A while ago, I wondered if modern stallions are a male morph adapted to domestication, one in which the strategy is mediated via the Y chromosome.
Looks as if I was right*. Check out “Decline of genetic diversity in ancient domestic stallions in Europe”.
Selection favored one particular kind of Y-chromosome. This had to be based on phenotype, not genealogy. Most likely it was favored under the new environment of domestication. Somehow, these stallions performed better, or were easier to get along with (my bet).
We already knew that Y-chromosomes could do things: Haplogroup I increases the risk of heart disease by about 50%, while the particular variant of Y chromosome influences aggression in mice.
Which means you have to re-examine the starburst phylogeny of R1b and R1a: it’s probably biology, rather than history, that drove those expansions. Some kind of selective advantage. Possibly one reason that those particular Y chromosomes far outraced steppe autosomal contributions. Most likely, R1a and R1b induce specific morphs – their carriers are somehow different. Maybe they’re born to be mild, or born to be princes of the universe. Maybe an R1b guy just finds it easier to cooperate with other R1b guys… Or maybe they’re resistant to typhoid.
* correct predictions mean nothing in biology. Ask any biologist.