Evolution of the Tribe Tropheini from Lake Tanganyika: Synchronized Explosive Speciation Producing Multiple Evolutionary Parallelism
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Genome Sequences of Tropheus Moorii and Petrochromis Trewavasae, Two Eco‑Morphologically Divergent Cichlid Fshes Endemic to Lake Tanganyika C
www.nature.com/scientificreports OPEN Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco‑morphologically divergent cichlid fshes endemic to Lake Tanganyika C. Fischer1,2, S. Koblmüller1, C. Börger1, G. Michelitsch3, S. Trajanoski3, C. Schlötterer4, C. Guelly3, G. G. Thallinger2,5* & C. Sturmbauer1,5* With more than 1000 species, East African cichlid fshes represent the fastest and most species‑rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversifcation. We add high‑quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so‑called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecifc), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecifc). GO enrichment analysis of gene regions afected by variants revealed several candidates which may infuence phenotype modifcations related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families. -
Indian and Madagascan Cichlids
FAMILY Cichlidae Bonaparte, 1835 - cichlids SUBFAMILY Etroplinae Kullander, 1998 - Indian and Madagascan cichlids [=Etroplinae H] GENUS Etroplus Cuvier, in Cuvier & Valenciennes, 1830 - cichlids [=Chaetolabrus, Microgaster] Species Etroplus canarensis Day, 1877 - Canara pearlspot Species Etroplus suratensis (Bloch, 1790) - green chromide [=caris, meleagris] GENUS Paretroplus Bleeker, 1868 - cichlids [=Lamena] Species Paretroplus dambabe Sparks, 2002 - dambabe cichlid Species Paretroplus damii Bleeker, 1868 - damba Species Paretroplus gymnopreopercularis Sparks, 2008 - Sparks' cichlid Species Paretroplus kieneri Arnoult, 1960 - kotsovato Species Paretroplus lamenabe Sparks, 2008 - big red cichlid Species Paretroplus loisellei Sparks & Schelly, 2011 - Loiselle's cichlid Species Paretroplus maculatus Kiener & Mauge, 1966 - damba mipentina Species Paretroplus maromandia Sparks & Reinthal, 1999 - maromandia cichlid Species Paretroplus menarambo Allgayer, 1996 - pinstripe damba Species Paretroplus nourissati (Allgayer, 1998) - lamena Species Paretroplus petiti Pellegrin, 1929 - kotso Species Paretroplus polyactis Bleeker, 1878 - Bleeker's paretroplus Species Paretroplus tsimoly Stiassny et al., 2001 - tsimoly cichlid GENUS Pseudetroplus Bleeker, in G, 1862 - cichlids Species Pseudetroplus maculatus (Bloch, 1795) - orange chromide [=coruchi] SUBFAMILY Ptychochrominae Sparks, 2004 - Malagasy cichlids [=Ptychochrominae S2002] GENUS Katria Stiassny & Sparks, 2006 - cichlids Species Katria katria (Reinthal & Stiassny, 1997) - Katria cichlid GENUS -
Outgroup Effects on Root Position and Tree Topology in the AFLP Phylogeny of a Rapidly Radiating Lineage of Cichlid Fish
Accepted Manuscript Short Communication Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish Paul C. Kirchberger, Kristina M. Sefc, Christian Sturmbauer, Stephan Koblmüller PII: S1055-7903(13)00347-3 DOI: http://dx.doi.org/10.1016/j.ympev.2013.09.005 Reference: YMPEV 4706 To appear in: Molecular Phylogenetics and Evolution Received Date: 5 December 2012 Revised Date: 4 September 2013 Accepted Date: 6 September 2013 Please cite this article as: Kirchberger, P.C., Sefc, K.M., Sturmbauer, C., Koblmüller, S., Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish, Molecular Phylogenetics and Evolution (2013), doi: http://dx.doi.org/10.1016/j.ympev.2013.09.005 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly 2 radiating lineage of cichlid fish 3 4 Paul C. Kirchbergera,b, Kristina M. Sefca, Christian Sturmbauera, Stephan Koblmüllera.* 5 6 a Department of Zoology, Karl‐Franzens‐University Graz, Universitätsplatz 2, A‐8010 Graz, 7 Austria 8 b present address: Department of Biological Sciences, University of Alberta, Edmonton, AB, 9 Canada T6G 2E9 10 11 * Corresponding author: Tel.:+43 316 380 3978; Fax: +43 316 380 9875; email: 12 stephan.koblmueller@uni‐graz.at (S. -
Presentation
Evolution in Darwin’s Dreampond: The genomic substrate for adaptive radiation in Lake Tanganyika cichlid fish Walter Salzburger Zoological Institute drawings: Julie Johnson drawings: !Charles R. Darwin’s (1809-1882) journey onboard of the HMS Beagle lasted from 27 December 1831 until 2 October 1836 Adaptive Radiation !Darwin’s specimens were classified as “an entirely new group” of 12 species by ornithologist John Gould (1804-1881) African Great Lakes taxonomic diversity at the species level L. Turkana 1 5 50 500 species 0 50 100 % endemics 4°N L. Tanganyika L. Tanganyika L. Albert 2°N L. Malawi L. Malawi L. Edward L. Victoria L. Victoria 0° L. Edward L. Edward L. Kivu L. Victoria 2°S L. Turkana L. Turkana L. Albert L. Albert 4°S L. Kivu L. Kivu L. Tanganyika 6°S taxonomic diversity at the genus level 10 20 30 40 50 genera 0 50 100 % endemics 8°S Rungwe L. Tanganyika L. Tanganyika Volcanic Field L. Malawi 10°S L. Malawi L. Victoria L. Victoria 12°S L. Malawi L. Edward L. Edward L. Turkana L. Turkana 14°S cichlid fish non-cichlid fish L. Albert L. Albert gastropods bivalves 28°E 30°E 32°E 34°E 36°E L. Kivu L. Kivu ostracods ••• W Salzburger, B Van Bockxlaer, AS Cohen (2017), AREES | AS Cohen & W Salzburger (2017) Scientific Drilling Cichlid Fishes Fotos: Angel M. Fitor Angel M. Fotos: !About every 20th fish species on our planet is the product of the ongoing explosive radiations of cichlids in the East African Great Lakes taxonomic~Diversity Victoria [~500 sp.] Tanganyika [250 sp.] Malawi [~1000 sp.] ••• ME Santos & W Salzburger (2012) Science ecological morphological~Diversity zooplanktivore insectivore piscivore algae scraper leaf eater fin biter eye biter mud digger scale eater ••• H Hofer & W Salzburger (2008) Biologie III ecological morphological~Diversity ••• W Salzburger (2009) Molecular Ecology astbur Astbur.:1-90001 Alignment 1 neobri 100% Neobri. -
Towards a Regional Information Base for Lake Tanganyika Research
RESEARCH FOR THE MANAGEMENT OF THE FISHERIES ON LAKE GCP/RAF/271/FIN-TD/Ol(En) TANGANYIKA GCP/RAF/271/FIN-TD/01 (En) January 1992 TOWARDS A REGIONAL INFORMATION BASE FOR LAKE TANGANYIKA RESEARCH by J. Eric Reynolds FINNISH INTERNATIONAL DEVELOPMENT AGENCY FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS Bujumbura, January 1992 The conclusions and recommendations given in this and other reports in the Research for the Management of the Fisheries on Lake Tanganyika Project series are those considered appropriate at the time of preparation. They may be modified in the light of further knowledge gained at subsequent stages of the Project. The designations employed and the presentation of material in this publication do not imply the expression of any opinion on the part of FAO or FINNIDA concerning the legal status of any country, territory, city or area, or concerning the determination of its frontiers or boundaries. PREFACE The Research for the Management of the Fisheries on Lake Tanganyika project (Tanganyika Research) became fully operational in January 1992. It is executed by the Food and Agriculture organization of the United Nations (FAO) and funded by the Finnish International Development Agency (FINNIDA). This project aims at the determination of the biological basis for fish production on Lake Tanganyika, in order to permit the formulation of a coherent lake-wide fisheries management policy for the four riparian States (Burundi, Tanzania, Zaïre and Zambia). Particular attention will be also given to the reinforcement of the skills and physical facilities of the fisheries research units in all four beneficiary countries as well as to the buildup of effective coordination mechanisms to ensure full collaboration between the Governments concerned. -
Morphology, Molecules, and Monogenean Parasites: an Example of an Integrative Approach to Cichlid Biodiversity
RESEARCH ARTICLE Morphology, Molecules, and Monogenean Parasites: An Example of an Integrative Approach to Cichlid Biodiversity Maarten Van Steenberge1,2,3*, Antoine Pariselle4¤a, Tine Huyse1,2, Filip A. M. Volckaert2, Jos Snoeks1,2, Maarten P. M. Vanhove1,2,5¤b 1 Biology Department, Royal Museum for Central Africa, Tervuren, Belgium, 2 Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium, 3 Institute of Zoology, University of Graz, Graz, Austria, 4 Institut des Sciences de l'Évolution, IRD-CNRS-Université Montpellier, Montpellier, France, 5 Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, Anavyssos, Greece ¤a Current address: IRD, ISE-M, Yaoundé, Cameroon ¤b Current address: Capacities for Biodiversity and Sustainable Development, Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium * [email protected] OPEN ACCESS Citation: Van Steenberge M, Pariselle A, Huyse T, Abstract Volckaert FAM, Snoeks J, Vanhove MPM (2015) Morphology, Molecules, and Monogenean Parasites: The unparalleled biodiversity of Lake Tanganyika (Africa) has fascinated biologists for over An Example of an Integrative Approach to Cichlid a century; its unique cichlid communities are a preferred model for evolutionary research. Biodiversity. PLoS ONE 10(4): e0124474. doi:10.1371/journal.pone.0124474 Although species delineation is, in most cases, relatively straightforward, higher-order clas- sifications were shown not to agree with monophyletic groups. Here, traditional morphologi- Academic Editor: Robert Guralnick, University of Colorado, UNITED STATES cal methods meet their limitations. A typical example are the tropheine cichlids currently belonging to Simochromis and Pseudosimochromis. The affiliations of these widespread Received: August 19, 2014 and abundant cichlids are poorly understood. -
Phylogenetic Congruence Between Lake Tanganyika Tropheine Cichlids and Their Monogenean Flatworm Parasites
CORE Metadata, citation and similar papers at core.ac.uk Provided by Ghent University Academic Bibliography www.nature.com/scientificreports OPEN Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika Received: 29 January 2015 Accepted: 23 July 2015 tropheine cichlids and their Published: 03 September 2015 monogenean flatworm parasites Maarten P. M. Vanhove1,2,3,4,†, Antoine Pariselle5,‡, Maarten Van Steenberge1,2,6, Joost A. M. Raeymaekers1, Pascal I. Hablützel1,¶, Céline Gillardin1,φ, Bart Hellemans1, Floris C. Breman2, Stephan Koblmüller6, Christian Sturmbauer6, Jos Snoeks1,2, Filip A. M. Volckaert1 & Tine Huyse1,2 The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. -
Hered 347 Master..Hered 347 .. Page702
Heredity 80 (1998) 702–714 Received 3 June 1997 Phylogeny of African cichlid fishes as revealed by molecular markers WERNER E. MAYER*, HERBERT TICHY & JAN KLEIN Max-Planck-Institut f¨ur Biologie, Abteilung Immungenetik, Corrensstr. 42, D-72076 T¨ubingen, Germany The species flocks of cichlid fish in the three great East African Lakes, Victoria, Malawi, and Tanganyika, have arisen in each lake by explosive adaptive radiation. Various questions concerning their phylogeny have not yet been answered. In particular, the identity of the ancestral founder species and the monophyletic origin of the haplochromine cichlids from the East African lakes have not been established conclusively. In the present study, we used the anonymous nuclear DNA marker DXTU1 as a step towards answering these questions. A 280 bp-fragment of the DXTU1 locus was amplified by the polymerase chain reaction from East African lacustrine species, the East African riverine cichlid species Haplochromis bloyeti, H. burtoni and H. sparsidens, and other African cichlids. Sequencing revealed several indels and substitutions that were used as cladistically informative markers to support a phylogenetic tree constructed by the neighbor-joining method. The topology, although not supported by high bootstrap values, corresponds well to the geographical distribution and previous classifica- tion of the cichlids. Markers could be defined that: (i) differentiate East African from West African cichlids; (ii) distinguish the riverine and Lake Victoria/Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicate the existence of a monophyletic Lake Victoria cichlid superflock which includes haplochromines from satellite lakes and East African rivers. In order to resolve further the relationship of East African riverine and lacustrine species, mtDNA cytochrome b and control region segments were sequenced. -
Morphometric, Molecular Phylogenetic and Gene Expression Approaches Towards the Understanding of the Adaptive Radiations of the East African Cichlids
Morphometric, Molecular Phylogenetic and Gene Expression Approaches towards the Understanding of the Adaptive Radiations of the East African Cichlids Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universitat Konstanz, Mathematisch-naturwissenschaftliche Sektion Fachbereich Biologie vorgelegt von Celine Clabaut, M.Sc. Konstanz, Dezember 2005 1 ACKNOWLEDGMENTS I first want to thank Prof. Axel Meyer for welcoming me in his laboratory and giving me the opportunity of completing a doctoral degree in the University of Konstanz. I also thank Dr. Walter Salzburger for getting me started on all the projects that could not have happened without his work. I am grateful for all the ideas he shared with me, and his availability to answer my questions. Dr. Paul Bunje gave me the chance of experiencing a fruitful collaboration by improving the morphometric work, and I am grateful to him for this (as well as all the corrections he did of my English writing). I am grateful to people belonging to the Meyer lab in general. I have never been denied or refused help, time, book or answers, each time I have been asking for them. I have to particularly acknowledge Arie and Dirk, since computer-related issues are the field where I have been more demanding, and Elke for being so efficient. I am so thankful to the friends I made here in Konstanz. It took a while for me to meet them, but they really made life here more enjoyable. Some even provided support in addition to fun, and I am particularly grateful to them. -
Limnological Study of Lake Tanganyika, Africa with Special Emphasis on Piscicultural Potentiality Lambert Niyoyitungiye
Limnological Study of Lake Tanganyika, Africa with Special Emphasis on Piscicultural Potentiality Lambert Niyoyitungiye To cite this version: Lambert Niyoyitungiye. Limnological Study of Lake Tanganyika, Africa with Special Emphasis on Piscicultural Potentiality. Biodiversity and Ecology. Assam University Silchar (Inde), 2019. English. tel-02536191 HAL Id: tel-02536191 https://hal.archives-ouvertes.fr/tel-02536191 Submitted on 9 Apr 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. “LIMNOLOGICAL STUDY OF LAKE TANGANYIKA, AFRICA WITH SPECIAL EMPHASIS ON PISCICULTURAL POTENTIALITY” A THESIS SUBMITTED TO ASSAM UNIVERSITY FOR PARTIAL FULFILLMENT OF THE REQUIREMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN LIFE SCIENCE AND BIOINFORMATICS By Lambert Niyoyitungiye (Ph.D. Registration No.Ph.D/3038/2016) Department of Life Science and Bioinformatics School of Life Sciences Assam University Silchar - 788011 India Under the Supervision of Dr.Anirudha Giri from Assam University, Silchar & Co-Supervision of Prof. Bhanu Prakash Mishra from Mizoram University, Aizawl Defence date: 17 September, 2019 To Almighty and merciful God & To My beloved parents with love i MEMBERS OF EXAMINATION BOARD iv Contents Niyoyitungiye, 2019 CONTENTS Page Numbers CHAPTER-I INTRODUCTION .............................................................. 1-7 I.1 Background and Motivation of the Study .......................................... -
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CICHLIFORMES: Cichlidae (part 2) · 1 The ETYFish Project © Christopher Scharpf and Kenneth J. Lazara COMMENTS: v. 4.0 - 30 April 2021 Order CICHLIFORMES (part 2 of 8) Family CICHLIDAE Cichlids (part 2 of 7) Subfamily Pseudocrenilabrinae African Cichlids (Abactochromis through Greenwoodochromis) Abactochromis Oliver & Arnegard 2010 abactus, driven away, banished or expelled, referring to both the solitary, wandering and apparently non-territorial habits of living individuals, and to the authors’ removal of its one species from Melanochromis, the genus in which it was originally described, where it mistakenly remained for 75 years; chromis, a name dating to Aristotle, possibly derived from chroemo (to neigh), referring to a drum (Sciaenidae) and its ability to make noise, later expanded to embrace cichlids, damselfishes, dottybacks and wrasses (all perch-like fishes once thought to be related), often used in the names of African cichlid genera following Chromis (now Oreochromis) mossambicus Peters 1852 Abactochromis labrosus (Trewavas 1935) thick-lipped, referring to lips produced into pointed lobes Allochromis Greenwood 1980 allos, different or strange, referring to unusual tooth shape and dental pattern, and to its lepidophagous habits; chromis, a name dating to Aristotle, possibly derived from chroemo (to neigh), referring to a drum (Sciaenidae) and its ability to make noise, later expanded to embrace cichlids, damselfishes, dottybacks and wrasses (all perch-like fishes once thought to be related), often used in the names of African cichlid genera following Chromis (now Oreochromis) mossambicus Peters 1852 Allochromis welcommei (Greenwood 1966) in honor of Robin Welcomme, fisheries biologist, East African Freshwater Fisheries Research Organization (Jinja, Uganda), who collected type and supplied ecological and other data Alticorpus Stauffer & McKaye 1988 altus, deep; corpus, body, referring to relatively deep body of all species Alticorpus geoffreyi Snoeks & Walapa 2004 in honor of British carcinologist, ecologist and ichthyologist Geoffrey Fryer (b. -
Depth Segregation and Diet Disparity Revealed by Stable Isotope Analyses
Hata et al. Zoological Letters (2015) 1:15 DOI 10.1186/s40851-015-0016-1 RESEARCH ARTICLE Open Access Depth segregation and diet disparity revealed by stable isotope analyses in sympatric herbivorous cichlids in Lake Tanganyika Hiroki Hata1*, Jyunya Shibata2,3, Koji Omori2, Masanori Kohda4 and Michio Hori5 Abstract Background: Lake Tanganyika in the African Great Rift Valley is known as a site of adaptive radiation in cichlid fishes. Diverse herbivorous fishes coexist on a rocky littoral of the lake. Herbivorous cichlids have acquired multiple feeding ecomorphs, including grazer, browser, scraper, and scooper, and are segregated by dietary niche. Within each ecomorph, however, multiple species apparently coexist sympatrically on a rocky slope. Previous observations of their behavior show that these cichlid species inhabit discrete depths separated by only a few meters. In this paper, using carbon (C) and nitrogen (N) stable isotope ratios as markers, we followed the nutritional uptake of cichlid fishes from periphyton in their feeding territories at various depths. Results: δ15N of fish muscles varied among cichlid ecomorphs; this was significantly lower in grazers than in browsers and scoopers, although δ15N levels in periphyton within territories did not differ among territorial species. This suggests that grazers depend more directly on primary production of periphyton, while others ingest animal matter from higher trophic levels. With respect to δ13C, only plankton eaters exhibited lower values, suggesting that these fishes depend on production of phytoplankton, while the others depend on production of periphyton. Irrespective of cichlid ecomorph, δ13C of periphyton correlated significantly with habitat depth, and decreased as habitat depth became deeper.