Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA

Abstract

The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's D and Fu's Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.

Keywords: Gallus gallus; Philippine chickens; demographic history; genetic structure; mtDNA; phylogeography.

FIGURE 1

Maximum likelihood phylogenetic tree for complete mtDNA D-loop nucleotide sequences of Philippine chickens. Node labels correspond to bootstrap support values evaluated with 1,000 ultrafast bootstrap replicates in IQ-TREE. The scale bar (0.007) indicates the genetic distance (substitution per site). Bootstrap values under 50% are not shown.

FIGURE 2

Median-joining network of the complete mtDNA D-loop region (1,232 bp) depicting relationship of Philippine chickens, Indonesian chickens, and Pacific chickens. The area of each circle is proportional to the frequency of the corresponding haplotypes. The length of branch connecting to other haplotypes correspond to mutational positions.

FIGURE 3

Mismatch distribution of the complete mtDNA D-loop sequences of (A,B,D) Philippine chickens [red junglefowls (RJFs) and NCs], (C) Pacific, (E) Indonesian, and (F) mainland Southeast Asian (SEA) chickens based on pairwise nucleotide site differences. The solid line indicates the theoretical distribution under population expansion model. The raggedness statistics and corresponding p-values for (A) Philippine RJFs; r = 0.0479, p = 0.049 and (D) RJFs–NCs–haplogroup D; r = 0.0210, p = 0.019, provided statistical support for the smoothness of the observed distributions.

FIGURE 4

Bayesian coalescent skyline plot showing estimated demographic history of Philippine chickens (haplogroup D). The central blue line is the median estimate effective population size. The shaded area shows the upper and lower estimates of 95% credibility interval. The vertical dotted line represents the median estimate of time to the most recent common ancestor. The x-axis is the time (in years before present), and the y-axis indicates population size (as the product of N_e and the generation length in years).

FIGURE 5

The proposed routes of translocation scenario of Philippine chickens expanding to the Pacific relating to the Austronesian speakers movement, as supported by the population pairwise genetic divergence (F_ST) estimates, mismatch distribution analyses, and demographic inference based on coalescent simulation of Bayesian skyline plot (BSP).