2015 – 2017 Report
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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. -
Didemnidae Didemnum Granulatum Tokioka, 1954
SOME ASCIDIANS (TUNICATA, ASCIDIACEA) FROM PARANA STATE, SOUTHERN BRAZIL 1 Rosana Moreira da Rocha 2 Cinthia Margareth Nasser 2 ABSTRACT. The records ofeleven species from the Parana State coast are presented. One ofthem, Ascidia curvata (Traustedt, 1882), is first registered in the Brazilian coast. Six other species had their geographic distribution extended to the south in West Atlantic waters. KEY WORDS. Ascidiacea, taxonomy, Parana, Brazil The coast of Parana State is one ofthe shortest in Brazil and the few rocky substrates are almost restricted to a few small islands near the coast. The invertebrate fauna of these islands is very poorly known, as well as the ascidians. The only publication on the ascidians ofParana (MOURE et at. 1954) registered the presence of three species: Didemnum candidum (probably a mixture of many species), Polysyncraton amethysteum (really abundant in the intertidal region), and Styela plicata (common species on piers and artificial substrate). In this paper we deal with specimens which were given to us for identification and some material collected during sporadic visits to the coast. This is probably the reason that most species are very common ones and will not be further described, though it is important to register them, because of the extension of the southern limit of distribution in the western Atlantic for most species. We chose not to present the whole synonymy of the species, but only previous references on Brazilian records. Other references are provided at "Distribution and Habitat" section. The specimens examined are deposited in the collection of the first author at Zoology Department ofUniversidade Federal do Parana (codes of vouchers are provided under the item "examined material"). -
MARINE FAUNA and FLORA of BERMUDA a Systematic Guide to the Identification of Marine Organisms
MARINE FAUNA AND FLORA OF BERMUDA A Systematic Guide to the Identification of Marine Organisms Edited by WOLFGANG STERRER Bermuda Biological Station St. George's, Bermuda in cooperation with Christiane Schoepfer-Sterrer and 63 text contributors A Wiley-Interscience Publication JOHN WILEY & SONS New York Chichester Brisbane Toronto Singapore ANTHOZOA 159 sucker) on the exumbrella. Color vari many Actiniaria and Ceriantharia can able, mostly greenish gray-blue, the move if exposed to unfavorable condi greenish color due to zooxanthellae tions. Actiniaria can creep along on their embedded in the mesoglea. Polyp pedal discs at 8-10 cm/hr, pull themselves slender; strobilation of the monodisc by their tentacles, move by peristalsis type. Medusae are found, upside through loose sediment, float in currents, down and usually in large congrega and even swim by coordinated tentacular tions, on the muddy bottoms of in motion. shore bays and ponds. Both subclasses are represented in Ber W. STERRER muda. Because the orders are so diverse morphologically, they are often discussed separately. In some classifications the an Class Anthozoa (Corals, anemones) thozoan orders are grouped into 3 (not the 2 considered here) subclasses, splitting off CHARACTERISTICS: Exclusively polypoid, sol the Ceriantharia and Antipatharia into a itary or colonial eNIDARIA. Oral end ex separate subclass, the Ceriantipatharia. panded into oral disc which bears the mouth and Corallimorpharia are sometimes consid one or more rings of hollow tentacles. ered a suborder of Scleractinia. Approxi Stomodeum well developed, often with 1 or 2 mately 6,500 species of Anthozoa are siphonoglyphs. Gastrovascular cavity compart known. Of 93 species reported from Ber mentalized by radially arranged mesenteries. -
Major Article Epidemiological Study of Snakebite Cases in Brazilian Western Amazonia
Rev Soc Bras Med Trop 51(3):338-346, May-June, 2018 doi: 10.1590/0037-8682-0489-2017 Major Article Epidemiological study of snakebite cases in Brazilian Western Amazonia Katia Regina Pena Schesquini Roriz[1], Kayena Delaix Zaqueo[2],[3], Sulamita Silva Setubal[2], Tony Hiroshi Katsuragawa[4], Renato Roriz da Silva[1], Carla Freire Celedônio Fernandes[2],[4], Luiz Augusto Paiva Cardoso[5], Moreno Magalhães de Souza Rodrigues[2], Andreimar Martins Soares[2], Rodrigo Guerino Stábeli[1],[2] and Juliana Pavan Zuliani[1],[2] [1]. Departamento de Medicina, Universidade Federal de Rondônia, Porto Velho, RO, Brasil. [2]. Fundação Oswaldo Cruz-Rondônia, Porto Velho, RO, Brasil. [3]. Centro de Referência de Jaciara, Instituto Federal de Educação, Ciência e Tecnologia de Mato Grosso, Campus São Vicente, Jaciara, MT, Brasil. [4]. Centro de Pesquisa em Medicina Tropical, Porto Velho, RO, Brasil. [5]. Centro de Medicina Tropical de Rondônia, Porto Velho, RO, Brasil. Abstract Introduction: Brazil has the largest number of snakebite cases in South America, of which the large majority is concentrated in the Midwest and North. Methods: In this descriptive observational study, we assessed the epidemiological and clinical snakebite cases referred to the Centro de Medicina Tropical de Rondônia from September 2008 to September 2010. Results: We followed up 92 cases from admission until discharge, namely 81 (88%) men and 11 (12%) women, with a mean age of 37 years, and mainly from rural areas (91.3%). The snakebites occurred while performing work activities (63%) during the Amazon rainy season (78.3%). The vast majority of individuals presented from the Porto Velho microregion (84.7%). -
Anura: Brachycephalidae) Com Base Em Dados Morfológicos
Pós-graduação em Biologia Animal Laboratório de Anatomia Comparada de Vertebrados Departamento de Ciências Fisiológicas Instituto de Ciências Biológicas da Universidade de Brasília Sistemática filogenética do gênero Brachycephalus Fitzinger, 1826 (Anura: Brachycephalidae) com base em dados morfológicos Tese apresentada ao Programa de pós-graduação em Biologia Animal para a obtenção do título de doutor em Biologia Animal Leandro Ambrósio Campos Orientador: Antonio Sebben Co-orientador: Helio Ricardo da Silva Maio de 2011 Universidade de Brasília Instituto de Ciências Biológicas Programa de Pós-graduação em Biologia Animal TESE DE DOUTORADO LEANDRO AMBRÓSIO CAMPOS Título: “Sistemática filogenética do gêneroBrachycephalus Fitzinger, 1826 (Anura: Brachycephalidae) com base em dados morfológicos.” Comissão Examinadora: Prof. Dr. Antonio Sebben Presidente / Orientador UnB Prof. Dr. José Peres Pombal Jr. Prof. Dr. Lílian Gimenes Giugliano Membro Titular Externo não Vinculado ao Programa Membro Titular Interno Vinculado ao Programa Museu Nacional - UFRJ UnB Prof. Dr. Cristiano de Campos Nogueira Prof. Dr. Rosana Tidon Membro Titular Interno Vinculado ao Programa Membro Titular Interno Vinculado ao Programa UnB UnB Brasília, 30 de maio de 2011 Dedico esse trabalho à minha mãe Corina e aos meus irmãos Flávio, Luciano e Eliane i Agradecimentos Ao Prof. Dr. Antônio Sebben, pela orientação, dedicação, paciência e companheirismo ao longo do trabalho. Ao Prof. Dr. Helio Ricardo da Silva pela orientação, companheirismo e pelo auxílio imprescindível nas expedições de campo. Aos professores Carlos Alberto Schwartz, Elizabeth Ferroni Schwartz, Mácia Renata Mortari e Osmindo Pires Jr. pelos auxílios prestados ao longo do trabalho. Aos técnicos Pedro Ivo Mollina Pelicano, Washington José de Oliveira e Valter Cézar Fernandes Silveira pelo companheirismo e auxílio ao longo do trabalho. -
2017 AAS Abstracts
2017 AAS Abstracts The American Arachnological Society 41st Annual Meeting July 24-28, 2017 Quéretaro, Juriquilla Fernando Álvarez Padilla Meeting Abstracts ( * denotes participation in student competition) Abstracts of keynote speakers are listed first in order of presentation, followed by other abstracts in alphabetical order by first author. Underlined indicates presenting author, *indicates presentation in student competition. Only students with an * are in the competition. MAPPING THE VARIATION IN SPIDER BODY COLOURATION FROM AN INSECT PERSPECTIVE Ajuria-Ibarra, H. 1 Tapia-McClung, H. 2 & D. Rao 1 1. INBIOTECA, Universidad Veracruzana, Xalapa, Veracruz, México. 2. Laboratorio Nacional de Informática Avanzada, A.C., Xalapa, Veracruz, México. Colour variation is frequently observed in orb web spiders. Such variation can impact fitness by affecting the way spiders are perceived by relevant observers such as prey (i.e. by resembling flower signals as visual lures) and predators (i.e. by disrupting search image formation). Verrucosa arenata is an orb-weaving spider that presents colour variation in a conspicuous triangular pattern on the dorsal part of the abdomen. This pattern has predominantly white or yellow colouration, but also reflects light in the UV part of the spectrum. We quantified colour variation in V. arenata from images obtained using a full spectrum digital camera. We obtained cone catch quanta and calculated chromatic and achromatic contrasts for the visual systems of Drosophila melanogaster and Apis mellifera. Cluster analyses of the colours of the triangular patch resulted in the formation of six and three statistically different groups in the colour space of D. melanogaster and A. mellifera, respectively. Thus, no continuous colour variation was found. -
Eudistoma (Ascidiacea: Polycitoridae) from Tropical Brazil
ZOOLOGIA 31 (2): 195–208, April, 2014 http://dx.doi.org/10.1590/S1984-46702014000200011 Eudistoma (Ascidiacea: Polycitoridae) from tropical Brazil Livia de Moura Oliveira1, Gustavo Antunes Gamba1 & Rosana Moreira da Rocha1,2 1 Programa de Pós-graduação em Zoologia, Departamento de Zoologia, Universidade Federal do Paraná. Caixa Postal 19020, 81531-980 Curitiba, PR, Brazil. 2 Corresponding author: E-mail: [email protected] ABSTRACT. We studied material in collections from coastal intertidal and subtidal tropical waters of the Brazilian states of Paraíba, Pernambuco, Alagoas, Bahia, and Espírito Santo. We identified seven species of Eudistoma, of which two are new to science. Eudistoma alvearium sp. nov. colonies have fecal pellets around each zooid and zooids are 6-8 mm long with seven straight and parallel pyloric tubules; the larval trunk is 0.6 mm long with three adhesive papillae and ten ampullae. Eudistoma versicolor sp. nov. colonies are cushion-shaped, variable in color (blue, purple, brown, light green, gray or white) and zooids have six straight and parallel pyloric tubules; the larval trunk is 0.8 mm long with three adhesive papillae and six ampules. Three species – E. carolinense Van Name, 1945, E. recifense Millar, 1977, and E. vannamei Millar, 1977 – are known from northeastern Brazil. The identification of two additional species will require confirmation. We also propose a synonymy for E. carolinense with E. repens Millar, 1977, also previously described in Brazil. KEY WORDS. Atlantic; colonial ascidians; new species; taxonomy. Eudistoma Caullery, 1909 is the most species-rich genus and comment on the implications of species richness for the in Polycitoridae, with 124 valid species found in tropical and distribution of Eudistoma. -
Interaction of the Toads Rhinella Rubescens (Lutz, 1925) and R
Herpetology Notes, volume 14: 1137-1139 (2021) (published online on 20 August 2021) Interaction of the toads Rhinella rubescens (Lutz, 1925) and R. diptycha (Cope, 1862) with artificial road lights in central Brazil Leonardo P. Fraga1,* and Helga C. Wiederhecker2 The impact of roads on biodiversity starts with In Brazil, the genus Rhinella is represented by 40 habitat destruction, persists through time, and might species (Segalla et al., 2019). Among them, species of the be aggravated by traffic and road characteristics R. marina group (sensu Pramuk, 2006) present cranial (Trombulak and Frissell, 2000; Coffin, 2007). Species crests and distinctive, large parotoid glands (Maciel characteristics may also play an important role, and et al., 2007; Pramuk et al., 2008). In Brasília, Distrito studies contemplating terrestrial vertebrates have Federal, Brazil, the R. marina group is represented by revealed amphibians as particularly vulnerable to three species: R. diptycha (Cope, 1862), R. rubescens traffic (Glista et al., 2007; Healey et al., 2020). Among (Lutz, 1925), and R. cerradensis Maciel et al., 2007 anurans, species that perform massive seasonal (Vaz-Silva et al., 2020). Despite their conspicuous size, migrations for resources, such as food and reproductive information regarding the interaction of these species sites, are particularly affected by traffic (Elzanowski with roads and artificial lights are scarce. Here we et al., 2009; Langen et al., 2009; Beebee, 2013). report on the interaction of individuals of two species of Additionally, some road structures, such as manholes, the R. marina group with the headlights of a car. drains, and basins, can accumulate rainwater, creating The interaction occurred on the 17 November 2019 at temporary bodies of water that attract anurans (Le Viol 19:30 h on a rural road (5 m wide) east of Santa Maria, et al., 2012; Cunnington et al., 2014; Sterrett et al., Distrito Federal, Brazil (16.0082°S, 47.8886°W). -
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. -
Amphibiaweb's Illustrated Amphibians of the Earth
AmphibiaWeb's Illustrated Amphibians of the Earth Created and Illustrated by the 2020-2021 AmphibiaWeb URAP Team: Alice Drozd, Arjun Mehta, Ash Reining, Kira Wiesinger, and Ann T. Chang This introduction to amphibians was written by University of California, Berkeley AmphibiaWeb Undergraduate Research Apprentices for people who love amphibians. Thank you to the many AmphibiaWeb apprentices over the last 21 years for their efforts. Edited by members of the AmphibiaWeb Steering Committee CC BY-NC-SA 2 Dedicated in loving memory of David B. Wake Founding Director of AmphibiaWeb (8 June 1936 - 29 April 2021) Dave Wake was a dedicated amphibian biologist who mentored and educated countless people. With the launch of AmphibiaWeb in 2000, Dave sought to bring the conservation science and basic fact-based biology of all amphibians to a single place where everyone could access the information freely. Until his last day, David remained a tirelessly dedicated scientist and ally of the amphibians of the world. 3 Table of Contents What are Amphibians? Their Characteristics ...................................................................................... 7 Orders of Amphibians.................................................................................... 7 Where are Amphibians? Where are Amphibians? ............................................................................... 9 What are Bioregions? ..................................................................................10 Conservation of Amphibians Why Save Amphibians? ............................................................................. -
DEEP SEA LEBANON RESULTS of the 2016 EXPEDITION EXPLORING SUBMARINE CANYONS Towards Deep-Sea Conservation in Lebanon Project
DEEP SEA LEBANON RESULTS OF THE 2016 EXPEDITION EXPLORING SUBMARINE CANYONS Towards Deep-Sea Conservation in Lebanon Project March 2018 DEEP SEA LEBANON RESULTS OF THE 2016 EXPEDITION EXPLORING SUBMARINE CANYONS Towards Deep-Sea Conservation in Lebanon Project Citation: Aguilar, R., García, S., Perry, A.L., Alvarez, H., Blanco, J., Bitar, G. 2018. 2016 Deep-sea Lebanon Expedition: Exploring Submarine Canyons. Oceana, Madrid. 94 p. DOI: 10.31230/osf.io/34cb9 Based on an official request from Lebanon’s Ministry of Environment back in 2013, Oceana has planned and carried out an expedition to survey Lebanese deep-sea canyons and escarpments. Cover: Cerianthus membranaceus © OCEANA All photos are © OCEANA Index 06 Introduction 11 Methods 16 Results 44 Areas 12 Rov surveys 16 Habitat types 44 Tarablus/Batroun 14 Infaunal surveys 16 Coralligenous habitat 44 Jounieh 14 Oceanographic and rhodolith/maërl 45 St. George beds measurements 46 Beirut 19 Sandy bottoms 15 Data analyses 46 Sayniq 15 Collaborations 20 Sandy-muddy bottoms 20 Rocky bottoms 22 Canyon heads 22 Bathyal muds 24 Species 27 Fishes 29 Crustaceans 30 Echinoderms 31 Cnidarians 36 Sponges 38 Molluscs 40 Bryozoans 40 Brachiopods 42 Tunicates 42 Annelids 42 Foraminifera 42 Algae | Deep sea Lebanon OCEANA 47 Human 50 Discussion and 68 Annex 1 85 Annex 2 impacts conclusions 68 Table A1. List of 85 Methodology for 47 Marine litter 51 Main expedition species identified assesing relative 49 Fisheries findings 84 Table A2. List conservation interest of 49 Other observations 52 Key community of threatened types and their species identified survey areas ecological importanc 84 Figure A1. -
Comprehensive Phylogenomic Analyses Resolve Cnidarian Relationships and the Origins of Key Organismal Traits
Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits Ehsan Kayal1,2, Bastian Bentlage1,3, M. Sabrina Pankey5, Aki H. Ohdera4, Monica Medina4, David C. Plachetzki5*, Allen G. Collins1,6, Joseph F. Ryan7,8* Authors Institutions: 1. Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution 2. UPMC, CNRS, FR2424, ABiMS, Station Biologique, 29680 Roscoff, France 3. Marine Laboratory, university of Guam, UOG Station, Mangilao, GU 96923, USA 4. Department of Biology, Pennsylvania State University, University Park, PA, USA 5. Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA 6. National Systematics Laboratory, NOAA Fisheries, National Museum of Natural History, Smithsonian Institution 7. Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA 8. Department of Biology, University of Florida, Gainesville, FL, USA PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3172v1 | CC BY 4.0 Open Access | rec: 21 Aug 2017, publ: 21 Aug 20171 Abstract Background: The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including symbiosis, colonial body plans and elaborate life histories, however, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome scale data for each major cnidarian lineage. Results: Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome scale data that includes representatives of all cnidarian classes.