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.

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.

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.

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.

There is increased evidence that incorporating evolutionary history directly in conservation actions is beneficial, particularly given the likelihood that extinction is not random and that phylogenetic diversity (PD) is lost at higher rates than species diversity. This evidence is even more compelling in biodiversity hotspots, such as Madagascar, where less than 10% of the original vegetation remains. Here, we use the Leguminosae, an ecologically and economically important plant family, and a combination of phylogenetics and species distribution modelling, to assess biodiversity patterns and identify regions, coevolutionary processes and ecological factors that are important in shaping this diversity, especially during the Quaternary. We show evidence that species distribution and community PD are predicted by watershed boundaries, which enable the identification of a network of refugia and dispersal corridors that were perhaps important for maintaining community integrity during past climate change. Phylogenetically clustered communities are found in the southwest of the island at low elevation and share a suite of morphological characters (especially fruit morphology) indicative of coevolution with their main dispersers, the extinct and extant lemurs. Phylogenetically over-dispersed communities are found along the eastern coast at sea level and may have resulted from many independent dispersal events from the drier and more seasonal regions of Madagascar.

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.

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.