The BTAX and Y carry a great number of SNP with
high difference in allelic frequencies between groups.
These chromosomes have probably undergone much
stronger selection or, more parsimoniously, higher genetic
drift, due to their unique inheritance [6], and the
history of domestication, selection, breed formation.
Furthermore, the intensive use of artificial insemination
techniques have likely contributed to the reduction of
genetic variability within breeds (or cattle types) in these
chromosomes. It is understood that in the case of the
SNP that are polymorphic in both cattle types, the alternative
allele likely arose within the cattle population before
the split between taurine and zebu, and remained in
both populations at variable frequencies. Alleles that are
fixed in one subspecies and variable in the other possibly
arose after the split. However, this understanding does
not take into account that alleles that were fixed in one
population also might have arisen before the split, but
were fixed due to different selection processes or as a
result of different bottlenecks on the populations. The
identification of the ancestral allele of these SNP, ideally
using whole genome sequences of other Bovids, would
contribute to understand the evolutionary processes
behind these monomorphic sites.