Data from: Genomic architecture drives population structuring in Amazonian birds

Geographic barriers are frequently invoked to explain genetic structuring
across the landscape. However, inferences on the spatial and temporal
origins of population variation have been largely limited to evolutionary
neutral models, ignoring the potential role of natural selection and
intrinsic genomic processes known as genomic architecture in producing
heterogeneity in differentiation across the genome. To test how genomic
architecture impacts our ability to reconstruct general patterns of
diversification in 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 found that
phylogenetic relationships within species and demographic parameters
varied across the genome in predictable ways. Genetic diversity was
positively associated with recombination rate and negatively associated
with species tree support. Gene flow was less pervasive in regions of low
recombination, making these windows more likely to retain patterns of
population structuring that matched the species tree. We further found
that approximately a third of the genome showed evidence of selective
sweeps and linked selection, skewing genome-wide estimates of effective
population sizes and gene flow between populations towards lower values.
In sum, we showed that the effects of intrinsic genomic characteristics
and selection can be disentangled from neutral processes to elucidate how
inferring spatial patterns of diversification are sensitive to genomic
architecture.