Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

Abstract

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.

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

“…These multiple ancestries suggest high genetic variation among PhNPs on different islands. Furthermore, it revealed that the Cordillera Clade (which includes the Benguet [B] population) has ancestry distant from the general Asian clade (Banayo et al., 2023 ; Basilio Jr. et al., 2022 ), similar to the findings in the related Lanyu pig of Taiwan (Li et al., 2017 ; Wu et al., 2007 ). Moreover, PhNP interbreeds with endemic wild pigs of the Philippines, such as Sus philippensis , S. cebifrons , S. ahoenobarbus , S. olivieri , and S .…”

“…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).…”

“…The PhNP is locally regarded as an indigenous species adapted to local conditions (FAO, 2011 ; Santiago et al., 2016 ). It is an Asian‐type Sus scrofa pig belonging to the East, Southeast, Pacific, and Cordillera clades, distinct from the wild pigs of the Philippines (i.e., S. philippensis and S. celebensis ; Banayo et al., 2023 ; Layos, Geromo, et al., 2022 ; Layos, Godinez, et al., 2022 ). PhNPs are traditionally associated with the indigenous communities who use them in rituals and to prepare ethnic foods, such as etag and kinuday (Alabado, 2017 ; Garambas et al., 2022 ; Lapena & Acabado, 2017 ; Ma, 2010 ; Maddul et al., 2015 ; Molintas, 2017 ; Voss, 1987 ).…”

“…Recent phylogenetic analyses indicated that PhNP may have at least four origins of domestication throughout Asia, that is Southeast Asia (SEA), East Asia (EA), the Cordillera region/Lanyu Island, and the Pacific (Banayo et al., 2023 ; Dichoso et al., 2022 ; Larson et al., 2005 ; Layos, Geromo, et al., 2022 ; Layos, Godinez, et al., 2022 ; Tanaka et al., 2008 ; Wu et al., 2007 ). These multiple ancestries suggest high genetic variation among PhNPs on different islands.…”

Population structure of Vietnamese pigs using mitochondrial DNA

“…Recent two studies (Banayo et al, 2023; Layos et al, 2022) reported the presence of a high frequency of MTSEA haplogroups (Layos et al, 2022, renamed MTSEA as D7) in native pigs in the Philippines, especially middle islands (South Luzon, Cebu, etc. ), as well as our result of the southern regions of Vietnam.…”