Comparative analysis of African cattle, sheep and goat genomes reveal convergence and divergence to contrasting environments

African livestock have co-existed and co-adapted to Africa’s diverse eco-climates which have likely impacted their genomes. Such impacts however remain poorly investigated across multiple livestock species. Using whole genome sequences of African cattle, sheep, and goats in Ethiopia, we conducted a cross and within-species comparative genomic analysis and identified seven common genes associated with high- and low-altitude adaptation. One gene CSMD3 was found in a genomic region under selection in low- and high-altitude individuals suggesting a potential role for convergent selection. CSMD3 was duplicated on chromosomes 9 and 10 in sheep and was enriched for Gene Ontology (GO) terms linked to cellular component organization, neuron projection development, and membrane dynamics. Shared selection signatures overlapping HOXC4 , HOXC5 , HOXC6 , HOXC9 , and MAN1C1 , were found in low-altitude individuals of the three species. The HOXC gene cluster was functionally enriched in sheep and goats for skeletal morphogenesis, embryonic development, and transcriptional regulation. MAN1C1 also showed species-specific roles including hydrolase activity and stress response in cattle, and ion binding and protein metabolism in sheep and goats, suggesting convergence within Caprinae and their divergence from Bovinae. PLEKHA1 was found in a candidate region in high-altitude individuals indicating possible convergent adaptation to hypoxia, and oxidative stress. These results provide insights into the genomic architecture of genomic convergence/divergence in African livestock and likely highlight possible mechanisms of adaptive evolution that could inform cross-species climate-resilient livestock breeding. Experimental validation will however be necessary to confirm the precise functional roles of the putative loci.