Ancient Horse DNA Shows Scythian Warriors Were Adept Domesticators

At least in the US, inbreeding is indeed extensive. The vast majority of male horses are castrated at a young age, since intact males are considered more difficult to train and control (therefore more dangerous to humans) and more expensive to house than castrated males or intact females. Therefore, a small percentage of males end up fathering all the offspring. There are American Quarter Horse stallions with literally thousands of offspring (sometimes to their detriment, as when a popular stallion was belatedly discovered to carry a recessive genetic disease[0]).

It's therefore interesting to a modern horse person to read that "the Scythians maintained the natural herd structure" (a "harem" structure in which one male tends to sexually dominate several females - but several, not thousands, and not generally for his entire life).

[0] https://en.wikipedia.org/wiki/Impressive_(horse)

That's just part of the Y chromosome.

But this is a better cite:

> We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication.

Wallner et al. (2013) Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

http://journals.plos.org/plosone/article?id=10.1371/journal....

So yes, it seems that all domestic stallions descend from just one ancestor stallion. That's amazing!