Many understory birds and other groups form genetically differentiated subspecies or closely related species on opposite sides of major rivers of Amazonia, but are proposed to come into geographic contact in headwater regions where narrower river widths may present less of a dispersal barrier. Whether such forms hybridize in headwater regions is generally unknown, but has important implications to our understanding of the role of rivers as drivers of speciation. We used a dataset of several thousand single nucleotide polymorphisms to show that seven taxon pairs that differentiate across a major Amazonian river come into geographic contact and hybridize in headwater regions. All taxon pairs possessed hybrids with low numbers of loci in which alleles were inherited from both parental species, suggesting they are backcrossed with parentals, and indicating gene flow between parental populations. Ongoing gene flow challenges rivers as the sole cause of in situ speciation, but is compatible with the view that the wide river courses in the heart of Amazonia may have driven interfluvial divergence during episodes of wet forest retraction away from headwater regions. Taxa as old as 4 Ma in our Amazonian dataset continue to hybridize at contact zones, suggesting reproductive isolation evolves at a slow pace.

Phylogeographical studies of the most species‐rich region of the planet—the Amazon basin—have repeatedly uncovered genetically distinctive, allopatric lineages within currently named species, but understanding whether such lineages are reproductively isolated species is challenging. Here we harness the power of genome‐wide data sets together with detailed phylogeographical sampling to both characterize the number of unique lineages and infer levels of reproductive isolation for three parapatric manakin species that make up the genus Pipra. The mitochondrial and nuclear genomes both support six distinctive lineages. The youngest lineages are now highly admixed with each other across major portions of their geographical ranges with one lineage now extinct in a genomically unadmixed state. In contrast, the oldest sets of lineages—dated to 1.4 million years—exhibit narrow hybrid zones. By fitting demographic models to parapatric lineage pairs we found that levels of gene flow and genomic homogenization decline with increasing evolutionary age. Only lineages descending from the basal node at 1.4 million years ago in the genus experience negligible gene flow, possess genomes resistant to homogenization and are separated by narrow hybrid zones. We conclude that a million years or more were required for Pipra manakins to become reproductively isolated. We suggest the six lineages be reclassified as two or three reproductively isolated species. Our unique approach to quantifying reproductive isolation in parapatric lineages could be applied broadly to other phylogeographical studies and would help determine species classification of the plethora of newly identified lineages in the Amazon basin and other regions.

∙ Few studies have investigated how the abundance of food resources influences the phenology of the annual cycles of tropical birds. Frugivorous birds are good models for such investigation because the abundance of their main food types, fruits and arthropods, vary independently from each other. We investigated how the consumption and availability of fruits and arthropods are related to breeding and molt cycles of frugivorous birds in a fragmented landscape of the Brazilian Atlantic forest. We recorded the occurrence of brood patches and the molting of flight feathers in mist‐netted birds, from which we also analyzed the contents of fecal samples. Using nonparametric and parametric correlation tests we investigated the relationships among breeding and molt stage with the availability of fruits and arthropods. We found that the availability of fruits and arthropods fluctuates temporally and independently, but both food sources have shortage periods, apparently more pronounced for fruits. During periods when fruit was scarce, birds relied more heavily on arthropods as food. Incubation occurred when fruit availability was high, whereas the molt period that followed was coincident with the availability of arthropods. Although our observational study does not permit definite conclusions regarding the relationship between food availability and the timing of the annual cycle events investigated, it is suggestive that avian breeding and molt cycles coincide with fruit and arthropod availability, respectively. Together with arthropods, fruits are important for nestlings of frugivorous birds, and protein from arthropods may be especially important for the development of new feathers.RESUMO ∙ Relação entre disponibilidade de alimento, muda de penas e reprodução de aves frugívoras Poucos estudos abordaram a influência da abundância de recursos alimentares sobre a fenologia do ciclo anual de aves tropicais. Aves frugívoras são bons modelos para esse propósito porque as abundâncias dos seus principais alimentos, frutas e artrópodes, podem variar no tempo de maneira independente. Neste trabalho investigamos como os ciclos de muda de penas de voo e reprodução estão relacionados com a disponibilidade e o consumo de frutos e artrópodes em uma paisagem fragmentada de Mata Atlântica. Para isso registramos a ocorrência de placa de choco e mudas nas penas de voo de aves capturadas em redes de neblina e sua relação temporal com a disponibilidade de frutos e artrópodes amostrados nas áreas das redes. A disponibilidade de frutos e artrópodes apresentaram flutuações temporais independentes, porém ambos apresentaram períodos de escassez, aparentemente mais pronunciado para os frutos. Durante períodos de escassez de frutos, as aves consumiram mais artrópodes. O período de incubação ocorreu quando a disponibilidade de frutos era maior, enquanto a muda de penas coincidiu com o período de maior disponibilidade de artrópodes. Embora nosso estudo observacional não permita conclusões definitivas sobre a relação entre a disponibilidade de alimentos e os eventos de ciclo anual investigados, é sugestivoque os períodos de reprodução e muda tenham coincidido com maior disponibilidade de frutos e artrópodes, respectivamente. Juntamente com artrópodes, frutos podem ser importantes para a criação dos filhotes das aves frugívoras, enquanto proteína proveniente dos artrópodes pode ser especialmente importante para o desenvolvimento de novas penas..