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.

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.

Abstract

The Paleotropical monocot family Pandanaceae includes ca. 700 species assigned to four genera: Pandanus (ca. 500 spp.), Freycinetia (ca. 200 spp.), Martellidendron (6 spp.) and Sararanga (2 spp.). The most speciose genus, Pandanus, was classically subdivided into eight subgenera. Previous cladistic analyses revealed that several key morphological characters might have evolved independently several times, thus highlighting the need for a robust molecular phylogenetic framework to elucidate phylogenetic relationships and infrafamilial and infrageneric classification within this group. In this study, three plastid DNA regions (matK, trnQ­rps16, trnL­trnF) and 200 individuals (representing 134 species and 609 newly produced sequences)—spanning the taxonomic and biogeographic diversity of the family—are analyzed to test the monophyly at the familial and generic levels, and to infer phylogenetic relationships within the family. Particular emphasis is devoted to Pandanus with the aim of recognizing key morphological characters that reflect the evolutionary history of the genus. Phylogenetic inferences support the monophyly of Pandanaceae and establish Sararanga as sister to the rest of the family, with Freycinetia as sister to the Pandanus­Martellidendron pair. Although relationships are not well­resolved within the latter clade, three supported lineages are retrieved: (1) the Acrostigma clade comprising taxa of P. subg. Acrostigma, (2) the Martellidendron clade including taxa assigned to the genus Martellidendron and (3) the core Pandanus clade including taxa of all other subgenera of Pandanus. Morphological and biogeographic evidence supporting clade definitions are discussed in detail. This study provides the first phylogenetic backbone for Pandanaceae, which is sufficiently robust to serve as a springboard for future research into the evolutionary history of this neglected family.