Elucidating the demographic and phylogeographic histories of species provides
insight into the processes responsible for generating biological diversity, and
genomic datasets are now permitting the estimation of histories and demographic
parameters with unprecedented accuracy. We used a genomic single nucleotide
polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the
historical demography and phylogeography of a widespread lowland Neotropical
bird (Xenops minutus). As expected, we found that prominent landscape features
that act as dispersal barriers, such as Amazonian rivers and the Andes
Mountains, are associated with the deepest phylogeographic breaks, and also
that isolation by distance is limited in areas between these barriers. In
addition, we inferred positive population growth for most populations and
detected evidence of historical gene flow between populations that are now
physically isolated. Even with genomic estimates of historical demographic
parameters, we found the prominent diversification hypotheses to be untestable.
We conclude that investigations into the multifarious processes shaping species
histories, aided by genomic datasets, will provide greater resolution of
diversification in the Neotropics, but that future efforts should focus on
understanding the processes shaping the histories of lineages rather than
trying to reconcile these histories with landscape and climatic events in Earth
history.Comment: 61 pages, 4 figures (+3 supplemental), 3 tables (+6 supplemental
