All 5 of the extant sapient Xindi species have the same holes (and a line of bumps) on their cheeks, as can be seen below:
Has it ever been explained what purpose they serve, or how such different species (which clearly diverged evolutionarily long ago) retain these cheek holes if they're purely cosmetic?
Answer
In-Universe, the common features shared by the 6 Xindi species; Xindi-Aquatics, Xindi-Arboreals, Xindi-Insectoids, Xindi-Primates, Xindi-Reptilians and Xindi-Avians are largely as a result of their shared genetic heritage. According to Wikipedia, they have over 99.5% of their DNA in common so it's hardly surprising that they'd have common physical features.
As you can see from the mask shots below, the ridges are sealed so there's little chance that they serve a physical purpose as glands or for breathing. It's more likely that the skin ridge is a function of supporting the bone ridge (and spines) below.
Out of universe, the decision to have the Xindis evolve from a common ancestor requires that they should look at least a little bit alike or fans would say "if they evolved from a common ancestor, how come they look completely different?"
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