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Molecular Analysis and Phylogeography of Neotropical Amphibians
Molecular analysis and Phylogeography of Neotropical Amphibians Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Marcelo Coelho Miguel Gehara aus Juiz de Fora - MG, Brasilien 1. Referentin oder Referent: Professor Dr. Miguel Vences 2. Referentin oder Referent: Professor Dr. Michael Veith eingereicht am: 01.10.2012 mündliche Prüfung (Disputation) am: 25.01.2013 Drukjahr 2013 2 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Keine Tagungsbeiträge Canedo, C; GEHARA, M ; Vences, M; HADDAD, CFB Molecular and acoustic analyses of Ischnocnema guentheri species complex (Anura: Brachycephalidae). In: IX Congresso Latinoamericano de Herpetologia, 2011 . Resumos do IX Congresso Latinoamericano de Herpetologia, 2011, Curitiba, Brazil (oral presentation) GEHARA, M ; Canedo, C; Haddad, C; Vences, M Molecular analysis of Ischnocnema guentheri highlights a complex of cryptic species. In: XI Congreso Luso-Espanol / XV Congreso Espanol de Herpetología. 2010 . Sevilla, Spain. (oral presentation) 3 When the mind is thinking it is talking to itself Plato 4 Table of contents I. Acknowledgments ............................................................................................................................... -
The Promise of Next-Generation Taxonomy
Megataxa 001 (1): 035–038 ISSN 2703-3082 (print edition) https://www.mapress.com/j/mt/ MEGATAXA Copyright © 2020 Magnolia Press Correspondence ISSN 2703-3090 (online edition) https://doi.org/10.11646/megataxa.1.1.6 The promise of next-generation taxonomy MIGUEL VENCES Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany �[email protected]; https://orcid.org/0000-0003-0747-0817 Documenting, naming and classifying the diversity and concepts. We should meet three main challenges, of life on Earth provides baseline information on the using new technological developments without throwing biosphere, which is crucially important to understand and the well-tried and successful foundations of Linnaean mitigate the global changes of the Anthropocene. Since nomenclature overboard. Linnaeus, taxonomists have named about 1.8 million species (Roskov et al. 2019) and continue doing so at 1. Fully embrace cybertaxonomy, machine learning a rate of about 15,000–20,000 species per year (IISE and DNA taxonomy to ease, not burden the workflow 2011). Natural history collections—museums, herbaria, of taxonomists. culture collections and others—hold billions of collection specimens (Brooke 2000) and have teamed up to Computer power and especially, DNA sequencing capacity assemble a cybertaxonomic infrastructure that mobilizes increases faster than exponentially (e.g., Rupp 2018) metadata and images of voucher specimens, now even and new technologies offer unprecedented opportunities at the scale of digitizing entire collections of millions for classifying specimens based on molecular evidence of insect or herbaria vouchers in automated imaging or image analysis. Yet, the vast majority of species lines (e.g., Tegelberg et al. -
A Molecular Phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)
Zootaxa 1945: 51–66 (2008) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2008 · Magnolia Press ISSN 1175-5334 (online edition) Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia) NICOLAS VIDAL1,10, WILLIAM R. BRANCH2, OLIVIER S.G. PAUWELS3,4, S. BLAIR HEDGES5, DONALD G. BROADLEY6, MICHAEL WINK7, CORINNE CRUAUD8, ULRICH JOGER9 & ZOLTÁN TAMÁS NAGY3 1UMR 7138, Systématique, Evolution, Adaptation, Département Systématique et Evolution, C. P. 26, Muséum National d’Histoire Naturelle, 43 Rue Cuvier, Paris 75005, France. E-mail: [email protected] 2Bayworld, P.O. Box 13147, Humewood 6013, South Africa. E-mail: [email protected] 3 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium. E-mail: [email protected], [email protected] 4Smithsonian Institution, Center for Conservation Education and Sustainability, B.P. 48, Gamba, Gabon. 5Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802-5301 USA. E-mail: [email protected] 6Biodiversity Foundation for Africa, P.O. Box FM 730, Bulawayo, Zimbabwe. E-mail: [email protected] 7 Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, INF 364, D-69120 Heidelberg, Germany. E-mail: [email protected] 8Centre national de séquençage, Genoscope, 2 rue Gaston-Crémieux, CP5706, 91057 Evry cedex, France. E-mail: www.genoscope.fr 9Staatliches Naturhistorisches Museum, Pockelsstr. 10, 38106 Braunschweig, Germany. E-mail: [email protected] 10Corresponding author Abstract The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radia- tion termed Lamprophiidae by Vidal et al. -
AHN-29-1999 Type
ISSN 1017-6187 AFRICAN HERP NEWS No.29 June 1999 CONTENTS EDITORIAL .............. ,................................................................ .............. ........... ................ I .1.\Jewsletter of the ARTICLES BURGER. M., BRANCH. W.R .. & IIAAGNER. G.V. Rcccnt African Herpetological Association of Africa Herpetological Literature: 18 ......................................................................................... 2 SCHMIDT. W.R .. & OLSEN. P. Using the Road as a Means of Conducting I lcrpi:to- logical Surveys: An Example from Warm baths ........................ ..................................... 24 LAMBIRIS, A.J. L. Privately Owncd Biological Collections: An Assessment of Principal Issues and Appropriatt: Legal Principles ........................................................ 27 BROADLEY, D.G. The Southern African Python. l'ython natafensis A. Smith I 8'10. is a Valid Species ...... .................................................................................................... 31 NATURAL HISTORY NOTES LOE I IR, V..1.T., & HARRIS, T.J. llomopus signaws: Natural Diet .................................... 33 I PORTER, B. W. Lygodactylus capensis: Predation by Bats .................................. .'............. 35 GREIFF, I. Philothamnus natalensis occidentalis: Sizc and Reproduction ......................... 36 GREIFF, I. Crotaphopeltis hotamboeia: Dict ..................................................................... 38 GREIFF. I. 1/emachatus haemachatus: Leucism ............................................................... -
Taxonomy and Geographic Distribution of Malagasy Frogs of the Gephyromantis Asper Clade, with Description of a New Subgenus
SALAMANDRA 53(1) Taxonomy77–98 and15 Februarydistribution 2017 of MalagasyISSN 0036–3375frogs of the Gephyromantis asper clade Taxonomy and geographic distribution of Malagasy frogs of the Gephyromantis asper clade, with description of a new subgenus and revalidation of Gephyromantis ceratophrys Miguel Vences1, Jörn Köhler2, Maciej Pabijan3, Molly C. Bletz1, Philip-Sebastian Gehring1,4, Oliver Hawlitschek5,6, Andolalao Rakotoarison1, Fanomezana M. Ratsoavina7, Franco Andreone8, Angelica Crottini9 & Frank Glaw5 1) Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany 2) Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany 3) Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, ul. Gronostajowa 9, 30–87, Kraków, Poland 4) Faculty of Biology / Biologiedidaktik, University Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany 5) Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 München, Germany 6) Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, 08003 Barcelona, Spain 7) Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo, 101 Madagascar 8) Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, 10123 Torino, Italy 9) CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Nº 7, 4485-661 Vairão, Portugal Corresponding author: Miguel Vences, e-mail: [email protected] Manuscript received: 17 April 2016 Accepted: 31 May 2016 by Stefan Lötters Abstract. We integrate molecular, bioacoustic and morphological data to provide a systematic revision of the frogs classi- fied in the Gephyromantis asper clade (Anura: Mantellidae), endemic to Madagascar. Based on concordant differentiation in a mitochondrial and a nuclear gene (16S rRNA and Rag1) we distinguish six different species in this clade: G. -
A Phylogeny and Revised Classification of Squamata, Including 4161 Species of Lizards and Snakes
BMC Evolutionary Biology This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes BMC Evolutionary Biology 2013, 13:93 doi:10.1186/1471-2148-13-93 Robert Alexander Pyron ([email protected]) Frank T Burbrink ([email protected]) John J Wiens ([email protected]) ISSN 1471-2148 Article type Research article Submission date 30 January 2013 Acceptance date 19 March 2013 Publication date 29 April 2013 Article URL http://www.biomedcentral.com/1471-2148/13/93 Like all articles in BMC journals, this peer-reviewed article can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central. For information about publishing your research in BMC journals or any BioMed Central journal, go to http://www.biomedcentral.com/info/authors/ © 2013 Pyron et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes Robert Alexander Pyron 1* * Corresponding author Email: [email protected] Frank T Burbrink 2,3 Email: [email protected] John J Wiens 4 Email: [email protected] 1 Department of Biological Sciences, The George Washington University, 2023 G St. -
Reconciling Molecular Phylogeny, Morphological Divergence and Classification of Madagascan Narrow-Mouthed Frogs (Amphibia: Micro
Molecular Phylogenetics and Evolution 100 (2016) 372–381 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Reconciling molecular phylogeny, morphological divergence and classification of Madagascan narrow-mouthed frogs (Amphibia: Microhylidae) Mark D. Scherz a, Miguel Vences b, Andolalao Rakotoarison b, Franco Andreone c, Jörn Köhler d, ⇑ Frank Glaw a, Angelica Crottini e, a Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 München, Germany b Zoologisches Institut, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany c Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, 10123 Torino, Italy d Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany e 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, Portugal article info abstract Article history: A recent study clarified several aspects of microhylid phylogeny by combining DNA sequences from Received 19 November 2015 Sanger sequencing and anchored phylogenomics, although numerous aspects of tree topology proved Revised 11 April 2016 highly susceptible to data partition and chosen model. Although the phylogenetic results of the study Accepted 12 April 2016 were in conflict with previous publications, the authors made several changes to the taxonomy of Available online 13 April 2016 Madagascar’s cophyline microhylids. We re-analyzed part of their data together with our own molecular and morphological data. Based on a supermatrix of 11 loci, we propose a new phylogeny of the Keywords: Cophylinae, and discuss it in the context of a newly generated osteological dataset. We found several Cophylinae sample misidentifications, partially explaining their deviant results, and propose to resurrect the genera Anilany gen. -
Comparing Species Tree Estimation with Large
City University of New York (CUNY) CUNY Academic Works Publications and Research College of Staten Island 2015 Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes Sara Ruane American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA Christopher J. Raxworthy American Museum of Natural History Alan R. Lemmon Florida State University Emily Moriarty Lemmon Florida State University Frank T. Burbrink CUNY College of Staten Island How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/si_pubs/58 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Ruane et al. BMC Evolutionary Biology (2015) 15:221 DOI 10.1186/s12862-015-0503-1 RESEARCH ARTICLE Open Access Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes Sara Ruane1*, Christopher J. Raxworthy1, Alan R. Lemmon2, Emily Moriarty Lemmon2 and Frank T. Burbrink1,3 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. -
08:30 – 09:15 09:20 – 10:40 09:20 – 09:40 09:40 – 10:00 10:00 – 10:20
Tuesday, September 19th – Morning Plenary Lecture: Nikolay Poyarkov: Herpetofaunal diversity and endemism in Indochina: new 08:30 – 09:15 discoveries and biogeographic patterns Chair: Peter Kaufmann Room 1 Room 2 09:20 – 10:40 Session 1a: Population Genetics, Genetic Diversity Session 2a: Anuran Larvae Chair: Peter Mikuliček Chair: Arne Schulze 09:20 – 09:40 Valerija Zakšek, Grega Makovec, Peter Trontelj: Arne Schulze, Jörn Köhler, Stefan Lötters, Bruno Viertel & Secondary contact and limited hybridization of two distinct Michael Veith: Proteus anguinus lineages in the underground of the Hidden treasures: old museum tadpole collections in the Classical Karst light of modern scientific research 09:40 – 10:00 Peter Trontelj, Valerija Zakšek: Jan M. Kaczmarek, Mikołaj Kaczmarski, Janusz Kloskowski: A leap forward in the conservation genetics of Proteus A matter of proportion? Associational effects in tadpole- populations fish predator system 10:00 – 10:20 Alejandro Ibáñez, Molly Bletz, Miguel Vences, Sebastian Veronika Bókony, Zsanett Mikó, Ágnes M. Móricz, Dániel Steinfartz: Krüzselyi, Attila Hettyey: Gut microbial diversity is related to host genetic diversity Chronic exposure to a glyphosate-based herbicide makes but is not affected by starvation during an el Niño event in common toad (Bufo bufo) larvae more toxic Galápagos marine iguanas 10:20 – 10:40 Hisanori Okamiya, Hirotaka Sugawara, Tamotsu Kusano: Dóra Holly, Zsanett Mikó, Attila Hettyey: Loss of genetic diversity prevents adaptation at the margin Effects of a glyphosate-based -
Integrative Review of Geckos of the Paroedura Bastardi Species Complex (Squamata, Gekkonidae)
Vertebrate Zoology 71, 2021, 27–48 | DOI 10.3897/vz.71.e59495 27 Completing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae) Aurélien Miralles1, Teddy Bruy1, Angelica Crottini2, Andolalao Rakotoarison3, Fanomezana M. Ratsoavina3, Mark D. Scherz4, Robin Schmidt5, Jörn Köhler6, Frank Glaw4, Miguel Vences5 1 Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France 2 CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Nº 7, 4485-661 Vairão, Portugal 3 Zoologie et Biodiversité Animale, Université d’Antananarivo, BP 906, Antananarivo, 101 Madagascar 4 Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany 5 Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany 6 Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany http://zoobank.org/08BE0686-2B92-461D-8BB0-592CFB025133 Corresponding author: Aurélien Miralles ([email protected]) Academic editor Uwe Fritz | Received 25 September 2020 | Accepted 21 December 2020 | Published 26 February 2021 Citation: Miralles A, Bruy T, Crottini A, Rakotoarison A, Ratsoavina FM, Scherz MD, Schmidt R, Köhler J, Glaw F, Vences M (2021) Complet- ing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae). Vertebrate Zoology 71: 27–48. https://doi.org/10.3897/vz.71.e59495 Abstract The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura, currently comprises four nominal species: P. bastardi, supposedly widely distributed in southern and western Madagascar, P. ibityensis, a montane endemic, and P. -
New Records, Distribution and Conservation of Mantella Bernhardi, an Endangered Frog Species from South-Eastern Madagascar
Oryx Vol 39 No 3 July 2005 Short Communication New records, distribution and conservation of Mantella bernhardi, an Endangered frog species from south-eastern Madagascar Falitiana Rabemananjara, Parfait Bora, John E. Cadle, Franco Andreone, Emile Rajeriarison, Pierre Talata, Frank Glaw, Miguel Vences and David R. Vieites Abstract We report on seven new localities for Mantella Reserve). An overlap analysis of the potential distribu- bernhardi, a Malagasy poison frog that was previously tion area of the species, based on the extent of remaining known only from a single site. This species has been primary vegetation, indicates that the habitat of M. considered threatened with extinction because of ongo- bernhardi in south-eastern Madagascar is fragmented and ing habitat destruction and collection for the pet trade populations may be relatively small and isolated. We (up to c. 3,000 specimens per year). The new localities support the IUCN Red List category of Endangered for considerably extend the known range of this species, this species and highlight the need for detailed studies of which has now been documented from c. 21.00d to its populations. 24.15dS and 47.00d to 48.00dE, and over 60–629 m altitude. Two of the sites are within protected areas Keywords Amphibia, distribution, Madagascar, (Ranomafana National Park and Manombo Special Mantella bernhardi, Mantellidae, status. Among the endemic amphibian fauna of Madagascar, (Raxworthy & Nussbaum, 2000). The original description the Malagasy poison frogs of the genus Mantella are (Vences et al., 1994) lacked precise locality data because outstanding for their bright, often aposematic coloration, the specimens upon which the description was based diurnal activity and toxicity (Vences et al., 1999). -
New Records, Distribution and Conservation of Mantella Bernhardi, an Endangered Frog Species from South-Eastern Madagascar
Oryx Vol 39 No 3 July 2005 Short Communication New records, distribution and conservation of Mantella bernhardi, an Endangered frog species from south-eastern Madagascar Falitiana Rabemananjara, Parfait Bora, John E. Cadle, Franco Andreone, Emile Rajeriarison, Pierre Talata, Frank Glaw, Miguel Vences and David R. Vieites Abstract We report on seven new localities for Mantella Reserve). An overlap analysis of the potential distribu- bernhardi, a Malagasy poison frog that was previously tion area of the species, based on the extent of remaining known only from a single site. This species has been primary vegetation, indicates that the habitat of M. considered threatened with extinction because of ongo- bernhardi in south-eastern Madagascar is fragmented and ing habitat destruction and collection for the pet trade populations may be relatively small and isolated. We (up to c. 3,000 specimens per year). The new localities support the IUCN Red List category of Endangered for considerably extend the known range of this species, this species and highlight the need for detailed studies of which has now been documented from c. 21.00d to its populations. 24.15dS and 47.00d to 48.00dE, and over 60–629 m altitude. Two of the sites are within protected areas Keywords Amphibia, distribution, Madagascar, (Ranomafana National Park and Manombo Special Mantella bernhardi, Mantellidae, status. Among the endemic amphibian fauna of Madagascar, (Raxworthy & Nussbaum, 2000). The original description the Malagasy poison frogs of the genus Mantella are (Vences et al., 1994) lacked precise locality data because outstanding for their bright, often aposematic coloration, the specimens upon which the description was based diurnal activity and toxicity (Vences et al., 1999).