Data from: Amazonian rivers are leaky barriers to gene flow in forest understory birds

Ever since Alfred Russel Wallace’s nineteenth-century observation that
related terrestrial species are often separated on opposing riverbanks,
major Amazonian rivers have been recognized as key drivers of speciation.
However, rivers are dynamic entities whose widths and courses may vary
through time. It thus remains unknown how effective rivers are at reducing
gene flow and promoting speciation over long timescales. We fit
demographic models to genomic sequence to reconstruct the history of gene
flow in three pairs of avian taxa fully separated by different Amazonian
rivers, and whose geographic ranges do not make contact in headwater
regions. Models with gene flow were best fit, but still supported an
initial period without any gene flow which ranged from 187,000 to over
959,000 years, suggesting that rivers are capable of initiating speciation
through long stretches of allopatric divergence. Allopatry was followed by
either bursts or prolonged episodes of gene flow that retarded genomic
differentiation but did not homogenize populations. Our results support
Amazonian rivers as key barriers that promoted speciation and the buildup
of species richness, but they also suggest that river barriers are often
leaky, with genomic divergence accumulating slowly due to episodes of
substantial gene flow.