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Cheng R, Xue D, Han H, Zhu C. Patterns of endemism of the Chinese Larentiinae (Lepidoptera: Geometridae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21891. [PMID: 35398935 DOI: 10.1002/arch.21891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Chinese Larentiinae is exceptionally rich in species since it spans the Palearctic realm and the Oriental realm, comprising 715 species belonging to 130 genera. Among them, nearly half species are endemic. This taxon is considered an ideal object for the study of endemic patterns. In this study, parsimony analysis of endemicity was used to delineate areas of endemisms (AOEs), and track compatibility analysis (TCA) was used to perform the TCA. Eight AOEs were supported. Except for five AOEs around the Qinghai-Tibet plateau (QTP), two AOEs from northern China and Taiwan islands were found. Twenty-two generalized tracks were obtained from the combination of the track analysis and the AOEs. The uplift of the QTP was assumed to greatly influence these endemic patterns, presented an appearance of highly centralized endemism and diversity in the eastern and southern edges of the QTP. And the AOE of Mt. Hengduan was considered as a major center of development through recent geological history, where strong evolutionary radiation might have taken place, resulting in the migration routes described by the generalized tracks from this center to various regions in various directions.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Chen YJ, Zhu L, Wu QN, Hu CC, Qu YF, Ji X. Geological and climatic influences on population differentiation of the Phrynocephalus vlangalii species complex (Sauria: Agamidae) in the northern Qinghai-Tibet Plateau. Mol Phylogenet Evol 2022; 169:107394. [PMID: 35045310 DOI: 10.1016/j.ympev.2022.107394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/06/2021] [Accepted: 12/25/2021] [Indexed: 11/26/2022]
Abstract
Extremely heterogeneous topography and complex paleoclimate history of the Qinghai-Tibet Plateau (QTP) have a key role in promoting genetic divergence and lineage/species formation. Here, we sequenced one nuclear and three mitochondrial markers of 532 individuals from the entire range of the Phrynocephalus vlangalii species complex including two species, P. putjatai and P. vlangalii, endemic to the northern QTP. We integrated multilocus phylogeny, demographic analysis and geographic barrier detection to evaluate the population structure and dynamics. We found a new mitochondrial clade (PV-I) in the Gonghe County population of P. vlangalii, partial mitochondrial DNA replacement within P. vlangalii and complete mitochondrial DNA replacement between P. putjatai and P. vlangalii. Neutrality test, mismatch distribution analysis and Extended Bayesian Skyline Plot (EBSP) analysis all supported a significant expansion of the Qaidam Basin population of P. vlangalii (PV-II-2) from 0.091 to 0.026 Ma after Penultimate Glaciation. The uplift of the Arjin and Anyemanqen Mountains during the Kunhuang Movement (∼1.2 Ma) split populations of P. vlangalii in Akesai, Qaidam Basin and source of the Yellow River. The uplift of the Elashan Mountains during the second phase of the Qingzang Movement (∼2.5 Ma) contributed to the divergence of the Gonghe County population of P. vlangalii from other conspecific populations. The third phase of the Qingzang Movement (∼1.7 Ma) contributed to the divergence of the Xinghai population of P. vlangalii from P. putjatai and to the divergence of the northern populations of P. putjatai from the southern conspecific populations. Our data support the idea that the geological and climatic changes following the orogeny of the QTP may have promoted population differentiation and shaped the current population patterns of the P. vlangalii species complex in the northeastern QTP.
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Affiliation(s)
- Yi-Jing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Qian-Nian Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Chao-Chao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China.
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China; College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, Zhejiang, China.
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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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Solovyeva EN, Lebedev VS, Dunayev EA, Nazarov RA, Bannikova AA, Che J, Murphy RW, Poyarkov NA. Cenozoic aridization in Central Eurasia shaped diversification of toad-headed agamas ( Phrynocephalus; Agamidae, Reptilia). PeerJ 2018; 6:e4543. [PMID: 29576991 PMCID: PMC5863718 DOI: 10.7717/peerj.4543] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/06/2018] [Indexed: 12/03/2022] Open
Abstract
We hypothesize the phylogenetic relationships of the agamid genus Phrynocephalus to assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors. Phrynocephalus is one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species of Phrynocephalus covering all major areas of the genus. Molecular data included four mtDNA (COI, ND2, ND4, Cytb; 2,703 bp) and four nuDNA protein-coding genes (RAG1, BDNF, AKAP9, NKTR; 4,188 bp). AU-tests were implemented to test for significant differences between mtDNA- and nuDNA-based topologies. A time-calibrated phylogeny was estimated using a Bayesian relaxed molecular clock with nine fossil calibrations. We reconstructed the ancestral area of origin, biogeographic scenarios, body size, and the evolution of habitat preference. Phylogenetic analyses of nuDNA genes recovered a well-resolved and supported topology. Analyses detected significant discordance with the less-supported mtDNA genealogy. The position of Phrynocephalus mystaceus conflicted greatly between the two datasets. MtDNA introgression due to ancient hybridization best explained this result. Monophyletic Phrynocephalus contained three main clades: (I) oviparous species from south-western and Middle Asia; (II) viviparous species of Qinghai–Tibetan Plateau (QTP); and (III) oviparous species of the Caspian Basin, Middle and Central Asia. Phrynocephalus originated in late Oligocene (26.9 Ma) and modern species diversified during the middle Miocene (14.8–13.5 Ma). The reconstruction of ancestral areas indicated that Phrynocephalus originated in Middle East–southern Middle Asia. Body size miniaturization likely occurred early in the history of Phrynocephalus. The common ancestor of Phrynocephalus probably preferred sandy substrates with the inclusion of clay or gravel. The time of Agaminae radiation and origin of Phrynocephalus in the late Oligocene significantly precedes the landbridge between Afro-Arabia and Eurasia in the Early Miocene. Diversification of Phrynocephalus coincides well with the mid-Miocene climatic transition when a rapid cooling of climate drove progressing aridification and the Paratethys salinity crisis. These factors likely triggered the spreading of desert habitats in Central Eurasia, which Phrynocephalus occupied. The origin of the viviparous Tibetan clade has been associated traditionally with uplifting of the QTP; however, further studies are needed to confirm this. Progressing late Miocene aridification, the decrease of the Paratethys Basin, orogenesis, and Plio–Pleistocene climate oscillations likely promoted further diversification within Phrynocephalus. We discuss Phrynocephalus taxonomy in scope of the new analyses.
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Affiliation(s)
| | | | - Evgeniy A Dunayev
- Zoological Museum, Lomonosov Moscow State University, Moscow, Russia
| | - Roman A Nazarov
- Zoological Museum, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A Bannikova
- Biological Faculty, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Faculty of Arts and Science, Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nikolay A Poyarkov
- Biological Faculty, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
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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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FENG PING, YANG GUANG, LU XIN. Development of twenty microsatellite loci from the Tibetan ground tit (Parus humilis). J Genet 2016. [DOI: 10.1007/s12041-013-0248-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Li X, Lin L, Cui A, Bai J, Wang X, Xin C, Zhang Z, Yang C, Gao R, Huang Y, Lei F. Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments. Mol Phylogenet Evol 2016; 104:14-20. [DOI: 10.1016/j.ympev.2016.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/20/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022]
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8
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Shao S, Quan Q, Cai T, Song G, Qu Y, Lei F. Evolution of body morphology and beak shape revealed by a morphometric analysis of 14 Paridae species. Front Zool 2016; 13:30. [PMID: 27366199 PMCID: PMC4928266 DOI: 10.1186/s12983-016-0162-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 06/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Morphological characters of birds reflect their adaptive evolution and ecological requirements and are also relevant to phylogenetic relationships within a group of related species. The tits (Paridae) are known to be outwardly homogeneous in shape, with one aberrant member, the Ground Tit (Pseudopodoces humilis), which is quite different from its relatives in both body morphology and beak shape. We combined traditional measurements and geometric morphometrics to quantify the variation in body morphology and beak shape of 14 Paridae species distributed in China. Based on these results, we sought to assess the contribution of phylogeny, altitude and species interactions to the evolution of morphological traits. RESULTS The basic features for discriminating among the 14 species studied here were overall body size, the ratio of body and tail length to culmen and tarsus length, and beak shape (long/slender/pointy vs. short/robust/blunt). These dimensions clearly separate Ps. humilis and Melanochlora sultanea from the other species in shape space. Body length and PC3 of beak shape (round outline vs. straight outline) show significant phylogenetic signals. Across 14 species, altitude is related to tarsus, culmen length and PC1 of beak shape. Within Parus major, altitude is related to body weight, body length, culmen length and PC1 of body morphology. Morphological distances and geographic distances among species are positively correlated. CONCLUSIONS The body morphology of Paridae species shows extensive evolutionary changes, while their beak has mainly evolved along the long/slender/pointy vs. short/robust/blunt dimension. Only body length and beak curvature show a phylogenetic signal. Altitude correlates with multiple traits both across and within species, suggesting that altitude is an important factor in promoting morphological divergence. The deviant appearance of Ps. humilis corresponds to its foraging and feeding adaptations to high-altitude steppe habitats. Our results also show a higher level of morphological divergence with greater difference in distribution ranges among the Paridae species involved in this study.
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Affiliation(s)
- Shimiao Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ; University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qing Quan
- Guangdong Entomological Institute, Chinese Academy of Sciences, Guangdong, 510260 China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ; University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, 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
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10
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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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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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Liu G, Zhou L, Li X, Lu D. Population Genetic Structure of the Invasive Red Swamp Crayfish in China Revealed by ITS1 Variation. Biochem Genet 2013; 51:841-52. [DOI: 10.1007/s10528-013-9611-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 01/08/2013] [Indexed: 10/26/2022]
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13
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Jin YT, Brown RP. Species history and divergence times of viviparous and oviparous Chinese toad-headed sand lizards (Phrynocephalus) on the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2013; 68:259-68. [PMID: 23567019 DOI: 10.1016/j.ympev.2013.03.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 03/11/2013] [Accepted: 03/24/2013] [Indexed: 11/26/2022]
Abstract
The Qinghai-Tibetan Plateau (QTP) is an important biogeographical area and has recently become a focus for biodiversity studies. Phyrnocephalus lizards form a widespread Eurasian group with oviparous and viviparous reproductive modes, but two previous mtDNA studies of species from around the QTP have provided different phylogenetic hypotheses. We analysed three loci (mtDNA, RAG-1, AME) from all recognised Chinese Phrynocephalus species to reconstruct the speciation history of the group and to estimate species divergence times. The effects of mtDNA partitioning strategy on phylogenetic inference were examined. Bayes factor comparisons of marginal likelihoods (mLs) estimated using stepping-stone sampling revealed that partitioning strategy had a major impact on mL. Nevertheless, it had a negligible effect on the inferred tree topology. The impact of hard-bound uniform or equivalent soft-bound gamma speciation time calibration priors as well as the use of a fixed topology (as opposed to integration over all possible species histories) on divergence time estimation were also assessed, and found to have little impact on posterior estimates. All three gene trees and the species tree supported the hypothesis that the Chinese species form oviparous and viviparous sister clades. This was in agreement with an early mtDNA study but differed from a subsequent reanalysis of the mtDNA data. Inclusion of mtDNA from more widely distributed Phrynocephalus (from previous studies) indicates that the oviparous P. interscapularis from Central Asia lies outside the clade of Chinese viviparous and oviparous species, but that other Asian oviparous species lie within the Chinese oviparous clade. The median of the posterior on the divergence time of Chinese oviparous and viviparous species was 9.7 Ma ago (95% interval: 7.2-13.0 Ma ago), which coincides with major uplifting of the QTP and indicates that viviparity evolved when this clade became restricted to regions of high elevation. We also found that cladogenesis within the viviparous clade began around 5 Ma ago whereas those in the oviparous clade began around 8.6 Ma ago. We establish more robust estimates of divergence times and relationships within this important group and so provide improved insights into the origins of Phrynocephalus diversity across the QTP.
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Affiliation(s)
- Y-T Jin
- Department of Biology, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, PR China
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Cao M, Jin Y, Liu N, Ji W. Effects of the Qinghai-Tibetan Plateau uplift and environmental changes on phylogeographic structure of the Daurian Partridge (Perdix dauuricae) in China. Mol Phylogenet Evol 2012; 65:823-30. [PMID: 22940153 DOI: 10.1016/j.ympev.2012.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 07/23/2012] [Accepted: 08/07/2012] [Indexed: 11/15/2022]
Abstract
Data from eight microsatellite loci were used to assess the evolutionary demographic processes of Daurian Partridges from 285 individuals distributed among 23 populations throughout much of the species' distribution range in China. Phylogenetic analysis using microsatellite DNA data indicated that the species were geographically structured and were split into two distinctive phylogroups A and B, splitting partridges geographically from high plateaus vs. lowlands in northern China with high bootstrap support in phylogenetic trees. Each of cluster A and cluster B was comprised with two subgroups respectively. Cluster A was further subdivided into the Loess Plateau group and the Qinghai-Tibetan group. Two subgroups of cluster B corresponded to populations of Liupan Mountains and northern China, respectively. This subdivision was confirmed by Bayesian clustering and population assignment analyses of microsatellite genotypes which indicated strong isolation of these groups/populations. Our results suggested that the vicariance patterns of genetic structures of Daurian Partridge may have resulted from: (1) the uplift of the Qinghai-Tibetan Plateau and the Loess Plateau followed by the increased aridification and desertification in northern China in Middle Pleistocene, (2) the monsoon and the existence of Qinling Mountains and Liupan Mountains, and (3) the glacial cycles from the late of Middle Pleistocene to early of Late Pleistocene. In addition, BOTTLENECK analysis indicated that Daurian Partridge had been experienced recent evolutionary bottlenecks.
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Affiliation(s)
- Manman Cao
- School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China
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15
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Liu S, Liu Y, Guo P, Sun Z, Murphy RW, Fan Z, Fu J, Zhang Y. Phylogeny of Oriental Voles (Rodentia: Muridae: Arvicolinae): Molecular and Morphological Evidence. Zoolog Sci 2012; 29:610-22. [DOI: 10.2108/zsj.29.610] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, Sichuan 610066, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, Sichuan 610066, China
| | - Peng Guo
- College of Life Sciences and Food Engineering, Yibin University, Yibin, Sichuan 644007, China
| | - Zhiyu Sun
- Sichuan Academy of Forestry, Chengdu, Sichuan 610066, China
| | - Robert W. Murphy
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, Yunnan 650223, China
| | - Zhenxin Fan
- College of Life Sciences, Sichuan University, Chengdu, Sichuan 610051, China
| | - Jianrong Fu
- Sichuan Academy of Forestry, Chengdu, Sichuan 610066, China
| | - Yaping Zhang
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, Yunnan 650223, China
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16
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Yu F, Li S, Kilpatrick WC, McGuire PM, He K, Wei W. Biogeographical Study of Plateau PikasOchotona curzoniae(Lagomorpha, Ochotonidae). Zoolog Sci 2012; 29:518-26. [DOI: 10.2108/zsj.29.518] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Molecular evidence for the subspecific differentiation of blue sheep (Pseudois nayaur) and polyphyletic origin of dwarf blue sheep (Pseudois schaeferi). Genetica 2012; 140:159-67. [DOI: 10.1007/s10709-012-9667-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 07/11/2012] [Indexed: 10/28/2022]
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18
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Fan Z, Liu S, Liu Y, Liao L, Zhang X, Yue B. Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia. PLoS One 2012; 7:e38184. [PMID: 22666478 PMCID: PMC3364228 DOI: 10.1371/journal.pone.0038184] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 05/01/2012] [Indexed: 11/30/2022] Open
Abstract
The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 individuals from 47 sampling sites. In addition, 23 cyt b sequences were collected from GenBank for analyses. Phylogenetic, demographic and landscape genetic methods were conducted. Seventy-six cyt b haplotypes were found and the genetic diversity was extremely high (π = 0.0368; h = 0.989). Five major evolutionary clades, based on geographic locations, were identified. Demographic analyses implied subclade 1A and subclade 1B experienced population expansions at about 0.052-0.013 Mya and 0.014-0.004 Mya, respectively. The divergence time analysis showed that the split between clade 1 and clade 2 occurred 0.26 Mya, which fell into the extensive glacial period (EGP, 0.5-0.17 Mya). The divergence times of other main clades (2.20-0.55 Mya) were congruent with the periods of the Qingzang Movement (3.6-1.7 Mya) and the Kun-Huang Movement (1.2-0.6 Mya), which were known as the most intense uplift events in the Tibetan Plateau. Our study supported the hypothesis that the SEMTP was a large late Pleistocene refugium, and further inferred that the Gongga Mountain Region and Hongya County were glacial refugia for A. draco in clade 1. We hypothesize that the evolutionary history of A. draco in the SEMTP primarily occurred in two stages. First, an initial divergence would have been shaped by uplift events of the Tibetan Plateau. Then, major glaciations in the Pleistocene added complexity to its demographic history and genetic structure.
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Affiliation(s)
- Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People’s Republic of China
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, People’s Republic of China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, People’s Republic of China
| | - Lihuan Liao
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), Sichuan University, Chengdu, People’s Republic of China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People’s Republic of China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), Sichuan University, Chengdu, People’s Republic of China
- * E-mail:
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Profound climatic effects on two East Asian black-throated tits (Ave: Aegithalidae), revealed by ecological niche models and phylogeographic analysis. PLoS One 2011; 6:e29329. [PMID: 22195047 PMCID: PMC3241714 DOI: 10.1371/journal.pone.0029329] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/25/2011] [Indexed: 11/19/2022] Open
Abstract
Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory.
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von Oheimb PV, Albrecht C, Riedel F, Du L, Yang J, Aldridge DC, Bössneck U, Zhang H, Wilke T. Freshwater biogeography and limnological evolution of the Tibetan Plateau--insights from a plateau-wide distributed gastropod taxon (Radix spp.). PLoS One 2011; 6:e26307. [PMID: 22028853 PMCID: PMC3197626 DOI: 10.1371/journal.pone.0026307] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 09/23/2011] [Indexed: 11/19/2022] Open
Abstract
Background The Tibetan Plateau is not only the highest and largest plateau on earth; it is also home to numerous freshwater lakes potentially harbouring endemic faunal elements. As it remains largely unknown whether these lakes have continuously existed during the Last Glacial Maximum (LGM), questions arise as to whether taxa have been able to exist on the plateau since before the latest Pleistocene, from where and how often the plateau was colonized, and by which mechanisms organisms conquered remote high altitude lentic freshwater systems. In this study, species of the plateau-wide distributed freshwater gastropod genus Radix are used to answer these biogeographical questions. Methodology/Principal Findings Based on a broad spatial sampling of Radix spp. on the Tibetan Plateau, and phylogenetic analyses of mtDNA sequence data, three probably endemic and one widespread major Radix clade could be identified on the plateau. Two of the endemic clades show a remarkably high genetic diversity, indicating a relatively great phylogenetic age. Phylogeographical analyses of individuals belonging to the most widely distributed clade indicate that intra-plateau distribution cannot be explained by drainage-related dispersal alone. Conclusions/Significance Our study reveals that Radix spp. persisted throughout the LGM on the Tibetan Plateau. Therefore, we assume the continuous existence of suitable water bodies during that time. The extant Radix diversity on the plateau might have been caused by multiple colonization events combined with a relatively long intra-plateau evolution. At least one colonization event has a Palaearctic origin. In contrast to freshwater fishes, passive dispersal, probably by water birds, might be an important mechanism for conquering remote areas on the plateau. Patterns found in Radix spp. are shared with some terrestrial plateau taxa, indicating that Radix may be a suitable model taxon for inferring general patterns of biotic origin, dispersal and survival on the Tibetan Plateau.
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Affiliation(s)
- Parm Viktor von Oheimb
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany.
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Past and present: Phylogeography of the Bufo gargarizans species complex inferred from multi-loci allele sequence and frequency data. Mol Phylogenet Evol 2011; 61:136-48. [DOI: 10.1016/j.ympev.2011.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/20/2022]
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Zhao K, Duan Z, Peng Z, Gan X, Zhang R, He S, Zhao X. Phylogeography of the endemic Gymnocypris chilianensis (Cyprinidae): sequential westward colonization followed by allopatric evolution in response to cyclical Pleistocene glaciations on the Tibetan Plateau. Mol Phylogenet Evol 2011; 59:303-10. [PMID: 21352931 DOI: 10.1016/j.ympev.2011.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 01/13/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
The schizothoracine Gymnocypris chilianensis is restricted to the Shiyang, Ruoshui and Shule Rivers, listed from east to west, along the northeast edge of the Tibetan Plateau. This distribution provides a valuable system to test hypotheses about postglacial colonization. We used mitochondrial DNA sequence data (a control region and the cytochrome b gene; 1894 bp) to assess the phylogeographic structure of this species based on 278 specimens sampled from throughout the species' entire geographical range. We found three lineages corresponding geographically to the three rivers, suggesting three independent glacial differentiation centers within the northeast edge of the Tibetan Plateau. The phylogenetic analysis suggested that the Shiyang River population forms a lineage that separated from the other populations of G. chilianensis at the basal phylogenetic split within this species. The molecular data further demonstrated a clear pattern of decreasing genetic diversity from the eastern Shiyang River towards the central Ruoshui River and western Shule River lineages, a pattern consistent with sequential western colonization. We therefore propose a phylogeographic scenario for G. chilianensis of a gradual westerly expansion from the Shiyang River population along the northeast edge of the Tibetan Plateau, with subsequent allopatric evolution at approximately 0.37 and 0.05 million years ago (Ma), through at least two glacial maxima. Together with the genetic evidence reported in other species, our findings suggest that this common biogeographic pattern emphasizes the importance of the northeastern edge region of the Tibetan Plateau as a hotspot of genetic diversity for some taxa.
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Affiliation(s)
- Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Plateau Institute of Biology, The Chinese Academy of Science, Xining 810001, China
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Fan Z, Liu S, Liu Y, Zhang X, Yue B. How Quaternary geologic and climatic events in the southeastern margin of the Tibetan Plateau influence the genetic structure of small mammals: inferences from phylogeography of two rodents, Neodon irene and Apodemus latronum. Genetica 2011; 139:339-51. [DOI: 10.1007/s10709-011-9553-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
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Chen W, Hao H, Liu Y, Chen S, Zhang X, Liu S, Yue B. Mitochondrial DNA genetic variation and phylogeography of the recently described vole speciesProedromys liangshanensisLiu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae). J NAT HIST 2010. [DOI: 10.1080/00222933.2010.501911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cun YZ, Wang XQ. Plant recolonization in the Himalaya from the southeastern Qinghai-Tibetan Plateau: Geographical isolation contributed to high population differentiation. Mol Phylogenet Evol 2010; 56:972-82. [DOI: 10.1016/j.ympev.2010.05.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 05/02/2010] [Accepted: 05/11/2010] [Indexed: 11/25/2022]
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Chen W, Liu S, Liu Y, Hao H, Zeng B, Chen S, Peng H, Yue B, Zhang X. Phylogeography of the Large White-Bellied RatNiviventer excelsiorSuggests the Influence of Pleistocene Glaciations in the Hengduan Mountains. Zoolog Sci 2010; 27:487-93. [DOI: 10.2108/zsj.27.487] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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QU Y, LEI F, ZHANG R, LU X. Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Mol Ecol 2009; 19:338-51. [DOI: 10.1111/j.1365-294x.2009.04445.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Ci HX, Lin GH, Cai ZY, Tang LZ, Su JP, Liu JQ. Population history of the plateau pika endemic to the Qinghai-Tibetan Plateau based on mtDNA sequence data. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00635.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau. Mol Phylogenet Evol 2009; 53:1025-31. [DOI: 10.1016/j.ympev.2009.03.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 03/11/2009] [Indexed: 11/15/2022]
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LIU YIFEI, WANG YONG, HUANG HONGWEN. Species-level phylogeographical history ofMyricariaplants in the mountain ranges of western China and the origin ofM. laxiflorain the Three Gorges mountain region. Mol Ecol 2009; 18:2700-12. [DOI: 10.1111/j.1365-294x.2009.04214.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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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32
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Phylogeography of Tibetan snowcock (Tetraogallus tibetanus) in Qinghai–Tibetan Plateau. Mol Phylogenet Evol 2009; 50:526-33. [DOI: 10.1016/j.ympev.2008.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 10/12/2008] [Accepted: 12/02/2008] [Indexed: 11/19/2022]
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33
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YANG FUSHENG, LI YUFEI, DING XIN, WANG XIAOQUAN. Extensive population expansion ofPedicularis longiflora(Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Mol Ecol 2008; 17:5135-45. [DOI: 10.1111/j.1365-294x.2008.03976.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Aowphol A, Voris HK, Feldheim KA, Harnyuttanakorn P, Thirakhupt K. Genetic homogeneity among colonies of the white-nest swiftlet (Aerodramus fuciphagus) in Thailand. Zoolog Sci 2008; 25:372-80. [PMID: 18459819 DOI: 10.2108/zsj.25.372] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 01/10/2008] [Indexed: 11/17/2022]
Abstract
The white-nest swiftlet, Aerodramus fuciphagus, originally lived in large colonies in natural caves, but now it also occurs in man-made buildings. We investigated the patterns of genetic differentiation in two mitochondrial DNA genes (cyt-b and ND2) and eight microsatellite loci among and within colonies of A. fuciphagus from across recently established man-made colonies in Thailand. Ten white-nest swiftlet colonies were sampled along the coast of the Gulf of Thailand and the Andaman Sea in Thailand during 2003-2006. The genetic diversity of mtDNA was very low, and few significant PhiST values were found between pairs of colonies. Analyses of haplotype relationships did not show genetic structure across the sampled distribution. The level of genetic diversity for microsatellite loci was high, but FST values were not significant. However, due to small sample sizes for some colonies that could limit conclusions on genetic differentiation from PhiST and FST, we also analyzed the microsatellite data using STRUCTURE and found that number of subpopulations of white-nest swiftlets in sampled colonies was one. The lack of genetic differentiation among swiftlet house colonies could be a result of high gene flow between colonies and large population sizes. Our results suggest that A. fuciphagus living in recently established man-made colonies in Thailand should be considered members of a single panmictic population. Future work will be necessary to determine whether this panmixia is stable or a temporary result of the recent explosive expansion of the number of colonies, and comparisons to natural colonies may provide an understanding of mechanisms producing the lack of genetic structure in swiftlet house colonies.
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Affiliation(s)
- Anchalee Aowphol
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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