I support the Yggdrasil theme, with inspiration drawn from neurons and blood vessels for their designs.
Perhaps blood and bone? Antlers are bone(Albeit dead bone), and bone marrow creates blood. Blood carries oxygen and nutrients to the rest of the body.
Xerneus definitely has the enough antlers to represent the "bone" part, and Yveltal is blood red and could definitely "carry" things being as big as it is. Perhaps as guardians of the tree, Xerneus creates something that nourishes Yveltal/Yggdrasil, and Yveltal carries it off to spread it all over the rest of the tree.
That way when the evil team inevitably catch one, the other would rampage and need to be caught by the player and defeat the one caught by the evil team and somehow make the tree self sustaining.
Or maybe I'm totally off base and ones simply red, and one has horns. I dunno.
EDIT: Blood/Bone also fit with the genetic link too.
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