Genomic signatures of diversification in large plant genera Begonia and Cyrtandra

Diverse plant groups often emerge from bursts of speciation and may experience reductions in effective population size through recurrent lineage splitting. This process is hypothesised to influence genome-wide patterns of variation, including increased genetic drift, random fixation of nearly neutral mutations, and relaxed selection. Such diversification signatures might contribute to stocks of genetic variation, enhancing populations' adaptive potential to future challenges. To investigate these signals in large, diverse taxa, we compared two phylogenetically disparate plant genera, <i>Begonia</i> (Begoniaceae) and <i>Cyrtandra</i> (Gesneriaceae), generating new transcriptomic resources for the speciose genus <i>Cyrtandra </i>and taking advantage of comparable transcriptomic resources in <i>Begonia</i>. Leveraging closely related species-poor outgroups for each diverse genus, we examined shifts in selection strength and gene duplication patterns. Contrary to expectations, we found no evidence of genome-wide relaxed selection in the diverse genera compared to their species-poor counterparts, with only approximately one fifth of tested loci showing signs of relaxed selection. Additionally, there were no substantial changes in gene duplication patterns between the diverse and species-poor genera. Our findings suggest that the effects of diversification are not strong enough to be detected on a genome-wide scale, and that any effects of reduced effective population size on the stochastic fixation of mutations or duplicate genes may be short lived. This study showcases the utility of transcriptomic data for studying patterns of evolution and diversification in non-model organisms, and underscores the importance of investment in genomic resources for understudied taxa.