Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boars

Abstract

34 35 The Philippine archipelago was believed to have never been connected to the Asian continent 36 even during the severe Quaternary sea-level drops. As a result, the history of pig dispersal in 37 the Philippines remains controversial and must have some anthropogenic origin associated with 38 some human migration events. In this study, the context of origin, dispersal, and the level of 39 genetic introgression in Philippine native pigs were deduced using mitochondrial DNA D-loop 40 analysis altogether with domestic pigs and wild boars corresponding to their geographic origin. 41 Results revealed a considerable genetic diversity (0.900±0.016), and a widespread Asian pig- 42 ancestry (94.60%) were revealed in the phylogenetic analysis with admixed European pig- 43 origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close 44 genetic connection between the continental wild boars and domestic pigs present in the 45 Philippine pigs corroborates our hypothesis of a genetic signal that could potentially be 46 associated with the recently reported multiple waves of human migrations to the Philippines 47 during the last 50,000 years. The high frequency of haplotypes (54.08%) that collapsed in the 48 D7 haplogroup represent an interesting challenge as its distribution does not coincide with the 49 hypothesized migratory route of the Neolithic Austronesian-speaking populations. We detected 50 the first Pacific Clade signature and ubiquitously distributed D2 haplotypes which postulate 51 the legitimate dispersal of pigs associated with the multiple waves of human migrations 52 involving the Philippines. The multimodal mismatch and neutrality test statistics both Fu’s 53 Fs and Tajima’s D correlates the long stationary period of effective population size revealed in 54 the Bayesian skyline plot. While the sudden decrease in population was consistent with the 55 pronounced population bottleneck of Asian and European pigs during the interglacial periods 56 of the Pleistocene. 57 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.23.453525; this version posted July 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. 3 58