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Nachman MW, Beckman EJ, Bowie RCK, Cicero C, Conroy CJ, Dudley R, Hayes TB, Koo MS, Lacey EA, Martin CH, McGuire JA, Patton JL, Spencer CL, Tarvin RD, Wake MH, Wang IJ, Achmadi A, Álvarez-Castañeda ST, Andersen MJ, Arroyave J, Austin CC, Barker FK, Barrow LN, Barrowclough GF, Bates J, Bauer AM, Bell KC, Bell RC, Bronson AW, Brown RM, Burbrink FT, Burns KJ, Cadena CD, Cannatella DC, Castoe TA, Chakrabarty P, Colella JP, Cook JA, Cracraft JL, Davis DR, Davis Rabosky AR, D’Elía G, Dumbacher JP, Dunnum JL, Edwards SV, Esselstyn JA, Faivovich J, Fjeldså J, Flores-Villela OA, Ford K, Fuchs J, Fujita MK, Good JM, Greenbaum E, Greene HW, Hackett S, Hamidy A, Hanken J, Haryoko T, Hawkins MTR, Heaney LR, Hillis DM, Hollingsworth BD, Hornsby AD, Hosner PA, Irham M, Jansa S, Jiménez RA, Joseph L, Kirchman JJ, LaDuc TJ, Leaché AD, Lessa EP, López-Fernández H, Mason NA, McCormack JE, McMahan CD, Moyle RG, Ojeda RA, Olson LE, Kin Onn C, Parenti LR, Parra-Olea G, Patterson BD, Pauly GB, Pavan SE, Peterson AT, Poe S, Rabosky DL, Raxworthy CJ, Reddy S, Rico-Guevara A, Riyanto A, Rocha LA, Ron SR, Rovito SM, Rowe KC, Rowley J, Ruane S, Salazar-Valenzuela D, Shultz AJ, Sidlauskas B, Sikes DS, Simmons NB, Stiassny MLJ, Streicher JW, Stuart BL, Summers AP, Tavera J, Teta P, Thompson CW, Timm RM, Torres-Carvajal O, Voelker G, Voss RS, Winker K, Witt C, Wommack EA, Zink RM. Specimen collection is essential for modern science. PLoS Biol 2023; 21:e3002318. [PMID: 37992027 PMCID: PMC10664955 DOI: 10.1371/journal.pbio.3002318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 11/24/2023] Open
Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
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Affiliation(s)
- Michael W. Nachman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Chris J. Conroy
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Robert Dudley
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Tyrone B. Hayes
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Michelle S. Koo
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Eileen A. Lacey
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Christopher H. Martin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carol L. Spencer
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Marvalee H. Wake
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Ian J. Wang
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Anang Achmadi
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | | | - Michael J. Andersen
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christopher C. Austin
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lisa N. Barrow
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | | | - John Bates
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Kayce C. Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Rayna C. Bell
- California Academy of Sciences, San Francisco, California, United States of America
| | - Allison W. Bronson
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - Rafe M. Brown
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Frank T. Burbrink
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin J. Burns
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | | | - David C. Cannatella
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jocelyn P. Colella
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joel L. Cracraft
- American Museum of Natural History, New York, New York, United States of America
| | - Drew R. Davis
- Natural History Museum and Dept. of Biology, Eastern New Mexico University, Portales, New Mexico, United States of America
| | | | - Guillermo D’Elía
- Instituto de Cs. Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - John P. Dumbacher
- California Academy of Sciences, San Francisco, California, United States of America
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Scott V. Edwards
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Julián Faivovich
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Kassandra Ford
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jérôme Fuchs
- ISYEB, Muséum national d’Histoire naturelle, Paris, France
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jeffrey M. Good
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Eli Greenbaum
- Biodiversity Collections and Dept. of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Harry W. Greene
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shannon Hackett
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Melissa TR Hawkins
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Lawrence R. Heaney
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - David M. Hillis
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Angela D. Hornsby
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Peter A. Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Sharon Jansa
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Rosa Alicia Jiménez
- Escuela de Biología, Universidad de San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | | | - Travis J. LaDuc
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Adam D. Leaché
- Burke Museum, University of Washington, Seattle, Washington, United States of America
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Universidad de la República, Montevideo, Uruguay
| | - Hernán López-Fernández
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas A. Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - John E. McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California, United States of America
| | - Caleb D. McMahan
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Ricardo A. Ojeda
- CONICET, Centro de Ciencia y Técnica Mendoza, Mendoza, Argentina
| | - Link E. Olson
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | | | - Lynne R. Parenti
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Bruce D. Patterson
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Gregory B. Pauly
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Silvia E. Pavan
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - A Townsend Peterson
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Steven Poe
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Daniel L. Rabosky
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Sushma Reddy
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | | | - Awal Riyanto
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Luiz A. Rocha
- California Academy of Sciences, San Francisco, California, United States of America
| | - Santiago R. Ron
- Museo de Zoología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Kevin C. Rowe
- Museums Victoria Research Institute, Melbourne, Australia
| | - Jodi Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Sara Ruane
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | | | - Allison J. Shultz
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Brian Sidlauskas
- Dept. of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Derek S. Sikes
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Nancy B. Simmons
- American Museum of Natural History, New York, New York, United States of America
| | | | | | - Bryan L. Stuart
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
| | - Adam P. Summers
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, United States of America
| | | | - Pablo Teta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Cody W. Thompson
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert M. Timm
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | | | - Gary Voelker
- Dept. Ecology and Conservation Biology, Texas A&M University, College Station, Texas, United States of America
| | - Robert S. Voss
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin Winker
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Christopher Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Elizabeth A. Wommack
- University of Wyoming Museum of Vertebrates, University of Wyoming, Laramie, Wyoming, United States of America
| | - Robert M. Zink
- University of Nebraska State Museum, Lincoln, Nebraska, United States of America
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Rabibisoa NHC, Welt RS, Raxworthy CJ. Revision of the Subgenus Ochthomantis Frogs from Madagascar (Amphibia: Mantellidae) with the Description of Four Species and Resurrection of Mantidactylus catalai and M. poissoni. Animals (Basel) 2023; 13:2800. [PMID: 37685064 PMCID: PMC10563080 DOI: 10.3390/ani13172800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The subgenus Ochthomantis is an obligate forest and stream-dwelling group of mantellid frogs, endemic to Madagascar, with six species currently recognized. However, this group suffers from ongoing taxonomic confusion due to low numbers of examined specimens, and failure to consider morphological variation from development and sexual dimorphism. Here, we examined the morphology of 637 sexed adult specimens collected by us in the field and from other museum collections. We also sequenced a DNA fragment of the 16S mtDNA gene for each lineage to determine congruence between morphological and molecular data sets and to help delimit species. Our results demonstrate that the subgenus Ochthomantis includes eleven valid species: five already recognized, M. catalai and M. poissoni that we resurrect from synonymy, and four new species which we describe for the first time here. In some analyses, Mantidactylus majori groups with other Mantidactylus subgenera, so we do not consider it a member of the subgenus Ochthomantis in this study. All species have restricted distributions and elevational ranges in the humid forests of Madagascar. This study demonstrates the utility of assessing cryptic species using both diagnostic morphological characters and molecular data. The discovery of this new cryptic biodiversity, and the taxonomic revision herein, will likely require conservation activities for those species with the most restricted distributions.
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Affiliation(s)
- Nirhy H. C. Rabibisoa
- Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Rachel S. Welt
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
| | - Christopher J. Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
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Burbrink FT, Ruane S, Rabibisoa N, Raselimanana AP, Raxworthy CJ, Kuhn A. Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes. Ecol Evol 2023; 13:e10344. [PMID: 37529593 PMCID: PMC10375368 DOI: 10.1002/ece3.10344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single-island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.
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Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'EnvironnementUniversité de MahajangaMahajangaMadagascar
| | - Achille P. Raselimanana
- Zoologie et Biodiversité Animale, Faculté des SciencesUniversité d'AntananarivoAntananarivoMadagascar
| | | | - Arianna Kuhn
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
- Virginia Museum of Natural HistoryMartinsvilleVirginiaUSA
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4
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Das S, Greenbaum E, Meiri S, Bauer AM, Burbrink FT, Raxworthy CJ, Weinell JL, Brown RM, Brecko J, Pauwels OSG, Rabibisoa N, Raselimanana AP, Merilä J. Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family. Mol Phylogenet Evol 2023; 180:107700. [PMID: 36603697 DOI: 10.1016/j.ympev.2022.107700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023]
Abstract
The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.
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Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland.
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX 79968, USA
| | - Shai Meiri
- School of Zoology, Tel Aviv University, Tel Aviv, Israel; The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA
| | - Jeffrey L Weinell
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA; Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Jonathan Brecko
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium; Royal Museum for Central Africa, Tervuren, Belgium
| | - Olivier S G Pauwels
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Campus Universitaire d'Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland; Area of Ecology and Biodiversity, School of Biological Sciences, Kadoorie Biological Sciences Building, Pokfulam Road, The University of Hong Kong, Hong Kong Special Administrative Region
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5
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DeBaun D, Rabibisoa N, Raselimanana AP, Raxworthy CJ, Burbrink FT. Widespread Reticulate Evolution in an Adaptive Radiation. Evolution 2023; 77:931-945. [PMID: 36688802 DOI: 10.1093/evolut/qpad011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
Abstract
A fundamental assumption of evolutionary biology is that phylogeny follows a bifurcating process. However, hybrid speciation and introgression are becoming more widely documented in many groups. Hybrid inference studies have been historically limited to small sets of taxa, while exploration of the prevalence and trends of reticulation at deep time scales remains unexplored. We study the evolutionary history of an adaptive radiation of 109 gemsnakes in Madagascar (Pseudoxyrhophiinae) to identify potential instances of introgression. Using several network inference methods, we find twelve reticulation events within the 22-million-year evolutionary history of gemsnakes, producing 28% of the diversity for the group, including one reticulation that resulted in the diversification of an 18 species radiation. These reticulations occur at nodes with high gene tree discordance. Hybridization events occurred between north-south distributed parentals which share similar ecologies. Younger hybrids occupy intermediate contact zones between the parentals, showing that post-speciation dispersal in this group has not eroded the spatial signatures of introgression. Reticulations accumulated consistently over time, despite drops in overall speciation rates during the Pleistocene. This suggests that while bifurcating speciation may decline as the result of species accumulation and environmental change, speciation by hybridization may be more robust to these processes.
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Affiliation(s)
- Dylan DeBaun
- American Museum of Natural History, New York, USA
| | - Nirhy Rabibisoa
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Madagascar
| | - Achille P Raselimanana
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, BP 906, Antananarivo, 101 Madagascar.,Association Vahatra, BP 3972, Antananarivo, 101 Madagascar
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6
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Nunes LA, Raxworthy CJ, Pearson RG. Evidence for ecological processes driving speciation among endemic lizards of Madagascar. Evolution 2021; 76:58-69. [PMID: 34862965 DOI: 10.1111/evo.14409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 09/06/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Although genetic patterns produced by population isolation during speciation are well documented, the biogeographic and ecological processes that trigger speciation remain poorly understood. Alternative hypotheses for the biogeography and ecology of speciation include geographic isolation combined with niche conservation (soft allopatry) or parapatric distribution on an environmental gradient with niche divergence (ecological speciation). Here, we use species' distributions, environmental data, and two null models (the Random Translation and Rotation and the Background Similarity Test) to test these alternative hypotheses among 28 sister pairs of microendemic lizards in Madagascar. Our results demonstrate strong bimodal peaks along a niche divergence-conservation spectrum, with at least 25 out of 28 sister pairs exhibiting either niche conservation or divergence, and the remaining pairs showing weak ecological signals. Yet despite these significant results, we do not find strong associations of niche conservation with allopatric distributions or niche divergence with parapatric distributions. Our findings thus provide strong evidence of a role for ecological processes driving speciation, rather than the classic expectation of speciation through geographic isolation, but demonstrate that the link between ecological speciation and parapatry is complex and requires further analysis of a broader taxonomic sample to fully resolve.
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Affiliation(s)
- Laura A Nunes
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom.,Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, New York, New York, 10024
| | - Richard G Pearson
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
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Welt RS, Raxworthy CJ. Dispersal, not vicariance, explains the biogeographic origin of iguanas on Madagascar. Mol Phylogenet Evol 2021; 167:107345. [PMID: 34748875 DOI: 10.1016/j.ympev.2021.107345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/23/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022]
Abstract
Lizards of the clade Iguanidae (sensu lato) are primarily a New World group. Thus, the remarkable presence of an endemic lineage of iguanas (family Opluridae) on the isolated Indian Ocean island of Madagascar has long been considered a biogeographic anomaly. Previous work attributed this disjunct extant distribution to: (1) vicariance at about 140-165 Ma, caused by the breakup of Gondwana and the separation of South America, Africa, and Madagascar (with subsequent extinction of iguanas on Africa, and potentially other Gondwanan landmasses), (2) vicariance at about 80-90 Ma, caused by the sundering of hypothesized land-bridge connections between South America, Antarctica, India, and Madagascar, or (3) long-distance overwater dispersal from South America to Madagascar. Each hypothesis has been supported with molecular divergence dating analyses, and thus the biogeographic origin of the Opluridae is not yet well resolved. Here we utilize genetic sequences of ultraconserved elements for all Iguania families and the majority of Iguanidae (s.l.) genera, and morphological data for extant and fossil taxa (used for divergence dating analyses), to produce the most comprehensive dataset applied to date to test these origin hypotheses. We find strong support for a sister relationship between the Opluridae (Madagascar) and Leiosauridae (South America). Divergence of the Opluridae from Leiosauridae is dated to between the late Cretaceous and mid-Paleogene, at a time when Madagascar was already an island and was isolated from all other Gondwanan landmasses. Consequently, our results support a hypothesis of long-distance overwater dispersal of the Opluridae lineage, either directly from South America to Madagascar or potentially via Antarctica or Africa, leading to this radiation of iguanas in the Indian Ocean.
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Affiliation(s)
- Rachel S Welt
- Department of Herpetology, American Museum of Natural History, USA.
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8
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Fieldsend TW, Dubos N, Krysko KL, Raxworthy CJ, Malone SL. In situ adaptation and ecological release facilitate the occupied niche expansion of a non-native Madagascan day gecko in Florida. Ecol Evol 2021; 11:9410-9422. [PMID: 34306631 PMCID: PMC8293743 DOI: 10.1002/ece3.7749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/21/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
AIM To investigate whether the frequently advocated climate-matching species distribution modeling approach could predict the well-characterized colonization of Florida by the Madagascar giant day gecko Phelsuma grandis. LOCATION Madagascar and Florida, USA. METHODS To determine the climatic conditions associated with the native range of P. grandis, we used native-range presence-only records and Bioclim climatic data to build a Maxent species distribution model and projected the climatic thresholds of the native range onto Florida. We then built an analogous model using Florida presence-only data and projected it onto Madagascar. We constructed a third model using native-range presences for both P. grandis and the closely related parapatric species P. kochi. RESULTS Despite performing well within the native range, our Madagascar Bioclim model failed to identify suitable climatic habitat currently occupied by P. grandis in Florida. The model constructed using Florida presences also failed to reflect the distribution in Madagascar by overpredicting distribution, especially in western areas occupied by P. kochi. The model built using the combined P. kochi/P. grandis dataset modestly improved the prediction of the range of P. grandis in Florida, thereby implying competitive exclusion of P. grandis by P. kochi from habitat within the former's fundamental niche. These findings thus suggest ecological release of P. grandis in Florida. However, because ecological release cannot fully explain the divergent occupied niches of P. grandis in Madagascar versus Florida, our findings also demonstrate some degree of in situ adaptation in Florida. MAIN CONCLUSIONS Our models suggest that the discrepancy between the predicted and observed range of P. grandis in Florida is attributable to either in situ adaptation by P. grandis within Florida, or a combination of such in situ adaptation and competition with P. kochi in Madagascar. Our study demonstrates that climate-matching species distribution models can severely underpredict the establishment risk posed by non-native herpetofauna.
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Affiliation(s)
| | - Nicolas Dubos
- Département Écologie et Gestion de la BiodiversitéMuséum National d'Histoire NaturelleParisFrance
| | - Kenneth L. Krysko
- Division of HerpetologyFlorida Museum of Natural HistoryGainesvilleFLUSA
| | - Christopher J. Raxworthy
- Division of Vertebrate ZoologyDepartment of HerpetologyAmerican Museum of Natural HistoryNew York CityNYUSA
| | - Sparkle L. Malone
- Department of Biological SciencesFlorida International UniversityMiamiFLUSA
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9
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Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Syst Biol 2021; 70:49-66. [PMID: 32359157 PMCID: PMC7823230 DOI: 10.1093/sysbio/syaa034] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/30/2022] Open
Abstract
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].
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Affiliation(s)
- Paul M Hime
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Elizabeth Prendini
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Justin D Kratovil
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Pedro L V Peloso
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, 66075-750, Brazil
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Stephen C Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | | | - Christopher J Raxworthy
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sandeep Das
- Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Kerala 680653, India
| | - Nikhil Gaitonde
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - David M Green
- Redpath Museum, McGill University, Montreal, Quebec H3A 0C4, Canada
| | - Jim Labisko
- The Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, The University of Kent, Canterbury, Kent, CT2 7NR, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, PO Box 1348, Anse Royale, Mahé, Seychelles
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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10
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Uetz P, Cherikh S, Shea G, Ineich I, Campbell PD, Doronin IV, Rosado J, Wynn A, Tighe KA, McDiarmid R, Lee JL, Köhler G, Ellis R, Doughty P, Raxworthy CJ, Scheinberg L, Resetar A, Sabaj M, Schneider G, Franzen M, Glaw F, Böhme W, Schweiger S, Gemel R, Couper P, Amey A, Dondorp E, Ofer G, Meiri S, Wallach VAN. A global catalog of primary reptile type specimens. Zootaxa 2019; 4695:zootaxa.4695.5.2. [PMID: 31719333 DOI: 10.11646/zootaxa.4695.5.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Indexed: 11/04/2022]
Abstract
We present information on primary type specimens for 13,282 species and subspecies of reptiles compiled in the Reptile Database, that is, holotypes, neotypes, lectotypes, and syntypes. These represent 99.4% of all 13,361 currently recognized taxa (11,050 species and 2311 subspecies). Type specimens of 653 taxa (4.9%) are either lost or not located, were never designated, or we did not find any information about them. 51 species are based on iconotypes. To map all types to physical collections we have consolidated all synonymous and ambiguous collection acronyms into an unambiguous list of 364 collections holding these primary types. The 10 largest collections possess more than 50% of all (primary) reptile types, the 36 largest collections possess more than 10,000 types and the largest 73 collections possess over 90% of all types. Of the 364 collections, 107 hold type specimens of only 1 species or subspecies. Dozens of types are still in private collections. In order to increase their utility, we recommend that the description of type specimens be supplemented with data from high-resolution images and CT-scans, and clear links to tissue samples and DNA sequence data (when available). We request members of the herpetological community provide us with any missing type information to complete the list.
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Affiliation(s)
- Peter Uetz
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA..
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11
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Burbrink FT, Grazziotin FG, Pyron RA, Cundall D, Donnellan S, Irish F, Keogh JS, Kraus F, Murphy RW, Noonan B, Raxworthy CJ, Ruane S, Lemmon AR, Lemmon EM, Zaher H. Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships. Syst Biol 2019; 69:502-520. [DOI: 10.1093/sysbio/syz062] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022] Open
Abstract
Abstract
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brasil, 1500—Butantã, São Paulo—SP 05503-900, Brazil
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - David Cundall
- Department of Biological Sciences, 1 W. Packer Avenue, Lehigh University, Bethlehem, PA 18015, USA
| | - Steve Donnellan
- South Australian Museum, North Terrace, Adelaide SA 5000, Australia
- School of Biological Sciences, University of Adelaide, SA 5005 Australia
| | - Frances Irish
- Department of Biological Sciences, Moravian College, 1200 Main St, Bethlehem, PA 18018, US
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON M5S 2C6, Canada
| | - Brice Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University, 195 University Avenue, Newark, NJ 07102, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil CEP 04263-000, Brazil
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), UMR 7207 CNRS/MNHN/Sorbonne Université, Muséum national d’Histoire naturelle, 8 rue Buffon, CP 38, 75005 Paris, France
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12
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Burbrink FT, Ruane S, Kuhn A, Rabibisoa N, Randriamahatantsoa B, Raselimanana AP, Andrianarimalala MSM, Cadle JE, Lemmon AR, Lemmon EM, Nussbaum RA, Jones LN, Pearson R, Raxworthy CJ. The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar. Syst Biol 2019; 68:918-936. [DOI: 10.1093/sysbio/syz026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world’s mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University-Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 Fifth Ave., New York, NY 10016, USA
| | - Nirhy Rabibisoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Bernard Randriamahatantsoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Mamy S M Andrianarimalala
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - John E Cadle
- Department of Biology, East Georgia State College, Swainsboro, GA 30401, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Ronald A Nussbaum
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Leonard N Jones
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Richard Pearson
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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13
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Yuan ZY, Zhang BL, Raxworthy CJ, Weisrock DW, Hime PM, Jin JQ, Lemmon EM, Lemmon AR, Holland SD, Kortyna ML, Zhou WW, Peng MS, Che J, Prendini E. Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean. Natl Sci Rev 2018; 6:10-14. [PMID: 34691821 PMCID: PMC8294181 DOI: 10.1093/nsr/nwy092] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/30/2018] [Accepted: 09/02/2018] [Indexed: 12/02/2022] Open
Affiliation(s)
- Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | | | - Paul M Hime
- Department of Biology, University of Kentucky, Lexington, USA
- Biodiversity Institute, University of Kansas, Lawrence, USA
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, Tallahassee, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, Tallahassee, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, USA
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Elizabeth Prendini
- Department of Herpetology, American Museum of Natural History, New York, USA
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14
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Ruane S, Myers EA, Lo K, Yuen S, Welt RS, Juman M, Futterman I, Nussbaum RA, Schneider G, Burbrink FT, Raxworthy CJ. Unrecognized species diversity and new insights into colour pattern polymorphism within the widespread Malagasy snake Mimophis (Serpentes: Lamprophiidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1375046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University, 195 University Ave, Newark, NJ 07102, USA
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Edward A. Myers
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kahmun Lo
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Sara Yuen
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Rachel S. Welt
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Maya Juman
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - India Futterman
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Ronald A. Nussbaum
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Gregory Schneider
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Christopher J. Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
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15
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Blumgart D, Dolhem J, Raxworthy CJ. Herpetological diversity across intact and modified habitats of Nosy Komba Island, Madagascar. J NAT HIST 2017. [DOI: 10.1080/00222933.2017.1287312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Ruane S, Burbrink FT, Randriamahatantsoa B, Raxworthy CJ. The Cat-eyed Snakes of Madagascar: Phylogeny and Description of a New Species ofMadagascarophis(Serpentes: Lamprophiidae) from the Tsingy of Ankarana. COPEIA 2016. [DOI: 10.1643/ch-15-346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Florio AM, Raxworthy CJ. A Phylogeographic Assessment of the Malagasy Giant Chameleons (Furcifer verrucosus and Furcifer oustaleti). PLoS One 2016; 11:e0154144. [PMID: 27257819 PMCID: PMC4892496 DOI: 10.1371/journal.pone.0154144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 04/08/2016] [Indexed: 01/27/2023] Open
Abstract
The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus) are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are nested within this chameleon group, and two subspecies have been described in F. verrucosus. In this study, we utilized a phylogeographic approach to assess genetic diversification within these chameleons. This was accomplished by (1) identifying clades within each species supported by both mitochondrial and nuclear DNA, (2) assessing divergence times between clades, and (3) testing for niche divergence or conservatism. We found that both F. oustaleti and F. verrucosus could be readily identified based on genetic data, and within each species, there are two well-supported clades. However, divergence times are not contemporary and spatial patterns are not congruent. Diversification within F. verrucosus occurred during the Plio-Pleistocene, and there is evidence for niche divergence between a southwestern and southeastern clade, in a region of Madagascar that shows no obvious landscape barriers to dispersal. Diversification in F. oustaleti occurred earlier in the Pliocene or Miocene, and niche conservatism is supported with two genetically distinct clades separated at the Sofia River in northwestern Madagascar. Divergence within F. verrucosus is most consistent with patterns expected from ecologically mediated speciation, whereas divergence in F. oustaleti most strongly matches the patterns expected from the riverine barrier hypothesis.
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Affiliation(s)
- Antonia M. Florio
- Department of Herpetology, American Museum of Natural History, New York, NY, United States of America
| | - Christopher J. Raxworthy
- Department of Herpetology, American Museum of Natural History, New York, NY, United States of America
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Abstract
Chameleons, lizards often synonymous with camouflage for their color-changing abilities, possess a variety of permanent coloration patterns whose evolutionary significance remains largely unknown. In this study, we explore the potential for white ventral line markings in species across the genus Chamaeleonidae to function as a camouflage pattern against diurnal predators. Diurnal behavioral field studies of the white-lined chameleon Furcifer viridis showed that individuals typically exposed ventral line markings during the characteristic ring-flip antipredator behavior in response to a predatory threat. These ventral line markings are largely inconspicuous in other postures. Comparative morphological analyses of 86 species found that there was a significant positive correlation between ventral line markings with arboreal habitat type, even when accounting for phylogeny. These results suggest that ventral line markings (and the ring-flip behavior) could act as a disruptive or mimetic coloration marking for arboreal chameleons against visual diurnal predators. Further work testing differential predation rates is necessary in order to verify the proposed function of these line markings.
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Biju SD, Senevirathne G, Garg S, Mahony S, Kamei RG, Thomas A, Shouche Y, Raxworthy CJ, Meegaskumbura M, Van Bocxlaer I. Frankixalus, a New Rhacophorid Genus of Tree Hole Breeding Frogs with Oophagous Tadpoles. PLoS One 2016; 11:e0145727. [PMID: 26790105 PMCID: PMC4720377 DOI: 10.1371/journal.pone.0145727] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/08/2015] [Indexed: 11/18/2022] Open
Abstract
Despite renewed interest in the biogeography and evolutionary history of Old World tree frogs (Rhacophoridae), this family still includes enigmatic frogs with ambiguous phylogenetic placement. During fieldwork in four northeastern states of India, we discovered several populations of tree hole breeding frogs with oophagous tadpoles. We used molecular data, consisting of two nuclear and three mitochondrial gene fragments for all known rhacophorid genera, to investigate the phylogenetic position of these new frogs. Our analyses identify a previously overlooked, yet distinct evolutionary lineage of frogs that warrants recognition as a new genus and is here described as Frankixalusgen. nov. This genus, which contains the enigmatic ‘Polypedates’ jerdonii described by Günther in 1876, forms the sister group of a clade containing Kurixalus, Pseudophilautus, Raorchestes, Mercurana and Beddomixalus. The distinctiveness of this evolutionary lineage is also corroborated by the external morphology of adults and tadpoles, adult osteology, breeding ecology, and life history features.
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Affiliation(s)
- S D Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
| | - Gayani Senevirathne
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
| | - Stephen Mahony
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India.,School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Rachunliu G Kamei
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India.,Department of Life Sciences, The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Ashish Thomas
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India.,Department of Environmental Studies, Hindu College, University of Delhi, Delhi, 110 007, India
| | - Yogesh Shouche
- Microbial Culture Collection, National Center for Cell Science, NCCS Complex, Pune University Campus, Ganeshkhind, Pune, 411 007, India
| | - Christopher J Raxworthy
- Herpetology Department, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, United States of America
| | - Madhava Meegaskumbura
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Ines Van Bocxlaer
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
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20
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Bletz MC, Rosa GM, Andreone F, Courtois EA, Schmeller DS, Rabibisoa NHC, Rabemananjara FCE, Raharivololoniaina L, Vences M, Weldon C, Edmonds D, Raxworthy CJ, Harris RN, Fisher MC, Crottini A. Consistency of Published Results on the Pathogen Batrachochytrium dendrobatidis in Madagascar: Formal Comment on Kolby et al. Rapid Response to Evaluate the Presence of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) and Ranavirus in Wild Amphibian Populations in Madagascar. PLoS One 2015; 10:e0135900. [PMID: 26465608 PMCID: PMC4605792 DOI: 10.1371/journal.pone.0135900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 07/28/2015] [Indexed: 11/24/2022] Open
Affiliation(s)
- Molly C. Bletz
- Technische Universitat Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstr. 4, 38106, Braunschweig, Germany
- * E-mail:
| | - Gonçalo M. Rosa
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, United Kingdom
- Institute of Zoology, Zoological Society of London, Regent’s Park, London, NW1 4RY, United Kingdom
- Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Bloco 2, Piso 5, Campo Grande, 1749–016, Lisbon, Portugal
| | - Franco Andreone
- Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, I-10123, Torino, Italy
- IUCN SSC Amphibian Specialist Group-Madagascar, Antananarivo, Madagascar
| | - Elodie A. Courtois
- CNRS-Guyane, USR 3456, 2 avenue Gustave Charlery, 97300, Cayenne, Guyane Française
- Station d’écologie expérimentale du CNRS à Moulis, USR 2936, 2 route du CNRS, 09200, Moulis, France
| | - Dirk S. Schmeller
- UFZ–Helmholtz Centre for Environmental Research, Department of Conservation Biology, Permoserstr. 15, 04318, Leipzig, Germany
- EcoLab (Laboratoire Ecologie Fonctionnelle et Environement), CNRS/Université de Toulouse, UPS, INPT, 118 route de Narbonne, 31062, Toulouse, France
| | - Nirhy H. C. Rabibisoa
- IUCN SSC Amphibian Specialist Group-Madagascar, Antananarivo, Madagascar
- Département de Biologie Animale et Ecologie, Faculté des Sciences, University of Mahajanga, Ambondrona, B.P. 652, Mahajanga 401, Madagascar
| | | | | | - Miguel Vences
- Technische Universitat Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Devin Edmonds
- Association Mitsinjo, Lot 104 A Andasibe Gare, Andasibe, 514, Madagascar
| | - Christopher J. Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79 St., New York, NY, 10024, United States of America
| | - Reid N. Harris
- Department of Biology, James Madison University, Harrisonburg, VA, 22807, United States of America
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, United Kingdom
| | - Angelica Crottini
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, N°7, 4485–661 Vairão, Vila do Conde, Portugal
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Ruane S, Raxworthy CJ, Lemmon AR, Lemmon EM, Burbrink FT. Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes. BMC Evol Biol 2015; 15:221. [PMID: 26459325 PMCID: PMC4603904 DOI: 10.1186/s12862-015-0503-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar's serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. METHODS Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. RESULTS Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. CONCLUSIONS Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees.
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Affiliation(s)
- Sara Ruane
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Alan R Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Biology Department, College of Staten Island/CUNY, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.
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22
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Oliver LA, Prendini E, Kraus F, Raxworthy CJ. Systematics and biogeography of the Hylarana frog (Anura: Ranidae) radiation across tropical Australasia, Southeast Asia, and Africa. Mol Phylogenet Evol 2015; 90:176-92. [PMID: 25987527 DOI: 10.1016/j.ympev.2015.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/29/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
We present an inclusive molecular phylogeny for Hylarana across its global distribution, utilizing two mitochondrial and four nuclear gene regions for 69 of the 97 currently described species. We use phylogenetic methods to test monophyly of Hylarana, determine relationships among ten putative subgenera, identify major clades, reconstruct biogeographic history, and estimate continental dispersal dates. Results support Hylarana as a monophyletic group originating approximately 26.9MYA and comprising eight clades that partly correspond to currently described subgenera plus two new groups. The African and Australasian species each form clades embedded within a paraphyletic Southeast Asian group. We estimate that Africa and Australasia were colonized by Hylarana s.l. from SE Asia approximately 18.7 and 10.8MYA, respectively. Biogeographic reconstructions also support three separate colonization events in India from Southeast Asia. Examination of museum specimens identified morphological characters useful for delineating subgenera and species. We herein elevate all supported subgenera to genus rank and formally describe two new genera to produce a revised taxonomy congruent with our new phylogenetic and biogeographic findings.
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Affiliation(s)
- Lauren A Oliver
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, United States; Department of Herpetology, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, United States.
| | - Elizabeth Prendini
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, United States; Department of Ecology, Evolution and Natural Resource Conservation, Rutgers University, New Brunswick, NJ 08901, United States
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, United States
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23
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Bletz MC, Rosa GM, Andreone F, Courtois EA, Schmeller DS, Rabibisoa NHC, Rabemananjara FCE, Raharivololoniaina L, Vences M, Weldon C, Edmonds D, Raxworthy CJ, Harris RN, Fisher MC, Crottini A. Widespread presence of the pathogenic fungus Batrachochytrium dendrobatidis in wild amphibian communities in Madagascar. Sci Rep 2015; 5:8633. [PMID: 25719857 PMCID: PMC4341422 DOI: 10.1038/srep08633] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/12/2015] [Indexed: 01/15/2023] Open
Abstract
Amphibian chytridiomycosis, an emerging infectious disease caused by the fungus Batrachochytrium dendrobatidis (Bd), has been a significant driver of amphibian declines. While globally widespread, Bd had not yet been reported from within Madagascar. We document surveys conducted across the country between 2005 and 2014, showing Bd's first record in 2010. Subsequently, Bd was detected in multiple areas, with prevalence reaching up to 100%. Detection of Bd appears to be associated with mid to high elevation sites and to have a seasonal pattern, with greater detectability during the dry season. Lineage-based PCR was performed on a subset of samples. While some did not amplify with any lineage probe, when a positive signal was observed, samples were most similar to the Global Panzootic Lineage (BdGPL). These results may suggest that Bd arrived recently, but do not exclude the existence of a previously undetected endemic Bd genotype. Representatives of all native anuran families have tested Bd-positive, and exposure trials confirm infection by Bd is possible. Bd's presence could pose significant threats to Madagascar's unique "megadiverse" amphibians.
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Affiliation(s)
- Molly C Bletz
- 1] Department of Biology, James Madison University, Harrisonburg, VA 22807, USA [2] Technische Universität Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Gonçalo M Rosa
- 1] Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent CT2 7NR, UK [2] Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK [3] Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências da Universidade de Lisboa, Bloco 2, Piso 5, Campo Grande, 1749-016 Lisbon, Portugal
| | - Franco Andreone
- 1] Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, I-10123, Torino, Italy [2] IUCN SSC Amphibian Specialist Group-Madagascar, 101 Antananarivo, Madagascar
| | - Elodie A Courtois
- 1] CNRS-Guyane, USR 3456, 2 avenue Gustave Charlery, 97300 Cayenne, Guyane Française [2] Station d'écologie expérimentale du CNRS à Moulis, USR 2936, 2 route du CNRS, 09200 Moulis, France
| | - Dirk S Schmeller
- 1] UFZ - Helmholtz Centre for Environmental Research, Department of Conservation Biology, Permoserstr. 15, 04318 Leipzig, Germany [2] EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), CNRS/Université de Toulouse; UPS, INPT; 118 route de Narbonne, 31062 Toulouse, France
| | - Nirhy H C Rabibisoa
- 1] IUCN SSC Amphibian Specialist Group-Madagascar, 101 Antananarivo, Madagascar [2] Département de Biologie Animale et Ecologie, Faculté des Sciences, University of Mahajanga, Ambondrona, B.P. 652, Mahajanga 401, Madagascar
| | - Falitiana C E Rabemananjara
- 1] IUCN SSC Amphibian Specialist Group-Madagascar, 101 Antananarivo, Madagascar [2] University of Antananarivo, BP 906, Antananarivo 101, Antananarivo, Madagascar
| | | | - Miguel Vences
- Technische Universität Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Devin Edmonds
- Association Mitsinjo, Lot 104 A Andasibe Gare, Andasibe 514, Madagascar
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th St. New York, NY 10024, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, W2 1PG, UK
| | - Angelica Crottini
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Vila do Conde, Portugal
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Jenkins RKB, Tognelli MF, Bowles P, Cox N, Brown JL, Chan L, Andreone F, Andriamazava A, Andriantsimanarilafy RR, Anjeriniaina M, Bora P, Brady LD, Hantalalaina EF, Glaw F, Griffiths RA, Hilton-Taylor C, Hoffmann M, Katariya V, Rabibisoa NH, Rafanomezantsoa J, Rakotomalala D, Rakotondravony H, Rakotondrazafy NA, Ralambonirainy J, Ramanamanjato JB, Randriamahazo H, Randrianantoandro JC, Randrianasolo HH, Randrianirina JE, Randrianizahana H, Raselimanana AP, Rasolohery A, Ratsoavina FM, Raxworthy CJ, Robsomanitrandrasana E, Rollande F, van Dijk PP, Yoder AD, Vences M. Extinction risks and the conservation of Madagascar's reptiles. PLoS One 2014; 9:e100173. [PMID: 25111137 PMCID: PMC4128600 DOI: 10.1371/journal.pone.0100173] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/22/2014] [Indexed: 01/08/2023] Open
Abstract
Background An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. Methodology/Principal Findings Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. Conclusions/Significance With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and western regions of Madagascar and this study highlights the importance of these arid regions to conserving the island's biodiversity.
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Affiliation(s)
| | - Marcelo F. Tognelli
- IUCN/CI Biodiversity Assessment Unit, Betty & Gordon Moore Center for Science & Oceans, Conservation International, Arlington, Virginia, United States of America
- IUCN Global Species Programme, Gland, Switzerland
| | - Philip Bowles
- IUCN/CI Biodiversity Assessment Unit, Betty & Gordon Moore Center for Science & Oceans, Conservation International, Arlington, Virginia, United States of America
- IUCN Global Species Programme, Gland, Switzerland
| | - Neil Cox
- IUCN/CI Biodiversity Assessment Unit, Betty & Gordon Moore Center for Science & Oceans, Conservation International, Arlington, Virginia, United States of America
- IUCN Global Species Programme, Gland, Switzerland
| | - Jason L. Brown
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Lauren Chan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, United States of America
| | | | - Alain Andriamazava
- Ligue pour la Protection de la Nature à Madagascar, Lot 313 Cité Civil Ambohipo, Antaninarenina, Antananarivo, Madagascar
| | | | - Mirana Anjeriniaina
- WWF Madagascar and West Indian Ocean Programme Office, Antananarivo, Madagascar
| | - Parfait Bora
- Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Lee D. Brady
- Calumma Ecological Services, Dunkirk, Faversham, Kent, United Kingdom
| | - Elisoa F. Hantalalaina
- Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Frank Glaw
- Zoologische Staatssammlung München, München, Germany
| | - Richard A. Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, United Kingdom
| | | | - Michael Hoffmann
- IUCN/CI Biodiversity Assessment Unit, Betty & Gordon Moore Center for Science & Oceans, Conservation International, Arlington, Virginia, United States of America
- IUCN Species Survival Commission, Gland, Switzerland
- United Nations Environment Programme World Conservation Monitoring Centre, Cambridge, United Kingdom
| | | | - Nirhy H. Rabibisoa
- Département de Zoologie et Ecologie, Faculté des Sciences Campus Ambondrona, Mahajanga, Madagascar
| | - Jeannot Rafanomezantsoa
- Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - Hery Rakotondravony
- Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ny A. Rakotondrazafy
- Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | | | | | | | | | | | | | | | | | | | - Fanomezana M. Ratsoavina
- Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
- Technical University of Braunschweig, Zoological Institute, Braunschweig, Germany
| | - Christopher J. Raxworthy
- Herpetology Department, American Museum of Natural History, New York, New York, United States of America
| | | | - Finoana Rollande
- Conservation International, Villa Hajanirina, Ankorahotra, Antananarivo, Madagascar
| | - Peter P. van Dijk
- IUCN/CI Biodiversity Assessment Unit, Betty & Gordon Moore Center for Science & Oceans, Conservation International, Arlington, Virginia, United States of America
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Miguel Vences
- Technical University of Braunschweig, Zoological Institute, Braunschweig, Germany
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Florio AM, Ingram CM, Rakotondravony HA, Louis EE, Raxworthy CJ. Detecting cryptic speciation in the widespread and morphologically conservative carpet chameleon (Furcifer lateralis) of Madagascar. J Evol Biol 2012; 25:1399-414. [PMID: 22686488 DOI: 10.1111/j.1420-9101.2012.02528.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation.
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Affiliation(s)
- A M Florio
- Richard Gilder Graduate School, Department of Herpetology, American Museum of Natural History, New York, NY, USA.
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Richards CM, Nussbaum RA, Raxworthy CJ. Phylogenetic relationships within the Madagascan boophids and mantellids as elucidated by mitochondrial ribosomal genes. AFR J HERPETOL 2010. [DOI: 10.1080/21564574.2000.9650013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Christina M. Richards
- a Department of Biological Sciences , Wayne State University , Detroit, MI, 48202, USA E-mail:
| | - Ronald A. Nussbaum
- b Division of Herpetology, Museum of Zoology , University of Michigan , Ann Arbor, MI, 48108, USA
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Andreone F, Rosa GM, Noël J, Crottini A, Vences M, Raxworthy CJ. Living within fallen palm leaves: the discovery of an unknown Blommersia (Mantellidae: Anura) reveals a new reproductive strategy in the amphibians of Madagascar. Naturwissenschaften 2010; 97:525-43. [PMID: 20401457 DOI: 10.1007/s00114-010-0667-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 03/23/2010] [Accepted: 03/25/2010] [Indexed: 10/19/2022]
Abstract
We describe a new mantelline frog of the genus Blommersia found in rainforest in North East Madagascar, from the protected areas of Ambatovaky, Betampona, Masoala, and Zahamena. Blommersia angolafa n.sp. is a small frog, with a body size of 17-21 mm, expanded finger and toe tips, and colouration ranging from yellow to dark brown, with pale-bluish spots on the flanks and light tips of fingers and toes. A peculiar aspect characterising this new species is its novel life history and reproductive mode. Both sexes live and breed in a phytotelmic habitat of water accumulated within fallen prophylls and fallen leaf sheaths of at least three species of Dypsis palms. Within these phytotelmata, egg laying and complete larval development occur. Thus, B. angolafa n.sp. represents a new evolutionary lineage of Malagasy frogs in which phytotelmy is known. Up to now, reproduction in phytotelmata in Malagasy frogs has been reported for many cophyline microhylids, most species of Guibemantis, Mantella laevigata, and possibly in a still-undescribed species belonging to the genus Spinomantis. We consider the reproductive mode of B. angolafa as a derived character, having evolved from the more typical reproduction in lentic water bodies. The general scarcity of lentic habitats in Malagasy rainforests may have provided the conditions that favoured the evolution of this phytotelmic breeding strategy. The new species, being specialised to a habitat represented by a few selected Dypsis species, potentially suffers the selective exploitation of these palms.
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Affiliation(s)
- Franco Andreone
- Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, 10123, Torino, Italy.
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Köhler G, Diethert HH, Nussbaum RA, Raxworthy CJ. A Revision of the Fish Scale Geckos, Genus Geckolepis Grandidier (Squamata, Gekkonidae) from Madagascar and the Comoros. HERPETOLOGICA 2009. [DOI: 10.1655/08-059.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Karsten KB, Andriamandimbiarisoa LN, Fox SF, Raxworthy CJ. Sexual selection on body size and secondary sexual characters in 2 closely related, sympatric chameleons in Madagascar. Behav Ecol 2009. [DOI: 10.1093/beheco/arp100] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Karsten KB, Andriamandimbiarisoa LN, Fox SF, Raxworthy CJ. Social Behavior of Two Species of Chameleons in Madagascar: Insights Into Sexual Selection. HERPETOLOGICA 2009. [DOI: 10.1655/08-035r1.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Pearson RG, Raxworthy CJ. The evolution of local endemism in madagascar: watershed versus climatic gradient hypotheses evaluated by null biogeographic models. Evolution 2009; 63:959-67. [PMID: 19210532 DOI: 10.1111/j.1558-5646.2008.00596.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Substantial insular speciation has resulted in exceptionally high levels of endemism in Madagascar, creating locally restricted species' ranges that remain poorly understood. The contributions of alternative processes that could influence patterns of local endemism-including speciation by geographic isolation or adaptation to environmental gradients-are widely debated, both for Madagascar and elsewhere. A recently proposed hypothesis (the "watershed hypothesis") suggests that allopatric speciation driven by isolation in watersheds during Quaternary climate shifts provides a general explanation for patterns of local endemism across taxa in Madagascar. Here we tested coincidence between species' distributions and areas of endemism predicted by two contrasting biogeographic hypotheses: (1) the watershed hypothesis, and (2) an alternative hypothesis driven by climatic gradients (the "current climate hypothesis"). Statistical significance of coincidence was assessed by comparing against a null model. Surprisingly, we found that extant distributions of lemurs, geckos, and chameleons reveal species patterns that are significantly coincident with the watershed and current climate hypotheses. These results strongly support local endemism developing from multiple processes, even among closely related species. Our findings thus indicate that pluralistic approaches will offer the best option both for understanding processes that generate local endemism, and for incorporating endemism within conservation priority setting.
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Affiliation(s)
- Richard G Pearson
- Department of Herpetology, American Nuseum of Natural History, New York, New York 10024, USA.
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Andreone F, Carpenter AI, Cox N, du Preez L, Freeman K, Furrer S, Garcia G, Glaw F, Glos J, Knox D, Köhler J, Mendelson JR, Mercurio V, Mittermeier RA, Moore RD, Rabibisoa NHC, Randriamahazo H, Randrianasolo H, Raminosoa NR, Ramilijaona OR, Raxworthy CJ, Vallan D, Vences M, Vieites DR, Weldon C. The challenge of conserving amphibian megadiversity in Madagascar. PLoS Biol 2008; 6:e118. [PMID: 18462021 PMCID: PMC2365978 DOI: 10.1371/journal.pbio.0060118] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Highly diverse and so far apparently untouched by emergent diseases, Malagasy frogs nevertheless are threatened by ongoing habitat destruction, making pro-active conservation actions especially important for preserving this unique, pre-decline, amphibian fauna.
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Affiliation(s)
- Franco Andreone
- Museo Regionale di Scienze Naturali di Torino, Torino, Italy.
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Cramer AF, Rabibisoa NHC, Raxworthy CJ. Descriptions of two new Spinomantis frogs from Madagascar (Amphibia: Mantellidae), and new morphological data for S. brunae and S. massorum. American Museum Novitates 2008. [DOI: 10.1206/594.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Frost DR, Grant T, Faivovich J, Bain RH, Haas A, Haddad CFB, de Sa RO, Channing A, Wilkinson M, Donnellan SC, Raxworthy CJ, Campbell JA, Blotto BL, Moler P, Drewes RC, Nussbaum RA, Lynch JD, Green DM, Wheeler WC. Is The Amphibian Tree of Life really fatally flawed? Cladistics 2008. [DOI: 10.1111/j.1096-0031.2007.00181.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Kremen C, Cameron A, Moilanen A, Phillips SJ, Thomas CD, Beentje H, Dransfield J, Fisher BL, Glaw F, Good TC, Harper GJ, Hijmans RJ, Lees DC, Louis E, Nussbaum RA, Raxworthy CJ, Razafimpahanana A, Schatz GE, Vences M, Vieites DR, Wright PC, Zjhra ML. Aligning Conservation Priorities Across Taxa in Madagascar with High-Resolution Planning Tools. Science 2008; 320:222-6. [PMID: 18403708 DOI: 10.1126/science.1155193] [Citation(s) in RCA: 379] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- C Kremen
- Department of Environmental Sciences, Policy and Management, 137 Mulford Hall, University of California, Berkeley, CA 94720-3114, USA.
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Raxworthy CJ, Ingram CM, Rabibisoa N, Pearson RG. Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar. Syst Biol 2008; 56:907-23. [PMID: 18066927 DOI: 10.1080/10635150701775111] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Although the systematic utility of ecological niche modeling is generally well known (e.g., concerning the recognition and discovery of areas of endemism for biogeographic analyses), there has been little discussion of applications concerning species delimitation, and to date, no empirical evaluation has been conducted. However, ecological niche modeling can provide compelling evidence for allopatry between populations, and can also detect divergent ecological niches between candidate species. Here we present results for two taxonomically problematic groups of Phelsuma day geckos from Madagascar, where we integrate ecological niche modeling with mitochondrial DNA and morphological data to evaluate species limits. Despite relatively modest levels of genetic and morphological divergence, for both species groups we find divergent ecological niches between closely related species and parapatric ecological niche models. Niche models based on the new species limits provide a better fit to the known distribution than models based upon the combined (lumped) species limits. Based on these results, we elevate three subspecies of Phelsuma madagascariensis to species rank and describe a new species of Phelsuma from the P. dubia species group. Our phylogeny continues to support a major endemic radiation of Phelsuma in Madagascar, with dispersals to Pemba Island and the Mascarene Islands. We conclude that ecological niche modeling offers great potential for species delimitation, especially for taxonomic groups exhibiting low vagility and localized endemism and for groups with more poorly known distributions. In particular, niche modeling should be especially sensitive for detecting recent parapatric speciation driven by ecological divergence, when the environmental gradients driving speciation are represented within the ecological niche models.
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Affiliation(s)
- Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, New York, NY 10024-5192, USA.
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Raxworthy CJ, Nussbaum RA. Six New Species of Occipital-lobed Calumma Chameleons (Squamata: Chamaeleonidae) from Montane Regions of Madagascar, with a New Description and Revision of Calumma Brevicorne. COPEIA 2006. [DOI: 10.1643/0045-8511(2006)6[711:snsooc]2.0.co;2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mendelson JR, Lips KR, Gagliardo RW, Rabb GB, Collins JP, Diffendorfer JE, Daszak P, Ibáñez D R, Zippel KC, Lawson DP, Wright KM, Stuart SN, Gascon C, da Silva HR, Burrowes PA, Joglar RL, La Marca E, Lötters S, du Preez LH, Weldon C, Hyatt A, Rodriguez-Mahecha JV, Hunt S, Robertson H, Lock B, Raxworthy CJ, Frost DR, Lacy RC, Alford RA, Campbell JA, Parra-Olea G, Bolaños F, Domingo JJC, Halliday T, Murphy JB, Wake MH, Coloma LA, Kuzmin SL, Price MS, Howell KM, Lau M, Pethiyagoda R, Boone M, Lannoo MJ, Blaustein AR, Dobson A, Griffiths RA, Crump ML, Wake DB, Brodie ED. Biodiversity. Confronting amphibian declines and extinctions. Science 2006; 313:48. [PMID: 16825553 DOI: 10.1126/science.1128396] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Le M, Raxworthy CJ, McCord WP, Mertz L. A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes. Mol Phylogenet Evol 2006; 40:517-31. [PMID: 16678445 DOI: 10.1016/j.ympev.2006.03.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2005] [Revised: 03/01/2006] [Accepted: 03/02/2006] [Indexed: 11/29/2022]
Abstract
Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.
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Affiliation(s)
- Minh Le
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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Greenbaum E, Campbell AC, Raxworthy CJ. A REVISION OF SUB-SAHARAN CHALCIDES (SQUAMATA: SCINCIDAE), WITH REDESCRIPTIONS OF TWO EAST AFRICAN SPECIES. HERPETOLOGICA 2006. [DOI: 10.1655/05-14.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Clark VC, Raxworthy CJ, Rakotomalala V, Sierwald P, Fisher BL. Convergent evolution of chemical defense in poison frogs and arthropod prey between Madagascar and the Neotropics. Proc Natl Acad Sci U S A 2005; 102:11617-22. [PMID: 16087888 PMCID: PMC1187980 DOI: 10.1073/pnas.0503502102] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Indexed: 11/18/2022] Open
Abstract
With few exceptions, aposematically colored poison frogs sequester defensive alkaloids, unchanged, from dietary arthropods. In the Neotropics, myrmicine and formicine ants and the siphonotid millipede Rhinotus purpureus are dietary sources for alkaloids in dendrobatid poison frogs, yet the arthropod sources for Mantella poison frogs in Madagascar remained unknown. We report GC-MS analyses of extracts of arthropods and microsympatric Malagasy poison frogs (Mantella) collected from Ranomafana, Madagascar. Arthropod sources for 11 "poison frog" alkaloids were discovered, 7 of which were also detected in microsympatric Mantella. These arthropod sources include three endemic Malagasy ants, Tetramorium electrum, Anochetus grandidieri, and Paratrechina amblyops (subfamilies Myrmicinae, Ponerinae, and Formicinae, respectively), and the pantropical tramp millipede R. purpureus. Two of these ant species, A. grandidieri and T. electrum, were also found in Mantella stomachs, and ants represented the dominant prey type (67.3% of 609 identified stomach arthropods). To our knowledge, detection of 5,8-disubstituted (ds) indolizidine iso-217B in T. electrum represents the first izidine having a branch point in its carbon skeleton to be identified from ants, and detection of 3,5-ds pyrrolizidine 251O in A. grandidieri represents the first ponerine ant proposed as a dietary source of poison frog alkaloids. Endemic Malagasy ants with defensive alkaloids (with the exception of Paratrechina) are not closely related to any Neotropical species sharing similar chemical defenses. Our results suggest convergent evolution for the acquisition of defensive alkaloids in these dietary ants, which may have been the critical prerequisite for subsequent convergence in poison frogs between Madagascar and the Neotropics.
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Affiliation(s)
- Valerie C Clark
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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Raxworthy CJ, Martinez-Meyer E, Horning N, Nussbaum RA, Schneider GE, Ortega-Huerta MA, Townsend Peterson A. Predicting distributions of known and unknown reptile species in Madagascar. Nature 2003; 426:837-41. [PMID: 14685238 DOI: 10.1038/nature02205] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Accepted: 11/11/2003] [Indexed: 11/08/2022]
Abstract
Despite the importance of tropical biodiversity, informative species distributional data are seldom available for biogeographical study or setting conservation priorities. Modelling ecological niche distributions of species offers a potential solution; however, the utility of old locality data from museums, and of more recent remotely sensed satellite data, remains poorly explored, especially for rapidly changing tropical landscapes. Using 29 modern data sets of environmental land coverage and 621 chameleon occurrence localities from Madagascar (historical and recent), here we demonstrate a significant ability of our niche models in predicting species distribution. At 11 recently inventoried sites, highest predictive success (85.1%) was obtained for models based only on modern occurrence data (74.7% and 82.8% predictive success, respectively, for pre-1978 and all data combined). Notably, these models also identified three intersecting areas of over-prediction that recently yielded seven chameleon species new to science. We conclude that ecological niche modelling using recent locality records and readily available environmental coverage data provides informative biogeographical data for poorly known tropical landscapes, and offers innovative potential for the discovery of unknown distributional areas and unknown species.
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Affiliation(s)
- Christopher J Raxworthy
- American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024-5192, USA.
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Abstract
Historical biogeography is dominated by vicariance methods that search for a congruent pattern of fragmentation of ancestral distributions produced by shared Earth history. A focus of vicariant studies has been austral area relationships and the break-up of the supercontinent Gondwana. Chameleons are one of the few extant terrestrial vertebrates thought to have biogeographic patterns that are congruent with the Gondwanan break-up of Madagascar and Africa. Here we show, using molecular and morphological evidence for 52 chameleon taxa, support for a phylogeny and area cladogram that does not fit a simple vicariant history. Oceanic dispersal--not Gondwanan break-up--facilitated species radiation, and the most parsimonious biogeographic hypothesis supports a Madagascan origin for chameleons, with multiple 'out-of-Madagascar' dispersal events to Africa, the Seychelles, the Comoros archipelago, and possibly Reunion Island. Although dispersal is evident in other Indian Ocean terrestrial animal groups, our study finds substantial out-of-Madagascar species radiation, and further highlights the importance of oceanic dispersal as a potential precursor for speciation.
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Affiliation(s)
- C J Raxworthy
- American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024-5192, USA.
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Nussbaum RA, Raxworthy CJ, Raselimanana AP, Ramanamanjato JB. New Species of Day Gecko,PhelsumaGray (Reptilia: Squamata: Gekkonidae), from the Réserve Naturelle Intégrale d'Andohahela, Southern Madagascar. COPEIA 2000. [DOI: 10.1643/0045-8511(2000)000[0763:nsodgp]2.0.co;2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Nussbaum RA, Raxworthy CJ, Ramanamanjato JB. Additional Species of Mabuya Fitzinger (Reptilia: Squamata: Scincidae) from Western Madagascar. J HERPETOL 1999. [DOI: 10.2307/1565724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nussbaum RA, Andreone F, Raxworthy CJ. New Rain-Forest Species of Pseudoxyrhopus Günther (Squamata: Colubridae) from Northern Madagascar. COPEIA 1998. [DOI: 10.2307/1447708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nussbaum RA, Raxworthy CJ. New Long-Tailed Mabuya Fitzinger from Lokobe Reserve, Nosy Be, Madagascar (Reptilia: Squamata: Scincidae). COPEIA 1998. [DOI: 10.2307/1447706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nussbaum RA, Raxworthy CJ. A New Mabuya (Reptilia: Squamata: Scincidae) of the Aureopunctata-Group from Southern Madagascar. J HERPETOL 1995. [DOI: 10.2307/1565082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nussbaum RA, Raxworthy CJ. New Uroplatus Duméril (Reptilia: Squamata: Gekkonidae) of the ebenaui-Group from the Anosy Mountains of Southern Madagascar. COPEIA 1995. [DOI: 10.2307/1446806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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