Genomics of speciation in sunflowers  (Helianthus spp.)

While at UBC, I worked on the origin and maintenance of species divergence using wild populations of Helianthus annuus and closely related species (H. argophyllusH. petiolarisH. debilis). These species remain largely reproductively isolated and ecologically distinct, yet also frequently hybridize and exchange parts of their genome.

1.Islands of divergence and geography of speciation

-Here (Renaut et al. 2013), we showed that genetic divergence was lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence were numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

2.Hybrid speciation and transposable elements

-Interspecific hybridization promotes genome restructuring and introduces new genetic variation. For example, certain wild species of sunflowers contain a hybrid genome that originates from two distinct parental species. The genome of these hybrids has also expanded in size and this is likely due to the proliferation of selfish (transposable) genetic elements. Using next generation DNA sequencing, we find that as predicted, transposable elements are more abundance in the hybrid species, compared to parental species. In addition, we identify genes that serve to regulate the activity of these elements. As such, our work provides a new approach to explore transposable elements proliferation in hybrid species (Renaut et al. 2014).

3.Repeatability of divergence

-The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in molding phenotypes. Using independent pairs of sister species of sunflowers, we find that repeated genome evolution appears to result from both similar selective pressures and shared local genomic landscapes (Renaut et al. 2014).

4. Accumulation of deleterious mutations during domestication

For individuals to stay well adapted to their environment, harmful mutations must be removed from populations by natural selection. Yet, under specific circumstances that impair the effectiveness of selection, such as during the domestication of plants and animals, these harmful mutations are predicted to accumulate. Here, we report that mutations impairing protein function are more abundant in domesticated sunflowers than in their wild relatives. We also identify similar patterns in other domesticated species of the sunflower family. Finally, we provide evidence that, as predicted by population genetic theory, deleterious mutations have accumulated preferentially in low recombining regions of the genome. A paucity of recombination is likely to frustrate attempts to eliminate these mutations by plant and animal breeding program, despite probable benefits to agricultural productivity.  (Renaut & Rieseberg 2015)