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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. -
USF Board of Trustees ( March 7, 2013)
Agenda item: (to be completed by Board staff) USF Board of Trustees ( March 7, 2013) Issue: Proposed Ph.D. in Integrative Biology ________________________________________________________________ Proposed action: New Degree Program Approval ________________________________________________________________ Background information: This application for a new Ph.D is driven by a recent reorganization of the Department of Biology. The reorganization began in 2006 and was completed in 2009. The reorganization of the Department of Biology, in part, reflected the enormity of the biological sciences, and in part, different research perspectives and directions taken by the faculty in each of the respective areas of biology. Part of the reorganization was to replace the original Ph.D. in Biology with two new doctoral degrees that better serve the needs of the State and our current graduate students by enabling greater focus of the research performed to earn the Ph.D. The well-established and highly productive faculty attracts students to the Tampa Campus from all over the United States as well as from foreign countries. The resources to support the two Ph.D. programs have already been established in the Department of Biology and are sufficient to support the two new degree programs. The reorganization created two new departments; the Department of Cell Biology, Microbiology, and Molecular Biology (CMMB) and the Department of Integrative Biology (IB). This proposal addresses the creation of a new Ph.D., in Integrative Biology offered by the Department of Integrative Biology (CIP Code 26.1399). The name of the Department, Integrative Biology, reflects the belief that the study of biological processes and systems can best be accomplished by the incorporation of numerous integrated approaches Strategic Goal(s) Item Supports: The proposed program directly supports the following: Goal 1 and Goal 2 Workgroup Review: ACE March 7, 2013 Supporting Documentation: See Complete Proposal below Prepared by: Dr. -
The Conservation Biology of Tortoises
The Conservation Biology of Tortoises Edited by Ian R. Swingland and Michael W. Klemens IUCN/SSC Tortoise and Freshwater Turtle Specialist Group and The Durrell Institute of Conservation and Ecology Occasional Papers of the IUCN Species Survival Commission (SSC) No. 5 IUCN—The World Conservation Union IUCN Species Survival Commission Role of the SSC 3. To cooperate with the World Conservation Monitoring Centre (WCMC) The Species Survival Commission (SSC) is IUCN's primary source of the in developing and evaluating a data base on the status of and trade in wild scientific and technical information required for the maintenance of biological flora and fauna, and to provide policy guidance to WCMC. diversity through the conservation of endangered and vulnerable species of 4. To provide advice, information, and expertise to the Secretariat of the fauna and flora, whilst recommending and promoting measures for their con- Convention on International Trade in Endangered Species of Wild Fauna servation, and for the management of other species of conservation concern. and Flora (CITES) and other international agreements affecting conser- Its objective is to mobilize action to prevent the extinction of species, sub- vation of species or biological diversity. species, and discrete populations of fauna and flora, thereby not only maintain- 5. To carry out specific tasks on behalf of the Union, including: ing biological diversity but improving the status of endangered and vulnerable species. • coordination of a programme of activities for the conservation of biological diversity within the framework of the IUCN Conserva- tion Programme. Objectives of the SSC • promotion of the maintenance of biological diversity by monitor- 1. -
Spiders of the Hawaiian Islands: Catalog and Bibliography1
Pacific Insects 6 (4) : 665-687 December 30, 1964 SPIDERS OF THE HAWAIIAN ISLANDS: CATALOG AND BIBLIOGRAPHY1 By Theodore W. Suman BISHOP MUSEUM, HONOLULU, HAWAII Abstract: This paper contains a systematic list of species, and the literature references, of the spiders occurring in the Hawaiian Islands. The species total 149 of which 17 are record ed here for the first time. This paper lists the records and literature of the spiders in the Hawaiian Islands. The islands included are Kure, Midway, Laysan, French Frigate Shoal, Kauai, Oahu, Molokai, Lanai, Maui and Hawaii. The only major work dealing with the spiders in the Hawaiian Is. was published 60 years ago in " Fauna Hawaiiensis " by Simon (1900 & 1904). All of the endemic spiders known today, except Pseudanapis aloha Forster, are described in that work which also in cludes a listing of several introduced species. The spider collection available to Simon re presented only a small part of the entire Hawaiian fauna. In all probability, the endemic species are only partly known. Since the appearance of Simon's work, there have been many new records and lists of introduced spiders. The known Hawaiian spider fauna now totals 149 species and 4 subspecies belonging to 21 families and 66 genera. Of this total, 82 species (5596) are believed to be endemic and belong to 10 families and 27 genera including 7 endemic genera. The introduced spe cies total 65 (44^). Two unidentified species placed in indigenous genera comprise the remaining \%. Seventeen species are recorded here for the first time. In the catalog section of this paper, families, genera and species are listed alphabetical ly for convenience. -
Records of the Hawaii Biological Survey for 1996
Records of the Hawaii Biological Survey for 1996. Bishop Museum Occasional Papers 49, 71 p. (1997) RECORDS OF THE HAWAII BIOLOGICAL SURVEY FOR 1996 Part 2: Notes1 This is the second of 2 parts to the Records of the Hawaii Biological Survey for 1996 and contains the notes on Hawaiian species of protists, fungi, plants, and animals includ- ing new state and island records, range extensions, and other information. Larger, more comprehensive treatments and papers describing new taxa are treated in the first part of this Records [Bishop Museum Occasional Papers 48]. Foraminifera of Hawaii: Literature Survey THOMAS A. BURCH & BEATRICE L. BURCH (Research Associates in Zoology, Hawaii Biological Survey, Bishop Museum, 1525 Bernice Street, Honolulu, HI 96817, USA) The result of a compilation of a checklist of Foraminifera of the Hawaiian Islands is a list of 755 taxa reported in the literature below. The entire list is planned to be published as a Bishop Museum Technical Report. This list also includes other names that have been applied to Hawaiian foraminiferans. Loeblich & Tappan (1994) and Jones (1994) dis- agree about which names should be used; therefore, each is cross referenced to the other. Literature Cited Bagg, R.M., Jr. 1980. Foraminifera collected near the Hawaiian Islands by the Steamer Albatross in 1902. Proc. U.S. Natl. Mus. 34(1603): 113–73. Barker, R.W. 1960. Taxonomic notes on the species figured by H. B. Brady in his report on the Foraminifera dredged by HMS Challenger during the years 1873–1876. Soc. Econ. Paleontol. Mineral. Spec. Publ. 9, 239 p. Belford, D.J. -
Living World 1995-1996.Pdf
Journal of The Trinidad and Tobago Field Naturalists' Club 1995-1996 Natura Maxime Miranda in Minimis Published July 1996 UVING WORLD is a published biennially by the Trinidad and Tobago Field Naturalists' Club. All rights reserved. Typesetting by Detta Buch, design and mechanical art by Ichris Industries, 63 School St, Carenage, Republic of Trinidad & Tobago. living World Journal of the Trinidad &. Tobago Field Naturalists' Club 1995-1996 EC:litorial Contents There were eight founders of the Freidric William Urich rinldad Field Naturalists' Club in Fr.Anthony de Verteuil C.S.Sp. ...................................3 1891, and biographies of five of the Forest Decline in Trinidad & Tobago I~ ere published in the centenary issu Paul L.Comeau .......................................6 of 1991-1992. This issue includes on The Revegetation of the McClean Monument ~f F.W. Urich, the last of the well Victor Quesnel, T.Frankie Farrell, Anne Hilton, John Hilton and Luisa Zuniaga •.•9 iknown founders. The remaining IW Back to Landscaping... and in style! left no published material and facts Dennis Nardin .......................................13 rabout their lives are so scant that more Guanapo Cave bea.ch will have to be done before we Joannah P.E.C.Darlington .......•.........................15 publish anything worthwhile. Fr d Some Recent Reptilian Introductions to Trinidad trteuil's account of the life of Uricli Hans E.A. Boos .................•................... .17 ~ as published in his book "The Noteworthy Bird Records for Trinidad & Tobago, 1993-1994 nnans in Trinidad" (1994) jUld he floyd E. Hayes .............•.........................20 ! ciously gave us permission t Distributional Ecology of Selected Ebstract what we wanted from lhis pnbJ Plants and Animals on Trinidad!s 1ication. -
Florida Tree Snail Species Conservation Measures and Permitting
SPECIES CONSERVATION MEASURES AND PERMITTING GUIDELINES Effective December, 2020 Florida Tree Snail Liguus fasciatus Species Overview Status: Removed from Florida’s Endangered and Threatened Species List. Current Protections • 68A-4.001, F.A.C., General Prohibitions and Photograph by Randy Grau, FWC. Requirement – Prohibits the take, transport, sale, and possession of wildlife. • 68A-1.004, F.A.C., Take – The term take shall include taking, attempting to take, pursuing, hunting, molesting, capturing, or killing any wildlife or freshwater fish, or their nests or eggs by any means whether or not such actions result in obtaining possession of such wildlife or freshwater fish or their nests or eggs. Biological Background This section describes the biological background for this species and provides context for the following sections. It focuses on the habitats that support the Florida tree snail, and the threats faced by the species. Florida tree snails (Liguus fasciatus) have historically been found in Collier, Palm Beach, Broward, Miami-Dade, and Monroe counties (Deisler-Seno 1994). Currently the species is primarily known from Miami-Dade, Monroe, and Collier counties (Emmel and Cotter 1995; see range map). The Florida tree snail has a conical shell 40 to 70 mm (1.6 to 2.7 in) in length. The shell color is extremely variable and can be matte or glossy (Pilsbry 1946). There are 58 named color morphs of the Florida tree snail (Jones et al. 1981, Roth and Bogan 1984, Emmel and Cotter 1995; Figure 1). Research shows very low genetic variation and suggests that all color morphs belong to a single species, Liguus fasciatus (Hillis 1995). -
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. -
Competitive Exclusion Between Podarcis Lizards from Tyrrhenian Islands: Inference from Comparative Species Distributions
Korsos, Z. &Kss, I. (eds) (1992) Proc. Sixth Ord. Gen. Meet. S. E. H., Budapest 1991, pp. 89-93. Competitive exclusion between Podarcis lizards from Tyrrhenian islands: Inference from comparative species distributions MASSIMO CAPULA Podarcis sicula is an opportunistic and eurikous lacertid lizard occurring as autochthon species in peninsular Italy, Sicily and in a number of Tyrrhenian islands and islets (HENLE & KLAVER 1986). It inhabits also the Adriatic coast of Yugosla- via and several Adriatic islands (NEVO et al. 1972). Distributional and genetic data indicate that in some Tyrrhenian islands, e.g. Sardinia, Corsica, Tuscan Archipelago, this lizard has been accidentally introduced by man in proto-historic or historic times, invading the range of other Podarcis species (e.g., P. tiliguerta, P. muralis) (LANZA 1983, 1988, CORTI et al. 1989). In these islands the allochthon P. sicula seems to have competed successfully with the native congeneric species, reducing their range (e.g., P. tiliguerta in Corsica and Sardinia) (LANZA 1983, 1988), or replacing them through competitive exclusion (e.g., P. muralis in the Tuscan Archipelago) (CORTI et al. 1989). In the present paper preliminary data are given on the occurrence of exclusion of P. wagleriana by P. sicula in the Aeolian Islands (Sicily). P. wagleriana is endemic to Sicily, Aegadian, Stagnone (Isola Grande) and Aeolian Islands, and has been traditionally considered closely related to P. sicula. Methods Competitive exclusion is one of the most dramatic natural effects of interspe- cific competition. The competitive superiority of a species has proved to be exceed- ingly difficult to analyze in natural conditions. To overcome this difficulty, we inferred the occurrence of competitive exclusion from the comparative distribu- tions and relative abundance of the two potentially competing species (GiLLER 1984). -
Driving Directions
ERICE Driving Directions: Make a left from the NAS 1 ABOUT ERICE gate. Drive about 3km Erice is a town within the Province of Make a right at the Autostrada Trapani. It is absolutely breathtaking and take the A19 for Palermo. sitting at 751 meters above sea level, Continue onto E90 You will overlooking the city of Trapani, the pass the Palermo exit. Egadi Islands and the coastlines of Continue onto A29 Racc Monte Cofano and San Vito Lo Capo. Bis/E90 Like so many towns of importance in Take the exit toward Sicily, Erice was conquered from one Trapani/Aeroporto Birgi. invader to another and each one left its Merge onto A29dir and take the architectural signature and cultural exit toward Trapani footprints. Originally named Eryx (by Keep on the A29dir and at the the Elymians were around before the roundabout, take the 1st exit Greeks came to Sicily), it has changed to Continue straight onto Strada Erice, to Gebal Hamed then to Monte Provinciale Torrebianca San Giuliano before reverting back to Erice once again in the 1930’s. Turn right to stay on Strada Provinciale Torrebianca an then take the first left onto Via delle Tremole Turn left onto SS187 After 100 meters make a sharp right onto Strada Provinciale 3/SP3 Sharp left to stay on Strada Provinciale 3/SP3 and follow MWR SIGONELLA signs for Erice. PSC 812 BOX 3390 FPO, AE 09627-3390 Estimated driving time: 3 ½ hours DSN: 624.4777 COMMERCIAL: 011.39.095.86.4777 Coordinates: 38.0333° N, 12.5333° E ISOLE EGADI beach and the remains of a Roman Erice settlement. -
The Olea Europaea L. Var. Sylvestris (Mill.) Lehr. Forests in the Mediterranean Area
Plant Sociology, Vol. 56, No. 2, December 2019, pp. 3-34 DOI 10.7338/pls2019562/01 The Olea europaea L. var. sylvestris (Mill.) Lehr. forests in the Mediterranean area L. Gianguzzi1, G. Bazan2 1Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy. 2Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy. Lorenzo Gianguzzi https://orcid.org/0000-0002-9007-7604, Giuseppe Bazan https://orcid.org/0000-0002-4827-9579 Abstract This paper examines the forest communities dominated by Olea europaea L. var. sylvestris (Mill.) Lehr. that have been described up until now in the Mediterranean Region (including other isolated extrazonal areas in the northwestern Iberian Peninsula and in Northern Turkey) as more or less evolved aspects of woods, microwoods and high maquis that principally tend to make up climacic and edapho-climacic “series heads”. These forma- tions maintain a significant large-scale distributive potential within the infra- and thermomediterranean bioclimate belts (with a few penetrations into the mesomediterranean) with a dry-subhumid (and sometimes humid) ombrotype; however, they are currently quite rare and fragmented in the wake of large-scale deforestation and the impoverishment of old-growth communities dominated by a species known to live for millennia. The study was conducted through the analysis of phytosociological data taken from the scientific literature and other unpublished data regarding North-Africa (Morocco, Algeria), the Iberian Peninsula, the Balearic Islands as well as other islands from the Tyrrhenian area (Sardinia, Corsica, Sicily and its minor islands), the Italian Peninsula, the Balkan Peninsula, the Aegean region, Turkey and the southern Anatolian coast. -
Biodiversity Summary: Port Phillip and Westernport, Victoria
Biodiversity Summary for NRM Regions Species List What is the summary for and where does it come from? This list has been produced by the Department of Sustainability, Environment, Water, Population and Communities (SEWPC) for the Natural Resource Management Spatial Information System. The list was produced using the AustralianAustralian Natural Natural Heritage Heritage Assessment Assessment Tool Tool (ANHAT), which analyses data from a range of plant and animal surveys and collections from across Australia to automatically generate a report for each NRM region. Data sources (Appendix 2) include national and state herbaria, museums, state governments, CSIRO, Birds Australia and a range of surveys conducted by or for DEWHA. For each family of plant and animal covered by ANHAT (Appendix 1), this document gives the number of species in the country and how many of them are found in the region. It also identifies species listed as Vulnerable, Critically Endangered, Endangered or Conservation Dependent under the EPBC Act. A biodiversity summary for this region is also available. For more information please see: www.environment.gov.au/heritage/anhat/index.html Limitations • ANHAT currently contains information on the distribution of over 30,000 Australian taxa. This includes all mammals, birds, reptiles, frogs and fish, 137 families of vascular plants (over 15,000 species) and a range of invertebrate groups. Groups notnot yet yet covered covered in inANHAT ANHAT are notnot included included in in the the list. list. • The data used come from authoritative sources, but they are not perfect. All species names have been confirmed as valid species names, but it is not possible to confirm all species locations.