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.

TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research.

Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.

From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae).

The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which included Bayesian phylogenies and haplotype networks, ancestral area reconstructions, and ecological niche modeling, allowed for exploring the evolutionary history of Dimorphandra. Within the subgenus Phaneropsia, the cpDNA sequence data were more closely-related to species from the genus Mora, while the ITS sequence data displayed a closer phylogenetic relationship with the subgenus Pocillum. This incongruence may be due to incomplete lineage sorting associated with ancient polymorphisms. The Amazonian Dimophandra lineages were highly polymorphic and divergent, while those from the Cerrado and the Atlantic Forest had low levels of polymorphisms. The Amazon likely gave rise to the Dimophandra lineage that produced the Cerrado species, while a Cerrado lineage likely gave rise to the Atlantic Forest species. Habitat shifts were identified as a key factor in shaping the late evolutionary history of Dimorphandra.

More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia.

Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.

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.

Landscape-scale forest cover drives the predictability of forest regeneration across the Neotropics.

Abandonment of agricultural lands promotes the global expansion of secondary forests, which are critical for preserving biodiversity and ecosystem functions and services. Such roles largely depend, however, on two essential successional attributes, trajectory and recovery rate, which are expected to depend on landscape-scale forest cover in nonlinear ways. Using a multi-scale approach and a large vegetation dataset (843 plots, 3511 tree species) from 22 secondary forest chronosequences distributed across the Neotropics, we show that successional trajectories of woody plant species richness, stem density and basal area are less predictable in landscapes (4 km radius) with intermediate (40-60%) forest cover than in landscapes with high (greater than 60%) forest cover. This supports theory suggesting that high spatial and environmental heterogeneity in intermediately deforested landscapes can increase the variation of key ecological factors for forest recovery (e.g. seed dispersal and seedling recruitment), increasing the uncertainty of successional trajectories. Regarding the recovery rate, only species richness is positively related to forest cover in relatively small (1 km radius) landscapes. These findings highlight the importance of using a spatially explicit landscape approach in restoration initiatives and suggest that these initiatives can be more effective in more forested landscapes, especially if implemented across spatial extents of 1-4 km radius.

Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava.

The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only c. 6 million years ago have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast Brazil's Atlantic Forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization, including into savannas and rainforests within South America. We identify the closest wild relatives to Manihot esculenta, including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species, including Manihot glaziovii, a species used widely in breeding programs. Finally, we show that this wild-to-crop introgression substantially shapes the mutation load in cassava. Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research.

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.

Contribution of the Brazilian National Forest Inventory to the knowledge of Cerrado woody flora / A contribuição do Inventário Florestal Nacional para o conhecimento da flora lenhosa do Cerrado

Abstract: The National Forest Inventory (Inventário Florestal Nacional-IFN) is a large initiative that uses standardised methods to survey Brazilian forestry resources. One target of the IFN is the Cerrado, which contains one of the richest floras in the world. The aim of this study was to assess the contribution of the IFN to the knowledge of Cerrado woody flora. We analysed data from field-collected vouchers sampled by the IFN Cerrado. We restricted our analyses to IFN collections of native trees and shrubs, including palms, which were identified at the species level. Habitat of each collection was obtained by overlaying specimens' geographic coordinates with land cover maps available in the Mapbiomas platform. Our final dataset comprised 28,602 specimens distributed in 2,779 sites (conglomerates) in Bahia, Distrito Federal, Goiás, Maranhão, Mato Grosso, Mato Grosso do Sul, Minas Gerais, Piauí, São Paulo and Tocantins. Collections were located in the following habitats: savannas (40.5%), forests (30.2%), anthropic areas (25.6%), grasslands (3.5%), and water (0.2%). We recorded 1,822 species belonging to 543 genera and 105 families, representing 34% of Cerrado woody species recorded on Flora do Brasil 2020. Fabaceae had the largest number of species, while Tapirira guianensis and Matayba guianensis were the most collected species. We highlight 60 potentially new records of occurrence for several states and 64 new records for the Cerrado, primarily in riparian forests where species from other biomes occur. In addition, 232 recorded species are Cerrado endemics, while 36 are cited in the CNCFlora's red list as endangered. The systematic sampling carried out by the IFN enabled vegetation sampling in remote and poorly known areas, which expanded the geographic range of many woody species and contributed to the knowledge of plant diversity in the Cerrado.

Resumo: O Inventário Florestal Nacional (IFN) é uma ampla iniciativa que emprega métodos padronizados para inventariar recursos florestais brasileiros. Um dos alvos do IFN é o Cerrado, o qual possui uma das floras mais ricas do mundo. O objetivo deste estudo foi avaliar a contribuição do IFN para o conhecimento da flora lenhosa do Cerrado. Nós analisamos dados de vouchers coletados em campo pelo IFN Cerrado. Nós restringimos nossas análises a coletas do IFN pertencentes a árvores e arbustos, incluindo palmeiras, identificadas ao nível de espécie. O habitat de cada coleta foi obtido pela intersecção entre as coordenadas geográficas dos espécimes com mapas de cobertura disponíveis na plataforma Mapbiomas. O conjunto final de dados foi composto por 28.602 coletas distribuídas em 2.779 sítios (conglomerados) localizados na Bahia, Distrito Federal, Goiás, Maranhão, Mato Grosso, Mato Grosso do Sul, Minas Gerais, Piauí, São Paulo e Tocantins. As coletas foram realizadas nos seguintes habitats: savanas (40,5%), florestas (30,2%), áreas antrópicas (25,6%), campos (3,5%) e água (0,2%). Ao todo foram registradas 1.822 espécies pertencentes a 543 gêneros e 105 famílias, representando 34% das espécies lenhosas do Cerrado registradas na Flora do Brasil 2020. Fabaceae apresentou o maior número de espécies, enquanto que Tapirira guianensis e Matayba guianensis foram as espécies mais coletadas. Destacam-se possíveis novos registros de ocorrência de 60 espécies para diversos estados e de 64 espécies para o Cerrado, predominantemente nas florestas ripárias onde geralmente ocorrem espécies de outros biomas. Além disso, foram registradas 232 espécies endêmicas do Cerrado, bem como 36 espécies citadas na lista vermelha do CNCFlora como ameaçadas. A amostragem sistemática realizada pelo IFN permitiu o inventário da vegetação em áreas remotas e pouco coletadas, permitindo a expansão da distribuição geográfica de diversas espécies lenhosas, e contribuindo para o conhecimento da diversidade vegetal no Cerrado.

High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae).

Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. "Campo Grande," S. capitata "RS024" and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.

The large mimosoid genus Inga Mill. (tribe Ingeae, Caesalpinioideae) is nodulated by diverse Bradyrhizobium strains in its main centers of diversity in Brazil.

Inga (Caesalpinioideae) is the type genus of the Ingeae tribe in the mimosoid clade. It comprises about 300 species, all trees or treelets, and has an exclusively neotropical distribution, with Brazil as its main center of diversity. In this study, we analyzed the diversity of 40 strains of rhizobia isolated from root nodules collected from ten species of Inga belonging to different types of vegetation in Brazil. Sequences of their housekeeping genes (dnaK, recA, rpoB, gyrB and glnII), 16S rRNA genes, internal transcribed spacer (ITS) regions, as well as their symbiosis-essential genes (nodC and nifH) were used to characterize them genetically. The ability of the rhizobia to form nodules on Inga spp., and on the promiscuous legume siratro (Macroptilium atropurpureum) was also evaluated. A multilocus sequence analysis (MLSA) combined with an analysis of the ITS region showed that the isolates were distributed into four main groups (A-D) within the large genus Bradyrhizobium. Analysis of the nodC and nifH genes showed that the isolates formed a separate branch from all described species of Bradyrhizobium, except for B. ingae. Most of the tested isolates formed nodules on siratro and all isolates tested nodulated Inga spp. Our results suggest a unique co-evolutionary history of Bradyrhizobium and Inga and demonstrate the existence of potential new species of microsymbionts nodulating this important and representative genus of leguminous tree from the Caesalpinioideae mimosoid clade.

Nodulation of the neotropical genus Calliandra by alpha or betaproteobacterial symbionts depends on the biogeographical origins of the host species.

The neotropical genus Calliandra is of great importance to ecology and agroforestry, but little is known about its nodulation or its rhizobia. The nodulation of several species from two restricted diversity centres with native/endemic species (Eastern Brazil and North-Central America) and species widespread in South America, as well as their nodule structure and the molecular characterization of their rhizobial symbionts based on phylogeny of the 16S rRNA, recA and nodC gene, is reported herein. Species representative of different regions were grown in Brazilian soil, their nodulation observed, and their symbionts characterized. Calliandra nodules have anatomy that is typical of mimosoid nodules regardless of the microsymbiont type. The rhizobial symbionts differed according to the geographical origin of the species, i.e. Alphaproteobacteria (Rhizobium) were the exclusive symbionts from North-Central America, Betaproteobacteria (Paraburkholderia) from Eastern Brazil, and a mixture of both nodulated the widespread species. The symbiont preferences of Calliandra species are the result of the host co-evolving with the "local" symbiotic bacteria that thrive in the different edaphoclimatic conditions, e.g. the acidic soils of NE Brazil are rich in acid-tolerant Paraburkholderia, whereas those of North-Central America are typically neutral-alkaline and harbour Rhizobium. It is hypothesized that the flexibility of widespread species in symbiont choice has assisted in their wider dispersal across the neotropics.

Mega-dams and extreme rainfall: Disentangling the drivers of extensive impacts of a large flooding event on Amazon Forests.

Extreme weather events and the presence of mega-hydroelectric dams, when combined, present an emerging threat to natural habitats in the Amazon region. To understand the magnitude of these impacts, we used remote sensing data to assess forest loss in areas affected by the extreme 2014 flood in the entire Madeira River basin, the location of two mega-dams. In addition, forest plots (26 ha) were monitored between 2011 and 2015 (14,328 trees) in order to evaluate changes in tree mortality, aboveground biomass (AGB), species composition and community structure around the Jirau reservoir (distance between plots varies from 1 to 80 km). We showed that the mega-dams were the main driver of tree mortality in Madeira basin forests after the 2014 extreme flood. Forest loss in the areas surrounding the reservoirs was 56 km2 in Santo Antônio, 190 km2 in Jirau (7.4-9.2% of the forest cover before flooding), and 79.9% above that predicted in environmental impact assessments. We also show that climatic anomalies, albeit with much smaller impact than that created by the mega-dams, resulted in forest loss along different Madeira sub-basins not affected by dams (34-173 km2; 0.5-1.7%). The impact of flooding was greater in várzea and transitional forests, resulting in high rates of tree mortality (88-100%), AGB decrease (89-100%), and reduction of species richness (78-100%). Conversely, campinarana forests were more flood-tolerant with a slight decrease in species richness (6%) and similar AGB after flooding. Taking together satellite and field measurements, we estimate that the 2014 flood event in the Madeira basin resulted in 8.81-12.47 ∙ 106 tons of dead biomass. Environmental impact studies required for environmental licensing of mega-dams by governmental agencies should consider the increasing trend of climatic anomalies and the high vulnerability of different habitats to minimize the serious impacts of dams on Amazonian biodiversity and carbon stocks.

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 Species of Mimosa L. ser. Bipinnatae DC. (Leguminosae) from the Cerrado: Taxonomic and Phylogenetic Insights.

Mimosa carolina (Leguminosae), a new species from the Parque Nacional Chapada das Mesas, located in the northern limit of the Brazilian Cerrado, is described and illustrated. In addition, a phylogenetic reconstruction was performed to recover the position of this species in relation to the main clades of the genus Mimosa. This new species is assigned to sect. Habbasia ser. Bipinnatae and exhibits relevant morphological differences with all described species of this series, most notably the prostate habit, glabrous stems, and absence of internal spicules. Our results indicate that this new entity is clearly nested in a strongly supported clade with other striated-corolla species of ser. Bipinnatae. Therefore, ser. Bipinnatae appears to be monophyletic, and a morphologically and ecologically cohesive group within Mimosa. An updated identification key for this series is provided.

Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains.

Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species richness is often associated with recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analysing plant diversification dynamics in the campo rupestre, an ecosystem associated with pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics exhibit fastest rates of diversification during the last 5 Myr, a climatically unstable period. However, results from ancestral range estimations using different models disagree on the age of the earliest in situ speciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated with these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, regardless of their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circumstances that can also result in higher extinction rates and fast species turnover, misleading the age estimates of endemic lineages.

Evolutionary diversity in tropical tree communities peaks at intermediate precipitation.

Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, however, is largely unexplored. Here we detail how evolutionary diversity varies along precipitation gradients by bringing together a comprehensive database on the composition of angiosperm tree communities across lowland tropical South America (2,025 inventories from wet to arid biomes), and a new, large-scale phylogenetic hypothesis for the genera that occur in these ecosystems. We find a marked reduction in the evolutionary diversity of communities at low precipitation. However, unlike species richness, evolutionary diversity does not continually increase with rainfall. Rather, our results show that the greatest evolutionary diversity is found in intermediate precipitation regimes, and that there is a decline in evolutionary diversity above 1,490 mm of mean annual rainfall. If conservation is to prioritise evolutionary diversity, areas of intermediate precipitation that are found in the South American 'arc of deforestation', but which have been neglected in the design of protected area networks in the tropics, merit increased conservation attention.

Low cytomolecular diversification in the genus Stylosanthes Sw. (Papilionoideae, Leguminosae).

Stylosanthes (Papilionoideae, Leguminosae) is a predominantly Neotropical genus with ~48 species that include worldwide important forage species. This study presents the chromosome number and morphology of eight species of the genus Stylosanthes (S. acuminata, S. gracilis, S. grandifolia, S. guianensis, S. hippocampoides, S. pilosa, S. macrocephala, and S. ruellioides). In addition, staining with CMA and DAPI, in situ hybridization with 5S and 35S rDNA probes, and estimation of DNA content were performed. The interpretation of Stylosanthes chromosome diversification was anchored by a comparison with the sister genus Arachis and a dated molecular phylogeny based on nuclear and plastid loci. Stylosanthes species showed 2n = 20, with low cytomolecular diversification regarding 5S rDNA, 35S rDNA, and genome size. Arachis has a more ancient diversification (~7 Mya in the Pliocene) than the relatively recent Stylosanthes (~2 Mya in the Pleistocene), and it seems more diverse than its sister lineage. Our data support the idea that the cytomolecular stability of Stylosanthes in relation to Arachis could be a result of its recent origin. The recent diversification of Stylosanthes could also be related to the low morphological differentiation among species, and to the recurrent formation of allopolyploid complexes.

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae.

Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4⁻7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitansrhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickiadabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickiasymbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits-diazotrophy and/or symbiotic nodulation, and pathogenesis-were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophyllinif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.