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Speak, Samuel A. 
ORCID: https://orcid.org/0000-0002-4207-7562, Birley, Thomas, Bortoluzzi, Chiara, Clark, Matthew D., Percival-Alwyn, Lawrence, Morales, Hernán E. and van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X
(2024)
Genomics‐informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.
Molecular Ecology Resources, 24 (7).
ISSN 1755-098X
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Abstract
Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.
| Item Type: | Article |
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| Additional Information: | Data Availability Statement: Genetic data: The Raw sequence reads for the six pink pigeon individuals have been deposited in the NCBI SRA (BioSample: PRJNA1018937, Accessions: SAMN37457073, SAMN37457074, SAMN37457075, SAMN37457076, SAMN37457077, SAMN37457078). The pink pigeon reference genome used for this project has been submitted to the NCBI BioSample: PRJNA1018937 (Speak et al., 2023). The Chicken bGalGal6 genome is publicly available on NCBI (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002315.5/). The chCADD scores are publicly available on the OSF (https://doi.org/10.17605/OSF.IO/8GDK9). Scripts: The LoadLift Snakemake pipeline is available on GitHub (https://github.com/saspeak/LoadLift). Research Funding: Royal Society. Grant Number: ICA/R1/201194; University of East Anglia. Grant Number: RTSG; 100162318RA1; Wellcome Trust. Grant Number: WT207492; Natural Environment Research Council. Grant Number: T209447; European Molecular Biology Organization. Grant Number: grant 1111-2018; H2020 Marie Skłodowska-Curie Actions. Grant Number: grant 840519; Biotechnology and Biological Sciences Research Council. Grant Numbers: BB/M011216/1, BB/S019669/1, BBS/E/T/000PR5885, BBS/E/T/000PR6193, BBS/E/T/000PR9816, BBS/E/T/000PR9818 |
| Faculty \ School: | Faculty of Science > School of Environmental Sciences |
| Depositing User: | LivePure Connector |
| Date Deposited: | 17 May 2024 16:31 |
| Last Modified: | 10 Oct 2024 00:00 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/95240 |
| DOI: | 10.1111/1755-0998.13967 |
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