Chambo: Is It Taste Or Something Else? Preference and Acceptability
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1 Exon Probe Sets and Bioinformatics Pipelines for All Levels of Fish Phylogenomics
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 2 3 Lily C. Hughes1,2,3,*, Guillermo Ortí1,3, Hadeel Saad1, Chenhong Li4, William T. White5, Carole 4 C. Baldwin3, Keith A. Crandall1,2, Dahiana Arcila3,6,7, and Ricardo Betancur-R.7 5 6 1 Department of Biological Sciences, George Washington University, Washington, D.C., U.S.A. 7 2 Computational Biology Institute, Milken Institute of Public Health, George Washington 8 University, Washington, D.C., U.S.A. 9 3 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian 10 Institution, Washington, D.C., U.S.A. 11 4 College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China 12 5 CSIRO Australian National Fish Collection, National Research Collections of Australia, 13 Hobart, TAS, Australia 14 6 Sam Noble Oklahoma Museum of Natural History, Norman, O.K., U.S.A. 15 7 Department of Biology, University of Oklahoma, Norman, O.K., U.S.A. 16 17 *Corresponding author: Lily C. Hughes, [email protected]. 18 Current address: Department of Organismal Biology and Anatomy, University of Chicago, 19 Chicago, IL. 20 21 Keywords: Actinopterygii, Protein coding, Systematics, Phylogenetics, Evolution, Target 22 capture 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. -
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CICHLIFORMES: Cichlidae (part 5) · 1 The ETYFish Project © Christopher Scharpf and Kenneth J. Lazara COMMENTS: v. 10.0 - 11 May 2021 Order CICHLIFORMES (part 5 of 8) Family CICHLIDAE Cichlids (part 5 of 7) Subfamily Pseudocrenilabrinae African Cichlids (Palaeoplex through Yssichromis) Palaeoplex Schedel, Kupriyanov, Katongo & Schliewen 2020 palaeoplex, a key concept in geoecodynamics representing the total genomic variation of a given species in a given landscape, the analysis of which theoretically allows for the reconstruction of that species’ history; since the distribution of P. palimpsest is tied to an ancient landscape (upper Congo River drainage, Zambia), the name refers to its potential to elucidate the complex landscape evolution of that region via its palaeoplex Palaeoplex palimpsest Schedel, Kupriyanov, Katongo & Schliewen 2020 named for how its palaeoplex (see genus) is like a palimpsest (a parchment manuscript page, common in medieval times that has been overwritten after layers of old handwritten letters had been scraped off, in which the old letters are often still visible), revealing how changes in its landscape and/or ecological conditions affected gene flow and left genetic signatures by overwriting the genome several times, whereas remnants of more ancient genomic signatures still persist in the background; this has led to contrasting hypotheses regarding this cichlid’s phylogenetic position Pallidochromis Turner 1994 pallidus, pale, referring to pale coloration of all specimens observed at the time; chromis, a name -
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. -
Similar Morphologies of Cichlid Fish in Lakes Tanganyika and Malawi Are Due to Convergence Thomas D
MOLECULAR PHYLOGENETICS AND EVOLUTION Vol. 2. No. 2, June. pp. 158-165. 1993 Similar Morphologies of Cichlid Fish in Lakes Tanganyika and Malawi Are Due to Convergence Thomas D. Kocher , * '1 Janet A. Conroy,* Kenneth R. McKaye,* and Jay R. Stauffer* * Department of Zoology, University of New Hampshire, Durham, New Hampshire 03824; t Appalachian Environmental Laboratory, University of Maryland, Frostburg, Maryland 21532; t School of Forest Resources, Pennsylvania State University, University Park, Pennsylvania 16802 Received March 22, 1993; revised June 29, 1993 ancestor for the Lake Victoria cichlid flock (Sage et al., The species flocks of cichlid fishes in the lakes of East 1984; Meyer et al., 1990). The mechanisms by which Africa are the most spectacular example of adaptive so many species have arisen in such a short time, radiation among living vertebrates. Similar highly de within closed lake basins, are a fascinating subject for rived morphologies are found among species in differ research. ent lakes. These similarities have been variously inter A separate, monophyletic origin for the species flock preted either as evidence for migration of ancestral in each lake has often been assumed, partly because species between the lakes, or of striking convergence of the high levels of endemicity found in the cichlid of morphology. To distinguish among these competing fauna, and partly because of the ancient and isolated hypotheses we sequenced a portion of the mitochon history of each lake (Fryer and lies, 1972). The lake drial UNA control region from six pairs of morphologi basins have arisen separately by a gradual lengthen cally similar taxa from Lakes Malawi and Tanganyika. -
Identification and Biology of Diplotaxodon, Rhamphochromis and Pallidochromis
190 Diplotaxodon, Rhamphochromis & Pallidochromis / Turner et al. Identification and Biology of Diplotaxodon, Rhamphochromis and Pallidochromis George F. Turner, Rosanna L. Robinson, Paul W. Shaw & Gary R. Carvalho Abstract Introduction We present preliminary morphological and mo- The genera Rhamphochromis Regan, 1922 and lecular taxonomic studies of the genera Rhampho- Diplotaxodon Trewavas, 1935 include the most chromis, Diplotaxodon and Pallidochromis, along with pelagic of Lake Malawi’s cichlids (Turner, 1996). notes on their identification, distribution and ecol- Pallidochromis Turner, 1994, a more benthic form, is ogy. We suggest that Rhamphochromis is comprised also considered in this chapter, as it appears mor- of eight to ten species: R. longiceps, R. woodi, R. phologically intermediate between Diplotaxodon macrophthalmus, R. esox, possibly R. ferox and four and Rhamphochromis (Turner 1994a). Rhampho- or five undescribed species. We suggest that R. chromis species are streamlined elongated predators lucius and R. brevis may be junior synonyms of R. of fish and zooplankton. They usually have large woodi. We also believe that Rhamphochromis teeth and jaws. Diplotaxodon comprises a heteroge- leptosoma and R. melanotus are junior synonyms of neous mix of small-toothed silvery species with R. esox. We consider that the two types of R. ferox upwardly-angled jaws. The genus includes zoo- are not conspecific and we designate a lectotype. planktivores and predators of small pelagic fish. However, we have not yet been able to positively The genus Rhamphochromis was described by identify this species from recent collections. Regan (1922), who took the type species as Diplotaxodon may contain anything from 11 to 22 or Rhamphochromis longiceps (Günther, 1864). -
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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. -
The Cichlid Fish Model
Genetic Basis of Vertebrate Diversity: the Cichlid Fish Model Proposed by The International Cichlid Genome Consortium (http://hcgs.unh.edu/cichlid/) March 28, 2006 Corresponding author: Thomas D. Kocher, Professor and Co-Director Hubbard Center for Genome Studies, University of New Hampshire Suite 400 Gregg Hall. 35 Colovos Road, Durham NH 03824 603-862-2115; FAX 862-2940; [email protected] From January 1, 2007: Department of Biology, University of Maryland College Park, MD 20742-5568 Additional authors: Jean-Francois Baroiller, CIRAD, Montpellier Russell Fernald, Stanford University Jody Hey, Rutgers University Hans Hofmann, Harvard University Axel Meyer, University of Konstanz Norihiro Okada, Tokyo Institute of Technology David Penman, University of Stirling Ole Seehausen, University of Bern Todd Streelman, Georgia Institute of Technology Cichlid Genome Executive Summary We advocate the development of genome sequences from cichlid fishes to support research into the genetic mechanisms which have contributed to the diversification of vertebrates. Cichlids have undergone a spectacular radiation in the lakes of East Africa which has generated a collection of ‘natural mutants’ that are amenable to genetic analysis in the laboratory. Cichlids exhibit tremendous diversity in features, such as jaws, teeth and pigmentation, that are derived from the neural crest. They also exhibit an extraordinary diversity and plasticity of behavior, which has contributed to their rapid speciation. Cichlids are perhaps the model system for understanding evolutionary mechanisms in vertebrates. We request a total of 10Gb of sequence from this group. The Nile tilapia is the obvious candidate for full (5x) draft assembly in this group, because of the availability of homozygous clonal lines and extensive genetic and physical maps for this species. -
Genome-Wide Microrna Screening in Nile Tilapia Reveals
www.nature.com/scientificreports OPEN Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased Received: 7 November 2016 Accepted: 15 May 2018 arm switching and increasing Published: xx xx xxxx complexity of expression throughout development Danillo Pinhal 1, Luiz A. Bovolenta2, Simon Moxon3, Arthur C. Oliveira1, Pedro G. Nachtigall1, Marcio L. Acencio4, James G. Patton5, Alexandre W. S. Hilsdorf6, Ney Lemke2 & Cesar Martins 7 MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identifcation and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fshes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identifed, many of which seem to be teleost-specifc, cichlid-specifc or tilapia-specifc. Abundant miRNA isoforms (isomiRs) were identifed with modifcations in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable diferential ratio of miRNA arms and isoforms infuenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs. -
Is Failure to Enforce Management Regulations Really the Cause of the Decline of Chambo Fishery? a Policy Agenda
IFPRI Eastern Africa Food Policy Network Network Report 12 November 2004 Is Failure to Enforce Management Regulations Really the Cause of the Decline of Chambo Fishery? A Policy Agenda E. Kaunda, D. Maliro, M. Mphepo, S. Khaila, L. Kamanga, L. Y. Phiri, and J. Valeta IFPRI Eastern Africa Food Policy Network 1 The International Food Policy Research Institute (IFPRI) was founded in 1975 to develop policy solutions for sustainably meeting the food needs of the developing world. Research, capacity strengthening, and policy communications at IFPRI concentrate on achieving economic growth and poverty reduction in low-income countries, improving food and nutrition security of poor people, and managing the natural resource base that supports agriculture. IFPRI researchers work closely with national counterparts and collaborate to strengthen research capacity in developing countries. IFPRI also strengthens the link between research and policymaking through its regional networks. It communicates the results of its research to influence policymaking and raise public awareness about food security, poverty, and natural resource issues. The IFPRI Eastern Africa Food Policy Network seeks to reduce poverty and improve food security in East Africa by generating policy-relevant information through collaborative research activities, improving the dissemination and use of such information, and strengthening local capacity to undertake and communicate policy research. The Network covers Ethiopia, Kenya, Malawi, Mozambique, Tanzania, and Uganda. The IFPRI Eastern Africa Food Policy Network Report series addresses policy problems related to food security in Eastern Africa. The reports are intended to be timely working documents of policy relevance to stakeholders in the region. The series includes research output from Network members supported by the Network’s competitive grants program. -
Replicated Divergence in Cichlid Radiations Mirrors a Major
Downloaded from http://rspb.royalsocietypublishing.org/ on January 27, 2016 Replicated divergence in cichlid radiations rspb.royalsocietypublishing.org mirrors a major vertebrate innovation Matthew D. McGee1, Brant C. Faircloth2, Samuel R. Borstein3, Jimmy Zheng4, C. Darrin Hulsey5, Peter C. Wainwright1 and Michael E. Alfaro4 Research 1Department of Evolution and Ecology, University of California, Davis, CA 95616, USA 2Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Cite this article: McGee MD, Faircloth BC, LA 70803, USA 3 Borstein SR, Zheng J, Darrin Hulsey C, Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA 4Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA Wainwright PC, Alfaro ME. 2016 Replicated 5Department of Biology, University of Konstanz, Konstanz, Germany divergence in cichlid radiations mirrors a major vertebrate innovation. Proc. R. Soc. B Decoupling of the upper jaw bones—jaw kinesis—is a distinctive feature of the 283: 20151413. ray-finned fishes, but it is not clear how the innovation is related to the extra- http://dx.doi.org/10.1098/rspb.2015.1413 ordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional diversity—African rift lake cichlids. We sequenced ultraconserved elements to generate a phylogenomic tree of the Received: 11 June 2015 Lake Tanganyika and Lake Malawi cichlid radiations. We filmed a diverse array of over 50 cichlid species capturing live prey and quantified the extent Accepted: 30 November 2015 of jaw kinesis in the premaxillary and maxillary bones. -
Fish Communities in the East African Great Lakes = Peuplement
277 Chapitre 13 FISH COMMUNITIES IN THE EAST AFRICAN GREAT LAKES PEUPLEMENTS ICHTHYOLOGIQUES DES GRANDS LACS D’AFRIQUE DE L’EST A.J. Ribbink D.H. Eccles Many fish communities of the East African Great Lakes (Lakes Victoria, Tanganyika and Malawi) are under intense pressure of exploitation to meet Man’s escalating needs for animal protein. Indeed, the requirement for fish protein is rising exponentially with the rapidly accele- rating increase in human populations and one cari confidently predict that these fish communi- ties Will be subjected to even greater fishing pressure in the future. A fiightening aspect of this exploitation is that SOlittle is known of the structure of the communities, or of the interac- tions within and between them, that it is impossible to predict, except in the broadest outline, the outcome of man-induced perturbations of such multispecific fisheries. There is already evi- dence of the effects of Man’s exploitation and manipulation of these resources (Fryer, 1972; Coulter, 1976 ; Turner, 1977a; 1977b ; Sharp, 1981; Witte, pers. Comm.) and it is clear that the fish communities of these lakes are particularly sensitive to exploitation. There are indications that in Lake Malawi several of the larger species of fish are either locally extinct or, by virtue of the patchy distribution of most species (see below), totally extinct (Turner, 1977a). The most basic ecological data consist of counts of individuals and of the species to which these individuals belong, of the trophic and habitat relations between these species and of the way that the counts and relations vary with time. -
Biostor-80351.Pdf
- f JUN i Phylogenetic versus convergent relationship USftARY between piscivorous cichlid fishes from Lakes Malawi and Tanganyika Melanie L. J. Stiassny Department of Morphology, Zoological Laboratory, University of Leiden, The Netherlands'. Contents Synopsis 67 Introduction 67 Methods, nomenclature and materials . 68 Methods 68 Nomenclature 69 Materials 70 Abbreviations used in text figures . 70 Anatomical description 73 Ethmovomerine region of the neurocranium 73 Cephalic muscles 77 Pharyngeal jaw apparatus .... 87 Discussion . 98 Acknowledgements 99 References 100 Synopsis The anatomy and phylogenetic relationships of two genera of African cichlid fishes, Rhamphochromis from Lake Malawi and Bathybates from Lake Tanganyika, are investigated. In accordance with the current methods of cladistic analysis data from representatives of a wide range of cichlid taxa are included for outgroup comparison. Particular emphasis is placed upon the anatomy of the ethmovo- merine region of the neurocranium, the cheek musculature, and the pharyngeal jaw apparatus. Based upon a number of synapomorphic characters an hypothesis of a sistergrbup relationship between the monophyletic genus, Bathybates, and a monophyletic assemblage consisting of the genera Hemibates and Trematocara is formulated. A similar resolution of the relationships of Rhampho- chromis has not been achieved; the differential success of the study is discussed and additional data relevant to unravelling the status and relationships of Rhamphochromis are introduced. Introduction The similarities that exist between individual species and whole communities of cichlid fishes in Lakes Malawi and Tanganyika have often been remarked upon (eg. Pellegrin, 1903; Regan, 1921, 1922; Fryer, 1959; Fryer & lies, 1972; Galis & Barel, 1980). Regan (1921) felt that the majority of the Malawian genera were phyletically distinct from any found else- where and that they formed a 'natural group'.