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

Abstract

33 34 Philippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. 35 They are valued locally for their various sociocultural roles. Recently, considerable literature has 36 accumulated in the field of native pig production and marketing. However, there is limited research on 37 the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among 38 native pigs from various islands and provinces in Luzon and Visayas, Philippines. In addition, a much- 39 debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild 40 pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of 41 PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n=157) were collected 42 from 10 provinces in Luzon and the Visayas, Philippines. Approximately 650 base pairs of the mtDNA 43 d-loop control region were sequenced and analyzed together with publicly available sequences. Pairwise- 44 distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL 45 with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig 46 domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). 47 We identified 19 haplotypes (1-38 samples each), forming 4 haplogroups i.e. North Luzon, South Luzon 48 and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the 49 native pig population, but the use of wild pig for interspecific hybridization was observed. This study 50 showed that the Philippine native pigs have ancestral origin from at least 3 Sus scrofa lineage and that 51 they were not domesticated from the endemic wild pigs of the Philippines. 52 53 54 Keywords: Mitochondrial DNA d-loop control region, Indigenous pig, Livestock, Biodiversity, 55 Haplotype, Conservation 56 3 bioRxiv preprint doi: https://doi.org/10.1101/2022.10.16.510730; this version posted October 20, 2022. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 57