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

Abstract

The Philippine archipelago was believed to have never been connected to the Asian continent, even during the severe Quaternary sea-level drops. As a result, the history of pig dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with some human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine native pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boars corresponding to their geographic origin. Results revealed a considerable genetic diversity (0.900±0.016), and a widespread Asian pig-ancestry (94.60%) were revealed in the phylogenetic analysis with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine pigs corroborates our hypothesis of a genetic signal that could potentially be associated with the recently reported multiple waves of human migrations to the Philippines during the last 50,000 years. The high frequency of haplotypes (54.08%) that collapsed in the D7 haplogroup represent an interesting challenge as its distribution does not coincide with the hypothesized migratory route of the Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes which postulate the legitimate dispersal of pigs associated with the multiple waves of human migrations involving the Philippines. The multimodal mismatch and neutrality test statistics both Fu’s Fs and Tajima’s D correlates the long stationary period of effective population size revealed in the Bayesian skyline plot. While the sudden decrease in population was consistent with the pronounced population bottleneck of Asian and European pigs during the interglacial periods of the Pleistocene.

Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA

“…Based on the patterns of mutational signatures, the most numerous haplotypes (20 haplotypes; n = 103/184, 55.98%) in our dataset which covered the largest area, formed an independent clade although this haplogroup was not present in Northern Luzon. While this study is the first analysis to resolve the complete mtDNA D-loop of a substantial number of sequences from these populations, it shows that it has an analogous signature to the previously documented haplogroup in MSEA, which was classified as D7 based on short/partial fragment analysis (510 bp) ( Tanaka et al, 2008 ; Layos et al, 2021 ). Using complete D-loop fragment analysis, we confirmed that this haplogroup is distinct from the available haplogroup that has been tentatively classified by haplogroup-specific motif recognition in porcine mtDNA ( Larson et al, 2005 ; Wu et al, 2007 ).…”

“…By screening and detecting the haplogroup-specific mutational motifs, we assigned each haplotype based on the smallest named sub-phylo groups to which it belongs. Recently, it has been proposed that the six major clusters of porcine mtDNA sequences, designated D1 to D6 ( Larson et al, 2005 ), with the addition of D7 (previously designated MTSEA, which is thought to be restricted to the Indo-Burma Biodiversity Hotspots (IBBH); Tanaka et al, 2008 ; Larson et al, 2010 ; Layos et al, 2021 ) reflect domestication from genetically distinct subpopulations of wild boars ( Supplementary Table S3 ). Our results showed that the D-loop sequences of Philippine pigs obtained in this study could be classified into five phylogenetically distinct haplogroups such as D1, D2, D6, D7, and Lanyu Clade, except for the Philippine wild pig haplotypes (PHL44-47).…”

“…This method calculates the net divergence of each taxon from all other taxa as the sum of the individual distances from variance within and among groups. The nomenclatures described by Larson et al (2005) with six clades (D1 to D6) including the newly proposed mitochondrial Southeast Asia (MTSEA) haplogroup ( Tanaka et al, 2008 ), previously renamed D7 by Layos et al (2021) , were used as a reference for clade notation. We also performed the network analysis on shorter sequences (509 bp) to accommodate the major representative haplotypes by partial mtDNA resolution, which were used in the previous studies for a thorough haplotype representation of the different haplogroups and geographical locations.…”