Insights into the mitochondrial DNA genetic diversity and affinities of village chickens from the Sulu Archipelago, Philippines

The Sulu archipelago in the Philippines witnessed significant human migration from prehistoric to subrecent periods, resulting in a tapestry of cultures, languages, and genes. However, many details remain unclear. Archaeological evidence shows that human populations traversing within and between regions in Island Southeast Asia (ISEA) and the Pacific brought a variety of domestic animals, including dogs, pigs, chickens, and commensal Pacific rats. Recent insights into the ancient movements of these species suggest that they have different origins and arrival times. Here, we leveraged chickens as a tool to investigate human interactions in the Sulu archipelago. We sequenced a 764-base pair fragment of the mitochondrial DNA control region to examine the genetic diversity and structure of 254 village chickens from the Sulu archipelago. Combined with comparable datasets from other islands of ISEA and the Pacific, our data reveal a higher maternal genetic affinity of chickens from the Sulu Archipelago with those from adjacent Indonesian islands than with chickens from the rest of the Philippines. This observation points to long-standing regional interactions between the Sulu archipelago and Indonesia. Furthermore, core haplogroup D lineages, which characterise ancient Pacific chickens, are not found in the Sulu archipelago, but are present elsewhere in the Philippines.