Genomics of divergence and hybridisation in the genus Antirrhinum L.

Plant’s sessile habit and extreme variation in ploidy level, mating system and dispersal provide excellent opportunities for the study of speciation. However substantial challenges remain in elucidating the role of different evolutionary processes in the generation of new species. The genus Antirrhinum, including the model system A. majus, has many resources for addressing a wide range of evolutionary questions about speciation. Here I use restriction site associated DNA (RAD-seq) to investigate the genomics of hybridisation and divergence in the genus Antirrhinum. First, I examined the phylogenetic relationships within the genus and estimate genetic structure and rates of hybridisation. My results show that geography has a strong influence on the phylogenetic relationships of the genus, and that hybridisation occurs repeatedly between the main taxonomic subsections. However I also found differences between the genetic clustering and the traditional taxonomy of the genus, with subsection Kickxiella appearing in several places in the tree. I recovered a Kickxiella like morphology as the ancestral state of the genus, and found several transition events to an Antirrhinum like morphology throughout the genus. Second, I measured the proportion of hybridisation in putative natural hybrid populations between species from different subsections (Antirrhinum and Kickxiella) and characterised the genetic structure of several populations in the South of Spain. I found a high proportion of hybrid individuals in the populations in the south of the Sierra Nevada and identified the role of this mountain range as an important barrier to gene flow. Third, I explored the genetic architecture of the morphological divergence between subsection Antirrhinum and Kickxiella and identified important genomic regions for the maintenance of species. In this thesis I provide multiple lines of evidence suggesting that natural selection via habitat preferences plays a major role in maintaining the morphological divergence of species in the wild