  More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences
have been deposited in GenBank for eight common domestic animals (i.e. cattle,
dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors
or relatives. Nevertheless, few efforts have been performed to evaluate the
sequence data quality, which heavily impact the original conclusion. Herein, we
conducted a phylogenetic survey of these complete or near-complete mtDNA
sequences based on mtDNA haplogroup trees for the eight animals. We show that,
errors due to artificial recombination, surplus of mutations, and phantom
mutations, do exist in 14.5% (194/1342) of mtDNA sequences and shall be treated
with wide caution. We propose some caveats for mtDNA studies of domestic
animals in the future.
