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The Amazon forest is far from uniform, containing different forest types and even savannas, but quantitative analyses of this variation are lacking. Here, we applied ordination analyses to test the floristic differentiation among Amazonian vegetation types using data for virtually all known tree species occurring in the Amazon (8224), distributed across 1584 sites. We also performed multiple regressions to assess the role of climate and substrate in shaping continental‐scale patterns of community composition across Amazonia. We find that the traditional classification of Amazonian vegetation types is consistent with quantitative patterns of tree species composition. High elevation and the extremes of substrate‐related factors underpin the floristic segregation of environmentally “marginal” vegetation types and terra firme forests with climatic factors being relatively unimportant. These patterns hold at continental scales, with sites of similar vegetation types showing higher similarity between them regardless of geographic distance, which contrasts with the idea of large‐scale variation among geographic regions (e.g., between the Guiana Shield and southwestern Amazon) representing the dominant floristic pattern in the Amazon. In contrast to other tropical biomes in South America, including the Mata Atlântica (second largest rain forest biome in the neotropics), the main floristic units in the Amazon are not geographically separated, but are edaphically driven and spatially interdigitated across Amazonia. Two thirds of terra firme tree species are restricted to this vegetation type, while among marginal vegetation types, only white‐sand forests (campinaranas) have a substantial proportion of restricted species, with other vegetation types sharing large numbers of species.

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.

Made available in DSpace on 2022-04-28T19:46:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 We introduce the concept of Biome Awareness Disparity (BAD)—defined as a failure to appreciate the significance of all biomes in conservation and restoration policy—and quantify disparities in (a) attention and interest, (b) action and (c) knowledge among biomes in tropical restoration science, practice and policy. By analysing 50,000 tweets from all Partner Institutions of the UN Decade of Ecosystem Restoration, and 45,000 tweets from the main science and environmental news media world-wide, we found strong disparities in attention and interest relative to biome extent and diversity. Tweets largely focused on forests, whereas open biomes (such as grasslands, savannas and shrublands) received less attention in relation to their area. In contrast to these differences in attention, there were equivalent likes and retweets between forest versus open biomes, suggesting the disparities may not reflect the views of the general public. Through a literature review, we found that restoration experiments are disproportionately concentrated in rainforests, dry forests and mangroves. More than half of the studies conducted in open biomes reported tree planting as the main restoration action, suggesting inappropriate application of forest-oriented techniques. Policy implications. We urge scientists, policymakers and land managers to recognise the value of open biomes for protecting biodiversity, securing ecosystem services, mitigating climate change and enhancing human livelihoods. Fixing Biome Awareness Disparity will increase the likelihood of the United Nations Decade on Ecosystem Restoration successfully delivering its promises. Department of Genetics Ecology and Evolution Federal University of Minas Gerais Institute Society Population and Nature Department of Ecology University of Brasília Research Institute for the Environment and Livelihoods Charles Darwin University Department of Biological Sciences University of Cape Town Institut Méditerranéen de Biodiversité et d'Ecologie CNRS IRD Aix Marseille Université Avignon Université IUT d'Avignon Instituto de Pesquisas Ambientais Lab of Vegetation Ecology Universidade Estadual Paulista (UNESP) Department of Plant Biology University of Campinas School of Environmental Sciences University of Liverpool Department of Zoology & Entomology University of Pretoria School of Animal Plant & Environmental Sciences University of the Witwatersrand Department of Geography College of Life and Environmental Sciences University of Exeter Department of Ecology and Conservation Biology Texas A&M University Royal Botanic Garden Edinburgh Lab of Vegetation Ecology Universidade Estadual Paulista (UNESP)

Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.

The Cerrado is a biodiversity hotspot in central Brazil that is the largest expanse of savanna in the Neotropics. Here, we aim to identify and delimit biogeographic districts within the Cerrado, to provide a geographic framework for conservation planning and scientific research prioritization. We used data from 588 sites with tree species inventories distributed across the entire Cerrado. To identify districts, we clustered sites based on their similarity in tree species composition. To investigate why districts differ in composition, we (1) determined the proportion of tree species in different districts that derive from other biomes, to assess the influence of neighbouring biomes upon geographically marginal districts and (2) assayed key climatic differences between districts, to test the effect of environmental factors upon compositional differences. We found seven biogeographic districts within the Cerrado. Marginal districts have a large proportion of tree species characteristic of Amazonia and Atlantic Forest, but the Cerrado endemic species are also important. Further, districts differed significantly for multiple climatic variables. Finally, to provide a preliminary conservation assessment of the different districts, we assessed their rate of land conversion and current coverage by protected areas. We found that districts in the south and southwest of the Cerrado have experienced the greatest land conversion and are the least protected, while those in the north and northeast are less impacted and better protected. Overall, our results show how biogeographic analyses can contribute to conservation planning by giving clear guidelines on which districts merit greater conservation and management attention.

This study investigated the current Leguminosae tree species composition in coastal forests over lithosoil soil or sandy plains in the eastern and central portion of Rio de Janeiro state, Brazil. A comparative study between the Atlantic Forest areas of the Southeast Region of Brazil was conducted to evaluate the influence of environmental variables on floristic differentiation. A total of 34 areas of the Southeast Region was selected from the NeoTropTree platform and the Leguminosae species in these areas were the basis for a similarity analysis. The Jaccard Similarity Index and the UPGMA method were applied for grouping analysis. The relationships between the Leguminosae species composition and the environmental variables were investigated via Cannonical Correspondance Analysis (CCA). The cluster analysis showed that the Leguminosae tree species group of this portion of Rio de Janeiro coastline share floristic affinity with seasonal forests, a result confirmed by CCA. This floristic differentiation is sustained by an exclusive group of Leguminosae species established over lithosoils or sandy plains, and signals that the extent of dry forests in Rio de Janeiro state might be larger than currently stated. The results justify distinct conservation actions in view of the floristic singularities of these areas. Resumo: O presente trabalho investigou a composição de espécies arbóreas de Leguminosae presentes em florestas litorâneas, estabelecidas sobre solos litólicos ou planície arenosa, na porção Central e Leste do estado do Rio de Janeiro, Brasil. Foi realizado um estudo comparativo entre áreas de Floresta Atlântica no Sudeste brasileiro para avaliar a influência de variáveis ambientais nas diferenciações florísticas. Foram elencadas 34 áreas da Região Sudeste na plataforma NeoTropTree e tabuladas as espécies de Leguminosae dessas áreas para análise de similaridade. Foi utilizado o índice de similaridade de Jaccard e o método UPGMA para as análises de agrupamento. As relações entre a composição de espécies de Leguminosae e as variáveis ambientais foram investigadas através da análise de Correspondência Canônica (CCA). A análise de agrupamento mostrou que o conjunto de espécies de Leguminosae arbóreas dessa porção do litoral fluminense possui afinidade florística com as florestas estacionais, resultado igualmente corroborado pela CCA. Essa diferenciação florística é sustentada por um conjunto exclusivo de espécies de Leguminosae, estabelecidas nessas florestas sobre solos litólicos ou planície arenosa e sinaliza que a extensão de matas secas no estado do Rio de Janeiro pode ser maior que o apresentado atualmente. Este resultado justifica ações diferenciadas em termos de conservação, tendo em vista a singularidade florística apresentada por estas áreas.

This special issue focuses on long‐term ecological monitoring in the tropics, with a particular focus, appropriate to Plants, People, Planet, on what it can offer both to local people and decision makers in tropical countries. Two of the contributed papers emphasise the role that long‐term, permanent monitoring plots can play in bringing together researchers, policymakers and communities, based on examples from Peru and Colombia (Baker et al., Norden et al.). The articles also highlight new plot‐based methods for monitoring the neglected tropical dry biomes of savannas and dry forests (The SEOSAW Partnership; Moonlight et al.) and new methods for field‐based monitoring of habitat degradation (Ahrends et al.) and the distribution of large trees (Harris et al.). Overall, the issue demonstrates that sustainable management of tropical environments requires long‐term, ground‐based monitoring that engages with the communities and institutions that manage these landscapes.

International audience; Understanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotaceae subfamily Chrysophylloideae, we collected 146 Chrysophylloideae accessions in previously under-explored areas, generating one of the most geographically complete data sets for neotropical Sapotaceae. Sapotaceae is a good model to test diversification hypotheses in lowland neotropical rain forests as it predominantly occurs

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191ha) and quantified tree palm (i.e., ≥10cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

We use DNA sequence data to understand the evolutionary history of the genus Cavanillesia (Malvaceae), with particular emphasis on C. chicamochae, an emblematic succulent-trunked tree endemic to seasonally dry tropical forests (SDTFs) of the Chicamocha Canyon of Colombia, South America. Based on field sampling of multiple individuals from different populations, we inferred a phylogeny calibrated into absolute time using robust macrofossil information. We show strong support for a monophyletic Cavanillesia chicamochae, with a mean stem age of 1.46 Ma. Two different mechanisms could explain its origin, either a late uplift age of the eastern cordillera or increased dryness of the Chicamocha Canyon during the Middle Pleistocene Transition. We also find marked genetic differentiation of its populations within the Chicamocha Canyon, likely driven by a combination of climate change and local landscape processes. Our results suggest that within northern inter-Andean SDTFs, as has been demonstrated in the central Andes, dispersal limitation leads to species and even population monophyly within individual valleys. The genetic differentiation of populations of C. chicamochae, together with the presence of other endemic and threatened species in the Chicamocha Canyon, calls for urgent management to conserve the unique biodiversity in the region. publishedVersion

The covid-19 pandemic led to rapid and large-scale government intervention in economies and societies. A common policy response to covid-19 outbreaks has been the lockdown or quarantine. Designed to slow the spread of the disease, lockdowns have unintended consequences for the environment. This article examines the impact of Colombia’s lockdown on forest fires, motivated by satellite data showing a particularly large upsurge of fires at around the time of lockdown implementation. We find that Colombia’s lockdown is associated with an increase in forest fires compared to three different counterfactuals, constructed to simulate the expected number of fires in the absence of the lockdown. To varying degrees across Colombia’s regions, the presence of armed groups is correlated with this fire upsurge. Mechanisms through which the lockdown might influence fire rates are discussed, including the mobilisation of armed groups and the reduction in the monitoring capacity of state and conservation organisations during the covid-19 outbreak. Given the fast-developing situation in Colombia, we conclude with some ideas for further research.

AimThe aim was to test whether species distribution models (SDMs) can reproduce major macroecological patterns in a species‐rich, tropical region and provide recommendations for using SDMs in areas with sparse biotic inventory data.LocationNorth‐east Brazil, including Minas Gerais.Time periodPresent.Major taxa studiedFlowering plants.MethodsSpecies composition estimates derived from stacked SDMs (s‐SDMs) were compared with data from 1,506 inventories of 933 woody plant species from north‐east Brazil. Both datasets were used in hierarchical clustering analyses to delimit floristic units that correspond to biomes. The ability of s‐SDMs to predict the identity, functional composition and floristic composition of biomes was compared across geographical and environmental space.ResultsThe s‐SDMs and inventory data both resolved four major biomes that largely corresponded in terms of their distribution, floristics and function. The s‐SDMs proved excellent at identifying broad‐scale biomes and their function, but misassigned many individual sites in complex savanna–forest mosaics.Main conclusionsOur results show that s‐SDMs have a unique role to play in describing macroecological patterns in areas lacking inventory data and for poorly known taxa. s‐SDMs accurately predict floristic and functional macroecological patterns but struggle in areas where non‐climatic factors, such as fire or soil, play key roles in governing distributions.

We investigate whether the Amotape—Huancabamba zone in the Andes acts as a barrier or corridor for plant species migration. We test this hypothesis based on data on trees, shrubs, and herbs collected in dry inter-Andean valleys (DIAVs) of Ecuador. We found that 72% of the species cross the Amotape—Huancabamba zone in a north—south direction and 13% of the species cross the Andes in an east—west direction. Southern DIAVs concentrate the highest numbers of endemic species. At the regional level we found that 43% of the species are exclusively Andean, while the remaining 57% are found in the Pacific lowlands, the Caribbean, and Mesoamerica. These results showing many species crossing the Amotape—Huancabamba zone in a north—south direction and also frequently found in neighboring lowland and highland ecosystems suggest that the Amotape—Huancabamba zone acts as a corridor for species migration of dry inter-Andean flora.

Bastin et al.’s estimate (Reports, 5 July 2019, p. 76) that tree planting for climate change mitigation could sequester 205 gigatonnes of carbon is approximately five times too large. Their analysis inflated soil organic carbon gains, failed to safeguard against warming from trees at high latitudes and elevations, and considered afforestation of savannas, grasslands, and shrublands to be restoration., Funding: Supported by the Texas A&M Sid Kyle Global Savanna Research Initiative (T.W.B.); Swiss National Science Foundation (20FI20_173691) (N.B.); Centre National pour la Recherche Scientifique CNRS PICS 2018-2020 (RESIGRASS) (E.B.); CNPq (Brazil, 303179/2016-3) (G.D.); CNPq (Brazil) (G.W.F.); CNPq (Brazil, 303988/2018-5) (A.F.); NASA award NNX17AK14G (F.F.); NSF award 1354943 (W.A.H.); Fundação de Amparo à Pesquisa do Estado de Minas Gerais (Brazil, 2016/13232-5) (S.L.S.); the Office of the Royal Society (IC170015) (C.E.R.L.); CNPq (Brazil, 310345/2018-9) (G.E.O.); the Spanish Government (FIROTIC, PGC2018-096569-B-I00) (J.G.P.); the National Research Foundation (ACCESS, 114695) (N.S.); CNPq (Brazil, 303568/2017-8) (F.A.O.S.); NSF awards 1342703 and 1926431 (C.J.S. and D.M.G.); NSF award EAR-1253713 (C.A.E.S.); Deutsche Forschungsgemeinschaft grant 5579 POEM (V.M.T.); and USDA-NIFA Sustainable Agricultural Systems Grant 12726253 (J.W.V.)

Freezing temperatures and water availability shape the distribution of evolutionary lineages of angiosperm trees in the Americas., The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are still a subject of debate. We unveil the evolutionary structure of tree species assemblages across the Americas to assess whether an inability to move or an inability to evolve is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity. Our study establishes the pervasive importance of niche conservatism to community assembly even at intercontinental scales.

Cynophalla polyantha (Capparaceae), new record for the Argentine flora. This paper records for the first time the presence in the Argentine flora of the small tree Cynophalla polyantha (Triana & Planch.) Cornejo & Iltis (Capparaceae), which was recently found in the north of the province of Salta, close to the Bolivian border.

AimTo 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.LocationLowland Tropical South America (LTSA), including Argentina, Bolivia, Brazil, Ecuador, Paraguay, Peru and Uruguay.Time periodPresent.Major taxa studiedTrees.MethodsWe 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.ResultsOur 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 conclusionsTree 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.

Tropical moist forests and savannas are iconic biomes. There is, however, a third principal biome in the lowland tropics that is less well known: tropical dry forest. Discussions on responses of vegetation in the tropics to climate and land-use change often focus on shifts between forests and savannas, but ignore dry forests. Tropical dry forests are distinct from moist forests in their seasonal drought stress and consequent deciduousness and differ from savannas in rarely experiencing fire. These factors lead tropical dry forests to have unique ecosystem function. Here, we discuss the underlying environmental drivers of transitions among tropical dry forests, moist forests and savannas, and demonstrate how incorporating tropical dry forests into our understanding of tropical biome transitions is critical to understanding the future of tropical vegetation under global environmental change.

In the tropics, research, conservation and public attention focus on rain forests, but this neglects that half of the global tropics have a seasonally dry climate. These regions are home to dry forests and savannas (Figures 1 and 2), and are the focus of this Primer. The attention given to rain forests is understandable. Their high species diversity, sheer stature and luxuriance thrill biologists today as much as they did the first explorers in the Age of Discovery. Although dry forest and savanna may make less of a first impression, they support a fascinating diversity of plant strategies to cope with stress and disturbance including fire, drought and herbivory. Savannas played a fundamental role in human evolution, and across Africa and India they support iconic megafauna.

1.The Cerrado Domain of central Brazil houses the largest extent of savanna in the Neotropics, but despite its simple characterisation as a giant savanna, it contains considerable vegetation heterogeneity that is poorly understood.2.We aimed to determine how vegetation types in the Cerrado diverge in their tree species composition and what role ecological factors play in driving compositional patterns.3.We used a dataset of 1,165 tree species inventories spread across the Cerrado Domain, which come from six vegetation types that have a substantial arboreal component: woody savannas, dystrophic cerradão, mesotrophic cerradão, seasonally dry tropical forests, semideciduous forests and evergreen forests. We found three extremes in terms of tree species composition, with clear underlying ecological drivers, which leads us to propose a ternary model, the ‘Cerrado Vegetation Triangle’, to characterize woody vegetation in the Cerrado. At one extreme, we found that semideciduous and evergreen forests are indistinguishable floristically and are found in areas with high water availability. At another extreme lie seasonally dry tropical forests which are found on more fertile soils. At the third extreme, we found that all types of savanna, and dystrophic cerradão, are highly similar in tree species composition and are commonly found in areas of poor soils and high flammability. Mesotrophic cerradão is transitional in tree species composition between savannas and seasonally dry tropical forest.4.The lack of variation in tree species composition attributed to climatic variables indicates that within homogeneous macroclimatic zones, many types of forest and savanna co‐exist due to complex mosaics of local substrate heterogeneity and fire history.5.Synthesis. Our findings highlight the complexity of forest‐savanna transitions in the Cerrado Domain, with relevance for understanding the future of Cerrado vegetation under environmental change. If nitrogen deposition is extensive, some savannas may be more likely to transition to mesotrophic cerradão or even seasonally dry tropical forest whereas if water availability increases these same savannas may transition to semideciduous or evergreen forest. Our ‘Cerrado Vegetation Triangle’ model offers a simple conceptual tool to frame discussions of conservation and management.

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.

The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.

Bastin et al . (Reports, 12 May 2017, p. 635) infer forest as more globally extensive than previously estimated using tree cover data. However, their forest definition does not reflect ecosystem function or biotic composition. These structural and climatic definitions inflate forest estimates across the tropics and undermine conservation goals, leading to inappropriate management policies and practices in tropical grassy ecosystems.

AimWe aimed to assess the contribution of marginal habitats to the tree species richness of the Mata Atlântica (Atlantic Forest) biodiversity hotspot. In addition, we aimed to determine which environmental factors drive the occurrence and distribution of these marginal habitats.LocationThe whole extension of the South American Atlantic Forest Domain plus forest intrusions into the neighbouring Cerrado and Pampa Domains, which comprises rain forests (“core” habitat) and five marginal habitats, namely high elevation forests, rock outcrop dwarf-forests, riverine forests, semi deciduous forests and restinga (coastal white-sand woodlands).MethodsWe compiled a dataset containing 366,875 occurrence records of 4,431 tree species from 1,753 site-checklists, which were a priori classified into 10 main vegetation types. We then performed ordination analyses of the species-by-site matrix to assess the floristic consistency of this classification. In order to assess the relative contribution of environmental predictors to the community turnover, we produced models using 26 climate and substrate-related variables as environmental predictors.ResultsOrdination diagrams supported the floristic segregation of vegetation types, with those considered as marginal habitats placed at the extremes of ordination axes. These marginal habitats are associated with the harshest extremes of five limiting factors: temperature seasonality (high elevation and subtropical riverine forests), flammability (rock outcrop dwarf-forests), high salinity (restinga), water deficit severity (semi deciduous forests) and waterlogged soils (tropical riverine forests). Importantly, 45% of all species endemic to the Atlantic Domain only occur in marginal habitats.Main conclusionsOur results showed the key role of the poorly protected marginal habitats in contributing to the high species richness of the Atlantic Domain. Various types of environmental harshness operate as environmental filters determining the distribution of the Atlantic Domain habitats. Our findings also stressed the importance of fire, a previously neglected environmental factor.

The rocky montane savannas of South America, known as campos rupestres in Brazil, where they largely occur, represent a megadiverse habitat housing c.15% of the Brazilian vascular flora in less than 1% of the Brazilian territory. Amongst other factors, the remarkable plant diversity in campos rupestres has been attributed to its occurrence as many isolated patches and to floristic influences from surrounding habitats, including lowland woody savannas (cerrado), Atlantic rain forests, seasonally dry woodlands and Amazonian rain forests. However, no study has assessed the degree to which the putative floristic influence from surrounding habitats drives compositional variation in campos rupestres. Here, we used a dataset on the composition of South American woody plant communities (>4,000 community surveys, with >100 representing campos rupestres), combined with environmental data, with the aim of characterising and explaining compositional variation of the campos rupestres woody flora. Our results showed that all campos rupestres, including the sites occurring in Amazonian ironstone formations, are more similar to cerrado woody savannas than to any other South American vegetation formations covered in our dataset. Also, multiple campo rupestre floristic groups may be recognized based on distinct species composition and environmental conditions, primarily related to substrate and climate. We stress the importance of considering this floristic heterogeneity in conservation, management and research planning.

Inter-bedded volcanic and organic sediments from Erazo (Ecuador) indicate the presence of four different forest assemblages on the eastern Andean flank during the middle Pleistocene. Radiometric dates (40Ar-39Ar) obtained from the volcanic ash indicate that deposition occurred between 620,000 and 192,000 years ago. Examination of the organic sediment composition and the fossil pollen, wood and charcoal it contains provides insight into depositional environment, vegetation assemblage and fire history. The high organic content and abundance of macro fossils found throughout the sediment suggest that during the period of deposition the local environment was either a swamp or a shallow water body. The correlation of fire activity (peaks in charcoal abundance) with volcanic ash deposits through most of the record suggests that volcanoes were the main source of ignition. The low abundance of grass (typically < 10%) throughout the sedimentary sequence along with the low abundance of other taxa indicative of open vegetation suggests the persistence of forest at Erazo. Four types of forest assemblage were identified (with the first taxa as the most dominant): i) Alnus-Arecaceae, ii) Miconia-Melastomataceae/Combretaceae-Moraceae/Urticaceae, iii) Arecaceae-Alnus, and iv) Podocarpus with Oreopanax sp. and Melastomataceae/Combretaceae. Changes in the forest floristic composition indicate high vegetation turnover and reassortment of taxa between upper and lower montane forests during the middle Pleistocene as well as the persistence of forest cover.

We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga. We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria. Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.

WE AGREE WITH Levis et al. that humans have influenced dry forests since their first arrival in the neotropics. This long interaction has had major effects, not least in leading to widespread destruction of this now highly threatened vegetation ([ 1 ][1]). It is also possible, as pointed out by

WE AGREE WITH Kuemmerle et al. that the forests in the Gran Chaco region are under massive threat, underprotected, and deserving of greater attention from scientists and conservationists. We could have included the Chaco woodlands in our analyses, and their distinctive flora would have reinforced

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., This paper is the result of the Latin American and Caribbean Seasonally Dry Tropical Forest Floristic Network (DRYFLOR), which has been supported at the Royal Botanic Garden Edinburgh by a Leverhulme Trust International Network Grant (IN-074). This work was also supported by the U.K. Natural Environment Research Council grant NE/ I028122/1; Colciencias Ph.D. scholarship 529; Synthesys Programme GBTAF-2824; the NSF (NSF 1118340 and 1118369); the Instituto Humboldt (IAvH)–Red colombiana de investigación y monitoreo en bosque seco; the Inter-American Institute for Global Change Research (IAI; Tropi-Dry, CRN2-021, funded by NSF GEO 0452325); Universidad Nacional de Rosario (UNR); and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). The data reported in this paper are available at www.dryflor.info. R.T.P. conceived the study. M.P., A.O.-F., K.B.-R., R.T.P., and J.W. designed the DRYFLOR database system. K.B.-R. and K.G.D. carried out most analyses. K.B.-R. R.T.P., and K.G.D. wrote the manuscript with substantial input from A.D.-S., R.L.-P., A.O.-F., D.P., C.Q., and R.R.

In spite of the existence of a vast body of information on the plant diversity of the Amazon, there remain significant obstacles to informed decision-making and management for conservation. Species distributions are poorly understood and the relationships between diversity and composition of vegetation, ecosystem services and resilience to climatic fluctuations are insufficiently clear. The geographic distribution of phylogenetic diversity in relation to current protected areas is unexplored and very little is known about intraspecific genetic variability and its practical significance. Interpretation of vegetation differentiation and distribution remains relatively simplistic; there are still large parts of the basin for which few or no botanical data exist, and many rare and sparsely distributed species remain undiscovered. Improved understanding of the ecological roles, dynamics and associations of the species of greatest importance for the maintenance of sustainable livelihoods and ecosystem services, habitat restoration and adaptation to climate change is a high priority. In many cases these are common and widespread species. Some of these issues are explored by looking at the Cristalino region in northern Mato Grosso as a case-study. Effective integration, quality assessment, synthesis and application of existing data on the plant diversity of the Amazon will help to address these issues. However, more targeted information is needed from the ground. Future prioritisation of research effort will require a careful and pragmatic balance between the ‘traditional’ focus on rare and endemic species and species-rich communities, and the growing need to understand the key ‘framework’ elements that will determine the future of the Amazon environment. Similar situations are faced elsewhere in the tropics: for botanical research institutes in the 21st century this demands an urgent re-evaluation of core activities and concerted engagement with the issues and challenges facing conservation in a context of rampant population growth, climate change and environmental destruction.

In order to develop niche models for tree species characteristic of thecerrado vegetation (woody savannas) of central South America, and tohindcast their distributions during the Last Glacial Maximum and Last Inter-Glacial, we compiled a dataset of tree species checklists for typical cerradovegetation (n=282) and other geographically co-occurring vegetationtypes, e.g. seasonally dry tropical forest (n=355). We then performed anIndicator Species Analysis to select ten species that best characterizetypical cerrado vegetation and developed niche models for them using theMaxent algorithm. We used these models to assess the probability ofoccurrence of each species across South America at the following timeslices: Current (0 ka pre-industrial), Holocene (6 ka BP), Last GlacialMaximum (LGM - 21 ka BP), and Last Interglacial (LIG - 130 ka BP). Theniche models were robust for all species and showed the highest probabilityof occurrence in the core area of the Cerrado Domain. The palaeomodelssuggested changes in the distributions of cerrado tree species throughoutthe Quaternary, with expansion during the LIG into the adjacentAmazonian and Atlantic moist forests, as well as connections with otherSouth American savannas. The LGM models suggested a retraction ofcerrado vegetation to inter-tableland depressions and slopes of the CentralBrazilian Highlands. Contrary to previous hypotheses, such as thePleistocene Refuge Theory, we found that the widest expansion of cerradotree species seems to have occurred during the LIG, most probably due toits warmer climate. On the other hand, the postulated retractions duringthe LGM were likely related to both decreased precipitation andtemperature. These results are congruent with palynological andphylogeographic studies in the Cerrado Domain.

The Amazon lowland rainforest flora is conventionally viewed as comprising lineages that evolved in biogeographic isolation after the split of west Gondwana ( ca . 100 Myr ago). Recent molecular phylogenies, however, identify immigrant lineages that arrived in South America during its period of oceanic isolation ( ca . 100–3 Myr ago). Long–distance sweepstakes dispersal across oceans played an important and possibly predominant role. Stepping–stone migration from Africa and North America through hypothesized Late Cretaceous and Tertiary island chains may have facilitated immigration. An analysis of inventory plot data suggests that immigrant lineages comprise ca . 20% of both the species and individuals of an Amazon tree community in Ecuador. This is more than an order of magnitude higher than previous estimates. We also present data on the community–level similarity between South American and palaeotropical rainforests, and suggest that most taxonomic similarity derives from trans–oceanic dispersal, rather than a shared Gondwanan history.

Los árboles filogenéticos basados ??en datos de secuencias de ADN, cuando se calibran con una dimensión de tiempo, permiten la inferencia de: (i) el patrón de acumulación de linajes a través del tiempo; (ii) el momento de origen de los grupos monofiléticos; (iii) cuando arribaron linajes en diferentes áreas geográficas; (iv) el momento de origen de las morfologías específicas del bioma. Esto brinda una nueva y poderosa visión de la historia de los biomas que en muchos casos no es proporcionada por el registro fósil de plantas incompleto. Filogenias de plantas fechadas para familias de angiospermas como Leguminoaceae (Fabaceae), Melastomataceae sensu stricto, Annonaceae y Rhamnaceae indican que la dispersión transoceánica a larga distancia ha jugado un papel importante en la configuración de sus distribuciones, y que esto puede oscurecer cualquier efecto de la historia tectónica, que anteriormente se suponía que había sido la principal causa de sus patrones biogeográficos. La dispersión de otros continentes también ha sido importante en el ensamblaje de la flora de la selva amazónica y la flora australiana. La comparación de patrones biogeográficos fechados de plantas y animales sugiere que la dispersión reciente a larga distancia podría ser más frecuente en las plantas, lo que tiene importantes implicaciones para el ensamblaje y coevolución de la comunidad. Las filogenias de plantas fechadas también revelan el papel de los cambios ambientales pasados ??en la evolución de los linajes en biomas ricos en especies, y muestran que la reciente diversificación Plio-Pleistoceno ha contribuido sustancialmente a su riqueza de especies actual. Debido al papel fundamental de los fósiles y los caracteres morfológicos en la asignación de edades a los nodos en los árboles filogenéticos, los estudios futuros deben incluir una consideración morfológica cuidadosa de los fósiles y sus parientes existentes en un contexto filogenético. Los sistemas de estudio ideales se basarán en datos de secuencias de ADN de múltiples loci y múltiples calibraciones fósiles. Esto permite la validación cruzada tanto de las estimaciones de edad de diferentes loci como de diferentes calibraciones de fósiles. Para obtener una visión más completa de la historia del bioma, los estudios futuros deben enfatizar el muestreo completo de taxones en grupos ecológicamente importantes y deben enfocarse en áreas geográficas para las cuales hay pocas filogenias a nivel de especie disponibles, como África tropical y Asia. Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminosae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio–Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

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.

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = 20.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyperfragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing.

Seasonally dry tropical forests have been largely ignored in discussions of vegetation changes during the Quaternary. We distinguish dry forests, which are essentially tree-dominated ecosystems, from open savannas that have a xeromorphic fire-tolerant, grass layer and grow on dystrophic, acid soils. Seasonally dry tropical forests grow on fertile soils, usually have a closed canopy, have woody floras dominated by the Leguminosae and Bignoniaceae and a sparse ground flora with few grasses. They occur in disjunct areas throughout the Neotropics. The Chaco forests of central South America experience regular annual frosts, and are considered a subtropical extension of temperate vegetation formations. At least 104 plant species from a wide range of families are each found in two or more of the isolated areas of seasonally dry tropical forest scattered across the Neotropics, and these repeated patterns of distribution suggest a more widespread expanse of this vegetation, presumably in drier and cooler periods of the Pleistocene. We propose a new vegetation model for some areas of the Ice-Age Amazon: a type of seasonally dry tropical forest, with rain forest and montane taxa largely confined to gallery forest. This model is consistent with the distributions of contemporary seasonally dry tropical forest species in Amazonia and existing palynological data. The hypothesis of vicariance of a wider historical area of seasonally dry tropical forests could be tested using a cladistic biogeographic approach focusing on plant genera that have species showing high levels of endemicity in the different areas of these forests.

7 p., [EN] The ‘‘Great American Biotic Interchange’’ (GABI) is regarded as a defining event in the biogeography of the Americas. It is hypothesized to have occurred when the Isthmus of Panama closed ca three million years ago (Ma), ending the isolation of South America and permitting the mixing of its biota with that of North America. This view of the GABI is based largely upon the animal fossil record, but recent molecular biogeographic studies of plants that show repeated instances of long-distance dispersal over major oceanic barriers suggest that perhaps the land bridge provided by the isthmus may have been less necessary for plant migration. Here we show that plants have significantly earlier divergence time estimates than animals for historical migration events across the Isthmus of Panama region. This difference in timing indicates that plants had a greater propensity for dispersal over the isthmus before its closure compared with animals. The GABI was therefore asynchronous for plants and animals, which has fundamental implications for the historical assembly of tropical biomes in the most species-rich forests on the planet.

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.

Puyasena et al . question our interpretation of climate-driven vegetation change on the Andean flank in western Amazonia during the middle Pleistocene and suggest that the use of Podocarpus spp. as a proxy of past climate change should be reassessed. We defend our assertion that vegetation change at the Erazo study site was predominantly driven by climate change due to concomitant changes recorded by multiple taxa in the fossil record.

Background Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. Results Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23–16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. Conclusions Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered.