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Ciezarek AG, Mehta TK, Man A, Ford AGP, Kavembe GD, Kasozi N, Ngatunga BP, Shechonge AH, Tamatamah R, Nyingi DW, Cnaani A, Ndiwa TC, Di Palma F, Turner GF, Genner MJ, Haerty W. Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes. Mol Biol Evol 2024; 41:msae116. [PMID: 38865496 PMCID: PMC11221657 DOI: 10.1093/molbev/msae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.
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Affiliation(s)
- Adam G Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Centre of Environment, Fisheries and Aquaculture Science (Cefas), Scientific Advice for Fisheries Management Team (SAFM), Lowestoft NR33 0H5, UK
| | - Tarang K Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Angela Man
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G P Ford
- School of Life and Health Sciences, Whitelands College, University of Roehampton, London SW15 4NA, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Buginyanya Zonal Agricultural Research and Development Institute, Mbale, Uganda
| | | | | | | | | | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion 7528809, Israel
| | - Titus C Ndiwa
- Department of Clinical Studies, University of Nairobi, Nairobi, Kenya
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - George F Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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Sawe S, Amasi A, Wynants M. Assessment of Potentially Toxic Metals in Fish from Lake Manyara, Northern Tanzania. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2023; 111:39. [PMID: 37704929 PMCID: PMC10499695 DOI: 10.1007/s00128-023-03794-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]
Abstract
Elemental tracer concentrations of copper, lead, nickel and zinc, were assessed in the muscles of Oreochromis amphimelas and Clarias gariepinus from Lake Manyara, Tanzania, to evaluate their safety to consumers, specifically humans. Results revealed that no elemental concentrations exceeded the FAO permissible levels, indicating fish from all sites are safe for human consumption. However, based on the highest found concentration of Pb, we recommend a maximum consumption of 2.2 kg of fish from Lake Manyara per week. No significant differences were observed in the metal concentrations between the two fish species, suggesting there is no bioaccumulation in the food chain. Moreover, no significant differences were found between fish landing sites, indicating there are no regions in the lake with higher pollution. These findings indicate that PTM concentrations have not increased to toxic levels due to increased mobilisation from the catchment. Continued monitoring of potential toxic metal concentrations in fish is recommended due to endorheic nature of Lake Manyara and increasing anthropogenic activities in its catchment area.
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Affiliation(s)
- Shovi Sawe
- Department of Research and Development, Tanzania Atomic Energy Commission, P O Box 743, Arusha, Tanzania
| | - Aloyce Amasi
- School of Materials, Energy, Water and Environmental Science, The Nelson Mandela African Institution of Science and Technology, P.O. Box 447, 23311 Arusha, Tanzania
| | - Maarten Wynants
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, 75007 Uppsala, Sweden
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3
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Mehta TK, Man A, Ciezarek A, Ranson K, Penman D, Di-Palma F, Haerty W. Chromatin accessibility in gill tissue identifies candidate genes and loci associated with aquaculture relevant traits in tilapia. Genomics 2023; 115:110633. [PMID: 37121445 DOI: 10.1016/j.ygeno.2023.110633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/02/2023]
Abstract
The Nile tilapia (Oreochromis niloticus) accounts for ∼9% of global freshwater finfish production however, extreme cold weather and decreasing freshwater resources has created the need to develop resilient strains. By determining the genetic bases of aquaculture relevant traits, we can genotype and breed desirable traits into farmed strains. We generated ATAC-seq and gene expression data from O. niloticus gill tissues, and through the integration of SNPs from 27 tilapia species, identified 1168 highly expressed genes (4% of all Nile tilapia genes) with highly accessible promoter regions with functional variation at transcription factor binding sites (TFBSs). Regulatory variation at these TFBSs is likely driving gene expression differences associated with tilapia gill adaptations, and differentially segregate in freshwater and euryhaline tilapia species. The generation of novel integrative data revealed candidate genes e.g., prolactin receptor 1 and claudin-h, genetic relationships, and loci associated with aquaculture relevant traits like salinity and osmotic stress acclimation.
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Affiliation(s)
| | | | | | - Keith Ranson
- Institute of Aquaculture, University of Stirling, Scotland, UK
| | - David Penman
- Institute of Aquaculture, University of Stirling, Scotland, UK
| | - Federica Di-Palma
- School of Biological Sciences, University of East Anglia, Norwich, UK; Genome British Columbia, Vancouver, Canada
| | - Wilfried Haerty
- Earlham Institute (EI), Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK
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4
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Nile Tilapia, Oreochromis niloticus (Teleostei: Cichlidae): a threat to native fishes of Lake Malawi? Biol Invasions 2022. [DOI: 10.1007/s10530-022-02756-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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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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Simulated encounters with a novel competitor reveal the potential for maladaptive behavioural responses to invasive species. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02690-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractDuring the early stage of biological invasions, interactions occur between native and non-native species that do not share an evolutionary history. This can result in ecological naïveté, causing native species to exhibit maladaptive behavioural responses to novel enemies, leading to negative consequences for individual fitness and ecosystem function. The behavioural response of native to non-native species during novel encounters can determine the impact of non-native species, and restrict or facilitate their establishment. In this study we simulated novel encounters between a widespread invasive fish species, the Nile tilapia (Oreochromis niloticus), and a threatened native Manyara tilapia (Oreochromis amphimelas). In the first experiment single adult O. niloticus were presented with a stimulus chamber (a transparent plastic cylinder) which was empty during control trials and contained a pair of juvenile O. amphimelas in stimulus trials. In the second experiment, the reciprocal set up was used, with pairs of juvenile O. amphimelas as the focal species and adult O. niloticus as the stimulus. Both species approached the stimulus chamber more readily during stimulus trials, a behavioural response which would increase the prevalence of interspecific interactions in situ. This included physical aggression, observed from the competitively dominant O. niloticus towards O. amphimelas. Despite an initial lack of fear shown by O. amphimelas, close inspection of the stimulus chamber often resulted in an energetically costly dart response. Under field conditions we predict that naïve native individuals may readily approach O. niloticus, increasing the likelihood of interactions and exacerbating widely reported negative outcomes.
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Tesfaye G, Curto M, Meulenbroek P, Englmaier GK, Tibihika PD, Alemayehu E, Getahun A, Meimberg H. Genetic diversity of Nile tilapia (Oreochromis niloticus) populations in Ethiopia: insights from nuclear DNA microsatellites and implications for conservation. BMC Ecol Evol 2021; 21:113. [PMID: 34098870 PMCID: PMC8183085 DOI: 10.1186/s12862-021-01829-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/09/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques. RESULTS The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High FST values (Global FST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq. CONCLUSIONS The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.
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Affiliation(s)
- Genanaw Tesfaye
- EIAR - National Fisheries and Other Aquatic Life Research Center, P.O. Box 64, Sebeta, Ethiopia.
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Vienna, Gregor Mendel-Straße 33, 1180, Vienna, Austria
- MARE-Marine and Environmental Sciences Centre, Universidade de Lisboa, Lisbon, Portugal
| | - Paul Meulenbroek
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel Straße 33, 1180, Vienna, Austria.
- WasserCluster Lunz - biologische Station, Lunz am See, Dr. Carl Kupelwieser Prom. 5, 3293, Lunz/See, Austria.
| | - Gernot K Englmaier
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010, Graz, Austria
| | | | - Esayas Alemayehu
- EIAR - National Fisheries and Other Aquatic Life Research Center, P.O. Box 64, Sebeta, Ethiopia
| | - Abebe Getahun
- Department of Zoological Sciences, Addis Ababa University, 1000, Addis Ababa, Ethiopia
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Vienna, Gregor Mendel-Straße 33, 1180, Vienna, Austria
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8
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Wing JDB, Champneys TS, Ioannou CC. The impact of turbidity on foraging and risk taking in the invasive Nile tilapia (Oreochromis niloticus) and a threatened native cichlid (Oreochromis amphimelas). Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-02984-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Anthropogenic activity can increase water turbidity, changing fish behaviour by reducing visibility. The spread of invasive species is also facilitated by human activity, further increasing the pressure on native species. In two experiments, we measured the foraging efficiency, risk perception and inter-individual consistency of risk-taking (personality variation in boldness) of an invasive species, the Nile tilapia (Oreochromis niloticus), and a threatened tilapia, the Manyara tilapia (Oreochromis amphimelas), in clear and turbid water. In experiment one, O. niloticus was faster to initiate feeding, encountered more food items and consumed more than O. amphimelas. The latency to start foraging by O. niloticus decreased in turbid water. Turbidity did not affect the latency to start foraging in O. amphimelas but the number of food items they encountered was highest at the intermediate turbidity. There was however no significant effect of turbidity in either species on the total food consumed. In contrast to this foraging context, in experiment two with a refuge and no food available, risk taking behaviour was similar in both species and they both responded with similarly reduced risk taking in turbid water. Evidence of personality variation was weak, being observed only in O. amphimelas when first leaving the shelter in turbid water. Overall, species differences were greater in the foraging context but turbidity was more important in the risk-taking context. O. amphimelas is more sensitive to turbidity during foraging, and O. niloticus is likely to have a competitive advantage in foraging situations, especially in degraded turbid habitats.
Significance statement
Under human-induced environmental change, native species are often exposed to multiple stressors. Here, we tested the responses of two cichlid fish to increasing turbidity, the Nile tilapia (Oreochromis niloticus), which is invasive throughout the tropics, and the Manyara tilapia (Oreochromis amphimelas), a threatened species, indigenous to Tanzania. We found that turbidity was beneficial to the foraging of O. niloticus, which in both clear and turbid water consumed and encountered more food than O. amphimelas. In contrast, without food present, both species displayed similar responses of increased risk perception in turbid water with little evidence of personality variation between individuals in either species. Our results suggest that invasive species tolerant of degraded habitats may outcompete less well-adapted native species for food.
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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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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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11
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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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12
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Moshobane MC, Nnzeru LR, Nelukalo K, Mothapo NP. Patterns of permit requests and issuance for regulated alien and invasive species in South Africa for the period 2015‐2018. Afr J Ecol 2020. [DOI: 10.1111/aje.12720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Moleseng C. Moshobane
- South African National Biodiversity Institute Pretoria National Botanical Garden Pretoria South Africa
| | - Livhuwani R. Nnzeru
- Department of Environmental Affairs Biosecurity Directorate Cape Town South Africa
| | | | - Natasha P. Mothapo
- Division for Research and Development Stellenbosch University Stellenbosch South Africa
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13
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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 2020. [PMID: 31921307 DOI: 10.3389/fgene.2019.01269.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] 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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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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15
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Abstract
The United Republic of Tanzania (Tanzania) is rich in freshwater resources and biodiversity. In this article, we highlight the importance of Tanzanian rivers and make a case for the conservation of the freshwater and terrestrial species that rely on these rivers. We provide an overview of current knowledge on Tanzanian rivers and discuss progress towards implementation of the National Water Policy (2002) and Water Management Act (2009), two legislative instruments that have motivated environmental flow assessments on at least six major rivers and offer legal backing for river conservation. We examine major challenges that pose significant threats to water security for river ecosystems and humans in Tanzania, among those: (1) human population growth, (2) agricultural expansion, (3) river flow alterations, (4) industrialization, (5) introduced species, and (6) climate change. We conclude by offering recommendations for future river conservation efforts in Tanzania.
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Lind CE, Agyakwah SK, Attipoe FY, Nugent C, Crooijmans RPMA, Toguyeni A. Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa. Sci Rep 2019; 9:16767. [PMID: 31727970 PMCID: PMC6856548 DOI: 10.1038/s41598-019-53295-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/29/2019] [Indexed: 01/17/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d’Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.
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Affiliation(s)
- Curtis E Lind
- WorldFish, Jalan Batu Maung, Batu Maung, 11960, Bayan Lepas, Penang, Malaysia. .,CSIRO Agriculture & Food, Castray Esplanade, Hobart, Australia.
| | - Seth K Agyakwah
- Aquaculture Research and Development Center (ARDEC), CSIR-Water Research Institute, PO Box 139, Akosombo, Ghana
| | - Felix Y Attipoe
- Aquaculture Research and Development Center (ARDEC), CSIR-Water Research Institute, PO Box 139, Akosombo, Ghana
| | - Christopher Nugent
- Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | | | - Aboubacar Toguyeni
- Centre International de Recherche-Développement sur l'Elevage en zone Subhumide (CIRDES) 01 BP 454 Bobo-Dioulasso 01, Bobo-Dioulasso, Burkina Faso.,Université Nazi BONI (UNB) 01 BP 1091 Bobo-Dioulasso 01, Bobo-Dioulasso, Burkina Faso
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17
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Lind CE, Agyakwah SK, Attipoe FY, Nugent C, Crooijmans RPMA, Toguyeni A. Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa. Sci Rep 2019. [PMID: 31727970 DOI: 10.1038/s41598-019-53295-y.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d'Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.
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Affiliation(s)
- Curtis E Lind
- WorldFish, Jalan Batu Maung, Batu Maung, 11960, Bayan Lepas, Penang, Malaysia. .,CSIRO Agriculture & Food, Castray Esplanade, Hobart, Australia.
| | - Seth K Agyakwah
- Aquaculture Research and Development Center (ARDEC), CSIR-Water Research Institute, PO Box 139, Akosombo, Ghana
| | - Felix Y Attipoe
- Aquaculture Research and Development Center (ARDEC), CSIR-Water Research Institute, PO Box 139, Akosombo, Ghana
| | - Christopher Nugent
- Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | | | - Aboubacar Toguyeni
- Centre International de Recherche-Développement sur l'Elevage en zone Subhumide (CIRDES) 01 BP 454 Bobo-Dioulasso 01, Bobo-Dioulasso, Burkina Faso.,Université Nazi BONI (UNB) 01 BP 1091 Bobo-Dioulasso 01, Bobo-Dioulasso, Burkina Faso
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Aquaculture-Mediated Invasion of the Genetically Improved Farmed Tilapia (Gift) into the Lower Volta Basin of Ghana. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11100188] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The need for improved aquaculture productivity has led to widespread pressure to introduce the Genetically Improved Farmed Tilapia (GIFT) strains of Nile tilapia (Oreochromis niloticus) into Africa. However, the physical and regulatory infrastructures for preventing the escape of farmed stocks into wild populations and ecosystems are generally lacking. This study characterized the genetic background of O. niloticus being farmed in Ghana and assessed the genetic effects of aquaculture on wild populations. We characterized O. niloticus collected in 2017 using mitochondrial and microsatellite DNA markers from 140 farmed individuals sampled from five major aquaculture facilities on the Volta Lake, and from 72 individuals sampled from the wild in the Lower Volta River downstream of the lake and the Black Volta tributary upstream of the lake. Our results revealed that two farms were culturing non-native O. niloticus stocks, which were distinct from the native Akosombo strain. The non-native tilapia stocks were identical to several GIFT strains, some of which showed introgression of mitochondrial DNA from non-native Oreochromis mossambicus. We also found that the non-native cultured tilapias have escaped into the wild and interbred with local populations, and also observed potentially admixed individuals on some farms. Our results highlight aquaculture as a vector in the spread of invasive non-native species and strains, and underscore the importance of genetic baseline studies to guide conservation planning for wild populations.
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19
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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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20
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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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