> Yes, some parts are inherently O(n²) (mate finding, crowd density, predator/prey proximity, pathogen spread). Ecology needs pairwise relationships.

You might be able to do a bit better for some of these, check this out https://en.wikipedia.org/wiki/N-body_simulation

Essentially the idea in some optimizations is to divide the space into cells, and so you can discard relations with elements in far away cells.

Could use quad trees, or similar bucketing. But I think he already stated that he tried to avoid the processing of long distance pairs. So probably he does some localized bucketing. Personally, I don't even fully understand what his simulation is doing. There are tradeoffs between accuracy / performance, depending on the specific problem. So hard to judge here.