Selective sweeps and the role of divergent and parallel selection in Amazonian and Andean bird diversification

Both divergent and parallel selection can contribute to genomic and population differentiation, and thus speciation. However, the relative importance of each type of selection in driving speciation is poorly understood, especially in the context of environmental change. We compared selective sweeps and time of divergence in avian sister species pairs from the Amazonian lowlands that each underwent the same set of shared climatic cycles in parallel since speciating ( n =9 pairs) with species pairs from different elevations and environments ( n =8 pairs). Using phylogenetic multilevel Bayesian modeling, we inferred divergent selection in elevationally-differentiated pairs, while the lowland-restricted species pairs exhibited patterns consistent with parallel selection acting during glacial cycles as the key driver of selective sweeps. Parallel selection may play the key role in driving speciation in the species-rich lowlands where wide rivers are often the only barriers separating newly diverging species in similar environments.