Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.
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 o...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1010551 |
| _version_ | 1797856331536793600 |
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| author | Meng Yue Wu Giovanni Forcina Gabriel Weijie Low Keren R Sadanandan Chyi Yin Gwee Hein van Grouw Shaoyuan Wu Scott V Edwards Maude W Baldwin Frank E Rheindt |
| author_facet | Meng Yue Wu Giovanni Forcina Gabriel Weijie Low Keren R Sadanandan Chyi Yin Gwee Hein van Grouw Shaoyuan Wu Scott V Edwards Maude W Baldwin Frank E Rheindt |
| author_sort | Meng Yue Wu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-09T20:38:44Z |
| format | Article |
| id | doaj.art-1c52499bfe7a4807b92efc63a8da28e1 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-09T20:38:44Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-1c52499bfe7a4807b92efc63a8da28e12023-03-30T05:31:16ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042023-01-01191e101055110.1371/journal.pgen.1010551Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.Meng Yue WuGiovanni ForcinaGabriel Weijie LowKeren R SadanandanChyi Yin GweeHein van GrouwShaoyuan WuScott V EdwardsMaude W BaldwinFrank E RheindtHuman 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.https://doi.org/10.1371/journal.pgen.1010551 |
| spellingShingle | Meng Yue Wu Giovanni Forcina Gabriel Weijie Low Keren R Sadanandan Chyi Yin Gwee Hein van Grouw Shaoyuan Wu Scott V Edwards Maude W Baldwin Frank E Rheindt Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. PLoS Genetics |
| title | Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. |
| title_full | Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. |
| title_fullStr | Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. |
| title_full_unstemmed | Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. |
| title_short | Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. |
| title_sort | historic samples reveal loss of wild genotype through domestic chicken introgression during the anthropocene |
| url | https://doi.org/10.1371/journal.pgen.1010551 |
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