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Most social animals don't seem to care whether they're associating with a male or female of the same species unless it's mating time--otherwise, wouldn't these horses also be socially rejecting geldings and spayed mares?
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Having raised and trained both horses and dogs I can, with certainty, state that both respond to gender, not to "apparent physical sex". I don't know if they get their cues from body language or scent but the difference in behavior can be very obvious particularly in a mixed-gender heard or pack where there is an established social structure.