An interesting passage from the horse genome paper:
We were unable to phylogenetically separate E. przewalskii from the domesticated horses, despite its different karyotype (2N = 66 versus 2N = 64 for the domesticated horse), which is in agreement with recent findings (16), whereas the donkey (E. africanus) is clearly a distinct taxon (fig. S9, table S14, and SOM text). This suggests that either intermixing of E. przewalskii and E. caballus occurred after subspecies separation or that E. przewalskii is recently derived from E. caballus.
My first thought on seeing they'd completed a horse genome draft was that this would be really useful as a model for understanding the origin and dispersal of a new species -- the idea being that we know a lot archaeologically about horse domestication, and introgression from the wild progenitor species would have been limited to a certain range that we can sort of predict. However, that passage makes it sound not-so-simple.
The paper also mentions the "widespread synteny" of human and horse genomes, which I suppose means there are different chromosomal pairings that stand out because the other known non-primate mammalian genomes are on different long branches (dog, cow, pig, mouse, elephant, etc.). We've got quite a decent sampling of long-diverged mammalian orders.
