Philippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. They are valued locally for their various sociocultural roles. Recently, considerable literature has accumulated in the field of native pig production and marketing. However, there is limited research on the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among native pigs from various islands and provinces in Luzon and the Visayas, Philippines. In addition, a much debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n = 157) were collected from 10 provinces in Luzon and the Visayas. Approximately 650 base pairs of the mtDNA D-loop region were sequenced and analyzed together with publicly available sequences. Pairwise-distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). We identified 19 haplotypes (1–38 samples each), forming 4 haplogroups, i.e., North Luzon, South Luzon and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the native pig population, but evidence of interspecific hybridization was observed. This study showed that the Philippine native pigs have originated from at least 3 Sus scrofa lineage and that they were not domesticated from the endemic wild pigs of the Philippines.

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.

Philippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. They are valued locally for their various sociocultural roles. Recently, considerable literature has accumulated in the field of native pig production and marketing. However, there is limited research on the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among native pigs from various islands and provinces in Luzon and Visayas, Philippines. In addition, a much-debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n=157) were collected from 10 provinces in Luzon and the Visayas, Philippines. Approximately 650 base pairs of the mtDNA d-loop region were sequenced and analyzed together with publicly available sequences. Pairwise-distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). We identified 19 haplotypes (1-38 samples each), forming 4 haplogroups i.e. North Luzon, South Luzon and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the native pig population, but the use of wild pig for interspecific hybridization was observed. This study showed that the Philippine native pigs have ancestral origin from at least 3 Sus scrofa lineage and that they were not domesticated from the endemic wild pigs of the Philippines.