstract
The subalpine warbler Sylvia cantillans is formally considered a polytypic species, with four subspecies, European S. c. cantillans, albistriata, moltonii (recently resumed name: subalpina) and North African S. c.inornata. They are very similar in external morphology but clearly differ in their vocalizations. We evaluated their uncertain taxonomic status reconstructing the phylogenetic and phylogeographic relationships among populations sampled across major biogeographical areas in the European species' range, using nucleotide sequences of the mitochondrial cytochrome b gene (mtDNA cyt b). A variety of phylogenetic analyses concordantly led to identify four major groups, only partially corresponding to the three European nominal subspecies. Phylogenetic trees showed a monophyletic group including all moltonii individuals, well diverged from all other taxa. Populations taxonomically assigned to cantillans were polyphyletic being split into two distinct clades (western and southern cantillans), with monophyletic albistriata closely related to southern cantillans. Individuals of moltonii and southern cantillans sampled in sites of sympatry in central Italy were assigned to their respective groups, with perfect concordance between phenotypic and genetic identifications. All findings indicate that moltonii should be ranked as a distinct species. Former subspecies cantillans is polyphyletic, but additional data are needed to define the taxonomic status of its two clades. Albistriata is phylogenetically related to southern cantillans and should be provisionally kept as a subspecies of S. cantillans. The cantillans complex thus provides an interesting case-study illustrating geographical structuring across small geographical ranges, and it exemplifies speciation through differentiation in allopatry leading to reproductive isolation after a secondary contact.
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JIN YUANTING, BROWN RICHARDP, LIU NAIFA. Cladogenesis and phylogeography of the lizardPhrynocephalus vlangalii(Agamidae) on the Tibetan plateau. Mol Ecol 2008; 17:1971-82. [DOI: 10.1111/j.1365-294x.2008.03721.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Peterson AT, Moyle RG, Nyári AS, Robbins MB, Brumfield RT, Remsen JV. The need for proper vouchering in phylogenetic studies of birds. Mol Phylogenet Evol 2007; 45:1042-4. [PMID: 17962047 DOI: 10.1016/j.ympev.2007.08.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 08/28/2007] [Accepted: 08/30/2007] [Indexed: 11/29/2022]
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