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’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. 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.

Mutualism discernibly connects the evolution of two or more interacting taxa. Endosymbioses, especially those that are obligate, are an intimate mutualism that link the evolution of host and endosymbiont. In these instances, we may expect codiversification of hosts and endosymbionts as well as host demography discernibly affecting the course of endosymbiont evolution. While many studies have demonstrated cospeciation of hosts and endosymbionts, detailed investigations of the impact of host demography on endosymbiont molecular evolution are generally lacking. Here, we sequenced complete genomes of carpenter ants (Genus Camponotus) and their Blochmannia endosymbionts to investigate their codiversification and test hypotheses about how host demography impacts molecular evolution in endosymbionts. Using whole genome phylogenomics, we identified strong signatures of codiversification between carpenter ants and their endosymbionts. We found that endosymbiont genes have evolved rapidly, at a pace of ~30x that of their hosts. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. We identified a positive relationship between host demography and shifts toward intensified selection in endosymbiont genes, but no relationship between host demography and shifts toward relaxed selection in endosymbiont genes. About 10% of the Blochmannia genes exhibited variable presence and absence across endosymbiont genomes. Of those, about half exhibited phylogenetic signal, indicating somewhat random patterns of gene loss in endosymbiont genomes. Lastly, we found no relationship between host demography and endosymbiont gene loss.