Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs

Abstract

Selection in genomic regions is prevalent in mammals; however, the effects of selection on the mitogenome are not clearly understood. We determined the complete mitochondrial DNA (mtDNA) sequences from six wild Tibetan pigs from the Tibetan plateau and four domestic pig breeds from the lowland of neighboring southwest China. Nucleotide diversity analysis using the sliding window method showed that the nucleotide diversity of wild Tibetan pigs in most regions of the mitogenome was higher than that of domestic pigs. The 12 s ribosomal RNA showed relatively lower nucleotide diversity in Tibetan pigs, suggesting purifying selection of these genes during high-altitude adaptation. More non-synonymous nucleotide substitutions in the ATP6 were found in wild Tibetan pigs, indicating adaptive selection in Tibetan pigs. The results suggested distinct impacts of natural selection and artificial selection upon the mitogenome, especially the mitochondrial signatures of adaptive evolution in wild Tibetan pigs under natural selection.

• Adaptation
• high altitude
• mitochondrial DNA
• natural selection

Declaration of interest

The authors have declared that no competing interests exist. This work was supported by grants from the National High Technology Research and Development Program of China (863 Program) (2013AA102502), the National Special Foundation for Transgenic Species of China (2014ZX0800950B and 2011ZX08006-003), the Fund for Distinguished Young Scientists of Sichuan Province (2013JQ0013), the Specialized Research Fund of Ministry of Agriculture of China (NYCYTX-009), the Program for Changjiang Scholars and Innovative Research Team in University (IRT13083), the Postdoctoral Fellowship of Peking-Tsinghua Center for Life Sciences, and the China Postdoctoral Science Foundation (2012M520123).