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Brunes TO, Pinto FCS, Taucce PPG, Santos MTT, Nascimento LB, Carvalho DC, Oliveira G, Vasconcelos S, Leite FSF. Traditional taxonomy underestimates the number of species of Bokermannohyla (Amphibia: Anura: Hylidae) diverging in the mountains of southeastern Brazil since the Miocene. SYST BIODIVERS 2023. [DOI: 10.1080/14772000.2022.2156001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Tuliana O. Brunes
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Felipe C. S. Pinto
- Programa de Pós-Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro P. G. Taucce
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Marcus Thadeu T. Santos
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, Brazil
| | - Luciana B. Nascimento
- Programa de Pós-Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Daniel C. Carvalho
- Programa de Pós-Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | - Felipe S. F. Leite
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Campus Florestal, Florestal, MG, Brazil
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2
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Booker WW, Lemmon EM, Lemmon AR, Ptacek MB, Hassinger ATB, Schul J, Gerhardt HC. Biogeography and the evolution of acoustic communication in the polyploid North American grey treefrog complex. Mol Ecol 2023; 32:4863-4879. [PMID: 37401503 DOI: 10.1111/mec.17061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
After polyploid species are formed, interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. Here, we estimate the biogeographical history of the North American grey treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, focusing specifically on the geographical origin of whole genome duplication and the expansion of lineages out of glacial refugia. We then test for lineage-specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Along with describing the overall biogeographical history and call diversity, we found evidence that the geographical origin of H. versicolor and the formation of the midwestern polyploid lineage are both associated with glacial limits, and that the southwestern polyploid lineage is associated with a shift in acoustic phenotype relative to the diploid lineage with which they share a mitochondrial lineage. In H. chrysoscelis, we see that acoustic signals are largely split by Eastern and Western lineages, but that northward expansion along either side of the Appalachian Mountains is associated with further acoustic diversification. Overall, results of this study provide substantial clarity on the evolution of grey treefrogs as it relates to their biogeography and acoustic communication.
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Affiliation(s)
- William W Booker
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emily Moriarty Lemmon
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, USA
| | - Margaret B Ptacek
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Alyssa T B Hassinger
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA
| | - Johannes Schul
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - H Carl Gerhardt
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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3
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Warwick AR, Barrow LN, Smith ML, Means DB, Lemmon AR, Lemmon EM. Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens tree frog, Hyla andersonii (Anura: Hylidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Range fragmentation poses challenges for species persistence over time and can be caused by both historical and contemporary processes. We combined genomic data, phylogeographical model testing and palaeoclimatic niche modelling to infer the evolutionary history of the Pine Barrens tree frog (Hyla andersonii), a seepage bog specialist, in eastern North America to gain a better understanding of the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species range: Alabama/Florida (AF), the Carolinas (CL) and New Jersey (NJ). Phylogenetic relationships within H. andersonii were consistent between the nuclear species tree and mitochondrial analyses, indicating divergence between AF and CL/NJ (Atlantic clade) ~0.9 Mya and divergence of the NJ clade ~0.15 Mya. Several predictions of north-eastern expansion along the Atlantic coast were supported by phylogeographical analyses. Model testing using genome-wide single nucleotide polymorphism data and species distribution models both provided evidence for multiple disjunct refugia. This comprehensive phylogeographical study of H. andersonii demonstrates a long history of range fragmentation within an endemic coastal plain species and highlights the influence of historical climate change on the current distribution of species and their genetic diversity.
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Affiliation(s)
- Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - D Bruce Means
- Coastal Plains Institute and Land Conservancy, Tallahassee, FL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
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4
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Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
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Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
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Cairns NA, Cicchino AS, Stewart KA, Austin JD, Lougheed SC. Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs. Mol Phylogenet Evol 2020; 156:107042. [PMID: 33338660 DOI: 10.1016/j.ympev.2020.107042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 10/28/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply sufficient time for species-level divergence. To understand why this species appears unified while congeners have radiated, we analyze and compare male advertisement calls, mitochondrial, and nuclear markers and speak to the complex processes that have potentially influenced its contemporary patterns. We find extensive geographic and topological mitonuclear discordance, with three nuclear lineages containing 6 more-structured mtDNA lineages, and nuclear introgression at some contact zones. Male advertisement call differentiation is incongruent with the genetic structure as only one lineage appears differentiated. Occupying the Interior Highlands of the central United States, this Western lineage also has the most concordant mitochondrial and nuclear geographic patterns. Based on our findings we suggest that the antiquity of common ancestors was not as important as the maintenance of allopatry in the divergence in P. crucifer genetic lineages. We use multiple lines of evidence to generate hypotheses of isolation, reticulation, and discordance within this species and to expand our understanding of the early stages of speciation.
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Affiliation(s)
- N A Cairns
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - A S Cicchino
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, United States.
| | - K A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098XH Amsterdam, North Holland, Netherlands
| | - J D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, United States.
| | - S C Lougheed
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
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Ospina OE, Tieu L, Apodaca JJ, Lemmon EM. Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States. COPEIA 2020. [DOI: 10.1643/ch2020009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Oscar E. Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Lynee Tieu
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Joseph J. Apodaca
- Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806;
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
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Bruschi DP, Peres EA, Lourenço LB, Bartoleti LFDM, Sobral-Souza T, Recco-Pimentel SM. Signature of the Paleo-Course Changes in the São Francisco River as Source of Genetic Structure in Neotropical Pithecopus nordestinus (Phyllomedusinae, Anura) Treefrog. Front Genet 2019; 10:728. [PMID: 31475035 PMCID: PMC6702341 DOI: 10.3389/fgene.2019.00728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/11/2019] [Indexed: 11/13/2022] Open
Abstract
Historical processes that have interrupted gene flow between distinct evolutionary lineages have played a fundamental role in the evolution of the enormous diversity of species found in the Neotropical region. Numerous studies have discussed the role of geographic barriers and Pleistocene forest refugia in the diversification of the region's biodiversity. In the present study, we investigated the relative contribution of these different factors to the evolutionary history of Pithecopus nordestinus, a Neotropical tree frog, which is amply distributed in the Brazilian Atlantic Forest and adjacent areas of the Caatinga biome. We used an extensive sample and multilocus DNA sequences to provide an overview of the intraspecific genetic diversity of P. nordestinus, characterize historical diversification patterns, and identify possible phylogenetic splits. We tested different scenarios of diversification based on Pleistocene Refugia and river barrier models using approximate Bayesian computation (ABC) and ecological niche modeling (ENM). The phylogenetic approach indicate the occurrence of processes of phylogeographic divergence in both time and space, related to historical shifts in the course of the São Francisco River during Plio-Pleistocene period, resulting in two principal, highly divergent clades. The ABC model provided strong statistical support for this scenario, confirming the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus. We believe that the climatic changes that occurred during the Pleistocene also played a secondary role in the genetic signatures identified, reinforcing the divergence of populations isolated by physical barriers. These findings reinforce the conclusion that the two models of diversification (geographic barriers and refugia) are not mutually exclusive in the Neotropical domain but may interact extensively during the diversification of species on a regional scale.
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Affiliation(s)
| | - Elen Arroyo Peres
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Luciana Bolsoni Lourenço
- Department of Structural and Functional Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Thadeu Sobral-Souza
- Spatial Ecology and Conservation Lab (LEEC), São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
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Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser's spotted newt (Neurergus kaiseri). Sci Rep 2019; 9:6239. [PMID: 30996234 PMCID: PMC6470216 DOI: 10.1038/s41598-019-41886-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/19/2019] [Indexed: 12/27/2022] Open
Abstract
The combination of niche modelling and landscape genetics (genomics) helps to disentangle processes that have shaped population structure in the evolutionary past and presence of species. Herein, we integrate a comprehensive genomic dataset with ecological parameters and niche modelling for the threatened Kaiser's newt, a newt species adapted to mountain spring-ponds in Iran. Genomic analysis suggests the existence of two highly differentiated clades North and South of the Dez River. Genetic variation between the two clades (76.62%) was much greater than within clades (16.25%), suggesting that the Dez River prevented gene flow. River disconnectivity, followed by geographic distance, contributed mostly to genetic differentiation between populations. Environmental niche and landscape resistance had no significant influence. Though a significant difference between climatic niches occupied by each clade at the landscape-scale, habitat niches at the local-scale were equivalent. 'Niche similarity analysis' supported niche conservatism between the two clades despite the southward shift in the climatic niche of the Southern clade. Accordingly, populations of different clades may occupy different climatic niches within their ancestral niche. Our results indicate that the change of climatic conditions of geographically and genetically separated populations does not necessarily result in the shift of an ecological niche.
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Muths E, Scherer RD, Amburgey SM, Corn PS. Twenty‐nine years of population dynamics in a small‐bodied montane amphibian. Ecosphere 2018. [DOI: 10.1002/ecs2.2522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- E. Muths
- Fort Collins Science Center U.S. Geological Survey 2150 Centre Avenue Fort Collins Colorado 80526 USA
| | - R. D. Scherer
- Conservation Science Partners 501 Old Town Square Fort Collins Colorado 80524 USA
| | - S. M. Amburgey
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
- Intercollege Degree Program in Ecology The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - P. S. Corn
- Northern Rocky Mountain Science Center U.S. Geological Survey Missoula Montana 59801 USA
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10
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Diversification of the widespread neotropical frog Physalaemus cuvieri in response to Neogene-Quaternary geological events and climate dynamics. Mol Phylogenet Evol 2018; 132:67-80. [PMID: 30508632 DOI: 10.1016/j.ympev.2018.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/10/2018] [Indexed: 11/24/2022]
Abstract
Here we reconstructed the demographical history and the dispersal dynamics of Physalemus cuvieri through the Neogene-Quaternary periods by coupling DNA regions with different mutation rates, ecological niche modelling, reconstruction of spatio-temporal lineage dispersal and coalescent simulations. Still, to test alternative diversification scenarios we used approximate Bayesian computation. Molecular phylogenetic analysis recovered four deep and strongly supported clades, which we interpret as population lineages. The ancestral location reconstruction placed the root in southcentral Amazonia, and the dispersal events indicate that spatial displacement was widespread early in the diversification of this species. The demographical scenario of "Multiple Refugia" with recent lineage admixture was the most likely hypothesis to predict the observed genetic parameters of P. cuvieri. Our results revealed that Neogene orogenic events might have played a prominent role in the early diversification of P. cuvieri. The species shows deep divergences with strong regional population structure, despite its widespread distribution. Final uplift of the central Brazilian Plateau and formation of the river basins in Central South America played an important role in the origin, diversification and the maintenance of P. cuvieri lineages.
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Cox CL, Stringer JF, Moseley MA, Chippindale PT, Streicher JW. Testing the geographical dimensions of genetic diversity following range expansion in a North American snake. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Christian L Cox
- Department of Biology, Georgia Southern University, Statesboro, GA, USA
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Joel F Stringer
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Matthew A Moseley
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Paul T Chippindale
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Jeffrey W Streicher
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
- Department of Life Sciences, The Natural History Museum, London, UK
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Mângia S, Koroiva R, Nunes PMS, Roberto IJ, Ávila RW, Sant'Anna AC, Santana DJ, Garda AA. A New Species of Proceratophrys (Amphibia: Anura: Odontophrynidae) from the Araripe Plateau, Ceará State, Northeastern Brazil. HERPETOLOGICA 2018. [DOI: 10.1655/herpetologica-d-16-00084.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sarah Mângia
- Programa de Pós-Graduação em Ciências Biológicas (Zoologia), Universidade Federal da Paraíba, Paraíba, Brazil
| | - Ricardo Koroiva
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Pedro M. Sales Nunes
- Universidade Federal de Pernambuco, Departamento de Zoologia, Centro de Biociências, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, Pernambuco, Brazil
| | - Igor Joventino Roberto
- Universidade Federal do Amazonas, Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas. Avenida General Rodrigo Octávio, 6200, 69077-000, Manaus, Amazonas, Brazil
| | - Robson W. Ávila
- Universidade Regional do Cariri (URCA). Campus do Pimenta. Rua Cel. Antônio Luiz, 1161, Bairro do Pimenta, Crato, Ceará, Brazil
| | - Anathielle Caroline Sant'Anna
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Diego J. Santana
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Adrian A. Garda
- Universidade Federal do Rio Grande do Norte, Departamento de Botânica e Zoologia, Campus Universitário, Lagoa Nova, 59078-900, Natal, Rio Grande do Norte, Brazil
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Faivovich J, Pereyra MO, Luna MC, Hertz A, Blotto BL, Vásquez-Almazán CR, McCranie JR, Sánchez DA, Baêta D, Araujo-Vieira K, Köhler G, Kubicki B, Campbell JA, Frost DR, Wheeler WC, Haddad CF. On the Monophyly and Relationships of Several Genera of Hylini (Anura: Hylidae: Hylinae), with Comments on Recent Taxonomic Changes in Hylids. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2018. [DOI: 10.2994/sajh-d-17-00115.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julián Faivovich
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Martín O. Pereyra
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - María Celeste Luna
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Andreas Hertz
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Boris L. Blotto
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090 São Paulo, São Paulo, Brazil
| | - Carlos R. Vásquez-Almazán
- Museo de Historia Natural, Escuela de Biología, Universidad de San Carlos de Guatemala, Calle Mariscal Cruz 1-56 zona 10, Ciudad de Guatemala, Guatemala
| | | | - David A. Sánchez
- Department of Biology, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Délio Baêta
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Katyuscia Araujo-Vieira
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Brian Kubicki
- Costa Rican Amphibian Research Center, Guayacán, Provincia de Limón, Costa Rica
| | - Jonathan A. Campbell
- Department of Biology, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Darrel R. Frost
- Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024, USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024, USA
| | - Célio F.B. Haddad
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
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Barrow LN, Lemmon AR, Lemmon EM. Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data. Syst Biol 2018; 67:979-996. [DOI: 10.1093/sysbio/syy021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lisa N Barrow
- Department of Biology, Museum of Southwestern Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
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15
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Jongsma GF, Barej MF, Barratt CD, Burger M, Conradie W, Ernst R, Greenbaum E, Hirschfeld M, Leaché AD, Penner J, Portik DM, Zassi-Boulou AG, Rödel MO, Blackburn DC. Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa. Mol Phylogenet Evol 2018; 120:274-285. [DOI: 10.1016/j.ympev.2017.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
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16
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Lemmon EM, Juenger TE. Geographic variation in hybridization across a reinforcement contact zone of chorus frogs ( Pseudacris). Ecol Evol 2017; 7:9485-9502. [PMID: 29187984 PMCID: PMC5696400 DOI: 10.1002/ece3.3443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/02/2017] [Accepted: 08/31/2017] [Indexed: 12/11/2022] Open
Abstract
Reinforcement contact zones, which are secondary contact zones where species are diverging in reproductive behaviors due to selection against hybridization, represent natural laboratories for studying speciation‐in‐action. Here, we examined replicate localities across the entire reinforcement contact zone between North American chorus frogs Pseudacris feriarum and P. nigrita to investigate geographic variation in hybridization frequencies and to assess whether reinforcement may have contributed to increased genetic divergence within species. Previous work indicated these species have undergone reproductive character displacement (RCD) in male acoustic signals and female preferences due to reinforcement. We also examined acoustic signal variation across the contact zone to assess whether signal characteristics reliably predict hybrid index and to elucidate whether the degree of RCD predicts hybridization rate. Using microsatellites, mitochondrial sequences, and acoustic signal information from >1,000 individuals across >50 localities and ten sympatric focal regions, we demonstrate: (1) hybridization occurs and (2) varies substantially across the geographic range of the contact zone, (3) hybridization is asymmetric and in the direction predicted from observed patterns of asymmetric RCD, (4) in one species, genetic distance is higher between conspecific localities where one or both have been reinforced than between nonreinforced localities, after controlling for geographic distance, (5) acoustic signal characters strongly predict hybrid index, and (6) the degree of RCD does not strongly predict admixture levels. By showing that hybridization occurs in all sympatric localities, this study provides the fifth and final line of evidence that reproductive character displacement is due to reinforcement in the chorus frog contact zone. Furthermore, this work suggests that the dual action of cascade reinforcement and partial geographic isolation is promoting genetic diversification within one of the reinforced species.
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Affiliation(s)
| | - Thomas E Juenger
- Department of Integrative Biology University of Texas, Austin Austin TX USA
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17
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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18
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Ecological divergence in the yellow-bellied kingsnake (Lampropeltis calligaster) at two North American biodiversity hotspots. Mol Phylogenet Evol 2017; 106:61-72. [DOI: 10.1016/j.ympev.2016.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 11/22/2022]
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19
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Muths E, Scherer R, Amburgey S, Matthews T, Spencer A, Corn P. First estimates of the probability of survival in a small-bodied, high-elevation frog (Boreal Chorus Frog, Pseudacris maculata), or how historical data can be useful. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2016-0024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In an era of shrinking budgets yet increasing demands for conservation, the value of existing (i.e., historical) data are elevated. Lengthy time series on common, or previously common, species are particularly valuable and may be available only through the use of historical information. We provide first estimates of the probability of survival and longevity (0.67–0.79 and 5–7 years, respectively) for a subalpine population of a small-bodied, ostensibly common amphibian, the Boreal Chorus Frog (Pseudacris maculata (Agassiz, 1850)), using historical data and contemporary, hypothesis-driven information–theoretic analyses. We also test a priori hypotheses about the effects of color morph (as suggested by early reports) and of drought (as suggested by recent climate predictions) on survival. Using robust mark–recapture models, we find some support for early hypotheses regarding the effect of color on survival, but we find no effect of drought. The congruence between early findings and our analyses highlights the usefulness of historical information in providing raw data for contemporary analyses and context for conservation and management decisions.
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Affiliation(s)
- E. Muths
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Building C, Fort Collins, CO 80526, USA
| | - R.D. Scherer
- Conservation Science Partners, 501 Old Town Square, Fort Collins, CO 80524 USA
| | - S.M. Amburgey
- Department of Ecosystem Science and Management, Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
| | - T. Matthews
- 1414 Nunn Creek Court, Fort Collins, CO 80526, USA
| | - A.W. Spencer
- Fort Lewis College, Department of Biology, Durango, CO 81301, USA
| | - P.S. Corn
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Aldo Leopold Wilderness Research Institute, Missoula, MT 59801, USA
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20
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Engebretsen KN, Barrow LN, Rittmeyer EN, Brown JM, Moriarty Lemmon E. Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years. Ecol Evol 2016; 6:5013-31. [PMID: 27547330 PMCID: PMC4979724 DOI: 10.1002/ece3.2232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/11/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022] Open
Abstract
Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep “tension zone,” in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30 years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.
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Affiliation(s)
- Kristin N Engebretsen
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
| | - Lisa N Barrow
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
| | - Eric N Rittmeyer
- Department of Biological Sciences Museum of Natural Science Louisiana State University 202 Life Sciences Building Baton Rouge Louisiana 70803; Research School of Biology The Australian National University Gould Building 116 Canberra ACT 2601 Australia
| | - Jeremy M Brown
- Department of Biological Sciences Museum of Natural Science Louisiana State University 202 Life Sciences Building Baton Rouge Louisiana 70803
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
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21
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Priti H, Roshmi RS, Ramya B, Sudhira HS, Ravikanth G, Aravind NA, Gururaja KV. Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats, India. PLoS One 2016; 11:e0149382. [PMID: 26934213 PMCID: PMC4774957 DOI: 10.1371/journal.pone.0149382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 02/01/2016] [Indexed: 11/19/2022] Open
Abstract
A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members--R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8-2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats.
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Affiliation(s)
- H. Priti
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
- Manipal University, Manipal, India
| | - Rekha Sarma Roshmi
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
- Manipal University, Manipal, India
| | - Badrinath Ramya
- Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India
| | - H. S. Sudhira
- Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India
- Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation and Development, Indian Institute of Science Campus, Bengaluru, India
| | - G. Ravikanth
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
| | - Neelavara Anantharam Aravind
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
| | - Kotambylu Vasudeva Gururaja
- Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India
- Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation and Development, Indian Institute of Science Campus, Bengaluru, India
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22
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Barrow LN, Bigelow AT, Phillips CA, Lemmon EM. Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex. Mol Ecol 2015; 24:4739-58. [DOI: 10.1111/mec.13343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Lisa N. Barrow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Alyssa T. Bigelow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois 185 Natural Resources Bldg, 607 E. Peabody Drive Champaign IL 61820 USA
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
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23
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Moseley MA, Cox CL, Streicher JW, Roelke CE, Chippindale PT. Phylogeography and lineage-specific patterns of genetic diversity and molecular evolution in a group of North American skinks. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew A. Moseley
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Christian L. Cox
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
- Department of Biology; The University of Virginia; Charlottesville VA 22903 USA
- Department of Biology; Georgia Southern University; Statesboro GA USA
| | - Jeffrey W. Streicher
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
- Department of Life Sciences; The Natural History Museum; London SW7 5BD UK
| | - Corey E. Roelke
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Paul T. Chippindale
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
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24
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Li JT, Wang JS, Nian HH, Litvinchuk SN, Wang J, Li Y, Rao DQ, Klaus S. Amphibians crossing the Bering Land Bridge: Evidence from holarctic treefrogs (Hyla, Hylidae, Anura). Mol Phylogenet Evol 2015; 87:80-90. [DOI: 10.1016/j.ympev.2015.02.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 02/21/2015] [Accepted: 02/24/2015] [Indexed: 10/23/2022]
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25
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dos Santos SP, Ibáñez R, Ron SR. Systematics of the Rhinellamargaritifera complex (Anura, Bufonidae) from western Ecuador and Panama with insights in the biogeography of Rhinellaalata. Zookeys 2015; 501:109-45. [PMID: 25987881 PMCID: PMC4432321 DOI: 10.3897/zookeys.501.8604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 04/02/2015] [Indexed: 11/12/2022] Open
Abstract
The Rhinellamargaritifera species group consists of 17 species of toads distributed in tropical and subtropical South America and eastern Central America. The identity of some of its species is poorly understood and there are numerous undescribed cryptic species. Among them, the status of Rhinellamargaritifera is one of the most problematic. Its range includes lowland rainforests separated by the Andes, the Chocoan rainforest to the west and the Amazonian rainforest to the east. This distribution is puzzling because the Andes are an old and formidable barrier to gene flow and therefore should generate vicariant speciation between disjunct lowland populations. Herein we clarify the taxonomy of populations of the Rhinellamargaritifera complex from Central America and the Chocó region of South America. The morphological and genetic variation of Rhinellamargaritifera was examined from 39 populations from Chocó, 24 from the upper Amazon region of Ecuador, and 37 from Panama, including the holotype of the Panamanian Rhinellaalata. Phylogenetic analyses were performed based on mitochondrial genes 12S rRNA, 16S rRNA, and cytochrome c oxidase I (COI) and the nuclear gene Tyrosinase (Tyr). The genetic and morphological data show that Panamanian and Chocoan populations are conspecific. In the phylogeny, populations from Chocó and Panama form a well-supported clade. The morphology of the holotype of Rhinellaalata falls within the variation range of Panamanian and Chocoan populations. Based on all this evidence, we assign the populations from western Ecuador and Panama to Rhinellaalata and demonstrate that the unusual distribution pattern of "Rhinellamargaritifera" on both sides of the Andes was an artifact of incorrectly defined species boundaries.
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Affiliation(s)
- Sueny P. dos Santos
- Museo de Zoología, Departamento de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre y Roca, Aptdo. 17–01–2184, Quito, Ecuador
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panama, República de Panama
- Departamento de Zoología, Universidad de Panama, Panama, República de Panama
| | - Santiago R. Ron
- Museo de Zoología, Departamento de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre y Roca, Aptdo. 17–01–2184, Quito, Ecuador
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26
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Schulte LJ, Clark JL, Novak SJ, Jeffries SK, Smith JF. Speciation within Columnea section Angustiflora (Gesneriaceae): islands, pollinators and climate. Mol Phylogenet Evol 2015; 84:125-44. [PMID: 25582068 DOI: 10.1016/j.ympev.2014.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 12/01/2022]
Abstract
Despite many advances in evolutionary biology, understanding the proximate mechanisms that lead to speciation for many taxonomic groups remains elusive. Phylogenetic analyses provide a means to generate well-supported estimates of species relationships. Understanding how genetic isolation (restricted gene flow) occurred in the past requires not only a well-supported molecular phylogenetic analysis, but also an understanding of when character states that define species may have changed. In this study, phylogenetic trees resolve species level relationships for fourteen of the fifteen species within Columnea section Angustiflorae (Gesneriaceae). The distributions of sister species pairs are compared and ancestral character states are reconstructed using Bayesian stochastic mapping. Climate variables were also assessed and shifts in ancestral climate conditions were mapped using SEEVA. The relationships between morphological character states and climate variables were assessed with correlation analyses. These results indicate that species in section Angustiflorae have likely diverged as a result of allopatric, parapatric, and sympatric speciation, with both biotic and abiotic forces driving morphological and phenological divergence.
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Affiliation(s)
- Lacie J Schulte
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | - John L Clark
- University of Alabama, Department of Biological Sciences, Box 870345, Tuscaloosa, AL 35487, USA
| | - Stephen J Novak
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | - Shandra K Jeffries
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | - James F Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA.
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27
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Gehara M, Crawford AJ, Orrico VGD, Rodríguez A, Lötters S, Fouquet A, Barrientos LS, Brusquetti F, De la Riva I, Ernst R, Urrutia GG, Glaw F, Guayasamin JM, Hölting M, Jansen M, Kok PJR, Kwet A, Lingnau R, Lyra M, Moravec J, Pombal JP, Rojas-Runjaic FJM, Schulze A, Señaris JC, Solé M, Rodrigues MT, Twomey E, Haddad CFB, Vences M, Köhler J. High levels of diversity uncovered in a widespread nominal taxon: continental phylogeography of the neotropical tree frog Dendropsophus minutus. PLoS One 2014; 9:e103958. [PMID: 25208078 PMCID: PMC4160190 DOI: 10.1371/journal.pone.0103958] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/04/2014] [Indexed: 11/24/2022] Open
Abstract
Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.
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Affiliation(s)
- Marcelo Gehara
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- Pós-graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, Natal, RN, Brasil
- * E-mail:
| | - Andrew J. Crawford
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
- Smithsonian Tropical Research Institute, Panamá, Republic of Panama
| | - Victor G. D. Orrico
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, Brasil
| | - Ariel Rodríguez
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
| | - Stefan Lötters
- Trier University, Biogeography Department, Trier, Germany
| | - Antoine Fouquet
- CNRS-Guyane - USR3456, Immeuble Le Relais - 2, Cayenne, French Guiana
| | - Lucas S. Barrientos
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Francisco Brusquetti
- Departamento de Zoologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil; Instituto de Investigación Biológica del Paraguay, Asunción, Paraguay
| | | | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | | | - Frank Glaw
- Zoologische Staatssammlung München, München, Germany
| | - Juan M. Guayasamin
- Universidad Tecnológica Indoamérica, Centro de Investigación de la Biodiversidad y el Cambio Climático (BioCamp), Cotocollao, Quito, Ecuador
| | - Monique Hölting
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Martin Jansen
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Philippe J. R. Kok
- Amphibian Evolution Lab, Department of Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Axel Kwet
- German Herpetological Society (DGHT), Mannheim, Germany
| | - Rodrigo Lingnau
- Universidade Tecnológica Federal do Paraná, Francisco Beltrão, PR, Brasil
| | - Mariana Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil
| | - Jiří Moravec
- Department of Zoology, National Museum, Prague, Czech Republic
| | - José P. Pombal
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Arne Schulze
- Hessisches Landesmuseum Darmstadt, Department of Zoology, Darmstadt, Germany
| | - J. Celsa Señaris
- Laboratorio de Ecología y Genética de Poblaciones, Centro de Ecología, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Mirco Solé
- Universidade Estadual de Santa Cruz, Departamento de Ciências Biológicas, Rodovia Ilhéus-Itabuna, Bahia, Brasil
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, Brasil
| | - Evan Twomey
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
| | - Celio F. B. Haddad
- Departamento de Zoologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
| | - Jörn Köhler
- Hessisches Landesmuseum Darmstadt, Department of Zoology, Darmstadt, Germany
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A stable niche assumption-free test of ecological divergence. Mol Phylogenet Evol 2014; 76:211-26. [DOI: 10.1016/j.ympev.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/23/2022]
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29
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Barrow LN, Ralicki HF, Emme SA, Lemmon EM. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Mol Phylogenet Evol 2014; 75:78-90. [DOI: 10.1016/j.ympev.2014.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 12/24/2013] [Accepted: 02/13/2014] [Indexed: 11/28/2022]
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30
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Hinsinger DD, Gaudeul M, Couloux A, Bousquet J, Frascaria-Lacoste N. The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation. Mol Phylogenet Evol 2014; 77:223-37. [PMID: 24795215 DOI: 10.1016/j.ympev.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.
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Affiliation(s)
- Damien D Hinsinger
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France; Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 'Origine, Structure et Evolution de la Biodiversité', 16 rue Buffon, CP 39, F-75005 Paris, France.
| | - Arnaud Couloux
- Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Nathalie Frascaria-Lacoste
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France.
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31
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Kieswetter CM, Schneider CJ. Phylogeography in the northern Andes: Complex history and cryptic diversity in a cloud forest frog, Pristimantis w-nigrum (Craugastoridae). Mol Phylogenet Evol 2013; 69:417-29. [DOI: 10.1016/j.ympev.2013.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 08/01/2013] [Accepted: 08/08/2013] [Indexed: 10/26/2022]
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32
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Yang Y, Xu M, Luo Q, Wang J, Li H. De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing. Gene 2013; 534:155-62. [PMID: 24239772 DOI: 10.1016/j.gene.2013.10.073] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/21/2013] [Accepted: 10/27/2013] [Indexed: 12/31/2022]
Abstract
Liriodendron chinense (Hemsl.) Sarg is an endangered species and occupies a pivotal position in phylogenetic studies of flowering plants, while its genomic resources are limited. In this study, we performed transcriptome sequencing for L. chinense petals and leaves using the Illumina paired-end sequencing technique. Approximately 17.02-Gb clean reads were obtained, and de novo assembly generated 87,841 unigenes, with an average length of 778 bp. Of these, there were 65,535 (74.61%) unigenes with significant similarity to publically available plant protein sequences. There were 3386 genes identified as significant differentially expressed between petals and leaves, among them 2969 (87.68%) were up-regulated and 417 (12.31%) down-regulated in petals. Metabolic pathway analysis revealed that 25 unigenes were predicted to be responsible for the biosynthesis of carotenoids, with 7 genes differentially expressed between these two tissues. This report is the first to identify genes associated with carotenoid biosynthesis in Liriodendron and represents a valuable resource for future genomic studies on the endangered species L. chinense.
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Affiliation(s)
- Ying Yang
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Meng Xu
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Qunfeng Luo
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jie Wang
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Huogen Li
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
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33
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Ye S, Huang H, Zheng R, Zhang J, Yang G, Xu S. Phylogeographic analyses strongly suggest cryptic speciation in the giant spiny frog (Dicroglossidae: Paa spinosa) and interspecies hybridization in Paa. PLoS One 2013; 8:e70403. [PMID: 23936199 PMCID: PMC3729840 DOI: 10.1371/journal.pone.0070403] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 06/17/2013] [Indexed: 11/23/2022] Open
Abstract
Species identification is one of the most basic yet crucial issues in biology with potentially far-reaching implications for fields such as conservation, population ecology, and epidemiology. The widely distributed but threatened frog Paa spinosa has been speculated to represent a complex of multiple species. In this study, 254 individuals representing species of the genus Paa were investigated along the entire range of P. spinosa: 196 specimens of P. spinosa, 8 specimens of P. jiulongensis, 5 specimens of P. boulengeri, 20 specimens of P. exilispinosa, and 25 specimens of P. shini. Approximately 1333 bp of mtDNA sequence data (genes 12S rRNA and 16S rRNA) were used. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood and Bayesian inference. BEAST was used to estimate divergence dates of major clades. Results suggest that P. spinosa can be divided into three distinct major lineages. Each major lineage totally corresponds to geographical regions, revealing the presence of three candidate cryptic species. Isolation and differentiation among lineages are further supported by the great genetic distances between the lineages. The bifurcating phylogenetic pattern also suggests an east-west dispersal trend during historic cryptic speciation. Dating analysis estimates that P. spinosa from Western China split from the remaining P. spinosa populations in the Miocene and that P. spinosa from Eastern China diverged from Central China in the Pliocene. We also found that P. exilispinosa from Mainland China and Hong Kong might have a complex of multiple species. After identifying cryptic lineages, we then determine the discrepancy between the mtDNA and the morphotypes in several individuals. This discrepancy may have been caused by introgressive hybridization between P. spinosa and P. shini.
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Affiliation(s)
- Shupei Ye
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Hua Huang
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Rongquan Zheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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34
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Zhang JB, Li RQ, Xiang XG, Manchester SR, Lin L, Wang W, Wen J, Chen ZD. Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.). PLoS One 2013; 8:e70449. [PMID: 23875028 PMCID: PMC3713062 DOI: 10.1371/journal.pone.0070449] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/18/2013] [Indexed: 12/01/2022] Open
Abstract
The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.
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Affiliation(s)
- Jing-Bo Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Steven R. Manchester
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Li Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- * E-mail: (ZDC); (JW)
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (ZDC); (JW)
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35
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Yang L, Hou Z, Li S. Marine incursion into East Asia: a forgotten driving force of biodiversity. Proc Biol Sci 2013; 280:20122892. [PMID: 23446524 DOI: 10.1098/rspb.2012.2892] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Episodic marine incursion has been a major driving force in the formation of present-day diversity. Marine incursion is considered to be one of the most productive 'species pumps' particularly because of its division and coalescence effects. Marine incursion events and their impacts on diversity are well documented from South America, North America and Africa; however, their history and impacts in continental East Asia largely remain unknown. Here, we propose a marine incursion scenario occurring in East Asia during the Miocene epoch, 10-17 Ma. Our molecular phylogenetic analysis of Platorchestia talitrids revealed that continental terrestrial populations (Platorchestia japonica) form a monophyletic group that is the sister group to the Northwest Pacific coastal species Platorchestia pacifica. The divergence time between the two species coincides with Middle Miocene high global sea levels. We suggest that the inland form arose as a consequence of a marine incursion event. This is the first solid case documenting the impact of marine incursion on extant biodiversity in continental East Asia. We believe that such incursion event has had major impacts on other organisms and has played an important role in the formation of biodiversity patterns in the region.
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Affiliation(s)
- Lu Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
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36
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Niemiller ML, McCandless JR, Reynolds RG, Caddle J, Near TJ, Tillquist CR, Pearson WD, Fitzpatrick BM. EFFECTS OF CLIMATIC AND GEOLOGICAL PROCESSES DURING THE PLEISTOCENE ON THE EVOLUTIONARY HISTORY OF THE NORTHERN CAVEFISH,AMBLYOPSIS SPELAEA(TELEOSTEI: AMBLYOPSIDAE). Evolution 2012; 67:1011-25. [DOI: 10.1111/evo.12017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Yan F, Zhou W, Zhao H, Yuan Z, Wang Y, Jiang K, Jin J, Murphy RW, Che J, Zhang Y. Geological events play a larger role than
P
leistocene climatic fluctuations in driving the genetic structure of
Q
uasipaa boulengeri
(
A
nura:
D
icroglossidae). Mol Ecol 2012; 22:1120-33. [DOI: 10.1111/mec.12153] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 10/23/2012] [Accepted: 10/25/2012] [Indexed: 01/23/2023]
Affiliation(s)
- Fang Yan
- 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
- Graduate School of the Chinese Academy of Sciences Beijing 100049 China
| | - Weiwei Zhou
- 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
| | - Haitao Zhao
- College of Life Sciences Bijie University Bijie 551700 China
| | - Zhiyong Yuan
- 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
- Graduate School of the Chinese Academy of Sciences Beijing 100049 China
| | - Yunyu Wang
- 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
| | - Ke Jiang
- 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
| | - Jieqiong Jin
- 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
| | - Robert W. Murphy
- 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
- Centre for Biodiversity and Conservation Biology Royal Ontario Museum 100 Queen's Park Toronto Ontario Canada M5S 2C6
| | - 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
| | - Yaping Zhang
- 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
- Laboratory for Conservation and Utilization of Bio‐resources Yunnan University Kunming 650091 China
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38
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Espregueira Themudo G, Nieman AM, Arntzen JW. Is dispersal guided by the environment? A comparison of interspecific gene flow estimates among differentiated regions of a newt hybrid zone. Mol Ecol 2012; 21:5324-35. [DOI: 10.1111/mec.12026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/19/2012] [Accepted: 08/08/2012] [Indexed: 11/28/2022]
Affiliation(s)
| | - A. M. Nieman
- Naturalis Biodiversity Center; P. O. Box 9517; 2300 RA; Leiden; The Netherlands
| | - J. W. Arntzen
- Naturalis Biodiversity Center; P. O. Box 9517; 2300 RA; Leiden; The Netherlands
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39
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Lemmon AR, Lemmon EM. High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography. Syst Biol 2012; 61:745-61. [DOI: 10.1093/sysbio/sys051] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Alan R. Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA
| | - Emily Moriarty Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA
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40
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Salerno PE, Ron SR, Señaris JC, Rojas-Runjaic FJM, Noonan BP, Cannatella DC. Ancient tepui summits harbor young rather than old lineages of endemic frogs. Evolution 2012; 66:3000-13. [PMID: 23025594 DOI: 10.1111/j.1558-5646.2012.01666.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The flattop mountains (tepuis) of South America are ancient remnants of the Precambrian Guiana Shield plateau. The tepui summits, isolated by their surrounding cliffs that can be up to 1000 m tall, are thought of as "islands in the sky," harboring relict flora and fauna that underwent vicariant speciation due to plateau fragmentation. High endemicity atop tepui summits support the idea of an ancient "Lost World" biota. However, recent work suggests that dispersal between lowlands and summits has occurred long after tepui formation indicating that tepui summits may not be as isolated from the lowlands as researchers have long suggested. Neither view of the origin of the tepui biota (i.e., ancient vicariance vs. recent dispersal) has strong empirical support owing to a lack of studies. We test diversification hypotheses of the Guiana Shield highlands by estimating divergence times of an endemic group of treefrogs, Tepuihyla. We find that diversification of this group does not support an ancient origin for this taxon; instead, divergence times among the highland species are 2-5 Ma. Our data indicate that most highland speciation occurred during the Pliocene. Thus, this unparalleled landscape known as "The Lost World" is inhabited, in part, not by Early Tertiary relicts but neoendemics.
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Affiliation(s)
- Patricia E Salerno
- Section of Integrative Biology, University of Texas at Austin, 1 University Station, C0900, Austin, Texas 78712, USA.
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41
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Nair A, Gopalan SV, George S, Kumar KS, Teacher AGF, Merilä J. High cryptic diversity of endemicIndiranafrogs in the Western Ghats biodiversity hotspot. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00539.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- A. Nair
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki; Finland
| | - S. V. Gopalan
- Chemical Biology; Rajiv Gandhi Centre for Biotechnology; Thiruvananthapuram; Kerala; India
| | - S. George
- Chemical Biology; Rajiv Gandhi Centre for Biotechnology; Thiruvananthapuram; Kerala; India
| | - K. S. Kumar
- Chemical Biology; Rajiv Gandhi Centre for Biotechnology; Thiruvananthapuram; Kerala; India
| | | | - J. Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki; Finland
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42
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Hether TD, Hoffman EA. Machine learning identifies specific habitats associated with genetic connectivity in Hyla squirella. J Evol Biol 2012; 25:1039-52. [PMID: 22487242 DOI: 10.1111/j.1420-9101.2012.02497.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The goal of this study was to identify and differentiate the influence of multiple habitat types that span a spectrum of suitability for Hyla squirella, a widespread frog species that occurs in a broad range of habitat types. We collected microsatellite data from 675 samples representing 20 localities from the southeastern USA and used machine-learning methodologies to identify significant habitat features associated with genetic structure. In simulation, we confirm that our machine-learning algorithm can successfully identify landscape features responsible for generating between-population genetic differentiation, suggesting that it can be a useful hypothesis-generating tool for landscape genetics. In our study system, we found that H. squirella were spatially structured and models including specific habitat types (i.e. upland oak forest and urbanization) consistently explained more variation in genetic distance (median pR(2) = 47.78) than spatial distance alone (median pR(2) = 23.81). Moreover, we estimate the relative importance that spatial distance, upland oak and urbanized habitat have in explaining genetic structure of H. squirella. We discuss how these habitat types may mechanistically facilitate dispersal in H. squirella. This study provides empirical support for the hypothesis that habitat-use can be an informative correlate of genetic differentiation, even for species that occur in a wide range of habitats.
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Affiliation(s)
- T D Hether
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA
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43
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Barber BR, Unmack PJ, Pérez-Losada M, Johnson JB, Crandall KA. Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage. BMC Evol Biol 2011; 11:343. [PMID: 22118288 PMCID: PMC3238299 DOI: 10.1186/1471-2148-11-343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 11/25/2011] [Indexed: 11/10/2022] Open
Abstract
Background Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergence in three clades of the Chilean freshwater species assemblage. Molecular studies of freshwater crabs (Aegla: Aeglidae: Anomura) and catfish (Trichomycterus arealatus: Trichomycteridae: Teleostei) exhibited similar levels of genetic divergences of mitochondrial lineages between species of crabs and phylogroups of the catfish, suggesting a shared evolutionary history among the three clades in this species assemblage. Results A phylogeny was constructed for Trichomycterus areolatus under the following best-fit molecular models of evolution GTR + I + R, HKY + I, and HKY for cytochrome b, growth hormone, and rag 1 respectively. A GTR + I + R model provided the best fit for both 28S and mitochondrial loci and was used to construct both Aegla phylogenies. Three different diversification models were observed and the three groups arose during different time periods, from 2.25 to 5.05 million years ago (Ma). Cladogenesis within Trichomycterus areolatus was initiated roughly 2.25 Ma (Late Pliocene - Early Pleistocene) some 1.7 - 2.8 million years after the basal divergences observed in both Aegla clades. These results reject the hypothesis of codivergence. Conclusions The similar genetic distances between terminal sister-lineages observed in these select taxa from the freshwater Chilean species assemblage were formed by different processes occurring over the last ~5.0 Ma. Dramatic changes in historic sea levels documented in the region appear to have independently shaped the evolutionary history of each group. Our study illustrates the important role that history plays in shaping a species assemblage and argues against assuming similar patterns equal a shared evolutionary history.
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Affiliation(s)
- Brian R Barber
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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44
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Conservation and genetics of the frosted flatwoods salamander (Ambystoma cingulatum) on the Atlantic coastal plain. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0274-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hoverman JT, Gray MJ, Haislip NA, Miller DL. Phylogeny, life history, and ecology contribute to differences in amphibian susceptibility to ranaviruses. ECOHEALTH 2011; 8:301-19. [PMID: 22071720 DOI: 10.1007/s10393-011-0717-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 09/27/2011] [Accepted: 10/11/2011] [Indexed: 05/23/2023]
Abstract
Research that identifies the potential host range of generalist pathogens as well as variation in host susceptibility is critical for understanding and predicting the dynamics of infectious diseases within ecological communities. Ranaviruses have been linked to amphibian die-off events worldwide with the greatest number of reported mortality events occurring in the United States. While reports of ranavirus-associated mortality events continue to accumulate, few data exist comparing the relative susceptibility of different species. Using a series of laboratory exposure experiments and comparative phylogenetics, we compared the susceptibilities of 19 amphibian species from two salamander families and five anurans families for two ranavirus isolates: frog virus 3 (FV3) and an FV3-like isolate from an American bullfrog culture facility. We discovered that ranaviruses were capable of infecting 17 of the 19 larval amphibian species tested with mortality ranging from 0 to 100%. Phylogenetic comparative methods demonstrated that species within the anuran family Ranidae were generally more susceptible to ranavirus infection compared to species from the other five families. We also found that susceptibility to infection was associated with species that breed in semi-permanent ponds, develop rapidly as larvae, and have limited range sizes. Collectively, these results suggest that phylogeny, life history characteristics, and habitat associations of amphibians have the potential to impact susceptibility to ranaviruses.
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Affiliation(s)
- Jason T Hoverman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
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Identification and characterization of nuclear microsatellite loci for multiple species of chorus frogs (Pseudacris) for population genetic analyses. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-010-9330-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Berendzen PB, Dugan JF, Gamble T. Post-glacial expansion into the Paleozoic Plateau: evidence of an Ozarkian refugium for the Ozark minnow Notropis nubilus (Teleostei: Cypriniformes). JOURNAL OF FISH BIOLOGY 2010; 77:1114-1136. [PMID: 21039494 DOI: 10.1111/j.1095-8649.2010.02769.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Genetic variation was examined within the Ozark minnow Notropis nubilus using complete mtDNA cytochrome b gene sequences from 160 individuals representing 30 localities to test hypotheses on the origin of the distribution. Phylogenetic analyses revealed three strongly supported clades of haplotypes consistent with geographic distributions: a clade from the Western Ozarks, a clade from the Southern Ozarks and a clade from the Northern Ozarks and upper Mississippi River basin. The estimated mean ages of these clades indicated that they diverged during pre-Illinoian glacial cycles extending from the late Pliocene into the early Pleistocene. Results of demographic analyses based on coalescent approaches supported the hypothesis that the Paleozoic Plateau was not a refugium for N. nubilus during periodic glacial advances. There is evidence of a genetic signature of northern expansion into the Paleozoic Plateau from a Southern Ozarkian refugium. Populations expanded out of drainages in the Northern Ozarks into the Paleozoic Plateau during the late Pleistocene. Subsequently, the two regions were isolated due to the recent extirpation of intervening populations caused by the loss of suitable habitat.
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Affiliation(s)
- P B Berendzen
- Department of Biology, McCollum Science Hall, University of Northern Iowa, Cedar Falls, IA 50614, USA.
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Lemmon AR, Lemmon EM. A likelihood framework for estimating phylogeographic history on a continuous landscape. Syst Biol 2010; 57:544-61. [PMID: 18686193 DOI: 10.1080/10635150802304761] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Due to lack of an adequate statistical framework, biologists studying phylogeography are abandoning traditional methods of estimating phylogeographic history in favor of statistical methods designed to test a priori hypotheses. These new methods may, however, have limited descriptive utility. Here, we develop a new statistical framework that can be used to both test a priori hypotheses and estimate phylogeographic history of a gene (and the statistical confidence in that history) in the absence of such hypotheses. The statistical approach concentrates on estimation of geographic locations of the ancestors of a set of sampled organisms. Now we use (2) to derive the likelihood of the ancestral geographic coordinates and the value of the scaled dispersal parameter, given the observed geographic coordinates (assuming known topology and branch lengths). Using a maximum likelihood approach, which is implemented in the new program PhyloMapper, we apply this statistical framework to a 246-taxon mitochondrial genealogy of North American chorus frogs, focusing in detail on one of these species. We demonstrate three lines of evidence for recent northward expansion of the mitochondrion of the coastal clade of Pseudacris feriarum: higher per-generation dispersal distance in the recently colonized region, a noncentral ancestral location, and directional migration. After illustrating one method of accommodating phylogenetic uncertainty, we conclude by discussing how extensions of this framework could function to incorporate a priori ecological and geological information into phylogeographic analyses.
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Affiliation(s)
- Alan R Lemmon
- Section of Integrative Biology, University of Texas-Austin, Austin, Texas 78712, USA.
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Wielstra B, Themudo GE, Güçlü Ö, Olgun K, Poyarkov N, Arntzen J. Cryptic crested newt diversity at the Eurasian transition: The mitochondrial DNA phylogeography of Near Eastern Triturus newts. Mol Phylogenet Evol 2010; 56:888-96. [DOI: 10.1016/j.ympev.2010.04.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 04/15/2010] [Accepted: 04/23/2010] [Indexed: 11/28/2022]
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CAMARGO ARLEY, SINERVO BARRY, SITES JACKW. Lizards as model organisms for linking phylogeographic and speciation studies. Mol Ecol 2010; 19:3250-70. [DOI: 10.1111/j.1365-294x.2010.04722.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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