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Grossi AA, Tian C, Ren M, Zou F, Gustafsson DR. Co-phylogeny of a hyper-symbiotic system: Endosymbiotic bacteria (Gammaproteobacteria), chewing lice (Insecta: Phthiraptera) and birds (Passeriformes). Mol Phylogenet Evol 2024; 190:107957. [PMID: 37914031 DOI: 10.1016/j.ympev.2023.107957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
Chewing lice are hosts to endosymbiotic bacteria as well as themselves being permanent parasites. This offers a unique opportunity to examine the cophylogenetic relationships between three ecologically interconnected organismal groups: birds, chewing lice, and bacteria. Here, we examine the cophylogenetic relationships between lice in the genus Guimaraesiella Eichler, 1949, their endosymbiotic Sodalis-allied bacteria, and a range of bird species from across South China. Both event and distance-based cophylogenetic analyses were explored to compare phylogenies of the three organismal groups. Pair-wise comparisons between lice-endosymbionts and bird-endosymbionts indicated that their evolutionary histories are not independent. However, comparisons between lice and birds, showed mixed results; the distance-based method of ParaFit indicated that their evolutionary histories are not independent, while the event-based method of Jane indicated that their phylogenies were no more congruent than expected by chance. Notably, louse host-switching does not seem to have affected bacterial strains, as conspecific lice sampled from distantly related hosts share bacteria belonging to the same clade.
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Affiliation(s)
- Alexandra A Grossi
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou 510260, Guangdong Province, China.
| | - Chunpo Tian
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou 510260, Guangdong Province, China; College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Street, Chang'an District, Xi'an City 710119, Shaanxi Province, China.
| | - Mengjiao Ren
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou 510260, Guangdong Province, China; College of Biology and Environmental Science, Jishou University, 120 Renmin Road, Jishou 416000, Hunan Province, China.
| | - Fasheng Zou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou 510260, Guangdong Province, China.
| | - Daniel R Gustafsson
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou 510260, Guangdong Province, China.
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Ji YT, Zhou XJ, Yang Q, Lu YB, Wang J, Zou JX. Adaptive evolution characteristics of mitochondrial genomes in genus Aparapotamon (Brachyura, Potamidae) of freshwater crabs. BMC Genomics 2023; 24:193. [PMID: 37041498 PMCID: PMC10091551 DOI: 10.1186/s12864-023-09290-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/01/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes. RESULTS A new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs. CONCLUSIONS Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.
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Affiliation(s)
- Yu-Tong Ji
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Xiao-Juan Zhou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Qian Yang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Yuan-Biao Lu
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Jun Wang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Jie-Xin Zou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China.
- Department of Parasitology, School of Basic Medical Science, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China.
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Dai C, Feng P. Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia. Mol Phylogenet Evol 2023; 180:107709. [PMID: 36657627 DOI: 10.1016/j.ympev.2023.107709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/29/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.
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Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China.
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
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Chen IS, Jang-Liaw NH. Phylogeography of Aphyocypris normalis Nichols and Pope, 1927 at Hainan Island and adjacent areas based on mitochondrial DNA data. PLoS One 2023; 18:e0282460. [PMID: 36854024 PMCID: PMC9974131 DOI: 10.1371/journal.pone.0282460] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
We investigated the genetic structure of the freshwater fish Aphyocypris normalis, in 33 populations around Hainan Island and southern mainland China. Sequencing of the mitochondrial DNA (mtDNA) cytochrome b from 127 specimens yielded 47 haplotypes, from which we inferred a Bayesian tree. This revealed three major divergences: a principal clade of specimens with widespread geographic distribution, plus two clades with limited distribution. We estimated that these diverged between 1.05-0.16 Ma. Additionally, based on molecular data and comparing with the climate patterns of Hainan Island, eight phylogeographic ranges (populations) of A. normalis were constructed: the eastern plain (E), northeastern hills and plain (NE), northwestern hills and lowlands (NW), central mountains (C), southeastern hills and plain (SE), southern mountains and hills (S), southwestern mountains and lowlands (SW), and western lowlands (W). The patterns of geographical divergence in this species do not reflect the isolation caused by the Qiongzhou (Hainan) Strait, which would generally be experienced by terrestrial animals on isolated islands. The present results indicate that the major clades within A. normalis have diverged before the temporary land bridge existed across the strait during the Last Glacial Maximum.
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Affiliation(s)
- I-Shiung Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Nian-Hong Jang-Liaw
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, Taipei, Taiwan
- * E-mail:
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Li B, Yang Z. Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae) in the Yili area, Xinjiang, China. Ecol Evol 2022; 12:e9504. [PMID: 36407909 PMCID: PMC9667411 DOI: 10.1002/ece3.9504] [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: 06/05/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Tianshan Mountains provide a model for studying biological evolution and speciation. Here we assess the evolutionary history of Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB), which are sympatric in the Yili River Valley in Xinjiang, China.Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI, COII, Cytb) and four nuclear DNA (nuDNA, EF-1α, Wingless, RPS5, CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan), and MNS (Manasi).Our results reveal that there is an asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggests that the genetic divergence between the two species in this area may have occurred in Holocene at 0.008 Mya. Neutrality tests (Tajima's D, Fu's F s), and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past. The demographic history and gene flow pattern between ACB and ECB may follow the "mountain isolation" hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are grouped together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear for both ACB and ECB, supporting that there has been frequent gene flow among the geographic populations in the Tianshan Mountains.These findings indicate that the Tianshan Mountains are less likely a barrier to gene flow of the two species.
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Affiliation(s)
- Bing Li
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- Key Laboratory of Plant Protection Resources and Pest MangagementNorthwest A&F UniversityYanglingChina
| | - Zhaofu Yang
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- Key Laboratory of Plant Protection Resources and Pest MangagementNorthwest A&F UniversityYanglingChina
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Fang DA, Luo H, He M, Mao C, Kuang Z, Qi H, Xu D, Tan L, Li Y. Genetic Diversity and Population Differentiation of Naked Carp (Gymnocypris przewalskii) Revealed by Cytochrome Oxidase Subunit I and D-Loop. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.827654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The genetic diversity in the naked carp (Gymnocypris przewalskii) of China is threatened by climate change, human activities, as well as natural factors, eliciting conservation concerns. To explore the genetic aspects of G. przewalskii, the genetic diversity, genetic structure, population differentiation, and historical demography of 566 representative individuals from seven geographically distinct ranges of Qinghai Lake were evaluated by mitochondrial DNA cytochrome oxidase subunit I (COI) and D-loop sequences. Estimates of genetic parameters showed that the seven populations of G. przewalskii had high levels of haplotype diversity (0.50243–0.94620) and low levels of nucleotide diversity (0.00079–0.00624). Haplotype genealogy indicated there was no obvious phylogenetic pattern between haplotypes. Both markers denoted the absence of population genetic structure [the genetic differentiation coefficient F-statistics (Fst) < 0] and the presence of high genetic flow (COI: 0.9731–1.0441; D-loop: 0.9480–1.0398). The mismatch between the distribution and neutrality tests supported the evidence of population expansion, which occurred during the late middle Pleistocene [COI: 0.36–0.108 MYA (Million Years Ago); D-loop: 0.497–0.165 MYA]. Furthermore, this work illustrated two simple, reliable, and inexpensive molecular markers for analysis of genetic diversity, while the sensitivity of the mitochondrial D-loop region as a reflection of genetic diversity in G. przewalskii is higher than that of the COI gene.
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Tian C, Yu X, Wang Z, Zou F, Gustafsson DR. PHYLOGENETIC RELATIONSHIPS OF GUIMARAESIELLA AND PRICEIELLA (PHTHIRAPTERA: ISCHNOCERA) FROM BABBLERS AND NON-BABBLERS (PASSERIFORMES). J Parasitol 2022; 108:107-121. [PMID: 35240688 DOI: 10.1645/21-91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Babblers (Passeriformes: Leiothrichidae, Pellorneidae, Timaliidae) are parasitized by more genera of lice of the Brueelia complex than any other group of songbirds. However, the relationships of these louse groups are poorly known. We here try to resolve the relationships between Guimaraesiella (Guimaraesiella), Guimaraesiella (Cicchinella), and their putative sister group Priceiella by using mitochondrial cytochrome c subunit 1 (COI), 12S, and 16S sequences. Our data indicate that G. (Cicchinella) forms a monophyletic group of lice from babblers, but the relationship between G. (Guimaraesiella), G. (Cicchinella), and Priceiella could not be resolved. Moreover, the position of the third lineage of babbler-specific lice, containing only the aberrant species Guimaraesiella montisodalis, is unresolved. Morphologically, this species is different from all other Guimaraesiella in several characters and may represent a distinct lineage. We present some data indicating that (1) the Nanling Mountain range may be a biogeographical barrier to chewing lice and (2) host participation in mixed-species feeding flocks may influence host associations in Brueelia-complex chewing lice.
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Affiliation(s)
- Chunpo Tian
- College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Street, Chang'an District, Xi'an City, 710119, Shaanxi Province, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Street, Chang'an District, Xi'an City, 710119, Shaanxi Province, China
| | - Zhengzhen Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
| | - Fasheng Zou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
| | - Daniel R Gustafsson
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
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Jha A, Seneviratne S, Prayag HS, Vasudevan K. Phylogeny identifies multiple colonisation events and Miocene aridification as drivers of South Asian bulbul (Passeriformes: Pycnonotidae) diversification. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00506-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jiang N, Xue DY, Han HX, Cheng R. Estimating hybridization as a consequence of climatic fluctuations: A case study of two geometridae species. Mol Phylogenet Evol 2021; 161:107168. [PMID: 33798671 DOI: 10.1016/j.ympev.2021.107168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/05/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
In some cases, the phylogenetic analysis based on the mitochondrial DNA (mtDNA) and the nuclear DNA (ncDNA) are discordant. There are three major causes of the discordance within insects, including hybridization, incomplete lineage sorting (ILS) and infection by Wolbachia. In this study, we used a combination of multilocus and coalescent analyses to explore these processes occurred during the evolutionary history of Limbatochlamys rosthorni Rothschild, 1894 and Limbatochlamys pararosthorni Han and Xue, 2005. The ncDNA phylogenetic tree supported two reciprocally monophyletic species, whereas the mtDNA results failed to reveal such a structure and revealed an extensive level of admixture between two species. Because of very low Wolbachia infection rates (<20%), we firstly excluded this reason for the discordance. The fixed nucleotide differences and large genetic distances (1.5-2.5%) at the ncDNA genes suggested that the lineage sorting process between these two species is nearly complete and two species have experienced a prolonged period of independent evolution. Thus, we secondly excluded ILS. Sharing haplotypes, mtDNA gene flow occurring and the transitional samples with morphological features supported hybridization. The distribution contraction during glaciations and postglacial distribution expansion might have facilitated hybridization. Taken together, our study indicates that the current genetic structure of L. rosthorni and L. pararosthorni is the results of contraction and fragmentation into separated refugia during glaciations, followed by postglacial expansion and admixture.
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Affiliation(s)
- Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Da-Yong Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Xiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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Luo Z, Wang X, Yang S, Cheng X, Liu Y, Hu J. Combining the responses of habitat suitability and connectivity to climate change for an East Asian endemic frog. Front Zool 2021; 18:14. [PMID: 33771163 PMCID: PMC7995727 DOI: 10.1186/s12983-021-00398-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/14/2021] [Indexed: 11/25/2022] Open
Abstract
Background Understanding the impacts of past and contemporary climate change on biodiversity is critical for effective conservation. Amphibians have weak dispersal abilities, putting them at risk of habitat fragmentation and loss. Both climate change and anthropogenic disturbances exacerbate these risks, increasing the likelihood of additional amphibian extinctions in the near future. The giant spiny frog (Quasipaa spinosa), an endemic species to East Asia, has faced a dramatic population decline over the last few decades. Using the giant spiny frog as an indicator to explore how past and future climate changes affect landscape connectivity, we characterized the shifts in the suitable habitat and habitat connectivity of the frog. Results We found a clear northward shift and a reduction in the extent of suitable habitat during the Last Glacial Maximum for giant spiny frogs; since that time, there has been an expansion of the available habitat. Our modelling showed that “overwarm” climatic conditions would most likely cause a decrease in the available habitat and an increase in the magnitude of population fragmentation in the future. We found that the habitat connectivity of the studied frogs will decrease by 50–75% under future climate change. Our results strengthen the notion that the mountains in southern China and the Sino-Vietnamese transboundary regions can act as critical refugia and priority areas of conservation planning going forward. Conclusions Given that amphibians are highly sensitive to environmental changes, our findings highlight that the responses of habitat suitability and connectivity to climate change can be critical considerations in future conservation measures for species with weak dispersal abilities and should not be neglected, as they all too often are. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-021-00398-w.
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Affiliation(s)
- Zhenhua Luo
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xiaoyi Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, China
| | - Shaofa Yang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xinlan Cheng
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, China.
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Cai H, Lyu L, Shrestha N, Tang Z, Su X, Xu X, Dimitrov D, Wang Z. Geographical patterns in phylogenetic diversity of Chinese woody plants and its application for conservation planning. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Hongyu Cai
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental Sciences Peking University Beijing China
| | - Lisha Lyu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental Sciences Peking University Beijing China
- School of Urban Planning and Design Shenzhen Graduate School Peking University Shenzhen China
- Landscape Ecology Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Nawal Shrestha
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental Sciences Peking University Beijing China
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Zhiyao Tang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental Sciences Peking University Beijing China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental Sciences Peking University Beijing China
| | - Xiaoting Xu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu China
| | - Dimitar Dimitrov
- Natural History Museum University of Oslo Oslo Norway
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark, University of Copenhagen Copenhagen Denmark
- Department of Natural History University Museum of Bergen University of Bergen Bergen Norway
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental Sciences Peking University Beijing China
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Othman SN, Chen YH, Chuang MF, Andersen D, Jang Y, Borzée A. Impact of the Mid-Pleistocene Revolution and Anthropogenic Factors on the Dispersion of Asian Black-Spined Toads ( Duttaphrynus melanostictus). Animals (Basel) 2020; 10:E1157. [PMID: 32650538 PMCID: PMC7401666 DOI: 10.3390/ani10071157] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 11/28/2022] Open
Abstract
Divergence-time estimation critically improves the understanding of biogeography processes underlying the distribution of species, especially when fossil data is not available. We hypothesise that the Asian black-spined toad, Duttaphrynus melanostictus, expanded into the Eastern Indomalaya following the Quaternary glaciations with the subsequent colonisation of new landscapes during the Last Glacial Maximum. Divergence dating inferred from 364 sequences of mitochondrial tRNAGly ND3 supported the emergence of a common ancestor to the three D. melanostictus clades around 1.85 (±0.77) Ma, matching with the Lower to Mid-Pleistocene transition. Duttaphrynus melanostictus then dispersed into Southeast Asia from the central Indo-Pacific and became isolated in the Southern Sundaic and Wallacea regions 1.43 (±0.10) Ma through vicariance as a result of sea level oscillations. The clade on the Southeast Asian mainland then colonised the peninsula from Myanmar to Vietnam and expanded towards Southeastern China at the end of the Mid-Pleistocene Revolution 0.84 (±0.32) Ma. Population dynamics further highlight an expansion of the Southeast Asian mainland population towards Taiwan, the Northeastern edge of the species' range after the last interglacial, and during the emergence of the Holocene human settlements around 7000 BP. Thus, the current divergence of D. melanostictus into three segregated clades was mostly shaped by Quaternary glaciations, followed by natural dispersion events over land bridges and accelerated by anthropogenic activities.
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Affiliation(s)
- Siti N. Othman
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yi-Huey Chen
- Department of Life Science, Chinese Culture University, Taipei 11114, Taiwan;
| | - Ming-Feng Chuang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Desiree Andersen
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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13
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Hu C, Pan T, Wu Y, Zhang C, Chen W, Chang Q. Spatial genetic structure and historical demography of East Asian wild boar. Anim Genet 2020; 51:557-567. [PMID: 32510675 DOI: 10.1111/age.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/21/2020] [Accepted: 05/01/2020] [Indexed: 11/30/2022]
Abstract
Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.
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Affiliation(s)
- C Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - T Pan
- School of Life Sciences, Anhui Normal University, Wuhu, Anhui, 230039, China
| | - Y Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - C Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, 210013, China
| | - W Chen
- College of Environment and Ecology, Jiangsu Open University (The City Vocational College of Jiangsu), Nanjing, Jiangsu, 210036, China
| | - Q Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
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14
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Li J, Song G, Liu N, Chang Y, Bao X. Deep south-north genetic divergence in Godlewski's bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences. BMC Evol Biol 2019; 19:161. [PMID: 31370783 PMCID: PMC6676563 DOI: 10.1186/s12862-019-1487-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 07/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski's Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species. RESULTS A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2-6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth. CONCLUSIONS Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.
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Affiliation(s)
- Jiande Li
- School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Naifa Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xinkang Bao
- School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
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15
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Xu X, Cheng F, Peng L, Sun Y, Hu X, Li S, Xian H, Jia K, Abbott RJ, Mao J. Late Pleistocene speciation of three closely related tree peonies endemic to the Qinling-Daba Mountains, a major glacial refugium in Central China. Ecol Evol 2019; 9:7528-7548. [PMID: 31346420 PMCID: PMC6635923 DOI: 10.1002/ece3.5284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/22/2019] [Accepted: 05/08/2019] [Indexed: 12/18/2022] Open
Abstract
Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling-Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling-Daba Mountains of Central China.
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Affiliation(s)
- Xing‐Xing Xu
- Peony International Research Institute, National Flower Engineering Research Centre, Key Laboratory for the Genetics and Breeding of Forest Trees and Ornamental Plants, College of Landscape ArchitectureBeijing Forestry UniversityBeijingChina
| | - Fang‐Yun Cheng
- Peony International Research Institute, National Flower Engineering Research Centre, Key Laboratory for the Genetics and Breeding of Forest Trees and Ornamental Plants, College of Landscape ArchitectureBeijing Forestry UniversityBeijingChina
| | - Li‐Ping Peng
- Peony International Research Institute, National Flower Engineering Research Centre, Key Laboratory for the Genetics and Breeding of Forest Trees and Ornamental Plants, College of Landscape ArchitectureBeijing Forestry UniversityBeijingChina
| | - Yan‐Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Xian‐Ge Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - San‐Yuan Li
- Forestry Department of Shaanxi ProvinceXi'anShaanxiChina
| | - Hong‐Li Xian
- Forestry Department of Shaanxi ProvinceXi'anShaanxiChina
| | - Kai‐Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Richard J. Abbott
- School of Biology, Mitchell BuildingUniversity of St AndrewsSt AndrewsFifeUK
| | - Jian‐Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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16
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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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17
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Li H, Kong L, Wang K, Zhang S, Motokawa M, Wu Y, Wang W, Li Y. Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex. Integr Zool 2019; 14:494-505. [PMID: 30688015 DOI: 10.1111/1749-4877.12378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages LN , LS and LHN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with LHN /LS split at 1.33 Ma and LN /(LHN +LS ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages LN and (LS +LHN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: LHN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; LS represents a cryptic species distributed throughout the southern Chinese continent; and LN represents the nominotypical species L. edwardsi.
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Affiliation(s)
- Haotian Li
- Marine College, Shandong University, Weihai, China
| | | | - Kaiyun Wang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | - Shuping Zhang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | | | - Yi Wu
- College of Life Science, Guangzhou University, Guangzhou, China
| | - Wenquan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China
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18
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Liu Y, Dietrich CH, Wei C. Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation? BMC Evol Biol 2019; 19:5. [PMID: 30621591 PMCID: PMC6323834 DOI: 10.1186/s12862-018-1317-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Results The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations. Conclusions Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas. Electronic supplementary material The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, 61820, USA
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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19
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Zhao M, Chang Y, Kimball RT, Zhao J, Lei F, Qu Y. Pleistocene glaciation explains the disjunct distribution of the Chestnut‐vented Nuthatch (Aves, Sittidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Min Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Department of Biology University of Florida Gainesville Florida
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | | | - Jian Zhao
- School of Life Sciences Sun Yat‐sen University Guangzhou China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
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20
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Wei C, Dong L, Li SH, Alström P, Liu Y, Xia C, Yao CT, Zhang Y. From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex. Mol Phylogenet Evol 2018; 131:219-227. [PMID: 30316948 DOI: 10.1016/j.ympev.2018.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/06/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.
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Affiliation(s)
- Chentao Wei
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-75007 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Biocontrol and Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Medium Altitude Experimental Station, Endemic Species Research Institute, Chichi, 15, Nantou 552, Taiwan, China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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21
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Sun Z, Wang H, Zhou W, Shi W, Zhu W, Zhang B. How rivers and historical climate oscillations impact on genetic structure in Chinese Muntjac ( Muntiacus reevesi)? DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Zhonglou Sun
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
- Department of Medicine; University of Utah; Salt Lake City Utah USA
| | - Hui Wang
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Wenliang Zhou
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Wenbo Shi
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Weiquan Zhu
- Department of Medicine; University of Utah; Salt Lake City Utah USA
| | - Baowei Zhang
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
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22
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Li J, Wei S, Hu M, Luo Z, Zhao M, Wu H. Reflection of paleoclimate oscillations and tectonic events in the phylogeography of moustache toads in southern China. J Zool (1987) 2018. [DOI: 10.1111/jzo.12537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- J. Li
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - S. Wei
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - M. Hu
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - Z. Luo
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - M. Zhao
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
| | - H. Wu
- School of Life Sciences Institute of Evolution and Ecology Central China Normal University Wuhan China
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23
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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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24
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Du Y, Wen Z, Zhang J, Lv X, Cheng J, Ge D, Xia L, Yang Q. The roles of environment, space, and phylogeny in determining functional dispersion of rodents (Rodentia) in the Hengduan Mountains, China. Ecol Evol 2017; 7:10941-10951. [PMID: 29299271 PMCID: PMC5743695 DOI: 10.1002/ece3.3613] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/21/2017] [Accepted: 10/08/2017] [Indexed: 11/07/2022] Open
Abstract
The recently described trait-based approach is becoming widely popular for a mechanistic understanding of species coexistence. However, the greatest challenge in functional analyses is decomposing the contributions of different ecological and evolutionary processes (e.g., niche-based process, neutral process, and evolutionary process) in determining trait structure. Taking rodents (Rodentia) in the Hengduan Mountains as our study model, we aim to (1) quantify the vertical patterns of functional structure for head-body length (HL), tail/body ratio (TR), animal component in diet (ACD), and all traits; (2) disentangle the relative importance of different assembly processes (environment, space, and phylogeny) in structuring trait dispersion; and (3) assess the feasibility of Bergmann's rule and Allen's rule along elevational gradient. Our results have suggested that the vertical functional structure pattern varied across these three traits, indicating distinct functional roles in the community assembly process. These nonrandom vertical patterns of HL, TR, and terminal ACD have demonstrated these traits were dominated by different ecological process along environmental gradient. In variance partitioning, high proportion of the spatial variations in trait dispersion was explained by environmental and spatial models, which have provided supporting strong evidence for niche-based and neutral processes in leading species coexistence. Although the three traits all exhibited apparent phylogenetic signals, phylogenetic relationship within community failed to predict the spatial variations of functional dispersion, confirming the enormous inference of phylogenetic signals in predicting trait structure. By assessing the vertical patterns of HL and TR at order and family levels, we argued that functional adaptation along an environmental gradient is a surrogate of series of complex processes (e.g., environmental filtering, interspecific interaction, and neutral dispersal) acting on multiple functional axes, which results in inconsistence with the empirical rules along elevational gradient.
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Affiliation(s)
- Yuanbao Du
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,College of Life Science University of Chinese Academy of Sciences Beijing China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jinlong Zhang
- Flora Conservation Department Kadoorie Farm and Botanic Garden Hong Kong SAR China
| | - Xue Lv
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,College of Life Science University of Chinese Academy of Sciences Beijing China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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25
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Feng B, Liu JW, Xu J, Zhao K, Ge ZW, Yang ZL. Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps). MYCORRHIZA 2017; 27:261-272. [PMID: 27909816 DOI: 10.1007/s00572-016-0751-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
The Alpine porcini, Boletus reticuloceps, is an ectomycorrhizal mushroom distributed in subalpine areas of Southwest China, central China, and Taiwan Island. This distribution pattern makes it an ideal organism to infer how ectomycorrhizal fungi have reacted to historical tectonic and climatic changes, and to illustrate the mechanism for the disjunction of organisms between Southwest China and Taiwan. In this study, we explored the phylogeographic pattern of B. reticuloceps by microsatellite genotyping, DNA sequencing, ecological factor analysis, and species distribution modeling. Three genetic groups from the East Himalayas (EH), northern Hengduan Mountains (NHM), and southern Hengduan Mountains (SHM), were identified. The earlier divergent SHM group is found under Abies in moister environments, whereas the EH and NHM groups, which are physically separated by the Mekong-Salween Divide, are found mainly under Picea in drier environments. Samples from Taiwan showed a close relationship with the SHM group. High mountains did not form dispersal barriers among populations in each of the EH, NHM, and SHM groups, probably due to the relatively weak host specificity of B. reticuloceps. Our study indicated that ecological heterogeneity could have contributed to the divergence between the SHM and the NHM-EH groups, while physical barriers could have led to the divergence of the NHM and the EH groups. Dispersal into Taiwan via Central China during the Quaternary glaciations is likely to have shaped its disjunct distribution.
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Affiliation(s)
- Bang Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian Wei Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON , L8S 4K1, Canada
| | - Kuan Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zai Wei Ge
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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26
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Gauffre-Autelin P, von Rintelen T, Stelbrink B, Albrecht C. Recent range expansion of an intermediate host for animal schistosome parasites in the Indo-Australian Archipelago: phylogeography of the freshwater gastropod Indoplanorbis exustus in South and Southeast Asia. Parasit Vectors 2017; 10:126. [PMID: 28264699 PMCID: PMC5339995 DOI: 10.1186/s13071-017-2043-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/17/2017] [Indexed: 03/13/2024] Open
Abstract
Background The planorbid snail Indoplanorbis exustus is the sole intermediate host for the Schistosoma indicum species group, trematode parasites responsible for cattle schistosomiasis and human cercarial dermatitis. This freshwater snail is widely distributed in Southern Asia, ranging from Iran to China eastwards including India and from the southeastern Himalayas to Southeast Asia southwards. The veterinary and medical importance of this snail explains the interest in understanding its geographical distribution patterns and evolutionary history. In this study, we used a large and comprehensive sampling throughout Indo-Malaya, including specimens from South India and Indonesia, areas that have been formerly less studied. Results The phylogenetic inference revealed five highly divergent clades (genetic distances among clades: 4.4–13.9%) that are morphologically indistinguishable, supporting the assumption that this presumed nominal species may represent a cryptic species complex. The species group may have originated in the humid subtropical plains of Nepal or in southern adjacent regions in the Early Miocene. The major cladogenetic events leading to the fives clades occurred successively from the Early Miocene to the Early Pleistocene, coinciding with major periods of monsoonal intensification associated with major regional paleogeographic events in the Miocene and repeated climate changes due to the Plio-Pleistocene climatic oscillations. Our coverage of the Indo-Australian Archipelago (IAA) highlights the presence of a single clade there. Contrary to expectations, an AMOVA did not reveal any population genetic structure among islands or along a widely recognised zoogeographical regional barrier, suggesting a recent colonisation independent of natural biogeographical constraints. Neutrality tests and mismatch distributions suggested a sudden demographic and spatial population expansion that could have occurred naturally in the Pleistocene or may possibly result of a modern colonisation triggered by anthropogenic activities. Conclusions Even though Indoplanorbis is the main focus of this study, our findings may also have important implications for fully understanding its role in hosting digenetic trematodes. The existence of a cryptic species complex, the historical phylogeographical patterns and the recent range expansion in the IAA provide meaningful insights to the understanding and monitoring of the parasites potential spread. It brings a substantial contribution to veterinary and public health issues. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2043-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Björn Stelbrink
- Department of Animal Ecology and Systematics, Justus Liebig University, Giessen, Germany
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University, Giessen, Germany
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27
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Chan J, Li W, Hu X, Liu Y, Xu Q. Genetic diversity and population structure analysis of Qinghai-Tibetan plateau schizothoracine fish (Gymnocypris dobula) based on mtDNA D-loop sequences. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Sun Z, Pan T, Wang H, Pang M, Zhang B. Yangtze River, an insignificant genetic boundary in tufted deer ( Elaphodus cephalophus): the evidence from a first population genetics study. PeerJ 2016; 4:e2654. [PMID: 27843712 PMCID: PMC5103815 DOI: 10.7717/peerj.2654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/04/2016] [Indexed: 12/02/2022] Open
Abstract
Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Tao Pan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Hui Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Mujia Pang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China.,School of Biosciences, Cardiff University, Cardiff, United Kingdom
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29
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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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30
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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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31
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Li J, Zhao M, Wei S, Luo Z, Wu H. Geologic events coupled with Pleistocene climatic oscillations drove genetic variation of Omei treefrog (Rhacophorus omeimontis) in southern China. BMC Evol Biol 2015; 15:289. [PMID: 26690899 PMCID: PMC4687352 DOI: 10.1186/s12862-015-0572-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pleistocene climatic oscillations and historical geological events may both influence current patterns of genetic variation, and the species in southern China that faced unique climatic and topographical events have complex evolutionary histories. However, the relative contributions of climatic oscillations and geographical events to the genetic variation of these species remain undetermined. To investigate patterns of genetic variation and to test the hypotheses about the factors that shaped the distribution of this genetic variation in species of southern China, mitochondrial genes (cytochrome b and NADH dehydrogenase subunit 2) and nine microsatellite loci of the Omei tree frog (Rhacophorus omeimontis) were amplified in this study. RESULTS The genetic diversity in the populations of R. omeimontis was high. The phylogenetic trees reconstructed from the mitochondrial DNA (mtDNA) haplotypes and the Bayesian genetic clustering analysis based on microsatellite data both revealed that all populations were divided into three lineages (SC, HG and YN). The two most recent splitting events among the lineages coincided with recent geological events (including the intense uplift of the Qinghai-Tibet Plateau, QTP and the subsequent movements of the Yun-Gui Plateau, YGP) and the Pleistocene glaciations. Significant expansion signals were not detected in mismatch analyses or neutrality tests. And the effective population size of each lineage was stable during the Pleistocene. CONCLUSIONS Based on the results of this study, complex geological events (the recent dramatic uplift of the QTP and the subsequent movements of the YGP) and the Pleistocene glaciations were apparent drivers of the rapid divergence of the R. omeimontis lineages. Each diverged lineages survived in situ with limited gene exchanges, and the stable demographics of lineages indicate that the Pleistocene climatic oscillations were inconsequential for this species. The analysis of genetic variation in populations of R. omeimontis contributes to the understanding of the effects of changes in climate and of geographical events on the dynamic development of contemporary patterns of genetic variation in the species of southern China.
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Affiliation(s)
- Jun Li
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Mian Zhao
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Shichao Wei
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Zhenhua Luo
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
| | - Hua Wu
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
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32
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Song G, Zhang R, DuBay SG, Qu Y, Dong L, Wang W, Zhang Y, Lambert DM, Lei F. East Asian allopatry and north Eurasian sympatry in Long-tailed Tit lineages despite similar population dynamics during the late Pleistocene. ZOOL SCR 2015. [DOI: 10.1111/zsc.12148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Center for Developmental Biology; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Shane G. DuBay
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Life Sciences Section; Integrative Research Center; Field Museum of Natural History; Chicago IL 60605 USA
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Wenjuan Wang
- Center for Watershed Ecology; Institute of Life Science; Nanchang University; Nanchang 330031 China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - David M. Lambert
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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33
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YE J, XIAO Z, LI C, WANG F, LIAO J, FU J, ZHANG Z. Past climate change and recent anthropogenic activities affect genetic structure and population demography of the greater long-tailed hamster in northern China. Integr Zool 2015. [DOI: 10.1111/1749-4877.12150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junbin YE
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Zhenlong XIAO
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Chuanhai LI
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Fusheng WANG
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Jicheng LIAO
- School of Life Sciences; Lanzhou University; Lanzhou China
| | - Jinzhong FU
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada
| | - Zhibin ZHANG
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
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34
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Li Y, Wu X, Zhang H, Yan P, Xue H, Wu X. Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae). PLoS One 2015; 10:e0138757. [PMID: 26394403 PMCID: PMC4578928 DOI: 10.1371/journal.pone.0138757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/03/2015] [Indexed: 11/26/2022] Open
Abstract
Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.
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Affiliation(s)
- Yongmin Li
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- School of Life Sciences, Fuyang Teachers College, Fuyang, Anhui, China
| | - Xiaoyou Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Huabin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Xue
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xiaobing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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35
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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: 35] [Impact Index Per Article: 3.9] [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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Wei S, Cao L, Gong Y, Shi B, Wang S, Zhang F, Guo X, Wang Y, Chen X. Population genetic structure and approximate
B
ayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth
G
rapholita molesta
(
L
epidoptera:
T
ortricidae) in its native range. Mol Ecol 2015; 24:4094-111. [DOI: 10.1111/mec.13300] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 06/22/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Shu‐Jun Wei
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Li‐Jun Cao
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Ya‐Jun Gong
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Bao‐Cai Shi
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Su Wang
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Fan Zhang
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Xiao‐Jun Guo
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Yuan‐Min Wang
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Xue‐Xin Chen
- Institute of Insect Sciences Zhejiang University 866 Yuhangtang Road Hangzhou 310058 China
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Grant WS. Problems and Cautions With Sequence Mismatch Analysis and Bayesian Skyline Plots to Infer Historical Demography. J Hered 2015; 106:333-46. [DOI: 10.1093/jhered/esv020] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 03/24/2015] [Indexed: 12/11/2022] Open
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Wang H, Luo X, Meng S, Bei Y, Song T, Meng T, Li G, Zhang B. The Phylogeography and Population Demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive Rivers as Barriers to Gene Flow. PLoS One 2015; 10:e0125770. [PMID: 25915933 PMCID: PMC4411157 DOI: 10.1371/journal.pone.0125770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/26/2015] [Indexed: 11/23/2022] Open
Abstract
Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15–17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.
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Affiliation(s)
- Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xia Luo
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Shaoquan Meng
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Yongjian Bei
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Tao Song
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Tao Meng
- Guangxi Forestry Inventory and Planning Institute, Nanning, 530011, Guangxi, China
| | - Guifen Li
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
- * E-mail: (GL); (BZ)
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- * E-mail: (GL); (BZ)
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Wu Y, Li H, Zou F, Hsu Y. Lineages differentiation and population structure of the light-vented bulbul Pycnonotus sinensis in China based on mitochondrial DNA and microsatellite analysis. Integr Zool 2015; 6:387-98. [PMID: 22182330 DOI: 10.1111/j.1749-4877.2011.00253.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The light-vented bulbul Pycnonotus sinensis is a small resident passerine that is found widely in central and south China, North Vietnam, and some East Asian islands, including Hainan, Taiwan and the Ryukyu Islands. Its subspecies status has been under considerable debate. A total of 10 subspecies have been proposed, but only 4 are widely recognized, including 1 continental taxon, P. s. sinensis, and 3 insular subspecies: P. s. hainanus, P. s. formosae and P. s. orii. Two mitochondrial DNA genes and 9 microsatellite loci were used to investigate the genetic divergence of this species, to identify the evolutionary status of 2 insular subspecies (P. s. hainanus and P. s. formosae) and to uncover probable historical causes that shaped them. The results reveal that P. s. formosae has diverged significantly from the other 2 subspecies because of a substantial time of isolation for populations on Taiwan Island. There was no significant genetic differentiation between P. s. sinensis and P. s. hainanus. The notable morphological difference in P. s. hainanus might be attributed to a rapid, recent adaptation to the tropical environment of Hainan Island. The low genetic divergence between P. s. sinensis and P. s. hainanus might result from a recent divergence or gene flow between them. Two insular subspecies of light-vented bulbul populations might have diverged recently from their continental relatives through a complex evolution history owing to island isolation, ecological isolation, and possibly even hybridization. Both P. s. hainanus and P. s. formosae should be considered important conservation units because of their morphological and genetic distinctiveness.
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Affiliation(s)
- Yuchun Wu
- South China Institute of Endangered Animals, Guangzhou, China
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Chen D, Chang J, Li SH, Liu Y, Liang W, Zhou F, Yao CT, Zhang Z. Was the exposed continental shelf a long-distance colonization route in the ice age? The Southeast Asia origin of Hainan and Taiwan partridges. Mol Phylogenet Evol 2015; 83:167-73. [DOI: 10.1016/j.ympev.2014.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/04/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
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41
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Reddy S, Sharief S, Yohe LR, Witkowski J, Hosner PA, Nyári ÁS, Moyle RG. Untangling taxonomic confusion and diversification patterns of the Streak-breasted Scimitar Babblers (Timaliidae: Pomatorhinus ruficollis complex) in southern Asia. Mol Phylogenet Evol 2014; 82 Pt A:183-92. [PMID: 25450499 DOI: 10.1016/j.ympev.2014.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/07/2014] [Accepted: 10/17/2014] [Indexed: 11/18/2022]
Abstract
Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa - P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a 'suture' zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The 'suture' zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Sarah Sharief
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Laurel R Yohe
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA; Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Julie Witkowski
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Peter A Hosner
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
| | - Árpád S Nyári
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA; Department of Zoology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA.
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
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42
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Qu Y, Ericson PGP, Quan Q, Song G, Zhang R, Gao B, Lei F. Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya. Mol Ecol 2014; 23:705-20. [DOI: 10.1111/mec.12619] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Per G. P. Ericson
- Department of Vertebrate Zoology; Swedish Museum of Natural History; PO Box 50007 SE-10405 Stockholm Sweden
| | - Qing Quan
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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Lu G, Lin A, Luo J, Blondel DV, Meiklejohn KA, Sun K, Feng J. Phylogeography of the Rickett's big-footed bat, Myotis pilosus (Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China. BMC Evol Biol 2013; 13:241. [PMID: 24188176 PMCID: PMC4228257 DOI: 10.1186/1471-2148-13-241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 10/29/2013] [Indexed: 12/03/2022] Open
Abstract
Background China is characterized by complex topographic structure and dramatic palaeoclimatic changes, making species biogeography studies particularly interesting. Previous researchers have also demonstrated multiple species experienced complex population histories, meanwhile multiple shelters existed in Chinese mainland. Despite this, species phylogeography is still largely unexplored. In the present study, we used a combination of microsatellites and mitochondrial DNA (mtDNA) to investigate the phylogeography of the east Asian fish-eating bat (Myotis pilosus). Results Phylogenetic analyses showed that M. pilosus comprised three main lineages: A, B and C, which corresponded to distinct geographic populations of the Yangtze Plain (YTP), Sichuan Basin (SCB) and North and South of China (NSC), respectively. The most recent common ancestor of M. pilosus was dated as 0.25 million years before present (BP). Population expansion events were inferred for populations of Clade C, North China Plain region, Clade B and YunGui Plateau region at 38,700, 15,900, 4,520 and 4,520 years BP, respectively. Conflicting results were obtained from mtDNA and microsatellite analyses; strong population genetic structure was obtained from mtDNA data but not microsatellite data. The microsatellite data indicated that genetic subdivision fits an isolation-by-distance (IBD) model, but the mtDNA data failed to support this model. Conclusions Our results suggested that Pleistocene climatic oscillations might have had a profound influence on the demographic history of M. pilosus. Spatial genetic structures of maternal lineages that are different from those observed in other sympatric bats species may be as a result of interactions among special population history and local environmental factors. There are at least three possible refugia for M. pilosus during glacial episodes. Apparently contradictory genetic structure patterns of mtDNA and microsatellite could be explained by male-mediated gene flow among populations. This study also provides insights on the necessity of conservation of M. pilosus populations to conserve this genetic biodiversity, especially in the areas of YTP, SCB and NSC regions.
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Affiliation(s)
| | | | | | | | | | - Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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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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Song G, Yu L, Gao B, Zhang R, Qu Y, Lambert DM, Li S, Zhou T, Lei F. Gene flow maintains genetic diversity and colonization potential in recently range-expanded populations of an Oriental bird, the Light-vented Bulbul (Pycnonotus sinensis, Aves: Pycnonotidae). DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12067] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- 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
| | | | - Shouhsien Li
- Department of Life Science; National Taiwan Normal University; Taipei; Taiwan
| | - Tianlin Zhou
- College of Life Science and Technology; Longdong University; Gansu; 745000; China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
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Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus). PLoS One 2013; 8:e55629. [PMID: 23405183 PMCID: PMC3566057 DOI: 10.1371/journal.pone.0055629] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 01/02/2013] [Indexed: 12/01/2022] Open
Abstract
We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus Pomatorhinus. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well as divergent evolution of members from within clades. Pomatorhinus species from different clades occupying Himalayan foothills show convergence towards similar climatic tolerances, whereas within a clade, allopatric sister-species occurring in the Himalayas have diverged to occupy different climatic parameter spaces. Comparisons of climatic tolerances of Himalayan foothills taxa with species distributed further south in Assam/Burma and Burma/Thailand indicate convergence towards similar parameter spaces in several climatic variables. Niche overlap was observed to be lower among species of the youngest clade (ruficollis) and higher among species of older clades (ferruginosus). Analysis of accumulation of ecological disparity through time indicates rapid divergence within recent time frames. As a result, Himalayan taxa originating at different temporal scales within the four main scimitar babbler clades have differentiated ecologically only in recently diverged taxa. Our study suggests that the repeated orogenic and climatic fluctuations of the Pliocene and Pleistocene within mainland Southeast Asia served as an important ecological speciation driver within scimitar babblers, by providing opportunities for rapid geographic expansion and filling of novel environmental niches.
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Wang B, Jiang J, Xie F, Li C. Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains. J Mol Evol 2013; 76:112-28. [PMID: 23381112 DOI: 10.1007/s00239-013-9544-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Accepted: 01/19/2013] [Indexed: 11/24/2022]
Abstract
Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F(ct) = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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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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Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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50
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Blair C, Davy CM, Ngo A, Orlov NL, Shi HT, Lu SQ, Gao L, Rao DQ, Murphy RW. Genealogy and Demographic History of a Widespread Amphibian throughout Indochina. J Hered 2012; 104:72-85. [PMID: 23125408 DOI: 10.1093/jhered/ess079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND1 and cytochrome b and tested hypotheses pertaining to climate, geology, and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio-Pleistocene diversification, with the former corresponding to periods of increased aridity and the onset of monsoonal weather systems. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia, suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina and further clarified the evolutionary history of lineages within P. leucomystax.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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