Phylogeny of a Rapidly Evolving Clade: the Cichlid Fishes of Lake Malawi
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Ecological Correlates of Ghost Lineages in Ruminants
Paleobiology, 38(1), 2012, pp. 101–111 Ecological correlates of ghost lineages in ruminants Juan L. Cantalapiedra, Manuel Herna´ndez Ferna´ndez, Gema M. Alcalde, Beatriz Azanza, Daniel DeMiguel, and Jorge Morales Abstract.—Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation. Juan L. Cantalapiedra, Gema Alcalde, and Jorge Morales. Departamento de Paleobiologı´a, Museo Nacional de Ciencias Naturales, UCM-CSIC, Pinar 25, 28006 Madrid, Spain. E-mail: [email protected] Manuel Herna´ndez Ferna´ndez. Departamento de Paleontologı´a, Facultad de Ciencias Geolo´gicas, Universidad Complutense de Madrid y Departamento de Cambio Medioambiental, Instituto de Geociencias, Consejo Superior de Investigaciones Cientı´ficas, Jose´ Antonio Novais 2, 28040 Madrid, Spain Daniel DeMiguel. -
Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
§4-71-6.5 LIST of CONDITIONALLY APPROVED ANIMALS November
§4-71-6.5 LIST OF CONDITIONALLY APPROVED ANIMALS November 28, 2006 SCIENTIFIC NAME COMMON NAME INVERTEBRATES PHYLUM Annelida CLASS Oligochaeta ORDER Plesiopora FAMILY Tubificidae Tubifex (all species in genus) worm, tubifex PHYLUM Arthropoda CLASS Crustacea ORDER Anostraca FAMILY Artemiidae Artemia (all species in genus) shrimp, brine ORDER Cladocera FAMILY Daphnidae Daphnia (all species in genus) flea, water ORDER Decapoda FAMILY Atelecyclidae Erimacrus isenbeckii crab, horsehair FAMILY Cancridae Cancer antennarius crab, California rock Cancer anthonyi crab, yellowstone Cancer borealis crab, Jonah Cancer magister crab, dungeness Cancer productus crab, rock (red) FAMILY Geryonidae Geryon affinis crab, golden FAMILY Lithodidae Paralithodes camtschatica crab, Alaskan king FAMILY Majidae Chionocetes bairdi crab, snow Chionocetes opilio crab, snow 1 CONDITIONAL ANIMAL LIST §4-71-6.5 SCIENTIFIC NAME COMMON NAME Chionocetes tanneri crab, snow FAMILY Nephropidae Homarus (all species in genus) lobster, true FAMILY Palaemonidae Macrobrachium lar shrimp, freshwater Macrobrachium rosenbergi prawn, giant long-legged FAMILY Palinuridae Jasus (all species in genus) crayfish, saltwater; lobster Panulirus argus lobster, Atlantic spiny Panulirus longipes femoristriga crayfish, saltwater Panulirus pencillatus lobster, spiny FAMILY Portunidae Callinectes sapidus crab, blue Scylla serrata crab, Samoan; serrate, swimming FAMILY Raninidae Ranina ranina crab, spanner; red frog, Hawaiian CLASS Insecta ORDER Coleoptera FAMILY Tenebrionidae Tenebrio molitor mealworm, -
"A Revision of the Freshwater Crabs of Lake Kivu, East Africa."
Northern Michigan University NMU Commons Journal Articles FacWorks 2011 "A revision of the freshwater crabs of Lake Kivu, East Africa." Neil Cumberlidge Northern Michigan University Kirstin S. Meyer Follow this and additional works at: https://commons.nmu.edu/facwork_journalarticles Part of the Biology Commons Recommended Citation Cumberlidge, Neil and Meyer, Kirstin S., " "A revision of the freshwater crabs of Lake Kivu, East Africa." " (2011). Journal Articles. 30. https://commons.nmu.edu/facwork_journalarticles/30 This Journal Article is brought to you for free and open access by the FacWorks at NMU Commons. It has been accepted for inclusion in Journal Articles by an authorized administrator of NMU Commons. For more information, please contact [email protected],[email protected]. This article was downloaded by: [Cumberlidge, Neil] On: 16 June 2011 Access details: Access Details: [subscription number 938476138] Publisher Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37- 41 Mortimer Street, London W1T 3JH, UK Journal of Natural History Publication details, including instructions for authors and subscription information: http://www.informaworld.com/smpp/title~content=t713192031 The freshwater crabs of Lake Kivu (Crustacea: Decapoda: Brachyura: Potamonautidae) Neil Cumberlidgea; Kirstin S. Meyera a Department of Biology, Northern Michigan University, Marquette, Michigan, USA Online publication date: 08 June 2011 To cite this Article Cumberlidge, Neil and Meyer, Kirstin S.(2011) 'The freshwater crabs of Lake Kivu (Crustacea: Decapoda: Brachyura: Potamonautidae)', Journal of Natural History, 45: 29, 1835 — 1857 To link to this Article: DOI: 10.1080/00222933.2011.562618 URL: http://dx.doi.org/10.1080/00222933.2011.562618 PLEASE SCROLL DOWN FOR ARTICLE Full terms and conditions of use: http://www.informaworld.com/terms-and-conditions-of-access.pdf This article may be used for research, teaching and private study purposes. -
Behaviour: an Important Diagnostic Tool for Lake Malawi Cichlids PDF
FISH and FISHERIES, 2002, 3, 213^224 Behaviour: an important diagnostic tool for Lake Malawi cichlids Jay R Stau¡er Jr1, Kenneth R McKaye2 & Ad F Konings3 1School of Forest Resources, Pennsylvania State University,University Park, Pennsylvania, PA16802, USA; 2Appalachian Laboratory,UMCES,301Braddock Road, Frostburg, Maryland, MD 21532, USA; 3Cichlid Press, PO Box13608, El Paso,Texas, T X 79913, USA Abstract Correspondence: Historically,the cichlid ¢shes of Lake Malawi, which probably represent one of the best Jay R. Stau¡er Jr, examples of rapid radiation of vertebrates, have been diagnosed with morphological School of Forest Resources, and genetic data. Many of the populations once thought to be conspeci¢c have been Pennsylvania State hypothesized to be separate species based on behavioural data. The use of behavioural University, data, as expressed in mate choice based on colour patterns or bower shapes, has been University Park, successfully used to diagnose both rock-dwelling and sand-dwelling cichlid species. Pennsylvania, PA Additionally,a combination of bower shapes and courtship patterns have been used as 16802, USA Tel.: þ1 814 863 0645 synapomorphies to diagnose genera within the Lake Malawi cichlid £ock. It is con- Fax: þ18148653725 cluded that taxonomists need to include behavioural data with morphological and E-mail:[email protected] genetic databases to diagnose species and to determine the phylogenetic relationships withinthis diverse assemblage of ¢shes. Received 5 Dec 2001 Accepted10Jun 2002 Keywords allopatry,behaviour, Cichlidae, -
Major Clades of Agaricales: a Multilocus Phylogenetic Overview
Mycologia, 98(6), 2006, pp. 982–995. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Major clades of Agaricales: a multilocus phylogenetic overview P. Brandon Matheny1 Duur K. Aanen Judd M. Curtis Laboratory of Genetics, Arboretumlaan 4, 6703 BD, Biology Department, Clark University, 950 Main Street, Wageningen, The Netherlands Worcester, Massachusetts, 01610 Matthew DeNitis Vale´rie Hofstetter 127 Harrington Way, Worcester, Massachusetts 01604 Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708 Graciela M. Daniele Instituto Multidisciplinario de Biologı´a Vegetal, M. Catherine Aime CONICET-Universidad Nacional de Co´rdoba, Casilla USDA-ARS, Systematic Botany and Mycology de Correo 495, 5000 Co´rdoba, Argentina Laboratory, Room 304, Building 011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350 Dennis E. Desjardin Department of Biology, San Francisco State University, Jean-Marc Moncalvo San Francisco, California 94132 Centre for Biodiversity and Conservation Biology, Royal Ontario Museum and Department of Botany, University Bradley R. Kropp of Toronto, Toronto, Ontario, M5S 2C6 Canada Department of Biology, Utah State University, Logan, Utah 84322 Zai-Wei Ge Zhu-Liang Yang Lorelei L. Norvell Kunming Institute of Botany, Chinese Academy of Pacific Northwest Mycology Service, 6720 NW Skyline Sciences, Kunming 650204, P.R. China Boulevard, Portland, Oregon 97229-1309 Jason C. Slot Andrew Parker Biology Department, Clark University, 950 Main Street, 127 Raven Way, Metaline Falls, Washington 99153- Worcester, Massachusetts, 01609 9720 Joseph F. Ammirati Else C. Vellinga University of Washington, Biology Department, Box Department of Plant and Microbial Biology, 111 355325, Seattle, Washington 98195 Koshland Hall, University of California, Berkeley, California 94720-3102 Timothy J. -
The Identity of Pseudotropheus Elongatus, with the Description of P. Longior from Mbamba Bay, Tanzania, and Notes on Genyochromis Mento (Teleostei: Cichlidae)
97 Ichthyol. Explor. Freshwaters, Vol. 7, No.2, pp. 97-110,12 figs.,1 tab., September 1996 © 1996 by Verlag Dr. Friedrich Pfeil, Miinchen, FRG- ISSN 0936-9902 The identity of Pseudotropheus elongatus, with the description of P. longior from Mbamba Bay, Tanzania, and notes on Genyochromis mento (Teleostei: Cichlidae) Lothar Seegers * Although Pseudotropheus elongatus was originally described from Mbamba Bay, Tanzania, a species of the P. elongatus-complex from Nkhata Bay, Malawi, has been considered to be the typical P. elongatus. Collections from Mbamba Bay revealed that at least two elongate Pseudotropheus species co-occur. The two extant syntypes of P. elongatus belong to the two species from Mbamba Bay. The specimen pictured by Fryer (1956) is selected as lectotype. The other species is described here as P. longior, new species. A third elongate cichlid, frequent at Mbamba Bay, is Genyochromis menta; some observations on this fish are included. 1956 beschrieb Fryer Pseudotropheus elongatus von Mbamba Bay, Tanzania, wahrend in der Literatur bisher eine Form aus dem P. elongatus-Komplex von Nkhata Bay, Malawi, als P. elongatus im Sinne der Typen angesehen wurde. In Mbamba Bay gibt es zwei gestreckte Pseudotropheus-Arten. Die beiden existierenden Syntypen gehoren unterschiedlichen Taxa an, namlich jeweils einer der beiden bei Mbamba Bay vorkommenden gestreckten Pseudotropheus-Arten. Als Lectotypus fur P. elongatus wurde das Exemplar festgelegt, das von Fryer (1956) abgebildet wurde. Die andere Pseudotropheus-Art wird hier als Pseudotropheus longior n. sp. beschrieben. Eine dritte gestreckte Cichlidenart, die in Mbamba Bay haufig vorkommt, ist Genyochromis menta Trewavas, 1935. Zu dieser Art werden einige Beobachtungen mitgeteilt. -
Rare Morph Lake Malawi Mbuna Cichlids Benefit from Reduced Aggression from Con- and Hetero-Specifics
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.08.439056; this version posted April 9, 2021. 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 4.0 International license. 1 Rare morph Lake Malawi mbuna cichlids benefit from reduced aggression from con- and hetero-specifics 2 Running title: Reduced aggression benefits rare morph mbuna 3 4 Alexandra M. Tyers*, Gavan M. Cooke & George F. Turner 5 School of Biological Sciences, Bangor University, Deniol Road, Bangor. Gwynedd. Wales. UK. LL57 2UW 6 * Current address: Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9B, 50931, Köln 7 8 Corresponding author: A.M. Tyers, [email protected] 9 10 Abstract 11 Balancing selection is important for the maintenance of polymorphism as it can prevent either fixation of one 12 morph through directional selection or genetic drift, or speciation by disruptive selection. Polychromatism can 13 be maintained if the fitness of alternative morphs depends on the relative frequency in a population. In 14 aggressive species, negative frequency-dependent antagonism can prevent an increase in the frequency of rare 15 morphs as they would only benefit from increased fitness while they are rare. Heterospecific aggression is 16 common in nature and has the potential to contribute to rare morph advantage. Here we carry out field 17 observations and laboratory aggression experiments with mbuna cichlids from Lake Malawi, to investigate the 18 role of con- and heterospecific aggression in the maintenance of polychromatism and identify benefits to rare 19 mores which are likely to result from reduced aggression. -
Kenyi Cichlid (Maylandia Lombardoi) Ecological Risk Screening Summary
Kenyi Cichlid (Maylandia lombardoi) Ecological Risk Screening Summary U.S. Fish and Wildlife Service, April 2011 Revised, July 2018 Web Version, 8/3/2018 Photo: Ged~commonswiki. Public domain. Available: https://commons.wikimedia.org/wiki/File:Maylandia_lombardoi.jpg. (July 2018). 1 Native Range and Status in the United States Native Range From Kasembe (2017): “Endemic to Lake Malawi. Occurs at Mbenji Island and Nkhomo reef [Malawi].” From Froese and Pauly (2018): “Africa: Endemic to Mbenji Island, Lake Malawi [Malawi].” 1 Status in the United States This species has not been reported as introduced or established in the United States. This species is in trade in the United States. From Imperial Tropicals (2018): “Kenyi Cichlid (Pseudotropheus lombardoi) […] $ 7.99 […] UNSEXED 1” FISH” Means of Introductions in the United States This species has not been reported as introduced or established in the United States. Remarks There is taxonomic uncertainty concerning Maylandia lombardoi. Because it has recently been grouped in the genera Metriaclima and Pseudotropheus, these names were also used when searching for information in preparation of this assessment. From Kasembe (2017): “This species previously appeared on the IUCN Red List in the genus Maylandia but is now considered valid in the genus Metriaclima (Konings 2016, Stauffer et al. 2016).” From Seriously Fish (2018): “There is ongoing debate as to the true genus of this species, it having been variously grouped in both Maylandia and Metriaclima, as well as the currently valid Pseudotropheus. -
Biology of Chordates Video Guide
Branches on the Tree of Life DVD – CHORDATES Written and photographed by David Denning and Bruce Russell ©2005, BioMEDIA ASSOCIATES (THUMBNAIL IMAGES IN THIS GUIDE ARE FROM THE DVD PROGRAM) .. .. To many students, the phylum Chordata doesn’t seem to make much sense. It contains such apparently disparate animals as tunicates (sea squirts), lancelets, fish and humans. This program explores the evolution, structure and classification of chordates with the main goal to clarify the unity of Phylum Chordata. All chordates possess four characteristics that define the phylum, although in most species, these characteristics can only be seen during a relatively small portion of the life cycle (and this is often an embryonic or larval stage, when the animal is difficult to observe). These defining characteristics are: the notochord (dorsal stiffening rod), a hollow dorsal nerve cord; pharyngeal gills; and a post anal tail that includes the notochord and nerve cord. Subphylum Urochordata The most primitive chordates are the tunicates or sea squirts, and closely related groups such as the larvaceans (Appendicularians). In tunicates, the chordate characteristics can be observed only by examining the entire life cycle. The adult feeds using a ‘pharyngeal basket’, a type of pharyngeal gill formed into a mesh-like basket. Cilia on the gill draw water into the mouth, through the basket mesh and out the excurrent siphon. Tunicates have an unusual heart which pumps by ‘wringing out’. It also reverses direction periodically. Tunicates are usually hermaphroditic, often casting eggs and sperm directly into the sea. After fertilization, the zygote develops into a ‘tadpole larva’. This swimming larva shows the remaining three chordate characters - notochord, dorsal nerve cord and post-anal tail. -
A Small Cichlid Species Flock from the Upper Miocene (9–10 MYA)
Hydrobiologia https://doi.org/10.1007/s10750-020-04358-z (0123456789().,-volV)(0123456789().,-volV) ADVANCES IN CICHLID RESEARCH IV A small cichlid species flock from the Upper Miocene (9–10 MYA) of Central Kenya Melanie Altner . Bettina Reichenbacher Received: 22 March 2020 / Revised: 16 June 2020 / Accepted: 13 July 2020 Ó The Author(s) 2020 Abstract Fossil cichlids from East Africa offer indicate that they represent an ancient small species unique insights into the evolutionary history and flock. Possible modern analogues of palaeolake Waril ancient diversity of the family on the African conti- and its species flock are discussed. The three species nent. Here we present three fossil species of the extinct of Baringochromis may have begun to subdivide haplotilapiine cichlid Baringochromis gen. nov. from their initial habitat by trophic differentiation. Possible the upper Miocene of the palaeolake Waril in Central sources of food could have been plant remains and Kenya, based on the analysis of a total of 78 articulated insects, as their fossilized remains are known from the skeletons. Baringochromis senutae sp. nov., B. same place where Baringochromis was found. sonyii sp. nov. and B. tallamae sp. nov. are super- ficially similar, but differ from each other in oral-tooth Keywords Cichlid fossils Á Pseudocrenilabrinae Á dentition and morphometric characters related to the Palaeolake Á Small species flock Á Late Miocene head, dorsal fin base and body depth. These findings Guest editors: S. Koblmu¨ller, R. C. Albertson, M. J. Genner, Introduction K. M. Sefc & T. Takahashi / Advances in Cichlid Research IV: Behavior, Ecology and Evolutionary Biology. The tropical freshwater fish family Cichlidae and its Electronic supplementary material The online version of estimated 2285 species is famous for its high degree of this article (https://doi.org/10.1007/s10750-020-04358-z) con- phenotypic diversity, trophic adaptations and special- tains supplementary material, which is available to authorized users. -
Fish Brains: Evolution and Environmental Relationships
Reviews in Fish Biology and Fisheries 8, 373±408 (1998) Fish brains: evolution and environmental relationships K. KOTRSCHAL1,Ã, M.J. VAN STAADEN2,3 and R. HUBER2,3 1Institute of Zoology, Department of Ethology, The University of Vienna and Konrad Lorenz Forschungsstelle, A±4645 GruÈnau 11, Austria 2Institute of Zoology, Department of Physiology, The University of Graz, UniversitaÈtsplatz 2, A±8010 Graz, Austria 3Department of Biological Sciences, Bowling Green State University, Life Science Bldg, Bowling Green, OH 43403, USA Contents Abstract page 373 Fish brains re¯ect an enormous evolutionary radiation 374 Based on morphology: how conclusions on sensory orientation are reached 376 Structure of ®sh brains 378 Large-scale evolutionary patterns of ®sh brains 384 Functional diversi®cation 386 Cyprinidae Gadidae Flat®shes Cichlidae and other modern perciforms How environments shape brains: turbidity, benthos and the pelagic realms 393 Variation of brain and senses with depth 395 Ontogenetic variation: a means of adaptation? 398 Intraspeci®c variation between `adult' age classes Intraspeci®c variation within age classes Conclusions: where to go from here? 400 Acknowledgements 401 References 402 Abstract Fish brains and sensory organs may vary greatly between species. With an estimated total of 25 000 species, ®sh represent the largest radiation of vertebrates. From the agnathans to the teleosts, they span an enormous taxonomic range and occupy virtually all aquatic habitats. This diversity offers ample opportunity to relate ecology with brains and sensory systems. In a broadly comparative approach emphasizing teleosts, we surveyed `classical' and more recent contributions on ®sh brains in search of evolutionary and ecological conditions of central nervous system diversi®cation.