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Lots of confusion here, sjp- so let's take your questions one by one:

"I've read all neos don't generally breed true"

Only true for some strains such as Blue Diamonds and some say Bloody Marys. Chocolates can sometimes throw "blonds," but the majority of colors in the hobby breed true.

" lets say if I leave my RCS tank and never cull them out...
would I eventually get natural color shirmps in the tank?"

If your shrimp throw a wild, then the wild genes will take over. Otherwise the shrimp will gravitate toward the lowest grade of whatever color you have.

"if one of my RCS mama let out yellow, blue, or whatever different color neos..."

Unless you happen to have a spontaneous mutation which is exceedingly rare, that just won't happen. Yellows, blues, etc are selectively bred varieties.

"If I get red rilli, blue rilli, carbon rilli from blue velvet and leave them without culling them out..."

You won't. Blue velvet has a mutation that fades red away by juvie age. They breed true and you won't get red rili, blue rili or carbons from them.

Now having said that, Red rilis can throw blue rilis and visa versa, but they will not throw carbons.

"would I eventually get natural color shrimps? "

These are referred to as "wilds" and if you breed two neo colors together, then this is often the case.
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