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.

Premise

The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family’s complex infra‐familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework.

Abstract

This study investigates the biogeography, evolution and systematics of Benstonea Callm. & Buerki (Pandanaceae) based on six plastid DNA regions and 54 specimens representing 36 species (60% of species generic diversity). Our maximum likelihood and Bayesian phylogenetic inferences support the monophyly of Benstonea and its close relationship with the speciose Pandanus Parkinson. Benstonea is subdivided into three clades exhibiting contrasting species diversities. Clades I and II have seven species each, whereas most of the species diversity occurs in clade III with 21 species. None of the sections defined by Stone in Pandanus subgenus Acrostigma (Kurz) B.C. Stone (now Benstonea) are retrieved monophyletic by our analyses. Biogeographical inference supports the origin of Benstonea on the Sunda shelf during the Miocene and shows several subsequent exchanges between Peninsular Malaysia and Borneo. Species in Indochina and the Indian continent originated in Peninsular Malaysia and all belong to clade I. Wallacea was colonized at least twice from Borneo sometimes during the Miocene and no back-dispersals were inferred. The Sunda shelf was colonized once, most likely from Halmahera. Finally, our analyses suggest that the Fijian endemic Benstonea thurstonii (C.H. Wright) Callm. & Buerki dispersed from either Australia or New Guinea during the Pleistocene.