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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. -
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. -
Mapa De Veracruz De Ignacio De La Llave. División Municipal
Veracruz de Ignacio de la Llave N O E 1 S 203 161 150 102 114 183 150154 060 155 150 109 129 063035 151 042 T1amaulipas50 013 192 056 153 023 078 154 055 034 197 150 056 055 167 010 163 095 060 096 057 187106 50 107 156 002 133 058 177 036 166 013 1213 51 160 009 189 086 194 132 112 152 136 093 53 027 026 076 001182 087 004 034 128 205 121 202 083 157 033 025 092 065 7 175 038 San Luis Potosí 170 161 150 180 025164 154 079 088 134 150 131 046 017 060 024 155 063 150 198 129 035 013 071521 069 056 153 162 078 040 1 055 034 056 051 124 188 160 055 167 158 179 189 066 146 058 037 160 103 064 211 071 043 Hidalgo 189 067 050 008 14 027 203 029 076 047 165 200 102 114 180680 007 202 083 157 183 062 175 033 127 170 180 109 101 022 044 131 042 192 068 021 125 072 198 023 081 157 00340 3 069 124 Golfo de México 197 138118 085 196 051 158 010 163 099 101595135 014 175 066 074 113 053 031 037 030 187001986 057 185 041 052 067103 064 211 106 140098 050 107 156 002 203 102 114 177 036 166 104709 168 086 194 112 117 183 132 006 137 131 136020693 020 201 109 042 192 023 001182 087 195 001471 197 128 184 010 163 095 110 173 096 057 092 065 191 061987106 025 019 156 107 002166 038 159 040 177 036 009 164 086 194 112 025 016 132 093 079 088 134 136026 046 024 017 051 124 128 001182 087 004 150658 191 162 025 092 126 038 188 193 079025164 088 134 016 146 179 193 066 046 024 017 028 037 162 126 071 043 188 193 100 146 179 193 008 148 064 028 029 103 071 024311 047 080 165 200 067 008 148 100 186 007 090 050 029 047 080 165 200 127 062 186 007 090 Escala -
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........................................................................................................................................................... -
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography of Rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus)
City University of New York (CUNY) CUNY Academic Works Publications and Research New York City College of Technology 2016 Diversity-dependent cladogenesis throughout western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) Christopher Blair CUNY New York City College of Technology Santiago Sánchez-Ramírez University of Toronto How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/ny_pubs/344 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] 1Blair, C., Sánchez-Ramírez, S., 2016. Diversity-dependent cladogenesis throughout 2 western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: 3 Crotalus and Sistrurus ). Molecular Phylogenetics and Evolution 97, 145–154. 4 https://doi.org/10.1016/j.ympev.2015.12.020. © 2016. This manuscript version is made 5 available under the CC-BY-NC-ND 4.0 license. 6 7 8 Diversity-dependent cladogenesis throughout western Mexico: evolutionary 9 biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) 10 11 12 CHRISTOPHER BLAIR1*, SANTIAGO SÁNCHEZ-RAMÍREZ2,3,4 13 14 15 1Department of Biological Sciences, New York City College of Technology, Biology PhD 16 Program, Graduate Center, The City University of New York, 300 Jay Street, Brooklyn, 17 NY 11201, USA. 18 2Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks 19 Street, Toronto, ON, M5S 3B2, Canada. 20 3Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, 21 ON, M5S 2C6, Canada. 22 4Present address: Environmental Genomics Group, Max Planck Institute for 23 Evolutionary Biology, August-Thienemann-Str. -
Ephemeral Pleistocene Woodlands Connect the Dots for Highland Rattlesnakes of the Crotalus Intermedius Group
Journal of Biogeography (J. Biogeogr.) (2011) ORIGINAL Ephemeral Pleistocene woodlands ARTICLE connect the dots for highland rattlesnakes of the Crotalus intermedius group Robert W. Bryson Jr1*, Robert W. Murphy2,3, Matthew R. Graham1, Amy Lathrop2 and David Lazcano4 1School of Life Sciences, University of Nevada, ABSTRACT Las Vegas, 4505 Maryland Parkway, Las Aim To test how Pleistocene climatic changes affected diversification of the Vegas, NV 89154-4004, USA, 2Centre for Biodiversity and Conservation Biology, Royal Crotalus intermedius species complex. Ontario Museum, Toronto, ON M5S 2C6, Location Highlands of Mexico and the south-western United States (Arizona). Canada, 3State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Methods We synthesize the matrilineal genealogy based on 2406 base pairs of Zoology, The Chinese Academy of Sciences, mitochondrial DNA sequences, fossil-calibrated molecular dating, reconstruction Kunming 650223, China, 4Laboratorio de of ancestral geographic ranges, and climate-based modelling of species Herpetologı´a, Universidad Auto´noma de distributions to evaluate the history of female dispersion. Nuevo Leo´n, San Nicolas de los Garza, Nuevo Results The presently fragmented distribution of the C. intermedius group is the Leo´n CP 66440, Mexico result of both Neogene vicariance and Pleistocene pine–oak habitat fragmentation. Most lineages appear to have a Quaternary origin. The Sierra Madre del Sur and northern Sierra Madre Oriental are likely to have been colonized during this time. Species distribution models for the Last Glacial Maximum predict expansions of suitable habitat for taxa in the southern Sierra Madre Occidental and northern Sierra Madre Oriental. Main conclusions Lineage diversification in the C. -
Magda. Patricia Montelongo Guerrero
MAGDA. PATRICIA MONTELONGO GUERRERO Nació en Poza Rica, Veracruz. Estudió la Licenciatura en la Facultad de Derecho de la Universidad Veracruzana, como integrante de la Generación 1980-1984. Cursó la Maestría en Derecho Privado en la Universidad Cristóbal Colón del puerto de Veracruz y la Maestría en Administración de Justicia, en la Universidad Autónoma Villa Rica de Boca del Río. Es Candidata a Doctora en Ciencias Jurídicas, Administrativas y de la Educación, por la Universidad de Las Naciones, de la Ciudad de Veracruz. La sólida preparación adquirida le permitió desempeñar importantes tareas como Catedrática de las Materias de Concurso Mercantil, Derecho Mercantil y Derecho Procesal Civil, en el Sistema Abierto del Instituto de Estudios Superiores de Xalapa. También diocátedra de las Materias de Derecho Pro- cesal Civil, Seminario de Ética y Formación Profesional, y Teoría General del Proceso, en la Universi- dad Cristóbal Colón, A. C., de la ciudad de Veracruz. Ha asistido a diversos cursos como el Segundo Curso de Capacitación para Aspirantes a Secretarios de Juzgados de Primera Instancia del Poder Judicial del Estado de Veracruz; el Curso para Secretario de Tribunales Colegiados, en el Centro de Capacitación del Poder Judicial de la Federación, en Xalapa, Veracruz; y el Taller de Derecho Oral Mercantil, en el nstituto Nacional de Posgrado en Derecho. Tiene los diplomados en Derecho Inmobiliario, en el Instituto de Investigaciones Jurídicas de la Uni- versidad Nacional Autónoma de México, del Centro de Estudios de Actualizaciones Jurídicas S. C., en la Ciudad de México; en Juicios Orales, en el Instituto Nacional de Posgrado en Derecho; en Derecho Procesal Civil y Mercantil, en el Instituto Nacional de Posgrado en Derecho. -
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. Amphib. Reptile Conserv. | http://redlist-ARC.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. -
Crocodylus Moreletii
ANFIBIOS Y REPTILES: DIVERSIDAD E HISTORIA NATURAL VOLUMEN 03 NÚMERO 02 NOVIEMBRE 2020 ISSN: 2594-2158 Es un publicación de la CONSEJO DIRECTIVO 2019-2021 COMITÉ EDITORIAL Presidente Editor-en-Jefe Dr. Hibraim Adán Pérez Mendoza Dra. Leticia M. Ochoa Ochoa Universidad Nacional Autónoma de México Senior Editors Vicepresidente Dr. Marcio Martins (Artigos em português) Dr. Óscar A. Flores Villela Dr. Sean M. Rovito (English papers) Universidad Nacional Autónoma de México Editores asociados Secretario Dr. Uri Omar García Vázquez Dra. Ana Bertha Gatica Colima Dr. Armando H. Escobedo-Galván Universidad Autónoma de Ciudad Juárez Dr. Oscar A. Flores Villela Dra. Irene Goyenechea Mayer Goyenechea Tesorero Dr. Rafael Lara Rezéndiz Dra. Anny Peralta García Dr. Norberto Martínez Méndez Conservación de Fauna del Noroeste Dra. Nancy R. Mejía Domínguez Dr. Jorge E. Morales Mavil Vocal Norte Dr. Hibraim A. Pérez Mendoza Dr. Juan Miguel Borja Jiménez Dr. Jacobo Reyes Velasco Universidad Juárez del Estado de Durango Dr. César A. Ríos Muñoz Dr. Marco A. Suárez Atilano Vocal Centro Dra. Ireri Suazo Ortuño M. en C. Ricardo Figueroa Huitrón Dr. Julián Velasco Vinasco Universidad Nacional Autónoma de México M. en C. Marco Antonio López Luna Dr. Adrián García Rodríguez Vocal Sur M. en C. Marco Antonio López Luna Universidad Juárez Autónoma de Tabasco English style corrector PhD candidate Brett Butler Diseño editorial Lic. Andrea Vargas Fernández M. en A. Rafael de Villa Magallón http://herpetologia.fciencias.unam.mx/index.php/revista NOTAS CIENTÍFICAS SKIN TEXTURE CHANGE IN DIASPORUS HYLAEFORMIS (ANURA: ELEUTHERODACTYLIDAE) ..................... 95 CONTENIDO Juan G. Abarca-Alvarado NOTES OF DIET IN HIGHLAND SNAKES RHADINAEA EDITORIAL CALLIGASTER AND RHADINELLA GODMANI (SQUAMATA:DIPSADIDAE) FROM COSTA RICA .....