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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. -
Descendants of Thomas Orton
AN ACCOUNT OF THE Descendants of Thomas Orton OF WINDSOR, CONNECTICUT, 1641 ( PRINCIPALLY IN THE MALE LINE) BY EDWARD ORTON, LL. D. Professor of Geology in Ohio State University State Geologist of Ohio COLUMBUS, OHIO PRESS OF NITSCHKE BROTHERS r896 TABLE OF CONTENTS. PAGES CHAPTER I.-lntrod11ctor11 . .......................................... Origin and distribution of tbt: name Orton.... • . 5 Ortons of the United States. 6 Acknowledgments . 7 Purpose and aim of the volume. 8 CHAPTER II.-7he .w~ttlernent of the Ortnns in New England........ 10 Section 1. Thomas Orton, of Windsor, Conn... 11 Removal to Farmington . 12 Last will and testament . 15 English homes of the Ortons . 16 .Section 2.. John Orton of Farmington. .....- . 21 H1sw1ves............. ...... ...... ...... ................. .... 22 Children . 23 SectioR: 3. Third. generation. .................................. (,i) Thomas of Farmington . 28 (b) John of Woodbury . 30 (c) Samuel of Litchfield . 34 CHAPTER III.-_De~cendants of Thomas of Windsor thro' Thornas of Fcrrro:i-n gto'n . Section 1. Fourth ge;neration. .. (a) Thro' Thomas of Tyringham . 43 (b) Thro' John of Tyringham . 45 Section 2. ·Fifth generation . ........ (a) Thro' Thomas of Tyringham . 47 ( b) Thro' John of Tyringham . 50 Section 3. Sixth generation . 55 (a) Thro' Thomas of Tyringham . 55 ( b) Thro' John of Tyringham . 61 PAGES Section 4. Seventh and later generations . 64 (a) Thro' Thomas of Tytingham . .. 64 (b) Thro' John of Tyringham . 76 CHAPTER IV.-Descendants of 1homas of Windsor thro' John of Wood- 1Yu,·y. • . • . 108 Section 1. Fourth generation ........................... 108 Section 2. Fifth and later generations. 111 (a) Thro' John............................ 111 (b) Thro' Samuel. ......... ., . 11~ CHAPTER V.-Descendants of 1 homas of Windsor thro' Samuel of Litch- :fie,ld . -
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. -
Zootaxa, Herpetological Results of the 2002 Expedition to Sarisarinama, A
ZOOTAXA 1942 Herpetological results of the 2002 expedition to Sarisariñama, a tepui in Venezuelan Guayana, with the description of five new species CESAR L. BARRIO-AMOROS & CHARLES BREWER-CARIAS Magnolia Press Auckland, New Zealand Cesar L. Barrio-Amoros & Charles Brewer-Carias Herpetological results of the 2002 expedition to Sarisariñama, a tepui in Venezuelan Guayana, with the description of five new species (Zootaxa 1942) 68 pp.; 30 cm. 26 Nov. 2008 ISBN 978-1-86977-269-7 (paperback) ISBN 978-1-86977-270-3 (Online edition) FIRST PUBLISHED IN 2008 BY Magnolia Press P.O. Box 41-383 Auckland 1346 New Zealand e-mail: [email protected] http://www.mapress.com/zootaxa/ © 2008 Magnolia Press All rights reserved. No part of this publication may be reproduced, stored, transmitted or disseminated, in any form, or by any means, without prior written permission from the publisher, to whom all requests to reproduce copyright material should be directed in writing. This authorization does not extend to any other kind of copying, by any means, in any form, and for any purpose other than private research use. ISSN 1175-5326 (Print edition) ISSN 1175-5334 (Online edition) 2 · Zootaxa 1942 © 2008 Magnolia Press BARRIO-AMORÓS & BREWER-CARÍAS Zootaxa 1942: 1–68 (2008) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2008 · Magnolia Press ISSN 1175-5334 (online edition) Herpetological results of the 2002 expedition to Sarisariñama, a tepui in Venezuelan Guayana, with the description of five new species CÉSAR L. BARRIO-AMORÓS1 & CHARLES BREWER-CARÍAS2 1Fundación AndígenA, Apartado Postal 210, 5101-A Mérida, Venezuela. -
Bibliography and Scientific Name Index to Amphibians
lb BIBLIOGRAPHY AND SCIENTIFIC NAME INDEX TO AMPHIBIANS AND REPTILES IN THE PUBLICATIONS OF THE BIOLOGICAL SOCIETY OF WASHINGTON BULLETIN 1-8, 1918-1988 AND PROCEEDINGS 1-100, 1882-1987 fi pp ERNEST A. LINER Houma, Louisiana SMITHSONIAN HERPETOLOGICAL INFORMATION SERVICE NO. 92 1992 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 The present alphabetical listing by author (s) covers all papers bearing on herpetology that have appeared in Volume 1-100, 1882-1987, of the Proceedings of the Biological Society of Washington and the four numbers of the Bulletin series concerning reference to amphibians and reptiles. From Volume 1 through 82 (in part) , the articles were issued as separates with only the volume number, page numbers and year printed on each. Articles in Volume 82 (in part) through 89 were issued with volume number, article number, page numbers and year. -
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. -
Mccutcheorfs Which Mrs
"You are a man *ith M,.. ,v^r/. ,,,.M ..thing for çroTrn <u j * o Ég¿^¡¡* ter«," Mrs. Van Wi« 8av- Heirs Wife Glances luí * P"»«"« Van "¡Ut* ,-<,,j «h^WlI Found to Fr»s« Wie, adding, .,. ^!a Her Used Wife roirtipd him in :-«r*. men on ; i h i* u dozen ning around with this Krrr., !Lhat ,, rt-,,,-rs''|f j Diary Against by Mrs. ' Frate in he »trinf.?<dtí» 2Ä*hcwn/cn »»«" rebte*. whereupon Mrs. >r;.(j l^' -j Which Is Better? Note; $250,000 sho's got me mixed un with th»'«»C*& $350,000 Left Who Names Brother '.*. one." '**: ,'¦' Husband, *r$ïï,rrïoî dozen. F * j of and ot Love Suit« Follow i »i«v« a «««-P^ntary,!always Vice-Chancellor Fotóer «f» . Safety principal good return, me.» for aï;,j. and as to the r^TJof^^nd days taking teitutrony -, tr^i $ Mrs. uncertainty* anxiety principal, Annie Ferrotta, b beautiful Italian hidden in a ne!il. In Easton no matter nightingale cqbwcb By how great the return? A trustee girl of twenty-three, for yours has h flowered thicket. My feet beat time "Here You Are flttnmilg lias but one answer. other person has poured all her afteret thought» into ft jovously to its music. I look in the Any* little red It is a volume rich in mirror and my eyes are like ArotmcfWitli Tfeii r'reneh Nephew and Two Nieces but one sensible answer. diary. silver poetic sophistry and occasional flashes stars, my cheeks like rarer blooms Mrs. Van liri Arc Sur- of wit. -
Reptilia, Squamata, Gymnophthalmidae, Potamites Erythrocularis Chávez & Catenazzi, 2014: Distribution Extension
Herpetology Notes, volume 8: 625-628 (2015) (published online on 20 December 2015) Reptilia, Squamata, Gymnophthalmidae, Potamites erythrocularis Chávez & Catenazzi, 2014: Distribution extension Juan C. Chávez-Arribasplata1,*, Vilma Duran2, and Germán Chávez3 The neotropical family Gymnophthalmidae Merrem, individuals of Potamites erythrocularis were recorded, 1820 comprises 36 genera that occur from Mexico representing the first record outside of the localities to Argentina (Goicoechea et al., 2012). This highly where the type series was collected. diversified family includes the semi-aquatic lizard A young female of Potamites erythrocularis (CORBIDI genus Potamites Doan & Castoe, 2005, which currently 13548) was found at El Parador, Inambari, 8.64 Km SE comprises eight species distributed from western Costa of Puerto Carlos (S 12.9699, W 70.2323; 266m) at 21:30 Rica and Panama to the Amazonian forests of Bolivia on 30 September 2013 by José Malqui and Germán (Chávez and Catenazzi, 2014). Likewise, with five Chávez. It was catched in the leaf-litter alongside a slow species Peru is the country with the highest diversity flowing stream 2-2.5 m in width. The stream drained a within this genus: P. flavogularis Altamirano-Benavides, closed canopy primary forest with riparian vegetation Zaher, Lobo, Grazziotin, Sales Nunes and Rodrigues, of ferns, lichens, plants of the family Heliconaceae and 2013; P. ecpleopus Cope 1876, P. montanicola Chavez Asteraceae and trees of the family Fabaceae. An adult y Vasquez, 2012; P. strangulatus Cope, 1868; and P. male (CORBIDI 15152) was also found at the locality erythrocularis Chavez and Catenazzi, 2014. Most of of El Parador (S 12.9804, W 70.2362; 253m) at 00:32 them are distributed in the Amazonian lowlands (Doan on 5 November 2014 by Juan C. -
The Herpetological Journal
Volume 16, Number 2 April 2006 ISSN 0268-0130 THE HERPETOLOGICAL JOURNAL Published by the BRITISH HERPETOLOGICAL SOCIETY The Herpetological Journal is published quarterly by the British Herpetological Society and is issued1 free to members. Articles are listed in Current Awareness in Biological Sciences, Current Contents, Science Citation Index and Zoological Record. Applications to purchase copies and/or for details of membership should be made to the Hon. Secretary, British Herpetological Society, The Zoological Society of London, Regent's Park, London NWl 4RY, UK. Instructions to authors are printed inside_the back cover. All contributions should be addressed to the Scientific Editor (address below). Scientific Editor: Wolfgang Wi.ister, School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, UK. E-mail: W.Wu [email protected] Associate Scientifi c Editors: J. W. Arntzen (Leiden), R. Brown (Liverpool) Managing Editor: Richard A. Griffi ths, The Durrell Institute of Conservation and Ecology, Marlowe Building, University of Kent, Canterbury, Kent, CT2 7NR, UK. E-mail: R.A.Griffi [email protected] Associate Managing Editors: M. Dos Santos, J. McKay, M. Lock Editorial Board: Donald Broadley (Zimbabwe) John Cooper (Trinidad and Tobago) John Davenport (Cork ) Andrew Gardner (Abu Dhabi) Tim Halliday (Milton Keynes) Michael Klemens (New York) Colin McCarthy (London) Andrew Milner (London) Richard Tinsley (Bristol) Copyright It is a fu ndamental condition that submitted manuscripts have not been published and will not be simultaneously submitted or published elsewhere. By submitting a manu script, the authors agree that the copyright for their article is transferred to the publisher ifand when the article is accepted for publication. -
Discovery of an Additional Piece of the Large Gymnophthalmid Puzzle: A
Zootaxa 4950 (2): 296–320 ISSN 1175-5326 (print edition) https://www.mapress.com/j/zt/ Article ZOOTAXA Copyright © 2021 Magnolia Press ISSN 1175-5334 (online edition) https://doi.org/10.11646/zootaxa.4950.2.4 http://zoobank.org/urn:lsid:zoobank.org:pub:9464FC1F-2F92-46B7-BA53-1CFC93981F09 Discovery of an additional piece of the large gymnophthalmid puzzle: a new genus and species of stream spiny lizard (Squamata: Gymnophthalmidae: Cercosaurinae) from the western Guiana Shield in Venezuela FERNANDO J.M. ROJAS-RUNJAIC1*, CÉSAR L. BARRIO-AMORÓS2, J. CELSA SEÑARIS3,4, IGNACIO DE LA RIVA5 & SANTIAGO CASTROVIEJO-FISHER4,6 1Museo de Historia Natural La Salle, Fundación La Salle de Ciencias Naturales, Caracas 1050, Distrito Capital, Venezuela 2Doc Frog Expeditions/CRWild, 60504, Bahía Ballena, Uvita, Costa Rica �[email protected]; https://orcid.org/0000-0001-5837-9381 3PROVITA, calle La Joya con Av. Libertador, Unidad Técnica del Este, piso 10, oficina 29-30, Caracas 1060, Miranda, Venezuela �[email protected]; https://orcid.org/0000-0001-8673-7385 4Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS 90619-900, Brazil 5Museo Nacional de Ciencias Naturales-CSIC, C/ José Gutiérrez Abascal 2, 28006 Madrid, Spain �[email protected]; https://orcid.org/0000-0001-5064-4507 6Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA �[email protected]; https://orcid.org/0000-0002-1048-2168 *Corresponding author. �[email protected]; https://orcid.org/0000-0001-5409-4231 Abstract Gymnophthalmids are a highly diverse group of Neotropical lizards and its species richness is still in process of discovery. -
A Rapid Biological Assessment of the Upper Palumeu River Watershed (Grensgebergte and Kasikasima) of Southeastern Suriname
Rapid Assessment Program A Rapid Biological Assessment of the Upper Palumeu River Watershed (Grensgebergte and Kasikasima) of Southeastern Suriname Editors: Leeanne E. Alonso and Trond H. Larsen 67 CONSERVATION INTERNATIONAL - SURINAME CONSERVATION INTERNATIONAL GLOBAL WILDLIFE CONSERVATION ANTON DE KOM UNIVERSITY OF SURINAME THE SURINAME FOREST SERVICE (LBB) NATURE CONSERVATION DIVISION (NB) FOUNDATION FOR FOREST MANAGEMENT AND PRODUCTION CONTROL (SBB) SURINAME CONSERVATION FOUNDATION THE HARBERS FAMILY FOUNDATION Rapid Assessment Program A Rapid Biological Assessment of the Upper Palumeu River Watershed RAP (Grensgebergte and Kasikasima) of Southeastern Suriname Bulletin of Biological Assessment 67 Editors: Leeanne E. Alonso and Trond H. Larsen CONSERVATION INTERNATIONAL - SURINAME CONSERVATION INTERNATIONAL GLOBAL WILDLIFE CONSERVATION ANTON DE KOM UNIVERSITY OF SURINAME THE SURINAME FOREST SERVICE (LBB) NATURE CONSERVATION DIVISION (NB) FOUNDATION FOR FOREST MANAGEMENT AND PRODUCTION CONTROL (SBB) SURINAME CONSERVATION FOUNDATION THE HARBERS FAMILY FOUNDATION The RAP Bulletin of Biological Assessment is published by: Conservation International 2011 Crystal Drive, Suite 500 Arlington, VA USA 22202 Tel : +1 703-341-2400 www.conservation.org Cover photos: The RAP team surveyed the Grensgebergte Mountains and Upper Palumeu Watershed, as well as the Middle Palumeu River and Kasikasima Mountains visible here. Freshwater resources originating here are vital for all of Suriname. (T. Larsen) Glass frogs (Hyalinobatrachium cf. taylori) lay their -
Diet of the Lizard Ecpleopus Gaudichaudii (Gymnophthalmidae) in Atlantic Rainforest, State of Rio De Janeiro, Brazil
ZOOLOGIA 28 (5): 587–592, October, 2011 doi: 10.1590/S1984-46702011000500006 Diet of the lizard Ecpleopus gaudichaudii (Gymnophthalmidae) in Atlantic Rainforest, state of Rio de Janeiro, Brazil Thiago Maia1, 5; Mauricio Almeida-Gomes1; Carla C. Siqueira2; Davor Vrcibradic3; Mara C. Kiefer4 & Carlos Frederico D. Rocha1 1 Departamento de Ecologia, Universidade do Estado do Rio de Janeiro. Rua São Francisco Xavier 524, 20550-019 Rio de Janeiro, RJ, Brazil. 2 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro. Avenida Carlos Chagas Filho 373, Bloco A, Cidade Universitária, 21941-902 Rio de Janeiro, RJ, Brazil. 3 Departamento de Zoologia, Universidade Federal do Estado do Rio de Janeiro. Avenida Pasteur 458, Urca, 22240-290 Rio de Janeiro, RJ, Brazil. 4 Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense. Caixa Postal 100436, Centro, 24020-971 Niterói, RJ, Brazil. 5 Corresponding author. E-mail: [email protected] ABSTRACT. In this study we analyzed the diet of the gymnophthalmid lizard Ecpleopus gaudichaudii Duméril & Bibron, 1839, a typical inhabitant of the forest-floor leaf litter, in an Atlantic Forest area in the state of Rio de Janeiro, southeast- ern Brazil. The 26 individuals sampled during the study had a mean snout-vent length (SVL) of 36.2 ± 4.2 mm and a mean jaw width (JW) of 4.1 ± 0.5 mm. We did not find differences in SVL between males and females, though the sexes differed in JW when the effect of body size was factored out, with females presenting higher values. The diet of the lizards was composed exclusively of arthropods, especially isopods and orthopterans.