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To date, a large amount of equine genetic data has been obtained regarding (i) extant domestic horses of various breeds from all over the world, (ii) ancient domestic horses, (iii) the extant Przewalski's wild horse, and (iv) the late Pleistocene wild horse from Eurasia and North America.

Here, a review of mt DNA and Y chromosome marker analyses is presented in the context of horse domestication.

High matrilineal (mt DNA) diversity, which can be found in both extant and ancient (domestic and wild) horses, has suggested that a high number of wild (and tamed) mares were domesticated.

Alternatively, Y chromosome marker analysis revealed a single haplotype in all domestic horses analyzed; interestingly even a small population of extant Przewalski's wild horses showed two different Y chromosome haplotypes.

It seems that an extreme male population bottleneck occurred due to domestication, while reduction in the female population was only moderate, leaving about 100 distinct haplotypes.

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