Asymmetric introgression reveals the genetic architecture of a plumage trait

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels

The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study “replicated” instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bistable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.

Spatial variation in introgression along a toad hybrid zone in France

The barrier effect is a restriction of gene flow between diverged populations by barrier genes. Restriction of gene flow and asymmetric introgression over multiple transects indicates species wide (genetic) adaptations, whereas transect-specific barrier loci may indicate local adaptation to gene flow. Asymmetric introgression can be caused by selection, hybrid zone movement, asymmetric reproductive isolation, or a combination of these. We study two widely separated transects (northwest and southeast France) for the 900 km long hybrid zone between Bufo bufo and B. spinosus toads, using ~1200 markers from restriction-site associated DNA (RAD) sequencing data. Genomic and geographic clines were used to identify outlier markers which show restricted or elevated introgression. Twenty-six barrier markers are shared between transects (the union of 56 and 123 barrier markers identified in each transect), which is more than would be expected by chance. However, the number of barrier markers is twice as high in the southeast transect. In the northwest transect a high amount of (asymmetric) introgression from B. spinosus into B. bufo is consistent with hybrid zone movement or asymmetric reproductive isolation. In the southeast transect, introgression is symmetric and consistent with a stable hybrid zone. Differences between transects may be related to genetic sub-structure within B. bufo. A longer period of secondary contact in southeast France appears to result in a relatively stronger barrier effect than in the northwest. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier to gene flow from local reductions in gene flow.