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.

Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a deep temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, i.e., at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.

Hybrid zones can provide clear documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a deep temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the under-sampled western portion of the zone (western Missouri) as well as investigating whether loci and pathways underpinning reproductive isolation were similar to those from the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016, 68 birds sampled between 1978 and 1980, and 5 additional reference birds sampled from outside the hybrid zone, we generated 11,669 SNPs via ddRADseq. We used these SNPs to interpolate spatially and assess the movement of the hybrid zone interface through time, and to assess variation in introgression among loci. We demonstrate that the interface has moved approximately 5-8 km to the northwest over the last 36-38 years, i.e., at only one-fifth the rate at which the eastern portion of the hybrid zone (e.g. Pennsylvania, Ohio) has moved. Temperature trends across the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Using genomic cline analyses, we detected four genes that showed restricted introgression in both Missouri and Pennsylvania, including Pnoc, a gene involved in metabolism, learning and memory, concordant with previous physiological and behavioral findings on hybrids and the parental species.