Abstract
BackgroundA major reduction of genetic diversity in mtDNA occurred during the domestication of East Asian pigs. However, the extent to which genetic diversity has been lost in the nuclear genome is uncertain. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationships and demographic history of domestic pigs and their ancestors, wild boars, we investigated 14 nuclear markers (including 8 functional genes, 2 pseudogenes and 4 intergenic regions) from 11 different chromosomes in East Asia-wide samples and pooled them with previously obtained mtDNA data for a combined analysis.Principal FindingsThe results indicated that domestic pigs and wild boars possess comparable levels of nucleotide diversity across the nuclear genome, which is inconsistent with patterns that have been found in mitochondrial genome.ConclusionsThis incongruence between the mtDNA and nuclear genomes is suggestive of a large-scale backcross between male wild boars and female domestic pigs in East Asia. Our data reveal the impacts of founder effects and backcross on the pig genome and help us better understand the complex demographic histories of East Asian pigs, which will be useful for future work on artificial selection.
Highlights
Domestication has been generally seen as a process that starts with a small number of wild individuals, which through succeeding generations of breeding, are integrated into human societies and thereby lose almost all opportunities to mate with their wild relatives [1,2,3,4,5]
Our data reveal the impacts of founder effects and backcross on the pig genome and help us better understand the complex demographic histories of East Asian pigs, which will be useful for future work on artificial selection
We conducted the analyses for wild boars and domestic pigs separately in addition to all samples combined since the hierarchical structure of wild boars or domestic pigs might not be detected if they both were combined into a single analysis
Summary
Domestication has been generally seen as a process that starts with a small number of wild individuals, which through succeeding generations of breeding, are integrated into human societies and thereby lose almost all opportunities to mate with their wild relatives [1,2,3,4,5]. Existing evidence has implicated artificial selection as another major cause of founder effects, in addition to domestication bottlenecks [7,18,19,20,21,22] The difference between these two factors is that domestication bottlenecks reduce genetic diversity across the entire genome, while artificial selection is expected to reduce diversity only at selected loci, plus linked regions. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationships and demographic history of domestic pigs and their ancestors, wild boars, we investigated 14 nuclear markers (including 8 functional genes, 2 pseudogenes and 4 intergenic regions) from 11 different chromosomes in East Asia-wide samples and pooled them with previously obtained mtDNA data for a combined analysis
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