The classification of the legume family proposed here addresses the long‐known non‐monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near‐complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well‐supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community‐endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade‐based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale. N eotropical seasonally dry forest (dry forest) is a biome with a wide and fragmented distribution, found from Mexico to Argentina and throughout the Caribbean (1, 2) ( Fig. 1). It is one of the most threatened tropical forests in the world (3), with less than 10% of its original extent remaining in many countries (4).Following other authors (5, 6), we define dry forest as having a closed canopy, distinguishing it from more open, grass-rich savanna. It occurs on fertile soils where the rainfall is less thañ 1800 mm per year, with a period of 3 to 6 months receiving less than 100 mm per month (5-7), during which the vegetation is mostly deciduous. Seasonally dry areas, especially in Peru and Mexico, were home to pre-Columbian civilizations, so human interaction with dry forest has a long history (8). The climates and fertile soils of dry forest regions have led to higher human population densities and an increasing demand for energy and land, enhancing degradation (9). More recently, destruction of dry forest has been accelerated by intensive cultivation of crops, such as sugar cane, rice and soy, or by conversion to pasture for cattle.Dry forest is in a critical state because so little of it is intact, and of the remnant areas, little is protected (3). For example, only 1.2% of the total Caatinga region of dry forest in Brazil is fully protected compared with 9.9% of the Brazilian Amazon (10). Conservation actions are urgently needed to protect dry forest's unique biodiversity-many plant species and even genera are restricted to it and reflect an evolutionary history confined to this biome (1).We evaluate the floristic relationships of the disjunct areas of neotropical dry forest and highlight those that contain the highest diversity and endemism of woody plant species. We also explore woody plant species turnover across geographic space among dry forests. Our results provide a framework to allow the conservation significance of each separate major region of dry forest to be assessed at a continental scale. Our analyses are based on a subset of a data set of 1602 inventories made in dry forest and related semi-deciduous forests from Mexico and the Caribbean to Argentina and Paraguay that covers 6958 woody species, which has been compiled by the Latin American and Caribbean Seasonally Dry Tropica...

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A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth’s plant biodiversity that are rare. A large fraction, ~36.5% of Earth’s ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth’s plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.

In order to develop niche models for tree species characteristic of the cerrado vegetation (woody savannas) of central South America, and to hindcast their distributions during the Last Glacial Maximum and Last Inter‐Glacial, we compiled a dataset of tree species checklists for typical cerrado vegetation (n = 282) and other geographically co‐occurring vegetation types, e.g. seasonally dry tropical forest (n = 355). We then performed an indicator species analysis to select ten species that best characterize typical cerrado vegetation and developed niche models for them using the Maxent algorithm. We used these models to assess the probability of occurrence of each species across South America at the following time slices: Current (0 ka pre‐industrial), Holocene (6 ka BP), Last Glacial Maximum (LGM – 21 ka BP), and Last Interglacial (LIG – 130 ka BP). The niche models were robust for all species and showed the highest probability of occurrence in the core area of the Cerrado Domain. The palaeomodels suggested changes in the distributions of cerrado tree species throughout the Quaternary, with expansion during the LIG into the adjacent Amazonian and Atlantic moist forests, as well as connections with other South American savannas. The LGM models suggested a retraction of cerrado vegetation to inter‐tableland depressions and slopes of the Central Brazilian Highlands. Contrary to previous hypotheses, such as the Pleistocene refuge theory, we found that the widest expansion of cerrado tree species seems to have occurred during the LIG, most probably due to its warmer climate. On the other hand, the postulated retractions during the LGM were likely related to both decreased precipitation and temperature. These results are congruent with palynological and phylogeographic studies in the Cerrado Domain.

Aim The aim of this study was to test the role of environmental factors and spatially autocorrelated processes, such as historical fragmentation and dispersal limitation, in driving floristic variation across seasonally dry tropical forests (SDTFs) in eastern South America.Location SDTFs extending from the Caatinga phytogeographical domain of north-eastern Brazil to the Chaco phytogeographical domain of northern Argentina, an area referred to as the Dry Diagonal.Methods We compiled a database of 282 inventories of woody vegetation in SDTFs from across the Dry Diagonal and combined this with data for 14 environmental variables. We assessed the relative contribution of spatially autocorrelated processes and environmental factors to the floristic turnover among SDTFs across the Dry Diagonal using variation partitioning methods. In addition, we used multivariate analyses to determine which environmental factors were most important in explaining the turnover.Results We found that the environmental factors measured (temperature, precipitation and edaphic conditions) explained 21.3% of the variation in species composition, with 14.1% of this occurring independently of spatial autocorrelation. A spatially structured fraction of 4.2% could not be accounted for by the environmental factors measured. The main axis of compositional variation was significantly correlated with a north-south gradient in temperature regime. At the extreme south of the Dry Diagonal, a cold temperature regime, in which frost occurred, appeared to underlie floristic similarities between chaco woodlands and southern SDTFs.Main conclusions Environmental variables, particularly those related to temperature regime, seem to be the most significant factors affecting variation in species composition of SDTFs. Thus historical fragmentation and isolation alone cannot explain the turnover in species composition within SDTFs, as is often assumed. Compositional and environmental heterogeneity needs to be taken into account both to understand the past distribution of SDTFs and to manage and conserve this key tropical biome.

35Aim: We aimed to assess the contribution of marginal habitats to the tree species 36 richness of the Mata Atlântica (Atlantic Forest) biodiversity hotspot. In addition, we 37 aimed to determine which environmental factors drive the occurrence and 38 distribution of these marginal habitats. Brazil where it largely occurs, stretches for over 3,500km across equatorial, tropical 73 and subtropical latitudes, and is renowned worldwide for being one of the 35 74 biodiversity hotspots for conservation prioritisation (Myers et al., 2000). Its 75 importance is also demonstrated by its designation as one of the five primary 76 vegetation 'Domains' of Brazil (IBGE, 1993; Ab'Sáber, 2003), the others being the The prevailing land cover of these bordering Domains are semi-arid thorn woodlands distribution of rain forest species in the Atlantic Domain, which at its harshest 88 extremes give rise to distinct habitats (one for each factor), referred to as marginal 89 habitats. Therefore, the rain forest is placed by Scarano (2009) (Galindo-Leal et al., 2003; Tabarelli et al., 2004; 2005; Joly et al., 2014 203The data were originally compiled from an extensive survey of published and 217It also excludes checklists with low species richness (< 20 species), because this is 218 often due to low sampling/collecting efforts, which results in poor descriptive power. 219This study used a subset of tree inventories from the NTT database, The distribution of the sites in the ordination space yielded by NMDS (Fig. 3a waterlogged soils at positive scores (tropical riverine forests). 377The floristic composition of marginal habitats is not simply a nested subset of 378 the more species rich rain forest. The turnover component accounts for most of the 379 floristic dissimilarity of each marginal habitat in relation to rain forests (Fig. 4). 380Nestedness is higher than the turnover component in very few cases (i.e., few The forward selection procedure retained 13 environmental variables in the 390 model to explain the variation in tree species composition (Table 1). In partitioning 391 the variation explained by the retained environmental and spatial predictors, we 392 found that the environmental fraction explained 27% of the variation, 5% of which 393 was independent of spatial autocorrelation (P < 0.01). The environmental predictors 394could not account for a spatially structured variation of 12% (P < 0.01), and 61% of 395 the variation remained unexplained (see discussion for more details). 396The harshest extremes of the retained environmental variables (Table 1) rock outcrops (including campos rupestres) from all others vegetation types (Fig. 3a). 404Within the rock outcrop habitat, the frequency of frost was associated with the forests and tropical riverine forests (Figs. 2b and 3b). At the harshest extreme of the 414 drought-stress gradient (Fig. 3b) Fig. S1). Because the overall floristic dissimilarity between cloud forests and rain 430forests was relatively low (Fig. 3), we assessed the rates of endemism con...

Aim To define and map the main biomes of lowland tropical South America (LTSA) using data from tree species inventories and to test the ability of climatic and edaphic variables to distinguish amongst them. Location Lowland Tropical South America (LTSA), including Argentina, Bolivia, Brazil, Ecuador, Paraguay, Peru and Uruguay. Time period Present. Major taxa studied Trees. Methods We compiled a database of 4,103 geo‐referenced tree species inventories distributed across LTSA. We used a priori vegetation classifications and cluster analyses of floristic composition to assign sites to biomes. We mapped these biomes geographically and assessed climatic overlaps amongst them. We implemented classification tree approaches to quantify how well climatic and edaphic data can assign inventories to biomes. Results Our analyses distinguish savanna and seasonally dry tropical forest (SDTF) as distinct biomes, with the Chaco woodlands potentially representing a third dry biome in LTSA. Amongst the wet forests, we find that the Amazon and Atlantic Forests might represent different biomes, because they are distinct in both climate and species composition. Our results show substantial environmental overlap amongst biomes, with error rates for classifying sites into biomes of 19–21 and 16–18% using only climatic data and with the inclusion of edaphic data, respectively. Main conclusions Tree species composition can be used to determine biome identity at continental scales. We find high biome heterogeneity at small spatial scales, probably attributable to variation in edaphic conditions and disturbance history. This points to the challenges of using climatic and/or interpolation‐based edaphic data or coarse‐resolution, remotely sensed imagery to map tropical biomes. From this perspective, we suggest that using floristic information in biome delimitation will allow for greater synergy between conservation efforts centred on species diversity and management efforts centred on ecosystem function.