Habitat specialization structures population divergence and demographic variation in Amazonian floodplain birds

Understanding how species respond to environmental change requires linking ecological traits to gene flow and demographic history across dynamic landscapes. Using population genomic data from twelve co-distributed Amazonian riverine island birds, we show that habitat specialization predicts genetic structure, divergence, and effective population size. Species specialized on dynamic sandbar scrub habitats exhibit higher gene flow, and higher genetic diversity despite smaller effective population sizes. These patterns are consistent with dispersal tracking shifting resources, which decouples genetic diversity from population size. In contrast, river-edge forest specialists show stronger spatial genetic structure and lower genetic diversity despite larger populations, consistent with long-term isolation in more stable habitats. We also detect regional variation in effective population sizes and genetic diversity across Amazonian river sub-basins, potentially reflecting historical differences in floodplain habitat availability. Overall, our results highlight how non-equilibrium dynamics shape genomic variation and emphasize habitat-driven dispersal in diversification and persistence in seasonal systems.