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

Abstract

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 civilizations across time. Archaezoological and linguistic evidence 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 chickens. It supports 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 in both 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 chickens 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 civilizations in Asia and East Africa.

Genetic diversity and population structure of indigenous chicken breeds in South China

“…1a). Consulting the suggestion from Pritchard et al [12] and Mwacharo et al [19] , as well as geographic information for the chicken breeds studied, K = 3 was chosen as the most optimal number of genetic clusters to reveal the biologically meaningful genetic structure of indigenous chicken breeds. For brevity, these three clusters of indigenous chicken breeds are referred to as cluster I (green), II (purple) and III (red) ( Table 1, Fig.…”

“…Indeed, the economically developed areas of South China in particular have had prolonged and sustained socioeconomic interactions with each other. Such interactions have facilitated the gene flow among indigenous chicken breeds, especially those in adjacent geographical regions, and between indigenous [19,21] . Different allelic proportions in these three clusters suggested the presence of an independent history of breed formation.…”

The past, present and future genetic improvement of indigenous chicken of Kenya

“…Maina (2000) characterized indigenous chicken based on morphology and feather colours, and reported wide variations in these features. They included Eastern (Kilifi, Taita-Taveta, Muranga, Kitui, Meru, Marsabit) and Western (Kisii, Nandi, HomaBay, Kakamega) Kenya (Mwacharo et al, 2013).This study also revealed population admixture between the two gene pools (Figure 3) with east to west genetic cline of gene pool two. There exists many morphological clades of indigenous chicken (Okeno, Kahi and Peters, 2012) and evidenced adaptive, biological, reproductive and production traits variations (Kingori, Wachira and Tuitoek, 2010).…”

“…Although the exact population of both genotypes and ecotypes for the Kenyan indigenous chicken are not well documented, the study by Okeno, Kahi and Peters (2011) could give an insight on the population structure for different genotypes and ecotypes. The genetic diversity of the Kenyan indigenous chicken could have been as a result of their dispersal from putative centres of domestication to different regions with diverse environmental conditions and people of different cultural orientations (Mwacharo et al, 2013). In the pooled data, they demonstrated the population structure for different genotypes within the farmers' households as presented in Figure 1.They also demonstrated that although the population is dominated by normal-feathered birds, the other genotypes are well represented in all the counties.…”

Evidence of balancing selection in multiple indigenous chicken populations

“…Of note, Mwacharo et al (2013) identified four microsatellites that were under positive selection at 30 loci in African village chickens, which revealed that not all microsatellite loci are subject to neutral selection or genetic drift.…”