Data for: Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow

Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplai..., Please see the README document (\"README.md\") and the accompanying published article: Johnson, O., C.C. Ribas, A. Aleixo, L.N. Naka, M.G. Harvey, and R.T. Brumfield. 2023. Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow. Molecular Ecology. Accepted.
In brief, we obtained ultraconserved element loci from 587 samples of 66 species of Amazonian birds. Species were approximately evenly split among three habitats that vary from highly dynamic riverine islands, floodplain forests, and stable upland forests. We employed a suite of phylogenetic and population genetic methods on each species to test for effects of gene flow and genetic structure among species in these three habitats. , Please see the README document (\"README.md\") and the accompanying published article: Johnson, O., C.C. Ribas, A. Aleixo, L.N. Naka, M.G. Harvey, and R.T. Brumfield. 2023. Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow. Molecular Ecology. Accepted.
Code is available at https://github.com/henicorhina/Riverine_islands_code, and is archived at Zenodo https://zenodo.org/badge/latestdoi/135321103.