Just occured to me that we have in-game confirmation that the Mystics
are a branch of humanity, specifically a magic using branch (and if magic, then presumably effected by Lavos and the frozen flame).
Spekkio, when you first meet him, says the following (with the retranslation next to it):
You are strong of will...! / Hm?
That's why the Old One let you / You guys have it.
through. / Power of the heart......
/ I get it, that's why the old man outside let you
/ in here.
Long before you were born... / Long before you guys were born......
...there was a kingdom where / There was a kingdom that prospered by magic.
magic flourished. /
Everyone there could use it! / Everyone in that world used magic.
But in time, people began to abuse / But that country grew addicted to magical power
their powers. It got so bad that no / and was destroyed......
one was allowed to use magic / After that, people became unable to use magic.
except wizards. / Except for the Demons anyway.
But you have it...determination, I / But you guys've got it. Strength of the heart.
mean! /
Magic needs power of the heart. /
It needs inner strength. / Magic's the heart's strength, power.
I bolded the important part. After the fall of zeal, no one who had been able to use magic was subsequently able to use magic... except for Demons/Wizards (which we know as Mystics).
Mystics are counted among people, which is a label usually applied only to humans. This very strongly implies that mystics aught be counted among humans. I'd propose the label Homo Enigmus or Homo Sapien Engimus, depending on if we count Mystics as a separate species of the same order or a subspecies of Homo Sapiens.
Given there behavior, I'd actually argue that they may have been effected more by the frozen flame than the Enlightened Ones. For one, they seem to be a rather violent lot (achieving a peaceful coexistence only with the help of the Entity via Chrono and Co). They have a close association is abominations such as the undead. The Mystic creature Retinite is in some way responsible for Fiona's forest dying out (and Fiona's Forest itself is strongly tied to the Entity, so Retinite is playing a lavos-like role). And it is by manipulating the Mystics that Magus was able to attempt to contact Lavos (thereby, offering a circumstantial connection between the Mystic and Lavos).
So, then, from that we might be able to actually propose a model of "human" evolution
/ -----------Mystics
Prehistoric Humans ---
\ /-----Enlightened Ones ----\
\---- --------- Modern Humans
\-----Earth Bound ----------/
Or possibly:
/-----------Earth Bound -------------------------\
Prehistoric Humans ---- --------- Modern Humans
\ /---- Enlightened Ones ---/
\----Magic Users---
\----- Mystics
Or even:
/-----------Earth Bound ----\
Prehistoric Humans ---- --------- Modern Humans
\ /
\---Enlightened Ones-----
\
\----- Mystics
Personally, I am inclined towards model 2 and 3, as an earlier deviation might also reduce the significance of Spekkio's "except" comment.