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 mulga complex ( Acacia aneura and closely related taxa) is a widespread group that is dominant in much of arid Australia. The group is taxonomically difficult, due to a complex interaction of sympatry and putative hybridisation between the major species, geographic variation within species and sympatric variation within A. aneura . Mulga is highly variable in a wide range of vegetative and reproductive characters and it is not unusual to find five or six distinct forms growing side by side. The aim of this project was to gain a better understanding of the relationships among mulga species and A. aneura varieties, as well as the maintenance of this variation. A single site in the Northern Territory, containing A. ayersiana , A. minyura and two varieties of A. aneura , was sampled intensively. Six morphotypes were observed in the field and five were strongly supported by morphometric analysis. Although the mulga complex is generally tetraploid (2 n = 52), triploid (2 n = 39) and pentaploid (2 n = 65) seedlings were produced in the study population. Microsatellite primers developed for A. mangium (sect. Juliflorae) were amplified in individuals of each morphotype, resulting in genetic marker patterns consistent with polyploidy. Genetic and morphometric distances were correlated and differences between morphotypes account for 63% of the total genetic variation (FPT = 0.63, P < 0.001). Allele sequences confirmed the presence of genuine heterozygosity and clonality was suggested by the low genotypic diversity and the lack of allele segregation. Seedlings had identical genotypes to the maternal plants and polyembryony was observed in each taxon, consistent with apomictic reproduction. Both variation of the ploidy level and apomixis may restrict gene flow among morphotypes, playing a role in the maintenance of morphological diversity at the study site. The success of the group in arid and semi-arid Australia may also be due, in part, to these factors.