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Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations

SIMPLE SUMMARY: Human activities have left indelible traces in the gene pool of livestock as well as recently domesticated wild animal species which are manifested by changes in their genome structure, often accompanied by the significant loss of biodiversity, especially in the case of small local p...

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Autores principales: Moravčíková, Nina, Kasarda, Radovan, Židek, Radoslav, McEwan, John Colin, Brauning, Rudiger, Landete-Castillejos, Tomás, Chonco, Louis, Ciberej, Juraj, Pokorádi, Jaroslav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10417186/
https://www.ncbi.nlm.nih.gov/pubmed/37570333
http://dx.doi.org/10.3390/ani13152525
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author Moravčíková, Nina
Kasarda, Radovan
Židek, Radoslav
McEwan, John Colin
Brauning, Rudiger
Landete-Castillejos, Tomás
Chonco, Louis
Ciberej, Juraj
Pokorádi, Jaroslav
author_facet Moravčíková, Nina
Kasarda, Radovan
Židek, Radoslav
McEwan, John Colin
Brauning, Rudiger
Landete-Castillejos, Tomás
Chonco, Louis
Ciberej, Juraj
Pokorádi, Jaroslav
author_sort Moravčíková, Nina
collection PubMed
description SIMPLE SUMMARY: Human activities have left indelible traces in the gene pool of livestock as well as recently domesticated wild animal species which are manifested by changes in their genome structure, often accompanied by the significant loss of biodiversity, especially in the case of small local populations. Despite the benefits of deer farming, intensive artificial selection associated with domestication can lead to several negative effects, including founder effects, inbreeding depression, or rapid decline in effective population size, which are also often present in traditional livestock. This study investigates the effect of human-mediated selection on the diversity of seven farmed red deer populations compared to two wild populations through the quantification of the level of genomic heterozygosity, inbreeding, admixture, and gene flow. These results will help to improve traditional breeding schemes and assist in a more sustainable utilisation of available animal genetic resources. ABSTRACT: In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (H(e) = 0.19) and the lowest genomic inbreeding (F(HOM) = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.
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spelling pubmed-104171862023-08-12 Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations Moravčíková, Nina Kasarda, Radovan Židek, Radoslav McEwan, John Colin Brauning, Rudiger Landete-Castillejos, Tomás Chonco, Louis Ciberej, Juraj Pokorádi, Jaroslav Animals (Basel) Article SIMPLE SUMMARY: Human activities have left indelible traces in the gene pool of livestock as well as recently domesticated wild animal species which are manifested by changes in their genome structure, often accompanied by the significant loss of biodiversity, especially in the case of small local populations. Despite the benefits of deer farming, intensive artificial selection associated with domestication can lead to several negative effects, including founder effects, inbreeding depression, or rapid decline in effective population size, which are also often present in traditional livestock. This study investigates the effect of human-mediated selection on the diversity of seven farmed red deer populations compared to two wild populations through the quantification of the level of genomic heterozygosity, inbreeding, admixture, and gene flow. These results will help to improve traditional breeding schemes and assist in a more sustainable utilisation of available animal genetic resources. ABSTRACT: In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (H(e) = 0.19) and the lowest genomic inbreeding (F(HOM) = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure. MDPI 2023-08-04 /pmc/articles/PMC10417186/ /pubmed/37570333 http://dx.doi.org/10.3390/ani13152525 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Moravčíková, Nina
Kasarda, Radovan
Židek, Radoslav
McEwan, John Colin
Brauning, Rudiger
Landete-Castillejos, Tomás
Chonco, Louis
Ciberej, Juraj
Pokorádi, Jaroslav
Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations
title Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations
title_full Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations
title_fullStr Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations
title_full_unstemmed Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations
title_short Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations
title_sort traces of human-mediated selection in the gene pool of red deer populations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10417186/
https://www.ncbi.nlm.nih.gov/pubmed/37570333
http://dx.doi.org/10.3390/ani13152525
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