Ephemeral habitats promote gene flow and limit population genetic structure in Amazonian birds

Species vary considerably in the degree of population genetic structure, but the factors that govern this variation are poorly understood. Genetic structure is known to correlate with many aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence how populations interact with the landscape to produce discontinuities in gene flow. Genetic data can reveal how traits shape gene flow, and comparative studies provide an opportunity to tease apart the importance of particular traits as predictors of genetic structure. Here, we use population genetic data from sets of species found across a series of Amazonian habitat types hypothesized to select for different dispersal abilities. Using loci from across the genome, we show that habitat type effects population genetic structure, with species in river island habitats, floodplain forest, and upland forest exhibiting progressively increasing levels of structure. Although morphological traits often used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species associated with dynamic and ephemeral riverine habitats. Our results suggest that species specialized on particular habitats, especially ephemeral riverine islands, have histories involving high levels of gene flow at evolutionary timescales, which shapes observed variation in population genetic structure across species and may lead to disparities in diversification among habitats.