Data from: Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilisations across time. Archaezoological and linguistic evidences suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chicken, supporting the importance of the region in understanding the history of the species and indirectly, of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur both in Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda’s hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chicken and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilisations in Asia and East Africa.

解析任一畜禽物种的遗传历史，是理解农业社会与农业经济的起源、发展与扩张的核心所在。乡村家养鸡在非洲分布广泛，它们与人类的紧密依附关系以及依赖人类进行长距离扩散的特性，使其成为追踪不同时期人类社会与文明间文化及贸易往来的重要生物标记物。考古动物学与语言学证据表明，该物种在非洲大陆的传入与扩散历程颇为复杂；针对东非乡村家养鸡的线粒体DNA（mtDNA）D环（D-loop）分析显示，其存在5个独特的单倍群，这一结果佐证了东非地区在理解该物种历史以及间接理解人类互动历程中的重要性。本研究针对东非四国（肯尼亚、乌干达、埃塞俄比亚、苏丹）的657只乡村家养鸡进行基因分型，共分析30个常染色体微卫星标记（microsatellite markers），最终鉴定出3个独立的常染色体基因库（I、II、III）。基因库I主要分布于埃塞俄比亚与苏丹境内，而基因库II与III则同时存在于肯尼亚与乌干达。研究观察到，在肯尼亚沿海至乌干达内陆区域之间，基因库II与III存在渐变性的混合现象（P=0.001），而基因库I则与另外两个基因库界限分明。我们认为，这三个基因库分别对应了非洲大陆历史上与该区域乡村家养鸡及人类的传入、扩散相关的三次独立事件的遗传印记。本研究结果为养鸡业历史提供了新的认知，而该历史正是由亚洲与东非地区古代、现代文明之间的陆路与海路交流所塑造的。