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Elucidating the demographic and phylogeographic histories of species providesinsight into the processes responsible for generating biological diversity, andgenomic datasets are now permitting the estimation of histories and demographicparameters with unprecedented accuracy. We used a genomic single nucleotidepolymorphism (SNP) dataset generated using a RAD-Seq method to investigate thehistorical demography and phylogeography of a widespread lowland Neotropicalbird (Xenops minutus). As expected, we found that prominent landscape featuresthat act as dispersal barriers, such as Amazonian rivers and the AndesMountains, are associated with the deepest phylogeographic breaks, and alsothat isolation by distance is limited in areas between these barriers. Inaddition, we inferred positive population growth for most populations anddetected evidence of historical gene flow between populations that are nowphysically isolated. Even with genomic estimates of historical demographicparameters, we found the prominent diversification hypotheses to be untestable.We conclude that investigations into the multifarious processes shaping specieshistories, aided by genomic datasets, will provide greater resolution ofdiversification in the Neotropics, but that future efforts should focus onunderstanding the processes shaping the histories of lineages rather thantrying to reconcile these histories with landscape and climatic events in Earthhistory.

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow