The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.

Understanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.