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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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Nuñez JJ, Suárez-Villota EY, Quercia CA, Olivares AP, Sites JW. Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia. PeerJ 2020; 8:e9980. [PMID: 33083116 PMCID: PMC7546244 DOI: 10.7717/peerj.9980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023] Open
Abstract
Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type I error: <0.094, type II error: 0.134). EBSP, mismatch distribution and neutrality indexes suggest sudden population expansion at ∼0.02 mya for all lineages. SDM infers fragmented distributions of B. leptopus associated with Pleistocene glaciations. Although the present populations of B. leptopus are found in zones affected by the last glacial maximum (∼0.023 mya), our analyses recover an older history of interglacial diversification (0.107–0.019 mya). In addition, we hypothesize two glacial refugia and three interglacial colonization routes, one of which gave rise to two expanding lineages in the south.
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Affiliation(s)
- José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Elkin Y Suárez-Villota
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Concepción, Región del Bio-Bío, Chile
| | - Camila A Quercia
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Angel P Olivares
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, UT, United States of America.,Current affiliation: Department of Biology, Austin Peay St University, Clarksville, TN, United States of America
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Trevisan CC, Batalha-Filho H, Garda AA, Menezes L, Dias IR, Solé M, Canedo C, Juncá FA, Napoli MF. Cryptic diversity and ancient diversification in the northern Atlantic Forest Pristimantis (Amphibia, Anura, Craugastoridae). Mol Phylogenet Evol 2020; 148:106811. [PMID: 32259656 DOI: 10.1016/j.ympev.2020.106811] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
Abstract
The Neotropical region is known both for its megadiverse fauna and for the significant deficiency of our knowledge on species limits. The Amazon and Atlantic Forest are the two most diverse and large rainforests in South America, and they harbor many groups of sister species and sister genera. The frog genus Pristimantis is the most speciose genus of terrestrial vertebrates with 546 species, but only three of them occur in the Atlantic forest. Herein, we investigate the diversification history and phylogenetic relationship among the Atlantic Forest Pristimantis lineages in a spatial-temporal framework, using mitochondrial and nuclear genes. Our results reveal a remarkable hidden diversity, with nine highly structure lineages that may correspond to undescribed species, with many cases of sympatry among these divergent lineages. Atlantic forest Pristimantis form a monophyletic group that started to diversify over 40 million years ago. This ancient group shows diversification events that remount the early bursts of the Atlantic Forest diversification history, as well as lineage diversification likely resulting from recent Pleistocene climatic fluctuations. Future work must concentrate in comparing these lineages under an integrative framework including morphology, advertisement calls and other ecology traits to confidently delimit species of Pristimantis in the Atlantic Forest.
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Affiliation(s)
- Camila Costa Trevisan
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil.
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil; Museu de História Natural ("Museu de Zoologia"), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Adrian Antonio Garda
- Laboratório de Anfíbios e Répteis - LAR, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Av. Salgado Filho S/N, Lagoa Nova, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Lucas Menezes
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Iuri Ribeiro Dias
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, Bahia, Brazil
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, Bahia, Brazil
| | - Clarissa Canedo
- Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Departamento de Zoologia, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, Rio de Janeiro, Brazil; Museu Nacional, Departamento de Vertebrados, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 São Cristóvão, Rio de Janeiro, Brazil
| | - Flora Acuña Juncá
- Museu de Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina, 44036-900 Feira de Santana, Bahia, Brazil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil; Museu de História Natural ("Museu de Zoologia"), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil
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Mângia S, Oliveira EF, Santana DJ, Koroiva R, Paiva F, Garda AA. Revising the taxonomy of
Proceratophrys
Miranda‐Ribeiro, 1920 (Anura: Odontophrynidae) from the Brazilian semiarid Caatinga: Morphology, calls and molecules support a single widespread species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Mângia
- Departamento de Sistemática e Ecologia Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Universidade Federal da Paraı́ba João Pessoa Brazil
| | - Eliana Faria Oliveira
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Diego José Santana
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Ricardo Koroiva
- Laboratório de Citotaxonomia e Insetos Aquáticos Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Fernando Paiva
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
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Stuart BL, Som HE, Neang T, Hoang HD, Le DTT, Dau VQ, Potter K, Rowley JJL. Integrative taxonomic analysis reveals a new species of Leptobrachium (Anura: Megophryidae) from north-eastern Cambodia and central Vietnam. J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1756498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Bryan L. Stuart
- Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Hannah E. Som
- Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Thy Neang
- Wild Earth Allies, Phnom Penh, Cambodia
| | - Huy Duc Hoang
- Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Duong Thi Thuy Le
- Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vinh Quang Dau
- Faculty of Natural Sciences, Hong Duc University, Thanh Hoa City, Vietnam
| | - Kathy Potter
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Jodi J. L. Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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de Sá FP, Haddad CFB, Gray MM, Verdade VK, Thomé MTC, Rodrigues MT, Zamudio KR. Male-male competition and repeated evolution of terrestrial breeding in Atlantic Coastal Forest frogs. Evolution 2019; 74:459-475. [PMID: 31710098 DOI: 10.1111/evo.13879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 11/28/2022]
Abstract
Terrestrial breeding is a derived condition in frogs, with multiple transitions from an aquatic ancestor. Shifts in reproductive mode often involve changes in habitat use, and these are typically associated with diversification in body plans, with repeated transitions imposing similar selective pressures. We examine the diversification of reproductive modes, male and female body sizes, and sexual size dimorphism (SSD) in the Neotropical frog genera Cycloramphus and Zachaenus, both endemic to the Atlantic rainforest of Brazil. Species in this clade either breed in rocky streams (saxicolous) or in terrestrial environments, allowing us to investigate reproductive habitat shifts. We constructed a multilocus molecular phylogeny and inferred evolutionary histories of reproductive habitats, body sizes, and SSD. The common ancestor was small, saxicolous, and had low SSD. Terrestrial breeding evolved independently three times and we found a significant association between reproductive habitat and SSD, with shifts to terrestrial breeding evolving in correlation with decreases in male body size, but not female body size. Terrestrial breeding increases the availability of breeding sites and results in concealment of amplexus, egg-laying, and parental care, therefore reducing male-male competition at all stages of reproduction. We conclude that correlated evolution of terrestrial reproduction and small males is due to release from intense male-male competition that is typical of exposed saxicolous breeding.
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Affiliation(s)
- Fábio P de Sá
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, UNESP - Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
| | - Célio F B Haddad
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, UNESP - Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
| | - Miranda M Gray
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Vanessa K Verdade
- Centro de Ciências Naturais e Humanas, UFABC - Universidade Federal do ABC, Santo André, 09210-580, São Paulo, Brazil
| | - Maria Tereza C Thomé
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, UNESP - Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, USP - Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
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Ansari MH, Cooper SJ, Schwarz MP, Ebrahimi M, Dolman G, Reinberger L, Saint KM, Donnellan SC, Bull CM, Gardner MG. Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species. Mol Phylogenet Evol 2019; 133:107-119. [DOI: 10.1016/j.ympev.2018.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022]
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8
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Suárez-Villota EY, Quercia CA, Díaz LM, Vera-Sovier V, Nuñez JJ. Speciation in a biodiversity hotspot: Phylogenetic relationships, species delimitation, and divergence times of Patagonian ground frogs from the Eupsophus roseus group (Alsodidae). PLoS One 2018; 13:e0204968. [PMID: 30543633 PMCID: PMC6292574 DOI: 10.1371/journal.pone.0204968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 11/19/2022] Open
Abstract
The alsodid ground frogs of the Eupsophus genus are divided into two groups, the roseus (2n = 30) and vertebralis (2n = 28), which are distributed throughout the temperate Nothofagus forests of South America. Currently, the roseus group is composed by four species, while the vertebralis group consists of two. Phylogenetic relationships and species delimitation within each group are controversial. In fact, previous analyses considered that the roseus group was composed of between four to nine species. In this work, we evaluated phylogenetic relationships, diversification times, and species delimitation within the roseus group using a multi-locus dataset. For this purpose, mitochondrial (D-loop, Cyt b, and COI) and nuclear (POMC and CRYBA1) partial sequences from 164 individuals were amplified, representing all species. Maximum Likelihood (ML) and Bayesian approaches were used to reconstruct phylogenetic relationships. Species tree was estimated using BEAST and singular value decomposition scores for species quartets (SVDquartets). Species limits were evaluated with six coalescent approaches. Diversification times were estimated using mitochondrial and nuclear rates with LogNormal relaxed clock in BEAST. Nine well-supported monophyletic lineages were recovered in Bayesian, ML, and SVDquartets, including eight named species and a lineage composed by specimens from the Villarrica population (Bootstrap:>70, PP:> 0.99). Single-locus species delimitation analyses overestimated the species number in E. migueli, E. calcaratus, and E. roseus lineages, while multi-locus analyses recovered as species the nine lineages observed in phylogenetic analyses (Ctax = 0.69). It is hypothesized that Eupsophus diversification occurred during Mid-Pleistocene (0.42-0.14 Mya), with most species having originated after the Last Southern Patagonian Glaciation (0.18 Mya). Our results revitalize the hypothesis that the E. roseus group is composed of eight species and support the Villarrica lineage as a new putative species.
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Affiliation(s)
| | - Camila A. Quercia
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Leila M. Díaz
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Victoria Vera-Sovier
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - José J. Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
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Keely CC, Hale JM, Heard GW, Parris KM, Sumner J, Hamer AJ, Melville J. Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140255. [PMID: 26361543 PMCID: PMC4555848 DOI: 10.1098/rsos.140255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 07/27/2015] [Indexed: 06/05/2023]
Abstract
Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog (Litoria raniformis) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis. However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.
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Affiliation(s)
- Claire C. Keely
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
- Sciences Department, Museum Victoria, Carlton 3053, Australia
| | - Joshua M. Hale
- Sciences Department, Museum Victoria, Carlton 3053, Australia
| | - Geoffrey W. Heard
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Kirsten M. Parris
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Joanna Sumner
- Sciences Department, Museum Victoria, Carlton 3053, Australia
| | - Andrew J. Hamer
- Australian Research Centre for Urban Ecology, Royal Botanic Gardens Melbourne c/o School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Jane Melville
- Sciences Department, Museum Victoria, Carlton 3053, Australia
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Cliff HB, Wapstra E, Burridge CP. Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania. BMC Evol Biol 2015; 15:121. [PMID: 26111715 PMCID: PMC4482293 DOI: 10.1186/s12862-015-0397-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background The aim of this research was to identify the effects of Pleistocene climate change on the distribution of fauna in Tasmania, and contrast this with biotic responses in other temperate regions in the Northern and Southern Hemisphere that experienced glacial activity during this epoch. This was achieved by examining the phylogeographic patterns in a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus. 204 individuals from 29 populations across the distributional range of N. ocellatus were surveyed for variation at two mitochondrial genes (ND2, ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships were reconstructed using a range of methods (maximum parsimony, Bayesian inference and haplotype networks), and the demographic histories of populations were assessed (AMOVA, Tajima’s D, Fu’s Fs, mismatch distributions, extended Bayesian skyline plots, and relaxed random walk analyses). Results There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania’s Northeast and a large area covering Southeast and Central Tasmania. Phylogeographic structure was also present within each major group, but the degree varied regionally, being highest in the Northeast. Only the Southeastern group had a signature of demographic expansion, occurring during the Pleistocene but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low levels of variation and a lack of phylogeographic structure, and further loci should be surveyed to corroborate the mitochondrial inferences. Conclusions The phylogeographic patterns of N. ocellatus indicate Pleistocene range and demographic expansion in N. ocellatus, particularly in the Southeast and Central areas of Tasmania. Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum. These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0397-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H B Cliff
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| | - E Wapstra
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| | - C P Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
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Phylogenetic evidence of historic mitochondrial introgression and cryptic diversity in the genus Pseudemoia (Squamata: Scincidae). Mol Phylogenet Evol 2014; 81:86-95. [DOI: 10.1016/j.ympev.2014.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/11/2014] [Accepted: 09/09/2014] [Indexed: 11/23/2022]
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12
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Pelletier TA, Crisafulli C, Wagner S, Zellmer AJ, Carstens BC. Historical Species Distribution Models Predict Species Limits in WesternPlethodonSalamanders. Syst Biol 2014; 64:909-25. [DOI: 10.1093/sysbio/syu090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/10/2014] [Indexed: 11/12/2022] Open
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Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding. Mol Phylogenet Evol 2013; 68:119-34. [DOI: 10.1016/j.ympev.2013.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/08/2013] [Indexed: 11/17/2022]
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14
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Singhal S, Moritz C. Testing hypotheses for genealogical discordance in a rainforest lizard. Mol Ecol 2012; 21:5059-72. [PMID: 22989358 DOI: 10.1111/j.1365-294x.2012.05747.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 06/27/2012] [Accepted: 07/01/2012] [Indexed: 12/26/2022]
Abstract
Genealogical discordance, or when different genes tell distinct stories although they evolved under a shared history, often emerges from either coalescent stochasticity or introgression. In this study, we present a strong case of mito-nuclear genealogical discordance in the Australian rainforest lizard species complex of Saproscincus basiliscus and S. lewisi. One of the lineages that comprises this complex, the Southern S. basiliscus lineage, is deeply divergent at the mitochondrial genome but shows markedly less divergence at the nuclear genome. By placing our results in a comparative context and reconstructing the lineages' demography via multilocus and coalescent-based approximate Bayesian computation methods, we test hypotheses for how coalescent variance and introgression contribute to this pattern. These analyses suggest that the observed genealogical discordance likely results from introgression. Further, to generate such strong discordance, introgression probably acted in concert with other factors promoting asymmetric gene flow between the mitochondrial and nuclear genomes, such as selection or sex-biased dispersal. This study offers a framework for testing sources of genealogical discordance and suggests that historical introgression can be an important force shaping the genetic diversity of species and their populations.
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Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA.
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A multilocus perspective on the speciation history of a North American aridland toad (Anaxyrus punctatus). Mol Phylogenet Evol 2012; 64:393-400. [DOI: 10.1016/j.ympev.2012.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/19/2012] [Accepted: 04/21/2012] [Indexed: 11/21/2022]
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16
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Singhal S, Moritz C. Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard. Evolution 2012; 66:1474-89. [PMID: 22519785 DOI: 10.1111/j.1558-5646.2011.01539.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (≈400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity.
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Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160, USA.
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17
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Fisher-Reid MC, Wiens JJ. What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evol Biol 2011; 11:300. [PMID: 21995558 PMCID: PMC3203092 DOI: 10.1186/1471-2148-11-300] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 10/13/2011] [Indexed: 11/15/2022] Open
Abstract
Background The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for Plethodon salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals). Results We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled). Conclusions Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like Plethodon, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.
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Affiliation(s)
- M Caitlin Fisher-Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY, 11794-5245, USA.
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18
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Bell RC, MacKenzie JB, Hickerson MJ, Chavarría KL, Cunningham M, Williams S, Moritz C. Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs. Proc Biol Sci 2011; 279:991-9. [PMID: 21900325 DOI: 10.1098/rspb.2011.1229] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the Late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum. Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of northeast Australia. Our results demonstrate at least two episodes of vicariance owing to climate-driven forest contractions: one in the Early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.
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Affiliation(s)
- Rayna C Bell
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
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19
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Miraldo A, Hewitt GM, Paulo OS, Emerson BC. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol Biol 2011; 11:170. [PMID: 21682856 PMCID: PMC3141430 DOI: 10.1186/1471-2148-11-170] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 06/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species. RESULTS Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry. CONCLUSIONS The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.
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Affiliation(s)
- Andreia Miraldo
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7J, UK.
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20
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Austin CC, Rittmeyer EN, Oliver LA, Andermann JO, Zug GR, Rodda GH, Jackson ND. The bioinvasion of Guam: inferring geographic origin, pace, pattern and process of an invasive lizard (Carlia) in the Pacific using multi-locus genomic data. Biol Invasions 2011. [DOI: 10.1007/s10530-011-0014-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Microsatellite analysis supports mitochondrial phylogeography of the hellbender (Cryptobranchus alleganiensis). Genetica 2010; 139:209-19. [PMID: 21161568 DOI: 10.1007/s10709-010-9538-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
We investigated genetic diversity of the hellbender (Cryptobranchus alleganiensis) throughout its range in the eastern US using nuclear markers and compared our results to a previously published mitochondrial analysis. A variety of nuclear markers, including protein-coding gene introns and microsatellites were tested but only microsatellites were variable enough for population level analysis. Microsatellite loci showed moderate among population sharing of alleles, in contrast to the reciprocal monophyly exhibited by mitochondrial DNA. However, analyses using F-statistics and Bayesian clustering algorithms showed considerable population subdivision and clustered hellbender populations into the same major groups as the mtDNA. The microsatellites combined with the mtDNA data suggest that gene flow is severely restricted or non-existent among eight major groups, and potentially among populations (rivers) within groups. The combined mtDNA and microsatellite data suggest that the currently recognized hellbender subspecies are paraphyletic. We suggest that the eight independent groups identified in our study should be managed as such, rather than basing conservation decisions on the two named subspecies of hellbender.
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Thomé MTC, Zamudio KR, Giovanelli JG, Haddad CF, Baldissera FA, Alexandrino J. Phylogeography of endemic toads and post-Pliocene persistence of the Brazilian Atlantic Forest. Mol Phylogenet Evol 2010; 55:1018-31. [DOI: 10.1016/j.ympev.2010.02.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Revised: 01/30/2010] [Accepted: 02/02/2010] [Indexed: 11/25/2022]
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23
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Bell RC, Parra JL, Tonione M, Hoskin CJ, Mackenzie JB, Williams SE, Moritz C. Patterns of persistence and isolation indicate resilience to climate change in montane rainforest lizards. Mol Ecol 2010; 19:2531-44. [PMID: 20497322 DOI: 10.1111/j.1365-294x.2010.04676.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Globally, montane tropical diversity is characterized by extraordinary local endemism that is not readily explained by current environmental variables indicating a strong imprint of history. Montane species often exist as isolated populations under current climatic conditions and may have remained isolated throughout recent climatic cycles, leading to substantial genetic and phenotypic divergence. Alternatively, populations may have become contiguous during colder climates resulting in less divergence. Here we compare responses to historical climate fluctuation in a montane specialist skink, Lampropholis robertsi, and its more broadly distributed congener, L. coggeri, both endemic to rainforests of northeast Australia. To do so, we combine spatial modelling of potential distributions under representative palaeoclimates, multi-locus phylogeography and analyses of phenotypic variation. Spatial modelling of L. robertsi predicts strong isolation among disjunct montane refugia during warm climates, but with potential for localized exchange during the most recent glacial period. In contrast, predicted stable areas are more widespread and connected in L. coggeri. Both species exhibit pronounced phylogeographic structuring for mitochondrial and nuclear genes, attesting to low dispersal and high persistence across multiple isolated regions. This is most prominent in L. robertsi, for which coalescent analyses indicate that most populations persisted in isolation throughout the climate cycles of the Pleistocene. Morphological divergence, principally in body size, is more evident among isolated populations of L. robertsi than L. coggeri. These results highlight the biodiversity value of isolated montane populations and support the general hypothesis that tropical montane regions harbour high levels of narrow-range taxa because of their resilience to past climate change.
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Affiliation(s)
- Rayna C Bell
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
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24
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Bryson RW, de Oca ANM, Jaeger JR, Riddle BR. Elucidation of cryptic diversity in a widespread nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution 2010; 64:2315-30. [PMID: 20394664 DOI: 10.1111/j.1558-5646.2010.01014.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We investigate the evolutionary history of the wide-ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range-wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well-supported clades, five of which correspond to well-defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate-driven range shifts, have all played a role in the historical diversification of H. arenicolor.
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Affiliation(s)
- Robert W Bryson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada 89154, USA.
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25
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Spinks PQ, Thomson RC, Barley AJ, Newman CE, Bradley Shaffer H. Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9184-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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WIENS JOHNJ, KUCZYNSKI CAITLINA, STEPHENS PATRICKR. Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01342.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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GIBBS HLISLE, DIAZ JOSE. Identification of single copy nuclear DNA markers for North American pit vipers. Mol Ecol Resour 2009; 10:177-80. [DOI: 10.1111/j.1755-0998.2009.02707.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- H. LISLE GIBBS
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH 43210‐1293, USA
| | - JOSE DIAZ
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH 43210‐1293, USA
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Pinho C, Rocha S, Carvalho BM, Lopes S, Mourão S, Vallinoto M, Brunes TO, Haddad CFB, Gonçalves H, Sequeira F, Ferrand N. New primers for the amplification and sequencing of nuclear loci in a taxonomically wide set of reptiles and amphibians. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9126-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Piskurek O, Nishihara H, Okada N. The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis. Gene 2008; 441:111-8. [PMID: 19118606 DOI: 10.1016/j.gene.2008.11.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 11/18/2008] [Accepted: 11/25/2008] [Indexed: 02/01/2023]
Abstract
Transposable elements have been characterized in a number of vertebrates, including whole genomes of mammals, birds, and fishes. The Anolis carolinensis draft assembly provides the first opportunity to study retroposons in a reptilian genome. Here, we identified and reconstructed a number of retroposons based on database searches: Five Sauria short interspersed element (SINE) subfamilies, 5S-Sauria SINE chimeras, Anolis Bov-B long interspersed element (LINE), Anolis SINE 2, Anolis LINE 2, Anolis LINE 1, Anolis CR 1, and a chromodomain-containing Ty3/Gypsy LTR element. We focused on two SINE families (Anolis Sauria SINE and Anolis SINE 2) and their partner LINE families (Anolis Bov-B LINE and Anolis LINE 2). We demonstrate that each SINE/LINE pair is distributed similarly and predict that the retrotransposition of evolutionarily younger Sauria SINE members is via younger Bov-B LINE members while a correlation also exists between their respective evolutionarily older SINE/LINE members. The evolutionarily youngest Sauria SINE sequences evolved as part of novel rolling-circle transposons. The evolutionary time frame when Bov-B LINEs and Sauria SINEs were less active in their retrotransposition is characterized by a high retrotransposition burst of Anolis SINE 2 and Anolis LINE 2 elements. We also characterized the first full-length chromoviral LTR element in amniotes (Amn-ichi). This newly identified chromovirus is widespread in the Anolis genome and has been very well preserved, indicating that it is still active. Transposable elements in the Anolis genome account for approximately 20% of the total DNA sequence, whereas the proportion is more than double that in many mammalian genomes in which such elements have important biological functions. Nevertheless, 20% transposable element coverage is sufficient to predict that Anolis retroposons and other mobile elements also may have biologically and evolutionarily relevant functions. The new SINEs and LINEs and other ubiquitous genomic elements characterized in the Anolis genome will prove very useful for studies in comparative genomics, phylogenetics, and functional genetics.
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Affiliation(s)
- Oliver Piskurek
- Department of Biological Sciences, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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30
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Dolman G. Evidence for differential assortative female preference in association with refugial isolation of rainbow skinks in Australia's tropical rainforests. PLoS One 2008; 3:e3499. [PMID: 18958149 PMCID: PMC2567034 DOI: 10.1371/journal.pone.0003499] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 09/22/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Divergence driven by female preference can give rise to pre-mating isolation more rapidly than post-mating isolation can evolve through the accumulation of allelic incompatibilities. Moreover pre-mating isolation may be more effective at maintaining morphological differentiation between divergent populations. In the context of Australian rainforest endemic skinks that were historically subjected to refugial isolation, this study examined the following predictions: 1) that assortative female preference is associated with more recent divergence of southern C. rubrigularis (S-RED) and C. rhomboidalis (BLUE), but not with deeply divergent S-RED and northern C. rubrigularis (N-RED); and 2) that upon secondary contact, morphological differentiation is maintained between S-RED and BLUE, whereas N-RED and S-RED remain morphogically indistinguishable. PRINCIPAL FINDINGS Female preference trials found no evidence for assortative female preference between N-RED and S-RED, supporting a previous genetic hybrid zone study which inferred post-mating but no pre-mating isolation. In contrast there is evidence for assortative female preference between S-RED and BLUE, with BLUE females preferring to associate with BLUE males, but S-RED females showing no preference. Multi-locus coalescent analyses, used to estimate post-divergence gene-flow between proximally located S-RED and BLUE populations, rejected zero gene-flow from BLUE to S-RED and thus RED and BLUE have maintained morphological differentiation despite secondary contact. Morphometric analyses confirmed a lack of morphological divergence between N-RED and S-RED and established that BLUE is morphologically divergent from RED in traits other than throat colour. CONCLUSIONS/SIGNIFICANCE Long-term isolation has been sufficient to generate post-mating isolation but no morphological divergence between N-RED and S-RED. In contrast, greater morphological differentiation is associated with evidence for assortative female preference between more recently diverged S-RED and BLUE. Combined with previous estimates of lineage-wide gene flow, these results are consistent with the suggestion that assortative female preference is more effective than post-mating isolation in maintaining morphological differentiation between divergent populations.
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Affiliation(s)
- Gaynor Dolman
- Australian National Wildlife Collection, CSIRO Sustainable Ecosystems, Canberra, Australia.
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31
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Gamble T, Berendzen PB, Bradley Shaffer H, Starkey DE, Simons AM. Species limits and phylogeography of North American cricket frogs (Acris: Hylidae). Mol Phylogenet Evol 2008; 48:112-25. [DOI: 10.1016/j.ympev.2008.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 02/22/2008] [Accepted: 03/10/2008] [Indexed: 10/22/2022]
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32
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Zarza E, Reynoso VH, Emerson BC. Diversification in the northern neotropics: mitochondrial and nuclear DNA phylogeography of the iguanaCtenosaura pectinataand related species. Mol Ecol 2008; 17:3259-75. [PMID: 18564087 DOI: 10.1111/j.1365-294x.2008.03826.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Eugenia Zarza
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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34
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Benavides E, Baum R, McClellan D, Sites JW. Molecular phylogenetics of the lizard genus Microlophus (squamata:tropiduridae): aligning and retrieving indel signal from nuclear introns. Syst Biol 2008; 56:776-97. [PMID: 17907054 DOI: 10.1080/10635150701618527] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylogenetic relationships in the South American "lava lizards" (genus Microlophus) and describe a strategy for aligning noncoding sequences that accounts for differences in tempo and class of mutational events. We focus on seven nuclear introns that vary in size and frequency of multibase length mutations (i.e., indels) and present a manual alignment strategy that incorporates insertions and deletions (indels) for each intron. Our method is based on mechanistic explanations of intron evolution that does not require a guide tree. We also use a progressive alignment algorithm (Probabilistic Alignment Kit; PRANK) and distinguishes insertions from deletions and avoids the "gapcost" conundrum. We describe an approach to selecting a guide tree purged of ambiguously aligned regions and use this to refine PRANK performance. We show that although manual alignment is successful in finding repeat motifs and the most obvious indels, some regions can only be subjectively aligned, and there are limits to the size and complexity of a data matrix for which this approach can be taken. PRANK alignments identified more parsimony-informative indels while simultaneously increasing nucleotide identity in conserved sequence blocks flanking the indel regions. When comparing manual and PRANK with two widely used methods (CLUSTAL, MUSCLE) for the alignment of the most length-variable intron, only PRANK recovered a tree congruent at deeper nodes with the combined data tree inferred from all nuclear gene regions. We take this concordance as an objective function of alignment quality and present a strongly supported phylogenetic hypothesis for Microlophus relationships. From this hypothesis we show that (1) a coded indel data partition derived from the PRANK alignment contributed significantly to nodal support and (2) the indel data set permitted detection of significant conflict between mitochondrial and nuclear data partitions, which we hypothesize arose from secondary contact of distantly related taxa, followed by hybridization and mtDNA introgression.
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Affiliation(s)
- Edgar Benavides
- Department of Integrative Biology, Brigham Young University, Provo, UT, USA.
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35
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Dolman G, Moritz C. A MULTILOCUS PERSPECTIVE ON REFUGIAL ISOLATION AND DIVERGENCE IN RAINFOREST SKINKS (CARLIA). Evolution 2007. [DOI: 10.1111/j.0014-3820.2006.tb01138.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gaynor Dolman
- School of Integrative Biology, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720–3160
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36
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Dolman G, Moritz C. A MULTILOCUS PERSPECTIVE ON REFUGIAL ISOLATION AND DIVERGENCE IN RAINFOREST SKINKS (CARLIA). Evolution 2006. [DOI: 10.1554/05-487.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Whiting AS, Sites JW, Pellegrino KCM, Rodrigues MT. Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae). Mol Phylogenet Evol 2005; 38:719-30. [PMID: 16364664 DOI: 10.1016/j.ympev.2005.11.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2005] [Revised: 11/04/2005] [Accepted: 11/04/2005] [Indexed: 11/22/2022]
Abstract
The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many fields. The recent flurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under different optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, specifically complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313).
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Affiliation(s)
- Alison S Whiting
- Department of Integrative Biology and M. L. Bean Museum, Brigham Young University, Provo, UT 84602, USA.
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Hoskin CJ, Higgie M, McDonald KR, Moritz C. Reinforcement drives rapid allopatric speciation. Nature 2005; 437:1353-6. [PMID: 16251964 DOI: 10.1038/nature04004] [Citation(s) in RCA: 295] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Accepted: 07/11/2005] [Indexed: 11/09/2022]
Abstract
Allopatric speciation results from geographic isolation between populations. In the absence of gene flow, reproductive isolation arises gradually and incidentally as a result of mutation, genetic drift and the indirect effects of natural selection driving local adaptation. In contrast, speciation by reinforcement is driven directly by natural selection against maladaptive hybridization. This gives individuals that choose the traits of their own lineage greater fitness, potentially leading to rapid speciation between the lineages. Reinforcing natural selection on a population of one of the lineages in a mosaic contact zone could also result in divergence of the population from the allopatric range of its own lineage outside the zone. Here we test this with molecular data, experimental crosses, field measurements and mate choice experiments in a mosaic contact zone between two lineages of a rainforest frog. We show that reinforcing natural selection has resulted in significant premating isolation of a population in the contact zone not only from the other lineage but also, incidentally, from the closely related main range of its own lineage. Thus we show the potential for reinforcement to drive rapid allopatric speciation.
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Affiliation(s)
- Conrad J Hoskin
- School of Integrative Biology, University of Queensland, St Lucia, Queensland 4072, Australia.
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Hickerson MJ, Dolman G, Moritz C. Comparative phylogeographic summary statistics for testing simultaneous vicariance. Mol Ecol 2005; 15:209-23. [PMID: 16367841 DOI: 10.1111/j.1365-294x.2005.02718.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Testing for simultaneous vicariance across comparative phylogeographic data sets is a notoriously difficult problem hindered by mutational variance, the coalescent variance, and variability across pairs of sister taxa in parameters that affect genetic divergence. We simulate vicariance to characterize the behaviour of several commonly used summary statistics across a range of divergence times, and to characterize this behaviour in comparative phylogeographic datasets having multiple taxon-pairs. We found Tajima's D to be relatively uncorrelated with other summary statistics across divergence times, and using simple hypothesis testing of simultaneous vicariance given variable population sizes, we counter-intuitively found that the variance across taxon pairs in Nei and Li's net nucleotide divergence (pi(net)), a common measure of population divergence, is often inferior to using the variance in Tajima's D across taxon pairs as a test statistic to distinguish ancient simultaneous vicariance from variable vicariance histories. The opposite and more intuitive pattern is found for testing more recent simultaneous vicariance, and overall we found that depending on the timing of vicariance, one of these two test statistics can achieve high statistical power for rejecting simultaneous vicariance, given a reasonable number of intron loci (> 5 loci, 400 bp) and a range of conditions. These results suggest that components of these two composite summary statistics should be used in future simulation-based methods which can simultaneously use a pool of summary statistics to test comparative the phylogeographic hypotheses we consider here.
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Affiliation(s)
- M J Hickerson
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, California 94720-3160, USA.
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