| One of the striking features of plant evolution is the high frequency of new species produced by genome duplication, or polyploidy. Nearly 30% of extant vascular plant species are the result of recent genome duplication. Despite this high incidence of neopolyploid species, we do not fully understand the historical role that polyploid species have played in the evolution of plant diversity. An outstanding feature of polyploid speciation is that ancient genome duplications, or paleopolyploidy, can be detected in the genomes of living plants. Using a combination of new bioinformatic pipelines and statistical approaches, I analyzed a phylogenetically diverse set of plant genome data. These analyses have uncovered nearly 60 ancient genome duplications in the ancestry of green plants. Strikingly, we observe a genome duplication in the history of nearly 70% of seed plant families. Comparisons of the timing of duplications in relation to subsequent lineage divergences are consistent with polyploid driven diversification and suggest that a substantial fraction of seed plant diversity may be the result of genome duplication. In contrast, the eukaryotes with the highest number of chromosome numbers, homosporous ferns, demonstrated far fewer genome duplications than expected. One explanation for this difference is that genome evolution proceeds differently in seed plants compared to ferns, with the latter possibly losing chromosomes at a much slower rate. We also observed biased patterns of duplicate gene retention in the largest family of flowering plants, the Compositae, that deviate from our expectations from studies of Arabidopsis. These results indicate that our current models of duplicate gene resolution are inadequate, and additional analyses are needed to better understand the forces that drive gene retention and loss. Overall, these results suggest that polyploidy has played a substantial role in the evolutionary success of seed plants and that duplications are a prominent feature of plant genome evolution. |
