Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹ provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus–based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.

Brassicaceae is an important family at both the agronomic and scientific level. The family not only inlcudes several model species, but it is also becoming an evolutionary model at the family level. However, resolving the phylogenetic relationships within the family has been problematic, and a large-scale molecular phylogeny in terms of generic sampling and number of genes is still lacking. In particular, the deeper relationships within the family, for example between the three major recognized lineages, prove particularly hard to resolve. Using a slow-evolving mitochondrial marker (nad4 intron 1), we reconstructed a comprehensive phylogeny in generic representation for the family. In addition, and because resolution was very low in previous single marker phylogenies, we adopted a supermatrix approach by concatenating all checked and reliable sequences available on GenBank as well as new sequences for a total 207 currently recognized genera and eight molecular markers representing a comprehensive coverage of all three genomes. The supermatrix was dated under an uncorrelated relaxed molecular clock using a direct fossil calibration approach. Finally, a lineage-through-time-plot and rates of diversification for the family were generated. The resulting tree, the largest in number of genera and markers sampled to date and covering the whole family in a representative way, provides important insights into the evolution of the family on a broad scale. The backbone of the tree remained largely unresolved and is interpreted as the consequence of early rapid radiation within the family. The age of the family was inferred to be 37.6 (24.2–49.4) Ma, which largely agrees with previous studies. The ages of all major lineages and tribes are also reported. Analysis of diversification suggests that Brassicaceae underwent a rapid period of diversification, after the split with the early diverging tribe Aethionemeae. Given the dates found here, the family appears to have originated under a warm and humid climate approximately 37 Ma. We suggest that the rapid radiation detected was caused by a global cooling during the Oligocene coupled with a genome duplication event. This duplication could have allowed the family to rapidly adapt to the changing climate.

Significance: Mechanisms of plant seed dormancy evolved to delay germination to a season favorable for seedling growth. Germination timing is an important adaptive early-life history trait which determines plant fitness in natural and agricultural ecosystems. The DELAY OF GERMINATION 1 ( DOG1 ) gene provides natural genetic variation in dormancy, was the first dormancy-specific gene cloned, and encodes a protein of unknown function. We show here that DOG1 controls dormancy of different species by setting the optimal ambient temperature window for germination. This timing is achieved by temperature-dependent alteration of the gibberellin hormone metabolism, which in turn leads to altered expression of genes required for the biomechanical weakening of the coat encasing the embryo. The conserved DOG1-mediated coat-dormancy mechanism controls the timing of seed germination in a temperature-dependent manner.