In some biomes or events you might encounter entirely unique species that you can not get through breeding base species.
These serve as low priority genes and when combined with base species genes (found in either hybrids or the base species themselves) will be ignored resulting in an "impure" version of the base species.
Any character where one or both genes is not a base species gene will be called impure by the game even though some otherwise act as a base species specimen.
For example a fusion of a seedling Girl and Lymean would look like a Lymean, have Lymean passives, and Lymean guaranteed skills (and inherited skills from both parents), yet would not provide any skill points through a ritual even if base Lymean was never ritualed.
Both pure and impure genes are still there and are still transferred, and in absence of base species genes impure genes WILL resurface (with one exception).
Continuing the example above if one were to fuse two such Lymean/SeedlingGirl characters one could chose to either create a normal Lymean or a normal Seedling Girl.
You could even make a normal hybrid out of two such (base+impure) mixes, so long as base genes are different.
One "impure" gene worthy of special note is the human gene. It never "resurfaces", and it is impossible to hatch a pure human. Any pure human egg has no stability and the stability cannot be raised through any means. Human units can be created either by fusing two pure human units, or via Siena's creation abilities, but that results in a unit using the portrait and default skills of the MC you are currently playing as. Human genes act as lower priority than any other genes, including spirits. So either breeding or fusing a human + seedling girl would result in a pure seedling girl. When breeding or fusing humans with basespecies hybrids, you will get a pure version of one of the two basespecies used to create the hybrid. So a human + lightbug will have offspring that are either Lymean or Insect.
Generally, species priority is something like:
Base genes>Impure humanoid/creature genes>spirit genes>human genes.
With two impure genes of the same priority, gene order seems to be the deciding factor. When fusing two impure humanoid genes, order is the deciding factor. For example a C_Unit/Elf will be a C_Unit, but an Elf/C_Unit will be an Elf. This is how you can breed new Infertile species like B_Unit or C_Unit.
With two spirits (either humanoid or creature) the second gene takes priority. With two creatures the first gene takes priority. With two humans an egg will fail. With two base species it's a hybrid, for which the order of genes means nothing.