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.