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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. -
Checklist of Helminths from Lizards and Amphisbaenians (Reptilia, Squamata) of South America Ticle R A
The Journal of Venomous Animals and Toxins including Tropical Diseases ISSN 1678-9199 | 2010 | volume 16 | issue 4 | pages 543-572 Checklist of helminths from lizards and amphisbaenians (Reptilia, Squamata) of South America TICLE R A Ávila RW (1), Silva RJ (1) EVIEW R (1) Department of Parasitology, Botucatu Biosciences Institute, São Paulo State University (UNESP – Univ Estadual Paulista), Botucatu, São Paulo State, Brazil. Abstract: A comprehensive and up to date summary of the literature on the helminth parasites of lizards and amphisbaenians from South America is herein presented. One-hundred eighteen lizard species from twelve countries were reported in the literature harboring a total of 155 helminth species, being none acanthocephalans, 15 cestodes, 20 trematodes and 111 nematodes. Of these, one record was from Chile and French Guiana, three from Colombia, three from Uruguay, eight from Bolivia, nine from Surinam, 13 from Paraguay, 12 from Venezuela, 27 from Ecuador, 17 from Argentina, 39 from Peru and 103 from Brazil. The present list provides host, geographical distribution (with the respective biome, when possible), site of infection and references from the parasites. A systematic parasite-host list is also provided. Key words: Cestoda, Nematoda, Trematoda, Squamata, neotropical. INTRODUCTION The present checklist summarizes the diversity of helminths from lizards and amphisbaenians Parasitological studies on helminths that of South America, providing a host-parasite list infect squamates (particularly lizards) in South with localities and biomes. America had recent increased in the past few years, with many new records of hosts and/or STUDIED REGIONS localities and description of several new species (1-3). -
Amazon Alive: a Decade of Discoveries 1999-2009
Amazon Alive! A decade of discovery 1999-2009 The Amazon is the planet’s largest rainforest and river basin. It supports countless thousands of species, as well as 30 million people. © Brent Stirton / Getty Images / WWF-UK © Brent Stirton / Getty Images The Amazon is the largest rainforest on Earth. It’s famed for its unrivalled biological diversity, with wildlife that includes jaguars, river dolphins, manatees, giant otters, capybaras, harpy eagles, anacondas and piranhas. The many unique habitats in this globally significant region conceal a wealth of hidden species, which scientists continue to discover at an incredible rate. Between 1999 and 2009, at least 1,200 new species of plants and vertebrates have been discovered in the Amazon biome (see page 6 for a map showing the extent of the region that this spans). The new species include 637 plants, 257 fish, 216 amphibians, 55 reptiles, 16 birds and 39 mammals. In addition, thousands of new invertebrate species have been uncovered. Owing to the sheer number of the latter, these are not covered in detail by this report. This report has tried to be comprehensive in its listing of new plants and vertebrates described from the Amazon biome in the last decade. But for the largest groups of life on Earth, such as invertebrates, such lists do not exist – so the number of new species presented here is no doubt an underestimate. Cover image: Ranitomeya benedicta, new poison frog species © Evan Twomey amazon alive! i a decade of discovery 1999-2009 1 Ahmed Djoghlaf, Executive Secretary, Foreword Convention on Biological Diversity The vital importance of the Amazon rainforest is very basic work on the natural history of the well known. -
Proctoporus Bolivianus Werner (Squamata: Gymnophthalmidae) with the Description of Three New Species and Resurrection of Proctoporus Lacertus Stejneger
AMERICAN MUSEUM NOVITATES Number 3786, 32 pp. October 30, 2013 A taxonomic revision of Proctoporus bolivianus Werner (Squamata: Gymnophthalmidae) with the description of three new species and resurrection of Proctoporus lacertus Stejneger NOEMÍ GOICOECHEA,1 JOSÉ M. PADIAL,2 JUAN CARLOS CHapaRRO,3 SANTIagO CasTROVIEJo-FiSHER,4, 5 AND IgnaCIO DE LA RIVA1 ABSTRACT The genus Proctoporus comprises seven montane species distributed across the Central Andes of Peru, Bolivia, and northern Argentina. Within this genus, the extensive morpho- logical variation observed in populations traditionally assigned to Proctoporus bolivianus suggested the presence of additional species. Using a combination of morphological character differences and a phylogenetic hypothesis based on mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) DNA sequences, we find P. bolivianus to be composed of six distinct lineages. Among these, we name and describe herein Proctoporus carabaya, P. iridescens, and P. kiziri- ani and we resurrect the name Proctoporus lacertus. The remaining two lineages are also considered unnamed species and are referred herein as confirmed candidate species (CCS), which we refrain from naming due to lack of appropriate material. The new species named 1 Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales-CSIC, C/ José Gutiérrez Abascal 2, 28006 Madrid, Spain. 2 Section of Amphibians and Reptiles, Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA, 15213-4080. 3 Museo de Historia Natural, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru. 4 Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192. 5 Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil. -
Zootaxa,A New Petracola and Re-Description of P. Ventrimaculatus
Zootaxa 1700: 53–62 (2008) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2008 · Magnolia Press ISSN 1175-5334 (online edition) A new Petracola and re-description of P. ventrimaculatus (Squamata: Gymnophthalmidae) DAVID KIZIRIAN1, 2, 3, 7, SARAH BAYEFSKY-ANAND1, 4, 6, 8, APRIL ERIKSSON5, MINH LE1, 10 & MAUREEN A. DONNELLY1, 3, 9 1Herpetology, American Museum of Natural History, 175 Central Park West, New York, NY 10024–5192, USA. 2Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA 90095–1606, USA. 3Department of Biological Sciences, Florida International University, Miami, FL 33199, USA. 4Abraham Joshua Heschel High School, 20 West End Avenue, New York, NY 10023–7809, USA. 5Early Entrance Program, California State University–Los Angeles, Los Angeles, CA 90032, USA. 6Harvard University, 1092 Harvard Yard Mail Center, Cambridge, Massachusetts, 02138, USA. E-mail: [email protected], 8 [email protected], [email protected], [email protected] Abstract We describe Petracola waka sp. nov. and re-describe the poorly known P. ventrimaculatus, both high-Andean gymnoph- thalmids from northern Peru. The new species is diagnosed by gracile habitus, smooth dorsal scales, an anterior supercil- iary that extends onto the dorsum, absence of loreal, three genials, 36–49 transverse dorsal scale rows, 23–28 transverse ventral scale rows, 0–7 femoral pores, absence of subocular-labial fusion, and a color pattern consisting of dark spots or fine lines or bands on a pale brown background. Petracola waka is known from the middle Río Marañon and Cajamara- Cajabamba basin (Río Crisnejos drainage) from small isolated syngamic systems at 2650–2900 m and is parapatrically distributed with respect to P. -
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. -
Tiago Rodrigues Simões
Diapsid Phylogeny and the Origin and Early Evolution of Squamates by Tiago Rodrigues Simões A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in SYSTEMATICS AND EVOLUTION Department of Biological Sciences University of Alberta © Tiago Rodrigues Simões, 2018 ABSTRACT Squamate reptiles comprise over 10,000 living species and hundreds of fossil species of lizards, snakes and amphisbaenians, with their origins dating back at least as far back as the Middle Jurassic. Despite this enormous diversity and a long evolutionary history, numerous fundamental questions remain to be answered regarding the early evolution and origin of this major clade of tetrapods. Such long-standing issues include identifying the oldest fossil squamate, when exactly did squamates originate, and why morphological and molecular analyses of squamate evolution have strong disagreements on fundamental aspects of the squamate tree of life. Additionally, despite much debate, there is no existing consensus over the composition of the Lepidosauromorpha (the clade that includes squamates and their sister taxon, the Rhynchocephalia), making the squamate origin problem part of a broader and more complex reptile phylogeny issue. In this thesis, I provide a series of taxonomic, phylogenetic, biogeographic and morpho-functional contributions to shed light on these problems. I describe a new taxon that overwhelms previous hypothesis of iguanian biogeography and evolution in Gondwana (Gueragama sulamericana). I re-describe and assess the functional morphology of some of the oldest known articulated lizards in the world (Eichstaettisaurus schroederi and Ardeosaurus digitatellus), providing clues to the ancestry of geckoes, and the early evolution of their scansorial behaviour. -
Focus on Dance Education
FOCUS ON DANCE EDUCATION: Engaging in the Artistic Processes: Creating, Performing, Responding, Connecting In Partnership with the International Guild of Musicians in Dance (IGMID) 17th Annual Conference October 7-11, 2015 Phoenix, Arizona CONFERENCE PROCEEDINGS National Dance Education Organization Kirsten Harvey, MFA Editor Focus on Dance Education: Engaging in the Artistic Processes: Creating Performing, Responding, Connecting Editorial Introduction In October 2015, the National Dance Education Organization met for their annual conference in Phoenix, Arizona to celebrate and honor the legacy, and individuality of the NDEO dance community. The warm spirit of Phoenix resonated with each educator and artist that came together at the beautiful Pointe Hilton Tapatio Cliffs Resort. Over 150 workshops, papers presentations, panels, master classes, social events, and performances were offered including full day pre-conference intensives that preceded the official start of the conference. The range of offerings for dance educators included a variety of experiences to foster inspiration, education, response, dialogue and connection to one another. Contributions to Focus on Dance Education: Engaging in the Artistic Processes: Creating Performing, Responding, Connecting Conference Proceedings include paper presentations, panel discussions, workshops, and movement sessions presented from October 7-11, 2015. The proceedings include 4 abstracts, 9 full papers, 6 movement session summaries, 6 summary of workshop presentations, 2 panel discussion summaries, and 1 special interest group summary. One of the broadest ranges of submissions since I have been editing the proceedings. The NDEO top paper selection committee selected Caroline Clark’s paper titled “We Learned to Perform by Performing: Oral Histories of Ballet Dancers in a Beer Hall” for the Top Paper Citation. -
A New Species of Riama from Ecuador Previously Referred to As Riama Hyposticta (Boulenger, 1902) (Squamata: Gymnophthalmidae)
AMERICAN MUSEUM NOVITATES Number 3719, 15 pp. June 3, 2011 A New Species of Riama from Ecuador Previously Referred to as Riama hyposticta (Boulenger, 1902) (Squamata: Gymnophthalmidae) SANTIAGO J. SANCHEZ-PACHECO,1 DAVID A. KIZIRIAN,2 AND PEDRO M. SALES NUNES3 ABSTRACT We describe Riama crypta, new species, from the western slopes of the Cordillera Occi¬ dental, Ecuador. This taxon was formerly referred to as Riama hyposticta, a rare species described on the basis of an adult male from northern Ecuador and here recorded from southwestern Colombia. The new species differs principally from Riama hyposticta by an incomplete super¬ ciliary series, formed just by the anteriormost superciliary scale (superciliary series complete in R. hyposticta, formed by five or six scales), no nasoloreal suture [= loreal absent] (complete [= loreal present] in R. hyposticta), distinct dorsolateral stripes at least anteriorly (scattered brown spots dorsally without dorsolateral stripes in R. hyposticta), and ventral coloration com¬ posed of small cream or brown spots or longitudinal stripes (dark brown with conspicuous transverse white bars and spots). Additionally, we document the presence of distal filiform appendages on the hemipenial lobes of both species. INTRODUCTION Although the diversity of Riama in Ecuador has been reviewed (Kizirian and Coloma, 1991; Kizirian, 1995, 1996; also see Reyes-Puig et al., 2008), some taxonomic uncertainties 1 Departamento de Zoologia, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Laboratorio de Herpetologia, CEP 91540-000, Porto Alegre, RS, Brazil. 2 Division of Vertebrate Zoology (Department of Herpetology), American Museum of Natural History. 3 Departamento de Zoologia, Instituto de Biociencias, Universidade de Sao Paulo, CEP 05422-970, Sao Paulo, SP, Brazil. -
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. -
Molecular Phylogenetics, Species Diversity, and Biogeography of the Andean Lizards of the Genus Proctoporus (Squamata: Gymnophthalmidae)
Molecular Phylogenetics and Evolution 65 (2012) 953–964 Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae) Noemí Goicoechea a, José M. Padial b, Juan C. Chaparro c, Santiago Castroviejo-Fisher b, ⇑ Ignacio De la Riva a,d, a Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain b Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, United States c Museo de Historia Natural, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru d School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia article info abstract Article history: The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed Received 25 February 2012 from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six Revised 20 August 2012 currently recognized species occurring across the yungas forests and wet montane grasslands of the Ama- Accepted 21 August 2012 zonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic Available online 7 September 2012 relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals Keywords: includes all currently recognized species of Proctoporus and 15 additional species representing the most Andes closely related groups to the genus. -
Digit Evolution in Gymnophthalmid Lizards JULIANA G
Int. J. Dev. Biol. 58: 895-908 (2014) doi: 10.1387/ijdb.140255jg www.intjdevbiol.com Digit evolution in gymnophthalmid lizards JULIANA G. ROSCITO*,1, PEDRO M.S. NUNES2 and MIGUEL T. RODRIGUES1 1Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo-SP and 2Departamento de Zoologia, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Brazil ABSTRACT The tetrapod limb is a highly diverse structure, and reduction or loss of this structure accounts for many of the limb phenotypes observed within species. Squamate reptiles are one of the many tetrapod lineages in which the limbs have been greatly modified from the pentadactyl generalized pattern, including different degrees of reduction in the number of limb elements to complete limblessness. Even though limb reduction is widespread, the evolutionary and develop- mental mechanisms involved in the formation of reduced limb morphologies remains unclear. In this study, we present an overview of limb morphology within the microteiid lizard group Gymn- ophthalmidae, focusing on digit arrangement. We show that there are two major groups of limb- reduced gymnophthalmids. The first group is formed by lizard-like (and frequently pentadactyl) species, in which minor reductions (such as the loss of 1-2 phalanges mainly in digits I and V) are the rule; these morphologies generally correspond to those seen in other squamates. The second group is formed by species showing more drastic losses, which can include the absence of an ex- ternally distinct limb in adults. We also present the expression patterns of Sonic Hedgehog (Shh) in the greatly reduced fore and hindlimb of a serpentiform gymnophthalmid.