Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia

Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected from the mountainous areas of Occidental Mindoro, Palawan, Agusan del Norte, Capiz, Leyte, Iloilo, and Guimaras were analyzed and compared with chicken reference sequences. Phylogenetic analysis revealed multiple maternal origins of the PH RJFs based on haplogroups D, E, and Y classification. This was supported by PH RJFs and RJFs from other Asian countries sharing a clade. A median-joining network also revealed the haplotype sharing of the PH RJFs and Indonesian RJF, demonstrating common maternal ancestry. High haplotype and nucleotide diversity were also observed at all sampling sites. Analysis of molecular variance indicated that the principal molecular variance existed within populations (81.23%) rather than among populations (18.77%). A population neutrality test and Bayesian skyline plot (BSP) analysis elucidated the RJF maternal effective population size expansion in the Philippines that possibly started approximately 2,800–3,000 years ago. The co-existence of Gallus gallus bankiva and Gallus gallus gallus in the Philippines was also verified. The haplotype sharing of the current RJF samples with commercial chickens suggested the need to formulate conservation programs that would protect the RJFs in the Philippines.