The traditional view is that species and their genomes evolve by vertical descent, leading to evolutionary histories that can be represented by bifurcating lineages. However, modern evolutionary thinking recognizes processes of reticulate evolution, such as horizontal gene transfers or hybridization, which involve total or partial merging of genetic material from two diverged species. Today it is widely recognized that such events are rampant in prokaryotes, but a prominent role in eukaryotes has only recently been acknowledged. Recent work has shown that reticulate evolution in eukaryotes is more common and has more complex outcomes than previously thought. However, we still have a very limited understanding of what are the impacts at the genomic and evolutionary levels. To address this, this project combined innovative computational and experimental approaches. The first goal is to infer patterns of reticulate evolution across the eukaryotic tree, and relate this to current biological knowledge. The second goal is to trace the genomic aftermath of inter-species hybridization at the i) short-term, by using re-sequencing and experimental evolution in yeast, ii) mid-term, by sequencing lineages of natural fungal hybrids, and iii) long-term, by analysing available genomes in selected eukaryotic taxa. A particular focus is placed on elucidating the role of hybridization in the origin of whole genome duplications, and in facilitating the spread of horizontally transferred genes. The results of this project have improved our understanding of reticular evolutionary processes as drivers of eukaryotic genome evolution. On the one hand we have elucidated genome evolution trends following hybridization in diverse yeast lineages, identifying the relative impact of neutral and selective evolutionary processes. On the other hand, we have charted reticulated processes across the major eukaryotic lineages, which have revealed differences that relate to certain life-history traits. For instance, we have observed that fungi, as compared to plants or animals, seem to better buffer the deleterious effects of the coexistence between diverged genomes. This may be related to the common occurrence of inter-species hybrids among unicellular fungi.
