Body Size Distributions at Community, Regional Or Taxonomic Scales Do Not
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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. -
Phylogenetic Diversity, Habitat Loss and Conservation in South
Diversity and Distributions, (Diversity Distrib.) (2014) 20, 1108–1119 BIODIVERSITY Phylogenetic diversity, habitat loss and RESEARCH conservation in South American pitvipers (Crotalinae: Bothrops and Bothrocophias) Jessica Fenker1, Leonardo G. Tedeschi1, Robert Alexander Pyron2 and Cristiano de C. Nogueira1*,† 1Departamento de Zoologia, Universidade de ABSTRACT Brasılia, 70910-9004 Brasılia, Distrito Aim To analyze impacts of habitat loss on evolutionary diversity and to test Federal, Brazil, 2Department of Biological widely used biodiversity metrics as surrogates for phylogenetic diversity, we Sciences, The George Washington University, 2023 G. St. NW, Washington, DC 20052, study spatial and taxonomic patterns of phylogenetic diversity in a wide-rang- USA ing endemic Neotropical snake lineage. Location South America and the Antilles. Methods We updated distribution maps for 41 taxa, using species distribution A Journal of Conservation Biogeography models and a revised presence-records database. We estimated evolutionary dis- tinctiveness (ED) for each taxon using recent molecular and morphological phylogenies and weighted these values with two measures of extinction risk: percentages of habitat loss and IUCN threat status. We mapped phylogenetic diversity and richness levels and compared phylogenetic distances in pitviper subsets selected via endemism, richness, threat, habitat loss, biome type and the presence in biodiversity hotspots to values obtained in randomized assemblages. Results Evolutionary distinctiveness differed according to the phylogeny used, and conservation assessment ranks varied according to the chosen proxy of extinction risk. Two of the three main areas of high phylogenetic diversity were coincident with areas of high species richness. A third area was identified only by one phylogeny and was not a richness hotspot. Faunal assemblages identified by level of endemism, habitat loss, biome type or the presence in biodiversity hotspots captured phylogenetic diversity levels no better than random assem- blages. -
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. -
Redalyc.ACCIÓN DEL ANTIVENENO BOTRÓPICO POLIVALENTE
Revista Peruana de Medicina Experimental y Salud Pública ISSN: 1726-4642 [email protected] Instituto Nacional de Salud Perú Yarlequé, Armando; Vivas, Dan; Inga, Rosío; Rodríguez, Edith; Adolfo Sandoval, Gustavo; Pessah, Silvia; Bonilla, César ACCIÓN DEL ANTIVENENO BOTRÓPICO POLIVALENTE SOBRE LAS ACTIVIDADES PROTEOLÍTICAS PRESENTES EN LOS VENENOS DE SERPIENTES PERUANAS Revista Peruana de Medicina Experimental y Salud Pública, vol. 25, núm. 2, 2008, pp. 169-173 Instituto Nacional de Salud Lima, Perú Disponible en: http://www.redalyc.org/articulo.oa?id=36311608002 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto Rev Peru Med Exp Salud Publica. 2008; 25(2):169-73. ARTÍCULO ORIGINAL ACCIÓN DEL ANTIVENENO BOTRÓPICO POLIVALENTE SOBRE LAS ACTIVIDADES PROTEOLÍTICAS PRESENTES EN LOS VENENOS DE SERPIENTES PERUANAS Armando Yarlequé1,a, Dan Vivas1,a, Rosío Inga1,a, Edith Rodríguez1,a, Gustavo Adolfo Sandoval1,a, Silvia Pessah2,b, César Bonilla2,a RESUMEN Los venenos de las serpientes peruanas causantes de la mayoría de accidentes ofídicos, contienen enzimas proteolíticas que pueden degradar proteínas tisulares y plasmáticas, así como causar hipotensión y coagulación sanguínea. Objetivos. Evaluar la capacidad inhibitoria del antiveneno botrópico polivalente al estado líquido producido por el Instituto Nacional de Salud del Perú (INS) sobre las actividades caseinolítica, coagulante y amidolítica de los venenos de Bothrops atrox, Bothrops brazili, Bothrops pictus y Bothrops barnetti. Materiales y métodos. Se usaron en cada caso sustratos como caseína, fibrinógeno bovino y el cromógeno benzoil-arginil-p-nitroanilida (BApNA) respectivamente, y se midieron los cambios en los valores de la actividad enzimática a ½, 1 y 2 dosis del antiveneno tanto al estado natural como calentado a 37 °C durante cinco días. -
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. -
Víbora De Campbell
Víbora de Campbell Bothrocophias campbelli (Freire-Lascano, 1991) P. D. Gutiérrez-Cárdenas Taxonomía Orden Squamata VU Familia Viperidae Categoría de amenaza ventrales (vs. 124-141 en B. colombianus y 143-153 en B. myersi) y 23 hileras de es- Nacional: Vulnerable VU B1ab(iii). camas dorsales (vs. 25 en B. colombianus) Global: no evaluada. (Campbell y Lamar 2004). Otro nombre común Distribución geográfica Serpiente boca de sapo. Países: Ecuador y Colombia. Descripción Departamentos: Nariño. Serpiente de tamaño mediano, hasta 123 Subregión biogeográfica: Cordillera cm de longitud total. La coloración varía Central. de café oscuro a gris oscuro con patrones Distribución altitudinal: 1.000 - 1.500 de “V” en el dorso, demarcadas por ban- m s.n.m. (Castro et al. 2005). das más claras. Presenta una franja oscura detrás del ojo. Un especimen presentó en Aspectos bioecológicos cada lado una mancha oscura entre las in- Hábitos terrestres, se encuentra sobre fralabiales 6-8. Se diferencia de Bothroco- la hojarasca en los bordes o el interior de phias colombianus por que presenta una es- bosques maduros (Cisneros-Heredia et cama lacunolabial, tiene 152-177 escamas al. 2006, Arteaga 2013). Se ha observado 113 ilícitos y minería ilegal. Adicional a esto, todas las especies de serpientes y en par- Vulnerables ticular los vipéridos son perseguidos por su peligrosidad potencial, aunque hasta el momento no se han reportado accidentes ofidicos con B. campbelli. Medidas de conservación existentes Ninguna. Oportunidades de conservación En la actualidad se está elaborando el Programa nacional para la conservación de serpientes en Colombia (Lynch, com. pers.). Aunque en este documento no se menciona explícitamente la especie B. -
Programação Do XVI Congresso Da SBBC E 10Th International
July 25th- 28th, 2012 Rio de Janeiro, Brazil 1 Contents www.sbbc.org.br Scientific Content Welcome to ICCB 2012 SBBC Council and Committees ICCB 10th Annual Meeting Supporters Meeting at a Glance Pre-Meeting Educational Activities Wednesday Program Thursday Program Friday Program Saturday Program Travel Awards General Information Meeting Registration Meeting Policies Meeting resources Transportation and Hotel Map General Travel Information Important phone numbers RioCentro Convention Center Attendee Resources RioCentro Convention Center Floor Plans Exhibitors Exhibitor Listings Exhibit Hall Floor Plan Poster Information Poster sessions and assignment Presentation instructions Poster title list Authors Author Index 2 Welcome! Welcome to the heart of biomedical sciences! As important as the function of cells for life, cell biology is at the center stage of science nowadays, either through the promises in therapy strategies and biotechnology or through the development of new tools and concepts, not to forget its importance and influence on science education. The program is dense, explores the many aspects of this fascinating area, and counts on the contribution from internationally recognized experts. We would like to express our sincere gratitude to invited speakers, guests, participants, exhibitors and the staff working to the different committees. This is also a great opportunity to thank the Brazilian Society for Cell Biology (SBBC) and the International Federation of Cell Biology (IFCB) for the partnership, and the different government agencies and institutions that contributed for both organizational and financial aspects, especially FIOCRUZ. The ICCB2012 is a happy and timely coincidence between the International Congress on Cell Biology and the Congress of the Brazilian Society for Cell Biology, which was detected and worked out in 2004. -
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. -
Proteomic and Toxicological Profiling of the Venom of Bothrocophias
Toxicon 90 (2014) 15e25 Contents lists available at ScienceDirect Toxicon journal homepage: www.elsevier.com/locate/toxicon Proteomic and toxicological profiling of the venom of Bothrocophias campbelli, a pitviper species from Ecuador and Colombia David Salazar-Valenzuela a, b, Diana Mora-Obando c, María Laura Fernandez c, * Amaru Loaiza-Lange b, H. Lisle Gibbs a, Bruno Lomonte c, a Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, 318 W. 12th Ave., Columbus, OH 43210-1293, USA b Escuela de Biología, Pontificia Universidad Catolica del Ecuador, Avenida 12 de Octubre y Roca, Apartado 17-01-2184, Quito, Ecuador c Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose 11501, Costa Rica article info abstract Article history: Detailed snake venom proteomes for nearly a hundred species in different pitviper genera Received 16 June 2014 have accumulated using ‘venomics’ methodologies. However, venom composition for Accepted 24 July 2014 some lineages remains poorly known. Bothrocophias (toad-headed pitvipers) is a genus Available online 1 August 2014 restricted to the northwestern portion of South America for which information on venom composition is lacking. Here, we describe the protein composition, toxicological profiling, Keywords: and antivenom neutralization of the venom of Bothrocophias campbelli, a species distrib- Snake venom uted in Colombia and Ecuador. Our analyses show that its venom mainly consists of Venomics Proteomic phospholipases A2 (43.1%), serine proteinases (21.3%), and metalloproteinases (15.8%). The Toxicity low proportion of metalloproteinases and high amount of a Lys49 phospholipase A2 ho- Viperidae mologue correlate well with the low hemorrhagic and high myotoxic effects found. -
Real-Time DNA Barcoding in a Remote Rainforest Using Nanopore Sequencing
bioRxiv preprint doi: https://doi.org/10.1101/189159; this version posted September 15, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Real-time DNA barcoding in a remote rainforest using nanopore sequencing 2 3 Aaron Pomerantz1,*, Nicolás Peñafiel2, Alejandro Arteaga3, Lucas Bustamante3, Frank Pichardo3, 4 Luis A. Coloma4, César L. Barrio-Amorós5, David Salazar-Valenzuela2, Stefan Prost 1,6,* 5 6 1 Department of Integrative Biology, University of California, Berkeley, CA, USA 7 2 Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en 8 Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad 9 Tecnológica Indoamérica, Machala y Sabanilla, Quito, Ecuador 10 3 Tropical Herping, Quito, Ecuador 11 4 Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Otonga, Quito, 12 Ecuador 13 5 Doc Frog Expeditions, Uvita, Costa Rica 14 6 Program for Conservation Genomics, Department of Biology, Stanford University, Stanford, CA, 15 USA 16 17 * Corresponding authors: [email protected] (A. Pomerantz) and 18 [email protected] (S. Prost) 19 20 Abstract 21 Advancements in portable scientific instruments provide promising avenues to expedite 22 field work in order to understand the diverse array of organisms that inhabit our planet. 23 Here we tested the feasibility for in situ molecular analyses of endemic fauna using a 24 portable laboratory fitting within a single backpack, in one of the world’s most imperiled 25 biodiversity hotspots: the Ecuadorian Chocó rainforest. -
Venom Characterization of the Three Species of Ophryacus and Proteomic Profiling of O. Sphenophrys Unveils Sphenotoxin, a Novel
Journal of Proteomics xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Journal of Proteomics journal homepage: www.elsevier.com/locate/jprot Venom characterization of the three species of Ophryacus and proteomic profiling of O. sphenophrys unveils Sphenotoxin, a novel Crotoxin-like heterodimeric β-neurotoxin Edgar Neri-Castroa,b, Bruno Lomontec, Mariel Valdésa,d, Roberto Ponce-Lópeza, Melisa Bénard-Vallea, Miguel Borjae, Jason L. Stricklandf, Jason M. Jonesg, Christoph Grünwaldg, ⁎ Fernando Zamudioa, Alejandro Alagóna, a Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, México b Programa de Doctorado en Ciencias Biomédicas UNAM, México. c Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica d Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, México e Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio C.P. 35010, México. f Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA. g Herp.mx A.C., Villa del Álvarez, Colima, México ABSTRACT Venoms of the three species of Ophryacus (O. sphenophrys, O. smaragdinus, and O. undulatus), a viperid genus endemic to Mexico, were analyzed for the first time in the present work. The three venoms lacked procoagulant activity on human plasma, but induced hemorrhage and were highly lethal to mice. These venoms also displayed proteolytic and phospholipase A2 activities in vitro. The venom of O. sphenophrys was the most lethal and caused hind-limb paralysis in mice. Proteomic profiling of O. -
New Observations on Diet of the South American Two-Striped Forest-Pitviper Bothrops Bilineatus Smaragdinus (Hoge, 1966)
CORE Metadata, citation and similar papers at core.ac.uk Provided by Servicio de Difusión de la Creación Intelectual Nota Cuad. herpetol. 33(1): 29-31 (2019) New observations on diet of the South American two-striped forest-pitviper Bothrops bilineatus smaragdinus (Hoge, 1966) Pablo J. Venegas1, Juan C. Chávez-Arribasplata1, Eduardo Almora1, Pablo Grilli2, Vilma Duran1 1 Centro de Ornitología y Biodiversidad (CORBIDI). Calle Santa Rita 105, Urb. Los Huertos de San Antonio, Surco, Lima 33, Perú. 2 Cátedra de Ecología General y Recursos Naturales, Universidad Nacional Arturo Jauretche. Av. Calchaquí 6299, Florencio Varela (CP 1888) Provincia de Buenos Aires, Argentina. Recibida: 14 Noviembre 2017 ABSTRACT Revisada: 28 Febrero 2018 The arboreal, nocturnal and widely distributed snake Bothrops bilineatus smaragdinus (Squamata, Aceptada: 29 Enero 2019 Viperidae) is known as a generalist whose diet items have rarely been identified to species level. Editor Asociado: J. Goldberg In this work we report three new items for its diet: an adult frog Dendropsophus marmoratus (Anura, Hylidae), an adult lizard Thecadactylus solimoensis (Squamata, Phyllodactylidae), and an adult bat Carollia brevicauda (Chiroptera, Phyllostomidae), the latter being the first record doi: 10.31017/CdH.2019.(2017-031) of predation of a Chiropteran by this species. Key Words: Anurophagy; Carollia brevicauda; Dendropsophus marmoratus; Diet; Thecadactylus solimoensis; Saurophagy. The venomous snake, Bothrops bilineatus smarag- marmoratus (Laurenti, 1768) at 1.4 m above the dinus (Hoge, 1966), is widely distributed across the ground on a branch at Cashiriari (11°51’53.4” S; western side of the Amazon basin, encompassing 72°46’45.4” W, 588 m a.s.l.), La Convención, Cusco Amazonian Colombia and southern Venezuela, department, Peru.