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Williamson G, Harris T, Bizior A, Hoskisson PA, Pritchard L, Javelle A. Biological ammonium transporters: evolution and diversification. FEBS J 2024. [PMID: 38265636 DOI: 10.1111/febs.17059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
Although ammonium is the preferred nitrogen source for microbes and plants, in animal cells it is a toxic product of nitrogen metabolism that needs to be excreted. Thus, ammonium movement across biological membranes, whether for uptake or excretion, is a fundamental and ubiquitous biological process catalysed by the superfamily of the Amt/Mep/Rh transporters. A remarkable feature of the Amt/Mep/Rh family is that they are ubiquitous and, despite sharing low amino acid sequence identity, are highly structurally conserved. Despite sharing a common structure, these proteins have become involved in a diverse range of physiological process spanning all domains of life, with reports describing their involvement in diverse biological processes being published regularly. In this context, we exhaustively present their range of biological roles across the domains of life and after explore current hypotheses concerning their evolution to help to understand how and why the conserved structure fulfils diverse physiological functions.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Paul Alan Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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2
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Yang S, Kar S. First report on chemometric modeling of tilapia fish aquatic toxicity to organic chemicals: Toxicity data gap filling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167991. [PMID: 37898216 DOI: 10.1016/j.scitotenv.2023.167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The Toxic Substances Control Act (TSCA) mandates the Environmental Protection Agency (EPA) to document chemicals entering the US. Due to the vast range of toxicity endpoints, experimental toxicological study for all chemicals is impossible to conduct. To address this, in silico methods like QSAR and read-across are strategically used to prioritize testing for chemicals lacking ecotoxicity data. Aquatic toxicity is one of the most critical endpoints directly related to aquatic species, mainly fish, followed by direct to indirect effects on humans through drinking water and fish as food, respectively. Therefore, we have employed the ToxValDB database to curate acute LC50 toxicity data for three Tilapia species covering two different genera, an ideal species for aquatic toxicity testing. Employing the curated dataset, we have developed multiple robust and predictive QSAR and quantitative read-across structure-activity relationship (q-RASAR) models for Tilapia zillii, Oreochromis niloticus, and Oreochromis mossambicus which helped to understand the toxicological mode of action (MoA) of the modeled chemicals and predict the aquatic toxicity of new untested chemicals followed by toxicity data gap filling. The best three QSAR models showed encouraging statistical quality in terms of determination coefficient R2 (0.94, 0.74, and 0.77), cross-validated leave-one-out Q2 (0.90, 0.67 and 0.70), and predictive capability in terms of R2pred (0.95, 0.77, and 0.74) for T. zillii, O. niloticus, and O. mossambicus datasets, respectively. The developed best mathematical models were used for the prediction of aquatic toxicity in terms of pLC50 for 297 untested organic chemicals across three major Tilapia species ranging from 1.841 to 8.561 M in terms of environmental risk assessment.
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Affiliation(s)
- Siyun Yang
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry, Kean University, 1000 Morris Avenue, Union, NJ 07083, USA
| | - Supratik Kar
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry, Kean University, 1000 Morris Avenue, Union, NJ 07083, USA.
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3
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Popoola MO, Schedel FDB, Hebert PDN, Schliewen UK. First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species. PeerJ 2022; 10:e13049. [PMID: 35437472 PMCID: PMC9013235 DOI: 10.7717/peerj.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 02/11/2022] [Indexed: 01/11/2023] Open
Abstract
Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats.
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4
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Ndimele PE, Owodeinde FG, Clarke EO, Whenu OO, Joseph OO. Population parameters, exploitation rate and diet of black-chinned Tilapia, Sarotherodon melanotheron Rüppell, 1852 (Pisces: Cichlidae), from Badagry Creek, Lagos, Nigeria. AFRICAN ZOOLOGY 2021. [DOI: 10.1080/15627020.2021.2006779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | | | - Olufemi Olabode Joseph
- Agricultural Education Department, Adeniran Ogunsanya College of Education, Oto/Ijanikin, Nigeria
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5
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Mojekwu TO, Cunningham MJ, Bills RI, Pretorius PC, Hoareau TB. Utility of DNA barcoding in native Oreochromis species. JOURNAL OF FISH BIOLOGY 2021; 98:498-506. [PMID: 33070327 DOI: 10.1111/jfb.14594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.
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Affiliation(s)
- Tonna O Mojekwu
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biotechnology, Nigerian Institute for Oceanography and Marine Research, Lagos, Nigeria
| | - Michael J Cunningham
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- South African Institute for Aquatic Biodiversity, Grahamstown, South Africa
| | - Roger I Bills
- South African Institute for Aquatic Biodiversity, Grahamstown, South Africa
| | - Petrus C Pretorius
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Thierry B Hoareau
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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6
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Akian DD, Yao K, Parmentier E, Joassard L, Clota F, Baroiller JF, Lozano P, Chatain B, Bégout ML. Acoustic signals produced by Nile tilapia Oreochromis niloticus and black-chinned tilapia Sarotherodon melanotheron during intra- and interspecific pairings. ZOOLOGY 2020; 143:125831. [PMID: 32949976 DOI: 10.1016/j.zool.2020.125831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 11/18/2022]
Abstract
We characterised, for the first-time, the sound production of black-chinned tilapia Sarotherodon melanotheron and show differences with that of Nile tilapia Oreochromis niloticus in a hybridization pairing context. Although both species were able to produce drum sounds, they showed different acoustic features. Drum sounds were produced in aggressive (chasing or lateral attack) and non-aggressive (courtship) contexts by O. niloticus but only in aggressive situations (fleeing or avoidance) by S. melanotheron. The second type of sounds produced by O. niloticus were grunts, produced in both aggressive (chasing and after biting) and non-aggressive contexts (nest building). The second type of sound produced by S. melanotheron was a rolling sound, produced only during courtship. Each species was able to produce common sounds (drum) and species-specific sounds (grunts and rolling). This implies that species can communicate without being able to understand each other because the sounds emitted may probably have different significance. Drumming corresponded only to aggressivity in S. melanotheron, whereas this was not true for O. niloticus. 11-ketotestosterone (11-kt) levels were significantly higher in male O. niloticus than male S. melanotheron, but there was no significant correlation between 11-kt or estradiol concentrations and the number of sounds produced in aggressive or non-aggressive behavioural contexts in either species. During interspecies interactions, O. niloticus drum sounds are likely considered to be aggressive by S. melanotheron and could potentially constitute a reproductive barrier between the two species.
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Affiliation(s)
- Dieudonné Djétouan Akian
- Département Eaux, Forêts et Environnement, Institut National Polytechnique Félix Houphouët Boigny, BP 1313, Yamoussoukro, Cote d'Ivoire; Laboratoire de Biologie et Cytologie Animales, Unité de Formation et de Recherche Science de la Nature, Université Nangui-Abrogoua, 02 BP 801, Abidjan 02, Cote d'Ivoire; Laboratoire Ressources Halieutiques, Institut Français de Recherche pour l'Exploitation de la Mer, L'Houmeau, 17137, France
| | - Kouakou Yao
- Laboratoire de Biologie et Cytologie Animales, Unité de Formation et de Recherche Science de la Nature, Université Nangui-Abrogoua, 02 BP 801, Abidjan 02, Cote d'Ivoire
| | - Eric Parmentier
- Laboratoire de Morphologie Fonctionnelle et Evolutive, AFFISH, Institut de chimie- B6C, Université de Liège, Sart Tilman, 4000, Liège, Belgium
| | - Lucette Joassard
- Laboratoire Ressources Halieutiques, Institut Français de Recherche pour l'Exploitation de la Mer, L'Houmeau, 17137, France
| | - Frédéric Clota
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-François Baroiller
- Unité Mixte de Recherche 116, Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Paul Lozano
- Unité Mixte de Recherche 116, Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Béatrice Chatain
- MARBEC, Université Montpellier, CNRS, Ifremer, IRD, Chemin de Maguelone, 34250, Palavas-les-Flots, France
| | - Marie-Laure Bégout
- Laboratoire Ressources Halieutiques, Institut Français de Recherche pour l'Exploitation de la Mer, L'Houmeau, 17137, France; MARBEC, Université Montpellier, CNRS, Ifremer, IRD, Chemin de Maguelone, 34250, Palavas-les-Flots, France.
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7
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Syaifudin M, Bekaert M, Taggart JB, Bartie KL, Wehner S, Palaiokostas C, Khan MGQ, Selly SLC, Hulata G, D'Cotta H, Baroiller JF, McAndrew BJ, Penman DJ. Species-Specific Marker Discovery in Tilapia. Sci Rep 2019; 9:13001. [PMID: 31506510 PMCID: PMC6737103 DOI: 10.1038/s41598-019-48339-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/22/2019] [Indexed: 11/12/2022] Open
Abstract
Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.
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Affiliation(s)
- Mochamad Syaifudin
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.,Program Study of Aquaculture, Agriculture Faculty, Universitas Sriwijaya, South Sumatra, Indonesia
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Kerry L Bartie
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Stefanie Wehner
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.,Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Christos Palaiokostas
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - M G Q Khan
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.,Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sarah-Louise C Selly
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Gideon Hulata
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel
| | - Helena D'Cotta
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France.,CIRAD, Campus Int. Baillarguet, 34398, Montpellier, France
| | - Jean-Francois Baroiller
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France.,CIRAD, Campus Int. Baillarguet, 34398, Montpellier, France
| | - Brendan J McAndrew
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - David J Penman
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.
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8
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Ford AG, Bullen TR, Pang L, Genner MJ, Bills R, Flouri T, Ngatunga BP, Rüber L, Schliewen UK, Seehausen O, Shechonge A, Stiassny ML, Turner GF, Day JJ. Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments. Mol Phylogenet Evol 2019; 136:215-226. [DOI: 10.1016/j.ympev.2019.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 03/26/2019] [Accepted: 04/06/2019] [Indexed: 12/15/2022]
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9
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Abdulmalik-Labe OP, Quilang JP. DNA barcoding of fishes from Lake Lanao, Philippines. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1614890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Onaya P. Abdulmalik-Labe
- Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Biology Department, College of Natural Sciences and Mathematics, Mindanao State University, Marawi City, Philippines
| | - Jonas P. Quilang
- Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
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10
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Bbole I, Zhao JL, Tang SJ, Katongo C. Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa. PLoS One 2018; 13:e0203095. [PMID: 30481181 PMCID: PMC6258479 DOI: 10.1371/journal.pone.0203095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022] Open
Abstract
Genetic characterization of southern African cichlids has not received much attention. Here, we describe the mitogenome sequences and phylogenetic positioning of Oreochromis andersonii and O. macrochir among the African cichlids. The complete mitochondrial DNA sequences were determined for O. andersonii and O. macrochir, two important aquaculture and fisheries species endemic to southern Africa. The complete mitogenome sequence lengths were 16642 bp and 16644 bp for O. andersonii and O. macrochir respectively. The general structural organization follows that of other teleost species with 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a non-coding control region. Phylogenetic placement of the two species among other African cichlids was performed using Maximum Likelihood (ML) and Bayesian Markov-Chain-Monte-Carlo (MCMC). The consensus trees confirmed the relative positions of the two cichlid species with O. andersonii being very closely related to O. mossambicus and O. macrochir showing a close relation to both species. Among the 13 mitochondrial DNA protein coding genes ND6 may have evolved more rapidly and COIII was the most conserved. There are signs that ND6 may have been subjected to positive selection in order for these cichlid lineages to diversify and adapt to new environments. More work is needed to characterize the southern Africa cichlids as they are important species for capture fisheries, aquaculture development and understanding biogeographic history of African cichlids. Bio-conservation of some endangered cichlids is also essential due to the threat by invasive species.
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Affiliation(s)
- Ian Bbole
- Department of Fisheries, Mansa, Zambia
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Jin-Liang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN), Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Shou-Jie Tang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Cyprian Katongo
- Biological Sciences Department, University of Zambia, Lusaka, Zambia
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11
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Gammerdinger WJ, Kocher TD. Unusual Diversity of Sex Chromosomes in African Cichlid Fishes. Genes (Basel) 2018; 9:E480. [PMID: 30287777 PMCID: PMC6210639 DOI: 10.3390/genes9100480] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.
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Affiliation(s)
- William J Gammerdinger
- Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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12
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Moser FN, van Rijssel JC, Mwaiko S, Meier JI, Ngatunga B, Seehausen O. The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes. Proc Biol Sci 2018; 285:rspb.2018.0171. [PMID: 30111604 DOI: 10.1098/rspb.2018.0171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/23/2018] [Indexed: 12/29/2022] Open
Abstract
Adaptive radiation research typically relies on the study of evolution in retrospective, leaving the predictive value of the concept hard to evaluate. Several radiations, including the cichlid fishes in the East African Great Lakes, have been studied extensively, yet no study has investigated the onset of the intraspecific processes of niche expansion and differentiation shortly after colonization of an adaptive zone by cichlids. Haplochromine cichlids of one of the two lineages that seeded the Lake Victoria radiation recently arrived in Lake Chala, a lake perfectly suited for within-lake cichlid speciation. Here, we infer the colonization and demographic history, quantify phenotypic, ecological and genomic diversity and diversification, and investigate the selection regime to ask if the population shows signs of diversification resembling the onset of adaptive radiation. We find that since their arrival in the lake, haplochromines have colonized a wide range of depth habitats associated with ecological and morphological expansion and the beginning of phenotypic differentiation and potentially nascent speciation, consistent with the very early onset of an adaptive radiation process. Moreover, we demonstrate evidence of rugged phenotypic fitness surfaces, indicating that current ecological selection may contribute to the phenotypic diversification.
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Affiliation(s)
- Florian N Moser
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Jacco C van Rijssel
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland.,Wageningen Marine Research, Wageningen University and Research, Ijmuiden, The Netherlands
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Benjamin Ngatunga
- Tanzania Fisheries Research Institute, Box 9750, Dar Es Salaam, Tanzania
| | - Ole Seehausen
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland .,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
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13
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Chiozzi G, Stiassny MLJ, Alter SE, De Marchi G, Mebrahtu Y, Tessema M, Asmamaw B, Fasola M, Bellati A. Fishes in the desert: mitochondrial variation and phylogeography of Danakilia (Actinopterygii: Cichlidae) and Aphanius (Actinopterygii: Cyprinodontidae) in the Danakil Depression of northeastern Africa. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1025-1040. [PMID: 29166850 DOI: 10.1080/24701394.2017.1404043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Danakil Depression in northeastern Africa represents one of the harshest arid environments on Earth, yet two genera of fishes, Danakilia (Cichlidae) and Aphanius (Cyprinodontidae), share its sparse aquatic habitats. The evolutionary history of these fishes is investigated here in the context of genetic, geological and paleoenvironmental information. We collected samples from seven sites and assessed phylogeographic relationships using concatenated COI and cytb mtDNA genes. Danakilia morphospecies show low differentiation at mitochondrial markers, but variation is partitioned between a northern cluster containing D. dinicolai plus three undescribed riverine populations, and a southern cluster including two creek populations of D. franchettii separated by the hypersaline waters of Lake Afrera. Aphanius displayed four genetically distinct clades (A. stiassnyae in Lake Afrera; one distributed across the entire area; one in Lake Abaeded; and one in the Shukoray River), but without clear large-scale geographic structure. However, Danakil Aphanius are clearly differentiated from A. dispar sensu stricto from the Sinai Peninsula. Geological evidence suggests that after the Late Pleistocene closure of the Danakil-Red Sea connection, increased post-glacial groundwater availability caused the formation of a brackish paleo-lake flooding the entire region below the -50 m contour. Fish populations previously isolated in coastal oases during glaciation were able to mix in the paleo-lake. Subsequently, in a more arid phase starting ∼7300 BP, paleo-lake regression isolated fishes in separate drainages, triggering their still ongoing diversification.
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Affiliation(s)
- Giorgio Chiozzi
- a Dipartimento di Scienze della Terra e dell'Ambiente , Università degli Studi di Pavia , Pavia , Italy.,b Museo di Storia Naturale di Milano , Milano , Italy
| | - Melanie L J Stiassny
- c Department of Ichthyology , American Museum of Natural History , New York , NY , USA
| | - S Elizabeth Alter
- c Department of Ichthyology , American Museum of Natural History , New York , NY , USA.,d Department of Biology , York College and the Graduate Center/The City University of New York , Jamaica , NY , USA
| | - Giuseppe De Marchi
- a Dipartimento di Scienze della Terra e dell'Ambiente , Università degli Studi di Pavia , Pavia , Italy
| | - Yohannes Mebrahtu
- e Research Division , Ministry of Marine Resources , Massawa , Eritrea
| | | | - Berhan Asmamaw
- f Ethiopian Biodiversity Institute , Addis Ababa , Ethiopia
| | - Mauro Fasola
- a Dipartimento di Scienze della Terra e dell'Ambiente , Università degli Studi di Pavia , Pavia , Italy
| | - Adriana Bellati
- a Dipartimento di Scienze della Terra e dell'Ambiente , Università degli Studi di Pavia , Pavia , Italy
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Soliman T, Aly W, Fahim RM, Berumen ML, Jenke-Kodama H, Bernardi G. Comparative population genetic structure of redbelly tilapia ( Coptodon zillii (Gervais, 1848)) from three different aquatic habitats in Egypt. Ecol Evol 2017; 7:11092-11099. [PMID: 29299284 PMCID: PMC5743693 DOI: 10.1002/ece3.3586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 11/21/2022] Open
Abstract
Recently, tilapia have become increasingly important in aquaculture and fisheries worldwide. They are one of the major protein sources in many African countries and are helping to combat malnutrition. Therefore, maintenance and conservation genetics of wild populations of tilapia are of great significance. In this study, we report the population genetic structure and genetic diversity of the redbelly tilapia (Coptodon zillii) in three different Egyptian aquatic environments: brackish (Lake Idku), marine (Al‐Max Bay), and freshwater (Lake Nasser). The habitat differences, environmental factors, and harvesting pressures are the main characteristics of the sampling sites. Three mitochondrial DNA markers (COI: cytochrome oxidase subunit I; the D‐loop; CYTB: cytochrome b) were used to assess population structure differences among the three populations. The population at Lake Nasser presented the highest genetic diversity (Hd = 0.8116, H = 6), and the marine population of Al‐Max Bay the lowest (Hd = 0.2391, H = 4) of the combined sequences. In addition, the phylogenetic haplotype network showed private haplotypes in each environmental habitat. Results presented here will be useful in aquaculture to introduce the appropriate broodstock for future aquaculture strategies of C. zillii. In addition, evidence of population structure may contribute to the management of tilapia fisheries in Egyptian waters.
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Affiliation(s)
- Taha Soliman
- Okinawa Institute of Science and Technology Graduate University (OIST) 1919-1 Tancha, Onna-son Kunigami-gun Okinawa Japan.,National Institute of Oceanography and Fisheries Cairo Egypt
| | - Walid Aly
- National Institute of Oceanography and Fisheries Cairo Egypt
| | - Reda M Fahim
- National Institute of Oceanography and Fisheries Cairo Egypt
| | - Michael L Berumen
- Division of Biological and Environmental Sciences and Engineering Red Sea Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Holger Jenke-Kodama
- Okinawa Institute of Science and Technology Graduate University (OIST) 1919-1 Tancha, Onna-son Kunigami-gun Okinawa Japan
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biologyns University of California Santa Cruz San ta Cruz CA USA
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15
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A new cichlid fish in the Sahara: The Ounianga Serir lakes (Chad), a biodiversity hotspot in the desert. C R Biol 2016; 339:529-536. [DOI: 10.1016/j.crvi.2016.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/29/2016] [Accepted: 08/30/2016] [Indexed: 11/17/2022]
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16
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Gammerdinger WJ, Conte MA, Baroiller JF, D'Cotta H, Kocher TD. Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron. BMC Genomics 2016; 17:808. [PMID: 27756226 PMCID: PMC5070092 DOI: 10.1186/s12864-016-3163-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 10/13/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation. RESULTS We found that Sarotherodon melanotheron segregates an XY system on LG1 in the same region identified in Oreochromis niloticus. Both species have higher densities of sex-patterned SNPs, as well as elevated number of ancestral copy number variants in this region when compared to the rest of the genome, but the pattern of differentiation along LG1 differs between species. The number of sex-patterned SNPs shared by the two species is small, but larger than expected by chance, suggesting that a novel Y-chromosome arose just before the divergence of the two species. We identified a shared sex-patterned SNP that alters a Gata4 binding site near Wilms tumor protein that might be responsible for sex-determination. CONCLUSIONS Shared sex-patterned SNPs, insertions and deletions suggest an ancestral sex-determination system that is common to both S. melanotheron and O. niloticus. Functional analyses are needed to evaluate shared SNPs near candidate genes that might play a role in sex-determination of these species. Interspecific variation in the sex chromosomes of tilapia species provides an excellent model system for understanding the evolution of vertebrate sex chromosomes.
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Affiliation(s)
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | | | | | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
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17
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Kide NG, Dunz A, Agnèse JF, Dilyte J, Pariselle A, Carneiro C, Correia E, Brito JC, Yarba LO, Kone Y, Durand JD. Cichlids of the Banc d'Arguin National Park, Mauritania: insight into the diversity of the genus Coptodon. JOURNAL OF FISH BIOLOGY 2016; 88:1369-1393. [PMID: 26856797 DOI: 10.1111/jfb.12899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
To determine the species diversity of cichlids in the Banc d'Arguin National Park (PNBA) and their phylogenetic relationships with other species in West Africa, a morphometric and meristic and molecular phylogenetic study was conducted. Both approaches not only confirm the presence of Sarotherodon melanotheron in PNBA but also demonstrate the presence of a second species from the genus Coptodon. While morphometric characteristics match the description of the Guinean tilapia Coptodon guineensis, phylogenetic reconstructions based on three mitochondrial and one nuclear DNA fragment demonstrate that C. guineensis is paraphyletic over its range. Because different lineages of C. guineensis are allopatric, the distribution of C. guineensis should be restricted to Ghana and Côte d'Ivoire. The many other lineages of this species should be considered as C. sp. aff. guineensis.
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Affiliation(s)
- N G Kide
- Université Abdel Maleck Essaâdi - Faculté des Sciences, Département de Biologie, Laboratoire Biologie Appliqué et Pathologie, Tétouan, Morocco
| | - A Dunz
- Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstr. 21, 81247, München, Germany
| | - J-F Agnèse
- Institut de Recherche pour le Développement (IRD), Université Montpellier, UMR 226, Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, CC 65, F-34095, Montpellier cedex 5, France
| | - J Dilyte
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - A Pariselle
- Institut de Recherche pour le Développement (IRD), Université Montpellier, UMR 226, Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, CC 65, F-34095, Montpellier cedex 5, France
- IRD, ISE-M, BP 1857, Yaoundé, Cameroon
| | - C Carneiro
- Observatoire du Parc National du Banc d'Arguin, Nouakchott, Mauritania
| | - E Correia
- Observatoire du Parc National du Banc d'Arguin, Nouakchott, Mauritania
| | - J C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - L O Yarba
- Observatoire du Parc National du Banc d'Arguin, Nouakchott, Mauritania
| | - Y Kone
- Faculté des Sciences de l'Université de Nouakchott, Nouakchott, Mauritania
| | - J-D Durand
- Institut de Recherche pour le Développement (IRD), Université Montpellier, UMR MARBEC, Place Eugène Bataillon, CC 93, F-34095, Montpellier cedex 5, France
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18
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Identification of wild tilapia species in the main rivers of south China using mitochondrial control region sequence and morphology. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Maranan JBD, Basiao ZU, Quilang JP. DNA barcoding of feral tilapias in Philippine lakes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4302-4313. [PMID: 26457820 DOI: 10.3109/19401736.2015.1089478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tilapia (Oreochromis mossambicus) was first introduced to the Philippines in 1950 for aquaculture. Since then, other species of tilapia have been introduced to the country and some of them (mainly Oreochromis niloticus) have become established in lakes and other water bodies. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene was done to assess the reliability of morphological identification and the degree of introgression among feral tilapias (Oreochromis spp.) in seven major Philippine lakes, namely Laguna de Bay, Lake Lanao, Taal Lake, Lake Mainit, Lake Naujan, Lake Bato, and Lake Buhi. Specimens were also collected from a private hatchery in Sual, Pangasinan to serve as reference. Morphological traits, Nucleotide BLAST (BLASTn), and Translated BLAST (BLASTx) analyses were used to classify the specimens. A Neighbor-Joining tree was constructed using the Kimura 2-Parameter method, incorporating 66 COI sequences generated from the study and 20 additional reference sequences obtained from GenBank. Three Oreochromis clusters were obtained and were classified as the O. niloticus group, O. mossambicus group, and O. aureus group, with bootstrap support values of 99%, 74%, and 99%, respectively. The mean K2P genetic distances within each group were 0.008%, 0.959%, and 0.086%, respectively. The clustering of COI sequences generated from this study corresponded with the results of the BLASTn analysis. Oreochromis hybrids were also found in all the lakes. The study highlights the usefulness of DNA barcoding for molecular identification and detection of introgressed individuals, with potential applications in management of feral stocks.
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Affiliation(s)
- Justin Bryan D Maranan
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
| | - Zubaida U Basiao
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
| | - Jonas P Quilang
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
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20
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Kinaro ZO, Xue L, Volatiana JA. Complete mitochondrial DNA sequences of the Victoria tilapia (Oreochromis variabilis) and Redbelly Tilapia (Tilapia zilli): genome characterization and phylogeny analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2455-7. [PMID: 27158785 DOI: 10.3109/19401736.2015.1033695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Cichlid fishes have played an important role in evolutionary biology, population studies and aquaculture industry with East African species representing a model suited for studying adaptive radiation and speciation for cichlid genome projects in which closely related genomes are fast emerging presenting questions on phenotype-genotype relations. The complete mitochondrial genomes presented here are for two closely related but eco-morphologically distinct Lake Victoria basin cichlids, Oreochromis variabilis, an endangered native species and Tilapia zilli, an invasive species, both of which are important economic fishes in local areas. The complete mitochondrial genomes determined for O. variabilis and T. zilli are 16 626 and 16,619 bp, respectively. Both the mitogenomes contain 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a non-coding control region, which are typical of vertebrate mitogenomes. Phylogenetic analyses of the two species revealed that though both lie within family Cichlidae, they are remotely related.
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Affiliation(s)
- Zachary Omambia Kinaro
- a Department of Aquaculture , College of Marine Sciences, Ningbo University , Ningbo , Zhejiang , China .,b Directorate of Fisheries, Kisii County Government, Kisii , Kenya , and
| | - Liangyi Xue
- a Department of Aquaculture , College of Marine Sciences, Ningbo University , Ningbo , Zhejiang , China .,c Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University , Ningbo , Zhejiang , China
| | - Josies Ancella Volatiana
- a Department of Aquaculture , College of Marine Sciences, Ningbo University , Ningbo , Zhejiang , China
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21
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Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol Ecol 2015; 24:3421-40. [PMID: 25997156 PMCID: PMC4973668 DOI: 10.1111/mec.13247] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022]
Abstract
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.
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Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, Bern, 3005, Switzerland
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Timothee Cezard
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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22
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Ronkin D, Seroussi E, Nitzan T, Doron-Faigenboim A, Cnaani A. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 13:35-43. [DOI: 10.1016/j.cbd.2015.01.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 11/27/2022]
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23
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Ovenden JR, Macbeth GM, Pope L, Thuesen P, Street R, Broderick D. Translocation between freshwater catchments has facilitated the spread of tilapia in eastern Australia. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0754-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Genetic and morphological analyses indicate high population mixing in the endangered cichlid Alcolapia flock of East Africa. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0551-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Dunz AR, Schliewen UK. Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”. Mol Phylogenet Evol 2013; 68:64-80. [DOI: 10.1016/j.ympev.2013.03.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 11/24/2022]
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26
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Firmat C, Alibert P, Losseau M, Baroiller JF, Schliewen UK. Successive invasion-mediated interspecific hybridizations and population structure in the endangered cichlid Oreochromis mossambicus. PLoS One 2013; 8:e63880. [PMID: 23671704 PMCID: PMC3650077 DOI: 10.1371/journal.pone.0063880] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 04/08/2013] [Indexed: 01/09/2023] Open
Abstract
Hybridization between invasive and native species accounts among the major and pernicious threats to biodiversity. The Mozambique tilapia Oreochromis mossambicus, a widely used freshwater aquaculture species, is especially imperiled by this phenomenon since it is recognized by the IUCN as an endangered taxon due to genetic admixture with O. niloticus an invasive congeneric species. The Lower Limpopo and the intermittent Changane River (Mozambique) drain large wetlands of potentially great importance for conservation of O. mossambicus, but their populations have remained unstudied until today. Therefore we aimed (1) to estimate the autochthonous diversity and population structure among genetically pure O. mossambicus populations to provide a baseline for the conservation genetics of this endangered species, (2) to quantify and describe genetic variation of the invasive populations and investigate the most likely factors influencing their spread, (3) to identify O. mossambicus populations unaffected by hybridization. Bayesian assignment tests based on 423 AFLP loci and the distribution of 36 species-specific mitochondrial haplotypes both indicate a low frequency of invasive and hybrid genotypes throughout the system, but nevertheless reveal evidence for limited expansion of two alien species (O. niloticus and O. andersonii) and their hybrids in the Lower Limpopo. O. mossambicus populations with no traces of hybridization are identified. They exhibit a significant genetic structure. This contrasts with previously published estimates and provides rather promising auspices for the conservation of O. mossambicus. Especially, parts of the Upper Changane drainage and surrounding wetlands are identified as refugial zones for O. mossambicus populations. They should therefore receive high conservation priority and could represent valuable candidates for the development of aquaculture strains based on local genetic resources.
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Affiliation(s)
- Cyril Firmat
- UMR CNRS 6282 Biogéosciences - Université de Bourgogne, Dijon, France.
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27
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Cnaani A. The Tilapias' Chromosomes Influencing Sex Determination. Cytogenet Genome Res 2013; 141:195-205. [DOI: 10.1159/000355304] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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28
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Wu L, Yang J. Identifications of captive and wild tilapia species existing in Hawaii by mitochondrial DNA control region sequence. PLoS One 2012; 7:e51731. [PMID: 23251613 PMCID: PMC3520857 DOI: 10.1371/journal.pone.0051731] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 11/09/2012] [Indexed: 11/18/2022] Open
Abstract
Background The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis. Methodology/Principal Findings In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization. Conclusions/Significance This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species identification. The suspected tilapia hybrids that consist of O. niloticus are present in captive and wild populations in Hawaii.
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Affiliation(s)
- Liang Wu
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- College of Animal Science & Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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29
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Microsatellites Cross-Species Amplification across Some African Cichlids. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:870935. [PMID: 22701809 PMCID: PMC3373121 DOI: 10.1155/2012/870935] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/26/2012] [Indexed: 12/21/2022]
Abstract
The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P95) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.
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30
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Organization of Mhc class II A and B genes in the tilapiine fish Oreochromis. Immunogenetics 2012; 64:679-90. [DOI: 10.1007/s00251-012-0618-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
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31
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Mendlová M, Desdevises Y, Civáňová K, Pariselle A, Šimková A. Monogeneans of West African cichlid fish: evolution and cophylogenetic interactions. PLoS One 2012; 7:e37268. [PMID: 22662139 PMCID: PMC3356412 DOI: 10.1371/journal.pone.0037268] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/18/2012] [Indexed: 11/19/2022] Open
Abstract
The goals of this paper were to investigate phylogenetic and evolutionary patterns of cichlid fish from West Africa and their Cichlidogyrus and Scutogyrus monogenean parasites, to uncover the presence of host-parasite cospeciation and to assess the level of morphological adaptation in parasites. This required the following steps, each one representing specific objectives of this paper: (1) to build phylogenetic trees for Cichlidogyrus and Scutogyrus species based on ribosomal DNA sequences, (2) to investigate phylogenetic relationships within West African cichlid fish based on the analysis of mitochondrial cytochrome b DNA sequences, (3) to investigate host-parasite cophylogenetic history to gain clues on parasite speciation process, and (4) to investigate the link between the morphology of the attachment apparatus and parasite phylogeny. Phylogenetic analyses supported the monophyletic origin of the Cichlidogyrus/Scutogyrus group, and suggested that Cichlidogyrus is polyphyletic and that Scutogyrus is monophyletic. The phylogeny of Cichlidae supported the separation of mouthbrooders and substrate-brooders and is consistent with the hypothesis that the mouthbrooding behavior of Oreochromis and Sarotherodon evolved from substrate-brooding behavior. The mapping of morphological characters of the haptor onto the parasite phylogenetic tree suggests that the attachment organ has evolved from a very simple form to a more complex one. The cophylogenetic analyses indicated a significant fit between trees using distance-based tests, but no significant cospeciation signal using tree-based tests, suggesting the presence of parasite duplications and host switches on related host species. This shed some light on the diversification process of Cichlidogyrus species parasitizing West African cichlids.
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Affiliation(s)
- Monika Mendlová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Yves Desdevises
- UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls/Mer, France
- CNRS, UMR 7232, BIOM, Observatoire Océanologique, Banyuls/Mer, France
| | - Kristína Civáňová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Antoine Pariselle
- Institut des Sciences de l'Evolution, IRD-CNRS-UM2, Université Montpellier 2 CC065, Montpellier, France
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Enhancement of Functional Properties of Wami Tilapia (Oreochromis urolepis hornorum) Skin Gelatin at Different pH Values. FOOD BIOPROCESS TECH 2012. [DOI: 10.1007/s11947-012-0859-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Szitenberg A, Goren M, Huchon D. Mitochondrial and morphological variation of Tilapia zillii in Israel. BMC Res Notes 2012; 5:172. [PMID: 22469095 PMCID: PMC3412729 DOI: 10.1186/1756-0500-5-172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 04/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tilapia zillii is widespread in the East Levant inland aquatic systems as well as in artificial water reservoirs. In this study we explore the genetic and morphological variation of this widespread species, using mitochondrial control region sequences and meristic characters. We examine the hypothesis that T. zillii's population structure corresponds to the four Israeli aquatic systems. RESULTS Out of seven natural water bodies, only two were found to possess genetically divergent populations of T. zillii. In addition to its presence in fish farms, the species was found in two artificial recreational ponds which were supposed to have been stocked only with other fish species. In these two artificial habitats, the haplotype frequencies diverged significantly from those of natural populations. Finally, fish from the Dead Sea springs of Ne'ot HaKikar appear to differ both genetically and morphologically from fish of the same aquatic system but not from fish of other water systems. CONCLUSIONS Our results show that the population structure of T. zillii does not match the geography of the Israeli water-basins, with the exception of the Dead Sea and Kishon River, when considering natural populations only. The absence of a significant divergence between basins is discussed. Our results and observations suggest that the Ne'ot HaKikar Dead Sea population and those of artificial ponds could have originated from the "hitchhiking" of T. zillii, at the expense of some other cultivated tilapiine species.
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Affiliation(s)
- Amir Szitenberg
- Department of Zoology, Tel-Aviv University, Tel Aviv, Israel
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He A, Luo Y, Yang H, Liu L, Li S, Wang C. Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): genome characterization and phylogeny applications. Mol Biol Rep 2010; 38:2015-21. [PMID: 20857213 DOI: 10.1007/s11033-010-0324-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 09/03/2010] [Indexed: 01/25/2023]
Abstract
Cichlid fishes have played an important role in evolutionary biology and aquaculture industry. Nile tilapia (Oreochromis niloticus), blue tilapia (Oreochromis aureus) and Mozambique tilapia (Oreochromis mossambicus), the useful models in studying evolutionary biology within Cichlid fishes, are also mainly cultured species in aquaculture with great economic importance. In this paper, the complete nucleotide sequence of the mitochondrial genome for O. niloticus and O. aureus were determined and phylogenetic analyses from mitochondrial protein-coding genes were conducted to explore their phylogenetic relationship within Cichlids. The mitogenome is 16,625 bp for O. niloticus and 16,628 bp for O. aureus, containing the same gene order and an identical number of genes or regions with the other Cichlid fishes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one putative control region. Phylogenetic analyses using three different computational algorithms (maximum parsimony, maximum likelihood and Bayesian method) show O. niloticus and O. mossambicus are closely related, and O. aureus has remotely phylogenetic relationship from above two fishes.
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Affiliation(s)
- Anyuan He
- Key Laboratory of Aquatic Genetic Resources and Utilization, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
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Poletto AB, Ferreira IA, Cabral-de-Mello DC, Nakajima RT, Mazzuchelli J, Ribeiro HB, Venere PC, Nirchio M, Kocher TD, Martins C. Chromosome differentiation patterns during cichlid fish evolution. BMC Genet 2010; 11:50. [PMID: 20550671 PMCID: PMC2896337 DOI: 10.1186/1471-2156-11-50] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cichlid fishes have been the subject of increasing scientific interest because of their rapid adaptive radiation which has led to an extensive ecological diversity and their enormous importance to tropical and subtropical aquaculture. To increase our understanding of chromosome evolution among cichlid species, karyotypes of one Asian, 22 African, and 30 South American cichlid species were investigated, and chromosomal data of the family was reviewed. RESULTS Although there is extensive variation in the karyotypes of cichlid fishes (from 2n = 32 to 2n = 60 chromosomes), the modal chromosome number for South American species was 2n = 48 and the modal number for the African ones was 2n = 44. The only Asian species analyzed, Etroplus maculatus, was observed to have 46 chromosomes. The presence of one or two macro B chromosomes was detected in two African species. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA) gene revealed a variable number of clusters among species varying from two to six. CONCLUSIONS The karyotype diversification of cichlids seems to have occurred through several chromosomal rearrangements involving fissions, fusions and inversions. It was possible to identify karyotype markers for the subfamilies Pseudocrenilabrinae (African) and Cichlinae (American). The karyotype analyses did not clarify the phylogenetic relationship among the Cichlinae tribes. On the other hand, the two major groups of Pseudocrenilabrinae (tilapiine and haplochromine) were clearly discriminated based on the characteristics of their karyotypes. The cytogenetic mapping of 18S ribosomal RNA (18S rRNA) gene did not follow the chromosome diversification in the family. The dynamic evolution of the repeated units of rRNA genes generates patterns of chromosomal distribution that do not help follows the phylogenetic relationships among taxa. The presence of B chromosomes in cichlids is of particular interest because they may not be represented in the reference genome sequences currently being obtained.
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Affiliation(s)
- Andréia B Poletto
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Irani A Ferreira
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Diogo C Cabral-de-Mello
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Rafael T Nakajima
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Juliana Mazzuchelli
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Heraldo B Ribeiro
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Paulo C Venere
- UFMT - Universidade Federal de Mato Grosso, Instituto Universitário do Araguaia, Pontal do Araguaia, MT, Brazil
| | - Mauro Nirchio
- Universidad de Oriente, Escuela de Ciencias Aplicadas del Mar, Boca de Rio, Venezuela
| | - Thomas D Kocher
- University of Maryland, Department of Biology, College Park, MD 20742 USA
| | - Cesar Martins
- UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil
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Ocalewicz K, Mota-Velasco JC, Campos-Ramos R, Penman DJ. FISH and DAPI staining of the synaptonemal complex of the Nile tilapia (Oreochromis niloticus) allow orientation of the unpaired region of bivalent 1 observed during early pachytene. Chromosome Res 2009; 17:773-82. [PMID: 19714475 DOI: 10.1007/s10577-009-9071-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 08/03/2009] [Indexed: 11/25/2022]
Abstract
Bivalent 1 of the synaptonemal complex (SC) in XY male Oreochromis niloticus shows an unpaired terminal region in early pachytene. This appears to be related to recombination suppression around a sex determination locus. To allow more detailed analysis of this, and unpaired regions in the karyotype of other Oreochromis species, we developed techniques for FISH on SC preparations, combined with DAPI staining. DAPI staining identified presumptive centromeres in SC bivalents, which appeared to correspond to the positions observed in the mitotic karyotype (the kinetochores could be identified only sporadically in silver-stained EM SC images). Furthermore, two BAC clones containing Dmo (dmrt4) and OniY227 markers that hybridize to known positions in chromosome pair 1 in mitotic spreads (near the centromere, Flpter 0.25, and the putative sex-determination locus, Flpter 0.57, respectively) were used as FISH probes on SCs to verify that the presumptive centromere identified by DAPI staining was located in the expected position. Visualization of both the centromere and FISH signals on bivalent 1 allowed the unpaired region to be positioned at Flpter 0.80 to 1.00, demonstrating that the unpaired region is located in the distal part of the long arm(s). Finally, differences between mitotic and meiotic measurements are discussed.
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Affiliation(s)
- Konrad Ocalewicz
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
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37
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Schwarzer J, Misof B, Tautz D, Schliewen UK. The root of the East African cichlid radiations. BMC Evol Biol 2009; 9:186. [PMID: 19656365 PMCID: PMC2739198 DOI: 10.1186/1471-2148-9-186] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/05/2009] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND For decades cichlid fishes (Perciformes: Cichlidae) of the East African cichlid radiations (Teleostei: Cichlidae) have served as natural experimental subjects for the study of speciation processes and the search for potential speciation key factors. Despite numerous phylogenetic studies dealing with their intragroup relationships, surprisingly little is known about the phylogenetic placement and time of origin of this enigmatic group. We used multilocus DNA-sequence data from five nuclear and four mitochondrial genes and refined divergence time estimates to fill this knowledge gap. RESULTS In concordance with previous studies, the root of the East African cichlid radiations is nested within the so called "Tilapias", which is a paraphyletic assemblage. For the first time, we clarified tilapiine intragroup relationships and established three new monophyletic groups:"Oreochromini", "Boreotilapiini" and a group with a distribution center in East/Central Africa, the "Austrotilapiini". The latter is the founder lineage of the East African radiations and emerged at the Miocene/Oligocene boundary at about 14 to 26 mya. CONCLUSION Our results provide the first resolved hypothesis for the phylogenetic placement of the megadiverse East African cichlid radiations as well as for the world's second most important aquaculture species, the Nile Tilapia, Oreochromis niloticus. Our analyses constitute not only a robust basis for African cichlid phylogenetics and systematics, but provide a valid and necessary framework for upcoming comparative phylogenomic studies in evolutionary biology and aquaculture.
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Affiliation(s)
- Julia Schwarzer
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
- Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 München, Germany
| | - Bernhard Misof
- Biozentrum Grindel & Zoologisches Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Diethard Tautz
- Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Str. 2 24306 Plön, Germany
| | - Ulrich K Schliewen
- Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 München, Germany
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38
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Cnaani A, Kocher TD. Sex-linked markers and microsatellite locus duplication in the cichlid species Oreochromis tanganicae. Biol Lett 2009; 4:700-3. [PMID: 18700198 DOI: 10.1098/rsbl.2008.0286] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cichlid species of the genus Oreochromis vary in their genetic sex-determination systems. In this study, we used microsatellite DNA markers to characterize the sex-determination system in Oreochromis tanganicae. Markers on linkage group 3 were associated with phenotypic sex, with an inheritance pattern typical of a female heterogametic species (WZ-ZZ). Further, locus duplication was observed for two separate microsatellite markers on the sex chromosome. These results further advance our understanding of the rapidly evolving sex-determination systems among these closely related tilapia species.
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Affiliation(s)
- Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization, Bet-Dagan 50250, Israel.
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Samonte IE, Satta Y, Sato A, Tichy H, Takahata N, Klein J. Gene flow between species of Lake Victoria haplochromine fishes. Mol Biol Evol 2007; 24:2069-80. [PMID: 17652334 DOI: 10.1093/molbev/msm138] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The haplochromine cichlid fishes of Lake Victoria (LV), East Africa, are a textbook example of adaptive radiation-a rapid divergence of multiple morphologically distinguishable forms from a few founding lineages. The forms are generally believed to constitute a "flock" of several hundred reproductively isolated species in a dozen or so genera. This belief has, until now, not been subjected to a test, however. Here, we compare genetic variation at 11 loci in 10 haplochromine populations of 6 different species. Although the genetic diversity in the populations is quite high, using a variety of statistical tests, we find no evidence of genetic differentiation among the populations of LV haplochromines. On genetic distance trees, populations of the same species intermingle with those of different species. At the molecular level, the species are indistinguishable from one another. Genetic comparisons with closely related species in 2 crater lakes indicate that the species within LV continue exchanging genes. These observations have important implications for phylogenetic reconstruction. The approach used in this study is applicable to other instances of adaptive radiation.
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Affiliation(s)
- Irene E Samonte
- Biology Department and Center for Natural Sciences and Environmental Research, College of Science, De La Salle University-Manila, Manila, Philippines
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40
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D’Amato ME, Esterhuyse MM, van der Waal BCW, Brink D, Volckaert FAM. Hybridization and phylogeography of the Mozambique tilapia Oreochromis mossambicus in southern Africa evidenced by mitochondrial and microsatellite DNA genotyping. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9186-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sato A, Dongak R, Hao L, Takezaki N, Shintani S, Aoki T, Klein J. Mhc class I genes of the cichlid fish Oreochromis niloticus. Immunogenetics 2006; 58:917-28. [PMID: 17033824 DOI: 10.1007/s00251-006-0151-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 08/10/2006] [Indexed: 10/24/2022]
Abstract
In terms of number of species, perciform (perch-like) fishes are one of the most diversified groups of modern vertebrates. Within this group, the family Cichlidae is best known for its spectacular adaptive radiation in the great lakes of East Africa. The molecular tool kit used in the study of this radiation includes the major histocompatibility complex (Mhc) genes. To refine this tool, information about the organization of the Mhc regions is badly needed. In this study, the first step was taken toward providing such information for the Mhc class one regions of Oreochromis niloticus, a representative species of the tilapiine branch of the Cichlidae, for which good bacterial artificial chromosome library is available. Screening of the library with class I gene probes led to the identification and isolation of 31 class-I-positive clones. Sequencing of one of these clones and partial characterization of the remaining clones for the presence of class I exons resulted in the construction of two contigs representing the class I region of this species as well as identification of seven additional class-I-positive singleton clones. The O. niloticus genome was shown to contain at least 28 class I genes or gene fragments. The shorter of the two contigs was approximately 330 kb long and contained eight class I genes/gene fragments; the longer contig encompassed 1,200 kb of sequence and contained minimally 17 class I genes/gene fragments; three additional class I genes were found to be borne by a clone that might be part of the shorter contig.
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Affiliation(s)
- Akie Sato
- Tsurumi University School of Dental Medicine, 2-1-3 Tsurumi, Yokohama 230-8501, Japan.
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42
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WERNER NOAMY, MOKADY OFER. Swimming out of Africa: mitochondrial DNA evidence for late Pliocene dispersal of a cichlid from Central Africa to the Levant. Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00321.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Terai Y, Takezaki N, Mayer WE, Tichy H, Takahata N, Klein J, Okada N. Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs). J Mol Evol 2004; 58:64-78. [PMID: 14743315 DOI: 10.1007/s00239-003-2526-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2002] [Accepted: 07/21/2003] [Indexed: 10/26/2022]
Abstract
Genomic DNA libraries were prepared from two endemic species of Lake Victoria haplochromine (cichlid) fish and used to isolate and characterize a set of short interspersed elements (SINEs). The distribution and sequences of the SINEs were used to infer phylogenetic relationships among East African haplochromines. The SINE-based classification divides the fish into four groups, which, in order of their divergence from a stem lineage, are the endemic Lake Tanganyika flock (group 1); fish of the nonendemic, monotypic, widely distributed genus Astatoreochromis (group 2); the endemic Lake Malawi flock (group 3); and group 4, which contains fish from widely dispersed East African localities including Lakes Victoria, Edward, George, Albert, and Rukwa, as well as many rivers. The group 4 haplochromines are characterized by a subset of polymorphic SINEs, each of which is present in some individuals and absent in others of the same population at a given locality, the same morphologically defined species, and the same mtDNA-defined haplogroup. SINE-defined group 4 contains six of the seven previously described mtDNA haplogroups. One of the polymorphic SINEs appears to be fixed in the endemic Lake Victoria flock; four others display the presence-or-absence polymorphism within the species of this flock. These findings have implications for the origin of Lake Victoria cichlids and for their founding population sizes.
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Affiliation(s)
- Yohey Terai
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Falk TM, Teugels GG, Abban EK, Villwock W, Renwrantz L. Phylogeographic patterns in populations of the black-chinned tilapia complex (Teleostei, Cichlidae) from coastal areas in West Africa: support for the refuge zone theory. Mol Phylogenet Evol 2003; 27:81-92. [PMID: 12679073 DOI: 10.1016/s1055-7903(02)00369-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Within the tilapiines, a major African cichlid lineage, quite limited genetic informations are available on phylogenetic interrelationships and phylogeographical patterns at both macro- and micro-evolutionary scales. The present study examines the genetic diversity of the black-chinned tilapia complex from coastal areas in West Africa (Senegal to Congo-Brazzaville) based on mtDNA control region sequences. Phylogenetic inferences provide support for the monophyly of both taxa involved. It is suggested that Sarotherodon melanotheron and Sarotherodon nigripinnis have diverged probably since the early Pleistocene. The occurrence of the main intraspecific lineages could be dated back to about 500,000-900,000 years. Our data suggest that West African Pleistocene refuge zones may have strongly influenced the degree and level of genetic differentiation among populations and thus the observed phylogeographic patterns. The spatial distribution of mtDNA lineages and the centres of intrapopulational genetic diversity clearly correspond to proposed lowland refuge zones and core areas of Central Africa. Moreover, this study genetically supports the existence of Sarotherodon melanotheron leonensis for the first time and further confirms the validity of the most recently introduced subspecies, e.g., Sarotherodon nigripinnis dolloi.
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Affiliation(s)
- Thomas M Falk
- Zoologisches Institut und Zoologisches Museum der Universität Hamburg, Martin Luther King Pl 3, 20146 Hamburg, Germany.
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Rognon X, Guyomard R. Large extent of mitochondrial DNA transfer from Oreochromis aureus to O. niloticus in West Africa. Mol Ecol 2003; 12:435-45. [PMID: 12535094 DOI: 10.1046/j.1365-294x.2003.01739.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introgressive hybridization has an important evolutionary significance in terms of gene diversity and speciation. Among the major groups of vertebrates, fish show a strong propensity to hybridize. In order to highlight the possible occurrence of gene flow between two tilapia species, Oreochromis niloticus and O. aureus, a comparison of allozyme and mitochondrial DNA (mtDNA) polymorphism was performed on sympatric and allopatric populations of these two species. Nuclear data were congruent with the morphological identification of O. niloticus and O. aureus populations. In opposition, the mtDNA analysis resulted in two strictly differentiated groups which did not follow the morphological and nuclear DNA classification. The first group consisted of East African O. niloticus populations and the second included all the O. aureus populations and the West African O. niloticus populations. Moreover, in some cases, the same sequences were detected in both species. These data strongly support a differential introgression of mtDNA from O. aureus to O. niloticus involving all the West African area. This work points out the risk of misinterpretation of mtDNA or nuclear DNA data when only one single class of marker is used.
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Affiliation(s)
- X Rognon
- Département des Sciences Animales, Institut National Agronomique Paris-Grignon, 16 rue Claude Bernard, 75231 Paris cedex 05, France.
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