Natural adaptation and human selection of northeast African sheep genomes

• Published in: Genomics (San Diego, Calif.) Vol. 114; no. 5; p. 110448
• Main Authors: Ahbara, Abulgasim M., Musa, Hassan H., Robert, Christelle, Abebe, Ayele, Al-Jumaili, Ahmed S., Kebede, Adebabay, Latairish, Suliman, Agoub, Mukhtar Omar, Clark, Emily, Hanotte, Olivier, Mwacharo, Joram M.
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01-09-2022
• Subjects: Demographic history; Diversity; Fat-rumped; Fat-tailed; Ovis aries; Thin-tailed; Demographic history; Fat-rumped; Ovis aries; Thin-tailed; Fat-tailed; Diversity
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2022.110448

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.
•Northeast Africa sheep are defined by three major genetic backgrounds associated with their introduction in Africa•Natural selection for adaptation to contrasting environments could be drivers of adaptive divergence in African sheep•Skeletal tail associated genes are most likely playing major roles in the unique adaptations of African sheep