DNA Barcoding of Red Jungle Fowls (Gallus gallus philipensis Hatchisuka) from Different Mountain Areas in the Philippines

Abstract

Initially proposed as a global standard for rapid species identification, DNA barcodes (cytochrome c oxidase subunit I or COI in the mitochondrial genome) were determined to assess diversity and genetic distances among 25 red jungle fowls (Gallus gallus philipensis Hatchisuka) obtained from different mountain areas in 23 provinces of 12 islands in the Philippines. Results of the evolutionary analyses using Kimura two-parameter model in MEGA5 indicated existence of two main evolutionary clades, and effectiveness of DNA barcodes in identifying and differentiatiang red jungle fowls between and within clades. Genbank-accessed COI sequences of three subspecies of red jungle fowls (Gallus gallus gallus, Gallus gallus bankiva, Gallus gallus spadiceus) and three Gallus species (G. lafayettei, G. sonneratii, G. varius) were clustered in the intermediate zone between differentiated populations of Philippine red jungle fowls, but more recently diverged with those in Clade A. Based on 627 positions from 25 COI sequences, average genetic distance among red jungle fowls was 0.254 units, demonstrating close resemblance within clade, but greater divergence between clades (d>1). Genetic divergence within Clade A (d=0.294) was higher than Clade B (d=0.215). Moreover, pooled pair-wise genetic distance was not significantly correlated (P>0.05) with geographical distances among red jungle fowls between and within clades. Evolutionary analysis of the DNA barcodes of Philippine red jungle fowls provided important information on genetic variability and population structure useful to support decisions on agrobiodiversity conservation and research in upland areas.