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.

In organisms reproducing sexually, speciation occurs when increasing divergence results in pre- or post-zygotic reproductive isolation between lineages. Studies focusing on reproductive isolation origin in early stages of speciation are common. Many rely on indirect measures of introgression providing limited information on the genomic architecture of reproductive isolation maintenance in the long term. This study focuses on direct measures of introgression between two species in a late stage of speciation. We used ddRADseq genotyping in a natural hybrid zone between Podarcis bocagei and P. carbonelli to examine admixture extent, estimate effective selection, analyse hybrid zone stability, and assess variation in selection against introgression across the genome. Hybridization was confirmed the narrow and bimodal hybrid zone demonstrating the existence of strong mechanisms of reproductive isolation. Simulations suggested that simple premating barriers were not enough to explain the observed distribution of admixture classes, pointing out the role of post-mating isolation. A geographic cline approach confirmed strong reproductive isolation and high effective selection preventing extensive introgression outside of the contact zone; and detected a signal of hybrid zone movement towards P. bocagei distribution. Genomic cline analysis revealed heterogeneous patterns of introgression among loci within the syntopy zone, but most of the loci do not introgress more or less than the genomic average maintaining a strong association with the genomic background of origin. However, genomic clines can be driven by confounding effects resulting in incongruences between both cline approaches. Importantly, overall patterns of introgression seem to result from strong intrinsic barriers across the genome, without clear “islands of differentiation”. Last, an important role of the Z chromosome in reproductive isolation is suggested.

Desertification is a major threat to biodiversity in arid areas of the world, in part because many organisms in these regions are already existing at or near the limits of their movement and physiology. Here, we used molecular data to investigate patterns of persistence and dispersal in an ecologically and economically important carpenter bee (Xylocopa grisescens Lepeletier) found throughout the semiarid Caatinga region of Brazil. We used a genome-wide approach (Restriction-site associated DNA sequencing, RAD-seq) to gather genetic data (>83,000 SNPs) from bees sampled from eight sites within an arid region subject to desertification in Northeastern Brazil. We observed low levels of population genetic diversity and differentiation across the study region, despite data collection from sites up to 300 km distant. Additionally, we detected evidence of a relatively severe genetic bottleneck occurring an estimated 60 years ago. Our data suggest that population genetic patterns of X. grisescens have been shaped by human-mediated changes in the Caatinga, but these patterns have also been heavily influenced by biological characteristics of this species, such as their relatively high capacity for movement.

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.