Taxon-specific characteristics and extrinsic climatic and geological
forces may both shape population differentiation and speciation. In
geographically and taxonomically focused investigations, differentiation
may occur synchronously as species respond to the same external
conditions. Conversely, when evolution is investigated in taxa with
largely varying traits, population differentiation and speciation is
complex and shaped by interactions of Earth’s template and
species-specific traits. As such, it is important to characterize
evolutionary histories broadly across the tree of life, especially in
geographic regions that are exceptionally diverse and under pressures
from human activities such as in biodiversity hotspots. Here, using
whole-genome sequencing data, we characterize genomic variation in
populations of six Ethiopian Highlands forest bird species separated by
a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six
species, populations on either side of the GRV exhibited significant but
varying levels of genetic differentiation. Species with lower dispersal
ability generally had higher levels of population differentiation.
Divergence dating indicated asynchronous population differentiation
histories, with at least three distinct diversification periods. We
found that demographic histories—estimated for each
individual—varied by both species and population but were consistent
between individuals of the same species and sampling region. We found
that genomic diversity varied by half an order of magnitude across
species, and that this variation could largely be explained by the
harmonic mean of effective population size over the past 200,000 years.
Overall, we found that even in highly dispersive species like birds, the
GRV acts as a substantial biogeographic barrier.