Genetic diversity and population structure analysis of Philippine native pigs highlights four priority populations for conservation

Abstract

The Philippine native pig (PhNP) is a unique genetic resource with complex genetics due to multiple ancestries and hybridizations with wild pigs. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed 157 native pigs representing 7 populations (Benguet (B), Kalinga (K), Nueva Vizcaya, Isabela (I), Quezon (Q), Marinduque (M), and Samar (S)) and 39 pigs of transboundary distribution (Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 21 ISAG–FAO recommended microsatellite markers. We tested for population structure at the island, administrative region and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by analysis of molecular variance (Frt: 0.08; F’st: 0.288-0.728), Bayesian clustering (k = 2) and Nei’s DA genetic distance (98% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.72), a high allele count (Na: 9.24) and a low inbreeding coefficient (Fis: -0.022 to 0.150). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), administrative region (k = 4) and population (k= 9) levels. The pairwise F’st between PhNP populations ranged from 0.130 (Q and M) to 0.427 (Q and K), confirming that PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that the seven previously assigned PhNP populations, roughly delimited by provincial origin, are unique genetic units for conservation. Furthermore, the small effective population sizes of B, Q, I, and S (Ne: 5, 17, 24, and 26, respectively) necessitate immediate conservation actions, such as incentivizing the farming of PhNP.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

“…The initial ancestral polymorphisms between the D2 and D7 clades could explain the two initial clusters ( k = 2) differentiating the NL and SLV regions, respectively (Figure 4 ). We previously hypothesized that the pigs of the D7 clade originated from the D2 clade via a genetic bottleneck event upon dispersal to Southeast Asia (Banayo, 2023 ). Thereafter, upon dispersal to various provinces in the Philippines, members of each clade formed further population structure via genetic drift (i.e., Q, M, and S of the D7 clade) due to the varied agroclimatic conditions and management practices of each province.…”

“…To visualize the Q‐matrices, DISTRUCT (Rosenberg, 2004) was used to generate membership probability plots. The raw data reported here are available in the Dryad database (Banayo et al., 2022).…”