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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. -
Other Contributions
Other Contributions NATURE NOTES Amphibia: Caudata Ambystoma ordinarium. Predation by a Black-necked Gartersnake (Thamnophis cyrtopsis). The Michoacán Stream Salamander (Ambystoma ordinarium) is a facultatively paedomorphic ambystomatid species. Paedomorphic adults and larvae are found in montane streams, while metamorphic adults are terrestrial, remaining near natal streams (Ruiz-Martínez et al., 2014). Streams inhabited by this species are immersed in pine, pine-oak, and fir for- ests in the central part of the Trans-Mexican Volcanic Belt (Luna-Vega et al., 2007). All known localities where A. ordinarium has been recorded are situated between the vicinity of Lake Patzcuaro in the north-central portion of the state of Michoacan and Tianguistenco in the western part of the state of México (Ruiz-Martínez et al., 2014). This species is considered Endangered by the IUCN (IUCN, 2015), is protected by the government of Mexico, under the category Pr (special protection) (AmphibiaWeb; accessed 1April 2016), and Wilson et al. (2013) scored it at the upper end of the medium vulnerability level. Data available on the life history and biology of A. ordinarium is restricted to the species description (Taylor, 1940), distribution (Shaffer, 1984; Anderson and Worthington, 1971), diet composition (Alvarado-Díaz et al., 2002), phylogeny (Weisrock et al., 2006) and the effect of habitat quality on diet diversity (Ruiz-Martínez et al., 2014). We did not find predation records on this species in the literature, and in this note we present information on a predation attack on an adult neotenic A. ordinarium by a Thamnophis cyrtopsis. On 13 July 2010 at 1300 h, while conducting an ecological study of A. -
Herpetological Information Service No
Type Descriptions and Type Publications OF HoBART M. Smith, 1933 through June 1999 Ernest A. Liner Houma, Louisiana smithsonian herpetological information service no. 127 2000 SMITHSONIAN HERPETOLOGICAL INFORMATION SERVICE The SHIS series publishes and distributes translations, bibliographies, indices, and similar items judged useful to individuals interested in the biology of amphibians and reptiles, but unlikely to be published in the normal technical journals. Single copies are distributed free to interested individuals. Libraries, herpetological associations, and research laboratories are invited to exchange their publications with the Division of Amphibians and Reptiles. We wish to encourage individuals to share their bibliographies, translations, etc. with other herpetologists through the SHIS series. If you have such items please contact George Zug for instructions on preparation and submission. Contributors receive 50 free copies. Please address all requests for copies and inquiries to George Zug, Division of Amphibians and Reptiles, National Museum of Natural History, Smithsonian Institution, Washington DC 20560 USA. Please include a self-addressed mailing label with requests. Introduction Hobart M. Smith is one of herpetology's most prolific autiiors. As of 30 June 1999, he authored or co-authored 1367 publications covering a range of scholarly and popular papers dealing with such diverse subjects as taxonomy, life history, geographical distribution, checklists, nomenclatural problems, bibliographies, herpetological coins, anatomy, comparative anatomy textbooks, pet books, book reviews, abstracts, encyclopedia entries, prefaces and forwords as well as updating volumes being repnnted. The checklists of the herpetofauna of Mexico authored with Dr. Edward H. Taylor are legendary as is the Synopsis of the Herpetofalhva of Mexico coauthored with his late wife, Rozella B. -
A Revision of the Mexican Anolis (Reptilia
Zootaxa 3862 (1): 001–210 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Monograph ZOOTAXA Copyright © 2014 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3862.1.1 http://zoobank.org/urn:lsid:zoobank.org:pub:3FA375FE-E4E0-4509-BE02-EE5E786B07C6 ZOOTAXA 3862 A revision of the Mexican Anolis (Reptilia, Squamata, Dactyloidae) from the Pacific versant west of the Isthmus de Tehuantepec in the states of Oaxaca, Guerrero, and Puebla, with the description of six new species GUNTHER KÖHLER1,5, RAÚL GÓMEZ TREJO PÉREZ2, CLAUS BO P. PETERSEN1,3 & FAUSTO R. MÉNDEZ DE LA CRUZ4 1 Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325 Frankfurt a.M., Germany 2Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios 1, Los Reyes Iztacala, C.P. 54090, Estado de México, México 3Zoological Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark 4Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), A.P. 70-153, C.P. 04510, México D.F. México 5Correspondence: [email protected] Magnolia Press Auckland, New Zealand Accepted by S. Carranza: 9 Jul. 2014; published: 19 Sept. 2014 GUNTHER KÖHLER, RAÚL GÓMEZ TREJO PÉREZ, CLAUS BO P. PETERSEN & FAUSTO R. MÉNDEZ DE LA CRUZ A revision of the Mexican Anolis (Reptilia, Squamata, Dactyloidae) from the Pacific versant west of the Isthmus de Tehuantepec in the states of Oaxaca, Guerrero, and Puebla, with the description of six new species (Zootaxa 3862) 210 pp.; 30 cm. 19 Sept. 2014 ISBN 978-1-77557-485-9 (paperback) ISBN 978-1-77557-486-6 (Online edition) FIRST PUBLISHED IN 2014 BY Magnolia Press P.O. -
Xenosaurus Tzacualtipantecus. the Zacualtipán Knob-Scaled Lizard Is Endemic to the Sierra Madre Oriental of Eastern Mexico
Xenosaurus tzacualtipantecus. The Zacualtipán knob-scaled lizard is endemic to the Sierra Madre Oriental of eastern Mexico. This medium-large lizard (female holotype measures 188 mm in total length) is known only from the vicinity of the type locality in eastern Hidalgo, at an elevation of 1,900 m in pine-oak forest, and a nearby locality at 2,000 m in northern Veracruz (Woolrich- Piña and Smith 2012). Xenosaurus tzacualtipantecus is thought to belong to the northern clade of the genus, which also contains X. newmanorum and X. platyceps (Bhullar 2011). As with its congeners, X. tzacualtipantecus is an inhabitant of crevices in limestone rocks. This species consumes beetles and lepidopteran larvae and gives birth to living young. The habitat of this lizard in the vicinity of the type locality is being deforested, and people in nearby towns have created an open garbage dump in this area. We determined its EVS as 17, in the middle of the high vulnerability category (see text for explanation), and its status by the IUCN and SEMAR- NAT presently are undetermined. This newly described endemic species is one of nine known species in the monogeneric family Xenosauridae, which is endemic to northern Mesoamerica (Mexico from Tamaulipas to Chiapas and into the montane portions of Alta Verapaz, Guatemala). All but one of these nine species is endemic to Mexico. Photo by Christian Berriozabal-Islas. amphibian-reptile-conservation.org 01 June 2013 | Volume 7 | Number 1 | e61 Copyright: © 2013 Wilson et al. This is an open-access article distributed under the terms of the Creative Com- mons Attribution–NonCommercial–NoDerivs 3.0 Unported License, which permits unrestricted use for non-com- Amphibian & Reptile Conservation 7(1): 1–47. -
Chec List a Checklist of the Amphibians and Reptiles of San
Check List 10(4): 870–877, 2014 © 2014 Check List and Authors Chec List ISSN 1809-127X (available at www.checklist.org.br) Journal of species lists and distribution PECIES S OF A checklist * of the amphibians and reptiles of San Isidro de ISTS L Dota, Reserva Forestal Los Santos, Costa Rica Erick Arias and Federico Bolaños [email protected] Universidad de Costa Rica, Escuela de Biología, Museo de Zoología. San Pedro, 11501-2060, San José, Costa Rica. * Corresponding author. E-mail: Abstract: We present an inventory of amphibians and reptiles of San Isidro de Dota, northwest of the Cordillera de Talamanca in the Central Pacific of Costa Rica.Leptodactylus The study was insularum conduced from January to August 2012 in premontane wet Coloptychonforest from 689 rhombifer m to 800 m elevation. We found a total of 56 species, including 30 species of amphibians and 26 of reptiles. It results striking the presence of the frog , uncommon above 400 m elevation, and the lizard , a very uncommon species. DOI: 10.15560/10.4.870 Introduction datum, from 689 m to 800 N, 83°58′32.41″ W, WGS84et al. Lower Central America represents one of the regions m elevation). The region is dominated by premontane with the highest numberet al of amphibianset describedal. in the wet forest (Bolaños 1999) with several sites used Neotropics in relation to the area it represent (Savage for agriculture and pastures. The region presents the 2002; Boza-Oviedo . 2012; Hertz 2012). Much climate of the pacific slope of the Cordillera de Talamanca, of this richness of species iset associated al. -
Diversificação Morfológica E Molecular Em Lagartos Dactyloidae Sul-Americanos
MUSEU PARAENSE EMÍLIO GOELDI UNIVERSIDADE FEDERAL DO PARÁ PROGRAMA DE PÓS-GRADUAÇÃO EM ZOOLOGIA CURSO DE DOUTORADO EM ZOOLOGIA DIVERSIFICAÇÃO MORFOLÓGICA E MOLECULAR EM LAGARTOS DACTYLOIDAE SUL-AMERICANOS ANNELISE BATISTA D’ANGIOLELLA Belém - PA 2015 ANNELISE BATISTA D’ANGIOLELLA DIVERSIFICAÇÃO MORFOLOGICA E MOLECULAR EM LAGARTOS DACTYLOIDAE SUL-AMERICANOS Tese apresenta ao Programa de Pós-Graduação em Zoologia do convênio Universidade Federal do Pará e Museu Paraense Emílio Goeldi, para obtenção do título de doutora em zoologia. Orientadora: Dra. Tereza Cristina Ávila Pires Co-Orientadora: Dra. Ana Carolina Carnaval Belém - PA 2015 “É capaz quem pensa que é capaz.” ii Agradecimento Ao CNPq pela concessão da minha bolsa de pesquisa. A Capes pela Bolsa de Doutorado Sanduiche no exterior. À Teresa Avila-Pires, minha orientadora, por estar sempre disponível para ajudar, escutar e puxar a orelha! A minha co-orientadora Carol Carnaval, por ter me recebido de braços abertos em seu lab e por toda confiança e apoio. A Ana Prudente pelo passe livre à Coleção e sugestões dadas ao trabalho de hemipenis. Ao Tibério Burlamaqui por toda a ajuda com as análises moleculares e momentos de descontração! A todo o pessoal do laboratório de Herpetologia do MPEG pela companhia e troca de ideias, sempre ajudando quando possível. Ao lab de molecular que foi a minha casa nesses últimos quatro anos e a todos que por ele passaram e contribuíram de alguma forma com meu conhecimento, em especial a Áurea, Geraldo, e Joice. Aos meus filhos de quatro patas Pukey e Bingo por me amarem incondicionalmente. A dança, por ser meu refúgio e por não ter me deixado pirar! Ao meu amor, Bruno, por me inspirar diariamente a ser uma pessoa melhor! Por me impulsionar a ir além e por simplesmente existir em minha vida.. -
BOA2.1 Caecilian Biology and Natural History.Key
The Biology of Amphibians @ Agnes Scott College Mark Mandica Executive Director The Amphibian Foundation [email protected] 678 379 TOAD (8623) 2.1: Introduction to Caecilians Microcaecilia dermatophaga Synapomorphies of Lissamphibia There are more than 20 synapomorphies (shared characters) uniting the group Lissamphibia Synapomorphies of Lissamphibia Integumen is Glandular Synapomorphies of Lissamphibia Glandular Skin, with 2 main types of glands. Mucous Glands Aid in cutaneous respiration, reproduction, thermoregulation and defense. Granular Glands Secrete toxic and/or noxious compounds and aid in defense Synapomorphies of Lissamphibia Pedicellate Teeth crown (dentine, with enamel covering) gum line suture (fibrous connective tissue, where tooth can break off) basal element (dentine) Synapomorphies of Lissamphibia Sacral Vertebrae Sacral Vertebrae Connects pelvic girdle to The spine. Amphibians have no more than one sacral vertebrae (caecilians have none) Synapomorphies of Lissamphibia Amphicoelus Vertebrae Synapomorphies of Lissamphibia Opercular apparatus Unique to amphibians and Operculum part of the sound conducting mechanism Synapomorphies of Lissamphibia Fat Bodies Surrounding Gonads Fat Bodies Insulate gonads Evolution of Amphibians † † † † Actinopterygian Coelacanth, Tetrapodomorpha †Amniota *Gerobatrachus (Ray-fin Fishes) Lungfish (stem-tetrapods) (Reptiles, Mammals)Lepospondyls † (’frogomander’) Eocaecilia GymnophionaKaraurus Caudata Triadobatrachus Anura (including Apoda Urodela Prosalirus †) Salientia Batrachia Lissamphibia -
Check List the Journal Of
12 1 1838 the journal of biodiversity data 6 February 2016 Check List NOTES ON GEOGRAPHIC DISTRIBUTION Check List 12(1): 1838, 6 February 2016 doi: http://dx.doi.org/10.15560/12.1.1838 ISSN 1809-127X © 2016 Check List and Authors Leptophis ahaetulla (Linnaeus, 1758) (Serpentes, Colubridae): first record for the state of Rio Grande do Sul, Brazil Roberto Baptista de Oliveira1*, Christian Beier2, Giancarlo Ribeiro Bilo3, Tiago Gomes dos Santos3 and Gláucia Maria Funk Pontes4 1 Fundação Zoobotânica do Rio Grande do Sul, Museu de Ciências Naturais, Seção de Zoologia de Vertebrados, Rua Dr. Salvador França 1427, CEP 90690-000, Porto Alegre, RS, Brazil 2 Pontifícia Universidade Católica do Rio Grande do Sul, Museu de Ciências e Tecnologia, Programa de Pós-Graduação em Zoologia, Laboratório de Ornitologia, Av. Ipiranga 6681, CEP 90619-900, Porto Alegre, RS, Brazil 3 Universidade Federal do Pampa, Laboratório de Estudos em Biodiversidade Pampiana (LEBIP), Av. Antônio Trilha 1847, CEP 97300- 000, São Gabriel, RS, Brazil 4 Pontifícia Universidade Católica do Rio Grande do Sul, Museu de Ciências e Tecnologia, Setor de Herpetologia, Av. Ipiranga 6681, CEP 90619-900, Porto Alegre, RS, Brazil * Corresponding author: E-mail: [email protected] Abstract: We present the first record of Leptophis the extreme North to the state of Paraná, occupying a ahaetulla for the State of Rio Grande do Sul, Brazil. wide range of biomes, including the Amazon, Pantanal, Between November and December 2014, and February Cerrado, Caatinga and Atlantic Forest (Cunha and 2015, three specimens were found, respectively: one male Nascimento 1978; Vanzolini et al. -
Multi-National Conservation of Alligator Lizards
MULTI-NATIONAL CONSERVATION OF ALLIGATOR LIZARDS: APPLIED SOCIOECOLOGICAL LESSONS FROM A FLAGSHIP GROUP by ADAM G. CLAUSE (Under the Direction of John Maerz) ABSTRACT The Anthropocene is defined by unprecedented human influence on the biosphere. Integrative conservation recognizes this inextricable coupling of human and natural systems, and mobilizes multiple epistemologies to seek equitable, enduring solutions to complex socioecological issues. Although a central motivation of global conservation practice is to protect at-risk species, such organisms may be the subject of competing social perspectives that can impede robust interventions. Furthermore, imperiled species are often chronically understudied, which prevents the immediate application of data-driven quantitative modeling approaches in conservation decision making. Instead, real-world management goals are regularly prioritized on the basis of expert opinion. Here, I explore how an organismal natural history perspective, when grounded in a critique of established human judgements, can help resolve socioecological conflicts and contextualize perceived threats related to threatened species conservation and policy development. To achieve this, I leverage a multi-national system anchored by a diverse, enigmatic, and often endangered New World clade: alligator lizards. Using a threat analysis and status assessment, I show that one recent petition to list a California alligator lizard, Elgaria panamintina, under the US Endangered Species Act often contradicts the best available science. -
Final Report for the University of Nottingham / Operation Wallacea Forest Projects, Honduras 2004
FINAL REPORT for the University of Nottingham / Operation Wallacea forest projects, Honduras 2004 TABLE OF CONTENTS FINAL REPORT FOR THE UNIVERSITY OF NOTTINGHAM / OPERATION WALLACEA FOREST PROJECTS, HONDURAS 2004 .....................................................................................................................................................1 INTRODUCTION AND OVERVIEW ..............................................................................................................................3 List of the projects undertaken in 2004, with scientists’ names .........................................................................4 Forest structure and composition ..................................................................................................................................... 4 Bat diversity and abundance ............................................................................................................................................ 4 Bird diversity, abundance and ecology ............................................................................................................................ 4 Herpetofaunal diversity, abundance and ecology............................................................................................................. 4 Invertebrate diversity, abundance and ecology ................................................................................................................ 4 Primate behaviour........................................................................................................................................................... -
Pseudoeurycea Naucampatepetl. the Cofre De Perote Salamander Is Endemic to the Sierra Madre Oriental of Eastern Mexico. This
Pseudoeurycea naucampatepetl. The Cofre de Perote salamander is endemic to the Sierra Madre Oriental of eastern Mexico. This relatively large salamander (reported to attain a total length of 150 mm) is recorded only from, “a narrow ridge extending east from Cofre de Perote and terminating [on] a small peak (Cerro Volcancillo) at the type locality,” in central Veracruz, at elevations from 2,500 to 3,000 m (Amphibian Species of the World website). Pseudoeurycea naucampatepetl has been assigned to the P. bellii complex of the P. bellii group (Raffaëlli 2007) and is considered most closely related to P. gigantea, a species endemic to the La specimens and has not been seen for 20 years, despite thorough surveys in 2003 and 2004 (EDGE; www.edgeofexistence.org), and thus it might be extinct. The habitat at the type locality (pine-oak forest with abundant bunch grass) lies within Lower Montane Wet Forest (Wilson and Johnson 2010; IUCN Red List website [accessed 21 April 2013]). The known specimens were “found beneath the surface of roadside banks” (www.edgeofexistence.org) along the road to Las Lajas Microwave Station, 15 kilometers (by road) south of Highway 140 from Las Vigas, Veracruz (Amphibian Species of the World website). This species is terrestrial and presumed to reproduce by direct development. Pseudoeurycea naucampatepetl is placed as number 89 in the top 100 Evolutionarily Distinct and Globally Endangered amphib- ians (EDGE; www.edgeofexistence.org). We calculated this animal’s EVS as 17, which is in the middle of the high vulnerability category (see text for explanation), and its IUCN status has been assessed as Critically Endangered.