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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. -
Northern Blue-Tongue Lizard)
Consultation Document on Listing Eligibility and Conservation Actions Tiliqua scincoides intermedia (Northern Blue-tongue Lizard) Image: Copyright, Rick Shine You are invited to provide your views and supporting reasons related to: 1) the eligibility of Tiliqua scincoides intermedia (Northern Blue-tongue Lizard) for inclusion on the EPBC Act threatened species list in the Critically Endangered category and 2) the necessary conservation actions for the above species. Evidence provided by experts, stakeholders and the general public are welcome. Responses can be provided by any interested person. Tiliqua scincoides intermedia (Northern Bluetongue Skink) consultation document Page 1 of 18 Anyone may nominate a native species, ecological community or threatening process for listing under the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) or for a transfer of an item already on the list to a new listing category. The Threatened Species Scientific Committee (the Committee) undertakes the assessment of species to determine eligibility for inclusion in the list of threatened species and provides its recommendation to the Australian Government Minister for the Environment. Responses are to be provided in writing either by email to: [email protected] or by mail to: The Director Species Information and Policy Section, Wildlife, Heritage and Marine Division Department of the Environment and Energy PO Box 787 Canberra ACT 2601 Responses are required to be submitted by Friday 14 May 2021. Contents of -
A Catalogue of Reptiles of Monfragüe National Park (Spain), with Molecular Characterization of Populations of Blanus Wagler, 1830 in This Protected Area
Basic and Applied Herpetology 33 (2019) 81-91 A catalogue of reptiles of Monfragüe National Park (Spain), with molecular characterization of populations of Blanus Wagler, 1830 in this protected area Daniel Fernández-Ortín1, Gregorio Sánchez-Montes2, Íñigo Martínez-Solano2,* 1 Betania, 1, bajo G, 10003 Cáceres, Spain. 2 Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, José Gutiér- rez Abascal, 2, 28006 Madrid, Spain. *Correspondence: E-mail: [email protected] Received: 17 July 2019; returned for review: 29 October 2019; accepted 06 November 2017. Monfragüe National Park (Cáceres, Extremadura, Spain) is a protected area in central‐western Iberia,including some of the best preserved primary Mediterranean vegetation. Legal protection dates back to 1979 (first as a Natural Park and then as a National Park), but knowledge about its reptile communities is so far limited to sparse records. In this paper we present an updated species list based on 521 records covering 163 1x1 km UTM grids in the study area, compiled in the period 2000‐2019. We detected 20 native species, representing 71.4% of the reptile fauna in Extremadura and 35% of the ibero‐balearic reptile fauna. Additionally, based on molecular analyses populations of the amphisbaenid genus Blanus in the study area are assigned to the oriental Iberian taxon, B. cinereus. The new records extend the known distribution of the different reptile species in the study area in 56 10x10 km UTM grids. Species presenting more restricted distributions in Monfragüe are Lacerta schreiberi (one 1x1 grid), Emys orbicularis, and Acanthodactylus erythrurus (four 10x10 grids each). -
Natural History of the Tropical Gecko Phyllopezus Pollicaris (Squamata, Phyllodactylidae) from a Sandstone Outcrop in Central Brazil
Herpetology Notes, volume 5: 49-58 (2012) (published online on 18 March 2012) Natural history of the tropical gecko Phyllopezus pollicaris (Squamata, Phyllodactylidae) from a sandstone outcrop in Central Brazil. Renato Recoder1*, Mauro Teixeira Junior1, Agustín Camacho1 and Miguel Trefaut Rodrigues1 Abstract. Natural history aspects of the Neotropical gecko Phyllopezus pollicaris were studied at Estação Ecológica Serra Geral do Tocantins, in the Cerrado region of Central Brazil. Despite initial prospection at different types of habitats, all individuals were collected at sandstone outcrops within savannahs. Most individuals were observed at night, but several specimens were found active during daytime. Body temperatures were significantly higher in day-active individuals. We did not detect sexual dimorphism in size, shape, weight, or body condition. All adult males were reproductively mature, in contrast to just two adult females (11%), one of which contained two oviductal eggs. Dietary data indicates that P. pollicaris feeds upon a variety of arthropods. Dietary overlap between sexes and age classes was moderate to high. The rate of caudal autotomy varied between age classes but not between sexes. Our data, the first for a population ofP. pollicaris from a savannah habitat, are in overall agreement with observations made in populations from Caatinga and Dry Forest, except for microhabitat use and reproductive cycle. Keywords. Cerrado, lizard, local variation, niche breadth, thermal ecology, sexual dimorphism, tail autotomy. Introduction information about aspects of the natural history (habitat Phyllopezus pollicaris (Spix, 1825) is a large-sized, use, morphology, diet, temperatures, reproductive nocturnal and insectivorous gecko native to central condition and caudal autotomy) of a population of South America (Rodrigues, 1986; Vanzolini, Costa P. -
N REPTILIA: SQUAMATA: SAURIA: PHRYNOSOMATIDAE PHRYNOSOMA Phrynosoma Modestum Girard
630.1 n REPTILIA: SQUAMATA: SAURIA: PHRYNOSOMATIDAE PHRYNOSOMAMODESTUM Catalogue of American Amphibians and Reptiles. Whiting, M.J. and J.R. Dixon. 1996. Phrynosoma modestum. Phrynosoma modestum Girard Roundtail Homed Lizard Phrynosoma modesturn Girard, in Baird and Girard, 1852:69 (see Banta, 1971). Type-locality, "from the valley of the Rio Grande west of San Antonio .....and from between San Antonio and El Paso del Norte." Syntypes, National Mu- seum of Natural History (USNM) 164 (7 specimens), sub- Figure. Adult Phrynosoma modestum from Doha Ana County, adult male, adult male, and 5 adult females, USNM 165660, New Mexico. Photograph by Suzanne L. Collins, courtesy of an adult male, and Museum of Natural History, University The Center for North American Amphibians and Reptiles. of Illinois at Urbana-Champaign (UIMNH) 40746, an adult male, collected by J.H. lark in May or June 1851 (Axtell, 1988) (not examined by authors). See Remarks. Phrynosomaplatyrhynus: Hemck,Terry, and Hemck, 1899: 136. Doliosaurus modestus: Girard, 1858:409. Phrynosoma modestrum: Morafka, Adest, Reyes, Aguirre L., A(nota). modesta: Cope, 1896:834. and Lieberman, 1992:2 14. Lapsus. Content. No subspecies have been described. and Degenhardt et al. (1996). Habitat photographs appeared in Sherbrooke (1981) and Switak (1979). Definition. Phrynosoma modestum is the smallest horned liz- ard, with a maximum SVL of 66 mm in males and 71 mm in Distribution. Phrynosoma modestum occurs in southern and females (Fitch, 1981). It is the sister taxon to l? platyrhinos, western Texas, southern New Mexico, southeastern Arizona and and is part of the "northern radiation" (sensu Montanucci, 1987). north-central Mexico. -
Anfibios Y Reptiles 1 Keiner Meza-Tilvez1,2, Adolfo Mulet-Paso1,2 & Ronald Zambrano-Cantillo1 1Universidad De Cartagena & 2Fauna Silvestre Fundación
Fauna del Jardín Botánico “Guillermo Piñeres” de Cartagena, Turbaco, COLOMBIA Anfibios y Reptiles 1 Keiner Meza-Tilvez1,2, Adolfo Mulet-Paso1,2 & Ronald Zambrano-Cantillo1 1 2 Universidad de Cartagena & Fauna Silvestre Fundación Fotos: Adolfo Mulet Paso (AMP) – Hugo Claessen (HC) – Jairo H. Maldonado (JHM) – Jesús Torres Meza (JTM) – José Luis Pérez-González (JPG) – Jose Luna (JL) – Keiner Meza-Tilvez (KMT) – Luis Alberto Rueda Solano (LRS) – Mauricio Rivera Correa (MRC) – Juan Salvador Mendoza (JSM). © Jardín Botánico de Cartagena “Guillermo Piñeres” [[email protected]] Macho = (M), Hembra = (H) y Juvenil = (Juv.) [fieldguides.fieldmuseum.org] [1097] versión 1 12/2018 1 Rhinella horribilis 2 Rhinella humboldti 3 Dendrobates truncatus 4 Boana pugnax BUFONIDAE (foto KMT) BUFONIDAE (foto KMT) DENDROBATIDAE (foto KMT) HYLIDAE (foto KMT) 5 Boana xerophylla 6 Dendropsophus microcephalus 7 Scarthyla vigilans 8 Scinax rostratus HYLIDAE (foto LRS) HYLIDAE (foto KMT) HYLIDAE (foto KMT) HYLIDAE (foto KMT) 9 Scinax ruber 10 Trachycephalus typhonius 11 Engystomops pustulosus 12 Leptodactylus fragilis HYLIDAE (foto KMT) HYLIDAE (foto KMT) LEPTODACTYLIDAE (foto KMT) LEPTODACTYLIDAE (foto LRS) 13 Leptodactylus insularum 14 Pleurodema brachyops 15 Elachistocleis pearsei 16 Agalychnis callidryas LEPTODACTYLIDAE (foto AMP) LEPTODACTYLIDAE (foto KMT) MICROHYLIDAE (foto MRC) PHYLLOMEDUSIDAE (foto HC) 17 Phyllomedusa venusta 18 Basiliscus basiliscus (M) 19 Basiliscus basiliscus (Juv.) 20 Anolis auratus PHYLLOMEDUSIDAE (foto AMP) CORYTOPHANIDAE (foto KMT) CORYTOPHANIDAE (foto AMP) DACTYLOIDAE (foto AMP) Fauna del Jardín Botánico “Guillermo Piñeres” de Cartagena, Turbaco, COLOMBIA Anfibios y Reptiles 2 Keiner Meza-Tilvez1,2, Adolfo Mulet-Paso1,2 & Ronald Zambrano-Cantillo1 1 2 Universidad de Cartagena & Fauna Silvestre Fundación Fotos: Adolfo Mulet Paso (AMP) – Hugo Claessen (HC) – Jairo H. -
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. -
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. -
REPTILIA: SQUAMATA: PHRYNOSOMATIDAE Sceloporus Poinsettii
856.1 REPTILIA: SQUAMATA: PHRYNOSOMATIDAE Sceloporus poinsettii Catalogue of American Amphibians and Reptiles. Webb, R.G. 2008. Sceloporus poinsettii. Sceloporus poinsettii Baird and Girard Crevice Spiny Lizard Sceloporus poinsettii Baird and Girard 1852:126. Type-locality, “Rio San Pedro of the Rio Grande del Norte, and the province of Sonora,” restricted to either the southern part of the Big Burro Moun- tains or the vicinity of Santa Rita, Grant County, New Mexico by Webb (1988). Lectotype, National Figure 1. Adult male Sceloporus poinsettii poinsettii (UTEP Museum of Natural History (USNM) 2952 (subse- 8714) from the Magdalena Mountains, Socorro County, quently recataloged as USNM 292580), adult New Mexico (photo by author). male, collected by John H. Clark in company with Col. James D. Graham during his tenure with the U.S.-Mexican Boundary Commission in late Au- gust 1851 (examined by author). See Remarks. Sceloporus poinsetii: Duméril 1858:547. Lapsus. Tropidolepis poinsetti: Dugès 1869:143. Invalid emendation (see Remarks). Sceloporus torquatus Var. C.: Bocourt 1874:173. Sceloporus poinsetti: Yarrow “1882"[1883]:58. Invalid emendation. S.[celoporus] t.[orquatus] poinsettii: Cope 1885:402. Seloporus poinsettiii: Herrick, Terry, and Herrick 1899:123. Lapsus. Sceloporus torquatus poinsetti: Brown 1903:546. Sceloporus poissetti: Král 1969:187. Lapsus. Figure 2. Adult female Sceloporus poinsettii axtelli (UTEP S.[celoporus] poinssetti: Méndez-De la Cruz and Gu- 11510) from Alamo Mountain (Cornudas Mountains), tiérrez-Mayén 1991:2. Lapsus. Otero County, New Mexico (photo by author). Scelophorus poinsettii: Cloud, Mallouf, Mercado-Al- linger, Hoyt, Kenmotsu, Sanchez, and Madrid 1994:119. Lapsus. Sceloporus poinsetti aureolus: Auth, Smith, Brown, and Lintz 2000:72. -
Iguanid and Varanid CAMP 1992.Pdf
CONSERVATION ASSESSMENT AND MANAGEMENT PLAN FOR IGUANIDAE AND VARANIDAE WORKING DOCUMENT December 1994 Report from the workshop held 1-3 September 1992 Edited by Rick Hudson, Allison Alberts, Susie Ellis, Onnie Byers Compiled by the Workshop Participants A Collaborative Workshop AZA Lizard Taxon Advisory Group IUCN/SSC Conservation Breeding Specialist Group SPECIES SURVIVAL COMMISSION A Publication of the IUCN/SSC Conservation Breeding Specialist Group 12101 Johnny Cake Ridge Road, Apple Valley, MN 55124 USA A contribution of the IUCN/SSC Conservation Breeding Specialist Group, and the AZA Lizard Taxon Advisory Group. Cover Photo: Provided by Steve Reichling Hudson, R. A. Alberts, S. Ellis, 0. Byers. 1994. Conservation Assessment and Management Plan for lguanidae and Varanidae. IUCN/SSC Conservation Breeding Specialist Group: Apple Valley, MN. Additional copies of this publication can be ordered through the IUCN/SSC Conservation Breeding Specialist Group, 12101 Johnny Cake Ridge Road, Apple Valley, MN 55124. Send checks for US $35.00 (for printing and shipping costs) payable to CBSG; checks must be drawn on a US Banlc Funds may be wired to First Bank NA ABA No. 091000022, for credit to CBSG Account No. 1100 1210 1736. The work of the Conservation Breeding Specialist Group is made possible by generous contributions from the following members of the CBSG Institutional Conservation Council Conservators ($10,000 and above) Australasian Species Management Program Gladys Porter Zoo Arizona-Sonora Desert Museum Sponsors ($50-$249) Chicago Zoological -
Microhabitat Selection of the Poorly Known Lizard Tropidurus Lagunablanca (Squamata: Tropiduridae) in the Pantanal, Brazil
ARTICLE Microhabitat selection of the poorly known lizard Tropidurus lagunablanca (Squamata: Tropiduridae) in the Pantanal, Brazil Ronildo Alves Benício¹; Daniel Cunha Passos²; Abraham Mencía³ & Zaida Ortega⁴ ¹ Universidade Regional do Cariri (URCA), Centro de Ciências Biológicas e da Saúde (CCBS), Departamento de Ciências Biológicas (DCB), Laboratório de Herpetologia, Programa de Pós-Graduação em Diversidade Biológica e Recursos Naturais (PPGDR). Crato, CE, Brasil. ORCID: http://orcid.org/0000-0002-7928-2172. E-mail: [email protected] (corresponding author) ² Universidade Federal Rural do Semi-Árido (UFERSA), Centro de Ciências Biológicas e da Saúde (CCBS), Departamento de Biociências (DBIO), Laboratório de Ecologia e Comportamento Animal (LECA), Programa de Pós-Graduação em Ecologia e Conservação (PPGEC). Mossoró, RN, Brasil. ORCID: http://orcid.org/0000-0002-4378-4496. E-mail: [email protected] ³ Universidade Federal de Mato Grosso do Sul (UFMS), Instituto de Biociências (INBIO), Programa de Pós-Graduação em Biologia Animal (PPGBA). Campo Grande, MS, Brasil. ORCID: http://orcid.org/0000-0001-5579-2031. E-mail: [email protected] ⁴ Universidade Federal de Mato Grosso do Sul (UFMS), Instituto de Biociências (INBIO), Programa de Pós-Graduação em Ecologia e Conservação (PPGEC). Campo Grande, MS, Brasil. ORCID: http://orcid.org/0000-0002-8167-1652. E-mail: [email protected] Abstract. Understanding how different environmental factors influence species occurrence is a key issue to address the study of natural populations. However, there is a lack of knowledge on how local traits influence the microhabitat use of tropical arboreal lizards. Here, we investigated the microhabitat selection of the poorly known lizard Tropidurus lagunablanca (Squamata: Tropiduridae) and evaluated how environmental microhabitat features influence animal’s presence. -
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.