Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification.

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Ceratonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.

Single-Base Gene Variants in MIR-146A and SCN1A Genes Related to the Epileptogenic Process in Drug-Responsive and Drug-Resistant Temporal Lobe Epilepsy-A Preliminary Study in a Brazilian Cohort Sample.

The drug-resistant temporal lobe epilepsy (TLE) has recently been associated with single nucleotide variants (SNVs) in microRNA(miR)-146a (MIR-146A) (rs2910164) and Sodium Voltage-Gated Channel Alpha Subunit 1 (SCN1A) (rs2298771 and rs3812718) genes. Moreover, no studies have shown an association between these SNVs and susceptibility to drug-resistant and drug-responsive TLE in Brazil. Thus, deoxyribonucleic acid (DNA) samples from 120 patients with TLE (55 drug-responsive and 65 drug-resistant) were evaluated by real-time polymerase chain reaction (RT-PCR). A total of 1171 healthy blood donor individuals from the Online Archive of Brazilian Mutations (ABraOM, from Portuguese Arquivo Brasileiro On-line de Mutações), a repository containing genomic variants of the Brazilian population, were added as a control population for the studied SNVs. MIR-146A and SCN1A relative expression was performed by quantitative RT-PCR (qRT-PCR). The statistical analysis protocol was performed using an alpha error of 0.05. TLE patient samples and ABraOM control samples were in Hardy-Weinberg equilibrium for all studied SNVs. For rs2910164, the frequencies of the homozygous genotype (CC) (15.00% vs. 9.65%) and C allele (37.80% vs. 29.97%) were superior in patients with TLE compared to controls with a higher risk for TLE disease [odds ratio (OR) = 1.89 (95% confidence interval (95%CI) = 1.06-3.37); OR = 1.38 (95%CI = 1.04-1.82), respectively]. Drug-responsive patients also presented higher frequencies of the CC genotype [21.81% vs. 9.65%; OR = 2.58 (95%CI = 1.25-5.30)] and C allele [39.09% vs. 29.97%; OR = 1.50 (95%CI = 1.01-2.22)] compared to controls. For rs2298771, the frequency of the heterozygous genotype (AG) (51.67% vs. 40.40%) was superior in patients with TLE compared to controls with a higher risk for TLE disease [OR = 2.42 (95%CI = 1.08-5.41)]. Drug-resistant patients presented a higher AG frequency [56.92% vs. 40.40%; OR = 3.36 (95%CI = 1.04-17.30)] compared to the control group. For rs3812718, the prevalence of genotypes and alleles were similar in both studied groups. The MIR-146A relative expression level was lower in drug-resistant compared to drug-responsive patients for GC (1.6 vs. 0.1, p-value = 0.049) and CC (1.8 vs. 0.6, p-value = 0.039). Also, the SCN1A relative expression levels in samples from TLE patients were significantly higher in AG [2.09 vs. 1.10, p-value = 0.038] and GG (3.19 vs. 1.10, p-value < 0.001) compared to the AA genotype. In conclusion, the rs2910164-CC and rs2298771-AG genotypes are exerting significant risk influence, respectively, on responsive disease and resistant disease, probably due to an upregulated nuclear factor kappa B (NF-kB) and SCN1A loss of function.

Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas.

Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.

The Role of MRI in the Diagnosis of Spinal Cord Tumors.

Spinal cord tumors are uncommon, and its multiple representatives not always have pathognomonic characteristics, which poses a challenge for both patients and caring physicians. The radiologist performs an important role in recognizing these tumors, as well as in differentiating between neoplastic and non-neoplastic processes, supporting clinical and surgical decision-making in patients with spinal cord injury. Magnetic Resonance Imaging (MRI) assessment, paired with a deep understanding of the various patterns of cord involvement allied to detailed clinical data can provide a diagnosis or significantly limit the differential diagnosis in most cases. In this article, we aim to review the most common and noteworthy intramedullary and extramedullary spinal tumors, as well as some other tumoral mimics, with an emphasis on their MRI morphologic characteristics.

Pseudomonas aeruginosa and Bacillus cereus Isolated from Brazilian Cerrado Soil Act as Phosphate-Solubilizing Bacteria.

The phosphate-solubilizing microorganism is essential for soil quality and plant development and can serve as an alternative to reduce such Brazilian needs for importing phosphate overseas. Here, we isolated and selected bacteria from Brazilian Cerrado soils capable of solubilize phosphate. We obtained 53 bacteria isolates, of which 23 could solubilize phosphate at a pH of 7.0, 17 could solubilize phosphate at a pH of 6.0, and 8 could solubilize at a pH of 5.5. Using 16S rRNA gene sequences, we identified nine bacteria species clustered in four groups: Bacillus sp., Pseudomonas sp., Priestia sp., and Klebsiella sp. Our results revealed that the UFT01 (P. aeruginosa) and UFT42 (B. cereus) isolates exhibited the best phosphate solubilization performance at all tested pH values. We further recorded higher levels of solubilization and phosphate availability six days after the soil inoculation with P. aeruginosa, and enzymatic analysis of the soil samples revealed that the P. aeruginosa-inoculated samples resulted in four-fold higher enzymatic activities when compared to non-inoculated soils. The B. cereus soil inoculation increased ß-glucosidase activities and resulted in reduced the activities of arylsulfatase. Altogether, our findings demonstrated that P. aeruginosa and B. cereus isolated from Cerrado soils showed high phosphate solubilization potential.

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.

High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community.

Microbial starter cultures are used in the production of many cheeses around the world, such as Parmigiano-Reggiano, in Italy, Époisses, in France, and Canastra, in Brazil, providing many of the unique features of these cheeses. Bacteriophages (phages) are ubiquitous and well known to modulate the structure of bacterial communities, and recent data indicate that cheeses contain a high abundance of naturally occurring phages. Here, we analyze the viral and bacterial metagenomes of Canastra cheese: a traditional artisanal Brazilian cheese produced using an endogenous starter culture and raw milk. Over 1,200 viral operational taxonomic units were recovered using both isolated viral-like particles and complete metagenomic DNA. Common viral families identified included Siphoviridae and Myoviridae, with 40% of putative phage genomes unidentified at the family level of classification. We observed very high phage diversity, which varied greatly across different cheese producers, with 28% of phage genomes detected in only one producer. Several metagenome-assembled genomes were recovered for lactic acid-producing bacteria, as well as nonstarter bacterial species, and we identified several phage-bacterium interactions, at the strain level of resolution, varying across distinct cheese producers. We postulate that at least one bacterial strain detected could be endogenous and unique to the Canastra cheese-producing region in Brazil and that its growth seems to be modulated by autochthonous phages present in this artisanal production system. This phage-host relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for other similar cheese production systems around the world. IMPORTANCE Our work demonstrated a dynamic yet stable microbial ecosystem during cheese production using an endogenous starter culture. This was observed across several distinct producers and was marked by genomic evidence of continued phage-bacterium interactions, such as the presence of bacterial defense mechanisms. Furthermore, we provide evidence of unique microbial signatures for each individual cheese producer studied in the region, a fact that may have profound consequences on product traceability. This was the first effort to describe and understand the bacteriophage composition and ecological dynamics within the Brazilian Canastra cheese production system. The study of this prototypical backslopping production system provides a solid background for further mechanistic studies of the production of many cheeses around the world.

Myxofibrosarcoma: Another mimicker of meningioma / Mixofibrosarcoma: otro imitador del meningioma

Primary intracranial malignant fibrous histiocytoma (MFH), or myxofibrosarcoma, is an extremely rare condition, with only a few cases reported in the literature. We report a case of a dural-based myxofibrosarcoma in a previously healthy 42-year-old man that was initially presumed to be an atypical meningioma. The findings based on conventional and advanced magnetic resonance sequences, including diffusion-weighted imaging, perfusion weighted imaging and proton magnetic resonance spectroscopy, as well as histopathological aspects, are discussed (AU)

El histiocitoma fibroso maligno intracraneal primario (HFM) o mixofibrosarcoma, es una condición extremadamente rara, con solo unos pocos casos reportados en la literatura. Presentamos un caso de mixofibrosarcoma de base dural en un varón de 42 años, previamente sano, que inicialmente se presumió que era un meningioma atípico. Se discuten los hallazgos basados en secuencias de resonancia magnética convencionales y avanzadas, que incluyen imágenes ponderadas por difusión, imágenes ponderadas por perfusión y espectroscopía de resonancia magnética de protones, así como aspectos histopatológicos (AU)

Myxofibrosarcoma: Another mimicker of meningioma.

Primary intracranial malignant fibrous histiocytoma (MFH), or myxofibrosarcoma, is an extremely rare condition, with only a few cases reported in the literature. We report a case of a dural-based myxofibrosarcoma in a previously healthy 42-year-old man that was initially presumed to be an atypical meningioma. The findings based on conventional and advanced magnetic resonance sequences, including diffusion-weighted imaging, perfusion weighted imaging and proton magnetic resonance spectroscopy, as well as histopathological aspects, are discussed.

Resource-oriented sanitation: Identifying appropriate technologies and environmental gains by coupling Santiago software and life cycle assessment in a Brazilian case study.

Implementation of resource recovery technologies is becoming increasingly important, as humans are exhausting the world's natural resources. Recovering nutrients and water from wastewater treatment systems will play an important role in changing the current trends towards a circular economy. However, guidance is still needed to determine the most appropriate way to do this. In this study two decision-support tools, sanitation planning software (Santiago) and life cycle assessment (LCA), were applied to identify appropriate technologies and their environmental impacts. As a case study, current and alternative scenarios for a wastewater treatment plant (WWTP) in Campo Grande, west-central Brazil, were used. Among 12 scenarios provided by Santiago for efficient nutrient recovery, eight were selected for further assessment. The current WWTP system (UASB reactors) resulted in the highest negative impacts in two of nine assessment categories (freshwater and marine eutrophication), due to nutrient discharge to water. A source separation scenario with urine stored in a urine bank and co-composting of feces showed best overall performance. Electricity consumption played a crucial role for impacts in several categories, while water consumption was not significantly affected by choice of toilet. One Santiago scenario matched the most appropriate scenario with the best environmental performance, but the other seven scenarios were not as beneficial, indicating a need for some adjustments in the software. These results highlight the importance of performing LCA to compare alternative scenarios, even when using a tool designed to identify locally appropriate technologies. The results also indicate that the current wastewater treatment system has reasonable environmental performance, but could be improved if measures were taken to recover energy and reuse water.

Improving biological removal of pharmaceutical active compounds and estrogenic activity in a mesophilic anaerobic osmotic membrane bioreactor treating municipal sewage.

The contamination of water sources by pharmaceutically active compounds (PhACs) and their effect on aquatic communities and human health have become an environmental concern worldwide. Membrane bioreactors (MBRs) are an alternative to improve biological removal of recalcitrant organic compounds from municipal sewage. Their efficiency can be increased by using high retention membranes such as forward osmosis (FO) and membrane distillation (MD). Thus, this research aimed to evaluate the performance of an anaerobic osmotic MBR coupled with MD (OMBR-MD) in the treatment of municipal sewage containing PhACs and estrogenic activity. A submerged hybrid FO-MD module was integrated into the bioreactor. PhACs removal was higher than 96% due to biological degradation, biosorption and membrane retention. Biological removal of the PhACs was affected by the salinity build-up in the bioreactor, with reduction in biodegradation after 32 d. However, salinity increment had little or no effect on biosorption removal. The anaerobic OMBR-MD removed >99.9% of estrogenic activity, resulting in a distillate with 0.14 ng L-1 E2-eq, after 22 d, and 0.04 ng L-1 E2-eq, after 32 d. OMBR-MD treatment promoted reduction in environmental and human health risks from high to low, except for ketoprofen, which led to medium acute environmental and human health risks. Carcinogenic risks were reduced from unacceptable to negligible, regarding estrogenic activity. Thus, the hybrid anaerobic OMBR-MD demonstrated strong performance in reducing risks, even when human health is considered.

Peritoneal metastasis of a brainstem anaplastic ganglioglioma in a 2-year-old boy: case report and literature review.

Anaplastic gangliogliomas (AGG) are rare tumors of the central nervous system (CNS) that commonly affect children and young adults, with an unusual infratentorial presentation, which is related to hydrocephalus and a worse prognosis. We report a case of a brainstem AGG in a 2-year-old boy who underwent a ventriculoperitoneal shunting (VPS) and later presented peritoneal metastasis. We also reviewed the related literature. Even though rare, disease dissemination through VPS should be sought in patients with CNS tumors and VPS who develop new abdominal symptoms. The early diagnosis and intervention may minimize morbidity and improve quality of life of such patients.

Structuring functional groups of aquatic insects along the resistance/resilience axis when facing water flow changes.

Understanding how differences in intensity and frequency of hydrological disturbances affect the resistance and resilience of aquatic organisms is key to manage aquatic systems in a fast-changing world. Some aquatic insects have strategies that improve the permanence (resistance), while others use strategies that favor recolonization (resilience). Therefore, we carried out a manipulative experiment to understand the influence of functional characteristics of aquatic insects in their permanence and recolonization against hydrological disturbances in streams in the biodiversity hotspot of the Cerrado of Brazil. We placed 200 artificial substrates in five streams and submitted them to changing water flow regimes that differed both in frequency and intensity, and we observed the response of the aquatic community for 39 days. We used a hierarchical Bayesian approach to estimate the probabilities of permanence and recolonization of each life strategy group (nine groups). We observed that the most intense changes in the water flow tended to affect the permanence of almost all groups, but the intensity of this effect reduced over time. On the other hand, less frequent disturbances, regardless of intensity, tended to reduce the permanence of most groups of aquatic insects over time. The different effects of disturbance intensity may have been related to a greater recolonization capacity of some groups. The results we present are worrisome in a scenario of reduced riparian vegetation around streams and with the expectation of precipitation becoming more concentrated in shorter periods of time due to climate change in the Cerrado hotspot, reducing the occurrence of many groups of aquatic insects in their habitat, particularly those with traits associated with resistance against hydrological disturbance.

Methane liquid-gas phase distribution during anaerobic sludge digestion: A thermodynamic approach.

Anaerobic digestion is certainly one of the options that can help solve the dilemma of energy demand, waste management and climate crisis mitigation mainly. Under ideal conditions, it is expected that all biomethane will be transferred from the liquid to the gaseous phase, ensuring maximum recovery. However, for concentrated wastewater or complex organic waste blends composed of functional groups with different sizes, the molecular interactions become important since the system is not only biphasic. Since the formation and transfer of a gas is related to the equilibrium condition, a thermodynamic approach could help to estimate the degree of variation of biomethane between the liquid and gaseous phases. Therefore, this investigation aimed to obtain the distribution between liquid and gaseous phases of the biomethane produced in the sewage sludge anaerobic digestion considering the substrate as a non-ideal solution. The nonlinear differential equations of the ADM1 were integrated with Aspen Plus® to verify the equilibrium conditions and the model was calibrated with data obtained through experiments conducted in a lab scale sequence batch reactor (SBR) fed with synthetic substrate (1500 mgCOD.L-1) and inoculated with flocculent sludge (500 mgSSV.L-1) from a full-scale UASB reactor. Considering the thermodynamic approach, the percentage of dissolved biomethane remains below the 2.97% percentage estimated by using the ADM1. It is possible to state that the principle of ideality is maintained in the system. On the other hand, CO2 phase distribution was considerably affected by the species defined in the equilibrium reactions. Therefore, it can be stated that Henry's Law simplification in ADM1 model is valid to represent the phenomenon investigated.

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.

Genomic and functional characterization of bacteriocinogenic lactic acid bacteria isolated from Boza, a traditional cereal-based beverage.

Boza is a traditional low-alcohol fermented beverage from the Balkan Peninsula, frequently explored as a functional food product. The product is rich in Lactic Acid Bacteria (LAB) and some of them can produce bacteriocins. In this study, a sample of Boza from Belogratchik, Bulgaria, was analyzed for the presence of bacteriocinogenic LAB, and after analyses by RAPD-PCR, three representative isolates were characterized by genomic analyses, using whole genome sequencing. Isolates identified as Pediococcus pentosaceus ST75BZ and Pediococcus pentosaceus ST87BZ contained operons encoding for bacteriocins pediocin PA-1 and penocin A, while isolate identified as Pediococcus acidilactici ST31BZ contained only the operon for pediocin PA-1 and a CRISPR/Cas system for protection against bacteriophage infection. The antimicrobial activity of bacteriocins produced by the three isolates was inhibited by treatment of the cell-free supernatants with proteolytic enzymes. The produced bacteriocins inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp., among other tested species. The levels of bacteriocin production varied from 3200 to 12,800 AU/ml recorded against L. monocytogenes 104, 637 and 711, measured at 24 h of incubation at 37 °C. All bacteriocins remained active after incubation at pH 2.0-10.0. The activity mode of the studied bacteriocins was bactericidal, as determined against L. monocytogenes 104, 637 and 711. In addition, bactericidal activity was demonstrated using a cell leakage ß-galactosidase assay, indicating a pore formation mechanism as a mode of action. The present study highlights the importance of combining genomic analyses and traditional microbiological approaches as way of characterizing microbial interactions in fermented foods.

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.