The phylogenetic relationship between Equus przewalskii and E. caballus is often a matter of debate. Although these taxa have different chromosome numbers, they do not form monophyletic clades in a phylogenetic tree based on mtDNA sequences. Here we report sequence variation from five newly identified Y chromosome regions of the horse. Two fixed nucleotide differences on the Y chromosome clearly display Przewalski"s horse and domestic horse as sister taxa. At both positions the Przewalski"s horse haplotype shows the ancestral state, in common with the members of the zebra/ass lineage. We discuss the factors that may have led to the differences in mtDNA and Y-chromosomal observations.
Animals Base Sequence DNA, Mitochondrial/genetics Genetic Variation/genetics* Horses/classification Horses/genetics* Male Molecular Sequence Data Phylogeny Probability Species Specificity Y Chromosome/genetics*