Abstract
A fine-grained mitochondrial DNA phylogenomic analysis was conducted in domestic pigs and wild boars, revealing that pig domestication in East Asia occurred in the Mekong and the middle and downstream regions of the Yangtze river.
Highlights
Reported evidence indicates that pigs were independently domesticated in multiple places throughout the world
The complete mitochondrial DNA (mtDNA) of 24 samples of wild boars and domestic pigs, each representing a unique haplotype in the major clades in this tree, were selected and sequenced
The African warthog is well known to be distinct from Eurasian wild boars and has frequently been used as the outgroup in previous phylogenetic studies of pigs [16,25,26,39,40,41,42]
Summary
Population phylogenomic analysis was conducted in domestic pigs and wild boars by screening the haplogroup-specific mutation motifs inferred from a phylogenetic tree of pig complete mitochondrial DNA (mtDNA) sequences. All domestic pigs are clustered into single clade D (which contains subclades D1, D2, D3, and D4), with wild boars from East Asia being interspersed. Three haplogroups within D1 are dominant in the Mekong region (D1a2 and D1b) and the middle and downstream regions of the Yangtze River (D1a1a), and may represent independent founders of domestic pigs. None of the domestic pig samples from North East Asia, the Yellow River region, and the upstream region of the Yangtze River share the same haplogroup status with the local wild boars. The limited regional distributions of haplogroups D1 (including its subhaplogroups), D2, D3, and D4 in domestic pigs suggest at least two different in situ domestication events
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