Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.
• We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy.
• We identified twenty-six ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy.
• Through dense phylog...