A New Jurassic Lizard from China
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Modeling and Partitioning the Nucleotide Evolutionary Process for Phylogenetic and Comparative Genomic Inference
University of Central Florida STARS Electronic Theses and Dissertations, 2004-2019 2007 Modeling And Partitioning The Nucleotide Evolutionary Process For Phylogenetic And Comparative Genomic Inference Todd Castoe University of Central Florida Part of the Biology Commons Find similar works at: https://stars.library.ucf.edu/etd University of Central Florida Libraries http://library.ucf.edu This Doctoral Dissertation (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2004-2019 by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Castoe, Todd, "Modeling And Partitioning The Nucleotide Evolutionary Process For Phylogenetic And Comparative Genomic Inference" (2007). Electronic Theses and Dissertations, 2004-2019. 3111. https://stars.library.ucf.edu/etd/3111 MODELING AND PARTITIONING THE NUCLEOTIDE EVOLUTIONARY PROCESS FOR PHYLOGENETIC AND COMPARATIVE GENOMIC INFERENCE by TODD A. CASTOE B.S. SUNY – College of Environmental Science and Forestry, 1999 M.S. The University of Texas at Arlington, 2001 A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomolecular Sciences in the Burnett College of Biomedical Sciences at the University of Central Florida Orlando, Florida Spring Term 2007 Major Professor: Christopher L. Parkinson © 2007 Todd A. Castoe ii ABSTRACT The transformation of genomic data into functionally relevant information about the composition of biological systems hinges critically on the field of computational genome biology, at the core of which lies comparative genomics. The aim of comparative genomics is to extract meaningful functional information from the differences and similarities observed across genomes of different organisms. -
AMANI NATURE RESERVE an Introduction
Field Guides AMANI NATURE RESERVE an introduction This guide was developed to help participants on Tropical Biology Association field courses to learn about the Amani Nature Reserve and the forests of the East Usambara Mountains. It includes an introduction to the East Usambaras and describes the ecology, flora and fauna of the area. The history of management and conservation of the Amani Nature Reserve, together with its current status, is outlined. This publication was funded by the European Commission (B7-6200/01/0370/ENV). For any queries concerning this document please contact: Tropical Biology Association Department of Zoology Downing Street, Cambridge CB2 3EJ United Kingdom Tel: +44 (0) 1223 336619 e-mail: [email protected] © Tropical Biology Association 2007 A Banson production Printed by Swaingrove Field Guides AMANI NATURE RESERVE an introduction TBA Field Guide CONTENTS EAST USAMBARA MOUNTAINS 3 Geographical history 3 Flora and fauna of the Usambara Mountains 3 Human impacts 3 History of Amani 5 History of Amani Botanical Garden 5 FLORA OF THE EASTERN USAMBARAS & AMANI 6 Vegetation cover of the East Usambara Mountains 6 Endemic plants in Amani 7 Introduced (alien and invasive) species 7 Case study of an introduced species: Maesopsis eminii (Rhamnaceae) 8 FAUNA OF AMANI 9 Vertebrates 9 Invertebrates 13 MANAGEMENT OF AMANI NATURE RESERVE 14 Conservation 14 REFERENCES 16 2 Amani Nature Reserve EAST USAMBARA MOUNTAINS An overview Geographical history The Amani Nature Reserve is located in the East Usambara region. This is part of the Eastern Arc Mountains, an isolated mountain chain of ancient crystalline rock formed through a cycle of block faulting and erosion that stretches from the Taita Hills in Kenya down to the Southern Highlands in Tanzania. -
A New Species of Dibamus (Squamata: Dibamidae) from West Malaysia
2004 Asiatic Herpetological Research Vol. 10, pp. 1-7 A New Species of Dibamus (Squamata: Dibamidae) from West Malaysia RAUL E. DIAZ1,2,*, MING TZI LEONG3, L. LEE GRISMER1, AND NORSHAM S. YAAKOB4 1Department of Biology, La Sierra University, Riverside, CA 92515-8247, USA 2Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA *Corresponding author E-mail: [email protected] 3Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 119260, Republic of Singapore 4Forest Research Institute Malaysia, Kepong, 52109 Kuala Lumpur, Malaysia Abstract. - A new lizard of the genus Dibamus is described from Pulau Tioman and Pulau Tulai, Pahang, West Malaysia. This species most closely resembles D. novaeguineae, D. kondaoensis, D. leucurus and D. montanus, but differs from all congeneric species in exhibiting the following combination of characters: postoculars 1, scales bor- dering first infralabial 4, SVL 123 mm, 25-26 midbody scale rows, frontonasal and rostral sutures complete, and the presence of slightly posteriorly notched cycloid body scales as an adult. Key words. - Dibamus, Dibamus tiomanensis, new species, Dibamidae, Pulau Tioman, West Malaysia. Introduction were sexed externally under a dissecting microscope; males were identified by having two small, flap-like The genus Dibamus presently contains 18 species (see limbs (one on each side of the vent) (Duméril and Greer, 1985; Darevsky, 1992; Das, 1996; Honda et al., Bibron, 1839). 1997; Ineich, 1999; Honda et al., 2001; Das and Lim, 2003; Das and Yaakob, 2003), a two-fold difference Taxonomy from the detailed review of the group by Greer (1985). Species of the genus Dibamus collectively range Dibamus tiomanensis, new species throughout southeast Asia, from southern China and the Figs. -
MADAGASCAR: the Wonders of the “8Th Continent” a Tropical Birding Custom Trip
MADAGASCAR: The Wonders of the “8th Continent” A Tropical Birding Custom Trip October 20—November 6, 2016 Guide: Ken Behrens All photos taken during this trip by Ken Behrens Annotated bird list by Jerry Connolly TOUR SUMMARY Madagascar has long been a core destination for Tropical Birding, and with the opening of a satellite office in the country several years ago, we further solidified our expertise in the “Eighth Continent.” This custom trip followed an itinerary similar to that of our main set-departure tour. Although this trip had a definite bird bias, it was really a general natural history tour. We took our time in observing and photographing whatever we could find, from lemurs to chameleons to bizarre invertebrates. Madagascar is rich in wonderful birds, and we enjoyed these to the fullest. But its mammals, reptiles, amphibians, and insects are just as wondrous and accessible, and a trip that ignored them would be sorely missing out. We also took time to enjoy the cultural riches of Madagascar, the small villages full of smiling children, the zebu carts which seem straight out of the Middle Ages, and the ingeniously engineered rice paddies. If you want to come to Madagascar and see it all… come with Tropical Birding! Madagascar is well known to pose some logistical challenges, especially in the form of the national airline Air Madagascar, but we enjoyed perfectly smooth sailing on this tour. We stayed in the most comfortable hotels available at each stop on the itinerary, including some that have just recently opened, and savored some remarkably good food, which many people rank as the best Madagascar Custom Tour October 20-November 6, 2016 they have ever had on any birding tour. -
História Das Paisagens Florestais Mésicas Dentro Da Diagonal De Formações Abertas: Contribuições De Paleomodelagem, Filoge
! ! Universidade de Brasília Instituto de Ciências Biológicas Programa de Pós-Graduação em Ecologia História das paisagens florestais mésicas dentro da diagonal de formações abertas: contribuições de paleomodelagem, filogeografia de espécies associadas e de conservação Roger Maia Dias Ledo Brasília – DF 2016 ! ! ! ! Universidade de Brasília Instituto de Ciências Biológicas Programa de Pós-Graduação em Ecologia História das paisagens florestais mésicas dentro da diagonal de formações abertas: contribuições de paleomodelagem, filogeografia de espécies associadas e de conservação Orientador: Dr. Guarino Rinaldi Colli Co-orientadora: Dra. Lilian G. Giugliano Tese apresentada ao Programa de Pós- Graduação em Ecologia da Universidade de Brasília como parte dos requisitos necessários para a obtenção do título de Doutor em Ecologia. Brasília – DF 2016 ! ! Roger Maia Dias Ledo História das paisagens florestais mésicas dentro da diagonal de formações abertas: contribuições de paleomodelagem, filogeografia de espécies associadas e conservação Tese realizada com o apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/SISBIOTA) e aprovada junto ao Programa de Pós-Graduação em Ecologia da Universidade de Brasília como requisito para obtenção do título de Doutor em Ecologia. Comissão Examinadora: Prof. Dr. Guarino R. Colli Prof. Dra. Lilian G. Giugliano Presidente/Orientador Co-orientadora UnB UnB Profa. Dra. Leonora P. Costa Prof. Dr. Adrian A. Garda Membro Externo não vinculado ao Programa Membro Externo não vinculado ao Programa UFES UFRN Prof. Dra. Rosane Collevatti Membro Prof. Dr. Ricardo Bomfim Machado Externo não vinculado ao Programa Membro Interno vinculado ao UFG Programa UnB Prof. Dr. Renato Caparroz Membro suplente vinculado ao Programa UnB Brasília, 29 de fevereiro de 2016 ! ! Agradecimentos Esta tese não sairia do papel (ou melhor, não se materializaria no papel) se não fosse a ajuda de inúmeras pessoas. -
A New Computing Environment for Modeling Species Distribution
EXPLORATORY RESEARCH RECOGNIZED WORLDWIDE Botany, ecology, zoology, plant and animal genetics. In these and other sub-areas of Biological Sciences, Brazilian scientists contributed with results recognized worldwide. FAPESP,São Paulo Research Foundation, is one of the main Brazilian agencies for the promotion of research.The foundation supports the training of human resources and the consolidation and expansion of research in the state of São Paulo. Thematic Projects are research projects that aim at world class results, usually gathering multidisciplinary teams around a major theme. Because of their exploratory nature, the projects can have a duration of up to five years. SCIENTIFIC OPPORTUNITIES IN SÃO PAULO,BRAZIL Brazil is one of the four main emerging nations. More than ten thousand doctorate level scientists are formed yearly and the country ranks 13th in the number of scientific papers published. The State of São Paulo, with 40 million people and 34% of Brazil’s GNP responds for 52% of the science created in Brazil.The state hosts important universities like the University of São Paulo (USP) and the State University of Campinas (Unicamp), the growing São Paulo State University (UNESP), Federal University of São Paulo (UNIFESP), Federal University of ABC (ABC is a metropolitan region in São Paulo), Federal University of São Carlos, the Aeronautics Technology Institute (ITA) and the National Space Research Institute (INPE). Universities in the state of São Paulo have strong graduate programs: the University of São Paulo forms two thousand doctorates every year, the State University of Campinas forms eight hundred and the University of the State of São Paulo six hundred. -
Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata)
Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) Item Type text; Electronic Dissertation Authors Lambert, Shea Maddock Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 07/10/2021 08:50:17 Link to Item http://hdl.handle.net/10150/630229 1 PHYLOGENETIC PERSPECTIVES ON VIVIPARITY, GENE-TREE DISCORDANCE, AND INTROGRESSION IN LIZARDS (SQUAMATA). by Shea Maddock Lambert ____________________________ Copyright © Shea Maddock Lambert 2018 A Dissertation Submitted to the Faculty of the DEPARTMENT OF ECOLOGY AND EVOLUTIONARY BIOLOGY In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2 THEUNIVERSITY OF ARIZONA GRADUATE COLLEGE Asmembers of the Dissertation Committee, we certify that we have read the dissertation prepared by Shea M. Lambert, titled "Phylogenetic perspectives on viviparity,gene-tree discordance, and introgressionin lizards {Squamata)" and recomme11dthat it be accepted as fulfillingthe dissertation requirem�t for the Degree of Doctor of Philosophy. _.c.---� ---------Date: May 21, 2018 _wJohn__ . �e� --�_:-_:-__:_ W_ -----�----'-------------------Date: May 21, 2018 Michael Barker M ichael ( s��t=t ��A". =----.�+o/-�i � -\.\----�--------._______ Date: May 21, 2018 Noa�man Final approval and acceptance· of this dissertation is contingent uporithe candidate's submission of the final copies of the· dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my ditettion and recommend that it be accepted as fulfillin_;the �issertation requirement. -
Integrative and Comparative Biology Integrative and Comparative Biology, Volume 60, Number 1, Pp
Integrative and Comparative Biology Integrative and Comparative Biology, volume 60, number 1, pp. 190–201 doi:10.1093/icb/icaa015 Society for Integrative and Comparative Biology SYMPOSIUM Convergent Evolution of Elongate Forms in Craniates and of Locomotion in Elongate Squamate Reptiles Downloaded from https://academic.oup.com/icb/article-abstract/60/1/190/5813730 by Clark University user on 24 July 2020 Philip J. Bergmann ,* Sara D. W. Mann,* Gen Morinaga,1,*,† Elyse S. Freitas‡ and Cameron D. Siler‡ *Department of Biology, Clark University, Worcester, MA, USA; †Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA; ‡Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK, USA From the symposium “Long Limbless Locomotors: The Mechanics and Biology of Elongate, Limbless Vertebrate Locomotion” presented at the annual meeting of the Society for Integrative and Comparative Biology January 3–7, 2020 at Austin, Texas. 1E-mail: [email protected] Synopsis Elongate, snake- or eel-like, body forms have evolved convergently many times in most major lineages of vertebrates. Despite studies of various clades with elongate species, we still lack an understanding of their evolutionary dynamics and distribution on the vertebrate tree of life. We also do not know whether this convergence in body form coincides with convergence at other biological levels. Here, we present the first craniate-wide analysis of how many times elongate body forms have evolved, as well as rates of its evolution and reversion to a non-elongate form. We then focus on five convergently elongate squamate species and test if they converged in vertebral number and shape, as well as their locomotor performance and kinematics. -
Evolution of the Iguanine Lizards (Sauria, Iguanidae) As Determined by Osteological and Myological Characters David F
Brigham Young University Science Bulletin, Biological Series Volume 12 | Number 3 Article 1 1-1971 Evolution of the iguanine lizards (Sauria, Iguanidae) as determined by osteological and myological characters David F. Avery Department of Biology, Southern Connecticut State College, New Haven, Connecticut Wilmer W. Tanner Department of Zoology, Brigham Young University, Provo, Utah Follow this and additional works at: https://scholarsarchive.byu.edu/byuscib Part of the Anatomy Commons, Botany Commons, Physiology Commons, and the Zoology Commons Recommended Citation Avery, David F. and Tanner, Wilmer W. (1971) "Evolution of the iguanine lizards (Sauria, Iguanidae) as determined by osteological and myological characters," Brigham Young University Science Bulletin, Biological Series: Vol. 12 : No. 3 , Article 1. Available at: https://scholarsarchive.byu.edu/byuscib/vol12/iss3/1 This Article is brought to you for free and open access by the Western North American Naturalist Publications at BYU ScholarsArchive. It has been accepted for inclusion in Brigham Young University Science Bulletin, Biological Series by an authorized editor of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. S-^' Brigham Young University f?!AR12j97d Science Bulletin \ EVOLUTION OF THE IGUANINE LIZARDS (SAURIA, IGUANIDAE) AS DETERMINED BY OSTEOLOGICAL AND MYOLOGICAL CHARACTERS by David F. Avery and Wilmer W. Tanner BIOLOGICAL SERIES — VOLUME Xil, NUMBER 3 JANUARY 1971 Brigham Young University Science Bulletin -
Literature Cited in Lizards Natural History Database
Literature Cited in Lizards Natural History database Abdala, C. S., A. S. Quinteros, and R. E. Espinoza. 2008. Two new species of Liolaemus (Iguania: Liolaemidae) from the puna of northwestern Argentina. Herpetologica 64:458-471. Abdala, C. S., D. Baldo, R. A. Juárez, and R. E. Espinoza. 2016. The first parthenogenetic pleurodont Iguanian: a new all-female Liolaemus (Squamata: Liolaemidae) from western Argentina. Copeia 104:487-497. Abdala, C. S., J. C. Acosta, M. R. Cabrera, H. J. Villaviciencio, and J. Marinero. 2009. A new Andean Liolaemus of the L. montanus series (Squamata: Iguania: Liolaemidae) from western Argentina. South American Journal of Herpetology 4:91-102. Abdala, C. S., J. L. Acosta, J. C. Acosta, B. B. Alvarez, F. Arias, L. J. Avila, . S. M. Zalba. 2012. Categorización del estado de conservación de las lagartijas y anfisbenas de la República Argentina. Cuadernos de Herpetologia 26 (Suppl. 1):215-248. Abell, A. J. 1999. Male-female spacing patterns in the lizard, Sceloporus virgatus. Amphibia-Reptilia 20:185-194. Abts, M. L. 1987. Environment and variation in life history traits of the Chuckwalla, Sauromalus obesus. Ecological Monographs 57:215-232. Achaval, F., and A. Olmos. 2003. Anfibios y reptiles del Uruguay. Montevideo, Uruguay: Facultad de Ciencias. Achaval, F., and A. Olmos. 2007. Anfibio y reptiles del Uruguay, 3rd edn. Montevideo, Uruguay: Serie Fauna 1. Ackermann, T. 2006. Schreibers Glatkopfleguan Leiocephalus schreibersii. Munich, Germany: Natur und Tier. Ackley, J. W., P. J. Muelleman, R. E. Carter, R. W. Henderson, and R. Powell. 2009. A rapid assessment of herpetofaunal diversity in variously altered habitats on Dominica. -
Description of a New Pygmy Chameleon (Chamaeleonidae: Brookesia) from Central Madagascar
Zootaxa 3490: 63–74 (2012) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2012 · Magnolia Press Article ISSN 1175-5334 (online edition) urn:lsid:zoobank.org:pub:FF22F75B-4A07-40D9-9609-1B8D269A921C Description of a new pygmy chameleon (Chamaeleonidae: Brookesia) from central Madagascar ANGELICA CROTTINI1,2,5, AURÉLIEN MIRALLES2, FRANK GLAW3, D. JAMES HARRIS1, ALEXANDRA LIMA1,4 & MIGUEL VENCES2 1CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão, Portugal. E-mail: [email protected] 2Zoological Institute, Division of Evolutionary Biology, Technical University of Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany 3Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany 4Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre s/n, 4169-007 Porto, Portugal 5Corresponding author Abstract We describe a new Brookesia species from a forest fragment located 13 km south of Ambalavao in the southern part of Madagascar's central high plateau. Brookesia brunoi sp. nov. is one of the few arid-adapted Brookesia species inhabiting deciduous forests on the western slope of the central high plateau of the island (around 950 m a.s.l.). So far the species has only been observed in the private Anja Reserve. The species belongs to the Brookesia decaryi group formed by arid-adapt- ed Brookesia species of western Madagascar: B. bonsi Ramanantsoa, B. perarmata (Angel), B. brygooi Raxworthy & Nussbaum and B. decaryi Angel. Brookesia brunoi differs from the other four species of the group by a genetic divergence of more than 17.6% in the mitochondrial ND2 gene, and by a combination of morphological characters: (1) nine pairs of laterovertebral pointed tubercles, (2) absence of enlarged pointed tubercles around the vent, (3) presence of poorly defined laterovertebral tubercles along the entire tail, (4) by the configuration of its cephalic crest, and (5) hemipenial morphology. -
Ancestral Reconstruction of Diet and Fang Condition in the Lamprophiidae: Implications for the Evolution of Venom Systems in Snakes
Journal of Herpetology, Vol. 55, No. 1, 1–10, 2021 Copyright 2021 Society for the Study of Amphibians and Reptiles Ancestral Reconstruction of Diet and Fang Condition in the Lamprophiidae: Implications for the Evolution of Venom Systems in Snakes 1,2 1 1 HIRAL NAIK, MIMMIE M. KGADITSE, AND GRAHAM J. ALEXANDER 1School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg. PO Wits, 2050, Gauteng, South Africa ABSTRACT.—The Colubroidea includes all venomous and some nonvenomous snakes, many of which have extraordinary dental morphology and functional capabilities. It has been proposed that the ancestral condition of the Colubroidea is venomous with tubular fangs. The venom system includes the production of venomous secretions by labial glands in the mouth and usually includes fangs for effective delivery of venom. Despite significant research on the evolution of the venom system in snakes, limited research exists on the driving forces for different fang and dental morphology at a broader phylogenetic scale. We assessed the patterns of fang and dental condition in the Lamprophiidae, a speciose family of advanced snakes within the Colubroidea, and we related fang and dental condition to diet. The Lamprophiidae is the only snake family that includes front-fanged, rear-fanged, and fangless species. We produced an ancestral reconstruction for the family and investigated the pattern of diet and fangs within the clade. We concluded that the ancestral lamprophiid was most likely rear-fanged and that the shift in dental morphology was associated with changes in diet. This pattern indicates that fang loss, and probably venom loss, has occurred multiple times within the Lamprophiidae.