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      Assessing the genetic diversity of farmed and wild Rufiji tilapia ( Oreochromis urolepis urolepis) populations using ddRAD sequencing

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          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.

          Abstract

          The objective of the current study was to assess the genetic variation among 10 Rufiji tilapia populations of both wild and farmed origin using ddRAD‐seq. We investigate for the existence of putative genetic clusters, test for the existence of isolation by distance, and assess the efficiency of predicting population of origin‐based only on the genomic profile using cross‐validation schemes.

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          Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

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            2b-RAD: a simple and flexible method for genome-wide genotyping.

            We describe 2b-RAD, a streamlined restriction site-associated DNA (RAD) genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Well-studied accessions of Arabidopsis thaliana were genotyped to validate the method's accuracy and to demonstrate fine-tuning of marker density as needed. The simplicity of the 2b-RAD protocol makes it particularly suitable for high-throughput genotyping as required for linkage mapping and profiling genetic variation in natural populations.
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              The importance of selective breeding in aquaculture to meet future demands for animal protein: A review

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                Author and article information

                Contributors
                christos.palaiokostas@slu.se
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                18 August 2020
                September 2020
                : 10
                : 18 ( doiID: 10.1002/ece3.v10.18 )
                : 10044-10056
                Affiliations
                [ 1 ] Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
                [ 2 ] Institute of Marine Sciences University of Dar es Salaam Zanzibar Tanzania
                [ 3 ] The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Edinburgh UK
                Author notes
                [*] [* ] Correspondence

                Christos Palaiokostas, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.

                Email: christos.palaiokostas@ 123456slu.se

                Author information
                https://orcid.org/0000-0002-4480-4612
                Article
                ECE36664
                10.1002/ece3.6664
                7520224
                33005362
                6b11693d-d5bb-426e-95d3-d48cbac7d405
                © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 20 May 2020
                : 16 July 2020
                : 20 July 2020
                Page count
                Figures: 7, Tables: 2, Pages: 13, Words: 8856
                Funding
                Funded by: Swedish International Development Agency
                Funded by: BBSRC Institute Strategic Program Grants , open-funder-registry 10.13039/501100000268;
                Award ID: BBS/E/D/20002172
                Award ID: BBS/E/D/30002275
                Award ID: BB/J004243/1
                Funded by: Roslin Institute
                Funded by: NERC
                Award ID: R8/H10/56
                Funded by: MRC
                Award ID: MR/K001744/1
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                September 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.1 mode:remove_FC converted:27.09.2020

                Evolutionary Biology
                ddrad‐seq,genetic diversity,rufiji tilapia
                Evolutionary Biology
                ddrad‐seq, genetic diversity, rufiji tilapia

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