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Liu Y, Li C, Shao H. Comparative Study of Potential Habitats for Simulium qinghaiense (Diptera: Simuliidae) in the Huangshui River Basin, Qinghai-Tibet Plateau: An Analysis Using Four Ecological Niche Models and Optimized Approaches. INSECTS 2024; 15:81. [PMID: 38392501 PMCID: PMC10889266 DOI: 10.3390/insects15020081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Abstract
The Huangshui River, a vital tributary in the upper reaches of the Yellow River within the eastern Qinghai-Tibet Plateau, is home to the endemic black fly species S. qinghaiense. In this study, we conducted a systematic survey of the distribution of the species in the Huangshui River basin, revealing its predominant presence along the river's main stem. Based on four ecological niche models-MaxEnt with parameter optimization; GARP; BIOCLIM; and DOMAIN-we conduct a comparative analysis; evaluating the accuracy of AUC and Kappa values. Our findings indicate that optimizing parameters significantly improves the MaxEnt model's predictive accuracy by reducing complexity and overfitting. Furthermore, all four models exhibit higher accuracy compared to a random model, with MaxEnt demonstrating the highest AUC and Kappa values (0.9756 and 0.8118, respectively), showcasing significant superiority over the other models (p < 0.05). Evaluation of predictions from the four models elucidates that potential areas of S. qinghaiense in the Huangshui River basin are primarily concentrated in the central and southern areas, with precipitation exerting a predominant influence. Building upon these results, we utilized the MaxEnt model to forecast changes in suitable areas and distribution centers during the Last Interglacial (LIG), Mid-Holocene (MH), and future periods under three climate scenarios. The results indicate significantly smaller suitable areas during LIG and MH compared to the present, with the center of distribution shifting southeastward from the Qilian Mountains to the central part of the basin. In the future, suitable areas under different climate scenarios are expected to contract, with the center of distribution shifting southeastward. These findings provide important theoretical references for monitoring, early warning, and control measures for S. qinghaiense in the region, contributing to ecological health assessment.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Provincial Key Laboratory of Agricultural Integrated Pest Management in Qinghai, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
| | - Chuanji Li
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Provincial Key Laboratory of Agricultural Integrated Pest Management in Qinghai, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
| | - Hainan Shao
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
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2
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Gong S, Suwannapoom C, Le M, Nguyen TQ, Ge Y, Wei Y, Gao Y. Genomic analyses reveal three phylogenetic species and their evolutionary histories in the big-headed turtle. iScience 2023; 26:107343. [PMID: 37539035 PMCID: PMC10393795 DOI: 10.1016/j.isci.2023.107343] [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: 02/09/2023] [Revised: 05/21/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
The critically endangered big-headed turtle (Platysternon megacephalum) is currently classified into three subspecies. However, the classification is still controversial and their evolutionary histories are still unclear. Here, multiple genetic analyses consistently revealed three phylogenetic groups with substantial genetic divergences and distinct demographic histories, suggesting three phylogenetic species (P. megacephalum, P. peguense, and Baise clade). Phylogeographical analyses revealed that the Red River plains and Guangxi basins are largely coincident with the boundaries between the three phylogenetic species, highlighting the key role of lowland areas in driving speciation in the big-headed turtle. The Baise clade is characterized by high-linkage disequilibrium but the lowest effective population size, indicating that the cryptic phylogenetic species is more vulnerable to human activities and environmental disturbance, and urgently needs more protection. Our findings provide fundamental insights into the taxonomy and scientific conservation of the family Platysternidae.
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Affiliation(s)
- Shiping Gong
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang Road West, Guangzhou 510260, China
| | | | - Minh Le
- Faculty of Environmental Sciences, University of Science & Central Institute for Natural Resources and Environmental Studies (CRES), Vietnam National University, Hanoi, Vietnam
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
| | - Yan Ge
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang Road West, Guangzhou 510260, China
| | - Yufeng Wei
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang Road West, Guangzhou 510260, China
| | - Yangchun Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang Road West, Guangzhou 510260, China
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3
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Liu Y, Bu Y, Wang J, Wei C. Geological events and climate change drive diversification and speciation of mute cicadas in eastern continental Asia. Mol Phylogenet Evol 2023; 184:107809. [PMID: 37172861 DOI: 10.1016/j.ympev.2023.107809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
The poor mobility of nymphs living underground, usually for many years and the weak flying ability of adults make cicadas unique for evolutionary biology and bio-geographical study. Cicadas of the genus Karenia are unusual in Cicadidae in lacking the timbals that produce sound. Population differentiation, genetic structure, dispersal and evolutionary history of the eastern Asian mute cicada Karenia caelatata were investigated based on morphological, acoustic and molecular data. The results reveal a high level of genetic differentiation in this species. Six independent clades with nearly unique sets of haplotypes corresponding to geographically isolated populations are recognized. Genetic and geographic distances are significantly correlated among lineages. The phenotypic differentiation is generally consistent with the high levels of genetic divergence across populations. Results of ecological niche modeling suggest that the potential distribution range of this mountain-habitat specialist during the Last Glacial Maximum was broader than its current range, indicating this species had benefited from the climate change during the early Pleistocene in southern China. Geological events such as orogeny in Southwest China and Pleistocene climate oscillations have driven the differentiation and divergence of this species, and basins, plains and rivers function as natural "barriers" to block the gene flow. Besides significant genetic divergence being found among clades, the populations occurring in the Wuyi Mountains and the Hengduan Mountains are significantly different in the calling song structure from other populations. This may have resulted from significant population differentiation and subsequent adaptation of related populations. We conclude that ecological differences in habitats, coupled with geographical isolation, have driven population divergence and allopatric speciation. This study provides a plausible example of incipient speciation in Cicadidae and improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this unusual cicada species. It informs future studies on population differentiation, speciation and phylogeography of other mountain-habitat insects in the East Asian continent.
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Affiliation(s)
- Yunxiang Liu
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory of Plateau Ecology and Agriculture, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, China
| | - Yifan Bu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiali Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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4
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Monroe AF, Hubbard SC, Rodriguez R, Kuhns FM, McClung MR, Moran MD, Gates MW. Biodiversity of Parasitic Hymenoptera Across Sky Islands of Arkansas, United States. ENVIRONMENTAL ENTOMOLOGY 2022; 51:922-926. [PMID: 35912716 DOI: 10.1093/ee/nvac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Sky islands are often areas of endemism and high species diversity around the world. In central North America, the Ozark and Ouachita Highlands contain numerous modestly high elevational islands that are slightly cooler and wetter than surrounding lowlands and these areas are known to contain many unique species. We studied parasitic Hymenoptera biodiversity on three sky islands in Arkansas, both in canopy and understory strata of mature post oak forests. We found that morphospecies diversity was high, and community structure varied both within (canopy versus understory) and between sky islands. Each mountaintop showed a high level of distinctiveness with few morphospecies found in multiple locations. The high intersky island variation indicates that individual sky islands in the region harbor unique Hymenoptera assemblages, a pattern that likely extends to the broader insect community. Our study suggests that these highland areas are important regions of North American biodiversity and that they should be evaluated individually for conservation efforts in order to preserve their distinctive community structure.
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Affiliation(s)
- Allison F Monroe
- Department of Biology & Health Sciences, Hendrix College, 1600 Washington Avenue, Conway, AR 72032, USA
| | - Sierra C Hubbard
- Department of Biology & Health Sciences, Hendrix College, 1600 Washington Avenue, Conway, AR 72032, USA
| | - Reynol Rodriguez
- Department of Biology & Health Sciences, Hendrix College, 1600 Washington Avenue, Conway, AR 72032, USA
| | - Faith M Kuhns
- Department of Biology & Health Sciences, Hendrix College, 1600 Washington Avenue, Conway, AR 72032, USA
| | - Maureen R McClung
- Department of Biology & Health Sciences, Hendrix College, 1600 Washington Avenue, Conway, AR 72032, USA
| | - Matthew D Moran
- Department of Biology & Health Sciences, Hendrix College, 1600 Washington Avenue, Conway, AR 72032, USA
| | - Michael W Gates
- Systematic Entomology Laboratory, USDA, Smithsonian Institution, P.O. Box 37012, National Museum of Natural History, Washington, DC 2001-37012, USA
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5
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Assessing the genetic consequences of habitat fragmentation on the federally threatened cheat mountain salamander (Plethodon nettingi): a comparative, multi-locus approach. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01449-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Christoph Liedtke H, Lyakurwa JV, Lawson LP, Menegon M, Garrido-Priego M, Mariaux J, Ngalason W, Channing A, Owen NR, Bittencourt-Silva GB, Wilkinson M, Larson JG, Loader SP. Thirty years of amphibian surveys in the Ukagurus Mountains of Tanzania reveal new species, yet others are in decline. AFR J HERPETOL 2022. [DOI: 10.1080/21564574.2022.2043945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- H Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - John V Lyakurwa
- Department of Zoology and Wildlife Conservation, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Lucinda P Lawson
- Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Michele Menegon
- Division of Biology & Conservation Ecology, School of Science & the Environment, Manchester Metropolitan University, Manchester, UK
- PAMS Foundation, Arusha, Tanzania
| | - Marina Garrido-Priego
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
- Division of Behavioural Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jean Mariaux
- Natural History Museum of Geneva, Geneva, Switzerland
| | - Wilirk Ngalason
- Department of Zoology and Wildlife Conservation, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Alan Channing
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Nisha R Owen
- On the EDGE Conservation, London, UK
- The Society for Environmental Exploration (Frontier), London, UK
| | - Gabriela B Bittencourt-Silva
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - Joanna G Larson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Simon P Loader
- Department of Life Sciences, Natural History Museum, London, UK
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7
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Tadeo E, Rull J. Hybridization, Behavioral Patterns, and Pre- and Postzygotic Isolation Between Two Recently Derived Species of Walnut-Infesting Rhagoletis Fruit Flies in the Highlands of Mexico. NEOTROPICAL ENTOMOLOGY 2021; 50:505-514. [PMID: 33765250 DOI: 10.1007/s13744-021-00865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Episodes of isolation and secondary contact among populations of insects of Nearctic origin during Pleistocene glacial/postglacial climatic cycles had a strong evolutionary influence on the diversity of flies in the genus Rhagoletis in mountainous areas of Mexico. As a series of experiments undertaken to gather support for phylogenetic hypotheses on the origin of three walnut-infesting species in the suavis group, we examined pre- and postzygotic isolation between Rhagoletis completa Cresson, 1929 and R. ramosae Hernández-Ortiz, 1985. Despite morphological, biological, and behavioral differences, these two species were found to be capable of hybridization. Mating experiments in large enclosures revealed asymmetric sexual isolation. There were notable differences in male sexual behavior. While R. ramosae males mated exclusively on host fruit, R. completa males used fruit and alternative mating locations. During fruit-guarding and male-male contests, R. completa and R. ramosae males adopted markedly different wing postures. R. completa females were more reluctant to copulate with heterospecific males than R. ramosae females. During no choice crosses in small enclosures, there was a reduction of egg hatch for the hybrid cross of R. completa males × R. ramosae females. Our results and previous studies on reproductive isolation between other species pairs in the suavis group support a clade in which R. ramosae, R. zoqui Bush, 1966, and R. completa are close relatives all still capable of hybridizing.
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Affiliation(s)
- Eduardo Tadeo
- Instituto de Neuroetología, Universidad Veracruzana, Veracruz, Mexico
| | - Juan Rull
- LIEMEN-División Control Biológico de Plagas, PROIMI Biotecnología-CONICET, Tucumán, Argentina.
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8
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Colihueque N, Gantz A, Parraguez M. Revealing the biodiversity of Chilean birds through the COI barcode approach. Zookeys 2021; 1016:143-161. [PMID: 33628081 PMCID: PMC7892532 DOI: 10.3897/zookeys.1016.51866] [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: 03/09/2020] [Accepted: 12/20/2020] [Indexed: 11/12/2022] Open
Abstract
The mitochondrial cytochrome c oxidase subunit I (COI) gene is an effective molecular tool for the estimation of genetic variation and the identification of bird species. This molecular marker is used to differentiate among Chilean bird species by analyzing barcodes for 76 species (197 individuals), comprising 28 species with no previous barcode data and 48 species with sequences retrieved from the BOLD and GenBank databases. The DNA barcodes correctly identified 94.7% of the species analyzed (72 of 76 species). Mean intraspecific K2P distance was 0.3% (range 0-8.7%). Within the intraspecific divergence range, three species, Phrygilus gayi, Sephanoides sephanoides and Curaeus curaeus, showed relatively high intraspecific divergence (1.5-8.7%), possibly due to the presence of a species complex or geographic isolation of sub-populations. Mean interspecific K2P distance was 24.7% (range 1.3-43.5%). Consequently, the intraspecific K2P distance showed limited overlap with interspecific K2P distance. The mean intraspecific divergence in our study was similar to that found in temperate regions of South America (0.24%). However, it was approximately one order of magnitude lower than values reported for bird species in tropical regions of northern South America (1.8-2.13%). This result suggests that bird species from Chile show low levels of genetic structure and divergence. The small overlap between intra- and inter-specific distances implies that COI barcodes could be used as an effective tool to identify nearly all the Chilean bird species analyzed.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avenida Alcalde Fuchslocher 1305, Casilla 933, Osorno, Chile Universidad de Los Lagos Osorno Chile
| | - Alberto Gantz
- Laboratorio de Ecología, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile Universidad de Los Lagos Osorno Chile
| | - Margarita Parraguez
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile Universidad de Los Lagos Osorno Chile
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Carvalho TR, Seger KR, Magalhães FM, Lourenço LB, Haddad CFB. Systematics and cryptic diversification of
Leptodactylus
frogs in the Brazilian campo rupestre. ZOOL SCR 2020. [DOI: 10.1111/zsc.12470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thiago R. Carvalho
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
| | - Karin R. Seger
- Laboratório de Estudos Cromossômicos Departamento de Biologia Estrutural e Funcional Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Felipe M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa Brazil
| | - Luciana B. Lourenço
- Laboratório de Estudos Cromossômicos Departamento de Biologia Estrutural e Funcional Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Célio F. B. Haddad
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
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10
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Garg KM, Chattopadhyay B, Koane B, Sam K, Rheindt FE. Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea. BMC Evol Biol 2020; 20:82. [PMID: 32652951 PMCID: PMC7353695 DOI: 10.1186/s12862-020-01646-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/24/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flora into smaller refugia, dramatically reducing species ranges. However, relatively less is known about the effects of cooling cycles on tropical biota. RESULTS We analyzed thousands of genome-wide DNA markers across an assemblage of three closely related understorey-inhabiting scrubwrens (Sericornis and Aethomyias; Aves) from montane forest along an elevational gradient on Mt. Wilhelm, the highest mountain of Papua New Guinea. Despite species-specific differences in elevational preference, we found limited differentiation within each scrubwren species, but detected a strong genomic signature of simultaneous population expansions at 27-29 ka, coinciding with the onset of the LGM. CONCLUSION The remarkable synchronous timing of population expansions of all three species demonstrates the importance of global cooling cycles in expanding highland habitat. Global cooling cycles have likely had strongly different impacts on tropical montane areas versus boreal and temperate latitudes, leading to population expansions in the former and serious fragmentation in the latter.
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Affiliation(s)
- Kritika M. Garg
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore
| | - Balaji Chattopadhyay
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore
| | - Bonny Koane
- The New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Katerina Sam
- Biology Centre CAS, Institute of Entomology, Branisovska 31, Ceske Budejovice, Czech Republic
- University of South Bohemia, Faculty of Science, Branisovska 1760, Ceske Budejovice, Czech Republic
| | - Frank E. Rheindt
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore
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11
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Patton AH, Margres MJ, Epstein B, Eastman J, Harmon LJ, Storfer A. Hybridizing salamanders experience accelerated diversification. Sci Rep 2020; 10:6566. [PMID: 32300150 PMCID: PMC7162952 DOI: 10.1038/s41598-020-63378-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/23/2020] [Indexed: 11/09/2022] Open
Abstract
Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.
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Affiliation(s)
- Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.
| | - Mark J Margres
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, 02138, USA
| | - Brendan Epstein
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,University of Minnesota, College of Biological Sciences, Saint Paul, MN, 55108, USA
| | | | - Luke J Harmon
- University of Idaho, Department of Biological Sciences and IBEST, Moscow, ID, 83844, USA
| | - Andrew Storfer
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA
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12
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Liu Y, Pham HT, He Z, Wei C. Phylogeography of the cicada Platypleura hilpa in subtropical and tropical East Asia based on mitochondrial and nuclear genes and microsatellite markers. Int J Biol Macromol 2020; 151:529-544. [PMID: 32084484 DOI: 10.1016/j.ijbiomac.2020.02.183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 10/25/2022]
Abstract
Climate change and geographical events play key roles in driving population genetic structure of organisms, but different scenarios were suggested for species occurring in tropical and subtropical areas. We investigated the population genetic structure, diversity and demographic history of the cicada Platypleura hilpa which occurs in coastal areas of southern China and northeastern Indo-Burma, and analysed the potential impact of climate change and geological events on its evolutionary history. Our data imply that P. hilpa comprises five main lineages with nearly unique sets of haplotypes and distinct geographic distributions. A major split of the lineages occurred in the Pleistocene. Geographic distance and geomorphic barriers serve as the primary factors shaping the genetic population structure, and several climatic factors are associated with the divergence. The potential range during the Last Glacial Maximum has apparently increased in south China and the exposed South China Sea Shelf. The Pleistocene sea-level fluctuations had profound effects on the regional genetic structure. The Beibu Gulf represents a more important geographic barrier than the Qiongzhou Strait in blocking gene flow among populations. These results contribute to a better understanding of the pressure climatic change and geographical events impose on insects in coastal areas of East Asia.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Thai Pham
- Vietnam National Museum of Nature Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Cau Giay, Hanoi, Viet Nam
| | - Zhiqiang He
- College of Plant Science, Tarim University, Alar, Xinjiang 843300, China
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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13
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- 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, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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14
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (
Anaxyrus canorus
). Evolution 2019; 73:2476-2496. [DOI: 10.1111/evo.13868] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/18/2019] [Accepted: 10/14/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Paul A. Maier
- Department of BiologySan Diego State University 5500 Campanile Dr. San Diego CA 92182
- FamilyTreeDNA Gene by Gene, 1445 N Loop W Houston TX 77008
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research CenterSan Diego Field Station 4165 Spruance Road, Suite 200 San Diego CA 92101
| | - Steven M. Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the EnvironmentUniversity of California, Davis 1 Shields Ave. Davis CA 95616
| | - Andres Aguilar
- Department of Biological SciencesCalifornia State University, Los Angeles 5151 State University Dr Los Angeles CA 90032
| | - Andrew J. Bohonak
- Department of BiologySan Diego State University 5500 Campanile Dr. San Diego CA 92182
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15
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Pan T, Zhou K, Zhang S, Shu Y, Zhang J, Li E, Wang M, Yan P, Wu H. Effects of dispersal barriers and geographic distance on the genetic structure of a narrowly distributed frog in a spatially structured landscape. J Zool (1987) 2019. [DOI: 10.1111/jzo.12730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Pan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - K. Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - S.‐L. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - Y.‐L. Shu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - J.‐H. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - E. Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - M.‐S. Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - P. Yan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - H.‐L. Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
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16
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Pan T, Sun Z, Lai X, Orozcoterwengel P, Yan P, Wu G, Wang H, Zhu W, Wu X, Zhang B. Hidden species diversity in Pachyhynobius: A multiple approaches species delimitation with mitogenomes. Mol Phylogenet Evol 2019; 137:138-145. [PMID: 31085325 DOI: 10.1016/j.ympev.2019.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 01/16/2023]
Abstract
The lack of distinct morphological features of cryptic species is a hard problem for taxonomy, especially when the taxa are closely related with considerable amounts of ancestral polymorphism. Lately, intensive coalescent-based analyses involving multiple loci have become the preferred method to assess the extent of genetic distinctiveness in otherwise phenotypically similar populations. Previously, phylogenetic studies on Pachyhynobius shangchengensis uncovered five extremely deeply divergent clades, which suggested that this species may be a cryptic species complex. In this study, we used the complete mitochondrial genome data and samples from the entire range of stout salamander (Pachyhynobius), as well as publicly available mitochondrial genomes to assess species boundaries within this genus using a suite of diverse methodologies (e.g. general mixed Yule coalescent model, Automatic Barcode Gap Discovery). The phylogenetic relationships recovered two major groups within P. shangchengensis, with one group formed by four of the six extant populations and corresponding to the central and eastern range of the Dabie mountains, while the other group encompassed two other lineages in the north west of the Dabie mountain range. The species delimitation comparison within Pachyhynobius supported the presence of recognized species within the genus, and consensus was observed across methods for the existence of up to five cryptic species within what has been traditionally considered to be P. shangchengensis. While this implies the existence of four taxa in addition to the described P. shangchengensis species, morphological data and life history information are further required to contribute to the species definition. The observed pattern of genetic variation is likely the outcome of a discontinuous habitat combined with niche conservatism, which produced the sky-island effect observed in Pachyhynobius, and which led to formation of a hidden species diversity in this genus.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; School of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Zhonglou Sun
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Department of Medicine, University of Utah, Salt Lake City 84112, UT, United States
| | - Xinlei Lai
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | | | - Peng Yan
- School of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Guiyou Wu
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Weiquan Zhu
- Department of Medicine, University of Utah, Salt Lake City 84112, UT, United States
| | - Xiaobing Wu
- School of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.
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17
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Isolation by elevation: mitochondrial divergence among sky island populations of Sacramento Mountain salamander (Aneides hardii). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01155-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Pan T, Wang H, Orozcoterwengel P, Hu CC, Wu GY, Qian LF, Sun ZL, Shi WB, Yan P, Wu XB, Zhang BW. Long-term sky islands generate highly divergent lineages of a narrowly distributed stream salamander (Pachyhynobius shangchengensis) in mid-latitude mountains of East Asia. BMC Evol Biol 2019; 19:1. [PMID: 30606099 PMCID: PMC6318985 DOI: 10.1186/s12862-018-1333-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/17/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Climate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands. RESULTS The Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. In the present study, we used mtDNA genes (Cyt b and ND2) of 193 individuals and 12 nuclear microsatellite loci genotyped on 370 individuals, representing 6 populations (JTX, KHJ, MW, TTZ, BYM and KJY) across the taxon's distribution area, to investigate their genetic variation and evolutionary history of P. shangchengensis. Most populations showed unusually high levels of genetic diversity. Phylogenetic analyses revealed five monophyletic clades with divergence times ranging from 3.96 to 1.4 Mya. Accordingly, significant genetic differentiation was present between these populations. Bayesian skyline plot analyses provided that all populations underwent long-term population expansions since the last inter-glacial (0.13 Mya ~ 0.12 Mya). Msvar analyses found recent signals of population decline for two northern populations (JTX and KHJ) reflecting a strong bottleneck (approximately 15-fold decrease) during the mid-Holocene (about 6000 years ago). Ecological niche modelling has shown a discontinuity in suitable habitats for P. shangchengensis under different historical climatic conditions. CONCLUSIONS Our results suggest that the niche conservatism of P. shangchengensis and sky island effects may have led to long-term isolation between populations. In sky island refuges, the mid-latitude Dabie Mountains have provided a long-term stable environment for P. shangchengensis, which has led to the accumulation of genetic diversity and has promoted genetic divergence.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- School of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China
| | - Hui Wang
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | | | - Chao-Chao Hu
- Analytical and Testing Center, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Gui-You Wu
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Li-Fu Qian
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Zhong-Lou Sun
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Wen-Bo Shi
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
| | - Peng Yan
- School of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China
| | - Xiao-Bing Wu
- School of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China
| | - Bao-Wei Zhang
- Anhui Key Laboratory of Eco–engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- School of Biosciences, Cardiff University, Cardiff, UK
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19
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Nascimento AC, Chaves AV, Leite FSF, Eterovick PC, dos Santos FR. Past vicariance promoting deep genetic divergence in an endemic frog species of the Espinhaço Range in Brazil: The historical biogeography of Bokermannohyla saxicola (Hylidae). PLoS One 2018; 13:e0206732. [PMID: 30395633 PMCID: PMC6218059 DOI: 10.1371/journal.pone.0206732] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 10/18/2018] [Indexed: 11/29/2022] Open
Abstract
The highland endemic frog Bokermannohyla saxicola occurs within the Espinhaço Range, the most extensive and continuous orogenic belt of the Brazilian territory, located in southeastern Brazil. We used mitochondrial DNA markers to test for spatial structure, to investigate the likely influence of past vicariant events, to evaluate demographic dynamics along the species range, and to understand the role of habitat discontinuities in promoting connectivity and diversity along the range. We found four major monophyletic lineages, each one associated with distinct mountain tops. The divergence time found between the four main clades clearly pre-dated the Pleistocene, except for the most recent separation. We observed no signs of population expansion for most of the sampling sites along the range, and a higher genetic diversity in the most continuous and central highland plateau, compared to smaller marginal regions. The Espinhaço Range harbors four deeply divergent lineages of B. saxicola within areas restricted by barriers for millions of years. These relatively isolated populations were kept apart by discontinuities represented by lowland habitats between mountain tops. Most of the lineage divergences occurred earlier than the Pleistocene, thus they cannot be solely explained by climatic oscillations of this epoch. However, within-lineage divergence times were all dated from the Pleistocene, suggesting an important effect in population dynamics. We also suggest that some marginal populations like those from Serra Negra and Serra de Itacambira can be the result of recent colonization events. Finally, in the southern Espinhaço region, the most continuous central highland area shows greater genetic diversity than the marginal discontinuous areas, where we have also observed a significant correlation between genetic and geographic distances. Bokermannohyla saxicola is a good model to study the biogeography of the Espinhaço Range because its high genetic structure reflects ancient as well as recent geological/climatic events, with important implications for conservation.
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Affiliation(s)
| | - Anderson Vieira Chaves
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Manejo e Conservação de Ecossistemas Naturais e Agrários, Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, campus Florestal, Minas Gerais, Brazil
- * E-mail: (AVC); (FRS)
| | - Felipe Sá Fortes Leite
- Programa de Pós-Graduação em Manejo e Conservação de Ecossistemas Naturais e Agrários, Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, campus Florestal, Minas Gerais, Brazil
| | - Paula Cabral Eterovick
- Programa de Pós Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
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20
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Shepard DB, Kuhns AR. Shifting rivers and stationary ground: biogeographic history of slimy salamanders on an isolated bluff in the Mississippi River floodplain. J Zool (1987) 2017. [DOI: 10.1111/jzo.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. B. Shepard
- School of Biological Sciences Louisiana Tech University Ruston LA USA
| | - A. R. Kuhns
- Illinois Natural History Survey Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign IL USA
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21
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Krysko KL, Nuñez LP, Newman CE, Bowen BW. Phylogenetics of Kingsnakes, Lampropeltis getula Complex (Serpentes: Colubridae), in Eastern North America. J Hered 2017; 108:226-238. [PMID: 28119446 DOI: 10.1093/jhered/esw086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/08/2016] [Indexed: 01/25/2023] Open
Abstract
Kingsnakes of the Lampropeltis getula complex range throughout much of temperate and subtropical North America. Studies over the last century have used morphology and color pattern to describe numerous subspecies. More recently, DNA analyses have made invaluable contributions to our understanding of their evolution and taxonomy. We use genetic and ecological methods to test previous hypotheses of distinct evolutionary lineages by examining 66 total snakes and 1) analyzing phylogeographic structure using 2 mtDNA loci and 1 nuclear locus, 2) estimating divergence dates and historical demography among lineages in a Bayesian coalescent framework, and 3) applying ecological niche modeling (ENM). Our molecular data and ENMs illustrate that 3 previously recognized subspecies in the eastern United States comprise well-supported monophyletic lineages that diverged during the Pleistocene. The geographic boundaries of these 3 lineages correspond closely to known biogeographic barriers (Florida peninsula, Appalachian Mountains, and Apalachicola River) previously identified for other plants and animals, indicating shared geographic influences on evolutionary history. We conclude that genetic, ecological, and morphological data support recognition of these 3 lineages as distinct species (Lampropeltis floridana, Lampropeltis getula, and Lampropeltis meansi).
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Affiliation(s)
- Kenneth L Krysko
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA
| | - Leroy P Nuñez
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA.,School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA
| | - Catherine E Newman
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
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22
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Meng HH, Su T, Gao XY, Li J, Jiang XL, Sun H, Zhou ZK. Warm-cold colonization: response of oaks to uplift of the Himalaya-Hengduan Mountains. Mol Ecol 2017; 26:3276-3294. [DOI: 10.1111/mec.14092] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Hong-Hu Meng
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
- Center for Integrative Conservation; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Kunming 650223 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Tao Su
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
| | - Xiao-Yang Gao
- Key Laboratory of Tropical Plant Resources and Sustainable Use; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
| | - Jie Li
- Center for Integrative Conservation; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Kunming 650223 China
| | - Xiao-Long Jiang
- Shanghai Chenshan Plant Science Research Center; Chinese Academy of Sciences; Shanghai 201602 China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - Zhe-Kun Zhou
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
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23
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Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, Che J, Zhang L, Ziegler T, Nguyen TQ, Burbrink FT. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri(Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Mol Ecol 2016; 25:2920-36. [DOI: 10.1111/mec.13658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Guo
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Qin Liu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Fei Zhu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Guang H. Zhong
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Xin Chen
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Edward A. Myers
- Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Avenue New York NY 10016 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Menglun Mengla Yunnan 666303 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Thomas Ziegler
- AG Zoologischer Garten Köln; Riehler Strasse 173 D-50735 Cologne Germany
| | - Truong Q. Nguyen
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Street Hanoi Vietnam
| | - Frank T. Burbrink
- Department of Herpetology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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24
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Lyons MP, Shepard DB, Kozak KH. Determinants of Range Limits in Montane Woodland Salamanders (GenusPlethodon). COPEIA 2016. [DOI: 10.1643/ot-14-222] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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26
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Deitloff J, Floyd C, Graham SP. Examining Head-shape Differences and Ecology in Morphologically Similar Salamanders at Their Zone of Contact. COPEIA 2016. [DOI: 10.1643/ce-15-319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Krysko KL, Nuñez LP, Lippi CA, Smith DJ, Granatosky MC. Pliocene-Pleistocene lineage diversifications in the Eastern Indigo Snake (Drymarchon couperi) in the Southeastern United States. Mol Phylogenet Evol 2016; 98:111-22. [PMID: 26778258 DOI: 10.1016/j.ympev.2015.12.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
Indigo Snakes (Drymarchon; with five currently recognized species) occur from northern Argentina, northward to the United States in southern Texas and eastward in disjunct populations in Florida and Georgia. Based on this known allopatry and a difference in supralabial morphology the two United States taxa previously considered as subspecies within D. corais (Boie 1827), the Western Indigo Snake, D. melanurus erebennus (Cope 1860), and Eastern Indigo Snake, D. couperi (Holbrook 1842), are currently recognized as separate species. Drymarchon couperi is a Federally-designated Threatened species by the United States Fish and Wildlife Service under the Endangered Species Act, and currently being incorporated into a translocation program. This, combined with its disjunct distribution makes it a prime candidate for studying speciation and genetic divergence. In this study, we (1) test the hypothesis that D. m. erebennus and D. couperi are distinct lineages by analyzing 2411 base pairs (bp) of two mitochondrial (mtDNA) loci and one single copy nuclear (scnDNA) locus; (2) estimate the timing of speciation using a relaxed phylogenetics method to determine if Milankovitch cycles during the Pleistocene might have had an influence on lineage diversifications; (3) examine historical population demography to determine if identified lineages have undergone population declines, expansions, or remained stable during the most recent Milankovitch cycles; and (4) use this information to assist in an effective and scientifically sound translocation program. Our molecular data support the initial hypothesis that D. melanurus and D. couperi should be recognized as distinct species, but further illustrate that D. couperi is split into two distinct genetic lineages that correspond to historical biogeography and sea level changes in peninsular Florida. These two well-supported genetic lineages (herein termed Atlantic and Gulf lineages) illustrate a common biogeographic distributional break previously identified for other plants and animals, suggesting that these organisms might have shared a common evolutionary history related to historic sea level changes caused by Milankovitch cycles. Our estimated divergence times suggest that the most recent common ancestor (MRCA) between D. melanurus and southeastern United States Drymarchon occurred ca. 5.9Ma (95% HPD=2.5-9.8Ma; during the late Blancan of the Pleistocene through the Hemphillian of the Miocene), whereas the MRCA between the Atlantic and Gulf lineages in the southeastern United States occurred ca. 2.0Ma (95% HPD=0.7-3.7Ma; during the Irvingtonian of the Pleistocene through the Blancan of the Pliocene). During one or more glacial intervals within these times, these two lineages must have become separated and evolved independently. Despite numerous Milankovitch cycles along with associated forming of physical barriers (i.e., sea level fluctuations, high elevation sand ridges, clayey soils, and/or insufficient habitats) since their initial lineage diversification, these two lineages have likely come in and out of contact with each other many times, yet today they still illustrate near discrete geographic distributions. Although the Atlantic and Gulf lineages appear to be cryptic, a thorough study examining morphological characters should be conducted. We believe that our molecular data is crucial and should be incorporated in making conscious decisions in the management of a translocation program. We suggest that source populations for translocations include maintaining the integrity of the known genetic lineages found herein, as well as those coming from the closest areas that currently support sizable Drymarchon populations.
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Affiliation(s)
- Kenneth L Krysko
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Leroy P Nuñez
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA; School of Natural Resources and Environment, 103 Black Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Catherine A Lippi
- Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, 13201 Bruce B Downs, MDC56, Tampa, FL 33612, USA.
| | - Daniel J Smith
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
| | - Michael C Granatosky
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
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Multi-locus phylogeny and divergence time estimates of Enallagma damselflies (Odonata: Coenagrionidae). Mol Phylogenet Evol 2016; 94:182-95. [DOI: 10.1016/j.ympev.2015.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/28/2015] [Accepted: 08/14/2015] [Indexed: 11/22/2022]
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29
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Santana DJ, Barros AB, Pontes R, Feio RN. A New Species of Glassfrog Genus Vitreorana (Anura, Centrolenidae) from the Cerrado Domain, Southeastern Brazil. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-14-00066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, Plethodon serratus. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9794-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Newman CE, Austin CC. Thriving in the Cold: Glacial Expansion and Post-Glacial Contraction of a Temperate Terrestrial Salamander (Plethodon serratus). PLoS One 2015; 10:e0130131. [PMID: 26132077 PMCID: PMC4488858 DOI: 10.1371/journal.pone.0130131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
The dynamic geologic history of the southeastern United States has played a major role in shaping the geographic distributions of amphibians in the region. In the phylogeographic literature, the predominant pattern of distribution shifts through time of temperate species is one of contraction during glacial maxima and persistence in refugia. However, the diverse biology and ecology of amphibian species suggest that a "one-size-fits-all" model may be inappropriate. Nearly 10% of amphibian species in the region have a current distribution comprised of multiple disjunct, restricted areas that resemble the shape of Pleistocene refugia identified for other temperate taxa in the literature. Here, we apply genetics and spatially explicit climate analyses to test the hypothesis that the disjunct regions of these species ranges are climatic refugia for species that were more broadly distributed during glacial maxima. We use the salamander Plethodon serratus as a model, as its range consists of four disjunct regions in the Southeast. Phylogenetic results show that P. serratus is comprised of multiple genetic lineages, and the four regions are not reciprocally monophyletic. The Appalachian salamanders form a clade sister to all other P. serratus. Niche and paleodistribution modeling results suggest that P. serratus expanded from the Appalachians during the cooler Last Glacial Maximum and has since been restricted to its current disjunct distribution by a warming climate. These data reject the universal applicability of the glacial contraction model to temperate taxa and reiterate the importance of considering the natural history of individual species.
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Affiliation(s)
- Catherine E. Newman
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Christopher C. Austin
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
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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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Giarla TC, Jansa SA. The impact of Quaternary climate oscillations on divergence times and historical population sizes inThylamysopossums from the Andes. Mol Ecol 2015; 24:2495-506. [DOI: 10.1111/mec.13173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/03/2015] [Accepted: 03/18/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas C. Giarla
- Department of Ecology, Evolution, and Behavior; University of Minnesota; St. Paul MN 55108 USA
- J.F. Bell Museum of Natural History; University of Minnesota; St. Paul MN 55108 USA
| | - Sharon A. Jansa
- Department of Ecology, Evolution, and Behavior; University of Minnesota; St. Paul MN 55108 USA
- J.F. Bell Museum of Natural History; University of Minnesota; St. Paul MN 55108 USA
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Chen S, Sun Z, He K, Jiang X, Liu Y, Koju NP, Zhang X, Tu F, Fan Z, Liu S, Yue B. Molecular phylogenetics and phylogeographic structure of Sorex bedfordiae based on mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 2015; 84:245-53. [PMID: 25617490 DOI: 10.1016/j.ympev.2014.12.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
The southeastern margin of the Tibetan Plateau is characterized by complex topography and a discontinuous landscape, creating a sky island situation. However, the way topography shapes genetic structures and demographic histories of endemic species has not been well studied. We examined the phylogeographic pattern and demographic histories of Sorex bedfordiae, a dispersal-limited small mammal, using three nuclear genes [1977bp] and two mitochondrial genes [1794bp] with comprehensive molecular approaches. We recovered five well-supported clades whose distributions are along mountain ridges and roughly subdivided by large rivers. Demographic expansions in the middle Pleistocene were strongly supported by both nuclear and mitochondrial genes. Our results support the hypothesis that sky island topography and river systems strongly affect the genetic structure of non-aquatic terrestrial species. We further clarify that S. bedfordiae and S. cylindricauda are valid sibling species, whereas S. excelsus is most likely a geographic subspecies of S. bedfordiae.
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Affiliation(s)
- Shunde Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China; College of Life Sciences, Sichuan Normal University, Chengdu 610066, China; Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhiyu Sun
- Sichuan Academy of Forestry, Chengdu 610081, China
| | - Kai He
- Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuelong Jiang
- Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu 610081, China
| | - Narayan Prasad Koju
- Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China
| | - Feiyun Tu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China
| | - Zhenxing Fan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu 610081, China.
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China.
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Bartolini S, Cioppi E, Rook L, Delfino M. Late Pleistocene fossils and the future distribution of Rana temporaria (Amphibia, Anura) along the Apennine Peninsula (Italy). Zool Stud 2014. [DOI: 10.1186/s40555-014-0076-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The effect of past climatic changes on the distribution of organisms is a fertile field of research that has been tackled in many different ways. Because the fossil record provides direct access to the chronological and geographic dimensions of biological events occurred in the past, it can be a useful tool for assessing range contractions and expansions related to climatic changes.
Results
Here, we provide support for the ‘recent’ shrinkage of the range of a frigophilous anuran, the common frog, Rana temporaria Linnaeus, 1758, by analyzing the amphibian fossil assemblage coming from the Grotta di Equi, a Late Pleistocene site (about 45 ka) located in the Apuan Alps (northern Apennine chain, Massa-Carrara Province, Italy). Besides, R. temporaria, the assemblage includes cf. Salamandra salamandra Linnaeus, 1758 and Bufo bufo Linnaeus, 1758.
Conclusions
The presence of R. temporaria in the Apuan Alps during a cold interglacial phase at an elevation that is much lower than the minimum current elevation in the region (about 300 m lower) supports the previously reported hypothesis that the Pleistocene coolings favored the dispersal of this frigophilous species along the Apennine chain and that its current, locally disjointed distribution is the effect of the post Pleistocene raise in temperature. Our results concur in predicting that the current global warming will further affect, negatively, the range of this frigophilous species by further reducing its distribution in the southern sectors of its range.
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Pelletier TA, Crisafulli C, Wagner S, Zellmer AJ, Carstens BC. Historical Species Distribution Models Predict Species Limits in WesternPlethodonSalamanders. Syst Biol 2014; 64:909-25. [DOI: 10.1093/sysbio/syu090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/10/2014] [Indexed: 11/12/2022] Open
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Cox SC, Prys-Jones RP, Habel JC, Amakobe BA, Day JJ. Niche divergence promotes rapid diversification of East African sky island white-eyes (Aves: Zosteropidae). Mol Ecol 2014; 23:4103-18. [PMID: 24954273 PMCID: PMC4255762 DOI: 10.1111/mec.12840] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 12/01/2022]
Abstract
The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species-rich white-eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1-2.5 Ma) during the fluctuating Plio-Pleistocene climate, which may have provided the primary driver for lineage diversification.
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Affiliation(s)
- Siobhan C Cox
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK; Bird Group, Department of Life Sciences, The Natural History Museum, Akeman Street, Tring, Hertfordshire, HP23 6AP, UK
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38
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Meng H, Li X, Qiao P. Population structure, historical biogeography and demographic history of the alpine toad Scutiger ningshanensis in the Tsinling Mountains of Central China. PLoS One 2014; 9:e100729. [PMID: 24956389 PMCID: PMC4067352 DOI: 10.1371/journal.pone.0100729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
Population genetic structure, historical biogeography and historical demography of the alpine toad Scutiger ningshanensis were studied using the combined data mtDNA cytochrome b (cyt b) and the mtDNA cytochrome c oxidase subunit I (COI) as the molecular markers. This species has high genetic variation. There was a significant genetic differentiation among most populations. Three lineages were detected. The phylogenetic relationship analyses and the SAMOVA (spatial analysis of molecular variance) results showed significant phylogeographic structure. 82.15% genetic variation occurred among populations whereas differentiation within populations only contributed 17.85% to the total. Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (regression coefficient = 0.001286, correlation coefficient = 0.77051, p (rrand≥robs) = 0.0185<0.05), indicating the existence of isolation-by-distance pattern of genetic divergence for cyt b + COI sequence, which suggests that the distribution of genetic variation is due to geographical separation rather than natural selection. The population expansion or contraction and genetic differentiation between populations or lineages could be explained by topography and the repetitive uplifts of the Tsinling Mountains and the climatic cycles during the late Pliocene and Pleistocene. S. ningshanensis experienced a rapid population expansion about 40,000 years before present. The current decline in population size was probably caused by anthropogenic disturbance. Current populations of S. ningshanensis are from different refugia though the location of these refugia could not be determined in our study. Topography, climatic changes and repetitive population expansion/contraction together led to the high level of genetic variation in S. ningshanensis. A total of three management units (MUs) was determined, which must be considered when conservation policy is made in the future.
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Affiliation(s)
- Hongzhe Meng
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaochen Li
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China
- * E-mail:
| | - Penghai Qiao
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China
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Metcalf JL, Prost S, Nogués-Bravo D, DeChaine EG, Anderson C, Batra P, Araújo MB, Cooper A, Guralnick RP. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study. Proc Biol Sci 2014; 281:20132782. [PMID: 24403338 PMCID: PMC3896022 DOI: 10.1098/rspb.2013.2782] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/04/2013] [Indexed: 01/30/2023] Open
Abstract
One of the grand goals of historical biogeography is to understand how and why species' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species's demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level.
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Affiliation(s)
- Jessica L. Metcalf
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Stefan Prost
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, University of Copenhagen, Copenhagen, Denmark
| | - Eric G. DeChaine
- Department of Biology, Western Washington University, Bellingham, WA, USA
| | - Christian Anderson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Persaram Batra
- Department of Geology, Greenfield Community College, Greenfield, MA, USA
| | - Miguel B. Araújo
- Center for Macroecology, Evolution, and Climate, University of Copenhagen, Copenhagen, Denmark
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Imperial College London, Silwood Park Campus, Berkshire, UK
| | - Alan Cooper
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
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40
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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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Bagley JC, Sandel M, Travis J, Lozano-Vilano MDL, Johnson JB. Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota. BMC Evol Biol 2013; 13:223. [PMID: 24107245 PMCID: PMC3851817 DOI: 10.1186/1471-2148-13-223] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 09/13/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Climatic and sea-level fluctuations throughout the last Pleistocene glacial cycle (~130-0 ka) profoundly influenced present-day distributions and genetic diversity of Northern Hemisphere biotas by forcing range contractions in many species during the glacial advance and allowing expansion following glacial retreat ('expansion-contraction' model). Evidence for such range dynamics and refugia in the unglaciated Gulf-Atlantic Coastal Plain stems largely from terrestrial species, and aquatic species Pleistocene responses remain relatively uninvestigated. Heterandria formosa, a wide-ranging regional endemic, presents an ideal system to test the expansion-contraction model within this biota. By integrating ecological niche modeling and phylogeography, we infer the Pleistocene history of this livebearing fish (Poeciliidae) and test for several predicted distributional and genetic effects of the last glaciation. RESULTS Paleoclimatic models predicted range contraction to a single southwest Florida peninsula refugium during the Last Glacial Maximum, followed by northward expansion. We inferred spatial-population subdivision into four groups that reflect genetic barriers outside this refuge. Several other features of the genetic data were consistent with predictions derived from an expansion-contraction model: limited intraspecific divergence (e.g. mean mtDNA p-distance = 0.66%); a pattern of mtDNA diversity (mean Hd = 0.934; mean π = 0.007) consistent with rapid, recent population expansion; a lack of mtDNA isolation-by-distance; and clinal variation in allozyme diversity with higher diversity at lower latitudes near the predicted refugium. Statistical tests of mismatch distributions and coalescent simulations of the gene tree lent greater support to a scenario of post-glacial expansion and diversification from a single refugium than to any other model examined (e.g. multiple-refugia scenarios). CONCLUSIONS Congruent results from diverse data indicate H. formosa fits the classic Pleistocene expansion-contraction model, even as the genetic data suggest additional ecological influences on population structure. While evidence for Plio-Pleistocene Gulf Coast vicariance is well described for many freshwater species presently codistributed with H. formosa, this species demography and diversification departs notably from this pattern. Species-specific expansion-contraction dynamics may therefore have figured more prominently in shaping Coastal Plain evolutionary history than previously thought. Our findings bolster growing appreciation for the complexity of phylogeographical structuring within North America's southern refugia, including responses of Coastal Plain freshwater biota to Pleistocene climatic fluctuations.
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Affiliation(s)
- Justin C Bagley
- Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA
| | - Michael Sandel
- Department of Biological Science, Biodiversity & Systematics, The University of Alabama, Box 870345, Tuscaloosa, AL 35487, USA
| | - Joseph Travis
- Department of Biological Science, The Florida State University, Tallahassee, FL 32306, USA
| | - María de Lourdes Lozano-Vilano
- Laboratorio de Ictiología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Jerald B Johnson
- Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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Leaché AD, Palacios JA, Minin VN, Bryson RW. Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south-eastern Mexico. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12172] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam D. Leaché
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Box 351800 Seattle WA 98195 USA
| | - Julia A. Palacios
- Department of Statistics; University of Washington; Seattle WA 98195-4322 USA
| | - Vladimir N. Minin
- Department of Statistics; University of Washington; Seattle WA 98195-4322 USA
| | - Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Box 351800 Seattle WA 98195 USA
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Valbuena-Ureña E, Amat F, Carranza S. Integrative phylogeography of Calotriton newts (Amphibia, Salamandridae), with special remarks on the conservation of the endangered Montseny brook newt (Calotriton arnoldi). PLoS One 2013; 8:e62542. [PMID: 23750201 PMCID: PMC3672179 DOI: 10.1371/journal.pone.0062542] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/22/2013] [Indexed: 02/01/2023] Open
Abstract
The genus Calotriton includes two species of newts highly adapted to live in cold and fast-flowing mountain springs. The Pyrenean brook newt (Calotriton asper), restricted to the Pyrenean region, and the Montseny brook newt (Calotriton arnoldi), endemic to the Montseny massif and one of the most endangered amphibian species in Europe. In the present manuscript, we use an integrative approach including species distribution modeling (SDM), molecular analyses of mitochondrial and nuclear DNA sequence data and morphology to unravel the historical processes that have contributed to shaping the biogeography and genetic structure of the genus Calotriton, with special emphasis on the conservation of C. arnoldi. The results of the molecular analyses confirm that, despite having originated recently, being ecologically similar and geographically very close, there is no signal of hybridization between C. asper and C. arnoldi. SDM results suggest that tough environmental conditions on mountains tops during glacial periods, together with subsequent warmer periods could have prevented the contact between the two species. Within the critically endangered C. arnoldi, a high genetic structure is revealed despite its extremely small distribution range compared to C. asper. Haplotype networks, AMOVA and SAMOVA analyses suggest that two distinct groups of populations can be clearly differentiated with absence of gene flow. This is in concordance with morphological differentiation and correlates with its geographical distribution, as the two groups are situated on the eastern and western sides of a river valley that acts as a barrier. The genetic and morphological results are highly important for the ongoing conservation program of C. arnoldi and strongly justify the management of this species into at least two independent evolutionary significant units (eastern and western sectors) to guarantee the long-term population viability.
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Affiliation(s)
- Emilio Valbuena-Ureña
- Unitat de Zoologia (Facultat de Biociències), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain.
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Rapson SA, Goldizen AW, Seddon JM. Gene flow in mongooses endemic to Namibia's granite inselbergs despite past climatic fluctuations and isolating landscape features. J Mammal 2013. [DOI: 10.1644/11-mamm-a-379.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Yan HF, Zhang CY, Wang FY, Hu CM, Ge XJ, Hao G. Population expanding with the phalanx model and lineages split by environmental heterogeneity: a case study of Primula obconica in subtropical China. PLoS One 2012; 7:e41315. [PMID: 23028425 PMCID: PMC3446961 DOI: 10.1371/journal.pone.0041315] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Current and historical events have both affected the current distribution patterns and intraspecific divergence of plants. While numerous studies have focused on the Qinghai-Tibetan Plateau (QTP), the impacts of such events on the flora of subtropical China remain poorly understood. Subtropical China is famous for its highly complex topography and the limited impact from glaciation during the Pleistocene; this may have resulted in a different genetic legacy for species in this region compared to fully glaciated areas. METHODOLOGY/PRINCIPAL FINDINGS We used plastid and nuclear DNA sequence data and distribution modeling to analyze the divergence patterns and demographic history of Primula obconica Hance, a widespread herbaceous montane species in subtropical China. The phylogenetic analysis revealed two major lineages (lineage A and lineage B), representing a west-east split into the Yunnan and Eastern groups, and the Sichuan and Central groups, respectively. The Eastern and Central groups comprised relatively new derived haplotypes. Nested Clade Analysis and Bayesian Skyline Plot analyses both indicated that P. obconica mainly experienced a gradual expansion of populations. In addition, the simulated distribution of P. obconica during the Last Glacial Maximum was slightly larger than its present-day distribution. CONCLUSION/SIGNIFICANCE Our results are the first to identify a west-east migration of P. obconica. The gradual expansion pattern and a larger potential distribution range in cold periods detected for P. obconica indicate that the population expansion of this species is consistent with the phalanx model. In addition, the current patterns of genetic differentiation have persisted as a result of the extensive environmental heterogeneity that exists in subtropical China.
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Affiliation(s)
- Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Cai-Yun Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Feng-Ying Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Chi-Ming Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Wang B, Jiang J, Xie F, Li C. Postglacial colonization of the Qinling Mountains: phylogeography of the swelled vent frog (Feirana quadranus). PLoS One 2012; 7:e41579. [PMID: 22848532 PMCID: PMC3405020 DOI: 10.1371/journal.pone.0041579] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/22/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling-Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia). METHODOLOGY/PRINCIPAL FINDINGS We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang-Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling-Micang-Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang-Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline. CONCLUSIONS/SIGNIFICANCE The Qinling-Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang-Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Feng Xie
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Cheng Li
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
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Concurrent speciation in the eastern woodland salamanders (Genus Plethodon): DNA sequences of the complete albumin nuclear and partial mitochondrial 12s genes. Mol Phylogenet Evol 2012; 63:278-90. [DOI: 10.1016/j.ympev.2011.12.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 12/16/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022]
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Chiari Y, van der Meijden A, Mucedda M, Lourenço JM, Hochkirch A, Veith M. Phylogeography of Sardinian cave salamanders (genus Hydromantes) is mainly determined by geomorphology. PLoS One 2012; 7:e32332. [PMID: 22427830 PMCID: PMC3299655 DOI: 10.1371/journal.pone.0032332] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 01/25/2012] [Indexed: 11/24/2022] Open
Abstract
Detecting the factors that determine the interruption of gene flow between populations is key to understanding how speciation occurs. In this context, caves are an excellent system for studying processes of colonization, differentiation and speciation, since they represent discrete geographical units often with known geological histories. Here, we asked whether discontinuous calcareous areas and cave systems represent major barriers to gene flow within and among the five species of Sardinian cave salamanders (genus Hydromantes) and whether intraspecific genetic structure parallels geographic distance within and among caves. We generated mitochondrial cytochrome b gene sequences from 184 individuals representing 48 populations, and used a Bayesian phylogeographic approach to infer possible areas of cladogenesis for these species and reconstruct historical and current dispersal routes among distinct populations. Our results show deep genetic divergence within and among all Sardinian cave salamander species, which can mostly be attributed to the effects of mountains and discontinuities in major calcareous areas and cave systems acting as barriers to gene flow. While these salamander species can also occur outside caves, our results indicate that there is a very poor dispersal of these species between separate cave systems.
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Affiliation(s)
- Ylenia Chiari
- Institut des Sciences de l'Evolution, CNRS-UMR n° 5554, CC 064, Université Montpellier II, Montpellier, France.
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Malaney JL, Frey JK, Cook JA. The biogeographic legacy of an imperilled taxon provides a foundation for assessing lineage diversification, demography and conservation genetics. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00866.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Shepard DB, Irwin KJ, Burbrink FT. Morphological Differentiation in Ouachita Mountain Endemic Salamanders. HERPETOLOGICA 2011. [DOI: 10.1655/herpetologica-d-11-00023.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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