Precipitation is the main axis of tropical plant phylogenetic turnover across space and time.

Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing.

The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae).

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.

Misleading fruits: The non-monophyly of Pseudopiptadenia and Pityrocarpa supports generic re-circumscriptions and a new genus within mimosoid legumes.

Generic delimitation in Piptadenia and allies (mimosoid legumes) has been in a state of flux, particularly caused by over-reliance on fruit and seed morphology to segregate species out of Piptadenia into the genera Parapiptadenia, Pityrocarpa and Pseudopiptadenia. Although supporting their segregation from Piptadenia, previous phylogenetic analyses suggested that some of these segregated genera are not monophyletic. Here, we test the monophyly of Parapiptadenia, Pityrocarpa and Pseudopiptadenia with dense taxon sampling across these genera, including the type species of each genus. Our analysis recovers Parapitadenia as monophyletic, but places Pseudopiptadenia species in two distinct lineages, one of which includes all three species of Pityrocarpa. Given that the type species of both Pseudopiptadenia and Pityrocarpa are nested in the same clade, we subsume Pseudopiptadenia under the older name Pityrocarpa. The remaining Pseudopiptadenia species are assigned to the new genus Marlimorimia. Alongside high molecular phylogenetic support, recognition of Parapiptadenia, Pityrocarpa and Marlimorimia as distinct genera is also supported by combinations of morphological traits, several of which were previously overlooked.

The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes.

The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation.

PREMISE: Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS: We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS: Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS: Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.

A new phylogeny-based tribal classification of subfamily Detarioideae, an early branching clade of florally diverse tropical arborescent legumes.

Detarioideae (81 genera, c. 760 species) is one of the six Leguminosae subfamilies recently reinstated by the Legume Phylogeny Working Group. This subfamily displays high morphological variability and is one of the early branching clades in the evolution of legumes. Using previously published and newly generated sequences from four loci (matK-trnK, rpL16, trnG-trnG2G and ITS), we develop a new densely sampled phylogeny to assess generic relationships and tribal delimitations within Detarioideae. The ITS phylogenetic trees are poorly resolved, but the plastid data recover several strongly supported clades, which also are supported in a concatenated plastid + ITS sequence analysis. We propose a new phylogeny-based tribal classification for Detarioideae that includes six tribes: re-circumscribed Detarieae and Amherstieae, and the four new tribes Afzelieae, Barnebydendreae, Saraceae and Schotieae. An identification key and descriptions for each of the tribes are also provided.

Flowers of the early-branching papilionoid legume Petaladenium urceoliferum display unique morphological and ontogenetic features.

PREMISE OF THE STUDY: Floral development can help to shed light on puzzling features across flowering plants. The enigmatic Amazonian monospecific genus Petaladenium of the legume family (Leguminosae) had rarely been collected and only recently became available for ontogenetic studies. The fimbriate-glandular wing petals of P. urceoliferum are unique among the more than 19000 legume species. Ontogenetic data illuminate the systematic position of the genus and foster our understanding on floral evolution during the early diversification of the papilionoid legumes. METHODS: Flower buds were collected in the field, fixed in 70% ethanol, and investigated using scanning electron microscopy (SEM). Results were compared with existing material from early-diverging papilionoid legumes. KEY RESULTS: Formation of sepals and petals shows bidirectional tendencies. Stamens arise in two whorls, and the single carpel arises concomitantly with the outer stamen whorl. Gland formation starts early on the edges of the wing petals. The carpel reopens for a short time when the initiation of ovules is visible. Stomata at the base of the hypanthium indicate that the flower functions like other standard flag blossoms. CONCLUSIONS: The floral ontogeny confirms the close affinity of P. urceoliferum with the florally heterogeneous, early-diverging papilionoid Amburaneae clade. The results strengthen the theory of a distinct experimental phase among early-branching papilionoid legumes during which a wider range of floral morphologies arose. Polysymmetry, monosymmetry, variable organ numbers, and a wide range of ontogenetic patterns laid the foundation for a successful canalization toward the more restricted but well-adapted dorsiventral papilionoid flag blossom.

Reinterpretation of the nomenclatural type of Pseudobombax heteromorphum (Malvaceae, Bombacoideae) reveals an overlooked new species from Bolivia.

In the course of a taxonomic revision of Pseudobombax Dugand, one of us (JGCS) frequently has observed herbarium specimens of Bombacoideae that comprise a mixture of different Angiosperm families. In particular, Pseudobombax heteromorphum (Kuntze) A. Robyns, a frequent name in checklists of the Bolivian flora, is based on type material of Bombax heteromorphum Kuntze that is clearly a mixture of Pseudobombax flowers and Tabebuia Gomes ex DC. (Bignoniaceae) leaves. We herein designate as the lectotype of Bombax heteromorphum the flowers of an herbarium sheet deposited in NY and as epitype a complete specimen (leaves, flowers, and fruit) in HUEFS. We consider Bombax heteromorphum to be a synonym of Pseudobombax longiflorum (Mart.) A. Robyns, a species widespread in Neotropical seasonally dry forest of Bolivia, Brazil, Paraguay, and Peru. Furthermore, we describe a new species, Pseudobombax pulchellum Carv.-Sobr., apparently endemic to seasonally dry tropical forest (SDTF) in Bolivia (Chiquitano dry forest), based on specimens commonly but incorrectly identified as Pseudobombax heteromorphum.We also comment on the morphology, distribution, and conservation status of this new species.

ResumenEn el curso de una revisión taxonómica de Pseudobombax Dugand, uno de nosotros (JGCS) con frecuencia se ha observado especímenes de herbario de Bombacoideae que comprenden una mezcla de diferentes familias de angiospermas. En particular, Pseudobombax heteromorphum (Kuntze) A.Robyns, un nombre frecuente en las listas de la flora boliviana, se basa en el material tipo de Bombax heteromorphum Kuntze que es claramente una mezcla de flores de Pseudobombax y hojas de Tabebuia Gomes ex DC. (Bignoniaceae). Aquí se designa como el lectotipo de Bombax heteromorphum las flores de uno espécimen de el herbario NY y como epitipo uno espécimen completo (hojas, flores y frutos) de el herbario HUEFS. Consideramos Bombax heteromorphum como sinónimo de Pseudobombax longiflorum (Mart.) A.Robyns, una especie ampliamente distribuida en los bosques neotropicales estacionalmente seco de Bolivia, Brasil, Paraguay y Perú. Por otra parte, se describe una especie nueva, Pseudobombax pulchellum Carv.-Sobr., aparentemente endémica de los Bosques secos Chiquitanos en Bolivia, con base en colecciones comúnmente, pero incorrectamente identificado, como Pseudobombax heteromorphum, con comentarios sobre su morfología, distribución y estado de conservación.

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages.

PREMISE OF STUDY: Phylogenetic relationships of the papilionoid legumes (Papilionoideae) reveal that the early branches are more highly diverse in floral morphology than are other clades of Papilionoideae. This study attempts for the first time to comprehensively sample the early-branching clades of this economically and ecologically important legume subfamily and thus to resolve relationships among them. • METHODS: Parsimony and Bayesian phylogenetic analyses of the plastid matK and trnL intron sequences included 29 genera not yet sampled in matK phylogenies of the Papilionoideae, 11 of which were sampled for DNA sequence data for the first time. • KEY RESULTS: The comprehensively sampled matK phylogeny better resolved the deep-branching relationships and increased support for many clades within Papilionoideae. The potentially earliest-branching papilionoid clade does not include any genus traditionally assigned to tribe Swartzieae. Dipterygeae is monophyletic with the inclusion of Monopteryx. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade within papilionoids. The quinolizidine-alkaloid-accumulating genistoid clade is expanded to include a strongly supported subclade containing Ormosia and the previously unplaced Clathrotropis s.s., Panurea, and Spirotropis. Camoensia is the first-branching genus of the core genistoids. • CONCLUSIONS: The well-resolved phylogeny of the earliest-branching papilionoids generated in this study will greatly facilitate the efforts to redefine and stabilize the classification of this legume subfamily. Many key floral traits did not often predict phylogenetic relationships, so comparative studies on floral evolution and plant-animal interactions, for example, should also benefit from this study.

Isolation and characterization of new ceramides from aerial parts of Lepidaploa cotoneaster.

Two new ceramides were isolated from the bulbs of Lepidaploa cotoneaster (Willd. ex Spreng.) H. Rob. [Vernonia cotoneaster (Willd. ex Spreng.) Less.)], in addition to germanicol, beta-sitosterol, stigmasterol, 3-beta-O-beta-D-glucopyranosyl-sitosterol, lupeol, lupeoyl acetate and tiliroside. The structures of the new compounds were elucidated by spectral techniques (MS, 1H NMR, 13C NMR, HSQC, HMBC, DEPT, and TOCSY) and were compared with data reported in literature, and were established as 2S*,2'R*,3S*,4R*,11E)-N-[2'-hydroxyhenicosanoyl]-2-amino-nonadec-11-ene-1,3,4-triol (1) and (2S*,2'R*,3S*,4R*,8E)-N-[2'-hydroxytricosanoyl]-2-amino-nonadec-8-ene-1,3,4-triol (2). To establish the structure and to locate the double bond, the methyl ester of the fatty acid and dimethyl disulfide (DMDS) derivatives were prepared for both ceramides.

The evolutionary history of Mimosa (Leguminosae): toward a phylogeny of the sensitive plants.

PREMISE OF THE STUDY: Large genera provide remarkable opportunities to investigate patterns of morphological evolution and historical biogeography in plants. A molecular phylogeny of the species-rich and morphologically and ecologically diverse genus Mimosa was generated to evaluate its infrageneric classification, reconstruct the evolution of a set of morphological characters, and establish the relationships of Old World species to the rest of the genus. METHODS: We used trnD-trnT plastid sequences for 259 species of Mimosa (ca. 50% of the total) to reconstruct the phylogeny of the genus. Six morphological characters (petiolar nectary, inflorescence type, number of stamens, number of petals, pollen type, and seismonasty) were optimized onto the molecular tree. KEY RESULTS: Mimosa was recovered as a monophyletic clade nested within the Piptadenia group and includes the former members of Schrankia, corroborating transfer of that genus to Mimosa. Although we found good support for several infrageneric groups, only one section (Mimadenia) was recovered as monophyletic. All but one of the morphological characters analyzed showed high levels of homoplasy. High levels of geographic structure were found, with species from the same area tending to group together in the phylogeny. Old World species of Mimosa form a monophyletic clade deeply nested within New World groups, indicating recent (6-10 Ma) long-distance dispersal. CONCLUSIONS: Although based on a single plastid region, our results establish a preliminary phylogenetic framework for Mimosa that can be used to infer patterns of morphological evolution and relationships and which provides pointers toward a revised infrageneric classification.

Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil.

*An extensive survey of nodulation in the legume genus Mimosa was undertaken in two major biomes in Brazil, the Cerrado and the Caatinga, in both of which there are high degrees of endemicity of the genus. *Nodules were collected from 67 of the 70 Mimosa spp. found. Thirteen of the species were newly reported as nodulating. Nodules were examined by light and electron microscopy, and all except for M. gatesiae had a structure typical of effective Mimosa nodules. The endosymbiotic bacteria in nodules from all of the Mimosa spp. were identified as Burkholderia via immunolabelling with an antibody against Burkholderia phymatum STM815. *Twenty of the 23 Mimosa nodules tested were shown to contain nitrogenase by immunolabelling with an antibody to the nitrogenase Fe- (nifH) protein, and using the delta(15)N ((15)N natural abundance) technique, contributions by biological N(2) fixation of up to 60% of total plant N were calculated for Caatinga Mimosa spp. *It is concluded that nodulation in Mimosa is a generic character, and that the preferred symbionts of Brazilian species are Burkholderia. This is the first study to demonstrate N(2) fixation by beta-rhizobial symbioses in the field.

Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire.

The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness.

Acetylcholinesterase activity of alkaloids from the leaves of Waltheria brachypetala.

Chemical investigation of the leaves of Waltheria brachypetala Turks (Sterculiaceae) resulted in the isolation of quinolinone alkaloids, waltherione-A, waltherione-B (N-methylwaltherione-A), 8-methoxyflindersine, and the cyclic peptide alkaloid waltherine. The inhibition of activity of acetylcholinesterase (AChE) by the alkaloids was evaluated. Waltherione-A, waltherione-B and waltherine showed significant activity.

Ryanodane diterpenes from two Erythroxylum species.

Ryanodane diterpenes, named 14-O-methyl-ryanodanol and ryanodanol, were isolated from ripe fruit of Erythroxylum passerinum. Compound 2 was also found in the leaves of this species, while 1 was obtained from the leaves of E. nummularia. Compound 1 showed insecticidal activity against Aedes aegypti larvae.

Radical scavenging, antioxidant and cytotoxic activity of Brazilian Caatinga plants.

Extracts of 32 plants from the Brazilian northeastern semi-arid region called Caatinga were evaluated through DPPH radical scavenging assay, beta-carotene bleaching, and brine shrimp lethality tests (BST). Among the extracts studied Byrsonima cf. gardneriana, Mascagnia coriacea, Cordia globosa, Diodia apiculata and Hypenia salzmannii showed the highest activities in DPPH radical scavenging test. In the beta-carotene bleaching test the highest activities were observed for Passiflora cincinnata, Chamaecrista repens, B. cf. gardneriana, Rollinia leptopetala, Serjania glabrata, Diospyros gaultheriifolia, C. globosa, Mimosa ophtalmocentra, M. coriacea and Lippia cf. microphylla. In contrast, R. leptopetala, Zornia cf. brasiliensis and Leonotis nepetifolia were the most active species in the BST.