Diversification mechanisms in Sub-Saharan Africa have long attracted research interest with varying support for either allopatric or parapatric models of speciation. However, studies have seldom been performed across the entire continent, a scale which could elucidate the relative importance of allopatric and parapatric models of divergence. To shed light on continental-scale patterns of African biogeography and diversification, we investigated the historical demography of a bird with a continent-wide distribution in Sub-Saharan Africa, the Yellow-rumped Tinkerbird, Pogoniulus bilineatus. We sampled populations from across the continent and using genomic data, assessed genetic diversity, structure, and differentiation, reconstructed the phylogeny, and performed alternative demographic model selection between neighbouring clade pairs. We uncovered substantial genetic structure and differentiation patterns which corroborated the phylogenetic topology. Structure was chiefly influenced by the arid corridor, a postulated biogeographical barrier in Sub-Saharan Africa. Moreover, peak genetic diversities coincided with postulated refugial areas while demographic reconstructions between genetic lineages supported allopatric models consistent with the Pleistocene Forest Refuge hypothesis. However, within lineages, divergence with gene flow was supported. Continent-wide patterns of diversification involve an integration of both allopatric and parapatric mechanisms, with a role for both periods of divergence in isolation and across ecological gradients. Furthermore, our study emphasises the importance of the arid corridor as a primary biogeographical feature across which diversification occurs, yet one that has hitherto received scant attention regarding its importance in avian diversification in Sub-Saharan Africa.

Physiological constraints related to atmospheric temperature pose a limit to body size in endothermic animals. This relationship has been summarized by two classical principles of biogeography: Bergmann’s and Allen’s rules. Body size may also constrain other phenotypic traits important in ecology, evolution and behaviour, and such effects have seldom been investigated at a continental scale. Through a multilevel-modelling approach, we demonstrate that continent-wide morphology of related African barbets follows predictions of both ecogeographic rules, and that body size mirrors variation in song pitch, an acoustic trait important in species recognition and sexual selection. Bergmann’s rule effects on song dwarf those of acoustic adaptation at a continental scale. Our findings suggest that macroecological patterns of body size can influence phenotypic traits important in ecology and evolution, and provide a baseline for further studies on the effects of environmental change on bird song.

It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. But evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones between related species provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with forecrown colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 79 individuals, measuring spectral reflectance of forecrown feathers as well as scoring colours from photographs. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird that we assembled. Admixture mapping using 104,933 SNPs identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score. The hybrid zone was bimodal with asymmetric backcrossing, consistent with the hypothesis that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males may reinforce species divergence and is consistent with the hypothesis that converted carotenoids are an honest signal of quality.