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.

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

In memory of Dr. Christopher Davidson

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.

Phylogenetic analyses of the family Sapindaceae inferred from nuclear and plastid sequence data have revealed a high level of para- and polyphyly at the subfamilial, tribal, and generic levels. A phylogenetic study focusing on taxa in the southern Pacific belonging to tribe Cupanieae has shown that the two most species-rich genera, Arytera Blume and Cupaniopsis Radlk., are polyphyletic. This study aims to clarify generic limits among the taxa currently placed in these two genera by identifying morphological features that support monophyletic groups suitable for recognition at the generic level. Specimens deposited in major herbaria holding material of these taxa were examined to complement extensive field observations. Careful consideration of morphological features in light of previous taxonomic treatments and the results of phylogenetic analyses enabled us to propose a re-aligned generic framework for Cupanieae in which two new genera are described to accommodate species previously placed in Arytera and Cupaniopsis: viz., Lepidocupania Buerki, Callm., Munzinger & Lowry (21 species) and Neoarytera Callm., Buerki, Munzinger & Lowry (4 species). A total of 25 new combinations are made, lectotypes are designated for nine names (two first step and seven second-step), and one new synonym is established. A key to the newly circumscribed genera Arytera and Cupaniopsis, along with allied genera, is provided, accompanied by information on the distribution and ecology of each species.

Halmahera is the largest (c. 18,000 km2) island of the Moluccan archipelago, but naturalists have only sporadically visited Halmahera and it has remained very poorly explored botanically. However, an intensive botanical inventory project was undertaken between 2012 and 2014 in part of the island to inform flora biodiversity management for certain proposed mining activities. This effort has contributed over 3600 plant collections and nearly doubled the number of Pandanus Parkinson (Pandanaceae) specimens (bringing the total to 55) available for Halmahera. After careful examination of all available material and comparison with other material from the region, we are able to present the first overview of the genus for the island. We have identified ten species from the island of which three are new to science and not known elsewhere, while the other seven are all representatives of species already described from other localities. The new species are formally described here as Pandanus beguinii Callm. & A. P. Keim, Pandanus benstoneoides Callm., Buerki & Phillipson and Pandanus halmaherensis Callm. & A. P. Keim. The new species are provided with notes on their respective morphology and known distributional and ecological ranges, line drawings. Those three new species are assigned a preliminary status of Endangered following IUCN Red List Categories and Criteria. All ten species are illustrated with colour photographs and a key to the species is provided.

Abstract

Benstonea (Pandanaceae) was circumscribed to include 57 species formerly placed in the genus Pandanus. Field observations, accompanied by the study of available herbarium material have brought new insights for the delimitation of certain problematic species, especially in the difficult group of species characterized by an axillary infructescence on a short peduncle covered by prophylls and the abscission of the basal portion of the drupe at maturity. New combinations, based on names in Pandanus previously treated as synonyms of Benstonea stenocarpa, are proposed for three distinct species of this group from Halmahera (Indonesia) and Papua New Guinea. The identity of Benstonea celebica, endemic to Sulawesi (Indonesia), is also elucidated and an epitype is designated for this species.

Sapindaceae (Sapindales) are a conspicuous and diversified element of the New Caledonian flora, with ca. 67 species (ca. 90 % endemic) in 13 genera (four endemic: Gongrodiscus, Loxodiscus, Podonephelium, Storthocalyx). The phylogeny of New Caledonian Sapindaceae is inferred by adding 97 new samples, encompassing the full distributional and morphological range of the archipelago's genera, to a broad plastid and nuclear DNA sequence dataset that is representative of the family worldwide. Results from phylogenetic analyses indicate that members of the family on New Caledonia belong to two major clades, the Dodonaea group (placed within subfamily Dodonaeoideae) and the Cupania group (subfamily Sapindoideae), which exhibit strikingly different species diversities (ca. 89% of the species on New Caledonia belong to the Cupania group). Results support the monophyly of all four endemic genera and most of those that also occur elsewhere, with the exception of the morphologically similar Austro‐Pacific genera Arytera and Cupaniopsis, both of which have representatives in each of two well‐supported subclades within the Cupania group, suggesting at least two dispersals to New Caledonia (most likely from Australia). The results provide a robust phylogenetic framework for ongoing taxonomic revisions of Sapindaceae genera on New Caledonia and for investigating the spatio‐temporal history of the family in this biogeographically intriguing archipelago, although expanded sampling (including from other areas) and further analyses will be required to resolve generic limits among the taxa currently placed in Arytera and Cupaniopsis.

Abstract

Pandanaceae, a palaeotropical monocot family of c. 700 species, comprises four currently recognized genera: Freycinetia Gaudich., Martellidendron (Pic. Serm.) Callm. & Chassot, Pandanus Parkinson and Sararanga Helms. Within Pandanus (c. 500 spp.), species of sect. Acrostigma Kurz [one of four sections comprising subg. Acrostigma (Kurz) B. C. Stone] possess highly distinctive morphological features (viz. sharp spiniform, linear styles with the stigmatic groove on the abaxial side of the style and a staminate flower reduced to 1 to 3 stamens) shared with two other species (likewise belonging to subg. Acrostigma but originally placed in sect. Fusiforma B. C. Stone) that separate them from all other congeners. Based on morphology, biogeography, and recent inferences from plastid DNA sequence data, we place these distinctive species in a new genus, Benstonea Callm. & Buerki, making the necessary new combinations for the 50 recognized species, accompanied by six lectotypifications, one epitytification and two neotypifications, and placing seventeen names in synonymy. A generic key is provided to facilitate distinguishing Benstonea from the four other genera of Pandanaceae. Comments are provided on the distribution, ecology and typification of each accepted species.