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Selection, Constraint, and Adaptation in the Visual Genes of Neotropical Cichlid Fishes and Other Vertebrates
SELECTION, CONSTRAINT, AND ADAPTATION IN THE VISUAL GENES OF NEOTROPICAL CICHLID FISHES AND OTHER VERTEBRATES by Frances Elisabeth Hauser A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Ecology and Evolutionary Biology University of Toronto © Copyright by Frances E. Hauser 2018 SELECTION, CONSTRAINT, AND ADAPTATION IN THE VISUAL GENES OF NEOTROPICAL CICHLID FISHES AND OTHER VERTEBRATES Frances E. Hauser Doctor of Philosophy, 2018 Department of Ecology and Evolutionary Biology University of Toronto 2018 ABSTRACT The visual system serves as a direct interface between an organism and its environment. Studies of the molecular components of the visual transduction cascade, in particular visual pigments, offer an important window into the relationship between genetic variation and organismal fitness. In this thesis, I use molecular evolutionary models as well as protein modeling and experimental characterization to assess the role of variable evolutionary rates on visual protein function. In Chapter 2, I review recent work on the ecological and evolutionary forces giving rise to the impressive variety of adaptations found in visual pigments. In Chapter 3, I use interspecific vertebrate and mammalian datasets of two visual genes (RH1 or rhodopsin, and RPE65, a retinoid isomerase) to assess different methods for estimating evolutionary rate across proteins and the reliability of inferring evolutionary conservation at individual amino acid sites, with a particular emphasis on sites implicated in impaired protein function. ii In Chapters 4, and 5, I narrow my focus to devote particular attention to visual pigments in Neotropical cichlids, a highly diverse clade of fishes distributed across South and Central America. -
Summary Report of Freshwater Nonindigenous Aquatic Species in U.S
Summary Report of Freshwater Nonindigenous Aquatic Species in U.S. Fish and Wildlife Service Region 4—An Update April 2013 Prepared by: Pam L. Fuller, Amy J. Benson, and Matthew J. Cannister U.S. Geological Survey Southeast Ecological Science Center Gainesville, Florida Prepared for: U.S. Fish and Wildlife Service Southeast Region Atlanta, Georgia Cover Photos: Silver Carp, Hypophthalmichthys molitrix – Auburn University Giant Applesnail, Pomacea maculata – David Knott Straightedge Crayfish, Procambarus hayi – U.S. Forest Service i Table of Contents Table of Contents ...................................................................................................................................... ii List of Figures ............................................................................................................................................ v List of Tables ............................................................................................................................................ vi INTRODUCTION ............................................................................................................................................. 1 Overview of Region 4 Introductions Since 2000 ....................................................................................... 1 Format of Species Accounts ...................................................................................................................... 2 Explanation of Maps ................................................................................................................................ -
Classifications and Other Ordering Systems
J. Zool. Syst. Evol. Research 40 (2002) 169–194 Received on 5 August 2002 Ó 2002 Blackwell Verlag, Berlin ISSN 0947–5745 1Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA; 2Department of Biological Sciences, Columbian University, NewYork, NY, USA Classifications and other ordering systems Ernst Mayr1 and W. J. Bock2 Abstract 9.5.1. Evidently descended from the same ancestor 1. Introduction 9.5.2. Parallelophyly 2. Why ordering systems should be of interest to the 9.5.3. Reversal philosopher? 9.5.4. Convergence 3. The universality of diversity 9.6. Significance of characters (weighing) 4. Objectives of ordering systems 9.7. Numerical approaches 4.1. Sorting 10. Ordering by using only the criterion of phylogeny – type 5 4.2. Information storage and retrieval is a major objective 10.1. Hennigian cladification of most ordering systems 10.2. Peculiarities of Hennigian terminology 4.3. Identification of an unknown item 10.2.1. Paraphyly 4.4. Inferences about not yet studied properties 10.2.2. Monophyly 4.5. To serve as base line in comparative studies 10.2.3. Relationship 5. Kinds of Ordering Systems 10.2.4. Classification 5.1 General considerations 10.2.5. Taxon 5.2. Ordering of single entities 10.3. Cladistic analysis 5.2.1. Assigning singular entities to a linear sequence 10.4. Recognition of clades (sequential listing) –type 1 11. Upward classification by two criteria, clustering by 5.2.1.1. Arbitrary sequence similarity and by common descent – type 6 5.2.1.2. Alphabetical listing 11.1. Pre-Darwinian classification 5.2.1.3. -
They're Not Just Convicts Anymore
2008 FAAS Publication Awards. Please follow reprint instructions at http://www.faas.info/2008_publication_awards_winners.html#reprintpolicy They’re Not Just Convicts Anymore By Daniel Spielman All Photos by Daniel Spielman Introduction Convicts get no respect, with many a cichlidophile turning up his or her nose at the sight of a group on Convicts in a tank or a bag of fry in an auction. It’s time for that to change. Easy to breed and exhibiting wonderful parental care, Convict cichlids (Cryptoheros nigrofasciatus) have long been staples in the hobby. Indeed, for many new fishkeepers, the satisfaction of watching a pair of Convict parents herd a group of fry around a tank sparks the initial desire to keep other mem bers of the cichlid family. Indeed, my fish cichlids were Convicts, and watch ing them care for their fry definitely got me hooked. The contrast with trying to keep guppies or swordtails from eating their own offspring is striking (how did eating one’s own young ever evolve in the first place?). However, the very fact that Convicts spawn so readily in the aquarium causes many hobbyists to quickly lose interest in the species. Although Convicts occasionally appear on experienced hobbyists’ lists of most favorite cichlid, the problem is they are just too common and too easy to breed. Typical Convict spawning jokes involve two fish and a wet paper towel, and one often feels fortunate to break the $1 barrier at the auction to avoid the indignity of having to bring one’s fish back home again at the end of the monthly club meeting. -
Neue Gattungseinteilung Der Mittelamerikanischen Cichliden
DCG_Info_07_2016_HR_20160621_DCG_Info 21.06.2016 06:51 Seite 146 Neue Gattungseinteilung der mittelamerikanischen Cichliden Rico Morgenstern Foto: Juan Miguel Artigas Azas Theraps irregularis verbleibt als einzige Art in der Gattung Theraps. Die Aufnahme entstand im Rio Lacanja im südlichen Chiapas, Mexiko. Inzwischen ist es fast 33 Jahre her, wenigstens Versuche, einzelne Gat- schien die Abhandlung „Diversity and dass KULLANDER (1983) die Gattung tungen neu zu definieren – aber eine evolution of the Middle American cich- Cichlasoma auf zwölf südamerikani- umfassende Gesamtbearbeitung er- lid fishes (Teleostei: Cichlidae) with re- sche, nahe mit der Typusart C. bima- folgte bisher nicht. Vielfach wurden vised classification“ (ŘIČAN et al. culatum verwandte Arten beschränkte. Zuordnungen vorgenommen, ohne 2016). Seither durfte der Name streng ge- dass man sich um eine wirkliche Be- nommen für die Mehrzahl der bis gründung bemühte. Die Arbeit berücksichtigt alle Cichliden dahin in dieser ehemaligen Sammel- Nord- und Mittelamerikas und der An- gattung untergebrachten, überwie- Bei der Gattungseinteilung der mittel- tillen sowie einige eng verwandte süd- gend mittelamerikanischen Arten amerikanischen Cichliden herrschte amerikanische Gattungen (Australoheros, nicht mehr verwendet werden. Man- somit bis vor kurzem ein ziemliches Caquetaia, Heroina, Mesoheros). gels geeigneter Alternativen ist das Chaos. Nun ist jedoch das Ende der An- Diese Fische gehören zu den „heroinen aber dennoch geschehen, wobei der führungszeichen (mit einer Ausnahme) -
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CICHLIFORMES: Cichlidae (part 6) · 1 The ETYFish Project © Christopher Scharpf and Kenneth J. Lazara COMMENTS: v. 6.0 - 18 April 2020 Order CICHLIFORMES (part 6 of 8) Family CICHLIDAE Cichlids (part 6 of 7) Subfamily Cichlinae American Cichlids (Acarichthys through Cryptoheros) Acarichthys Eigenmann 1912 Acara (=Astronotus, from acará, Tupí-Guaraní word for cichlids), original genus of A. heckelii; ichthys, fish Acarichthys heckelii (Müller & Troschel 1849) in honor of Austrian ichthyologist Johann Jakob Heckel (1790-1857), who proposed the original genus, Acara (=Astronotus) in 1840, and was the first to seriously study cichlids and revise the family Acaronia Myers 1940 -ia, belonging to: Acara (=Astronotus, from acará, Tupí-Guaraní word for cichlids), original genus of A. nassa [replacement name for Acaropsis Steindachner 1875, preoccupied by Acaropsis Moquin-Tandon 1863 in Arachnida] Acaronia nassa (Heckel 1840) wicker basket or fish trap, presumably based on its local name, Bocca de Juquia, meaning “fish trap mouth,” referring to its protractile jaws and gape-and-suck feeding strategy Acaronia vultuosa Kullander 1989 full of facial expressions or grimaces, referring to diagnostic conspicuous black markings on head Aequidens Eigenmann & Bray 1894 aequus, same or equal; dens, teeth, referring to even-sized teeth of A. tetramerus, proposed as a subgenus of Astronotus, which has enlarged anterior teeth Aequidens chimantanus Inger 1956 -anus, belonging to: Chimantá-tepui, Venezuela, where type locality (Río Abácapa, elevation 396 m) is -
Appendix A. Taxa Included in the Study Indicating Samples Used, Catalog Number of Museum Vouchers When Available, and General Collection Locality
Appendix A. Taxa included in the study indicating samples used, catalog number of museum vouchers when available, and general collection locality. Museum abbreviations are: AMNH – American Museum of Natural History, New York, USA; ANSP – Academy of Natural Sciences of Philadelphia, USA; AUM – Auburn University Museum, Auburn, Alabama, USA; ECOSUR – Fish Collection at Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, Mexico; MCNG – Museo de Ciencias Naturales de Guanare, Venezuela; MNHN – Muséum National d’Histoire Naturelle, Paris, France; ROM – Royal Ontario Museum, Toronto, Canada; UFRGS – Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; UTFTC – University of Tennessee Fish Collection, Knoxville, Tennessee, USA. ROM Catalogue Current taxonomy name Tissue Cat No No Locality Description Notes Outgroup Pseudetroplus maculatus T14743 ROM 98998 Aquarium trade India-Madagascar Etroplus suratensis T13505 ROM 93809 Aquarium trade Paratilapia polleni T13100 ROM 88333 Aquarium trade Lake Andrapongy, Paretroplus damii 201936 AMNH 201936 Madagascar Paretroplus polyactis T12265 AMNH Africa Chromidotilapia guntheri T11700 AMNH I-226361 Beffa River, Benin Aquarium trade, wild caught, Etia nguti T10792 ROM 88042 Cameroon Hemichromis bimaculatus T11719 Tchan Duga, Benin Aquarium trade, wild caught, Heterochromis multidens T07136 ROM 88350 Lobeke, Cameroon Oreochromis niloticus 9092S AMNH254194 Littoral Province, Guinea Aquarium trade, wild caught, Congo River, Democratic Orthochromis stormsi T10766 ROM 88041 Republic of -
Cichlasoma Sieboldii and C. Tuba
Rev. Biol Trop., 23 (2) : 189-211, 1975 Taxonomy and biological aspects 01 the Central Amer'ican cichlid fishes Cichlasoma sieboldii and C. tuba by William A. Bussing'lí< (Received for publication May 22, 1975) ABSTRACTo' The complex taxonomic history of Cichlasoma sieboldii is re· viewed. Cichlasoma punctatum and its synonym Theraps terrabae are induded for the first time in the synoymy of C. sieboldii. A report of C. guttulatum from Pa namá is attributable to a misidentification of C. tuba, which had not been pre viously reported from that countIy. The morphologic and meristic variation, coloration, ecology and geographic distribution of C. sieboldii and C. tuba are discussed.. M:orphologic and distri butional evidence suggest that these twÜ' species are Pacific and Atlantic slope de rivatives of a common Pliocene' ancestor. There is a marked resemblance between the ciehlid fauna of the Atlan tic slope of lower Central Ameriea and the southeastern region of Costa Rica. The historieal reasons fo! this similarity have been discussed (4). The present study reviews the taxonomic history and discusses the biology of a Pacifie slope species, Ci¡h/asoma sieboldii, and its Atlantic versant counterpart, Cieh/asoma. tu ba (Fig. 1). MATERIAL AND METHODS Body measureinents are expressed in standard length (SL) in millime ters (mm). Body propartions of C. sieboldir as parts per mil appear in Table 1. The last two dorsal and anal rays are counted as ane only when their bases are in contact; when the base of the last ray is not touching the penultimate ray, each ray is counted separately. -
Phylogenetic Relationships of Middle American Cichlids (Cichlidae, Heroini) Based on Combined Evidence from Nuclear Genes, Mtdna, and Morphology
Molecular Phylogenetics and Evolution 49 (2008) 941–957 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology Oldrˇich Rˇícˇan a,b,*, Rafael Zardoya c, Ignacio Doadrio c a Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005, Cˇeské Budeˇjovice, Czech Republic b Institute of Animal Physiology and Genetics of the Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Libeˇchov, Czech Republic c Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain article info abstract Article history: Heroine cichlids are the second largest and very diverse tribe of Neotropical cichlids, and the only cichlid Received 2 June 2008 group that inhabits Mesoamerica. The taxonomy of heroines is complex because monophyly of most gen- Revised 26 July 2008 era has never been demonstrated, and many species groups are without applicable generic names after Accepted 31 July 2008 their removal from the catch-all genus Cichlasoma (sensu Regan, 1905). Hence, a robust phylogeny for the Available online 7 August 2008 group is largely wanting. A rather complete heroine phylogeny based on cytb sequence data is available [Concheiro Pérez, G.A., Rˇícˇan O., Ortí G., Bermingham, E., Doadrio, I., Zardoya, R. 2007. Phylogeny and bio- Keywords: geography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b Cichlidae gene. Mol. Phylogenet. Evol. 43, 91–110], and in the present study, we have added and analyzed indepen- Middle America Central America dent data sets (nuclear and morphological) to further confirm and strengthen the cytb-phylogenetic Biogeography hypothesis. -
Blue-Eye Cichlid (Cryptoheros Spilurus) Ecological Risk Screening Summary
Blue-eye Cichlid (Cryptoheros spilurus) Ecological Risk Screening Summary U.S. Fish & Wildlife Service, April 2011 Revised, February 2019 Web Version, 10/10/2019 1 Native Range and Status in the United States Native Range From Froese and Pauly (2019a): “Central America: Atlantic slope from Belize to Nicaragua.” From Fricke et al. (2019): “Rivers flowing into Lake Isabel, Atlantic slope from Belize to Nicaragua: Belize, Guatemala, Honduras and Nicaragua;” From Nico (2019): “Tropical America. Atlantic Slope drainages of Middle America [Conkel 1993]; from the Yucatan Peninsula, Mexico, throughout Belize, south to Panama [Greenfield and Thomerson 1997].” 1 Status in the United States From Mundy (2005): “This species was reported to have been introduced to O‘ahu in 1984 (Devick, 1991; Fuller et al., [1999]). Yamamoto & Tagawa (2000) stated that it was well established in Nu‘uanu Reservoir and Hausten Ditch but disappeared from the reservoir after the 1984 drought, which suggests that the species was introduced prior to that year. Given the species’ occurrence in two disjunct habitats of O‘ahu, more investigation of its persistence on O‘ahu might be warranted to demonstrate its absence from open waters of the state.” From Nico (2019): “Reported as established in Nu'uanu Reservoir by Yamamoto and Tagawa (2000), but disappeared after the 1984 drought. Unclear at this time whether it is extirpated.” While the means of introduction in Hawaii (aquarium release) implies trade in this species within the United States the author could not find evidence of current trade in the species. Means of Introductions in the United States From Froese and Pauly (2019a): “Aquarium escape; considered an accidental introduction.” Remarks No additional remarks. -
Exon-Based Phylogenomics Strengthens the Phylogeny of Neotropical Cichlids And
bioRxiv preprint doi: https://doi.org/10.1101/133512; this version posted July 13, 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 Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and 2 identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae) 3 4 Katriina L. Ilves1,2*, Dax Torti3,4, and Hernán López-Fernández1 5 1 Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, 6 ON M5S 2C6 Canada 7 2 Current address: Biology Department, Pace University, 1 Pace Plaza, New York, NY 8 10038 9 3 Donnelly Sequencing Center, University of Toronto, 160 College Street, Toronto, ON 10 M5S 3E1 Canada 11 4 Current address: Ontario Institute for Cancer Research, MaRS Center, 661 University 12 Avenue, Toronto, ON M5G 0A3 Canada 13 *Corresponding author at: Biology Department, Pace University, 1 Pace Plaza, New 14 York, NY 10038; email: [email protected] 15 16 Abstract 17 The phenotypic, geographic, and species diversity of cichlid fishes have made them a 18 group of great interest for studying evolutionary processes. Here we present a targeted- 19 exon next-generation sequencing approach for investigating the evolutionary 20 relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily 21 Cichlinae using a set of 923 primarily single-copy exons designed through mining of the 22 Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were 23 robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that 1 bioRxiv preprint doi: https://doi.org/10.1101/133512; this version posted July 13, 2017. -
Teleostei: Cichlidae)
TERMS OF USE This pdf is provided by Magnolia Press for private/research use. Commercial sale or deposition in a public library or website is prohibited. Zootaxa 2833: 1–14 (2011) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Article ZOOTAXA Copyright © 2011 · Magnolia Press ISSN 1175-5334 (online edition) Paraneetroplus synspilus is a Junior Synonym of Paraneetroplus melanurus (Teleostei: Cichlidae) CALEB D. MCMAHAN1,2, CHRISTOPHER M. MURRAY2, AARON D. GEHEBER3,2, CHRISTOPHER D. BOECKMAN2 & KYLE R. PILLER2 1Division of Ichthyology, LSU Museum of Natural Science, Baton Rouge, LA 70803 USA. E-mail: [email protected] 2Department of Biological Sciences, Southeastern Louisiana University, Hammond LA 70402 USA 3Department of Zoology, University of Oklahoma, Norman OK 73019 USA Abstract The genus Paraneetroplus (Teleostei: Cichlidae) currently consists of 11 species that naturally occur from southern Mex- ico south to Panama. Paraneetroplus melanurus (Günther 1862) is found in the Lago de Petén system of Guatemala, and P. synspilus (Hubbs 1935) in the Río Grijalva-Usumacinta system, and other systems in Mexico, Belize, and Guatemala. Reported morphological differences between the two nominal species in the literature are vague but center around char- acteristics of a dark band that begins at the caudal fin and tapers anteriorly near mid-body. This band is reported as straight (horizontal) in P. melanurus but ventrally sloped in P. synspilus. Some authors have previously suggested that these two forms are not distinct. The purpose of this study was to conduct a systematic morphological comparison of P. melanurus and P. synspilus to further investigate their validity. We examined meristic, morphometric, and geometric morphometric characters and failed to recover diagnostic differences between these two forms.