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Natural adaptation and human selection of northeast African sheep genomes

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.

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Abulgasim M. Ahbara

Hassan H. Musa

Christelle Robert

Ayele Abebe

Ahmed S. Al-Jumaili

Adebabay Kebede

Suliman Latairish

Mukhtar Omar Agoub

Emily Clark

Director of Frozen Ark Project & Professor of Genetics & Conservation

Joram M. Mwacharo


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.


Ahbara, A. M., Musa, H. H., Robert, C., Abebe, A., Al-Jumaili, A. S., Kebede, A., …Mwacharo, J. M. (2022). Natural adaptation and human selection of northeast African sheep genomes. Genomics, 114(5), Article 110448.

Journal Article Type Article
Acceptance Date Aug 7, 2022
Online Publication Date Aug 12, 2022
Publication Date Sep 1, 2022
Deposit Date Feb 4, 2023
Publicly Available Date Feb 6, 2023
Journal Genomics
Print ISSN 0888-7543
Electronic ISSN 1089-8646
Publisher Elsevier BV
Peer Reviewed Peer Reviewed
Volume 114
Issue 5
Article Number 110448
Keywords Genetics
Public URL
Publisher URL
Additional Information This article is maintained by: Elsevier; Article Title: Natural adaptation and human selection of northeast African sheep genomes; Journal Title: Genomics; CrossRef DOI link to publisher maintained version:; Content Type: article; Copyright: Crown Copyright © 2022 Published by Elsevier Inc.


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