How long ago was this?
Plus, is it just male primates and other mammals that have a Y chromosome or do all male species have one now?
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This was millions and millions of years ago, back when mammals first split from reptiles. Not all males species have the Y chromosome, in butterflies, fishes, birds and reptiles the male has XX chromosomes and females have XY. Also in some insects like grasshoppers and cockroaches the females are XX and the males have an unpaired X chromosme (X0).