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Guo Q, Zhu QD, Zhou ZJ, Shi FM. Phylogeography and Genetic Structure of the Bush Cricket Decma fissa (Orthoptera, Tettigoniidae) in Southern China. Zool Stud 2023; 62:e32. [PMID: 37671174 PMCID: PMC10475508 DOI: 10.6620/zs.2023.62-32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/28/2023] [Indexed: 09/07/2023]
Abstract
Decma fissa is the most widely distributed species of the genus Decma occuring in southern China. This study presents the first phylogeographic work of D. fissa based on COI, Cytb and ITS sequence. We examined genetic diversity with ITS and mitochondrial sequence respectively, and phylogenetic work was based on the mitochondrial data. A high-level genetic diversity was revealed based on mitochondrial data but a low-level diversity was shown with ITS sequence. For the mitochondrial data, divergence time analysis displayed five lineages. Based on the Mantel test, geographic and genetic distances among D. fissa populations revealed a significant positive correlation. Bayesian skyline plot (BSP) analyses implied that none of three major lineages of D. fissa was seemingly affected by the last glacial maximum (LGM, 0.015-0.025 Mya). Ecological niche modeling was used to predict the distribution of D. fissa in four periods (LGM, Mid-Holocene, current and 2070) in China. Analysis of the ancestral area reconstruction indicated that D. fissa occurred in the South China area.
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Affiliation(s)
- Qi Guo
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China. E-mail: (Shi); (Guo); (Zhu); or (Zhou)
| | - Qi-Di Zhu
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China. E-mail: (Shi); (Guo); (Zhu); or (Zhou)
| | - Zhi-Jun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China. E-mail: (Shi); (Guo); (Zhu); or (Zhou)
| | - Fu-Ming Shi
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China. E-mail: (Shi); (Guo); (Zhu); or (Zhou)
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2
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The genetic drivers for the successful invasive potential of a generalist bird, the House crow. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02684-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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4
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Zhou Z, Zhen Y, Guan B, Ma L, Wang W. Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China. Ecol Evol 2021; 11:4276-4294. [PMID: 33976810 PMCID: PMC8093711 DOI: 10.1002/ece3.7324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 11/12/2022] Open
Abstract
Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI-5P lineages. The distribution of COI-5P haplotypes may not demonstrate significant phylogeographic structure (N ST > G ST, p > .05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI-5P haplotypes. For both COI-5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plot (BSP) analyses indicated that the population size of D. japonica's three major mitochondrial COI-5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015-0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species' distribution during the LGM period and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.
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Affiliation(s)
- Zhi‐Jun Zhou
- College of Life ScienceInstitute of Life Science and Green DevelopmentHebei UniversityBaodingChina
| | - Yun‐Xia Zhen
- College of Life ScienceInstitute of Life Science and Green DevelopmentHebei UniversityBaodingChina
| | - Bei Guan
- College of Life ScienceInstitute of Life Science and Green DevelopmentHebei UniversityBaodingChina
| | - Lan Ma
- College of Life ScienceInstitute of Life Science and Green DevelopmentHebei UniversityBaodingChina
| | - Wen‐Jing Wang
- College of Life ScienceInstitute of Life Science and Green DevelopmentHebei UniversityBaodingChina
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5
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Nandakumar M, Ishtiaq F. Genetic drift and bottleneck do not influence diversity in Toll-like receptor genes at a small spatial scale in a Himalayan passerine. Ecol Evol 2020; 10:12246-12263. [PMID: 33209285 PMCID: PMC7663051 DOI: 10.1002/ece3.6855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is important for long-term viability of a population. Low genetic diversity reduces persistence and survival of populations and increases susceptibility to diseases. Comparisons of the neutral markers with functional loci such as immune genes [Toll-like receptors; TLR] can provide useful insights into evolutionary potential of a species and how the diversity of pathogens and selection pressures on their hosts are directly linked to their environment. In this study, we compare genetic diversity in neutral (eleven microsatellite loci) and adaptive (seven TLR loci) loci to determine genetic variation in a nonmigratory western Himalayan passerine, the black-throated tit (Aegithalos concinnus), distributed across an elevation gradient with varying degree of pathogen-mediated selection pressure. We further compare the diversity in TLR loci with a high-elevation sister species, the white-throated tit (Aegithalos niveogularis). Our results indicate a lack of population genetic structure in the black-throated tit and signatures of a past bottleneck. In contrast, we found high diversity in TLR loci and locus-specific (TLR7) signatures of pathogen-mediated selection, which was comparable to diversity in the white-throated tit. Levels of diversity at TLR5 locus corresponded very closely with neutral microsatellite variation. We found evidence of positive selection in TLR1LA, TLR5, and TLR7 loci highlighting the importance in pathogen recognition. Our finding demonstrates that reduction in neutral variation does not necessarily lead to reduction in functional genetic diversity and probably helps in revival of population in a widespread species.
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Affiliation(s)
- Mridula Nandakumar
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
- Present address:
Department of BiologyLund UniversityLundSweden
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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6
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Dai C, Dong F, Yang X. Morphotypes or distinct species? A multilocus assessment of two East Asian scimitar babblers (Aves, Timaliidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University) Ministry of Education Guilin China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology Guangxi Normal University Guilin China
- School of Biological Sciences Guizhou Normal College Guiyang China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
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7
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Lu RS, Chen Y, Tamaki I, Sakaguchi S, Ding YQ, Takahashi D, Li P, Isaji Y, Chen J, Qiu YX. Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Mol Phylogenet Evol 2019; 143:106693. [PMID: 31778814 DOI: 10.1016/j.ympev.2019.106693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022]
Abstract
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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Affiliation(s)
- Rui-Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yan-Qian Ding
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuji Isaji
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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8
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Xue J, Zhang H, Ning X, Bu W, Yu X. Evolutionary history of a beautiful damselfly, Matrona basilaris, revealed by phylogeographic analyses: the first study of an odonate species in mainland China. Heredity (Edinb) 2018; 122:570-581. [PMID: 30356221 DOI: 10.1038/s41437-018-0158-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/18/2018] [Indexed: 11/09/2022] Open
Abstract
Matrona basilaris Selys, 1853 is a damselfly distributed mainly in mainland China. A total of 423 individuals from 48 populations covering almost the entire range were sampled to explore the genetic diversity, phylogeographic structure, and demographic dynamics of the species using sequences of three mitochondrial genes (COI, COII, and ND1) and a nuclear (ITS1 + 5.8 S + ITS2) gene. Phylogenetic tree, median-joining network, and BAPS analyses indicated a four-group division of the entire population, and the divergence event was estimated to have occurred in the middle Pleistocene. The diverse terrain of mainland China as well as past climatic oscillations were assumed to have shaped the current phylogeographic pattern of M. basilaris. Multiple lines of evidence supported population expansion in Group 1 and Group 2 but not in Group 3 or Group 4. The expansion times corresponded to the transition phase from the LIG (∼0.14-0.12 Mya) to the LGM (∼0.021-0.018 Mya). The pre-LGM expansion model reflected a different pattern affecting the historical dynamics of the population of East Asian species caused by Pleistocene climatic changes. Interestingly, Group 2 exhibited a disjunctive distribution pattern. The possible reasons were introgression caused by female-biased dispersal or human phoresy during construction of the Forbidden City during the Ming Dynasty of China.
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Affiliation(s)
- Junli Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Haiguang Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Ning
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Yu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.
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9
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Dai C, Hao Y, He Y, Lei F. The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone. BMC Evol Biol 2017; 17:266. [PMID: 29262786 PMCID: PMC5738821 DOI: 10.1186/s12862-017-1114-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses. RESULTS ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids. CONCLUSIONS Isolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.
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Affiliation(s)
- Chuanyin Dai
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yong He
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
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10
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Improved sampling at the subspecies level solves a taxonomic dilemma - A case study of two enigmatic Chinese tit species (Aves, Passeriformes, Paridae, Poecile). Mol Phylogenet Evol 2016; 107:538-550. [PMID: 27965081 DOI: 10.1016/j.ympev.2016.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/25/2016] [Accepted: 12/09/2016] [Indexed: 11/24/2022]
Abstract
A recent full species-level phylogeny of tits, titmice and chickadees (Paridae) has placed the Chinese endemic black-bibbed tit (Poecile hypermelaenus) as the sister to the Palearctic willow tit (P. montanus). Because this sister-group relationship is in striking disagreement with the traditional affiliation of P. hypermelaenus close to the marsh tit (P. palustris) we tested this phylogenetic hypothesis in a multi-locus analysis with an extended taxon sampling including sixteen subspecies of willow tits and marsh tits. As a taxonomic reference we included type specimens in our analysis. The molecular genetic study was complemented with an analysis of biometric data obtained from museum specimens. Our phylogenetic reconstructions, including a comparison of all GenBank data available for our target species, clearly show that the genetic lineage previously identified as P. hypermelaenus actually refers to P. weigoldicus because sequences were identical to that of a syntype of this taxon. The close relationship of P. weigoldicus and P. montanus - despite large genetic distances between the two taxa - is in accordance with current taxonomy and systematics. In disagreement with the previous phylogenetic hypothesis but in accordance with most taxonomic authorities, all our P. hypermelaenus specimens fell in the sister clade of all western and eastern Palearctic P. palustris. Though shared haplotypes among the Chinese populations of the two latter species might indicate mitochondrial introgression in this part of the breeding range, further research is needed here due to the limitations of our own sampling.
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11
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Zhang YH, Wang IJ, Comes HP, Peng H, Qiu YX. Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae). Sci Rep 2016; 6:24041. [PMID: 27137438 PMCID: PMC4853719 DOI: 10.1038/srep24041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.
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Affiliation(s)
- Yong-Hua Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Hans Peter Comes
- Department of Ecology &Evolution, Salzburg University, A-5020 Salzburg, Austria
| | - Hua Peng
- Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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12
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Yuan ZY, Suwannapoom C, Yan F, Poyarkov NA, Nguyen SN, Chen HM, Chomdej S, Murphy RW, Che J. Red River barrier and Pleistocene climatic fluctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina. Curr Zool 2016; 62:531-543. [PMID: 29491943 PMCID: PMC5804247 DOI: 10.1093/cz/zow042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions.
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Affiliation(s)
- Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological faculty, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Center, A.N. Severtsov Institute of Ecology and Evolution RAS, South Branch, District 10, Ho Chi Minh 700000, Vietnam
| | - Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., District 3, Ho Chi Minh 700000, Vietnam
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand, and
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
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13
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Phylogeography of a semi-aquatic bug, Microvelia horvathi (Hemiptera: Veliidae): an evaluation of historical, geographical and ecological factors. Sci Rep 2016; 6:21932. [PMID: 26923804 PMCID: PMC4770413 DOI: 10.1038/srep21932] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 02/03/2016] [Indexed: 11/23/2022] Open
Abstract
Subtropical China is a centre of speciation and well known for its high biological diversity and endemism. To understand the impact of historical, geographical and ecological factors on the intraspecific lineage divergence of invertebrates, we examined these processes in a semiaquatic bug, Microvelia horvathi (Hemiptera: Veliidae). Three hypotheses were developed using ecological niche models (ENM). We tested these hypotheses using mitochondrial (COI + COII) and nuclear data (ITS1 + 5.8S + ITS2). The phylogenic analysis revealed a shallow divergence in mitochondrial data. Clade I was mostly confined to the northern region and clade II was nearly restricted to the southern region. The historical process of Pleistocene climatic fluctuations during the LGM promoted divergence, along with such geographical barriers as the Wuyi, Nanling and Xuefeng mountains and ecological factors of temperature and vegetation type, contributed to these shallow genetic divergences and helped maintain them. The north-south population differentiation probably occurred during the transition from LIG to LGM, with post-LGM population expansion. The results of genetic data were mostly consistent with the spatial predictions from ENM. Our study emphasizes the multiple effects influencing genetic population differentiation, and also contributes to our knowledge of the phylogeography of other aquatic organisms in subtropical China.
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14
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Chen D, Liu Q, Chang J, Jiang A, Zhou F, Zhang Y, Zhang Z. Multi-locus analysis supports the taxonomic validity of Arborophila gingica guangxiensis Fang Zhou & Aiwu Jiang, 2008. Zookeys 2016:125-36. [PMID: 26877690 PMCID: PMC4740825 DOI: 10.3897/zookeys.555.6814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 11/22/2015] [Indexed: 11/12/2022] Open
Abstract
The taxonomic status of subspecies has long been debated, especially in conservation biology. Some proposed subspecies must be evolutionarily distinct to be considered conservation units. White-necklaced Partridge (Arborophilagingica) comprises two subspecies, Arborophilagingicagingica and Arborophilagingicaguangxiensis. Arborophilagingicaguangxiensis, restricted to three isolated small areas in Guangxi, China, with limited population sizes, is a newly discovered subspecies based on recently identified geographic and phenotypic differences between Arborophilagingicagingica; however, evidence is lacking that can effectively identify whether the subspecies is evolutionarily distinct. Here, three mitochondrial DNA segments and four nuclear introns were used to test whether the two subspecies are reciprocally monophyletic, which has been proposed as an objective method to evaluate evolutionary distinctiveness. The results indicate that the two subspecies are genetically divergent and form reciprocal monophyletic groups. Therefore, this study further supports the taxonomic validity and distinctiveness of Arborophilagingicaguangxiensis and suggests that this subspecies be considered as a conservation unit.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qiong Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Aiwu Jiang
- College of Forestry, Guangxi University, Nanning 530004, Guangxi, China
| | - Fang Zhou
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yanyun Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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15
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Liu S, Jiang N, Xue D, Cheng R, Qu Y, Li X, Lei F, Han H. Evolutionary history ofApocheima cinerarius(Lepidoptera: Geometridae), a female flightless moth in northern China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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16
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Lei F, Qu Y, Song G, Alström P, Fjeldså J. The potential drivers in forming avian biodiversity hotspots in the East Himalaya Mountains of Southwest China. Integr Zool 2015; 10:171-81. [PMID: 25316284 DOI: 10.1111/1749-4877.12121] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Little has been published to describe or interpret Asian biodiversity hotspots, including those in the East Himalayan Mountains of Southwest China (HMSC), thus making necessary a review of the current knowledge. The Pliocene and Pleistocene geological and glacial histories of the Asian continent differ from those of Europe and North America, suggesting different mechanisms of speciation and extinction, and, thus, different responses to climate changes during the Quaternary glaciations. This short review summarizes potential drivers in shaping and maintaining high species richness and endemism of birds in the HMSC. The geographical location at the junction of different biogeographical realms, the wide range of habitats and climates along the extensive elevational range, the complex topography and the distinct geological history of this region have probably contributed to the evolution of an exceptionally species-rich and endemic-rich, specialized montane avian fauna. The Mountain systems in the HMSC may have provided refugia where species survived during the glacial periods and barriers for preventing species dispersal after the glacial periods. More studies are required to further test this refugia hypothesis by comparing more cold-tolerent and warm-tolerent species.
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Affiliation(s)
- Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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17
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Wang X, Huang Y, Liu N, Yang J, Lei F. Seven complete mitochondrial genome sequences of bushtits (Passeriformes, Aegithalidae, Aegithalos): the evolution pattern in duplicated control regions. ACTA ACUST UNITED AC 2015; 26:350-6. [PMID: 25633179 DOI: 10.3109/19401736.2014.1003821] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The control region (CR) of the mitochondrial DNA exhibits important functions in replication and transcription, and duplications of the CR have been reported in a wide range of animal groups. In most cases, concerted evolution is expected to explain the high similarity of duplicated CRs. In this paper, we present seven complete mitochondrial genome sequences from the bushtits (genus Aegithalos), in which we discovered two duplicated CRs, and try to survey the evolution pattern of these duplicated CRs. We also found that the duplicated CRs within one individual were almost identical, and variations were concentrated in two sections, one located between a poly-C site and a potential TAS (termination associated sequence) element, the other one located at the 3' end of the duplicated CRs. The phylogenetic analyses of paralogous CRs showed that the tree topology were depending on whether the two high variable regions at the upstream of TAS element and the 3'end of duplicated CRs: when they were concluded, the orthologous copies were closely related; when they were excluded, the paralogous copies in the same lineages were closely related. This may suggest the role of recombination in the evolution of duplicated CRs. Consequently, the recombination was detected, and the breakpoints were found at ∼120 bp (the upstream of the potential TAS element) and ∼1150 bp of the alignment of duplicated CRs. According to these results, we supposed that homologous recombination occurred between paralogous CRs from different mtDNA molecule was proposed as the most suitable mechanism for concerted evolution of the duplicated CRs, and the recombination took place in every replication cycle, so that most part of the duplicated regions remain identical within an individual, while the 5' and 3'end of the duplicated CRs were not involved in recombination, and evolved independently.
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Affiliation(s)
- Xiaoyang Wang
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University , Xi'an , China and
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18
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Chelomina GN, Tatonova YV, Hung NM, Ngo HD. Genetic diversity of the Chinese liver fluke Clonorchis sinensis from Russia and Vietnam. Int J Parasitol 2014; 44:795-810. [DOI: 10.1016/j.ijpara.2014.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 11/24/2022]
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19
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Ye Z, Zhu G, Chen P, Zhang D, Bu W. Molecular data and ecological niche modelling reveal the Pleistocene history of a semi-aquatic bug (Microvelia douglasi douglasi) in East Asia. Mol Ecol 2014; 23:3080-96. [PMID: 24845196 DOI: 10.1111/mec.12797] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 05/14/2014] [Accepted: 05/14/2014] [Indexed: 11/29/2022]
Abstract
This study investigated the Pleistocene history of a semi-aquatic bug, Microvelia douglasi douglasi Scott, 1874 (Hemiptera: Veliidae) in East Asia. We used M. douglasi douglasi as a model species to explore the effects of historical climatic fluctuations on montane semi-aquatic invertebrate species. Two hypotheses were developed using ecological niche models (ENMs). First, we hypothesized that M. douglasi douglasi persisted in suitable habitats in southern Guizhou, southern Yunnan, Hainan, Taiwan and southeast China during the LIG. After that, the populations expanded (Hypothesis 1). As the spatial prediction in the LGM was significantly larger than in the LIG, we then hypothesized that the population expanded during the LIG to LGM transition (Hypothesis 2). We tested these hypotheses using mitochondrial data (COI+COII) and nuclear data (ITS1+5.8S+ITS2). Young lineages, relatively deep splits, lineage differentiation among mountain ranges in central, south and southwest China and high genetic diversities were observed in these suitable habitats. Evidence of mismatch distributions and neutrality tests indicate that a population expansion occurred in the late Pleistocene. The Bayesian skyline plot (BSP) revealed an unusual population expansion that likely happened during the cooling transition between LIG and LGM. The results of genetic data were mostly consistent with the spatial predictions from ENM, a finding that can profoundly improve phylogeographic research. The ecological requirements of M. douglasi douglasi, together with the geographical heterogeneity and climatic fluctuations of Pleistocene in East Asia, could have shaped this unusual demographic history. Our study contributes to our knowledge of semi-aquatic bug/invertebrate responses to Pleistocene climatic fluctuations in East Asia.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
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20
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Genetic diversity of Echinococcus granulosus in southwest China determined by the mitochondrial NADH dehydrogenase subunit 2 gene. ScientificWorldJournal 2014; 2014:867839. [PMID: 24592194 PMCID: PMC3925532 DOI: 10.1155/2014/867839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/24/2013] [Indexed: 12/21/2022] Open
Abstract
We evaluated genetic diversity and structure of Echinococcus granulosus by analyzing the complete mitochondrial NADH dehydrogenase subunit 2 (ND2) gene in 51 isolates of E. granulosus sensu stricto metacestodes collected at three locations in this region. We detected 19 haplotypes, which formed a distinct clade with the standard sheep strain (G1). Hence, all 51 isolates were identified as E. granulosus sensu stricto (G1–G3). Genetic relationships among haplotypes were not associated with geographical divisions, and fixation indices (Fst) among sampling localities were low. Hence, regional populations of E. granulosus in the southwest China are not differentiated, as gene flow among them remains high. This information is important for formulating unified region-wide prevention and control measures. We found large negative Fu's Fs and Tajima's D values and a unimodal mismatch distribution, indicating that the population has undergone a demographic expansion. We observed high genetic diversity among the E. granulosus s. s. isolates, indicating that the parasite population in this important bioregion is genetically robust and likely to survive and spread. The data from this study will prove valuable for future studies focusing on improving diagnosis and prevention methods and developing robust control strategies.
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21
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Qu Y, Ericson PGP, Quan Q, Song G, Zhang R, Gao B, Lei F. Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya. Mol Ecol 2014; 23:705-20. [DOI: 10.1111/mec.12619] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Per G. P. Ericson
- Department of Vertebrate Zoology; Swedish Museum of Natural History; PO Box 50007 SE-10405 Stockholm Sweden
| | - Qing Quan
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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22
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Dong L, Heckel G, Liang W, Zhang Y. Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers. Mol Ecol 2013; 22:3376-90. [PMID: 23692215 DOI: 10.1111/mec.12315] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 11/27/2022]
Abstract
The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.
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Affiliation(s)
- Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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23
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Multilocus phylogeography (mitochondrial, autosomal and Z-chromosomal loci) and genetic consequence of long-distance male dispersal in Black-throated tits (Aegithalos concinnus). Heredity (Edinb) 2013; 110:457-65. [PMID: 23299099 DOI: 10.1038/hdy.2012.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Multilocus data from the different genomes are essential to understand the phylogeographic history of species, particularly when a species has the male-biased dispersal pattern. Although Black-throated tits (Aegithalos concinnus) are socially monogamous and cooperatively breeding birds, limited observational data suggested that males may have the ability of long-distance dispersal. We have previously detected three highly supported mitochondrial populations within two subspecies of Black-throated tits (A. c. concinnus and A. c. talifuensis). Here, we used several genetic markers with different inheritance patterns to gain insights about their phylogeographic history. Phylogenetic and individual-based Bayesian analysis showed weak geographical structure amongst nuclear sequences (autosomal and Z-chromosomal loci). Coalescent analysis revealed high levels of gene flow among mitochondrial populations, even between allopatric populations. These results strongly suggested that male-biased gene flow was responsible for the discordant cytonuclear phylogeographic patterns. Consistent with expectation on the genetic consequence of long-distance male dispersal, mantel tests revealed a significant pattern of isolation by distance for mitochondrial sequences, but failed to provide a similar pattern for nuclear genes within a continuous population; female Black-throated tits showed a stronger but not significantly different relationship of isolation by distance than males when using mitochondrial DNA alone. We discussed the contribution of male juveniles with delayed dispersal to the non-significantly different IBD patterns between sexes. Our results using multilocus genetic data revealed aspects of the complex evolutionary history of Black-throated tits and the important role of long-distance male dispersal in the population structuring.
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24
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Fang F, Sun H, Zhao Q, Lin C, Sun Y, Gao W, Xu J, Zhou J, Ge F, Liu N. Patterns of diversity, areas of endemism, and multiple glacial refuges for freshwater crabs of the genus Sinopotamon in China (Decapoda: Brachyura: Potamidae). PLoS One 2013; 8:e53143. [PMID: 23308152 PMCID: PMC3537761 DOI: 10.1371/journal.pone.0053143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 11/23/2012] [Indexed: 11/25/2022] Open
Abstract
Previous research has shown that the geographical distribution patterns of freshwater fishes and amphibians have been influenced by past climatic oscillations in China resulting from Pleistocene glacial activity. However, it remains unknown how these past changes have impacted the present-day distribution of Chinese freshwater crabs. This work describes the diversity and endemism of freshwater crabs belonging to Sinopotamon, a highly speciose genus endemic to China, and evaluates its distribution in terms of topography and past climatic fluctuations. Species diversity within Sinopotamon was found to be concentrated in an area from the northeastern edge of the Yunnan-Guizhou Plateau to the Jiangnan Hills, and three areas of endemism were identified. Multiple regression analysis between current climatic variables and Sinopotamon diversity suggested that regional annual precipitation, minimum temperature in the coldest month, and annual temperature range significantly influenced species diversity and may explain the diversity patterns of Sinopotamon. A comparison of ecological niche models (ENMs) between current conditions and the last glacial maximum (LGM) showed that suitable habitat for Sinopotamon in China severely contracted during the LGM. The coincidence of ENMs and the areas of endemism indicated that southeast of the Daba Mountains, and central and southeastern China, are potential Pleistocene refuges for Sinopotamon. The presence of multiple Pleistocene refuges within the range of this genus could further promote inter- and intraspecific differentiations, and may have led to high Sinopotamon species diversity, a high endemism rate and widespread distribution.
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Affiliation(s)
- Fang Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiang Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Congtian Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yufang Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Gao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Juanjuan Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Junying Zhou
- Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Feng Ge
- Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Naifa Liu
- School of Life Sciences, Lanzou University, Lanzhou, China
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Zhu G, Liu G, Bu W, Lis JA. Geographic distribution and niche divergence of two stinkbugs, Parastrachia japonensis and Parastrachia nagaensis. JOURNAL OF INSECT SCIENCE (ONLINE) 2013; 13:102. [PMID: 24738857 PMCID: PMC4012745 DOI: 10.1673/031.013.10201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 10/05/2013] [Indexed: 06/03/2023]
Abstract
Parastrachiidae is a small stinkbug family containing only one genus and two species, Parastrachia japonensis (Scott) (Hemiptera: Heteroptera: Pentatomoidea) and Parastrachia nagaensis Distant. The geographic distribution of the genus has been poorly studied. Niche conservatism refers to that idea that closely related species are more ecologically similar than would be expected, whereas niche divergence predicts they occupy distinct niche spaces. The existence of only two species within one genus suggests niche conservatism or differentiation might exist among them. Herein, the distribution of the genus was mapped, potential distributions were predicted using ecological niche modeling, and climate spaces occupied by the two species were identified and compared. Our outlined map supports the general spreading route proposed by Schaefer et al. The potential distributions suggest that the genus' range could extend beyond its presently known distribution, and further investigation into this area could aid in their conservation, particularly P. nagaensis. The niche space inferred by ecological niche modeling suggests the two species do not occupy identical habitat, but the differences between their models could simply be due to the differential availability of habitat in the different regions that they occupy.
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Affiliation(s)
- Gengping Zhu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Guoqing Liu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jerzy A. Lis
- Department of Biosystematics, Opole University, Oleska 22, 45–052 Opole, Poland
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26
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Huang P, Schaal BA. Association between the geographic distribution during the last glacial maximum of Asian wild rice, Oryza rufipogon (Poaceae), and its current genetic variation. AMERICAN JOURNAL OF BOTANY 2012; 99:1866-1874. [PMID: 23125436 DOI: 10.3732/ajb.1200348] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY The combination of traditional population genetic studies and species distribution modeling (SDM) provides many new insights in detecting phylogeographic signals. In Asian wild rice (Oryza rufipogon), the progenitor of cultivated Asian rice, geographical subdivision has been documented in many genetic studies although the root cause of this subdivision remains unknown. Surprisingly, environmental factors associated with the spatial and temporal distribution of O. rufipogon have rarely been examined. The aim of this study is to understand the historical distribution of O. rufipogon and its relationship to the current geographical pattern of genetic variation. METHODS We used SDM to examine the present, past, and future distribution of O. rufipogon. The estimated distribution during the Last Glacial Maximum was then compared with genetic data from our previous work. KEY RESULTS The predicted paleodistribution of O. rufipogon at the Last Glacial Maximum was separated into disconnected east and west ranges. This past distribution is consistent with the current geographic pattern of genetic variation, with two genetic groups that intergrade. Annual precipitation is the single factor that contributes most to SDM estimates. SDM predictions for 2080 indicate a general trend of increasing probability of presence and range expansion. CONCLUSIONS (1) The historically disjunct distribution potentially contributes to the current genetic subdivision of O. rufipogon. (2) Water availability is an important factor that limits the distribution of O. rufipogon. (3) Global warming is a lesser threat than other human-mediated factors to the conservation of this endangered species.
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Affiliation(s)
- Pu Huang
- Department of Biology Washington University, Campus Box 1137, 1 Brookings Dr., St. Louis, Missouri 63130, USA.
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Liu H, Wang W, Song G, Qu Y, Li SH, Fjeldså J, Lei F. Interpreting the process behind endemism in China by integrating the phylogeography and ecological niche models of the Stachyridopsis ruficeps. PLoS One 2012; 7:e46761. [PMID: 23056441 PMCID: PMC3462788 DOI: 10.1371/journal.pone.0046761] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 09/10/2012] [Indexed: 11/29/2022] Open
Abstract
An area of endemism (AOE) is a complex expression of the ecological and evolutionary history of a species. Here we aim to address the principal drivers of avian diversification in shaping patterns of endemism in China by integrating genetic, ecological, and distributional data on the Red-headed Tree Babbler (Stachyridopsis ruficeps), which is distributed across the eastern Himalayas and south China. We sequenced two mtDNA markers from 182 individuals representing all three of the primary AOEs in China. Phylogenetic inferences were used to reconstruct intraspecific phylogenetic relationships. Divergence time and population demography were estimated to gain insight into the evolutionary history of the species. We used Ecological niche modeling to predict species' distributions during the Last Glacial Maximum (LGM) and in the present. Finally, we also used two quantitative tests, an identity test and background test to assess the similarity of ecological niche preferences between adjacent lineages. We found five primary reciprocally monophyletic clades, typically separated approximately 0.2-2.27 MYA, of which three were deeply isolated endemic lineages located in the three AOEs. All phylogroups were detected to have undergone population expansion during the past 0.3 MY. Niche models showed discontinuous habitats, and there were three barriers of less suitable habitat during the LGM and in modern times. Ecoclimatic niches may diverge significantly even over recent timescales, as each phylogroup had a unique distribution, and unique niche characteristics. Vicariant events associated with geographical and ecological barriers, glacial refuges and ecological differentiation may be the main drivers forming the pattern of endemism in China.
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Affiliation(s)
- Huatao Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- 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
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan
| | - Jon Fjeldså
- Center of Macroecology, Evolution and Climate, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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