Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

Hybridisation has the potential to generate or homogenize biodiversity and
is a particularly common phenomenon in plants, with an estimated 25% of
plant species undergoing inter-specific gene flow. However, hybridisation
in Amazonia’s megadiverse tree flora was assumed to be extremely rare
despite extensive sympatry between closely related species, and its role
in diversification remains enigmatic because it has not yet been examined
empirically. Using members of a dominant Amazonian tree family (Brownea,
Fabaceae) as a model to address this knowledge gap, our study recovered
extensive evidence of hybridisation among multiple lineages across
phylogenetic scales. More specifically, using targeted sequence capture
our results uncovered several historical introgression events between
Brownea lineages and indicated that gene tree incongruence in Brownea is
best explained by reticulation, rather than solely by incomplete lineage
sorting. Furthermore, investigation of recent hybridisation using ~19,000
ddRAD loci recovered a high degree of shared variation between two Brownea
species that co-occur in the Ecuadorian Amazon. Our analyses also showed
that these sympatric lineages exhibit homogeneous rates of introgression
among loci relative to the genome-wide average, implying a lack of
selection against hybrid genotypes and persistent hybridisation. Our
results demonstrate that gene flow between multiple Amazonian tree species
has occurred across temporal scales, and contrasts with the prevailing
view of hybridisation’s rarity in Amazonia. Overall, our results provide
novel evidence that reticulate evolution influenced diversification in
part of the Amazonian tree flora, which is the most diverse on Earth.