Comparative patterns of population structure.
Montane Ethiopian species share at least four biogeographic barriers (briefly reviewed by Manthey et al., 2017), with the GRV being the most studied to date. A diversity of taxa exhibit population or species level differentiation on either side of the GRV, including brush-furred rats, groove-toothed rats, Ethiopian wolf, gelada, frogs of several genera, giant lobelia, coffee, and the species studied here (Belay & Mori, 2006; Evans et al., 2011; Freilich et al., 2016; Gottelli et al., 2004; Kebede et al., 2007; Komarova et al., 2021; Manthey et al., 2017; Reyes-Velasco et al., 2018; Reyes‐Velasco et al., 2018; Silvestrini et al., 2007).
While the GRV has impacted a plethora of taxa, species’ evolutionary responses have varied in timing and/or magnitude. For example, the Ethiopian wolf (Canis simensis ) is a relatively good disperser and exhibits weakly differentiated populations on either side of the GRV; this differentiation is hypothesized to have occurred over the last 20,000 years since the Last Glacial Maximum of the Pleistocene Epoch (Gottelli et al., 2004). In contrast, semi-arboreal frogs (GenusLeptopelis ) are relatively poor dispersers and exhibit many distinct lineages across the Ethiopian Highlands with divergence dates predating the Pleistocene (Reyes‐Velasco et al., 2018). Based on this study, songbirds have diversified during Pleistocene glacial cycles, with population differentiation and cessation of connectivity dating to the past 50 kya to 350 kya (Fig. 4). Interestingly, population differentiation in most taxa appears to have occurred during a pulse Great Rift Valley volcanism that took place between 170 kya and 320 kya (Hutchison et al., 2016).
The asynchronous and varied patterns of diversification in Ethiopian montane taxa exemplify the complex geological and climatic history of the region. The formation of the GRV is old (~ 20 Mya) and ongoing (Frisch et al., 2010; Sepulchre et al., 2006), which has provided growing and continuous elevational heterogeneity in the central portion of the Ethiopian Highlands. During the last few million years, the Pleistocene climatic cycles have added climatic heterogeneity to the topographic variation; during glacial minima (e.g., contemporary periods), the GRV was likely relatively arid and hot compared to glacial maxima (e.g., the Last Glacial Maximum). These oscillations would have generally resulted in elevational shifts and greater potential geographic range in montane taxa during glacial maxima. Montane species inhabiting the Ethiopian Highlands would have experienced these combined geological and climatic forces; their population differentiation throughout these periods would have likely been shaped by the age of the lineage inhabiting the highlands (i.e., time of colonization) and species-specific dispersal ability, niche breadth, and interpopulation reproductive compatibility shaping whether populations underwent gene flow during periods of relatively higher habitat connectivity.
Drivers of genomic diversity. Genomic diversity is expected to be influenced by mutation rates, patterns of selection and linked selection, and effective population sizes (Amos & Harwood, 1998; Ellegren & Galtier, 2016). The largest effectors of mutation rates and effective population sizes are life history characteristics, namely fecundity rates (Romiguier et al., 2014). When focusing on species with similar life history strategies—as we do here with passerine birds—we may expect most of the variation in genomic diversity to be shaped by patterns of long-term linked selection across the genome and the demographic histories of populations that in turn shape effective population sizes. We find a negative correlation between genome wide estimates of FST and DXY, indicative of the effects of widespread linked selection in all six taxa (Fig. S5) (Cruickshank & Hahn, 2014), although with our limited sample sizes it wouldn’t be practical to identify direct effects of linked selection on genomic diversity. Overall, we find that the strongest predictors of genomic diversity across Ethiopian montane bird populations are recent population sizes and harmonic mean of population sizes over the past 200,000 years (Fig. 3).