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Magalhães RF, K S Ramos E, Bandeira LN, Ferreira JS, Werneck FP, Anciães M, Bruschi DP. Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas. Mol Phylogenet Evol 2024; 190:107959. [PMID: 37918682 DOI: 10.1016/j.ympev.2023.107959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.
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Affiliation(s)
- Rafael F Magalhães
- Department of Natural Sciences, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio, 70, São João del-Rei, MG 36301-160, Brazil; Postgraduate Programme in Zoology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG 31270-010, Brazil.
| | - Elisa K S Ramos
- Faculty of Philosophy and Natural Sciences, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland.
| | - Lucas N Bandeira
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Johnny S Ferreira
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
| | - Fernanda P Werneck
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Marina Anciães
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Daniel P Bruschi
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
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McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.530646. [PMID: 36993716 PMCID: PMC10055050 DOI: 10.1101/2023.03.15.530646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.
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Affiliation(s)
- J. F. McLaughlin
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Celestino Aguilar
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Justin M. Bernstein
- Department of Biology, Villanova University, Villanova, PA, USA
- Center for Genomics, University of Kansas, Lawrence, KS, USA
| | - Wayra G. Navia-Gine
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA, USA
| | | | | | | | - Rugger Collier
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Anshule Takyar
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Sidney J. Vong
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | | | - Robert Driver
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Jose R. Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Luis F. De León
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | | | | | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
| | - Kinsey M. Brock
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Matthew J. Miller
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
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3
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Jameson TJ, Streicher JW, Manuelli L, Head JJ, Smith EN. Miniaturization in Direct-Developing Frogs from Mexico with the Description of Six New Species. HERPETOLOGICAL MONOGRAPHS 2022. [DOI: 10.1655/0733-1347-36.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Tom J.M. Jameson
- Department of Zoology and University Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jeffrey W. Streicher
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas at Arlington, 701 S. Nedderman Drive, Arlington, TX 76019, USA
| | - Luigi Manuelli
- Department of Life Sciences, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Jason J. Head
- Department of Zoology and University Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Eric N. Smith
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas at Arlington, 701 S. Nedderman Drive, Arlington, TX 76019, USA
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Populational Differentiation in Boana bischoffi (Anura, Hylidae): Revisiting the Issue Using Molecular, Morphological, and Acoustic Data. J HERPETOL 2022. [DOI: 10.1670/20-121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Clark MI, Bradburd GS, Akopyan M, Vega A, Rosenblum EB, Robertson JM. Genetic isolation by distance underlies colour pattern divergence in red-eyed treefrogs (Agalychnis callidryas). Mol Ecol 2022; 31:1666-1681. [PMID: 35034406 PMCID: PMC8923152 DOI: 10.1111/mec.16350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond to individual measures of colour pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that colour-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance indicates that colour-pattern variation was either retained through other processes such as ancestral colour polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on colour pattern at a small geographic scale.
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Affiliation(s)
- Meaghan I. Clark
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Gideon S. Bradburd
- Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Maria Akopyan
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Jeanne M. Robertson
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Herpetology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
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Booker WW, Gerhardt HC, Lemmon AR, Ptacek MB, Hassinger ATB, Schul J, Lemmon EM. The complex history of genome duplication and hybridization in North American gray treefrogs. Mol Biol Evol 2021; 39:6427635. [PMID: 34791374 PMCID: PMC8826561 DOI: 10.1093/molbev/msab316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.
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Affiliation(s)
- William W Booker
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
| | - H Carl Gerhardt
- Division of Biological Sciences, University of Missouri, Columbia, USA, 65211-7400, MO
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, 32306-4192, USA
| | - Margaret B Ptacek
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Alyssa T B Hassinger
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Johannes Schul
- Division of Biological Sciences, University of Missouri, Columbia, USA, 65211-7400, MO
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
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7
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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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García-Rodríguez A, Guarnizo CE, Crawford AJ, Garda AA, Costa GC. Idiosyncratic responses to drivers of genetic differentiation in the complex landscapes of Isthmian Central America. Heredity (Edinb) 2021; 126:251-265. [PMID: 33051599 PMCID: PMC8027409 DOI: 10.1038/s41437-020-00376-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/08/2022] Open
Abstract
Isthmian Central America (ICA) is one of the most biodiverse regions in the world, hosting an exceptionally high number of species per unit area. ICA was formed <25 million years ago and, consequently, its biotic assemblage is relatively young and derived from both colonization and in situ diversification. Despite intensive taxonomic work on the local fauna, the potential forces driving genetic divergences and ultimately speciation in ICA remain poorly studied. Here, we used a landscape genetics approach to test whether isolation by distance, topography, habitat suitability, or environment drive the genetic diversity of the regional frog assemblage. To this end, we combined data on landscape features and mitochondrial DNA sequence variation for nine codistributed amphibian species with disparate life histories. In five species, we found that at least one of the factors tested explained patterns of genetic divergence. However, rather than finding a general pattern, our results revealed idiosyncratic responses to historical and ecological processes, indicating that intrinsic life-history characteristics may determine the effect of different drivers of isolation on genetic divergence in ICA. Our work also suggests that the convergence of several factors promoting isolation among populations over a heterogeneous landscape might maximize genetic differentiation, despite short geographical distances. In conclusion, abiotic factors and geographical features have differentially affected the genetic diversity across the regional frog assemblage. Much more complex models (i.e., considering multiple drivers), beyond simple vicariance of Caribbean and Pacific lineages, are needed to better understand the evolutionary history of ICA's diverse biotas.
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Affiliation(s)
- Adrián García-Rodríguez
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, AP 70-153, Ciudad Universitaria, CP, 04510, Ciudad de México, México.
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, 59078-900, RN, Brazil.
- Escuela de Biología, Universidad de Costa Rica, San Pedro, 11501-2060, San José, Costa Rica.
| | - Carlos E Guarnizo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Andrew J Crawford
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Panamá, Republic of Panama
| | - Adrian A Garda
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, 59078-900, RN, Brazil
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL, 36124, USA
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Magalhães RF, Lemes P, Santos MTT, Mol RM, Ramos EKS, Oswald CB, Pezzuti TL, Santos FR, Brandão RA, Garcia PCA. Evidence of introgression in endemic frogs from the campo rupestre contradicts the reduced hybridization hypothesis. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The campo rupestre ecosystem is considered an old, climatically buffered, infertile landscape. As a consequence, long-term isolation is thought to have played an important role in the diversification of its biota. Here, we tested for hybridization between two endemic leaf frogs from the campo rupestre. We used sequence markers and coalescent models to verify haplotype sharing between the species, to test the existence and direction of gene flow, and to reconstruct the spatiotemporal dynamics of gene flow. Additionally, ecological niche modelling (ENM) was used to assess for potential co-occurrence by overlapping the climatic niche of these species since the middle Pleistocene. We found haplotype sharing and/or lack of differentiation in four nuclear fragments, one of them associated with introgression. The coalescent models support introgressive hybridization unidirectionally from Pithecopus megacephalus to P. ayeaye, occurring ~300 kya. ENM corroborates this scenario, revealing areas of potential environmental niche overlap for the species at about 787 kya. These results contradict the expectation of reduced hybridization, while ENM suggests climatic fluctuation rather than stability for the two species. The reduced hybridization hypothesis needs to be further investigated because our results suggest that it may have unrealistic premises at least for animals.
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Affiliation(s)
- Rafael F Magalhães
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, São João del-Rei, Minas Gerais, Brazil
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Priscila Lemes
- Laboratorio de Ecologia e Conservação, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Marcus Thadeu T Santos
- Programa de Pós-Graduação em Zoologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, Brazil
| | - Rafael M Mol
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elisa K S Ramos
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Caroline B Oswald
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago L Pezzuti
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fabrício R Santos
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Reuber A Brandão
- Laboratório de Fauna e Unidades de Conservação, Departamento de Engenharia Florestal, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Paulo C A Garcia
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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10
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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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11
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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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Puschendorf R, Wallace M, Chavarría MM, Crawford AJ, Wynne F, Knight M, Janzen DH, Hallwachs W, Palmer C, Price SJ. Cryptic diversity and ranavirus infection of a critically endangered Neotropical frog before and after population collapse. Anim Conserv 2019. [DOI: 10.1111/acv.12498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- R. Puschendorf
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - M. Wallace
- Department of Zoology University of Oxford Oxford UK
| | - M. M. Chavarría
- Programa de Investigación Área de Conservación Guanacaste Liberia Costa Rica
| | - A. J. Crawford
- Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
| | - F. Wynne
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - M. Knight
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - D. H. Janzen
- Department of Biology University of Pennsylvania Philadelphia PA USA
| | - W. Hallwachs
- Department of Biology University of Pennsylvania Philadelphia PA USA
| | - C.V. Palmer
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - S. J. Price
- UCL Genetics Institute London UK
- Institute of Zoology, ZSL London UK
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13
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Cryer J, Wynne F, Price SJ, Puschendorf R. Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae). Zookeys 2019; 838:49-69. [PMID: 31048968 PMCID: PMC6477815 DOI: 10.3897/zookeys.838.29635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.
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Affiliation(s)
- James Cryer
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
| | - Felicity Wynne
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
| | - Stephen J. Price
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UKUCL Genetics InstituteLondonUnited Kingdom
- Institute of Zoology, ZSL, Regents Park, London NW1 4RY, UKInstitute of Zoology, ZSLLondonUnited Kingdom
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
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14
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Nascimento AC, Chaves AV, Leite FSF, Eterovick PC, dos Santos FR. Past vicariance promoting deep genetic divergence in an endemic frog species of the Espinhaço Range in Brazil: The historical biogeography of Bokermannohyla saxicola (Hylidae). PLoS One 2018; 13:e0206732. [PMID: 30395633 PMCID: PMC6218059 DOI: 10.1371/journal.pone.0206732] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 10/18/2018] [Indexed: 11/29/2022] Open
Abstract
The highland endemic frog Bokermannohyla saxicola occurs within the Espinhaço Range, the most extensive and continuous orogenic belt of the Brazilian territory, located in southeastern Brazil. We used mitochondrial DNA markers to test for spatial structure, to investigate the likely influence of past vicariant events, to evaluate demographic dynamics along the species range, and to understand the role of habitat discontinuities in promoting connectivity and diversity along the range. We found four major monophyletic lineages, each one associated with distinct mountain tops. The divergence time found between the four main clades clearly pre-dated the Pleistocene, except for the most recent separation. We observed no signs of population expansion for most of the sampling sites along the range, and a higher genetic diversity in the most continuous and central highland plateau, compared to smaller marginal regions. The Espinhaço Range harbors four deeply divergent lineages of B. saxicola within areas restricted by barriers for millions of years. These relatively isolated populations were kept apart by discontinuities represented by lowland habitats between mountain tops. Most of the lineage divergences occurred earlier than the Pleistocene, thus they cannot be solely explained by climatic oscillations of this epoch. However, within-lineage divergence times were all dated from the Pleistocene, suggesting an important effect in population dynamics. We also suggest that some marginal populations like those from Serra Negra and Serra de Itacambira can be the result of recent colonization events. Finally, in the southern Espinhaço region, the most continuous central highland area shows greater genetic diversity than the marginal discontinuous areas, where we have also observed a significant correlation between genetic and geographic distances. Bokermannohyla saxicola is a good model to study the biogeography of the Espinhaço Range because its high genetic structure reflects ancient as well as recent geological/climatic events, with important implications for conservation.
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Affiliation(s)
| | - Anderson Vieira Chaves
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Manejo e Conservação de Ecossistemas Naturais e Agrários, Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, campus Florestal, Minas Gerais, Brazil
- * E-mail: (AVC); (FRS)
| | - Felipe Sá Fortes Leite
- Programa de Pós-Graduação em Manejo e Conservação de Ecossistemas Naturais e Agrários, Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, campus Florestal, Minas Gerais, Brazil
| | - Paula Cabral Eterovick
- Programa de Pós Graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
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Testing Hypotheses of Diversification in Panamanian Frogs and Freshwater Fishes Using Hierarchical Approximate Bayesian Computation with Model Averaging. DIVERSITY 2018. [DOI: 10.3390/d10040120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.
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Su-Keene EJ, Bonilla MM, Padua MV, Zeh DW, Zeh JA. Simulated climate warming and mitochondrial haplogroup modulate testicular small non-coding RNA expression in the neotropical pseudoscorpion, Cordylochernes scorpioides. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy027. [PMID: 30595847 PMCID: PMC6305488 DOI: 10.1093/eep/dvy027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/22/2018] [Accepted: 10/21/2018] [Indexed: 06/01/2023]
Abstract
Recent theory suggests that tropical terrestrial arthropods are at significant risk from climate warming. Metabolic rate in such ectothermic species increases exponentially with environmental temperature, and a small temperature increase in a hot environment can therefore have a greater physiological impact than a large temperature increase in a cool environment. In two recent studies of the neotropical pseudoscorpion, Cordylochernes scorpioides, simulated climate warming significantly decreased survival, body size and level of sexual dimorphism. However, these effects were minor compared with catastrophic consequences for male fertility and female fecundity, identifying reproduction as the life stage most vulnerable to climate warming. Here, we examine the effects of chronic high-temperature exposure on epigenetic regulation in C. scorpioides in the context of naturally occurring variation in mitochondrial DNA. Epigenetic mechanisms, including DNA methylation, histone modifications and small non-coding RNA (sncRNA) expression, are particularly sensitive to environmental factors such as temperature, which can induce changes in epigenetic states and phenotypes that may be heritable across generations. Our results indicate that exposure of male pseudoscorpions to elevated temperature significantly altered the expression of >60 sncRNAs in testicular tissue, specifically microRNAs and piwi-interacting RNAs. Mitochondrial haplogroup was also a significant factor influencing both sncRNAs and mitochondrial gene expression. These findings demonstrate that chronic heat stress causes changes in epigenetic profiles that may account for reproductive dysfunction in C. scorpioides males. Moreover, through its effects on epigenetic regulation, mitochondrial DNA polymorphism may provide the potential for an adaptive evolutionary response to climate warming.
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Affiliation(s)
- Eleanor J Su-Keene
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Educational Leadership and Research Methodology, Florida Atlantic University, Boca Raton, FL, USA
| | - Melvin M Bonilla
- Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Michael V Padua
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - David W Zeh
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, Reno, NV, USA
| | - Jeanne A Zeh
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, Reno, NV, USA
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17
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Waddell EH, Crotti M, Lougheed SC, Cannatella DC, Elmer KR. Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical Pristimantis leaf litter frogs. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1503202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Emily H. Waddell
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, EH26 0QB, UK
| | - Marco Crotti
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Stephen C. Lougheed
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - David C. Cannatella
- Section of Integrative Biology and Texas Memorial Museum, University of Texas, Austin, TX 78712, USA
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
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18
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More sex chromosomes than autosomes in the Amazonian frog Leptodactylus pentadactylus. Chromosoma 2018; 127:269-278. [PMID: 29372309 DOI: 10.1007/s00412-018-0663-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process.
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19
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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de Magalhães RF, Lemes P, Camargo A, Oliveira U, Brandão RA, Thomassen H, Garcia PCDA, Leite FSF, Santos FR. Evolutionarily significant units of the critically endangered leaf frog Pithecopus ayeaye (Anura, Phyllomedusidae) are not effectively preserved by the Brazilian protected areas network. Ecol Evol 2017; 7:8812-8828. [PMID: 29177033 PMCID: PMC5689491 DOI: 10.1002/ece3.3261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/29/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Protected areas (PAs) are essential for biodiversity conservation, but their coverage is considered inefficient for the preservation of all species. Many species are subdivided into evolutionarily significant units (ESUs) and the effectiveness of PAs in protecting them needs to be investigated. We evaluated the usefulness of the Brazilian PAs network in protecting ESUs of the critically endangered Pithecopus ayeaye through ongoing climate change. This species occurs in a threatened mountaintop ecosystem known as campos rupestres. We used multilocus DNA sequences to delimit geographic clusters, which were further validated as ESUs with a coalescent approach. Ecological niche modeling was used to estimate spatial changes in ESUs' potential distributions, and a gap analysis was carried out to evaluate the effectiveness of the Brazilian PAs network to protect P. ayeaye in the face of climate changes. We tested the niche overlap between ESUs to gain insights for potential management alternatives for the species. Pithecopus ayeaye contains at least three ESUs isolated in distinct mountain regions, and one of them is not protected by any PA. There are no climatic niche differences between the units, and only 4% of the suitable potential area of the species is protected in present and future projections. The current PAs are not effective in preserving the intraspecific diversity of P. ayeaye in its present and future range distributions. The genetic structure of P. ayeaye could represent a typical pattern in campos rupestres endemics, which should be considered for evaluating its conservation status.
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Affiliation(s)
- Rafael Félix de Magalhães
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
- Programa de Desarrollo UniversitarioCentro Universitario de RiveraUniversidad de la República – UdelaRRiveraUruguay
| | - Priscila Lemes
- Laboratório de HerpetologiaDepartamento de ZoologiaInstituto de Biociências de Rio ClaroUniversidade Estadual “Júlio Mesquita Filho” – UNESPRio ClaroSão PauloBrasil
| | - Arley Camargo
- Programa de Desarrollo UniversitarioCentro Universitario de RiveraUniversidad de la República – UdelaRRiveraUruguay
| | - Ubirajara Oliveira
- Centro de Sensoriamento RemotoInstituto de GeociênciasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Reuber Albuquerque Brandão
- Laboratório de Fauna e Unidades de ConservaçãoDepartamento de Engenharia FlorestalFaculdade de TecnologiaUniversidade de Brasília – UnBBrasíliaDistrito FederalBrasil
| | - Hans Thomassen
- Graduação em Ciências BiológicasInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Paulo Christiano de Anchietta Garcia
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Felipe Sá Fortes Leite
- Laboratório SagaranaInstituto de Ciências Biológicas e da SaúdeUniversidade Federal de Viçosa – UFVFlorestalMinas GeraisBrasil
| | - Fabrício Rodrigues Santos
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
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21
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Gehara M, Garda AA, Werneck FP, Oliveira EF, Fonseca EM, Camurugi F, Magalhães FDM, Lanna FM, Sites JW, Marques R, Silveira‐Filho R, São Pedro VA, Colli GR, Costa GC, Burbrink FT. Estimating synchronous demographic changes across populations using
hABC
and its application for a herpetological community from northeastern Brazil. Mol Ecol 2017; 26:4756-4771. [DOI: 10.1111/mec.14239] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/30/2017] [Accepted: 07/02/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Marcelo Gehara
- Department of Herpetology American Museum of Natural History New York NY USA
| | - Adrian A. Garda
- Departamento de Botânica e Zoologia Centro de Biociências Universidade Federal do Rio Grande do Norte Lagoa Nova Natal RN Brazil
| | - Fernanda P. Werneck
- Coordenação de Biodiversidade Programa de Coleções Científicas Biológicas Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus AM Brazil
| | - Eliana F. Oliveira
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências Biológicas e da Saúde Laboratório de Zoologia Cidade Universitária Universidade Federal do Mato Grosso do Sul Campo Grand MS Brazil
| | - Emanuel M. Fonseca
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Felipe Camurugi
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Felipe de M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Flávia M. Lanna
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum Brigham Young University Provo UT USA
| | - Ricardo Marques
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Ricardo Silveira‐Filho
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Vinícius A. São Pedro
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências da Natureza Universidade Federal de São Carlos Buri SP Brazil
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Gabriel C. Costa
- Department of Biology Auburn University at Montgomery Montgomery AL USA
| | - Frank T. Burbrink
- Department of Herpetology American Museum of Natural History New York NY USA
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22
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Genetic evidence supporting the taxonomic separation of the Arabian and Northwest African subspecies of the desert hedgehog ( Paraechinus aethiopicus ). Gene 2017; 620:54-65. [DOI: 10.1016/j.gene.2017.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/30/2017] [Accepted: 04/07/2017] [Indexed: 11/21/2022]
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23
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Evolutionary processes in populations of Cryptosporidium inferred from gp60 sequence data. Parasitol Res 2017; 116:1855-1861. [PMID: 28502018 DOI: 10.1007/s00436-017-5459-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
Abstract
Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure. Here, we analyzed the genetic variation in time and space within two putative populations of Cryptosporidium in New Zealand to infer the processes behind the patterns of sequence polymorphism. Analyses using Tajima's D, Fu, and Li's D* and F* tests show significant departures from neutrality in some populations and indicate the selective maintenance of alleles within some populations. Demographic analyses showed distortions in the pattern of the genetic variability caused by high recombination rates and population expansion, which was observed in case notification data. Our results showed that processes acting on populations that have similar effects can be distinguished from one another and multiple processes can be detected acting at the same time. These results are significant for prediction of the parasite dynamics and potential mechanisms of long-term changes in the risk of cryptosporidiosis in humans.
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24
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Vertucci S, Pepper M, Edwards DL, Roberts JD, Mitchell N, Keogh JS. Evolutionary and natural history of the turtle frog, Myobatrachus gouldii, a bizarre myobatrachid frog in the southwestern Australian biodiversity hotspot. PLoS One 2017; 12:e0173348. [PMID: 28296914 PMCID: PMC5351994 DOI: 10.1371/journal.pone.0173348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/20/2017] [Indexed: 11/19/2022] Open
Abstract
Southwest Australia (SWA) is a global biodiversity hotspot and a centre of diversity and endemism for the Australo-Papuan myobatrachid frogs. Myobatrachus gouldii (the turtle frog) has a highly derived morphology associated with its forward burrowing behaviour, largely subterranean habit, and unusual mode of reproduction. Its sister genera Metacrinia and Arenophryne have restricted distributions in Western Australia with significant phylogeographic structure, leading to the recent description of a new species in the latter. In contrast, Myobatrachus is distributed widely throughout SWA over multiple climatic zones, but little is known of its population structure, geographic variation in morphology, or reproduction. We generated molecular and morphological data to test for genetic and morphological variation, and to assess whether substrate specialisation in this species may have led to phylogeographic structuring similar to that of other plant and animal taxa in SWA. We assembled sequence data for one mitochondrial and four nuclear DNA loci (3628 base pairs) for 42 turtle frogs sampled throughout their range. Likelihood phylogenetic analyses revealed shallow phylogeographic structure in the mtDNA locus (up to 3.3% genetic distance) and little variation in three of the four nDNA loci. The mtDNA haplotype network suggests five geographically allopatric groups, with no shared haplotypes between regions. These geographic patterns are congruent with several other SWA species, with genetic groups restricted to major hydrological divisions, the Swan Coastal Plain, and the Darling Scarp. The geographically structured genetic groups showed no evidence of significant morphological differentiation (242 individuals), and there was little sexual size dimorphism, but subtle differences in reproductive traits suggest more opportunistic breeding in lower rainfall zones. Call data were compared to sister genera Metacrinia and Arenophryne and found to be highly conservative across the three genera. Like many taxa in SWA, topographic variation and Plio-Pleistocene arid fluctuations likely were historic drivers of diversification in M. gouldii.
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Affiliation(s)
- Samantha Vertucci
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
| | - Mitzy Pepper
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
| | - Danielle L. Edwards
- School of Natural Sciences, University of California, Merced, CA, United States of America
| | - J. Dale Roberts
- Centre of Excellence in Natural Resource Management, The University of Western Australia, Albany, Western Australia
| | - Nicola Mitchell
- School of Animal Biology, The University of Western Australia, Crawley, Australia
| | - J. Scott Keogh
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
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Grismer LL, Wood PL, Aowphol A, Cota M, Grismer MS, Murdoch ML, Aguilar C, Grismer JL. Out of Borneo, again and again: biogeography of the Stream Toad genusAnsoniaStoliczka (Anura: Bufonidae) and the discovery of the first limestone cave-dwelling species. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12886] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Lee Grismer
- Herpetology Laboratory; Department of Biology; La Sierra University; 4500 Riverwalk Parkway Riverside CA 92515 USA
| | - Perry L. Wood
- Department of Biology; Brigham Young University; 150 East Bulldog Boulevard Provo UT 84602 USA
| | - Anchalee Aowphol
- Department of Zoology; Faculty of Science; Kasetsart University; Bangkok 10900 Thailand
| | - Michael Cota
- Natural History Museum; National Science Museum, Thailand; Technopolis Khlong 5 Khlong Luang Pathum Thani 12120 Thailand
| | - Marta S. Grismer
- Herpetology Laboratory; Department of Biology; La Sierra University; 4500 Riverwalk Parkway Riverside CA 92515 USA
| | - Matthew L. Murdoch
- Herpetology Laboratory; Department of Biology; La Sierra University; 4500 Riverwalk Parkway Riverside CA 92515 USA
| | - Cesar Aguilar
- Department of Biology; Brigham Young University; 150 East Bulldog Boulevard Provo UT 84602 USA
| | - Jesse L. Grismer
- Department of Biological Sciences; Auburn University; 331 Funchess Hall Auburn AL 36849 USA
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Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB. Phylogeography and species delimitation in convict cichlids (Cichlidae:Amatitlania): implications for taxonomy and Plio-Pleistocene evolutionary history in Central America. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Justin C. Bagley
- Evolutionary Ecology Laboratories; Department of Biology; Brigham Young University; Provo UT 84602 USA
| | - Wilfredo A. Matamoros
- Facultad de Ciencias Biológicas, Museo de Zoología; Colección de Ictiología; Universidad de Ciencias y Artes de Chiapas; CP 29039 Tuxtla Gutierrez Chiapas México
| | - Caleb D. McMahan
- Museum of Natural Science (Ichthyology); Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605 USA
| | - Michael Tobler
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
| | - Prosanta Chakrabarty
- Museum of Natural Science (Ichthyology); Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | - Jerald B. Johnson
- Evolutionary Ecology Laboratories; Department of Biology; Brigham Young University; Provo UT 84602 USA
- Monte L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
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Davis LR, Klonoski K, Rutschow HL, Van Wijk KJ, Sun Q, Haribal MM, Saporito RA, Vega A, Rosenblum EB, Zamudio KR, Robertson JM. Host Defense Skin Peptides Vary with Color Pattern in the Highly Polymorphic Red-Eyed Treefrog. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Whitfield SM, Lips KR, Donnelly MA. Amphibian Decline and Conservation in Central America. COPEIA 2016. [DOI: 10.1643/ch-15-300] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Menezes L, Canedo C, Batalha-Filho H, Garda AA, Gehara M, Napoli MF. Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest. PLoS One 2016; 11:e0154626. [PMID: 27248688 PMCID: PMC4889069 DOI: 10.1371/journal.pone.0154626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/16/2016] [Indexed: 11/21/2022] Open
Abstract
We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.
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Affiliation(s)
- Lucas Menezes
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Clarissa Canedo
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica, Ecologia e Zoologia, Laboratório de Anfíbios e Répteis-LAR, Campus Universitário, Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Gehara
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
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Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin. PLoS One 2015; 10:e0143392. [PMID: 26600198 PMCID: PMC4658055 DOI: 10.1371/journal.pone.0143392] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 11/04/2015] [Indexed: 11/19/2022] Open
Abstract
Pluralistic approaches to taxonomy facilitate a more complete appraisal of biodiversity, especially the diversification of cryptic species. Although species delimitation has traditionally been based primarily on morphological differences, the integration of new methods allows diverse lines of evidence to solve the problem. Robber frogs (Pristimantis) are exemplary, as many of the species show high morphological variation within populations, but few traits that are diagnostic of species. We used a combination of DNA sequences from three mitochondrial genes, morphometric data, and comparisons of ecological niche models (ENMs) to infer a phylogenetic hypothesis for the Pristimantis acuminatus complex. Molecular phylogenetic analyses revealed a close relationship between three new species—Pristimantis enigmaticus sp. nov., P. limoncochensis sp. nov. and P. omeviridis sp. nov.—originally confused with Pristimantis acuminatus. In combination with morphometric data and geographic distributions, several morphological characters such as degree of tympanum exposure, skin texture, ulnar/tarsal tubercles and sexual secondary characters (vocal slits and nuptial pads in males) were found to be useful for diagnosing species in the complex. Multivariate discriminant analyses provided a successful classification rate for 83–100% of specimens. Discriminant analysis of localities in environmental niche space showed a successful classification rate of 75–98%. Identity tests of ENMs rejected hypotheses of niche equivalency, although not strongly because the high values on niche overlap. Pristimantis acuminatus and P. enigmaticus sp. nov. are distributed along the lowlands of central–southern Ecuador and northern Peru, in contrast with P. limoncochensis sp. nov. and P. omeviridis sp. nov., which are found in northern Ecuador and southern Colombia, up to 1200 m in the upper Amazon Basin. The methods used herein provide an integrated framework for inventorying the greatly underestimated biodiversity in Amazonia.
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Li Y, Wu X, Zhang H, Yan P, Xue H, Wu X. Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae). PLoS One 2015; 10:e0138757. [PMID: 26394403 PMCID: PMC4578928 DOI: 10.1371/journal.pone.0138757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/03/2015] [Indexed: 11/26/2022] Open
Abstract
Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.
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Affiliation(s)
- Yongmin Li
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- School of Life Sciences, Fuyang Teachers College, Fuyang, Anhui, China
| | - Xiaoyou Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Huabin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Xue
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xiaobing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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Gonçalves H, Maia-Carvalho B, Sousa-Neves T, García-París M, Sequeira F, Ferrand N, Martínez-Solano I. Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium. Mol Phylogenet Evol 2015; 93:363-79. [PMID: 26282950 DOI: 10.1016/j.ympev.2015.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
Recent investigations on the evolutionary history of the common midwife toad (Alytes obstetricans) revealed high levels of geographically structured genetic diversity but also a situation where delineation of major historical lineages and resolution of their relationships are much more complex than previously thought. We studied sequence variation in one mitochondrial and four nuclear genes throughout the entire distribution range of all recognized A. obstetricans subspecies to infer the evolutionary processes that shaped current patterns of genetic diversity and population subdivision. We found six divergent, geographically structured mtDNA haplogroups diagnosing population lineages, and varying levels of admixture in nuclear markers. Given the timeframe inferred for the splits between major lineages, the climatic and environmental changes that occurred during the Pleistocene seem to have shaped the diversification history of A. obstetricans. Survival of populations in allopatric refugia through the Ice Ages supports the generality of the "refugia-within-refugia" scenario for the Iberian Peninsula. However, lineages corresponding to subspecies A. o. almogavarii, A. o. pertinax, A. o. obstetricans, and A. o. boscai responded differently to Pleistocene climatic oscillations after diverging from a common ancestor. Alytes o. obstetricans expanded northward from a northern Iberian refugium through the western Pyrenees, leaving a signal of contrasting patterns of genetic diversity, with a single mtDNA haplotype north of the Pyrenees from SW France to Germany. Both A. o. pertinax and A. o. boscai are widespread and genetically diverse in Iberia, the latter comprising two divergent lineages with a long independent history. Finally, A. o. almogavarii is mostly restricted to the north-eastern corner of Iberia north of the Ebro river, with additional populations in a small region in south-eastern France. This taxon exhibits unparalleled levels of genetic diversity and little haplotype sharing with other lineages, suggesting a process of incipient speciation.
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Affiliation(s)
- H Gonçalves
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - B Maia-Carvalho
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal
| | - T Sousa-Neves
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Museu Paraense Emílio Goeldi, Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - M García-París
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - F Sequeira
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - N Ferrand
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal; Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - I Martínez-Solano
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, s/n, 13005 Ciudad Real, Spain; Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio, s/n, 41092 Sevilla, Spain
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Peloso PL, Frost DR, Richards SJ, Rodrigues MT, Donnellan S, Matsui M, Raxworthy CJ, Biju S, Lemmon EM, Lemmon AR, Wheeler WC. The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura, Microhylidae). Cladistics 2015; 32:113-140. [DOI: 10.1111/cla.12118] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2015] [Indexed: 02/02/2023] Open
Affiliation(s)
- Pedro L.V. Peloso
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
- Richard Gilder Graduate School American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Darrel R. Frost
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Stephen J. Richards
- Herpetology Department South Australian Museum North Terrace Adelaide SA 5000 Australia
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo, Rua do Matão Trav. 14, n 321, Cidade Universitária, Caixa Postal 11461 CEP 05422‐970 São Paulo São Paulo Brazil
| | - Stephen Donnellan
- Centre for Evolutionary Biology and Biodiversity The University of Adelaide Adelaide SA 5005 Australia
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies Kyoto University Sakyo‐ku Kyoto 606‐8501 Japan
| | - Cristopher J. Raxworthy
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - S.D. Biju
- Systematics Lab Department of Environmental Studies University of Delhi Delhi 110 007 India
| | | | - Alan R. Lemmon
- Department of Scientific Computing Florida State University Dirac Science Library Tallahassee FL 32306‐4120 USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
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Molecular phylogeny, species limits, and biogeography of the Brazilian endemic lizard genus Enyalius (Squamata: Leiosauridae): An example of the historical relationship between Atlantic Forests and Amazonia. Mol Phylogenet Evol 2014; 81:137-46. [DOI: 10.1016/j.ympev.2014.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 06/07/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022]
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Thomé MTC, Zamudio KR, Haddad CFB, Alexandrino J. Barriers, rather than refugia, underlie the origin of diversity in toads endemic to the Brazilian Atlantic Forest. Mol Ecol 2014; 23:6152-64. [DOI: 10.1111/mec.12986] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/17/2014] [Accepted: 10/28/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Maria Tereza C. Thomé
- Departamento de Zoologia; Instituto de Biociências; UNESP - Univ Estadual Paulista; Campus Rio Claro; Caixa Postal 199, 13506-900 Rio Claro SP Brazil
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology; Cornell University; E209 Corson Hall Ithaca NY 14853-2701 USA
| | - Célio F. B. Haddad
- Departamento de Zoologia; Instituto de Biociências; UNESP - Univ Estadual Paulista; Campus Rio Claro; Caixa Postal 199, 13506-900 Rio Claro SP Brazil
| | - João Alexandrino
- Departamento de Ciências Biológicas; UNIFESP - Univ Federal de São Paulo; Campus Diadema; Rua Professor Artur Riedel 275 09972-270 Diadema SP Brazil
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Maia-Carvalho B, Gonçalves H, Ferrand N, Martínez-Solano I. Multilocus assessment of phylogenetic relationships in Alytes (Anura, Alytidae). Mol Phylogenet Evol 2014; 79:270-8. [DOI: 10.1016/j.ympev.2014.05.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
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Fahey AL, Ricklefs RE, Dewoody JA. DNA-based approaches for evaluating historical demography in terrestrial vertebrates. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12259] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L. Fahey
- Departments of Forestry and Natural Resource; Purdue University; West Lafayette Indiana 47907 USA
| | - Robert E. Ricklefs
- Department of Biology; University of Missouri at St Louis; St Louis MO 63121 USA
| | - J. Andrew Dewoody
- Departments of Forestry and Natural Resource; Purdue University; West Lafayette Indiana 47907 USA
- Biological Sciences; Purdue University; West Lafayette Indiana 47907 USA
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Streicher JW, García-Vázquez UO, Ponce-Campos P, Flores-Villela O, Campbell JA, Smith EN. Evolutionary relationships amongst polymorphic direct-developing frogs in theCraugastor rhodopisSpecies Group (Anura: Craugastoridae). SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.882428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
AbstractRose's mountain toad Capensibufo rosei survives in a few isolated montane populations in the south-western Cape of South Africa. It comprises several cryptic species but it is uncertain whether the lineage on the Cape Peninsula is distinct. We tested the hypothesis that toads from the Peninsula form a single genetic lineage but that different breeding sites are divergent at a population level as a result of limited dispersal abilities. Directed surveys were carried out to locate breeding sites and samples obtained were analysed in a phylogenetic and population genetic framework, using two mitochondrial markers. We found toads breeding at only one of five known historical breeding sites, although one new breeding site was also recorded. No toads were observed at 15 other non-breeding localities where they were historically observed. Toads from the two active breeding sites formed a single lineage that was sufficiently distinct to be given species status. However, these were discrete at a population level, with no shared haplotypes, suggesting no gene flow between sites. One site was particularly low in genetic diversity, implying increased vulnerability to stochastic events and elevated risk of extinction. These results, coupled with the failure to locate historically known sites on the Cape Peninsula, make this newly recognized Peninsula endemic a conservation priority. Efforts should focus on the protection and expansion of the two known surviving populations and the patches of habitat upon which they rely.
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Bagley JC, Johnson JB. Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas. Biol Rev Camb Philos Soc 2014; 89:767-90. [PMID: 24495219 DOI: 10.1111/brv.12076] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 01/06/2023]
Abstract
Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.
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Affiliation(s)
- Justin C Bagley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, 401 WIDB (Widtsoe Building), Provo, UT, 84602, U.S.A
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Guarnizo CE, Cannatella DC. Geographic determinants of gene flow in two sister species of tropical Andean frogs. J Hered 2013; 105:216-25. [PMID: 24336965 DOI: 10.1093/jhered/est092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Complex interactions between topographic heterogeneity, climatic and environmental gradients, and thermal niche conservatism are commonly assumed to indicate the degree of biotic diversification in montane regions. Our aim was to investigate factors that disrupt gene flow between populations and to determine if there is evidence of downslope asymmetric migration in highland frogs with wide elevational ranges and thermal niches. We determined the role of putative impediments to gene flow (as measured by least-cost path (LCP) distances, topographic complexity, and elevational range) in promoting genetic divergence between populations of 2 tropical Andean frog sister species (Dendropsophus luddeckei, N = 114; Dendropsophus labialis, N = 74) using causal modeling and multiple matrix regression. Although the effect of geographic features was species specific, elevational range and LCP distances had the strongest effect on gene flow, with mean effect sizes (Mantel r and regression coefficients β), between 5 and 10 times greater than topographic complexity. Even though causal modeling and multiple matrix regression produced congruent results, the latter provided more information on the contribution of each geographic variable. We found moderate support for downslope migration. We conclude that the climatic heterogeneity of the landscape, the elevational distance between populations, and the inability to colonize suboptimal habitats due to thermal niche conservatism influence the magnitude of gene flow. Asymmetric migration, however, seems to be influenced by life history traits.
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Affiliation(s)
- Carlos E Guarnizo
- the Department of Integrative Biology, University of Texas at Austin, 1 University Station, CO990, Austin, TX 78712
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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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From widespread to microendemic: molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia: Brachycephalidae) is endemic to Rio de Janeiro, Brazil. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0488-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Elmer KR, Bonett RM, Wake DB, Lougheed SC. Early Miocene origin and cryptic diversification of South American salamanders. BMC Evol Biol 2013; 13:59. [PMID: 23497060 PMCID: PMC3602097 DOI: 10.1186/1471-2148-13-59] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 02/18/2013] [Indexed: 11/30/2022] Open
Abstract
Background The currently recognized species richness of South American salamanders is surprisingly low compared to North and Central America. In part, this low richness may be due to the salamanders being a recent arrival to South America. Additionally, the number of South American salamander species may be underestimated because of cryptic diversity. The aims of our present study were to infer evolutionary relationships, lineage diversity, and timing of divergence of the South American Bolitoglossa using mitochondrial and nuclear sequence data from specimens primarily from localities in the Andes and upper Amazon Basin. We also estimated time of colonization of South America to test whether it is consistent with arrival via the Panamanian Isthmus, or land bridge connection, at its traditionally assumed age of 3 million years. Results Divergence time estimates suggest that Bolitoglossa arrived in South America from Central America by at least the Early Miocene, ca. 23.6 MYA (95% HPD 15.9-30.3 MYA), and subsequently diversified. South American salamanders of the genus Bolitoglossa show strong phylogeographic structure at fine geographic scales and deep divergences at the mitochondrial gene cytochrome b (Cytb) and high diversity at the nuclear recombination activating gene-1 (Rag1). Species often contain multiple genetically divergent lineages that are occasionally geographically overlapping. Single specimens from two southeastern localities in Ecuador are sister to the equatoriana-peruviana clade and genetically distinct from all other species investigated to date. Another single exemplar from the Andes of northwestern Ecuador is highly divergent from all other specimens and is sister to all newly studied samples. Nevertheless, all sampled species of South American Bolitoglossa are members of a single clade that is one of several constituting the subgenus Eladinea, one of seven subgenera in this large genus. Conclusions The ancestors of South American salamanders likely arrived at least by the Early Miocene, well before the completion of the Late Pliocene Panamanian land bridge (widely accepted as ca. 3 MYA). This date is in agreement with recent, controversial, arguments that an older, perhaps short-lived, land connection may have existed between South America and present-day Panama 23–25 MYA. Since its arrival in South America, Bolitoglossa has diversified more extensively than previously presumed and currently includes several cryptic species within a relatively small geographic area. Rather than two upper Amazonian species currently recorded for this region, we propose that at least eight should be recognized, although these additional lineages remain to be formally described.
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Affiliation(s)
- Kathryn R Elmer
- Department of Biology, Queen's University, Kingston, Ontario, Canada.
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Tonini JFR, Costa LP, Carnaval AC. Phylogeographic structure is strong in the Atlantic Forest; predictive power of correlative paleodistribution models, not always. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- João Filipe Riva Tonini
- Laboratório de Mastozoologia e Biogeografia; Departamento de Ciências Biológicas; Universidade Federal do Espírito Santo; Vitória ES Brazil
- Department of Biology; City College of New York; City University of New York; New York NY USA
- Department of Biology; University of Richmond; Richmond VA USA
| | - Leonora Pires Costa
- Laboratório de Mastozoologia e Biogeografia; Departamento de Ciências Biológicas; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Ana Carolina Carnaval
- Department of Biology; City College of New York; City University of New York; New York NY USA
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Thomé MTC, Zamudio KR, Haddad CFB, Alexandrino J. Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization. BMC Evol Biol 2012; 12:242. [PMID: 23228224 PMCID: PMC3574056 DOI: 10.1186/1471-2148-12-242] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/04/2012] [Indexed: 11/29/2022] Open
Abstract
Background Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification. The six species within the Rhinella crucifer group of toads were defined under morphological criteria alone. Previous data suggest limited correspondence of these species to mitochondrial lineages, and morphological intergradation at transitions between forms suggests hybridization. Here we extensively sampled populations throughout the geographic distribution of the group and analyzed mitochondrial and nuclear sequence data to delimit genetic units using tree–based and allele frequency–based approaches. Results These approaches yielded complementary results, with allele frequency-based methods performing unexpectedly well given the limited number of loci examined. Both mitochondrial and nuclear markers supported a genetic structure of five units within the group, with three of the inferred units distributed within its main range, while two other units occur in separate isolates. The inferred units are mostly discordant with currently described forms: unequivocal association exists for only two of the six species in the group. Genetic evidence for hybridization exists for two pairs of units, with clear cyto–nuclear allele mixing observed in one case. Conclusions Our results confirmed that current taxonomy does not represent evolutionary units in the Rhinella crucifer group. Correspondence between genetically distinguishable units and the currently recognized species is only possible for Rhinella henseli and R. inopina. The recognition of other species relies on the reassessment of the geographic range of R. crucifer, the examination of the type series of R. ornata for hybrids, and on the use of additional markers to verify the genetic distinctiveness of R. abei. We state that R. pombali should not remain a valid species since its description appears to be based on hybrids, and that the name R. pombali should be considered a synonym of both R. crucifer and R. ornata. The fifth inferred but undescribed genetic unit may represent a new species. Our results underscore the potential of the R. crucifer species group to contribute to a better understanding of diversification processes and hybridization patterns in the Neotropics, and provide the basis for future evolutionary and taxonomic studies.
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Affiliation(s)
- Maria Tereza C Thomé
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Caixa Postal 19913506-900, Rio Claro, SP, Brazil.
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Barker BS, Rodríguez-Robles JA, Aran VS, Montoya A, Waide RB, Cook JA. Sea level, topography and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis. Mol Ecol 2012; 21:6033-52. [PMID: 23163292 DOI: 10.1111/mec.12020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 01/08/2023]
Abstract
Quaternary climatic oscillations caused changes in sea level that altered the size, number and degree of isolation of islands, particularly in land-bridge archipelagoes. Elucidating the demographic effects of these oscillations increases our understanding of the role of climate change in shaping evolutionary processes in archipelagoes. The Puerto Rican Bank (PRB) (Puerto Rico and the Eastern Islands, which comprise Vieques, Culebra, the Virgin Islands and associated islets) in the eastern Caribbean Sea periodically coalesced during glaciations and fragmented during interglacial periods of the quaternary. To explore population-level consequences of sea level changes, we studied the phylogeography of the frog Eleutherodactylus antillensis across the archipelago. We tested hypotheses encompassing vicariance and dispersal narratives by sequencing mtDNA (c. 552 bp) of 285 individuals from 58 localities, and four nuDNA introns (totalling c. 1633 bp) from 173 of these individuals. We found low support for a hypothesis of divergence of the Eastern Islands populations prior to the start of the penultimate interglacial c. 250 kya, and higher support for a hypothesis of colonization of the Eastern Islands from sources in eastern Puerto Rico during the penultimate and last glacial period, when a land bridge united the PRB. The Río Grande de Loíza Basin in eastern Puerto Rico delineates a phylogeographic break. Haplotypes shared between the PRB and St. Croix (an island c. 105 km south-east of this archipelago) likely represent human-mediated introductions. Our findings illustrate how varying degrees of connectivity and isolation influence the evolution of tropical island organisms.
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Affiliation(s)
- Brittany S Barker
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA.
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Kaefer IL, Tsuji-Nishikido BM, Mota EP, Farias IP, Lima AP. The Early Stages of Speciation in Amazonian Forest Frogs: Phenotypic Conservatism Despite Strong Genetic Structure. Evol Biol 2012. [DOI: 10.1007/s11692-012-9205-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wu Y, Wang Y, Jiang K, Hanken J. Significance of pre-Quaternary climate change for montane species diversity: insights from Asian salamanders (Salamandridae: Pachytriton). Mol Phylogenet Evol 2012; 66:380-90. [PMID: 23110935 DOI: 10.1016/j.ympev.2012.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 01/20/2023]
Abstract
Despite extensive focus on the genetic legacy of Pleistocene glaciation, impacts of earlier climatic change on biodiversity are poorly understood. Because amphibians are highly sensitive to variations in precipitation and temperature, we use a genus of Chinese montane salamanders (Salamandridae: Pachytriton) to study paleoclimatic change in East Asia, which experienced intensification of its monsoon circulation in the late Miocene associated with subsequent Pliocene warming. Using both nuclear and mitochondrial DNA sequences, we reconstruct the species tree under a coalescent model and demonstrate that all major lineages originated before the Quaternary. Initial speciation within the genus occurred after the summer monsoon entered a stage of substantial intensification. Heavy summer precipitation established temporary water connectivity through overflows between adjacent stream systems, which may facilitate geographic range expansion by aquatic species such as Pachytriton. Species were formed in allopatry likely through vicariant isolation during or after range expansion. To evaluate the influence of Pliocene warming on these cold-adapted salamanders, we construct a novel temperature buffer-zone model, which suggests widespread physiological stress or even extinction during the warming period. A significant deceleration of species accumulation rate is consistent with Pliocene range contraction, which affected P. granulosus and P. archospotus the most because they lack large temperature buffer zones. In contrast, demographic growth occurred in species for which refugia persist. The buffer-zone model reveals the Huangshan Mountain as a potential climatic refugium, which is similar to that found for other East Asian organisms. Our approach can incorporate future climatic data to evaluate the potential impact of ongoing global warming on montane species (particularly amphibians) and to predict possible population declines.
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Affiliation(s)
- Yunke Wu
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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