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De León LF, Arias CF, Sharpe DMT, Bravo V, González R, Krahe R, Aguilar C. Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis. Mol Phylogenet Evol 2023; 189:107941. [PMID: 37804958 DOI: 10.1016/j.ympev.2023.107941] [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: 05/10/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA; Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama.
| | - Carlos F Arias
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington DC, USA
| | - Diana M T Sharpe
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Víctor Bravo
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Rigoberto González
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
| | - Rüdiger Krahe
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
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2
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Edwards AW, Harrison XA, Smith MA, Chavarría Díaz MM, Sasa M, Janzen DH, Hallwachs W, Chaves G, Fernández R, Palmer C, Wilson C, North A, Puschendorf R. Amphibian diversity across three adjacent ecosystems in Área de Conservación Guanacaste, Costa Rica. PeerJ 2023; 11:e16185. [PMID: 38034867 PMCID: PMC10688307 DOI: 10.7717/peerj.16185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/05/2023] [Indexed: 12/02/2023] Open
Abstract
Amphibians are the most threatened species-rich vertebrate group, with species extinctions and population declines occurring globally, even in protected and seemingly pristine habitats. These 'enigmatic declines' are generated by climate change and infectious diseases. However, the consequences of these declines are undocumented as no baseline ecological data exists for most affected areas. Like other neotropical countries, Costa Rica, including Área de Conservación Guanacaste (ACG) in north-western Costa Rica, experienced rapid amphibian population declines and apparent extinctions during the past three decades. To delineate amphibian diversity patterns within ACG, a large-scale comparison of multiple sites and habitats was conducted. Distance and time constrained visual encounter surveys characterised species richness at five sites-Murciélago (dry forest), Santa Rosa (dry forest), Maritza (mid-elevation dry-rain forest intersect), San Gerardo (rainforest) and Cacao (cloud forest). Furthermore, species-richness patterns for Cacao were compared with historic data from 1987-8, before amphibians declined in the area. Rainforests had the highest species richness, with triple the species of their dry forest counterparts. A decline of 45% (20 to 11 species) in amphibian species richness was encountered when comparing historic and contemporary data for Cacao. Conservation efforts sometimes focus on increasing the resilience of protected areas, by increasing their range of ecosystems. In this sense ACG is unique containing many tropical ecosystems compressed in a small geographic space, all protected and recognised as a UNESCO world heritage site. It thus provides an extraordinary platform to understand changes, past and present, and the resilience of tropical ecosystems and assemblages, or lack thereof, to climate change.
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Affiliation(s)
- Alex W. Edwards
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Xavier A. Harrison
- Centre for Ecology & Conservation, University of Exeter, Penryn, Cornwall, UK
| | - M. Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Mahmood Sasa
- School of Biology, Universidad de Costa Rica, San Pedro, San Jose, Costa Rica
| | - Daniel H. Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Gerardo Chaves
- School of Biology, Universidad de Costa Rica, San Pedro, San Jose, Costa Rica
| | - Roberto Fernández
- Guanacaste Dry Forest Conservation Fund, Philadelphia, United States of America
| | - Caroline Palmer
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Chloe Wilson
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Alexandra North
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
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3
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Finch KN, Jones FA, Cronn RC. Cryptic species diversity in a widespread neotropical tree genus: The case of Cedrela odorata. AMERICAN JOURNAL OF BOTANY 2022; 109:1622-1640. [PMID: 36098061 PMCID: PMC9827871 DOI: 10.1002/ajb2.16064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Reconciling the use of taxonomy to partition morphological variation and describe genetic divergence within and among closely related species is a persistent challenge in phylogenetics. We reconstructed phylogenetic relationships among Cedrela odorata (Meliaceae) and five closely allied species to test the genetic basis for the current model of species delimitation in this economically valuable and threatened genus. METHODS We prepared a nuclear species tree with the program SNPhylo and 16,000 single-nucleotide polymorphisms from 168 Cedrela specimens. Based on clades present and ancestral patterns ADMIXTURE, we designed nine species delimitation models and compared each model to current taxonomy with Bayes factor delimitation. Timing of major lineage divergences was estimated with the program SNAPP. RESULTS The resulting analysis revealed that modern C. odorata evolved from two genetically distinct ancestral sources. All species delimitation models tested better fit the data than the model representing current taxonomic delimitation. Models with the greatest marginal likelihoods separated Mesoamerican C. odorata and South American C. odorata into two species and lumped C. angustifolia and C. montana as a single species. We estimated that Cedrela diversified in South America within the last 19 million years following one or more dispersal events from Mesoamerican lineages. CONCLUSIONS Our analyses show that the present taxonomic understanding within the genus obscures divergent lineages in C. odorata due in part to morphological differentiation and taxonomic distinctions that are not predictably associated with genetic divergence. A more accurate application of taxonomy to C. odorata and related species may aid in its conservation, management, and restoration efforts.
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Affiliation(s)
- Kristen N. Finch
- Department of Botany and Plant PathologyOregon State University2082 Cordley Hall, 2701 SW Campus WayCorvallisOR97331USA
| | - F. Andrew Jones
- Department of Botany and Plant PathologyOregon State University2082 Cordley Hall, 2701 SW Campus WayCorvallisOR97331USA
- Smithsonian Tropical Research InstituteBalboa, AnconRepublic of Panama
| | - Richard C. Cronn
- USFS PNW Research Station3200 SW Jefferson WayCorvallisOR97331USA
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4
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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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5
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Yu L, Zhao S, Shi Y, Meng F, Xu C. Evolutionary history of the oriental fire-bellied toad ( Bombina orientalis) in Northeast China. Ecol Evol 2021; 11:4232-4242. [PMID: 33976806 PMCID: PMC8093726 DOI: 10.1002/ece3.7318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan-Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire-bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan-Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire-bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.
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Affiliation(s)
- Liqun Yu
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Shuai Zhao
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Yanshuang Shi
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Fanbing Meng
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
| | - Chunzhu Xu
- College of Life ScienceNortheast Agricultural UniversityHarbinChina
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6
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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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7
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Recent and Rapid Radiation of the Highly Endangered Harlequin Frogs (Atelopus) into Central America Inferred from Mitochondrial DNA Sequences. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12090360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Populations of amphibians are experiencing severe declines worldwide. One group with the most catastrophic declines is the Neotropical genus Atelopus (Anura: Bufonidae). Many species of Atelopus have not been seen for decades and all eight Central American species are considered “Critically Endangered”, three of them very likely extinct. Nonetheless, the taxonomy, phylogeny, and biogeographic history of Central American Atelopus are still poorly known. In this study, the phylogenetic relationships among seven of the eight described species in Central America were inferred based on mitochondrial DNA sequences from 103 individuals, including decades-old museum samples and two likely extinct species, plus ten South American species. Among Central American samples, we discovered two candidate species that should be incorporated into conservation programs. Phylogenetic inference revealed a ladderized topology, placing species geographically furthest from South America more nested in the tree. Model-based ancestral area estimation supported either one or two colonization events from South America. Relaxed-clock analysis of divergence times indicated that Atelopus colonized Central America prior to 4 million years ago (Ma), supporting a slightly older than traditional date for the closure of the Isthmus. This study highlights the invaluable role of museum collections in documenting past biodiversity, and these results could guide future conservation efforts. An abstract in Spanish (Resumen) is available as supplementary material.
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Rodríguez-Correa H, Oyama K, Quesada M, Fuchs EJ, González-Rodríguez A. Contrasting Patterns of Population History and Seed-mediated Gene Flow in Two Endemic Costa Rican Oak Species. J Hered 2019; 109:530-542. [PMID: 29509902 DOI: 10.1093/jhered/esy011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in 2 partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. The phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.
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Affiliation(s)
- Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán, México
| | - Mauricio Quesada
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán, México.,Laboratorio de Ecología y Evolución de Polinización y Sistemas Reproductivos de Plantas, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Eric J Fuchs
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán, México.,Escuela de Biología. Universidad de Costa Rica. San Pedro Montes de Oca 11501-2060, San José, Costa Rica
| | - Antonio González-Rodríguez
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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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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10
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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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11
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Mendoza AM, Bolívar-García W, Vázquez-Domínguez E, Ibáñez R, Parra Olea G. The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae). PeerJ 2019; 7:e6115. [PMID: 30627486 PMCID: PMC6321759 DOI: 10.7717/peerj.6115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/15/2018] [Indexed: 12/02/2022] Open
Abstract
The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansion, likely related to sea-level and climatic oscillations during the Pleistocene, whereas the structure of the northern clade has probably been driven by dispersal through the Isthmus of Tehuantepec and isolation by the Motagua–Polochic–Jocotán fault system and the Mexican highlands.
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Affiliation(s)
- Angela M Mendoza
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico city, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wilmar Bolívar-García
- Departamento de Biología, Grupo de Investigación en Ecología Animal, Universidad del Valle, Cali, Colombia
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Roberto Ibáñez
- Departamento de Zoología, Smithsonian Tropical Research Institute, Balboa, Panamá.,Universidad de Panamá, Panamá.,Sistema Nacional de Investigación, Panamá
| | - Gabriela Parra Olea
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico city, México
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Loaiza JR, Miller MJ. Historical and contemporary forces combine to shape patterns of genetic differentiation in two species of MesoamericanAnophelesmosquitoes. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jose R Loaiza
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Clayton, Republic of Panama
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Republic of Panama
| | - Matthew J Miller
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
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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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McCranie JR. A Discussion of the Phenetic-basedCraugastor laticepsSpecies Group (Anura: Brachycephaloidea: Craugastoridae) from North-central Honduras, with the Description of Two New Species. HERPETOLOGICA 2018. [DOI: 10.1655/herpetologica-d-17-00023.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proc Natl Acad Sci U S A 2017; 113:7978-85. [PMID: 27432951 DOI: 10.1073/pnas.1601063113] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.
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Saldarriaga-Córdoba M, Parkinson CL, Daza JM, Wüster W, Sasa M. Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE). PLoS One 2017; 12:e0187969. [PMID: 29176806 PMCID: PMC5703453 DOI: 10.1371/journal.pone.0187969] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/30/2017] [Indexed: 11/18/2022] Open
Abstract
The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species’ distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O´Higgins, Santiago, Chile
| | - Christopher L. Parkinson
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Juan M. Daza
- Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Wolfgang Wüster
- School of Biological Sciences, Bangor University, Bangor, United states of Kingdom
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
- Organization for Tropical Studies, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- * E-mail:
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Fan D, Sun Z, Li B, Kou Y, Hodel RGJ, Jin Z, Zhang Z. Dispersal corridors for plant species in the Poyang Lake Basin of southeast China identified by integration of phylogeographic and geospatial data. Ecol Evol 2017; 7:5140-5148. [PMID: 28770054 PMCID: PMC5528243 DOI: 10.1002/ece3.2999] [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: 11/24/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Measuring the dispersal of wildlife through landscapes is notoriously difficult. Recently, the categorical least cost path algorithm that integrates population genetic data with species distribution models has been applied to reveal population connectivity. In this study, we use this method to identify the possible dispersal corridors of five plant species (Castanopsis tibetana, Schima superba, Cyclocarya paliurus, Sargentodoxa cuneata, Eomecon chionantha) in the Poyang Lake Basin (PLB, largely coinciding with Jiangxi Province), China, in the late Quaternary. The results showed that the strongest population connectivity for the five species occurred in the Wuyi Mountains and the Yu Mountains of the eastern PLB (East Corridor) during the late Quaternary. In the western PLB, populations of the five species were connected by the Luoxiao Mountains and the Jiuling Mountains (West Corridor) but with a lower degree of connectivity. There were some minor connections between the eastern and the western populations across the Gannan Hills. When the corridors of five species were overlaid, the East Corridor and the West Corridor were mostly shared by multiple species. These results indicate that plant species in the PLB could have responded to the Quaternary climate changes by moving along the East Corridor and the West Corridor. Given that dispersal corridors have seldom been considered in the governmental strategies of biodiversity conservation in the PLB, preserving and restoring natural vegetation along these corridors should be prioritized to mitigate the effects of anthropogenic climate change by facilitating migration of plant species and other biota.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Zhixia Sun
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Bo Li
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | | | - Zhinong Jin
- Nanchang Institute of Technology Nanchang Jiangxi China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
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Guayasamin JM, Hutter CR, Tapia EE, Culebras J, Peñafiel N, Pyron RA, Morochz C, Funk WC, Arteaga A. Diversification of the rainfrog Pristimantis ornatissimus in the lowlands and Andean foothills of Ecuador. PLoS One 2017; 12:e0172615. [PMID: 28329011 PMCID: PMC5362048 DOI: 10.1371/journal.pone.0172615] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/01/2017] [Indexed: 11/28/2022] Open
Abstract
Geographic barriers and elevational gradients have long been recognized as important in species diversification. Here, we illustrate an example where both mechanisms have shaped the genetic structure of the Neotropical rainfrog, Pristimantis ornatissimus, which has also resulted in speciation. This species was thought to be a single evolutionary lineage distributed throughout the Ecuadorian Chocó and the adjacent foothills of the Andes. Based on recent sampling of P. ornatissimus sensu lato, we provide molecular and morphological evidence that support the validity of a new species, which we name Pristimantis ecuadorensis sp. nov. The sister species are elevational replacements of each other; the distribution of Pristimantis ornatissimus sensu stricto is limited to the Ecuadorian Chocó ecoregion (< 1100 m), whereas the new species has only been found at Andean localities between 1450-1480 m. Given the results of the Multiple Matrix Regression with Randomization analysis, the genetic difference between P. ecuadorensis and P. ornatissimus is not explained by geographic distance nor environment, although environmental variables at a finer scale need to be tested. Therefore this speciation event might be the byproduct of stochastic historic extinction of connected populations or biogeographic events caused by barriers to dispersal such as rivers. Within P. ornatissimus sensu stricto, morphological patterns and genetic structure seem to be related to geographic isolation (e.g., rivers). Finally, we provide an updated phylogeny for the genus, including the new species, as well as other Ecuadorian Pristimantis.
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Affiliation(s)
- Juan M. Guayasamin
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Investigaciones Biológicas y Ambientales BIÓSFERA, Laboratorio de Biología Evolutiva, Campus Cumbayá, Quito, Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Ingeniería en Biodiversidad y Cambio Climático, Facultad de Medio Ambiente, Universidad Tecnológica Indoamérica, Calle Machala y Sabanilla, Quito, Ecuador
| | - Carl R. Hutter
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Elicio E. Tapia
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Otonga, San Rafael, Quito, Ecuador
| | - Jaime Culebras
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Ingeniería en Biodiversidad y Cambio Climático, Facultad de Medio Ambiente, Universidad Tecnológica Indoamérica, Calle Machala y Sabanilla, Quito, Ecuador
| | - Nicolás Peñafiel
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Ingeniería en Biodiversidad y Cambio Climático, Facultad de Medio Ambiente, Universidad Tecnológica Indoamérica, Calle Machala y Sabanilla, Quito, Ecuador
| | - R. Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, D.C., United States of America
| | | | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, United States of America
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Hoyos M, Bloor P, Defler T, Vermeer J, Röhe F, Farias I. Phylogenetic relationships within the Callicebus cupreus species group (Pitheciidae: Primates): Biogeographic and taxonomic implications. Mol Phylogenet Evol 2016; 102:208-19. [PMID: 27235549 DOI: 10.1016/j.ympev.2016.05.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
Abstract
The genus Callicebus (Thomas, 1903) is one of the most diverse of Neotropical primate genera and the only extant member of the Callicebinae subfamily. It has a widespread distribution from Colombia to Brazil, Bolivia, Peru and northern Paraguay. Coat colouring and colour pattern vary substantially within the genus, and this has led to the description of numerous species and subspecies, as well as numerous species groups. However, a lack of molecular phylogenetic analyses on the genus means that phylogenetic relationships and biogeographic history of species are poorly understood. Here, we examined phylogenetic relationships and patterns of diversification within the Callicebus cupreus species Group (sensu Kobayashi, 1995) using complete mitochondrial DNA cytochrome b gene sequence. Analyses indicate that the Callicebus cupreus Group underwent recent and extensive diversification. The common ancestor appears to have emerged some 2.3 million years ago (Ma) from a centre of origin in the western Amazon region, followed by diversification of the group between about 1.5 and 1.2Ma. Phylogenetic analyses were able to recover most previously described species (including the recently described Colombian endemic Callicebus caquetensis). However, there are some notable inconsistences between the obtained phylogeny and current taxonomy. Some previously recognized taxa were not separated by our data (e.g., Callicebus caligatus and Callicebus dubius), while currently unrecognized species diversity was uncovered within C. cupreus in the form of two divergent lineages: one of which exhibited greater phylogenetic similarity to species from the C. moloch Group. Based on the present study, we challenge current taxonomic arrangements for the C. cupreus species Group and call for a thorough taxonomic revision within the genus Callicebus.
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Affiliation(s)
- Manuel Hoyos
- Instituto de Genética, Universidad Nacional de Colombia, Edificio 426, Bogotá D.C., Colombia.
| | - Paul Bloor
- Instituto de Genética, Universidad Nacional de Colombia, Edificio 426, Bogotá D.C., Colombia
| | - Thomas Defler
- Departamento de Biología, Universidad Nacional de Colombia, Edificio 421, Bogotá D.C., Colombia
| | - Jan Vermeer
- Le Conservatoire pour la Protection des Primates. La Vallée des Singes, 86700 Romagne, France
| | - Fabio Röhe
- Wildlife Conservation Society, Manaus, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil
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Priti H, Roshmi RS, Ramya B, Sudhira HS, Ravikanth G, Aravind NA, Gururaja KV. Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats, India. PLoS One 2016; 11:e0149382. [PMID: 26934213 PMCID: PMC4774957 DOI: 10.1371/journal.pone.0149382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 02/01/2016] [Indexed: 11/19/2022] Open
Abstract
A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members--R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8-2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats.
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Affiliation(s)
- H. Priti
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
- Manipal University, Manipal, India
| | - Rekha Sarma Roshmi
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
- Manipal University, Manipal, India
| | - Badrinath Ramya
- Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India
| | - H. S. Sudhira
- Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India
- Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation and Development, Indian Institute of Science Campus, Bengaluru, India
| | - G. Ravikanth
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
| | - Neelavara Anantharam Aravind
- Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India
| | - Kotambylu Vasudeva Gururaja
- Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India
- Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation and Development, Indian Institute of Science Campus, Bengaluru, India
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Molecular phylogenetics and biogeography of the Neotropical skink genus Mabuya Fitzinger (Squamata: Scincidae) with emphasis on Colombian populations. Mol Phylogenet Evol 2015; 93:188-211. [DOI: 10.1016/j.ympev.2015.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/23/2015] [Accepted: 07/24/2015] [Indexed: 01/05/2023]
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Barker BS, Rodríguez-Robles JA, Cook JA. Climate as a driver of tropical insular diversity: comparative phylogeography of two ecologically distinctive frogs in Puerto Rico. ECOGRAPHY 2015; 38:769-781. [PMID: 26508809 PMCID: PMC4620057 DOI: 10.1111/ecog.01327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/04/2014] [Indexed: 06/05/2023]
Abstract
The effects of late Quaternary climate on distributions and evolutionary dynamics of insular species are poorly understood in most tropical archipelagoes. We used ecological niche models under past and current climate to derive hypotheses regarding how stable climatic conditions shaped genetic diversity in two ecologically distinctive frogs in Puerto Rico. Whereas the Mountain Coquí, Eleutherodactylus portoricensis, is restricted to montane forest in the Cayey and Luquillo Mountains, the Red-eyed Coquí, E. antillensis, is a habitat generalist distributed across the entire Puerto Rican Bank (Puerto Rico and the Virgin Islands, excluding St. Croix). To test our hypotheses, we conducted phylogeographic and population genetic analyses based on mitochondrial and nuclear loci of each species across their range in Puerto Rico. Patterns of population differentiation in E. portoricensis, but not in E. antillensis, supported our hypotheses. For E. portoricensis, these patterns include: individuals isolated by long-term unsuitable climate in the Río Grande de Loíza Basin in eastern Puerto Rico belong to different genetic clusters; past and current climate strongly predicted genetic differentiation; and Cayey and Luquillo Mountains populations split prior to the last interglacial. For E. antillensis, these patterns include: genetic clusters did not fully correspond to predicted long-term unsuitable climate; and past and current climate weakly predicted patterns of genetic differentiation. Genetic signatures in E. antillensis are consistent with a recent range expansion into western Puerto Rico, possibly resulting from climate change and anthropogenic influences. As predicted, regions with a large area of long-term suitable climate were associated with higher genetic diversity in both species, suggesting larger and more stable populations. Finally, we discussed the implications of our findings for developing evidence-based management decisions for E. portoricensis, a taxon of special concern. Our findings illustrate the role of persistent suitable climatic conditions in promoting the persistence and diversification of tropical island organisms.
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Affiliation(s)
- Brittany S. Barker
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Javier A. Rodríguez-Robles
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
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Paz A, Ibáñez R, Lips KR, Crawford AJ. Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach. Mol Ecol 2015; 24:3723-37. [DOI: 10.1111/mec.13275] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Paz
- Department of Biological Sciences; Universidad de los Andes; A.A. 4976 Bogotá Colombia
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Círculo Herpetológico de Panamá; Apartado 0824-00122 Panama City Republic of Panama
| | - Karen R. Lips
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Department of Biology; University of Maryland; College Park MD 20742-4415 USA
| | - Andrew J. Crawford
- Department of Biological Sciences; Universidad de los Andes; A.A. 4976 Bogotá Colombia
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Círculo Herpetológico de Panamá; Apartado 0824-00122 Panama City Republic of Panama
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Berkman LK, Nielsen CK, Roy CL, Heist EJ. Comparative genetic structure of sympatric leporids in southern Illinois. J Mammal 2015. [DOI: 10.1093/jmammal/gyv060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mendoza ÁM, Ospina OE, Cárdenas-Henao H, García-R JC. A likelihood inference of historical biogeography in the world's most diverse terrestrial vertebrate genus: diversification of direct-developing frogs (Craugastoridae: Pristimantis) across the Neotropics. Mol Phylogenet Evol 2015; 85:50-8. [PMID: 25681675 DOI: 10.1016/j.ympev.2015.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/26/2015] [Accepted: 02/01/2015] [Indexed: 11/27/2022]
Abstract
The geology of the northern Andean region has driven the evolutionary history of Neotropical fauna through the creation of barriers and connections that have resulted in speciation and dispersal events, respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic placement of 12 species from the montane Andes of Colombia in a broader geographical context with a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40million years and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic history of the genus using ancestral range reconstruction by biogeographic regions and elevational ranges. We recognized the middle elevational band (between 1000 and 3000m) in the Northwestern Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species. Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion of lowland species.
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Affiliation(s)
- Ángela María Mendoza
- Grupo de estudios en genética, ecología molecular y fisiología animal, Universidad del Valle, 760032 Cali, Colombia; Grupo de investigación en ecología y conservación neotropical, Samanea Foundation, 760046 Cali, Colombia; Conservation Genetics Laboratory, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, 6713 Cali, Colombia.
| | - Oscar E Ospina
- Grupo de estudios en genética, ecología molecular y fisiología animal, Universidad del Valle, 760032 Cali, Colombia; Department of Biology, University of Puerto Rico, Rio Piedras 00931-3360, Puerto Rico
| | - Heiber Cárdenas-Henao
- Grupo de estudios en genética, ecología molecular y fisiología animal, Universidad del Valle, 760032 Cali, Colombia; Departamento de Biología, Universidad del Valle, 760032 Cali, Colombia
| | - Juan C García-R
- Grupo de estudios en genética, ecología molecular y fisiología animal, Universidad del Valle, 760032 Cali, Colombia; Institute of Agriculture and Environment, Massey University, Palmerston North, Private Bag 11-222, New Zealand
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Zumbado-Ulate H, Bolaños F, Gutiérrez-Espeleta G, Puschendorf R. Extremely low prevalence of Batrachochytrium dendrobatidis in frog populations from neotropical dry forest of Costa Rica supports the existence of a climatic refuge from disease. ECOHEALTH 2014; 11:593-602. [PMID: 25212725 DOI: 10.1007/s10393-014-0967-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 06/03/2023]
Abstract
Population declines and extinctions of numerous species of amphibians, especially stream-breeding frogs, have been linked to the emerging infectious disease chytridiomycosis, caused by the chytrid fungus, Batrachochytrium dendrobatidis. In Central America, most of the 34 species of the Craugastor punctariolus species group have disappeared in recent years in high- and low-elevation rainforests. Distribution models for B. dendrobatidis and the continuous presence of the extirpated stream-dwelling species, Craugastor ranoides, in the driest site of Costa Rica (Santa Elena Peninsula), suggest that environmental conditions might restrict the growth and development of B. dendrobatidis, existing as a refuge from chytridiomycosis-driven extinction. We conducted field surveys to detect and quantify the pathogen using Real-time PCR in samples from 15 species of frogs in two locations of tropical dry forest. In Santa Elena Peninsula, we swabbed 310 frogs, and only one sample of the species, C. ranoides, tested positive for B. dendrobatidis (prevalence <0.1%). In Santa Rosa Station, we swabbed 100 frogs, and nine samples from three species tested positive (prevalence = 9.0%). We failed to detect signs of chytridiomycosis in any of the 410 sampled frogs, and low quantities of genetic equivalents (between 0 and 1073) were obtained from the ten positive samples. The difference in the prevalence between locations might be due not only to the hotter and drier conditions of Santa Elena Peninsula but also to the different compositions of species in both locations. Our results suggest that B. dendrobatidis is at the edge of its distribution in these dry and hot environments of tropical dry forest. This study supports the existence of climatic refuges from chytridiomycosis and highlights the importance of tropical dry forest conservation for amphibians in the face of epidemic disease.
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Affiliation(s)
- Héctor Zumbado-Ulate
- School of Biology, University of Costa Rica, San Pedro de Montes de Oca, San Jose, Costa Rica,
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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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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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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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Alda F, Reina RG, Doadrio I, Bermingham E. Phylogeny and biogeography of the Poecilia sphenops species complex (Actinopterygii, Poeciliidae) in Central America. Mol Phylogenet Evol 2012; 66:1011-26. [PMID: 23277160 DOI: 10.1016/j.ympev.2012.12.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 11/06/2012] [Accepted: 12/15/2012] [Indexed: 11/16/2022]
Abstract
We inferred the phylogenetic relationships among members of the Poecilia sphenops species complex to resolve the colonization process and radiation of this group in Central America. We analyzed 2550 base pairs (bp) of mitochondrial DNA (mtDNA), including ATP synthase 6 and 8, cytochrome oxidase subunit I and NADH dehydrogenase subunit 2 genes, and 906bp of the nuclear S7 ribosomal protein of 86 ingroup individuals from 61 localities spanning most of its distribution from Mexico to Panama. Our mitochondrial data rendered a well-supported phylogeny for the P. sphenops complex that differed with the nuclear data set topology, which did not recover the monophyly of the P. mexicana mitochondrial lineage. Coalescent-based simulations tests indicated that, although hybridization cannot be completely ruled out, this incongruence is most likely due to incomplete lineage sorting in this group, which also showed the widest geographic distribution. A single colonization event of Central America from South America was estimated to have occurred between the early Paleocene and Oligocene (53-22millionyears ago). Subsequently, two largely differentiated evolutionary lineages diverged around the Early Oligocene-Miocene (38-13million years ago), which are considered two separate species complexes: P. sphenops and P. mexicana, which can also be distinguished by their tricuspid and unicuspid inner jaw teeth, respectively. Ultimately, within lineage diversification occurred mainly during the Miocene (22-5million years ago). All major cladogenetic events predated the final closure of the Isthmus of Panama. The allopatric distribution of lineages together with the long basal internodes suggest that vicariance and long term isolations could be the main evolutionary forces promoting radiation in this group, although dispersal through water barriers might also have occurred. Lastly, our results suggest the need to review the current species distribution and taxonomy of the P. sphenops complex sensu lato.
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Affiliation(s)
- Fernando Alda
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama, Spain.
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Crawford AJ, Cruz C, Griffith E, Ross H, Ibáñez R, Lips KR, Driskell AC, Bermingham E, Crump P. DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations. Mol Ecol Resour 2012; 13:1005-18. [PMID: 23280343 DOI: 10.1111/1755-0998.12054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/10/2012] [Accepted: 11/21/2012] [Indexed: 11/26/2022]
Abstract
Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.
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Affiliation(s)
- Andrew J Crawford
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panama, Republic of Panama; Círculo Herpetológico de Panamá, Apartado 0824-00122, Panama, Republic of Panama; Departamento de Ciencias Biológicas, Universidad de los Andes, A.A. 4976, Bogotá, Colombia
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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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33
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García-R JC, Crawford AJ, Mendoza AM, Ospina O, Cardenas H, Castro F. Comparative phylogeography of direct-developing frogs (Anura: Craugastoridae: Pristimantis) in the southern Andes of Colombia. PLoS One 2012; 7:e46077. [PMID: 23049941 PMCID: PMC3457947 DOI: 10.1371/journal.pone.0046077] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 08/28/2012] [Indexed: 11/18/2022] Open
Abstract
The Andes of South America hosts perhaps the highest amphibian species diversity in the world, and a sizable component of that diversity is comprised of direct-developing frogs of the genus Pristimantis (Anura: Craugastoridae). In order to better understand the initial stages of species formation in these frogs, this study quantified local-scale spatial genetic structuring in three species of Pristimantis. DNA sequences of two mitochondrial gene fragments (16S and COI) were obtained from P. brevifrons, P. palmeri and P. jubatus at different locations in the Cordillera Occidental. We found high levels of genetic diversity in the three species, with highly structured populations (as measured by F(ST)) in P. brevifrons and P. palmeri while P. jubatus showed panmixia. Large effective population sizes, inferred from the high levels of genetic diversity, were found in the three species and two highly divergent lineages were detected within P. jubatus and P. palmeri. Estimated divergence times among populations within P. brevifrons and P. palmeri coincide with the Pleistocene, perhaps due to similar responses to climatic cycling or recent geological history. Such insights have important implications for linking alpha and beta diversity, suggesting regional scale patterns may be associated with local scale processes in promoting differentiation among populations in the Andes.
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Affiliation(s)
- Juan C García-R
- Department of Biology, Universidad del Valle, Cali, Colombia.
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Harding LE, Dragoo JW. Out of the tropics: a phylogeographic history of the long-tailed weasel,Mustela frenata. J Mammal 2012. [DOI: 10.1644/11-mamm-a-280.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Smith BT, Amei A, Klicka J. Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama. Proc Biol Sci 2012; 279:3520-6. [PMID: 22673352 DOI: 10.1098/rspb.2012.0706] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Climatic and geological changes across time are presumed to have shaped the rich biodiversity of tropical regions. However, the impact climatic drying and subsequent tropical rainforest contraction had on speciation has been controversial because of inconsistent palaeoecological and genetic data. Despite the strong interest in examining the role of climatic change on speciation in the Neotropics there has been few comparative studies, particularly, those that include non-rainforest taxa. We used bird species that inhabit humid or dry habitats that dispersed across the Panamanian Isthmus to characterize temporal and spatial patterns of speciation across this barrier. Here, we show that these two assemblages of birds exhibit temporally different speciation time patterns that supports multiple cycles of speciation. Evidence for these cycles is further corroborated by the finding that both assemblages consist of 'young' and 'old' species, despite dry habitat species pairs being geographically more distant than pairs of humid habitat species. The matrix of humid and dry habitats in the tropics not only allows for the maintenance of high species richness, but additionally this study suggests that these environments may have promoted speciation. We conclude that differentially expanding and contracting distributions of dry and humid habitats was probably an important contributor to speciation in the tropics.
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Affiliation(s)
- Brian Tilston Smith
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway Box 4505, Las Vegas, NV 89154, USA.
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FOUQUET ANTOINE, LEDOUX JEANBAPTISTE, DUBUT VINCENT, NOONAN BRICEP, SCOTTI IVAN. The interplay of dispersal limitation, rivers, and historical events shapes the genetic structure of an Amazonian frog. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01871.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.
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Affiliation(s)
- Miguel Vences
- Division of Evolutionary Biology Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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Pinto-Sánchez NR, Ibáñez R, Madriñán S, Sanjur OI, Bermingham E, Crawford AJ. The Great American Biotic Interchange in frogs: multiple and early colonization of Central America by the South American genus Pristimantis (Anura: Craugastoridae). Mol Phylogenet Evol 2011; 62:954-72. [PMID: 22178362 DOI: 10.1016/j.ympev.2011.11.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/20/2011] [Accepted: 11/24/2011] [Indexed: 10/14/2022]
Abstract
The completion of the land bridge between North and South America approximately 3.5-3.1 million years ago (Ma) initiated a tremendous biogeographic event called the Great American Biotic Interchange (GABI), described principally from the mammalian fossil record. The history of biotic interchange between continents for taxonomic groups with poor fossil records, however, is not well understood. Molecular and fossil data suggest that a number of plant and animal lineages crossed the Isthmus of Panama well before 3.5 Ma, leading biologists to speculate about trans-oceanic dispersal mechanisms. Here we present a molecular phylogenetic analysis of the frog genus Pristimantis based on 189 individuals of 137 species, including 71 individuals of 31 species from Panama and Colombia. DNA sequence data were obtained from three mitochondrial (COI, 12S, 16S) and two nuclear (RAG-1 and Tyr) genes, for a total of 4074 base pairs. The resulting phylogenetic hypothesis showed statistically significant conflict with most recognized taxonomic groups within Pristimantis, supporting only the rubicundus Species Series, and the Pristimantis myersi and Pristimantis pardalis Species Groups as monophyletic. Inference of ancestral areas based on a likelihood model of geographic range evolution via dispersal, local extinction, and cladogenesis (DEC) suggested that the colonization of Central America by South American Pristimantis involved at least 11 independent events. Relaxed-clock analyses of divergence times suggested that at least eight of these invasions into Central America took place prior to 4 Ma, mainly in the Miocene. These findings contribute to a growing list of molecular-based biogeographic studies presenting apparent temporal conflicts with the traditional GABI model.
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BEAVIS AMBERS, SUNNUCKS PAUL, ROWELL DAVIDM. Microhabitat preferences drive phylogeographic disparities in two Australian funnel web spiders. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01753.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Lim HC, Sheldon FH. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Mol Ecol 2011; 20:3414-38. [PMID: 21777318 DOI: 10.1111/j.1365-294x.2011.05190.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co-distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now-submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross-shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post-divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid-Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630-690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.
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Affiliation(s)
- Haw Chuan Lim
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
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41
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Chan LM, Brown JL, Yoder AD. Integrating statistical genetic and geospatial methods brings new power to phylogeography. Mol Phylogenet Evol 2011; 59:523-37. [DOI: 10.1016/j.ympev.2011.01.020] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/31/2011] [Accepted: 01/31/2011] [Indexed: 01/29/2023]
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Gonzalez-Voyer A, Padial JM, Castroviejo-Fisher S, de la Riva I, Vilà C. Correlates of species richness in the largest Neotropical amphibian radiation. J Evol Biol 2011; 24:931-42. [PMID: 21401771 PMCID: PMC3116151 DOI: 10.1111/j.1420-9101.2011.02243.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Although tropical environments are often considered biodiversity hotspots, it is precisely in such environments where least is known about the factors that drive species richness. Here, we use phylogenetic comparative analyses to study correlates of species richness for the largest Neotropical amphibian radiation: New World direct-developing frogs. Clade-age and species richness were nonsignificantly, negatively correlated, suggesting that clade age alone does not explain among-clade variation in species richness. A combination of ecological and morphological traits explained 65% of the variance in species richness. A more vascularized ventral skin, the ability to colonize high-altitude ranges, encompassing a large variety of vegetation types, correlated significantly with species richness, whereas larger body size was marginally correlated with species richness. Hence, whereas high-altitude ranges play a role in shaping clade diversity in the Neotropics, intrinsic factors, such as skin structures and possibly body size, might ultimately determine which clades are more speciose than others.
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Affiliation(s)
- A Gonzalez-Voyer
- Department of Integrative Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio s/n, Seville, Spain.
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Pröhl H, Ron SR, Ryan MJ. Ecological and genetic divergence between two lineages of middle American túngara frogs Physalaemus (= Engystomops) pustulosus. BMC Evol Biol 2010; 10:146. [PMID: 20482771 PMCID: PMC2882927 DOI: 10.1186/1471-2148-10-146] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 05/18/2010] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. Here we combine population genetic methods (microsatellites) with phylogenetic information (mtDNA) to define genetic population clusters of the wide-spread Neotropical túngara frog (Physalaemus pustulosus). We measure gene flow and migration within and between population clusters and compare genetic diversity between population clusters. By applying ecological niche modeling we determine whether the two most divergent genetic groups of the túngara frog (1) inhabit different habitats, and (2) are separated geographically by unsuitable habitat across a gap in the distribution. RESULTS Most population structure is captured by dividing all sample localities into two allopatric genetic lineages. The Northern genetic lineage (NW Costa Rica) is genetically homogenous while the Southern lineage (SW Costa Rica and Panama) is sub-divided into three population clusters by both microsatellite and mtDNA analyses. Gene flow is higher within the Northern lineage than within the Southern lineage, perhaps due to increased landscape heterogeneity in the South. Niche modeling reveals differences in suitable habitat between the Northern and Southern lineages: the Northern lineage inhabits dry/pine-oak forests, while the Southern lineage is confined to tropical moist forests. Both lineages seem to have had little movement across the distribution gap, which persisted during the last glacial maximum. The lack of movement was more pronounced for the Southern lineage than for the Northern lineage. CONCLUSIONS This study confirms the finding of previous studies that túngara frogs diverged into two allopatric genetic lineages north and south of the gap in the distribution in central Costa Rica several million years ago. The allopatric distribution is attributed to unsuitable habitat and probably other unknown ecological factors present across the distribution gap. Niche conservatism possibly contributes to preventing movements across the gap and gene flow between both groups. Genetic and ecological data indicate that there is the potential for ecological divergence in allopatry between lineages. In this context we discuss whether the Northern and Southern lineages should be recognized as separate species, and we conclude that further studies of pre- and post-zygotic isolation are needed for a final assessment. Identified population clusters should motivate future behavioral and ecological research regarding within-species biodiversity and speciation mechanisms.
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Affiliation(s)
- Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine, Bünteweg 17, 30559 Hannover, Germany
- Section of Integrative Biology, 1 University Station C09300, The University of Texas, TX78712, USA
- Smithsonian Tropical Research Institute, P.O. Box 0943-03092 Balboa Ancón, Republic of Panamá
| | - Santiago R Ron
- Museo de Zoología, Centro de Biodiversidad y Ambiente, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Aptdo. 17-01-2184, Quito Ecuador
| | - Michael J Ryan
- Section of Integrative Biology, 1 University Station C09300, The University of Texas, TX78712, USA
- Smithsonian Tropical Research Institute, P.O. Box 0943-03092 Balboa Ancón, Republic of Panamá
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Complex evolution in the Neotropics: The origin and diversification of the widespread genus Leptodeira (Serpentes: Colubridae). Mol Phylogenet Evol 2009; 53:653-67. [DOI: 10.1016/j.ympev.2009.07.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 07/08/2009] [Accepted: 07/11/2009] [Indexed: 11/19/2022]
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45
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Streicher JW, Crawford AJ, Edwards CW. Multilocus molecular phylogenetic analysis of the montane Craugastor podiciferus species complex (Anura: Craugastoridae) in Isthmian Central America. Mol Phylogenet Evol 2009; 53:620-30. [DOI: 10.1016/j.ympev.2009.07.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 07/04/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
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46
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Robertson JM, Zamudio KR. Genetic diversification, vicariance, and selection in a polytypic frog. J Hered 2009; 100:715-31. [PMID: 19589848 DOI: 10.1093/jhered/esp041] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spatial patterns of heritable phenotypic diversity reflect the relative roles of gene flow and selection in determining geographic variation within a species. We quantified color differentiation and genetic divergence among 20 populations of the red-eyed tree frog (Agalychnis callidryas) in lower Central America. Phylogenetic analyses revealed 5 well-supported mitochondrial DNA clades, and we infer from our phylogeny that geographic barriers have played a large role in structuring populations. Two phenotypic characters varied independently among isolated population groups: Flank coloration distinguished Caribbean from Pacific individuals, whereas leg coloration exhibited a more complex geographic pattern. We detected 3 generalized spatial patterns of genetic and phenotypic diversity: 1) phenotypic differentiation in the presence of historical connectivity, 2) phenotypic uniformity across genetically differentiated regions, and 3) codistribution of genetic and phenotypic characters. These patterns indicate that phenotypic diversification is highly regionalized and can result from spatial variation in localized adaptations, geographic isolation, genetic drift, and/or evolutionary stasis. Although the mode of selection underlying color variation was not the focal objective of this study, we discuss the possible roles of natural and sexual selection in mediating population differentiation. Our study underscores the fact that selection gradients vary across relatively small spatial scales, even in species that occupy relatively homogeneous environments.
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Affiliation(s)
- Jeanne M Robertson
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY 14853-2701, USA.
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47
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ROBERTSON JEANNEM, DURYEA MCATHERINE, ZAMUDIO KELLYR. Discordant patterns of evolutionary differentiation in two Neotropical treefrogs. Mol Ecol 2009; 18:1375-95. [DOI: 10.1111/j.1365-294x.2009.04126.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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48
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Wang IJ, Shaffer HB. Rapid color evolution in an aposematic species: a phylogenetic analysis of color variation in the strikingly polymorphic strawberry poison-dart frog. Evolution 2008; 62:2742-59. [PMID: 18764916 DOI: 10.1111/j.1558-5646.2008.00507.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Aposematism is one of the great mysteries of evolutionary biology. The evolution of aposematic coloration is poorly understood, but even less understood is the evolution of polymorphism in aposematic signals. Here, we use a phylogeographic approach to investigate the evolution of color polymorphism in Dendrobates pumilio, a well-known poison-dart frog (family Dendrobatidae), which displays perhaps the most striking color variation of any aposematic species. With over a dozen color morphs, ranging from bright red to dull green, D. pumilio provides an ideal opportunity to examine the evolution of color polymorphism and evolutionary shifts to cryptic coloration in an otherwise aposematic species. We constructed a phylogenetic tree for all D. pumilio color morphs from 3051bp of mtDNA sequence data, reconstructed ancestral states using parsimony and Bayesian methods, and tested the recovered tree against constraint trees using parametric bootstrapping to determine the number of changes to each color type. We find strong evidence for nearly maximal numbers of changes in all color traits, including five independent shifts to dull dorsal coloration. Our results indicate that shifts in coloration in aposematic species may occur more regularly than predicted and that convergence in coloration may indicate that similar forces are repeatedly driving these shifts.
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Affiliation(s)
- Ian J Wang
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA.
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Wang IJ, Crawford AJ, Bermingham E. Phylogeography of the Pygmy Rain Frog (Pristimantis ridens) across the lowland wet forests of isthmian Central America. Mol Phylogenet Evol 2008; 47:992-1004. [PMID: 18424088 DOI: 10.1016/j.ympev.2008.02.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Revised: 02/06/2008] [Accepted: 02/28/2008] [Indexed: 11/29/2022]
Abstract
We used a phylogeographic approach to elucidate the evolutionary history of a lineage of frogs, known as Pristimantis (formerly Eleutherodactylus) ridens (Anura: Brachycephalidae), restricted to the wet forests occurring along the Caribbean versant of isthmian Central America as well as the disjunct wet forest on the Pacific slope of Costa Rica. We placed our phylogeographic study of P. ridens within a larger molecular phylogenetic analysis of Central American Pristimantis. All phylogenetic inferences were based on a 1455 base pair fragment of mitochondrial DNA, containing the complete ND2 gene and five flanking tRNA genes. Our reconstruction of the intraspecific phylogeny of P. ridens yielded a basal trichotomy dating to an estimated 12+ million years ago (Ma), consisting of central Panama, western Panama, and Costa Rica plus Honduras. Thus, the presence of P. ridens appears to predate the completion of the Isthmus 3.1Ma. Using a parametric bootstrap (SOWH) test, we evaluated four a priori zoogeographic hypotheses for the origin and spread of P. ridens. This analysis suggested that the P. ridens populations on the Caribbean versant of Costa Rica were established by Pacific versant ancestors only recently, in contrast to the very old lineages found in Panama. Our results support a model of Miocene colonization, long-term geographic stasis, followed by rapid dispersal across the Caribbean lowlands during the Pliocene or Pleistocene.
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Affiliation(s)
- Ian J Wang
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancón, Panama
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