Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene
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Wu et al. 2023 PLOS Genetics ...
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Authors
Wu, Meng YueForcina, Giovanni
Low, Gabriel Weijie
Sadanandan, Keren R
Gwee, Chyi Yin
van Grouw, Hein

Wu, Shaoyuan
Edwards, Scott V
Baldwin, Maude W
Rheindt, Frank E
Issue date
2023-01-19Submitted date
2022-04-29Subject Terms
chickensintrogression
domestic animals
genomics
single nucleotide polymorphisms
principal component analysis
phylogenetic analysis
population genetics
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Show full item recordAbstract
<Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20–50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.Citation
Wu MY, Forcina G, Low GW, Sadanandan KR, Gwee CY, et al. (2023) Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. PLOS Genetics 19(1): e1010551. https://doi.org/10.1371/journal.pgen.1010551Publisher
Public Library of Science (PLoS)Journal
PLOS GeneticsType
Journal ArticleItem Description
Copyright: © 2023 Wu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.EISSN
1553-7404ae974a485f413a2113503eed53cd6c53
10.1371/journal.pgen.1010551
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