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Amoutchi AI, Kersten P, Vogt A, Kohlmann K, Kouamelan EP, Mehner T. Population genetics of the African snakehead fish Parachanna obscura along West Africa's water networks: Implications for sustainable management and conservation. Ecol Evol 2023; 13:e9724. [PMID: 36694547 PMCID: PMC9842884 DOI: 10.1002/ece3.9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023] Open
Abstract
An essential factor for aquatic conservation is genetic diversity or population divergence, which in natural populations reflects the interplay between geographical isolation with restricted gene flow and local evolution of populations. The long geological history of Africa may induce stronger among-population divergence and lower within-population divergence in fish populations of African watersheds. As an example, we studied population structure of the African snakehead fish Parachanna obscura. Our study aimed: (1) to develop a set of highly polymorphic microsatellite markers suitable for the analysis of genetic diversity among P. obscura and (2) to study the genetic diversity and structure of P. obscura populations from the West Africa region and mostly from Côte d'Ivoire, with respect to the effects of climate region and geographical distance on the genetic differentiation. A total of 259 specimens from 15 locations of P. obscura were collected over the West Africa region reflecting a high variability of pairwise geographical distances and variability of hydrological connectivity of the area. We developed a set of 21 polymorphic microsatellite markers for studying population genetics of the fish. The results showed relatively low intragenetic diversity for all the 15 locations, certainly attributable to confinement of fish in segregated catchments, resulting in limited gene flow. We also found evidence for local adaptation processes, suggested by five out of 21 microsatellite loci being under putative selection, according to BAYESCAN analysis. In turn, there was strong genetic differentiation (F ST > 0.5) among fish from most locations, reflecting the allopatric development in watersheds without hydraulic connectivity. Neighbor-joining dendrogram, Principal Coordinate Analysis, and analysis of ancestral groups by STRUCTURE suggested that the 15 locations can be divided into three clusters, mainly matching the dominant climate zones and the segregation of the watersheds in the region. The distinct genetic structure of the fish from the 15 locations obtained in this study suggests that conservation and sustainable management actions of this fish resource should avoid genetic mixing of potentially locally adapted populations.
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Affiliation(s)
- Amien Isaac Amoutchi
- West African Science Service Centre on Climate Change and Adapted Land Use (WASCAL) Graduate Research Program on Climate Change and BiodiversityUniversité Felix Houphouet‐BoignyAbidjanCôte d'Ivoire,Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Petra Kersten
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Asja Vogt
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Klaus Kohlmann
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Essetchi Paul Kouamelan
- Laboratoire d'Hydrobiologie, UFR BiosciencesUniversité Felix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Thomas Mehner
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
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2
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Tibihika PD, Meimberg H, Curto M. Understanding the translocation dynamics of Nile tilapia ( Oreochromis niloticus) and its ecological consequences in East Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2154169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Papius Dias Tibihika
- National Fisheries Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
- MARE−Marine and Environmental Sciences Centre, University of Lisbon, Lisbon, Portugal
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3
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Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Absence of Figla-like Gene Is Concordant with Femaleness in Cichlids Harboring the LG1 Sex-Determination System. Int J Mol Sci 2022; 23:ijms23147636. [PMID: 35886982 PMCID: PMC9316214 DOI: 10.3390/ijms23147636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Oreochromis niloticus has been used as a reference genome for studies of tilapia sex determination (SD) revealing segregating genetic loci on linkage groups (LGs) 1, 3, and 23. The master key regulator genes (MKR) underlying the SD regions on LGs 3 and 23 have been already found. To identify the MKR in fish that segregate for the LG1 XX/XY SD-system, we applied short variant discovery within the sequence reads of the genomic libraries of the Amherst hybrid stock, Coptodon zillii and Sarotherodon galilaeus, which were aligned to a 3-Mbp-region of the O. aureus genome. We obtained 66,372 variants of which six were concordant with the XX/XY model of SD and were conserved across these species, disclosing the male specific figla-like gene. We further validated this observation in O. mossambicus and in the Chitralada hybrid stock. Genome alignment of the 1252-bp transcript showed that the figla-like gene’s size was 2664 bp, and that its three exons were capable of encoding 99 amino acids including a 45-amino-acid basic helix–loop–helix domain that is typical of the ovary development regulator—factor-in-the-germline-alpha (FIGLA). In Amherst gonads, the figla-like gene was exclusively expressed in testes. Thus, the figla-like genomic presence determines male fate by interrupting the female developmental program. This indicates that the figla-like gene is the long-sought SD MKR on LG1.
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Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shay Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Correspondence:
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4
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Geraerts M, Vangestel C, Artois T, Fernandes JMDO, Jorissen MWP, Chocha Manda A, Danadu Mizani C, Smeets K, Snoeks J, Sonet G, Tingbao Y, Van Steenberge M, Vreven E, Lunkayilakio Wamuini S, Vanhove MPM, Huyse T. Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources. Mol Ecol 2022; 31:3304-3322. [PMID: 35460297 DOI: 10.1111/mec.16479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.
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Affiliation(s)
- Mare Geraerts
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Carl Vangestel
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unit, Ghent University, Ghent, Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Michiel W P Jorissen
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Auguste Chocha Manda
- Unité de recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Célestin Danadu Mizani
- Département d'Ecologie et Biodiversité des Ressources Aquatique, Centre de Surveillance de la Biodiversité (CSB), Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jos Snoeks
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Gontran Sonet
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Yang Tingbao
- Institute of Aquatic Economic Animals and Key Laboratory for Improved Variety Reproduction of Aquatic Economic Animals, Zhongshan University, Ghangzhou, China
| | - Maarten Van Steenberge
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Emmanuel Vreven
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Soleil Lunkayilakio Wamuini
- Département de Biologie, I.S.P. Mbanza-Ngungu, Mbanza-Ngungu, Democratic Republic of the Congo.,Functional and Evolutionary Morphology Laboratory, University of Liège, Liège, Belgium
| | - Maarten P M Vanhove
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
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5
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Ciezarek A, Ford AG, Etherington GJ, Kasozi N, Malinsky M, Mehta TK, Penso-Dolfin L, Ngatunga BP, Shechonge A, Tamatamah R, Haerty W, Di Palma F, Genner MJ, Turner GF. Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2022; 548:737637. [PMID: 35177872 PMCID: PMC8655616 DOI: 10.1016/j.aquaculture.2021.737637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.
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Affiliation(s)
- A. Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G.P. Ford
- Department of Life Sciences, Roehampton University, London SW15 4JD, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Abi Zonal Agricultural Research and Development Institute, P.O. Box 219, Arua, Uganda
| | - Milan Malinsky
- Zoological Institute, Department of Environmental Sciences, University of Basel, 4051 Basel, Switzerland
| | - Tarang K. Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Luca Penso-Dolfin
- Silence Therapeutics GmbH, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Benjamin P. Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), PO. Box 9750, Dar es Salaam. Tanzania
| | - Asilatu Shechonge
- Tanzania Fisheries Research Institute (TAFIRI), PO. Box 9750, Dar es Salaam. Tanzania
| | - Rashid Tamatamah
- Tanzania Fisheries Research Institute (TAFIRI), PO. Box 9750, Dar es Salaam. Tanzania
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - George F. Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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6
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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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7
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Blackwell T, Ford AGP, Ciezarek AG, Bradbeer SJ, Gracida Juarez CA, Smith AM, Ngatunga BP, Shechonge A, Tamatamah R, Etherington G, Haerty W, Di Palma F, Turner GF, Genner MJ. Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species. Mol Ecol 2020; 30:895-911. [PMID: 33063411 DOI: 10.1111/mec.15638] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe × niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.
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Affiliation(s)
| | - Antonia G P Ford
- Department of Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Adam G Ciezarek
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, UK
| | | | | | - Alan M Smith
- Department of Biological Sciences, University of Hull, Hull, UK
| | | | - Asilatu Shechonge
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Rashid Tamatamah
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | | | - Wilfried Haerty
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, UK
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, UK.,Department of Biological and Medical Sciences, University of East Anglia, Norwich, UK
| | - George F Turner
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
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8
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Nyinondi CS, Mtolera MSP, Mmochi AJ, Lopes Pinto FA, Houston RD, de Koning DJ, Palaiokostas C. Assessing the genetic diversity of farmed and wild Rufiji tilapia ( Oreochromis urolepis urolepis) populations using ddRAD sequencing. Ecol Evol 2020; 10:10044-10056. [PMID: 33005362 PMCID: PMC7520224 DOI: 10.1002/ece3.6664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022] Open
Abstract
Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F st = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p-value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross-validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.
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Affiliation(s)
- Christer S. Nyinondi
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Institute of Marine SciencesUniversity of Dar es SalaamZanzibarTanzania
| | | | - Aviti J. Mmochi
- Institute of Marine SciencesUniversity of Dar es SalaamZanzibarTanzania
| | - Fernando A. Lopes Pinto
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
| | - Dirk J. de Koning
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Christos Palaiokostas
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
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9
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Tibihika PD, Curto M, Alemayehu E, Waidbacher H, Masembe C, Akoll P, Meimberg H. Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations. BMC Evol Biol 2020; 20:16. [PMID: 32000675 PMCID: PMC6990601 DOI: 10.1186/s12862-020-1583-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. RESULTS All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. CONCLUSIONS The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.
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Affiliation(s)
- Papius Dias Tibihika
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
| | - Esayas Alemayehu
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33/DG, 1180 Wien, Austria
| | - Herwig Waidbacher
- National Fishery and Aquatic Life Research Centre, P.O. Box 64, Addis Ababa, Sebeta Ethiopia
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Peter Akoll
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
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10
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Kajungiro RA, Palaiokostas C, Pinto FAL, Mmochi AJ, Mtolera M, Houston RD, de Koning DJ. Population Structure and Genetic Diversity of Nile Tilapia ( Oreochromis niloticus) Strains Cultured in Tanzania. Front Genet 2019; 10:1269. [PMID: 31921307 PMCID: PMC6933018 DOI: 10.3389/fgene.2019.01269] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 11/18/2019] [Indexed: 01/15/2023] Open
Abstract
Understanding population structure and genetic diversity within and between local Nile tilapia lines cultured in Tanzania is important for sustainable aquaculture production. This study investigated the genetic structure and diversity among seven Nile tilapia populations in Tanzania (Karanga, Igunga, Ruhila, Fisheries Education and Training Agency, Tanzania Fisheries Research Institute, Kunduchi, and Lake Victoria). Double-digest restriction site-associated DNA (ddRAD) libraries were prepared from 140 individual fish (20 per population) and sequenced using an Illumina HiSeq 4000 resulting in the identification of 2,180 informative single nucleotide polymorphisms (SNPs). Pairwise Fst values revealed strong genetic differentiation between the closely related populations; FETA, Lake Victoria, and Igunga and those from TAFIRI and Karanga with values ranging between 0.45 and 0.55. Population structure was further evaluated using Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC). Admixture was detected among Karanga, Kunduchi, and Ruhila populations. A cross-validation approach (25% of individual fish from each population was considered of unknown origin) was conducted in order to test the efficiency of the SNP markers to correctly assign individual fish to the population of origin. The cross-validation procedure was repeated 10 times resulting in 77% of the tested individual fish being allocated to the correct population. Overall our results provide a new database of informative SNP markers for both conservation management and aquaculture activities of Nile tilapia strains in Tanzania.
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Affiliation(s)
- Redempta A. Kajungiro
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Aquatic Science and Fisheries, College of Agricultural Sciences and Fisheries Technology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fernando A. Lopes Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Aviti J. Mmochi
- Institute of Marine Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marten Mtolera
- Institute of Marine Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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11
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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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12
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Shechonge A, Ngatunga BP, Tamatamah R, Bradbeer SJ, Harrington J, Ford AGP, Turner GF, Genner MJ. Losing cichlid fish biodiversity: genetic and morphological homogenization of tilapia following colonization by introduced species. CONSERV GENET 2018; 19:1199-1209. [PMID: 30363773 PMCID: PMC6182432 DOI: 10.1007/s10592-018-1088-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/09/2018] [Indexed: 11/04/2022]
Abstract
Among the many negative impacts of invasive species, hybridization with indigenous species has increasingly become recognized as a major issue. However, relatively few studies have characterized the phenotypic outcomes of hybridization following biological invasions. Here we investigate the genetic and morphological consequences of stocking invasive tilapia species in two water bodies in central Tanzania. We sampled individuals from the Mindu Reservoir on the Ruvu river system, and at Kidatu on the Great Ruaha-Rufiji river system. We screened individuals at 16 microsatellite loci, and quantified morphology using geometric morphometrics and linear measurements. In both the Mindu and Kidatu systems, we identified evidence of hybridization between indigenous Wami tilapia (Oreochromis urolepis) and the introduced Nile tilapia (Oreochromis niloticus) or blue-spotted tilapia (Oreochromis leucostictus). At both sites, purebred individuals could largely be separated using geometric morphometric variables, with hybrids occupying a broad morphospace among the parental species. Our data demonstrate that the gene pools and phenotypic identity of the indigenous O. urolepis have been severely impacted by the stocking of the invasive species. Given the lack of evidence for clear commercial benefits from stocking invasive tilapia species in waters already populated by indigenous congenerics, we suggest further spread of introduced species should be undertaken with considerable caution.
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Affiliation(s)
- Asilatu Shechonge
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Benjamin P. Ngatunga
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Rashid Tamatamah
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Stephanie J. Bradbeer
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Jack Harrington
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Antonia G. P. Ford
- Department of Life Sciences, Whitelands College, University of Roehampton, Holybourne Avenue, London, SW15 4JD UK
| | - George F. Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
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13
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Bradbeer SJ, Harrington J, Watson H, Warraich A, Shechonge A, Smith A, Tamatamah R, Ngatunga BP, Turner GF, Genner MJ. Limited hybridization between introduced and Critically Endangered indigenous tilapia fishes in northern Tanzania. HYDROBIOLOGIA 2018; 832:257-268. [PMID: 30880834 PMCID: PMC6394572 DOI: 10.1007/s10750-018-3572-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 06/09/2023]
Abstract
Hybridization between introduced and indigenous species can lead to loss of unique genetic resources and precipitate extinction. In Tanzania, the Nile tilapia (Oreochromis niloticus) and blue-spotted tilapia (Oreochromis leucostictus) have been widely introduced to non-native habitats for aquaculture and development of capture fisheries. Here, we aimed to quantify interspecific hybridization between these introduced species and the indigenous species Oreochromis esculentus, Oreochromis jipe and Oreochromis korogwe. In the Pangani basin, several hybrids were observed (O. niloticus × O. jipe, O. leucostictus × O. jipe, O. niloticus × O. korogwe), although hybrids were relatively uncommon within samples relative to purebreds. Hybrids between the native O. jipe × O. korogwe were also observed. In the Lake Victoria basin, no evidence of hybrids was found. Analysis of body shape using geometric morphometrics suggested that although purebreds could be discriminated from one another, hybrids could not be readily identified on body and head shape alone. These results provide the first evidence of hybridization between the introduced species and the Critically Endangered O. jipe in Tanzania. Given uncertainty regarding benefits of introduced species over large-bodied indigenous species in aquaculture and capture fisheries, we suggest that future introductions of hybridization-prone species should be carefully evaluated.
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Affiliation(s)
- Stephanie J. Bradbeer
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
- School of Biology, University of Leeds, Miall Building, Leeds, LS2 9JT UK
| | - Jack Harrington
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Henry Watson
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Abrahim Warraich
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Asilatu Shechonge
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Alan Smith
- Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Hull, HU5 7RX UK
| | - Rashid Tamatamah
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Benjamin P. Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - George F. Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
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14
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Shechonge A, Ngatunga BP, Bradbeer SJ, Day JJ, Freer JJ, Ford AGP, Kihedu J, Richmond T, Mzighani S, Smith AM, Sweke EA, Tamatamah R, Tyers AM, Turner GF, Genner MJ. Widespread colonisation of Tanzanian catchments by introduced Oreochromis tilapia fishes: the legacy from decades of deliberate introduction. HYDROBIOLOGIA 2018; 832:235-253. [PMID: 30880833 PMCID: PMC6394791 DOI: 10.1007/s10750-018-3597-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 06/09/2023]
Abstract
From the 1950s onwards, programmes to promote aquaculture and improve capture fisheries in East Africa have relied heavily on the promise held by introduced species. In Tanzania these introductions have been poorly documented. Here we report the findings of surveys of inland water bodies across Tanzania between 2011 and 2017 that clarify distributions of tilapiine cichlids of the genus Oreochromis. We identified Oreochromis from 123 sampling locations, including 14 taxa restricted to their native range and three species that have established populations beyond their native range. Of these three species, the only exotic species found was blue-spotted tilapia (Oreochromis leucostictus), while Nile tilapia (Oreochromis niloticus) and Singida tilapia (Oreochromis esculentus), which are both naturally found within the country of Tanzania, have been translocated beyond their native range. Using our records, we developed models of suitable habitat for the introduced species based on recent (1960-1990) and projected (2050, 2070) East African climate. These models indicated that presence of suitable habitat for these introduced species will persist and potentially expand across the region. The clarification of distributions provided here can help inform the monitoring and management of biodiversity, and inform policy related to the future role of introduced species in fisheries and aquaculture.
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Affiliation(s)
- Asilatu Shechonge
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Benjamin P. Ngatunga
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Stephanie J. Bradbeer
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Julia J. Day
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT UK
| | - Jennifer J. Freer
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Antonia G. P. Ford
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
- Department of Life Sciences, Centre for Research in Ecology, Whitelands College, University of Roehampton, Holybourne Avenue, London, SW15 4JD UK
| | - Jonathan Kihedu
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Tabitha Richmond
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Semvua Mzighani
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Alan M. Smith
- Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Hull, HU5 7RX UK
| | - Emmanuel A. Sweke
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Rashid Tamatamah
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Alexandra M. Tyers
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | - George F. Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
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15
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An important natural genetic resource of Oreochromis niloticus (Linnaeus, 1758) threatened by aquaculture activities in Loboi drainage, Kenya. PLoS One 2014; 9:e106972. [PMID: 25222491 PMCID: PMC4164595 DOI: 10.1371/journal.pone.0106972] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/04/2014] [Indexed: 11/19/2022] Open
Abstract
The need to improve food security in Africa through culture of tilapias has led to transfer of different species from their natural ranges causing negative impacts on wild fish genetic resources. Loboi swamp in Kenya is fed by three hot springs: Lake Bogoria Hotel, Chelaba and Turtle Springs, hosting natural populations of Oreochromis niloticus. The present study aimed at better genetic characterization of these threatened populations. Partial mtDNA sequences of the D-loop region and variations at 16 microsatellite loci were assessed in the three hot spring populations and compared with three other natural populations of O. niloticus in the region. Results obtained indicated that the hot spring populations had mitochondrial and nuclear genetic variability similar to or higher than the large closely related populations. This may be attributed to the perennial nature of the hot springs, which do not depend on rainfall but rather receive permanent water supply from deep aquifers. The study also revealed that gene flow between the three different hot spring populations was sufficiently low thus allowing their differentiation. This differentiation was unexpected considering the very close proximity of the springs to each other. It is possible that the swamp creates a barrier to free movement of fish from one spring to the other thereby diminishing gene flow. Finally, the most surprising and worrying results were that the three hot spring populations are introgressed by mtDNA genes of O. leucostictus, while microsatellite analysis suggested that some nuclear genes may also have crossed the species barrier. It is very likely that the recent intensification of aquaculture activities in the Loboi drainage may be responsible for these introgressions. Taking into account the importance of these new genetic resources, protection and management actions of the Loboi swamp should be accorded top priority to prevent the loss of these spring populations.
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16
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Hashimoto DT, Senhorini JA, Foresti F, Martínez P, Porto-Foresti F. Genetic identification of F1 and post-F1 serrasalmid juvenile hybrids in Brazilian aquaculture. PLoS One 2014; 9:e89902. [PMID: 24594674 PMCID: PMC3940687 DOI: 10.1371/journal.pone.0089902] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 01/29/2014] [Indexed: 11/18/2022] Open
Abstract
Juvenile fish trade monitoring is an important task on Brazilian fish farms. However, the identification of juvenile fish through morphological analysis is not feasible, particularly between interspecific hybrids and pure species individuals, making the monitoring of these individuals difficult. Hybrids can be erroneously identified as pure species in breeding facilities, which might reduce production on farms and negatively affect native populations due to escapes or stocking practices. In the present study, we used a multi-approach analysis (molecular and cytogenetic markers) to identify juveniles of three serrasalmid species (Colossoma macropomum, Piaractus mesopotamicus and Piaractus brachypomus) and their hybrids in different stocks purchased from three seed producers in Brazil. The main findings of this study were the detection of intergenus backcrossing between the hybrid ♀ patinga (P. mesopotamicus×P. brachypomus)×♂ C. macropomum and the occurrence of one hybrid triploid individual. This atypical specimen might result from automixis, a mechanism that produces unreduced gametes in some organisms. Moreover, molecular identification indicated that hybrid individuals are traded as pure species or other types of interspecific hybrids, particularly post-F1 individuals. These results show that serrasalmid fish genomes exhibit high genetic heterogeneity, and multi-approach methods and regulators could improve the surveillance of the production and trade of fish species and their hybrids, thereby facilitating the sustainable development of fish farming.
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Affiliation(s)
- Diogo Teruo Hashimoto
- Centro de Aquicultura, Universidade Estadual Paulista, (UNESP), Campus de Jaboticabal, Jaboticabal, SP, Brazil
- * E-mail:
| | - José Augusto Senhorini
- Centro de Pesquisa e Gestão de Recursos Pesqueiros Continentais, Instituto Chico Mendes de Conservação da Biodiversidade, Pirassununga, SP, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
| | - Paulino Martínez
- Departamento de Genética, Universidad de Santiago de Compostela, Facultad de Veterinaria, Lugo, Spain
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, (UNESP), Campus de Bauru, Bauru, SP, Brazil
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17
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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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18
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DUPUIS JULIANR, ROE AMANDAD, SPERLING FELIXAH. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol 2012; 21:4422-36. [DOI: 10.1111/j.1365-294x.2012.05642.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Jones JC, Perez-Sato JA, Meyer A. A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico. Mol Ecol 2012; 21:2692-712. [PMID: 22494472 DOI: 10.1111/j.1365-294x.2012.05571.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hybrid speciation may contribute significantly to generating biodiversity, but only a few well-documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae- the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation-by-distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.
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Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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20
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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