A few years ago, I was thinking about genetic male morphs. Turns out that you find qualitatively different forms of males in many species: Barry Sinervos’s lizards, Shuster’s isopods, Lank’s ruffs, jack salmon, etc. Logically, the Y chromosome would be the best place for a such a genetic switch, since that would avoid negative side effects in females. The problem is that the Y carries very few genes.
Alternate strategies don’t have to to be as complicated as they are in ruffs or Uta stansburiana. Different levels of aggressiveness, or different points on the cad/dad axis, would have different selective payoffs in different environments. If a new environment favored lower (or higher) aggressiveness in males , a Y-chromosome that induced lower (or higher) aggressiveness would take off. And since different Y chromosomes do indeed affect the level of aggressiveness in mice [which I just found out], possibly by affecting testosterone production – this mechanism is plausible.
This could explain a funny genetic pattern in the domestication of horses. There’s a fair amount of diversity in horse mtDNA: it looks as if many different mares were domesticated. On the other hand, it looks as if only one stallion was ever domesticated. All living stallions today are his descendants.
Stallions are pretty aggressive, and must have been hard to tame. Maybe one was genetically unusual – wimpier. Tameable.
Fortunately for all concerned, the selective value of aggressiveness, etc. has been the same for all human populations forever and ever, before and after the development of agriculture. Otherwise you might see weirdly rapid expansions of particular Y-chromosome haplogroups – common, yet only a few thousand years old.