The wild species genome ancestry of domestic chickens

Abstract

42Hybridization and/or introgression play a key role in the evolutionary history of animal species. 43 It is commonly observed in several orders in wild birds. The domestic chicken Gallus gallus 44domesticus is the commonest livestock species exploited for the benefit of mankind. The origin 45 of its diversity remains unsettled. Here, we report a genome-wide analyses for signatures of 46 introgression within domestic village chicken. We first established the genome-wide 47 phylogeny and divergence time across the genus Gallus, showing the sister relationships 48between Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii and that the Green 49 junglefowl is the first diverging lineage within the genus Gallus. Then, by analysing the whole-50 genome sequences of geographically diverse chicken populations, we reveal extensive 51 bidirectional introgression between Grey junglefowl and domestic chicken and to a much less 52 extent with Ceylon junglefowl. A single case of Green junglefowl G. varius introgression was 53 identified. These introgressed regions include biological functions related to the control of gene 54 expression. Our results show that while the Red junglefowl is the main ancestral species, 55introgressive hybridization episodes have impacted the genome and contributed to the diversity 56 of domestic chicken, although likely at different level across its geographic range. 57

Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

“…In our analyses, we adopt the dominance parameter h = 1 since the derived TSHR allele is recessive, and set the population size N = 180000 (95% HPD 26000-460000) estimated by Loog et al (2017). We pick a uniform prior over the interval [−1,1] for the selection coefficient s and a uniform prior over the set {−9000, −8999,…, 0} for the selection time k s , which covers the time period of chicken domestication dated to about 8000 years ago (95% CI 7014-8768 years) (Lawal et al, 2020). We choose a uniform prior over the interval [0,1] for the migration rate m and take the migration time to be k m = −250.…”

“…. , 0} for the selection time k s , which covers the time period of chicken domestication dated to about 8000 years ago (95% CI 7014-8768 years) (Lawal et al, 2020). We choose a uniform prior over the interval [0,1] for the migration rate m and take the migration time to be k m = −250.…”

Domestic chicken diversity: Origin, distribution, and adaptation

“…It also indicates a common ancestor between the Red junglefowl and these two species of ~2.6 to 2.9 mya and that the Green junglefowl is the oldest Gallus lineage with a divergence time of ~4 mya (Lawal et al . 2020). This phylogeny, (see also Tiley et al .…”

“…Topologies weighting (Martin & Van Belleghem 2017) for the relationships within the genus Gallus , adapted from Lawal et al . (2020). (a) The 15 possible topologies (T1–T15) from five taxa [Red junglefowl (RJ), Grey junglefowl (Gy), Ceylon junglefowl (Cy), Green junglefowl (Gn), and common pheasant (CP)].…”

Molecular Clocks without Rocks: New Solutions for Old Problems

“…Recently, whole-genome sequencing data from pedigree trios have been used to estimate the de novo mutation rate for many animals [74][75][76][77][78] and parent-progeny pairs in plants [79]. Recent examples of divergence time estimation based on mutation rates and coalescent age estimates include the age of human migration events [80] and of domestication histories among agriculturally important species [81][82][83].…”