Phylogeny and Genetic Diversity of Philippine Mallard Ducks Based on the Mitochondrial DNA D-loop Region

Abstract As with other locally adapted species, Philippine mallard ducks risk population fragmentation and indiscriminate hybridization. To allow for targeted breed improvement, this study aimed to unravel the maternal genetic relationships, phylogeny, and levels of genetic diversity in Philippine mallard ducks. We sequenced the mitochondrial DNA D-loop region of 118 ducks sampled from the Southern Leyte, Samar, and Cebu Provinces. Sequence data analysis revealed nine transition base substitutions and eight distinct haplotypes. Overall haplotypic diversity (Hd = 0.666 ± 0.038) exceeded that reported for Javanese ducks, but was comparable to that of Thai, Chinese, and Indian domestic duck populations. The matrilineal phylogenetic tree positioned all Philippine mallard ducks within the Old-World Haplogroup A. Specifically, they clustered into subhaplogroup A3 (75/118), together with domestic ducks from China and Southeast Asia; putative ancestral subhaplogroups A0 (6/118) and A1a (5/118) in a basal position, showing close genetic affinities with Eurasian wild mallards and Eastern spot-billed ducks; and subhaplogroup A1b (6/118), showing genetic relatedness to the Indian Runner duck. Notably, 26 individuals formed a distinct cluster corresponding to subhaplogroup A2, which appeared to be unique to this population. This study provides the first mitochondrial DNA D-loop-based genetic characterization of Philippine mallard ducks, placing this population within the broader Haplogroup A lineage and highlighting how its genetics was shaped by island biogeography. Collectively, these results establish the basis for future research on animal genetic resources and phenomics, supporting the sustainable management of mallard duck populations in the Philippines.