Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus.

@article{Wallner2003FixedND,
  title={Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus.},
  author={Barbara Wallner and Gottfried Brem and M. M{\"u}ller and Roland Achmann},
  journal={Animal genetics},
  year={2003},
  volume={34 6},
  pages={
          453-6
        }
}
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… 

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