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Plants are widely recognized as chemical factories, with each species producing dozens to hundreds of unique secondary metabolites. These compounds shape the interactions between plants and their natural enemies. We explore the evolutionary patterns and processes by which plants generate chemical diversity, from evolving novel compounds to unique chemical profiles. We characterized the chemical profile of one-third of the species of tropical rainforest trees in the genus Inga (c. 100, Fabaceae) using ultraperformance liquid chromatography-mass spectrometry-based metabolomics and applied phylogenetic comparative methods to understand the mode of chemical evolution. We show: each Inga species contain structurally unrelated compounds and high levels of phytochemical diversity; closely related species have divergent chemical profiles, with individual compounds, compound classes, and chemical profiles showing little-to-no phylogenetic signal; at the evolutionary time scale, a species' chemical profile shows a signature of divergent adaptation. At the ecological time scale, sympatric species were the most divergent, implying it is also advantageous to maintain a unique chemical profile from community members; finally, we integrate these patterns with a model for how chemical diversity evolves. Taken together, these results show that phytochemical diversity and divergence are fundamental to the ecology and evolution of plants.

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See 'Read me.rtf' (included in 'Data S1.rar') for a description of the files included in this dataset. Abstract of study: 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. 3,500 species, we show that the water availability gradient from deserts to rainforests 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.

There is high potential for ecosystem restoration across tropical savannah-dominated regions, but the benefits that could be gained from this restoration are rarely assessed. This study focuses on the Brazilian Cerrado, a highly species-rich savannah-dominated region, as an exemplar to review potential restoration benefits using three metrics: net biomass gains, plant species richness and ability to connect restored and native vegetation. Localized estimates of the most appropriate restoration vegetation type (grassland, savannah, woodland/forest) for pasturelands are produced. Carbon sequestration potential is significant for savannah and woodland/forest restoration in the seasonally dry tropics (net biomass gains of 58.2 ± 37.7 and 130.0 ± 69.4 Mg ha −1 ). Modelled restoration species richness gains were highest in the central and south-east of the Cerrado for savannahs and grasslands, and in the west and north-west for woodlands/forests. The potential to initiate restoration projects across the whole of the Cerrado is high and four hotspot areas are identified. We demonstrate that landscape restoration across all vegetation types within heterogeneous tropical savannah-dominated regions can maximize biodiversity and carbon gains. However, conservation of existing vegetation is essential to minimizing the cost and improving the chances of restoration success. This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.

As the United Nations develops a post-2020 global biodiversity framework for the Convention on Biological Diversity, attention is focusing on how new goals and targets for ecosystem conservation might serve its vision of ‘living in harmony with nature’1,2. Advancing dual imperatives to conserve biodiversity and sustain ecosystem services requires reliable and resilient generalizations and predictions about ecosystem responses to environmental change and management3. Ecosystems vary in their biota4, service provision5 and relative exposure to risks6, yet there is no globally consistent classification of ecosystems that reflects functional responses to change and management. This hampers progress on developing conservation targets and sustainability goals. Here we present the International Union for Conservation of Nature (IUCN) Global Ecosystem Typology, a conceptually robust, scalable, spatially explicit approach for generalizations and predictions about functions, biota, risks and management remedies across the entire biosphere. The outcome of a major cross-disciplinary collaboration, this novel framework places all of Earth’s ecosystems into a unifying theoretical context to guide the transformation of ecosystem policy and management from global to local scales. This new information infrastructure will support knowledge transfer for ecosystem-specific management and restoration, globally standardized ecosystem risk assessments, natural capital accounting and progress on the post-2020 global biodiversity framework.

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.

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

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events betweenBrownealineages and indicated that gene tree incongruence inBrowneais best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ∼19,000 ddRAD loci recovered a high degree of shared variation between twoBrowneaspecies which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization’s rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

Early natural historians – Compte de Buffon, von Humboldt and De Candolle – established ecology 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, an pantropical plant clade of 3,400 species, we show that the water availability gradient from deserts to rainforests 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. Fil: Ringelberg, Jens J. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza Fil: Koenen, Erik J.M. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza. Université Libre de Bruxelles. Faculté des Sciences. Evolutionary Biology & Ecology; Bélgica Fil: Sauter, Benjamín. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza Fil: Aebli, Anahita. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza. Abteling Umweltschutz und Energie. Departement Bau und Umwelt; Suiza Fil: Rando, Juliana G. Universidade Federal do Oeste da Bahia. Centro das Ciências Biológicas e da Saúde. Programa de Pós Graduação em Ciências Ambientais; Brasil Fil: Iganci, João R. Universidade Federal de Pelotas. Campus Universitário Capão do Leão. Instituto de Biologia; Brasil. Universidade Federal do Rio Grande do Sul. Programa de Pós-Graduação em Botânica; Brasil Fil: de Queiroz, Luciano P. Universidade Estadual de Feira de Santana. Departamento Ciências Biológicas; Brasil Fil: Murphy, Daniel J. Royal Botanic Gardens Victoria: Australia Fil: Gaudeul, Myriam. Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA: Francia Fil: Bruneau, Anne. Université de Montréal. Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques; Canadá Fil: Luckow, Melissa. Cornell University. School of Integrative Plant Science. Plant Biology Section; Estados Unidos Fil: Morales, Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentina

1. The outstanding diversity of Amazonian forests is predicted to be the result of several processes. While tree lineages have dispersed repeatedly across the Amazon, interactions between plants and insects may be the principal mechanism structuring the communities at local scales.2. Using metabolomic and phylogenetic approaches, we investigated the patterns of historical assembly of plant communities across the Amazon based on the Neotropical genus of trees Inga (Leguminosae) at four, widely separated sites.3. Our results show a low degree of phylogenetic structure and a mixing of chemotypes across the whole Amazon basin, suggesting that although biogeography may play a role, the metacommunity for any local community in the Amazon is the entire basin. Yet, local communities are assembled by ecological processes, with the suite of Inga at a given site more divergent in chemical defenses than expected by chance4.Synthesis. This is the first study to present metabolomics data for nearly 100 species in a diverse Neotropical plant clade across the whole Amazonia. Our results demonstrate a role for plant‐herbivore interactions in shaping the clade’s community assembly at a local scale, and suggest that the high alpha diversity in Amazonian tree communities must be due in part to the interactions of diverse tree lineages with their natural enemies providing a high number of niche dimensions.

SummaryPlants are widely recognized as chemical factories, with each species producing dozens to hundreds of unique secondary metabolites. These compounds shape the interactions between plants and their natural enemies. Here we explore how plants generate chemical diversity, and what evolutionary processes have led to novel compounds and unique chemical profiles.We comprehensively characterized the chemical profile of one-third of the species of tropical rainforest trees in the genusInga(∼ 100, Fabaceae) and applied phylogenetic comparative methods to understand the mode of chemical defense evolution.We show that: 1) EachIngaspecies produces exceptionally high levels of phytochemical diversity, despite costs, tradeoffs and biosynthetic constraints. 2) Closely related species have highly divergent defense profiles, with individual compounds, major compound classes and complete profiles showing little to no phylogenetic signal. 3) We show that the evolution of a species’ chemical profile shows a signature of divergent adaptation, implying that it is advantageous for a species to have distinct chemistry from close relatives to avoid shared natural enemies. 4) Finally, we hypothesize a model where deep homology of biosynthetic pathways and rapid changes in regulatory mechanisms may better explain the observed large shifts in defense chemicals between closely related taxa.

Hybridization can facilitate both evolutionary diversification and extinction and has had a critical role in plant evolution, with c. 25% of species known to hybridize in some temperate floras. However, in the species-rich Neotropical flora, the role of hybridization in the evolution of diversity remains unclear. Our review examines studies of hybridization in seed plants from across the Neotropics and explores its outcomes on Neotropical plant evolution. We review studies on a per-biome basis and a spectrum of evolutionary outcomes from hybridization are evident across Neotropical biomes and taxa. These range from short-term impacts, such as the broadening of ecological amplitude in hybrid progeny with transgressive phenotypes and genetic swamping, through to long term impacts, such as the generation of new lineages. Among these studies certain themes emerge, such as the pervasive hybridization among species-rich plant radiations from the Andean páramos, suggesting a role for hybridization in rapid diversification events. Finally, we highlight that hybridization is relatively understudied in the Neotropical flora, despite its remarkable species richness. The advent of genomic techniques can facilitate the study of hybridization and its effects in understudied biomes and plant groups. The increasing availability of genomic resources will eventually allow comparisons between tropical and temperate floras and therefore shed light on the evolutionary impacts of hybridization across the latitudinal biodiversity gradient.

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.

The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events], info:eu-repo/semantics/published

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.

The Neotropics is the most species-rich area in the world, and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba Mill. (Malvaceae, Bombacoideae). Ceiba comprises 18 mostly Neotropical species, largely endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests. Its species are among the most characteristic elements of Neotropical SDTF, one of the most threatened biomes in the tropics. Phylogenetic analyses of DNA sequence data (from the nuclear ribosomal internal transcribed spacers [nrITS] for 30 accessions representing 14 species of Ceiba) recovered the genus as monophyletic. The phylogeny showed geographic and ecological structure in three main clades: (i) a rain forest lineage of nine accessions of C. pentandra sister to the remaining species; (ii) a highly supported clade composed of C. schottii and C. aesculifolia from Central American and Mexican SDTF, plus two accessions of C. samauma from semi-humid, inter Andean valleys in Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American SDTF clade, no species represented by multiple accessions were resolved as monophyletic. We demonstrate that the patterns of species age, monophyly, and geographic structure previously reported for SDTF species within the Leguminosae family are not shared by Ceiba, suggesting that further phylogenetic studies of unrelated groups are required to understand general patterns.

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

Premise of the study: 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 c. 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 generate transcriptomes to select low-copy nuclear genes, enrich the sevia hybrid capture for representative species of most mimosoid genera and analyse 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. Key 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 hyper-fast 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 tax on sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.

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.

The Neotropics is the most species-rich area in the world and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genusCeibaMill. (Malvaceae: Bombacoideae).Ceibacomprises 18 mostly neotropical species endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests and its species are one of the most characteristic elements of neotropical SDTF, one of the most threatened biomes in the tropics. Phylogenetic analyses of DNA sequence data from the nuclear ribosomal internal transcribed spacers (ITS) for 30 accessions representing 14 species ofCeibarecovered the genus as monophyletic and showed geographical and ecological structure in three main clades: (i) a rain forest lineage of nine accessions ofC. pentandrasister to the remaining species; (ii) a highly supported clade composed ofC. schottiiandC. aesculifoliafrom Central American and Mexican SDTF plus two accessions ofC. samaumafrom inter Andean valleys from Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American clade, no species represented by multiple accessions were resolved as monophyletic. We demonstrate that the patterns of species age, monophyly and geographical structure previously reported for SDTF species within the Leguminosae family are not shared byCeiba, suggesting that further phylogenetic studies of unrelated groups are required.HIGHLIGHTSThis paper provides a well sampled phylogeny of the iconic genusCeiba, one of the most characteristic tree genera of neotropical Seasonally Dry Tropical Forest (SDTF).There is a clear phylogenetic signal for biome preference and geographic structure inCeiba.We estimate a mid Miocene origin forCeiba, with the stem node age of the genus estimated at 21.1 Ma and the crown node age at 12.7 Ma.Ceibaspecies have young stem ages in the SDTF clade but old stem ages in rain forest species.Patterns of species age, monophyly, ecological and geographical structure reported for SDTF species are only partially shared byCeiba, an iconic genus of neotropical SDTF.

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.

This is the author accepted manuscript. The final version is available from nternational Association for Plant Taxonomy via the DOI in this record

The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL–F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous “Boreotropical” distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace’s Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern 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.

Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera, we investigated the association between taxonomic and evolutionary metrics of diversity and two key measures of ecosystem function: aboveground wood productivity and biomass storage. While taxonomic and phylogenetic diversity were not important predictors of variation in biomass, both emerged as independent predictors of wood productivity. Amazon forests that contain greater evolutionary diversity and a higher proportion of rare species have higher productivity. While climatic and edaphic variables are together the strongest predictors of productivity, our results show that the evolutionary diversity of tree species in diverse forest stands also influences productivity. As our models accounted for wood density and tree size, they also suggest that additional, unstudied, evolutionarily correlated traits have significant effects on ecosystem function in tropical forests. Overall, our pan-Amazonian analysis shows that greater phylogenetic diversity translates into higher levels of ecosystem function: tropical forest communities with more distantly related taxa have greater wood productivity.