Genomic architecture predicts tree topology, population structuring, and demographic history in Amazonian birds

To test how variation in genomic characteristics (e.g., recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that co-occur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia.We resequenced 87 whole-genomes for three species of birds, Phlegopsis nigromaculata (n = 33; mean coverage = 10.5x with SD = 1.95; mean missing proportion = 0.17 with SD = 0.07), Xiphorhynchus spixii (n = 33; mean coverage = 11.0x with SD = 1.72; mean missing proportion = 0.16 with SD = 0.07), and Lipaugus vociferans (n = 30; mean coverage = 9.40x with SD = 1.73; mean missing proportion = 0.19 with SD = 0.09) that are co-distributed across three Amazonian areas of endemism, the Tapajos, Xingu, and Belem. Our samples consisted of tissues preserved in ethanol and toe pads from recently collected museum specimens.