Small Ruminant Research 132 (2015) 137–142 Contents lists available at ScienceDirect Small Ruminant Research journal h om epa ge: www.elsevier.com/locate/smallrumres Genetic diversity and structure in Egyptian indigenous sheep populations mirror patterns of anthropological interactions A.R. Elbeltagy a , A.M. Aboul-Naga a , H. Hassen b , B. Rischkowsky b , J.M. Mwacharo b,* a Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture. Nadi Elsaid Street, Dokki, Cairo, Egypt b Small Ruminant Genetics and Genomics Group, International Centre for Agricultural Research in Dry Areas, P.O. Box 5689 Addis Ababa, Ethiopia a r t i c l e i n f o Article history: Received 13 July 2015 Received in revised form 12 October 2015 Accepted 13 October 2015 Available online 19 October 2015 Keywords: Gene flow Human interactions Nile River Mediterranean Sea Ovis aries a b s t r a c t Human exchange networks are instrumental in influencing gene flow among domesticates. Here, we investigated levels of within- and between-population genetic diversity in 289 animals from six indige- nous sheep populations in Egypt (Barki, Farafra, Ossimi, Rahmani, Saidi, Souhagi) and 119 individuals of Awassi breed from Egypt, Turkey and Syria using 13 autosomal microsatellites. Although our analy- sis revealed genetic differentiation between Souhagi and other Egyptian populations, and between the Awassi from Egypt and the ones from Syria and Turkey, most likely due to reproductive isolation, Bayesian analysis identified two gene pools underlying the ancestral genetic diversity while multivariate analysis identified nine genetic clusters which could be subdivided into four broad genetic groups. Further analy- sis revealed that this genetic structure was the result of the exchange of genetic stocks along the Nile River valley and the Mediterranean Sea coast, but, minimal gene flow between flocks found in the Northern, Central and Southern Egypt across the Western desert. Our results support the fact that human interac- tion networks have shaped the genetic architecture of domestic animals while harsh environments such as deserts tend to limit human interactions and hence gene flow among domesticates. © 2015 Elsevier B.V. All rights reserved. 1. Introduction In natural populations, gene flow is influenced by the extent to which landscape topography facilitate interactions among pop- ulations (Taylor et al., 1993). Among domesticates, gene flow is mediated by human socio-cultural and economic networks, which may lead to a unique combination of genotypes as well as geo- spatial patterns of livestock genetic diversity and structure. Such human networks have shaped the genetic structure of several domestic animals including the Lipizzan horse breed (Achmann et al., 2004), local goat populations in Vietnam (Berthouly et al., 2009) and traditional breeds of sheep in Belgium (Dumasy et al., 2012). Warmuth et al. (2013) showed that ancient trading networks influenced the genetic structure of eastern Eurasian horses. Geo- graphic features can constrain human mobility and indirectly gene flow among domesticates. For instance, mountain ranges and the Yangtze River have been associated with increased levels of genetic differentiation in Yak (Xuebin et al., 2005) and Water Buffaloes (Zhang et al., 2007). * Corresponding author: Small Ruminant Genetics and Genomics Group, Inter- national Center for Agricultural Research in the Dry Areas (ICARDA). P.O. Box 5689 Addis Ababa, Ethiopia. E-mail address: j.mwacharo@cgiar.org (J.M. Mwacharo). In Egypt, livestock play pivotal roles to most communities whose common history may attenuate and/or enhance their interactions which in turn may sculpture the genetic diversity and demographic dynamics of their livestock. Sheep and goats (Shoats) have been an important livestock species in Egypt since the fifth millennium BC (Galal et al., 2005) and offer themselves as biological candidates to analyse the effects of human socio-cultural and economic inter- actions on livestock genetic diversity and structure. Unlike cattle or water buffaloes, shoats have been raised by most communities and they fulfill various socio-cultural and economic roles to their owners as well as entire villages. Livestock in Egypt offer an extra layer of information, the insights into the historical phenomenon that have shaped livestock biodiversity, because of the country’s strategic location at the entry point of most domestic species (ani- mals and plants) into the African continent (Fuller et al., 2011) and its long history of interaction with Eurasia. We therefore inves- tigated the genetic landscape of indigenous sheep populations in Egypt using autosomal microsatellites to better understand the influence of different factors (such as founder effect, reproductive isolation, admixture) in shaping their genetic diversity and struc- ture. To account for the possible complex scenario that may arise in reconstructing the genetic profiles of the indigenous sheep pop- ulations, we included in the study three populations of Awassi, a breed of sheep that occurs in central Asia and the Middle East. Data generated here provides a fine-scale overview on the knowledge http://dx.doi.org/10.1016/j.smallrumres.2015.10.020 0921-4488/© 2015 Elsevier B.V. All rights reserved.