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.

中文翻译：

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家鸡的野生物种基因组祖先。


背景技术杂交和基因渗入在动物物种的进化史上发挥着关键作用。它们通常在野生鸟类的几个目中观察到。家鸡鸡鸡是最常见的家畜品种。每年饲养超过 650 亿只鸡，生产肉类和 8000 万吨鸡蛋，供全球人类商业部门消费。揭示其遗传多样性的起源对于可持续育种改良计划具有重大应用。结果在这项研究中，我们报告了对本土乡村鸡和四种野生原鸡种之间基因渗入特征的全基因组分析。我们首先评估原鸡属的全基因组系统发育和分化时间。全基因组序列差异分析支持灰原鸡 G. sonneratii 和锡兰原鸡 G. lafayettii 之间的姐妹关系。这两个物种形成一个分支，是红原鸡 G. gallus 的姐妹，而绿原鸡 G. varius 是该属中最古老的谱系。我们揭示了灰原鸡和家鸡之间广泛的双向渐渗，以及与锡兰原鸡的程度较小的双向渐渗。我们发现了一个绿原鸡基因渗入的案例。这些渗入区域包括具有与发育和免疫系统相关的生物功能的基因。结论我们的研究表明，虽然红原鸡是主要的祖先物种，但渐渗杂交事件影响了基因组并促进了家鸡的多样性，尽管在其地理范围内可能处于不同的水平。