Domestication Process of the Goat Revealed by an Analysis of the Nearly Complete Mitochondrial Protein-Encoding Genes

Abstract

Goats (Capra hircus) are one of the oldest domesticated species, and they are kept all over the world as an essential resource for meat, milk, and fiber. Although recent archeological and molecular biological studies suggested that they originated in West Asia, their domestication processes such as the timing of population expansion and the dynamics of their selection pressures are little known. With the aim of addressing these issues, the nearly complete mitochondrial protein-encoding genes were determined from East, Southeast, and South Asian populations. Our coalescent time estimations suggest that the timing of their major population expansions was in the Late Pleistocene and significantly predates the beginning of their domestication in the Neolithic era (≈10,000 years ago). The ω (ratio of non-synonymous rate/synonymous substitution rate) for each lineage was also estimated. We found that the ω of the globally distributed haplogroup A which is inherited by more than 90% of goats examined, turned out to be extremely low, suggesting that they are under severe selection pressure probably due to their large population size. Conversely, the ω of the Asian-specific haplogroup B inherited by about 5% of goats was relatively high. Although recent molecular studies suggest that domestication of animals may tend to relax selective constraints, the opposite pattern observed in our goat mitochondrial genome data indicates the process of domestication is more complex than may be presently appreciated and cannot be explained only by a simple relaxation model.

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica

“…; Nomura et al . ). In several cases, sub‐stoichiometric shifting has been associated with fertility reversion in cytoplasmic male sterility (Arrieta‐Montiel & Mackenzie ).…”

Mitochondrial DNA diversity of Anatolian indigenous domestic goats

“…These dates are consistent with the results observed by Nomura et al . (), suggesting that the timing of the major population expansions of the East, South‐East and South Asian populations was in the late Pleistocene period.…”

“…A mutation rate of 2.73 × 10 −7 /site/year, estimated by Nomura et al . (), was used. The distributions of pairwise differences were obtained using dnasp v4.90.1.…”

The characterization of goat genetic diversity: Towards a genomic approach

“…The analysis of complete mitochondrial genomes has been recently extended also to goat, to provide a more comprehensive molecular phylogeny of the species. A first study by Nomura et al (2013) goat domestication dynamics through the analysis of about 10 Kbp of mtDNA protein-encoding genes. Further (and still unpublished) analyses of more than 70 complete mtDNA sequences representative of C. hircus from western Eurasia and one wild goat (C. aegagrus) from Iran confirmed a restricted number of mtDNA haplogroups.…”