Hmm, I think the EA meaning is pretty similar to the evobio meaning.

I think that in EA, "founder effects" are when a new group (e.g. people interested in existential risk) is initialized by some unusual individuals, and it grows, leading the group to retain some of those peculiarities. It's especially used for describing properties that arose from happenstance (e.g. they like Harry Potter), rather than expected differences (e.g. they like abstract thinking).

In evolutionary theory, they seem to be exclusively focused on the effects of randomly sub-sampling a population, but it's basically the same idea.

Edit: This looks like it is be wrong - the oldest reference I found on the EA Forum to it is explicitly the biology one: https://forum.effectivealtruism.org/posts/WAhFnueRgHkAf8KHc/making-ea-groups-more-welcoming.

My guess would be that people have accidentally swapped "founder's syndrome" with "founder effects." Founder's syndrome is widely used outside EA to refer to the things people are talking about: https://en.wikipedia.org/wiki/Founder's_syndrome. EA seems to use it to refer to a wider range of things, but this seems more likely than people intentionally applying founder effects from bio, since the meaning of founder effects in bio is pretty different and very specific.