Expansion From Lowland Pleistocene Refugia Followed by Cryptic Introgression in an African Elevational Generalist...

The immense biodiversity observed in tropical forests has inspired the study of evolution since its inception, and numerous hypotheses have been generated to explain this diversity. One major driver of tropical forest biodiversity has been the repeated climatic fluctuations due to the Pleistocene glacial cycles. The Afrotropics are one region that has seen a particularly rich debate about the origin of its avifauna. Lowland and highland Afrotropical forests responded in different ways to Pleistocene climatic cycling, likely shaping the population genetic structure of species tracking these habitats. Here we study the role of shifting forests throughout the Pleistocene in shaping population genetic structure in a forest generalist, the Yellow-whiskered Greenbul (Eurillas latirostris). We sequenced genomes from individuals across the continent with forest thought to span three Pleistocene refugia. At a coarse scale, we found evidence for three lineages that expanded from these refugia, with a western lineage west of the Dahomey gap, a central lineage across the Congo Basin, and an eastern lineage in the Albertine rift and adjacent rainforest. However, finer scale analysis revealed a more complex story. First, we found that the most stable eastern lineage demonstrated population genetic structure between its montane populations. This included one population that was likely admixed between the sampled Albertine Rift locations and an unsampled region. Second, we found surprisingly strong divergence between the parapatric eastern and central lineages. However, despite this divergence, we found signals of mitochondrial introgression from the eastern lineage far into the eastern sampling localities of the central lineage. This suggests a largely untapped promise for evolutionary genomic research across the Congo Basin, where populations expanding from alternate refugia likely meet and have their species boundaries tested.