Supplementary data from: Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade

Genomic analyses of hybrid zones provide excellent opportunities to
investigate the consequences of introgression in nature. In combination
with phylogenomics analyses, hybrid zone studies may illuminate the role
of ancient and contemporary gene flow in shaping variation of phylogenetic
signals across the genome, but this avenue has not been explored yet. We
combined phylogenomic and geographic cline analyses in a Pogoniulus
tinkerbird clade to determine whether contemporary introgression through
hybrid zones contributes to gene-tree heterogeneity across the species
ranges. We found diverse phylogenetic signals across the genome with the
most common topologies supporting monophyly among taxa connected by
secondary contact zones. Remarkably, these systematic conflicts were also
recovered when selecting only individuals from each taxon’s core range.
Using analyses of derived allele sharing and “recombination aware”
phylogenomics, we found that introgression shapes gene-tree heterogeneity,
and the species tree most likely supports monophyletic red-fronted
tinkerbirds, as recovered in previous reconstructions based on
mitochondrial DNA. Furthermore, by fitting geographic clines across two
secondary contact zones, we found that introgression rates were lower in
genomic regions supporting the putative species tree compared to those
supporting the two taxa in contact as monophyletic. This demonstrates that
introgression through narrow contact zones shapes gene-tree heterogeneity
even in allopatric populations. Finally, we did not find evidence that
mitochondria-interacting nuclear genes acted as barrier loci. Our results
show that species can withstand important amounts of introgression while
maintaining their phenotypic integrity and ecological separation, raising
questions regarding the genomic architecture of adaptation and barriers to
gene flow.