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

Both divergent and parallel selection can contribute to evolutionary change, yet their relative contributions to adaptation and speciation are poorly understood, especially during environmental change. We quantified selective sweep signatures and divergence times in Amazonian avian sister species pairs that either differ in elevation and are expected to have experienced strong divergent selection; or occur in similar lowland habitats and are expected to have experienced strong parallel selection. We found that elevational differentiation resulted in a greater accumulation of selective sweep signatures over the five-million-year timespan covered by our dataset, supporting the importance of divergent selection. Nevertheless, lowland-restricted species pairs accumulated more selective sweeps over the most recent two million years, suggesting that parallel selection, driven by major Pleistocene glacial cycles, produced faster evolutionary change than divergent selection in elevationally differentiated species pairs. Our results highlight parallel selection as an important driver of adaptation and evolution, especially during environmental instability.