Genomic perspective on speciation and hybridisation in Antirrhinum

Abstract

Rapidly speciating lineages are important for generating diversity. However, the factors underlying the origins of diversity in evolutionary radiations are not well understood. Adaptive introgression has been identified as one potential cause of rapid speciation. The plant genus Antirrhinum provides an ideal study system to explore the potential role adaptive introgression may play in rapid speciation. Antirrhinum species can be split into three morphological sections: Antirrhinum, Streptosepalum and Kickxiella. There has been recurrent evolution of species with the alpine Kickxiella morphology. One possibility behind this recurrent evolution is that it is caused by adaptive introgression of genes responsible for the Kickxiella morphology. The overall aim of this thesis is to determine how the Kickxiella morphology evolved multiple times in the Antirrhinum genus. First, I used RAD sequencing and whole genome sequencing datasets to build phylogenetic trees for Antirrhinum (Chapter 2). Phylogenetic trees produced conflicting results for how many times the Kickxiella morphology may have evolved. There was a high level of discordance present in the phylogenies, potentially caused by both incomplete lineage sorting and hybridisation. Hybridisation across the genus was supported by the lack of runs of homozygosity and the potential geographic clustering present in the chloroplast phylogeny rather than the species tree observed from the nuclear genome. D-statistic and phylogeny-based analyses were used to test for evidence of introgression between Kickxiella groups to determine support for the recurrent evolution of Kickxiella species via introgression (Chapter 3). Using short read whole genome sequence data D-statistics identified regions of the genome with signal of introgression between Kickxiella groups. However, genes contained within these regions were not clearly associated with the Kickxiella morphology and regions with signal of introgression were short, suggesting any introgression events occurred sufficient generations ago for introgressed regions to be eroded by recombination. Finally, a pangenome for the genus Antirrhinum was built using genome assemblies from across the Antirrhinum genus (Chapter 4). This aids the identification of structural variants that are shared across Kickxiella samples and may underlie their morphology. From the pangenome over 82,000 structural variants with a minimum length of 50 bp were identified across the genus. Two structural variants were found in all Kickxiella species and absent from other species, however they were not clearly associated with any aspect of Kickxiella morphology.

Overall, these findings suggest that standing genetic variation or de novo mutations at the nucleotide level may be responsible for the repeated evolution of the Kickxiella morphology. These findings offer insights into the evolutionary complexity that may have shaped the rapid evolution of the Antirrhinum genus.