Further resolution of porcine phylogeny in Southeast Asia by Thai mtDNA haplotypes

Summary The mtDNA control region of 72 Thai native pigs and 11 Thai wild boars indigenous to Northern Thailand was comparatively sequenced. In total, 36 nucleotide variations that accounted for 24 haplotypes have been described (TNH01 to TNH20 and TWH01 to TWH04). These haplotypes and further publicly available mtDNA haplotypes were used to assess phylogenetic relationships. Twenty‐three of the 24 haplotypes became integrated into the Asian clade of the phylogenetic tree and eight of them recapitulated another major cluster of haplotypes within this clade (Thai haplogroup, THG). Only haplotype TNH01 fit in with the European clade of the phylogenetic tree. An additional analysis using 510 bp of the mtDNA incorporated the THG haplotypes in to clade MTSEA (mountainous and Southeast Asian distribution) to form haplogroup MTSEA‐THG. Recently, MTSEA was renamed in MC3. MC3 contains only signatures of pigs scattered across the Indo‐Burma Biodiversity Hotspot (IBBH), a region including Thailand to the Kra Isthmus. Here we propose a putative independent porcine domestication event in South‐east Asia (SEA). All haplotypes of haplogroup MTSEA‐THG have revealed unique and previously unknown nucleotide signatures at positions 24 (nucleotide A) and at positions 183 (nucleotide C) that differentiate them from all other porcine mtDNA haplotypes.