Horse domestication incorporated most wild horses, mtDNA suggest

Welsh Pony

A new paper on equine mitochondrial DNA, focusing on shedding light on the origins of domestic horse (Equus caballus) is available:

Sebastian Lippold et al. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evolutionary Biology 2011. Open access.

From the Results section:

Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.

As always, I have a general attitude of caution on molecular clock estimates (and in this case the authors agree with such precautionary attitude). So I take these figures as mere loose references, however the overall notion of most mitochondrial DNA being ample spectrum pre-domestic seems correct and has been demonstrated in the past.

This wide maternal ancestry seems to persist even within breeds. Only the Welsh pony of all breeds sample showed some tendency towards a single matrilineage. 

Bayesian Skyline Plot of effective population size through time based on the
whole mtDNA sequence from 63 horses. The beginning of the recent effective population
size expansion is marked in red (median 7,000 years BP).

Actually, if we take this estimated chronology at face value and use oly the median values (blue line), the expansion would seem to go strong only towards 6000 years ago, 4000 BCE, roughly the age of horse domestication per the usual archaeological understanding.

See also: category: horse genetics.