Chicken Genetic Signatures Reveal a Long-Term Historical Relationship Between Zanzibar and Oman

Abstract

Background and Objective: Understanding the historical dispersal of indigenous chickens offers valuable insights into past human mobility, trade networks and livestock adaptation. This study examined the maternal genetic relationships between indigenous chicken populations from Zanzibar (Unguja and Pemba) and Oman using mitochondrial DNA (mtDNA) D-loop sequence analysis.

Materials and Methods: mtDNA sequences were analyzed to assess genetic diversity, population structure, phylogenetic relationships and historical gene flow. Haplotype and nucleotide diversity indices, Analysis of Molecular Variance (AMOVA), pairwise F_ST values, phylogenetic networks and neutrality tests were employed to infer evolutionary and demographic patterns.

Results: High haplotype diversity and a predominance of within-population genetic variation (81.39%) were observed, indicating repeated introductions followed by local population expansion rather than long-term isolation. Extensive sharing of maternal haplotypes between Zanzibar and several Omani ecotypes, particularly Dhofar and Musandam, was detected. A dominant ancestral haplogroup accounted for nearly 79% of all haplotypes and exhibited a star-like topology, consistent with demographic expansion from a common maternal source. Gene flow estimates (Nm >1) across most population pairs suggest sustained historical maternal exchange sufficient to counteract genetic drift. Notably, some Omani ecotypes showed greater genetic differentiation among themselves than relative to Zanzibar populations, reflecting localized divergence following dispersal.

Conclusion: These genetic patterns closely correspond with archaeological and historical evidence of Indian Ocean maritime trade linking East Africa and the Arabian Peninsula. The findings indicate that chickens were repeatedly transported as part of long-standing trade, settlement and provisioning systems. Overall, this study highlights the utility of mtDNA in reconstructing livestock dispersal histories and underscores the importance of conserving indigenous chicken populations as reservoirs of genetic, cultural and adaptive diversity.