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The two "wildcard" factors to me are the bad genes and the mutagenic genes. From what I gather, the mutagenic genes make it more likely that a member of the subspecies will spawn with different loci than what you've specified, but that's mostly just a guess. It could also relate to them spawning as new subspecies or just same variance in stats. It's hard to say without any official documentation being made available yet. I think the bad genes just cancel out any potential connections between the loci they're touching. They're not well explained anywhere nor are the effects super obvious to me. But I can say for sure that giving a creature a genome full of bad genes makes it trivial to kill them off, so The Accomplished achievement became completely trivial to unlock. Also, the effects of loci DO stack, so you can fill up a genome with whatever locus you want over and over again to make something hilarious. I made giant ants to subject the world to EDF-style shenanigans, which was a lot of fun.
It's not like normal DNA, where A pairs with T and G pairs with C, instead it just needs to be the same letter on both genes?
Though, looking at other genes, they don't follow the same pattern, so maybe it's just a coincidence.
Harmful genes halve the effects of neighboring genes. Multiple harmful genes don't reduce it any further. For whatever reason, Health I, Speed I, and Damage I round up instead of down, meaning they are unaffected by harmful genes. Attack Speed isn't rounded at all and will provide +0.5 instead of +1 if affected.
Amplifiers act like mutagenic genes, except they don't increase Mutation Rate and can't be moved.
Mutagenic genes affected by harmful genes will still connect to neighbors but won't increase Mutation Rate.
Tainted Amplifiers are caused by an amplifier being affected by a harmful gene. They won't ever connect to neighboring genes which means neighboring genes will never achieve synergy.
A gene with no neighbors at all will always be synergized.
Amplifiers sometimes have no neighbors.
Also, uplifted species keep the same genes.
I encountered the same a couple of times. It gave an error in the games console window as well when it happened so i think its a bug currently.
You did not imagine it