Background Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. Results In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. Conclusions Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

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

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