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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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Saatoglu D, Niskanen AK, Kuismin M, Ranke PS, Hagen IJ, Araya-Ajoy YG, Kvalnes T, Pärn H, Rønning B, Ringsby TH, Saether BE, Husby A, Sillanpää MJ, Jensen H. Dispersal in a house sparrow metapopulation: An integrative case study of genetic assignment calibrated with ecological data and pedigree information. Mol Ecol 2021; 30:4740-4756. [PMID: 34270821 DOI: 10.1111/mec.16083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 01/12/2023]
Abstract
Dispersal has a crucial role determining ecoevolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used genome-wide 200K Single Nucleotide Polymorphism data and two different genetic assignment approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation) to identify the dispersers in a house sparrow (Passer domesticus) metapopulation sampled over 16 years. Our results showed higher assignment accuracy with BONE. Hence, we proceeded to diagnose potential sources of errors in the assignment results from the BONE method due to variation in levels of interpopulation genetic differentiation, intrapopulation genetic variation and sample size. We show that assignment accuracy is high even at low levels of genetic differentiation and that it increases with the proportion of a population that has been sampled. Finally, we highlight that dispersal studies integrating both ecological and genetic data provide robust assessments of the dispersal patterns in natural populations.
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Affiliation(s)
- Dilan Saatoglu
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alina K Niskanen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Markku Kuismin
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Finland
| | - Peter S Ranke
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingerid J Hagen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Norwegian Institute for Nature Research, Trondheim, Norway
| | - Yimen G Araya-Ajoy
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Henrik Pärn
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bernt Rønning
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thor Harald Ringsby
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bernt-Erik Saether
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mikko J Sillanpää
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Finland.,Infotech Oulu, University of Oulu, Oulu, Finland
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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