Polyploidy increases overall diversity despite higher turnover than diploids in the Brassicaceae

Although polyploidy, or whole-genome duplication, is widespread across the Plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here we examine the effects of polyploidy in driving macroevolutionary patterns within the angiosperm family Brassicaceae, a speciose clade exhibiting extensive inter-specific variation in chromosome numbers. We inferred ploidal levels from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae published to date. After evaluating a total of 54 phylogenetic models of diversification, we found that ploidy drives diversification rates across the Brassicaceae, with polyploids experiencing faster rates of speciation and extinction, but relatively slower rates of diversification. Nevertheless, diversification rates are, on average, positive for both polyploids and diploids. We also found that despite diversifying significantly slower than diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, although most polyploids go extinct before sustainable populations are established, rare successful polyploids persist and significantly contribute to the long-term evolution of lineages. Our findings suggest that polyploidy has played a major role in shaping the long-term evolution of the Brassicaceae and highlight the importance of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.Significance statementAlthough polyploidy is a source of innovation, its long-term evolutionary significance is still debated. Here we analyze the evolutionary role of polyploidy within the Brassicaceae, a diverse clade exhibiting extensive variation in chromosome numbers among species. We found that, although polyploids diversify slower than diploids, polyploids have faster extinction and speciation rates. Our results also suggest that polyploidy has played an important role in shaping present-day differences in species richness within the Brassicaceae, with potential implications in explaining diversity patterns across the plant Tree of Life.