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Aim To evaluate the relative importance of climatic versus soil data when predicting species distributions for Amazonian plants and to gain understanding of potential range shifts under climate change. Location Amazon rain forest. Methods We produced species distribution models (SDM) at 5-km spatial resolution for 42 plant species (trees, palms, lianas, monocot herbs and ferns) using species occurrence data from herbarium records and plot-based inventories. We modelled species distribution with Bayesian logistic regression using either climate data only, soil data only or climate and soil data together to estimate their relative predictive powers. For areas defined as unsuitable to species occurrence, we mapped the difference between the suitability predictions obtained with climate-only versus soil-only models to identify regions where climate and soil might restrict species ranges independently or jointly. Results For 40 out of the 42 species, the best models included both climate and soil predictors. The models including only soil predictors performed better than the models including only climate predictors, but we still detected a drought-sensitive response for most of the species. Edaphic conditions were predicted to restrict species occurrence in the centre, the north-west and in the north-east of Amazonia, while the climatic conditions were identified as the restricting factor in the eastern Amazonia, at the border of Roraima and Venezuela and in the Andean foothills. Main conclusions Our results revealed that soil data are a more important predictor than climate of plant species range in Amazonia. The strong control of species ranges by edaphic features might reduce species’ abilities to track suitable climate conditions under a drought-increase scenario. Future challenges are to improve the quality of soil data and couple them with process-based models to better predict species range dynamics under climate change.

Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories. We estimate the impact of different factors on fern diversification over the past 400 million years by analysing a comprehensive dataset of fossil occurrences and complement these findings by analysing a large molecular phylogeny. We show that origination and extinction rates are governed by fundamentally different processes: originations depend on within-group diversity but are largely unaffected by environmental changes, whereas extinctions are strongly affected by external factors such as climate and geology. Our results indicate that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy.

Summary Understanding the responses of individual plant species along different edaphic gradients is a key question in ecology, with implications to community assembly, functioning of forest ecosystems, niche theory, and conservation planning. In tropical rain forests, responses to soil nutrients have been described only for a handful of species. Even abundant and conspicuous components of the forest, such as the palms (Arecaceae), are largely unknown in this respect. We inventoried all palm species and analysed soil chemistry in 96 sites across western Amazonia to (i) assess the relative importance of some micronutrients vs. macronutrients as drivers of patterns in palm species composition, (ii) model the response shapes of 61 palm taxa and of canopy vs. understory palms along gradients of selected soil nutrients, (iii) determine if the response shapes of conspecific palm varieties differ in relation to the most important observed soil nutrient, and (iv) assess if the rank-order of the most abundant canopy species changes along edaphic gradients. Patterns in palm species composition were best explained by Mehlich-III extractable exchangeable bases (Ca, K, Mg) and phosphorus (P), with the different palm species clearly separating along the soil cation concentration gradient. All 61 palm taxa exhibited statistical responses along soil nutrient gradients. Response shapes in relation to exchangeable bases varied among bimodal skewed (51% of species), unimodal skewed (47%), and monotonic (2%). There were no significant differences between canopy vs. understory species in their mean response shapes to the exchangeable bases, but canopy species had significantly higher mean optimum value for soil P and greater mean niche width along the Ca, K, Mg, P, and boron (B) gradients. Varieties of the same species of Bactris, Desmoncus and Geonoma generally had different response shapes and different optima for the exchangeable bases. Synthesis: Among the soil variables we studied, macronutrients (especially exchangeable bases and P) emerged as more important than micronutrients in predicting species abundances in palm communities of western Amazonian non-inundated forests. Non-gaussian responses were predominant, conspecific palm varieties exhibited different response types, and the rank-order of dominance of canopy palms varied along the gradients of exchangeable bases and P. Together, these findings advance niche theory about palms and may be used for generating better predictive models of palm species distributions and for experimental studies that search for the physiological mechanisms underlying inter- and infra-specific trade-offs along edaphic gradients. This article is protected by copyright. All rights reserved.

Biodiversity mapping in extensive tropical forest areas poses a major challenge for the interpretation of Landsat images, because floristically clearly distinct forest types may show little difference in reflectance. In such cases, the effects of the bidirectional reflection distribution function (BRDF) can be sufficiently strong to cause erroneous image interpretation and classification. Since the opening of the Landsat archive in 2008, several BRDF normalization methods for Landsat have been developed. The simplest of these consist of an empirical view angle normalization, whereas more complex approaches apply the semi-empirical Ross–Li BRDF model and the MODIS MCD43-series of products to normalize directional Landsat reflectance to standard view and solar angles. Here we quantify the effect of surface anisotropy on Landsat TM/ETM+ images over old-growth Amazonian forests, and evaluate five angular normalization approaches. Even for the narrow swath of the Landsat sensors, we observed directional effects in all spectral bands. Those normalization methods that are based on removing the surface reflectance gradient as observed in each image were adequate to normalize TM/ETM+ imagery to nadir viewing, but were less suitable for multitemporal analysis when the solar vector varied strongly among images. Approaches based on the MODIS BRDF model parameters successfully reduced directional effects in the visible bands, but removed only half of the systematic errors in the infrared bands. The best results were obtained when the semi-empirical BRDF model was calibrated using pairs of Landsat observation. This method produces a single set of BRDF parameters, which can then be used to operationally normalize Landsat TM/ETM+ imagery over Amazonian forests to nadir viewing and a standard solar configuration.

The factors explaining species turnover at different spatial scales have been intensively studied, but most work in Amazonia has mainly focused on plants. For animals, it is not as obvious which environmental variables most affect differences in species composition among sites. We sought to identify what causes anuran turnover in Amazonian terra firme forests, and how the effectiveness of these factors varies among regions and across spatial scales. We sampled frogs in 56 plots along ponds and streams distributed over three terra firme forest areas in Eastern Amazonia. Using multiple regressions on distance matrices, we partitioned the variation in species turnover into components explained by variation in environmental and spatial distances. This was done in parallel for each area separately, and for all areas together, to assess the consistency of results between scales and across areas at the same scale. Each community seemed to respond to a set of factors specific to that area, and the identity of the variables that emerged as significant differed among areas and scales. Both geographical distances and environmental differences had larger explanatory power at the regional scale than at the local scale. The large differences among results from different areas caution against making broad generalizations about species turnover patterns from a single community, as real differences may exist among areas.

Amazonian white-sand vegetation has unique tree communities tolerant to nutrient-poor soils of interest for interpreting processes of adaptation in neotropical forests. Part of this phytophysionomy is confined to Late Quaternary megafan palaeo-landforms, thus we posit that sedimentary disturbance is the main ecological factor controlling tree distribution and structuring in this environment. In this study, we characterize the topographic trend of one megafan palaeo-landform using a digital elevation model and verify its relationship to the forest by modelling the canopy height with remote sensing data. We also compare the composition and structure (i.e. canopy height and diameter at breast height) of tree groups from the outer and inner megafan environments based on the integration of remote sensing and floristic data. The latter consist of field inventories of trees ≥ 10 cm dbh using six (500 × 20 m) plots in várzea, terra firme and igapó from the outer megafan and 20 (50 × 20 m) plots in woodlands and forests from the inner megafan. The unweighted pair group method with arithmetic mean (UPGMA) and the non-metric multidimensional scaling (NMDS) were applied for clustering and dissimilarity analyses, respectively. The megafan is a sand-dominated triangular wetland with a topographic gradient of < 15 cm km−1, being more elevated along its axis. The outer megafan has a higher number of tree species (367), taller canopy height (mean of 14.1 m) and higher diameter at breast height (mean of 18.2 cm) than the white-sand forest. The latter records 89 tree species, mean canopy height of 8.4 cm and mean diameter at breast height of 15.3 cm. Trees increase in frequency closer to channels and toward the megafan's axis. The flooded and nutrient-poor sandy megafan substrate favoured the establishment of white-sand vegetation according to the overall megafan topography and morphological heterogeneities inherent to megafan sub-environments.

The changes in the publishing landscape are inevitable and the transition is bound to create challenges and occasional dysfunctions. Ecography is a journal of the Nordic Society Oikos and, as such, is committed to explore solutions that will enable adherence to open science policies while minimising the adverse effects of inequality that can emerge from them.

The riverine barrier hypothesis is a central concept in Amazonian biogeography. It states that large rivers limit species distributions and trigger vicariant speciation. Although the hypothesis has explanatory power, many recent biogeographical observations addressing it have produced conflicting results. We propose that the controversies arise because tributary arrangements in the Amazon river system have changed in geologically recent times, such that large tracts of forest that were on the same side of a river at one time got separated to different sides at another. Based on topographical data and sediment dating, we map about 20 major avulsion and river capture events that have rearranged the river network in central Amazonia during the late Pleistocene and Holocene. We identify areas where past riverine barrier effects might still linger in the absence of a major river, as well as areas where such effects may not yet have accumulated across an existing river. These results call for a reinterpretation of previous biogeographical studies and a reorientation of future works to take into account the idiosyncratic histories of individual rivers.

AIM: To map and interpret floristic and geoecological patterns across the Amazon basin by combining extensive field data with basin‐wide Landsat imagery and climatic data. LOCATION: Amazonia. TAXON: Ground truth data on ferns and lycophytes; remote sensing results reflect forest canopy properties. METHODS: We used field plot data to assess main ecological gradients across Amazonia and to relate floristic ordination axes to soil base cation concentration, Climatologies at High Resolution for the Earth's Land Surface Areas (CHELSA) climatic variables and reflectance values from a basin‐wide Landsat image composite with generalized linear models. Ordination axes were then predicted across all Amazonia using Landsat and CHELSA, and a regional subdivision was obtained using k‐medoid classification. RESULTS: The primary floristic gradient was strongly related to base cation concentration in the soil, and the secondary gradient to climatic variables. The Landsat image composite revealed a tapestry of broad‐scale variation in canopy reflectance characteristics across Amazonia. Ordination axis scores predicted using Landsat and CHELSA variables produced spatial patterns consistent with existing knowledge on soils, geology and vegetation, but also suggested new floristic patterns. The clearest dichotomy was between central Amazonia and the peripheral areas, and the available data supported a classification into at least eight subregions. MAIN CONCLUSIONS: Landsat data are capable of predicting soil‐related species compositional patterns of understorey ferns and lycophytes across the Amazon basin with surprisingly high accuracy. Although the exact floristic relationships may differ among plant groups, the observed ecological gradients must be relevant for other plants as well, since surface reflectance recorded by satellites is mostly influenced by the tree canopy. This opens exciting prospects for species distribution modelling, conservation planning, and biogeographical and ecological studies on Amazonian biota. Our maps provide a preliminary geoecological subdivision of Amazonia that can now be tested and refined using field data of other plant groups and from hitherto unsampled areas.

Salpichlaena is a distinctive fern genus characterised by 2-pinnate climbing fronds with indeterminate growth. The number of species in the genus has been a matter of debate. Taxonomic studies are made difficult by within-frond variability in pinna morphology and size, and by herbarium material being incomplete. We systematically documented 62 morphological traits in 283 herbarium specimens and sequenced 52 Salpichlaena and 11 outgroup specimens. DNA sequences included plastid genes (rbcL, rpoC1 and rps4), intergenic spacers (rps4-trnS, trnHpsbA and trnG-trnR) and a nuclear gene (pgiC). Phylogenetic analyses based on the plastid markers divided the samples into six major clades. We recognise the three deepest clades as distinct species (S. hookeriana, S. papyrus sp. nov. and S. volubilis), and each of the four shallower clades as a subspecies of S. volubilis. Furthermore, we suggest that a group of specimens, placed into different clades in the plastid and nuclear trees and showing mixed morphological characters, represent a fourth species of hybrid origin (S. hybrida sp. nov.). The most important diagnostic characters are: degree of lamina reduction in fertile pinnules; pinna/pinnule apex incisions, pinna/pinnule margin thickness and lamina texture in sterile pinna/pinnules; presence or absence of foliar buds; shape of scales; and the appearance of the abaxial surface of the lamina (uniform or with stomata on small white protuberances). Each of the four species can be identified by several diagnostic characters, and their geographical ranges are broad and partly overlapping. In contrast, the subspecies are mostly allopatric and their morphological limits are diffuse.

EMBO Reports (2019) 20: e47395[OpenUrl][1][FREE Full Text][2] Humanity is facing the twin challenge of producing sufficient and nutritious food for a growing and increasingly affluent population while reducing the environmental impact of agriculture. Livestock in particular is a major environmental stressor [1] as it produces an estimated 15% of global anthropogenic greenhouse gas (GHG) emissions [2], which is more than the whole transportation sector. The main sources of these emissions are methane from ruminants' enteric fermentation, emissions related to feed production, manure management and use of energy. In addition, cutting down forests for pasture and feed production substantially contributes to carbon dioxide emissions and biodiversity loss, especially in tropical regions. Livestock production also releases nitrogen and phosphorus into waterways, which causes eutrophication, disturbs ecosystems and can even result in oxygen depletion in lakes and oceans with drastic consequences for fish and other aquatic species. Lastly, livestock production consumes around a quarter of all fresh water available. > Population growth and rising average incomes mean that the global demand for livestock products will further increase by up to 70% between 2010 and 2050… Population growth and rising average incomes mean that the global demand for livestock products will further increase by up to 70% between 2010 and 2050 [2], which will have dramatic environmental consequences. However, the possibilities for increasing livestock production without increasing its environmental impact are very limited. Intensive livestock systems may help to use resources more efficiently and to better control emissions, but it has negative effects on animal welfare owing to limited space and cramped living conditions. > Cultured meat has often been heralded as a silver bullet for solving the environmental problems caused by livestock production. One possible solution is substituting meat with plant‐based alternatives [3]. Nonetheless, despite the increasing availability … [1]: {openurl}?query=rft.jtitle%253DEMBO%2BReports%26rft_id%253Dinfo%253Adoi%252F10.15252%252Fembr.201847395%26rft_id%253Dinfo%253Apmid%252F30552146%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [2]: /lookup/ijlink?linkType=FULL&journalCode=embor&resid=20/1/e47395&atom=%2Fembor%2F20%2F1%2Fe47395.atom

The outstanding biodiversity found in the American tropics (the Neotropics ) has attracted the attention of naturalists for centuries. Despite major advances in the generation of biodiversity data, many questions remain to be answered. In this review, we first summarize some of the knowns and unknowns about Neotropical biodiversity, and discuss how human impact may have drastically affected some of the patterns o bserved today. We then link biodiversity to landscape, and outline major advances in biogeographical research. In particular, we argue that it is crucial to test the effect of landscape and climatic evolution to biotic diversification and distribution in o rder to achieve a comprehensive understanding of current patterns. In this context, it is also important to consider extant and extinct taxa, as well as to use probabilistic and parametric methods that explicitly include landscape evolution models. We subs equently explore different scales in Neotropical biogeography, focusing on the intersection between biogeography and community ecology, both of which often address similar questions from different angles. The concepts of community assembly, island biogeogr aphy, neutral processes, and ecological interactions are then discussed as important components of the complex processes that determine the patterns observed today. Single - taxon and cross - taxonomic studies are complementary and greatly needed, but achievin g synthesis remains challenging. Finally, w e argue that phylogenetic approaches hold great potential to connect across taxonomic, spatial and temporal scales, despite current difficulties to generate and cross - analyze large volumes of molecular data. We co nclude by outlining major prospects and hindrances for further advancing our knowledge on the rich Neotropical biodiversity

The globally growing demand to produce more food with fewer inputs, less energy, and lower greenhouse gas (GHG) emissions challenges current agricultural practices. Recycled fertilizers made of various side streams and types of biomass have been developed mainly to improve nutrient recycling in food systems. However, the knowledge of the impacts of different recycled fertilizers on GHG emissions and energy use is lacking. There is also a need for developing environmental assessment methods for quantifying the impacts of recycling processes, particularly in terms of choosing reasonable methods for co-product allocation. The aims of this study were to address the above mentioned research gaps by i) assessing energy use and GHG emissions of various recycled fertilizers, ii) comparing the recycled fertilizers with mineral fertilizers, and iii) comparing the impacts of using different co-product allocation methods for the recycled fertilizers. Attributional Life Cycle Assessment (LCA) was used for estimating energy use and GHG emissions of recycled fertilizers, including ammonium sulfate, biogas digestate, and meat and bone meal, using kg of nitrogen in the fertilizers as a functional unit. In addition, the energy use and GHG emissions of oat production when using the recycled and mineral fertilizers were quantified. The data were obtained from field experiments, LCA databases, published literature, and fertilizer companies. The life-cycle energy consumption and GHG emissions of recycled fertilizers were found to be lower than that of mineral fertilizer, but also differences between recycled fertilizer products were notable. The biggest differences between fertilizers occurred in manufacturing and transportation. However, this conclusion is highly sensitive to several decisions, such as data sources and LCA methods used. Handling the raw materials of recycled fertilizers as by-products instead of residues adds burdens from primary production to fertilizers. Also handling the materials as waste increases the impacts due to burdens from the recycling process. Since the raw materials of fertilizers have only little economic value, applying economic allocation results to significantly lower impacts than mass allocation. Consequential LCA studies would be needed to improve the understanding of the wider impacts of recycled fertilizers, e.g. considering the benefits of avoided waste management processes. (C) 2020 Elsevier Ltd. All rights reserved.

Understanding the structure of and spatial variability in the species composition of ecological communities is at the heart of biogeography. In particular, there has been recent controversy about possible latitudinal trends in compositional heterogeneity across localities (β-diversity). A gradient in the size of the regional species pool alone can be expected to impose a parallel gradient on β-diversity, but whether β-diversity also varies independently of the size of the species pool remains unclear. A recently suggested methodological approach to correct latitudinal β-diversity gradients for the species pool effect is based on randomization null models that remove the effects of gradients in α- and γ-diversity on β-diversity. However, the randomization process imposes constraints on the variability of α-diversity, which in turn force γ- and β-diversity to become interdependent, such that any change in one is mirrored in the other. We argue that simple null model approaches are inadequate to discern whether correlations between α-, β- and γ-diversity reflect processes of ecological interest or merely differences in the size of the species pool among localities. We demonstrate that this kind of Narcissus effect may also apply to other metrics of spatial or phylogenetic species distribution. We highlight that Narcissus effects may lead to artificially high rejection rates for the focal pattern (Type II errors) and caution that these errors have not received sufficient attention in the ecological literature.

Aim To assess the relative roles of geologically defined terrain types ( environmental heterogeneity) and a major river ( physical dispersal barrier) as predictors of ecological structuring and biogeographical differentiation within Amazonian forests.Location Western Brazilian Amazonia, where the Jurua river and its terraces cross a 1000-km-long boundary between two geological formations ( the Solimoes and Ica Formations).Methods We sampled a 500-km stretch of the Jurua with 71 transects ( 5 m by 500 m) that spanned both the river and the geological boundary. All transects were inventoried for pteridophytes ( ferns and lycophytes) and Melastomataceae, and a subset of 39 transects also for palms and Zingiberales. Three surface soil samples were collected from each transect. The data were analysed using ordinations, regression trees, indicator species analyses and Mantel tests.Results All plant groups showed congruent species turnover between geologically defined terrain types, but little evidence of isolation by the river or geographical distance. Soil cation concentration differed between the Solimoes Formation and other terrain types and emerged as the main explanatory factor for species turnover. A large proportion of the plant species were significant indicators for specific parts of the soil cation concentration gradient, and these edaphic associations were congruent with those found in other parts of Amazonia. Pteridophytes had a larger proportion of species in the cation-rich soils than the other plant groups did, and palms had a higher proportion of generalists.Main conclusions The geological boundary between the Solimoes and Ica formations is confirmed as significant floristic turnover zone. As it runs in a north-south orientation for more than 1000 km, the edaphic differences associated with this boundary have wide-ranging implications for speciation and biogeographical patterns in Amazonia.

Remotely sensed image interpretation or classification of tropical forests can be severely hampered by the effects of the bidirectional reflection distribution function (BRDF). Even for narrow swath sensors like Landsat TM/ETM+, the influence of reflectance anisotropy can be sufficiently strong to introduce a cross-track reflectance gradient. If the BRDF could be assumed to be linear for the limited swath of Landsat, it would be possible to remove this gradient during image preprocessing using a simple empirical method. However, the existence of natural gradients in reflectance caused by spatial variation in floristic composition of the forest can restrict the applicability of such simple corrections. Here we use floristic information over Peruvian and Brazilian Amazonia acquired through field surveys, complemented with information from geological maps, to investigate the interaction of real floristic gradients and the effect of reflectance anisotropy on the observed reflectances in Landsat data. In addition, we test the assumption of linearity of the BRDF for a limited swath width, and whether different primary non-inundated forest types are characterized by different magnitudes of the directional reflectance gradient. Our results show that a linear function is adequate to empirically correct for view angle effects, and that the magnitude of the across-track reflectance gradient is independent of floristic composition in the non-inundated forests we studied. This makes a routine correction of view angle effects possible. However, floristic variation complicates the issue, because different forest types have different mean reflectances. This must be taken into account when deriving the correction function in order to avoid eliminating natural gradients.

Grain (size of sampling units) affects the spatial resolution at which ecological patterns can be observed and analysed, and potentially has an important effect on the results of broad-scale studies on diversity gradients. Here we examine the effect of grain on patterns of species richness and turnover in lowland rainforests of western Amazonia (Peru and Colombia). We inventoried pteridophytes (ferns and lycophytes), melastomes (Melastomataceae) and palms (Arecaceae) in four line transects of 22–29 km length. Different grains were obtained by aggregating original 100-m-long sampling units into larger segments up to 19.2 km long. With any given grain and plant group, local species richness varied considerably both within and among transects, and a transect segment that was species-rich with one grain could be relatively species-poor with another. Which transect had the highest vs lowest mean species richness per sampling unit (α richness) differed among plant groups. It also varied to some degree with grain, as transects differed in how rapidly local species richness increased with increasing grain. Patterns of species turnover were more consistently correlated among plant groups than patterns of species richness were, and NMDS ordinations were rather similar with all grains and plant groups. Floristic heterogeneity within the Amazonian terra firme rainforest seems to contain a general compositional pattern that is sufficiently robust to be detectable with various sampling schemes, but patterns of species richness appear more case-specific. Therefore, using one plant group as an indicator for patterns in other plant groups can be expected to work better for species turnover than for species richness.

© 2016 Elsevier Ltd. This work presents a novel meta-analysis for methane yields from anaerobically digesting dairy cattle manure. A database is compiled from 115 articles (2181 cases) by systematically assessing the academic literature. YCH4 and secondary variables collected in the database describe performance, operation conditions of digester and manure composition. Inputs to the database are normalised to enable inter-study uni- and multi-variate analysis, according to different types of digesters. Most cases (N = 1299) are reported for batch digesters and meta-analysis results in a mean YCH4 of 0.230±0.016 m3kg-1. CSTR (N = 241), results in mean of 0.190±0.016 m3kg-1 (random-effect model). Other continuous digesters, such as fixed-film, plug-flow and UASB require further cases for the application of meta-analysis. For non-specified semi-continuous digesters (N = 347), the mean calculated by the random-effect model is 0.204±0.032 m3kg-1 (N = 27). With respect to multi-variate analysis of operation conditions, batch digesters form four clusters, while two clusters are identified for CSTR and three for semi-continuous digesters. For variables describing manure composition, batch digesters present eight clusters, while CSTR and semi-continuous digesters have insufficient cases. The strongest correlations found for these secondary variables (Spearman's rho: -0.685 and -0.696) result for pH and YCH4 in batch and CSTR, respectively. Maximum YCH4 estimated by meta-analysis are proposed to replace the default IPCC values because they are based on a larger sample size and integrate updated literature. In particular, markedly higher YCH4 are obtained for Asia, Middle East and Indian Subcontinent than those in the IPCC guidelines.

Two core questions in plant community ecology are to what extent the distributions of species are structured by local environmental conditions, and whether taxa differ in this regard. We compared the distributions of trees, Melastomataceae and ferns on soil and topographic gradients in a Costa Rican lowland rain forest (trees and ferns 983 plots, Melastomataceae 277 plots). To test whether these plant groups differed in the prevalence or type of habitat specialization, we calculated species’ environmental optima and tolerances on each gradient. Habitat specialization was defined as a significantly biased optimum, or a narrow tolerance, relative to values obtained under spatially restricted randomizations of species occurrences. Within plant groups, we also asked whether the dispersion of species optima differed from random expectation on each gradient. Fern optima were over-dispersed on multiple gradients, implying considerable interspecific habitat partitioning, and tree optima were over-dispersed in relation to topographic position. Habitat specialization was more prevalent in the two predominantly understorey groups than in trees (75% of Melastomataceae species, 81–87% of ferns, 57–58% of trees). Species optima of Melastomataceae and ferns also tended towards lower landscape positions than did those of trees, perhaps reflecting a higher proportion of drought-sensitive species in these two groups.

This article examines how future diets could reduce the environmental impacts of food systems, and thus, enable movement into the post-Anthropocene. Such non-anthropocentric diets are proposed to address global food systems challenges inherent in the current geological epoch known as the Anthropocene&mdash, a period when human activity is the dominant cause of environmental change. Using non-anthropocentric indigenous worldviews and object-oriented ecosophy, the article discusses changes in ontologies around diets to consider choices made in the present for sustainable future food systems. This article conceptually addresses, how can pre-Anthropocene ontologies guide an exit of current approaches to diets? Considering temporality, what post-Anthropocene ontologies are possible in future diets for sustainable food systems? Through the ontological positions defining three distinct temporalities, considerations for guiding future diets in(to) the post-Anthropocene are proposed. Indigenous ontologies are presented as pre-Anthropocene examples that depict humans and non-humans in relational diets. Underlying Anthropocene ontologies define current unsustainable diets. These ontologies are described to present the context for the food systems challenges this article aims to address. A post-Anthropocene illustration then employs object-oriented ecosophy along with indigenous ontologies as theoretical foundations for shifting from the dominant neoliberal paradigm in current ontologies. Ontologically-based dietary guidelines for the post-Anthropocene diet present the ontological turns, consideration of temporality, and outline technological orientations proposed for sustainable future food systems. This is a novel attempt to integrate non-anthropocentric theories to suggest possible futures for human diets in order to exit the Anthropocene epoch. These non-anthropocentric ontologies demonstrate how temporal considerations and relational worldviews can be guidelines for transforming diets to address public health concerns, the environmental crisis, and socioeconomic challenges.

Background: Environmental changes are predicted to threaten human health, agricultural production and food security. Whilst their impact has been evaluated for major cereals, legumes and vegetables, no systematic evidence synthesis has been performed to date evaluating impact of environmental change on fruits, nuts and seeds (FN&S)—valuable sources of nutrients and pivotal in reducing risks of non-communicable disease. Methods: We systematically searched seven databases, identifying available published literature (1970–2018) evaluating impacts of water availability and salinity, temperature, carbon dioxide (CO2) and ozone (O3) on yields and nutritional quality of FN&S. Dose-response relationships were assessed and, where possible, mean yield changes relative to baseline conditions were calculated. Results: 81 papers on fruits and 24 papers on nuts and seeds were identified, detailing 582 and 167 experiments respectively. A 50% reduction in water availability and a 3–4dS m−1 increase in water salinity resulted in significant fruit yield reductions (mean yield changes: −20.7% [95%CI −43.1% to −1.7%]; and −28.2% [95%CI −53.0% to −3.4%] respectively). A 75%–100% increase in CO2 concentrations resulted in positive yield impacts (+37.8%; [95%CI 4.1% to 71.5%]; and 10.1%; [95%CI −30.0% to 50.3%] for fruits and nuts respectively). Evidence on yield impacts of increased O3 concentrations and elevated temperatures (>25 °C) was scarce, but consistently negative. The positive effect of elevated CO2 levels appeared to attenuate with simultaneous exposure to elevated temperatures. Data on impacts of environmental change on nutritional quality of FN&S were sparse, with mixed results. Discussion: In the absence of adaptation strategies, predicted environmental changes will reduce yields of FN&S. With global intake already well-below WHO recommendations, declining FN&S yields may adversely affect population health. Adaptation strategies and careful agricultural and food system planning will be essential to optimise crop productivity in the context of future environmental changes, thereby supporting and safeguarding sustainable and resilient food systems.

The scene for regional biogeography and human settlements in Central Amazonia is set by the river network, which presumably consolidated in the Pliocene. However, we present geomorphological and sediment chronological data showing that the river network has been anything but stable. Even during the last 50 kyr, the tributary relationships have repeatedly changed for four major rivers, together corresponding to one third of the discharge of the Amazon. The latest major river capture event converted the Japurá from a tributary of the Rio Negro to a tributary of the Amazon only 1000 years ago.Such broad-scale lability implies that rivers cannot have been as efficient biogeographical dispersal barriers as has generally been assumed, but that their effects on human societies can have been even more profound.Climate change and deforestation scenarios predict increasing water levels during peak floods, which will likely increase the risk of future river avulsions. This may have disastrous consequences for the local human societies, especially in those areas where the current floodplains are at only marginally lower elevations than the nearest water divide.We suggest that the prevailing paradigm of rivers as principal structuring elements of Amazonian biogeography needs to be re-evaluated, and that land use planning and civil risk assessment should take the possibility of river avulsions into account.

BackgroundKnowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.MethodsWe used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.ResultsSoil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).DiscussionIn spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world’s largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.

Environmental changes threaten agricultural production, food security, and health. Previous reviews suggest that environmental changes will substantially affect future yields of starchy dietary staples. To date, no comprehensive global analysis of the impacts of environmental change on (nonstaple) vegetables and legumes-important constituents of healthy diets-has been reported. We systematically searched for articles published between 1975 and 2016 on the effects of ambient temperature, tropospheric carbon dioxide (CO2), and ozone (O3) concentrations, water availability, and salinization on yields and nutritional quality of vegetables and legumes. We estimated mean effects of standardized environmental changes using observed exposure-response relationships and conducted meta-analyses where possible. We identified 174 relevant papers reporting 1,540 experiments. The mean (95% CI) reported yield changes for all vegetables and legumes combined were +22.0% (+11.6% to +32.5%) for a 250-ppm increase in CO2 concentration, -8.9% (-15.6% to -2.2%) for a 25% increase in O3 concentration,-34.7% (-44.6% to -24.9%) for a 50% reduction in water availability, and -2.3% (-3.7% to -0.9%) for a 25% increase in salinity. In papers with baseline temperatures >20 °C, a 4 °C increase in temperature reduced mean yields by -31.5% (-41.4% to -21.5%). Impacts of environmental changes on nutritional quality were mixed. In a business-as-usual scenario, predicted changes in environmental exposures would lead to reductions in yields of nonstaple vegetables and legumes. Where adaptation possibilities are limited, this may substantially change their global availability, affordability, and consumption in the mid to long term. Our results stress the importance of prioritizing agricultural developments, to minimize potential reductions in vegetable and legume yields and associated negative health effects.

The old idea that parasitoid wasps (Ichneumonidae) show an inverse latitudinal diversity gradient has recently been challenged, but how ichneumonid species richness varies across the globe is still not well understood. We carried out field inventories in 21 sites on three continents to clarify this question, focusing on the subfamilies Pimplinae and Rhyssinae. Our total sampling effort was 628 Malaise trap months and the total catch exceeded 65 000 individuals. Our main focus was in two intensively inventoried areas in Amazonia, together yielding 257 Malaise trap months and 26 390 ichneumonid individuals. To expand the scope and assess global species diversity patterns of the Pimplinae and Rhyssinae, we compiled published species lists from a total of 97 study localities around the world. The highest observed species richness in any locality, 105 species, was found in one of our field sites in Peruvian Amazonia. None of the other localities reported more than 70 species, even the ones with a sampling effort comparable to ours. Despite the local thoroughness of our field inventories in Amazonia, data analyses indicated that a substantial proportion of the parasitoid wasp species occurring in each site remained unobserved. The highest local species richness values were reported from the tropics. Nevertheless parasitoid wasps are still too sparsely sampled to draw solid conclusions about whether or not their species richness follows a particular latitudinal trend, and if so, where their richness peaks., The study was partly funded by the Kone Foundation, Finland (a grant awarded to the project: Biodiversity and multiple trophic interactions lead by Ilari E. Sääksjärvi). Isrrael C. Gómez thanks the support of the following foundations: the Amazon Conservation Association (Peru), Conservation International Foundation‐Peru and the Turku University Foundation. Marc Pollet is indebted to the Leopold III Fund (Belgium) for providing support for the Chilean survey. Field work in Los Queules and Huinay (Chile) was funded by research projects FONDECYT 1050745 and “Ayudas para la realización de estancias de investigación en el centro científico de la Fundación Huinay” (CSIC‐Endesa), grants to J. L. Nieves‐Aldrey.

The EAT-Lancet Commission proposes a universal healthy diet that could help to limit environmental changes within the planetary boundaries, but further work is needed to adapt this diet to local conditions and limit unintended environmental and health impacts of changing diets.

Various hypotheses have been proposed for why the traits distinguishing humans from other primates originally evolved, and any given trait may have been explained both as an adaptation to different environments and as a result of demands from social organization or sexual selection. To find out how popular the different explanations are among scientists, we carried out an online survey among authors of recent scientific papers in journals covering relevant fields of science (paleoanthropology, paleontology, ecology, evolution, human biology). Some of the hypotheses were clearly more popular among the 1,266 respondents than others, but none was universally accepted or rejected. Even the most popular of the hypotheses were assessed “very likely” by 70% of the respondents. An ordination of the hypotheses identified two strong gradients. Along one gradient, the hypotheses were sorted by their popularity, measured by the average credibility score given by the respondents. The second gradient separated all hypotheses postulating adaptation to swimming or diving into their own group. The average credibility scores given for different subgroups of the hypotheses were not related to respondent's age or number of publications authored. However, (paleo)anthropologists were more critical of all hypotheses, and much more critical of the water‐related ones, than were respondents representing other fields of expertise. Although most respondents did not find the water‐related hypotheses likely, only a small minority found them unscientific. The most popular hypotheses were based on inherent drivers; that is, they assumed the evolution of a trait to have been triggered by the prior emergence of another human‐specific behavioral or morphological trait, but opinions differed as to which of the traits came first.

The soil provides a great variety of microhabitats for myriad organisms of different size, physiological activity, behavior and ecosystem function. Besides abundance of participating soil organisms, their species diversity facilitates maximum exploitation of the resources available in the different habitats. At various levels of resolution, species can be categorized into classes performing ecosystem functions and, within each functional class, into guilds of species with similar life course characteristics. Measurement of the diversity and abundance of species within a functional class provides insights into the nature of ecosystem functions and services and to the health of the soil. At higher resolution, species diversity within guilds of a functional class may infer the degree of exploitation of available resources and the complementarity of an ecosystem service; diversity among the guilds of a functional class may indicate successional complementarity of the services. A diversity of guilds within a functional class expands the range of conditions over which ecosystem services are performed while species diversity within a functional class and its guilds contributes to the magnitude of the services. Consequently, diversity of species within functional classes is a key element of the biological component of soil health. In the context of ecosystem services and soil health, the biomass or metabolic activity of species are more useful measures of their abundance than numbers of individuals. Thus, understanding of soil health and ecosystem function requires, besides knowledge of species diversity within functional classes, assessment of the range of functions currently performed in the system and the abundances of organisms by which they are performed. We propose a diversity-weighted abundance product for comparison of the functional magnitude of different assemblages of like organisms.

Direct greenhouse gas (GHG) emissions from agriculture accounted for approximately 10% of total European Union (EU) emissions in 2010. To reduce farming-related GHG emissions, appropriate policy measures and supporting tools for promoting low-C farming practices may be efficacious. This article presents the methodology and testing results of a new EU-wide, farm-level C footprint calculator. The Carbon Calculator quantifies GHG emissions based on international standards and technical specifications on Life Cycle Assessment (LCA) and C footprinting. The tool delivers its results both at the farm level and as allocated to up to 5 main products of the farm. In addition to the quantification of GHG emissions, the calculator proposes mitigation options and sequestration actions that may be suitable for individual farms. The results obtained during a survey made on 54 farms from 8 EU Member States are presented. These farms were selected in view of representing the diversity of farm types across different environmental zones in the EU. The results of the C footprint of products in the data set show wide range of variation between minimum and maximum values. The results of the mitigation actions showed that the tool can help identify practices that can lead to substantial emission reductions. To avoid burden-shifting from climate change to other environmental issues, the future improvements of the tool should include incorporation of other environmental impact categories in place of solely focusing on GHG emissions. Integr Environ Assess Manag 2015;11:404–416. © 2015 The Authors. Published by Wiley Periodicals, Inc. on behalf of SETAC.

This meta-analysis quantifies the changes in greenhouse gas (GHG) emissions from dairy farms, caused by anaerobically digesting (AD) cattle manure. As this is a novel quantifiable synthesis of the literature, a database of GHG emissions from dairy farms is created. Each case in the database consists of a baseline (reference with no AD system) and an AD scenario. To enable interstudy comparison, emissions are normalized by calculating relative changes (RCs). The distributions of RCs are reported by specific GHGs and operation units. Nonparametric tests are applied to the RCs in order to identify a statistical difference of AD with respect to baseline scenarios (Wilcoxon rank test), correlations (Spearman test), and best estimation for changes in emissions (Kernel density distribution estimator). From 749 studies identified, 30 papers yield 89 independent cases. The median reductions in emissions from the baseline scenarios, according to operation units, are -43.2% (n.s.) for storage, -6.3% for field application of slurries, -11.0% for offset of energy from fossil fuel, and +0.4% (n.s.) for offset of inorganic fertilizers. The leaks from digesters are found to significantly increase the emissions from baseline scenarios (median = +1.4%).

Aim To examine the relative importance of gradients in soil fertility and rainfall for the phylogenetic structure of Neotropical forest fern communities, and to quantify how much the results are affected by phylogenetic resolution. Location Tropical lowland forests in Brazil (central Amazonia) and Panama (the Panama canal watershed). Methods We inventoried local fern communities at a total of 87 sites to model how their species richness and phylogenetic relatedness varied along gradients in soil fertility and rainfall. We produced a time-calibrated species-level molecular phylogeny of ferns, and quantified the phylogenetic relatedness of species within local communities using Faith’s phylogenetic diversity (PD) and mean phylogenetic diversity (MPD). Calculations were compared for phylogenies resolved to the species and genus levels. Results (1) We found significant and consistent effects of soil nutrient status on local phylogenetic community structure in both regions. In contrast, phylogenetic structure showed only a weak or no relationship with rainfall. (2) In both regions, MPD declined with increasing soil fertility, which means that fern communities on poor soils consisted, on average, of less closely related lineages than fern communities on rich soils. (3) Different fern genera were over-represented in different sections of the soil nutrient gradient.(4) Qualitatively similar results were obtained whether phylogenies were resolved to the species or the genus level. Main conclusions Our results highlight the importance of edaphic variation in structuring plant communities over evolutionary time-scales. Within the tropical forests studied, the effects of soil variation on local phylogenetic community structure seem to outweigh those of climate. Several fern genera show strong edaphic niche conservatism to either poor or rich soils, whereas many other genera have radiated to span a rather broad edaphic range. PD-based measures are so dominated by deep relationships that genus-level phylogenies are sufficient to investigate these patterns in tropical fern communities.

Insects are major contributors to farmland biodiversity, and their economic roles are also diverse. Many herbivorous species are crop pests, while predatory insects have the potential to act as biological controls against pests. Overall insect diversity has declined as a result of intensified agricultural practices. Riparian buffers may support insect populations in intensively cultivated areas, but their actual impact on the balance between harmful pests and beneficial predators is not known. It can be postulated that this impact may vary depending on the characteristics and location of the riparian buffer itself. We investigated the possibility that the biotic and abiotic attributes of agricultural riparian buffers adjoining crop fields and watercourses can explain the species composition of hemipteran assemblages. In particular, we were interested in the abundances of species belonging to the genus Nabis (generalist predators) and recognized and potential pests of cereal crops. Riparian buffer width and the presence or absence of woody plants were not associated with hemipteran species turnover among riparian buffers. In contrast, differences in the degree of dominance by grasses, in plant species turnover, and in which crop plant was cultivated in the adjacent field, explained a significant proportion of the variance in hemipteran species turnover. The abundance of predatory Nabis species increased with increasing riparian buffer width, whereas the abundance of recognized and potential crop pests decreased. The reverse patterns in the predatory and herbivorous Heteroptera suggest that increasing riparian buffer width might enhance biological control by Nabis predators.

Background Environmental changes—including climatic change, land degradation, water scarcity, and biodiversity loss—threaten agricultural production and quality and pose challenges to global food security. Most research in this area has focused on staple crop yields. By contrast, relatively little attention has been given to fruits and vegetables that are important for nutrition and health, including for the prevention of non-communicable diseases. In this study, we review the evidence of the effects of environmental change on the yield and quality of fruits and vegetables, and assess possible implications for nutrition and health outcomes. Methods We undertook two systematic reviews of the global published literature on the effect of environmental change on (1) yields and (2) nutritional quality of fruits and vegetables. We evaluated the evidence for 12 different environmental stressors: here we focus on atmospheric temperature and CO 2 concentrations, and precipitation patterns. Data were analysed from two study types: greenhouse experiments and model simulations. We used the review findings to assess the possible health consequences of changed availability and quality of fruits and vegetables in low-income, middle-income, and high-income settings. Findings Although findings varied between crop type and climatic zones, we did identify some consistent trends. In tropical countries, there were largely adverse effect on yield of increased temperature and changing precipitation patterns, although in more temperate zones some beneficial effects on yield were reported. Increased CO 2 concentration had a predominantly positive effect on yield. The effects of (moderate) increases in temperature and reduced precipitation on nutritional quality of fruits and vegetables were mostly positive with higher vitamin, mineral and soluble solid contents measured in many crops, largely as a result of plant stress responses. Increased atmospheric CO 2 concentrations had predominantly negative effects on nutritional quality of fruits and vegetables. Because most studies investigated one change, the combined and interactive effects of all environmental stressors remain unclear. Adverse health implications, including the potential for nutrient deficiencies and related chronic diseases were estimated to be largest in areas characterised by high vulnerability to environmental change and high rates of poverty and food insecurity, as well as areas that are highly dependent on local markets. Interpretation Our reviews identified effects of environmental change on yields and quality of fruits and vegetables that might pose threats to population health, especially in areas vulnerable to climate-change and food insecurity: directly through reduced consumption, and indirectly through income pathways that might result in restricted household dietary energy intake and dietary diversity. To obtain more precise estimates of the change in burden of disease and mortality attributable to affected yields and quality of fruits and vegetables, further research is needed on farmers' and consumers' adaptation and substitution strategies. Furthermore, the combined effect of multiple environmental stressors on fruit and vegetable yield and quality should be further quantified. These data would allow development of future scenarios, based on projected environmental changes and simulations of human behaviour change. Funding Wellcome Trust.

A practical definition of diversity is the effective number of types (such as species), or the number of equally-abundant types that gives the observed mean proportional abundance of the types. Diversity indices represent other phenomena, such as entropy and probability. Richness is the actual rather than effective number of types. Total (gamma) diversity can be partitioned multiplicatively into alpha diversity (mean diversity per subunit) and beta diversity (the effective number of compositionally distinct subunits) or additionally into species diversity in an average subunit and species turnover. Resemblance indices can be derived as monotonic transformations of beta diversity or beta richness.

Aim A major problem for conservation in Amazonia is that species distribution maps are inaccurate. Consequently, conservation planning needs to be based on other information sources such as vegetation and soil maps, which are also inaccurate. We propose and test the use of biotic data on a common and relatively easily inventoried group of plants to infer environmental conditions that can be used to improve maps of floristic patterns for plants in general. Location Brazilian Amazonia. Methods We sampled 326 plots of 250 m × 2 m separated by distances of 1–1800 km. Terrestrial fern individuals were identified and counted. Edaphic data were obtained from soil samples and analysed for cation concentration and texture. Climatic data were obtained from Worldclim. We used a multivariate regression tree to evaluate the hierarchical importance of soils and climate for fern communities and identified significant indicator species for the resultant classification. We then tested how well the edaphic properties of the plots could be predicted on the basis of their floristic composition using two calibration methods, weighted averaging and k-nearest neighbour estimation. Results Soil cation concentration emerged as the most important variable in the regression tree, whereas soil textural and climatic variation played secondary roles. Almost all the plot classes had several fern species with high indicator values for that class. Soil cation concentration was also the variable most accurately predicted on the basis of fern community composition (R2 = 0.65–0.75 for log-transformed data). Predictive accuracy varied little among the calibration methods, and was not improved by the use of abundance data instead of presence–absence data. Conclusions Fern species composition can be used as an indicator of soil cation concentration, which can be expected to be relevant also for other components of rain forests. Presence–absence data are adequate for this purpose, which makes the collecting of additional data potentially very rapid. Comparison with earlier studies suggests that edaphic preferences of fern species have good transferability across geographical regions within lowland Amazonia. Therefore, species and environmental data sets already available in the Amazon region represent a good starting point for generating better environmental and floristic maps for conservation planning.

1. Utilising short-term but geographically extensive sampling in Guatemala, Honduras, and Nicaragua, we examined altitudinal trends in species richness and diversity of ichneumonid parasitoid wasps. This study covered 19 subfamilies, including four globally large subfamilies that have not yet been taxonomically revised in the Neotropics. 2. Sampling was done at 25 sites classified into three elevational categories on the basis of the average elevation of traps at each site (low 34–659 m a.s.l., middle 1033–1709 m a.s.l., and high 1930–2565 m a.s.l.). A total of 2847 ichneumonid individuals were captured and sorted into 751 morphospecies, most of which were identified to the genus level. 3. We found a clear compositional gradient in ichneumonid communities along the elevational gradient, as the majority of species were restricted to either one elevational zone or two adjacent zones. In our data, mid- and highelevation sites had generally higher ichneumonid species richness and diversity than low-elevation sites. These trends were largely similar to those found in larger scale Mesoamerican ichneumonid studies. 4. Yet, the low ichneumonid richness at low elevations may partly be a sampling artefact. This provides a new piece of evidence for the suggestion that extensive sampling is needed for uncovering the real diversity of ichneumonids in tropical lowland forests, and that the reputation of Ichneumonidae as a notable example of a reversed latitudinal diversity gradient may be undeserved. This study was supported by the Finnish Society of Forest Science, Jenny and Antti Wihuri Foundation, Smithsonian Institution Graduate Student Fellowship, and SYNTHESYS (Anu Veijalainen), and Kone Foundation (Ilari E. Sääksjärvi, Biodiversity and multitrophic interactions-project). Project LLAMA was funded by the National Science Foundation grant DEB-0640015 (Project LLAMA).

The fern genus Osmolindsaea has recently been recognized as separate from Lindsaea on the basis of molecular data. Here we provide a taxonomic revision of Osmolindsaea based on morphological examination of herbarium specimens and molecular phylogenetic analysis of five plastid loci (trnL-tmF, trnH-psbA, rpoC1, rps4, and rps4-trnS). We recognize seven species in the genus, two of which are here described as new to science (O. latisquama and O. leptolepida) and three are transferred to this genus from Lindsaea (O. himalaica, O. minor, and O. plumula). A key to the species is provided, as well as descriptions, illustrations, synonymy, and a list of examined specimens for each species.

Summary Soil quality is an important determinant of primary productivity and species occurrence patterns. Therefore, plant species composition can be used as an indicator of soil quality when direct sampling of soils is impractical. We test how well the species composition of the plant family Melastomataceae can predict soil properties in western Amazonian rain forests. We examine nine soil variables: pH; loss-on-ignition; the concentrations of Al and P; and the concentrations of Ca, K, Mg, Na and the sum of these base cations. We compare two commonly used prediction techniques, k-nearest neighbour (k-NN) estimation and weighted averaging calibration via species indicator values. The Melastomataceae and soil data come from 311 localities widely distributed in western Amazonia. We use two different sets of Melastomataceae: a full set including all 283 observed species and an easy set containing 58 species that are both abundant in the data set and relatively easy to identify in the field. Weighted averaging calibration and k-NN performed approximately equally well. Both were found to be useful techniques to convert information on Melastomataceae species composition to estimates of soil cation concentration, especially magnesium and calcium, and to a lesser degree potassium. In nearly all cases, the full set of Melastomataceae species gave more accurate predictions than the easy set, but the differences were relatively small. Synthesis and applications. Our results show that Melastomataceae can be used as an indicator group that facilitates the field estimation of soil cation concentration and hence the assessment and mapping of soil variation over large areas. This provides important background information for all types of land-use planning, including systematic conservation planning that aims at representativeness of conservation area networks.

Normalization and weighting steps used in life cycle impact assessment (LCIA) are often ignored as the weighting factors currently available are seen as being uncertain, subjective and unreliable. This article aims to contribute to the development of a new approach towards weighting, exploring the application of the concept of a planetary safe operating space for human welfare. Based on this approach, the boundaries included in this study relate to: climate change, rate of biodiversity loss, nitrogen cycle, phosphorus cycle, stratospheric ozone depletion, global freshwater use and change in land use. The weighting factors are then applied to a case study comparing environmental impacts of organic, conventional and integrated farming systems with alternative land uses. An integrated farming system that uses a part of the land for natural forest was found to have the lowest total impact score. Conventional farming systems with Miscanthus and managed forest had the highest total impact scores. The main source of uncertainty in the results arose from the wide range of assessments for the safe boundary of the biodiversity loss impact category. As the weighting factors proposed in this paper are not based on the common LCA impact categories, more work is needed to adjust the weighting factors to be suitable for use in LCA studies. More research is also needed for further defining the safe planetary boundaries.

Organic farming practices have been promoted as, inter alia, reducing the environmental impacts of agriculture. This meta-analysis systematically analyses published studies that compare environmental impacts of organic and conventional farming in Europe. The results show that organic farming practices generally have positive impacts on the environment per unit of area, but not necessarily per product unit. Organic farms tend to have higher soil organic matter content and lower nutrient losses (nitrogen leaching, nitrous oxide emissions and ammonia emissions) per unit of field area. However, ammonia emissions, nitrogen leaching and nitrous oxide emissions per product unit were higher from organic systems. Organic systems had lower energy requirements, but higher land use, eutrophication potential and acidification potential per product unit. The variation within the results across different studies was wide due to differences in the systems compared and research methods used. The only impacts that were found to differ significantly between the systems were soil organic matter content, nitrogen leaching, nitrous oxide emissions per unit of field area, energy use and land use. Most of the studies that compared biodiversity in organic and conventional farming demonstrated lower environmental impacts from organic farming. The key challenges in conventional farming are to improve soil quality (by versatile crop rotations and additions of organic material), recycle nutrients and enhance and protect biodiversity. In organic farming, the main challenges are to improve the nutrient management and increase yields. In order to reduce the environmental impacts of farming in Europe, research efforts and policies should be targeted to developing farming systems that produce high yields with low negative environmental impacts drawing on techniques from both organic and conventional systems.

This article describes a method for detailed mapping of ecological variation in a tropical rainforest based on field inventory of pteridophytes ferns and lycophytes and remote sensing using Landsat Enhanced Thematic Mapper Plus ETM+ imagery. Previously known soil cation optima of the pteridophyte species were first used in calibration, i.e. to infer soil cation concentrations for sites on the basis of their pteridophyte species composition. Multiple linear regression based on spectral reflectance values in the Landsat image was then used to derive an equation that allowed the prediction of these calibrated soil values for unvisited sites in the study area. The predictive accuracy turned out to be high: the mean absolute error, as estimated by leave-one-out cross-validation, was just 7% of the total range of calibrated soil values. This method for detailed mapping of natural environmental variability in lowland tropical rainforest has applications for land-use planning, such as wildlife management, forestry, biodiversity conservation, and payments for carbon sequestration.

For a long time, the genus Metaxya was treated as monotypic with a single species, M. rostrata. A second species, M. lanosa, was described in 2001 on the basis of morphological features and rbcL gene sequences with a suggestion that the genus may contain even more species. We have now systematically compared morphological traits in a large number of Metaxya specimens collected in tropical America. We have also carried out phylogenetic analyses of 32 Metaxya and 5 outgroup specimens based on four markers of the plastid genome (rbcL, matK, and rps4 genes, and trnG-trnR intergenic spacer). Based on the morphological variation among the Metaxya specimens, we accept six distinct species, three of which we describe as new in this paper. Molecular phylogenetic analyses resolved five distinct clades. Four of these corresponded with the morphologically delineated species (M. contamanensis sp. nov., M. elongata sp. nov., M. lanosa, and M. parkeri). The fifth clade contained all the individuals of the remaining two species, of which M. rostrata was rendered paraphyletic by M. scalaris sp. nov. being nested within it. Since M. scalaris was resolved as monophyletic, and the two are clearly distinguishable morphologically, we consider them true species despite the incomplete genetic differentiation.

Aim To provide a mechanistic and probabilistic framework for defining the species pool based on species-specific probabilities of dispersal, environmental suitability and biotic interactions within a specific temporal extent, and to show how probabilistic species pools can help disentangle the geographical structure of different community assembly processes. Innovation Probabilistic species pools provide an improved species pool definition based on probabilities in conjunction with the associated species list, which explicitly recognize the indeterminate nature of species pool membership for a given focal unit of interest and better capture real-world complexity. Probabilistic species pools provide a quantitative assessment of how dispersal, environmental or biotic factors influence estimates of species pool composition and size for a given temporal extent. Conclusions Based on one simulated and two empirical examples we demonstrate that probabilistic species pools allow us to disentangle the geographical variation in dispersal, environmental and biotic assembly processes for species assemblages in focal units. We also show that probabilistic species pools are fully compatible with traditional definitions of species pools and are applicable over a wide range of spatial and temporal extents. Additionally they are robust to missing data and provide a quantified and transparent approach to estimating the size and composition of species pools in a mechanistic way, providing a valuable tool for studies from community ecology to macroecology.

Agriculture is one of the largest anthropogenic sources of greenhouse gases (GHGs), with dairy and beef production accounting for nearly two-thirds of emissions. Several recent papers suggest that dung beetles may affect fluxes of GHGs from cattle farming. Here, we put these previous findings into context. Using Finland as an example, we assessed GHG emissions at three scales: the dung pat, pasture ecosystem and whole lifecycle of milk or beef production. At the first two levels, dung beetles reduced GHG emissions by up to 7% and 12% respectively, mainly through large reductions in methane (CH4) emissions. However, at the lifecycle level, dung beetles accounted for only a 0.05–0.13% reduction of overall GHG emissions. This mismatch derives from the fact that in intensive production systems, only a limited fraction of all cow pats end up on pastures, offering limited scope for dung beetle mitigation of GHG fluxes. In contrast, we suggest that the effects of dung beetles may be accentuated in tropical countries, where more manure is left on pastures and dung beetles remove and aerate dung faster and that this is thus a key area for future research. These considerations give a new perspective on previous results and suggest that studies of biotic effects on GHG emissions from dung pats on a global scale are a priority for current research.

Vegetation maps are the starting point for the design of protected areas and regional conservation plans. Accurate vegetation maps are missing for much of Amazonia, preventing the development of effective and compelling conservation strategies. Here we used a network of 160 inventories across northwestern Amazonia to evaluate the use of Landsat and Shuttle Radar Topography Mission (SRTM) data to identify floristic and edaphic patterns in Amazonian forests. We first calculated the strength of the relationship between these remotely-sensed data, and edaphic and floristic patterns in these forests, and asked how sensitive these results are to image processing and enhancement. We additionally asked if SRTM data can be used to model patterns in plant species composition in our study areas. We find that variations in Landsat and SRTM data are strongly correlated with variations in soils and plant species composition, and that these patterns can be mapped solely on the basis of SRTM data over limited areas. Using these data, we furthermore identified widespread patch-matrix floristic patterns across northwestern Amazonia, with implications for conservation planning and study. Our findings provide further evidence that Landsat and SRTM data can provide a cost-effective means for mapping these forests, and we recommend that maps generated from a combination of remotely-sensed and field data be used as the basis for conservation prioritization and planning in these vast and remote forests.

Establishing which factors determine species distributions is of major relevance for practical applications such as conservation planning. The Amazonian lowlands exhibit considerable internal heterogeneity that is not apparent in existing vegetation maps. We used ferns as a model group to study patterns in plant species distributions and community composition at regional and landscape scales. Fern species composition and environmental data were collected in 109 plots of 250 × 2 m distributed among four sites in Brazilian Amazonia. Interplot distances varied from 1 to ca 670 km. When floristically heterogeneous datasets were analyzed, the use of an extended Sorensen dissimilarity index rather than the traditional Sorensen index improved model fit and made interpretation of the results easier. Major factors associated with species composition varied among sites, difference in cation concentration was a strong predictor of floristic dissimilarity in those sites with pronounced heterogeneity in cation concentration. Difference in clay content was the most relevant variable in sites with uniform cation concentrations. In every case, environmental differences were invariably better than geographic distances in predicting species compositional differences. Our results are consistent with the ideas that: (1) the relative predictive capacity of the explanatory variables depend on the relative lengths of the observed gradients; and (2) environmental gradients can be hierarchically structured such that gradients occur inside gradients. Therefore, site-specific relationships among variables can mask the bigger picture and make it more difficult to unravel the factors structuring plant communities in Amazonia. Resumo Estabelecer quais fatores determinam a distribuicao das especies e de grande relevância as aplicacoes praticas, tais como o planejamento da conservacao. As planicies amazonicas exibem consideravel heterogeneidade interna que nao e visivel nos mapas de vegetacao existentes. No presente trabalho, utilizamos samambaias como grupo modelo para estudar os padroes de distribuicao de especies de plantas em escalas regionais e de paisagem. Foram coletados dados ambientais e de composicao de especies de samambaias em 109 parcelas de 250 m × 2 m em quatro localidades na Amazonia brasileira. A distância entre parcelas variou de 1 ate ca. 670 km. Quando conjuntos de dados muito heterogeneos floristicamente foram analisados, a utilizacao de um indice de distância floristica de Sorensen estendido, em vez do Sorensen classico, permitiu um melhor ajuste do modelo e tornou a interpretacao dos resultados mais facil. Os principais fatores associados a composicao de especies variaram entre os locais, a diferenca de concentracao de cations foi um forte preditor da dissimilaridade floristica em locais cuja heterogeneidade na concentracao de cations era acentuda. A diferenca no teor de argila foi a variavel mais relevante em locais cuja concentracao de cations era relativamente uniforme entre as parcelas. Em todos os casos, as diferencas ambientais foram melhores preditoras da composicao de especies do que as distâncias geograficas. Nossos resultados sao consistentes as ideias de que: 1) os papeis relativos das variaveis explicativas dependem dos comprimentos relativos dos gradientes observados e 2) gradientes ambientais podem ser hierarquicamente estruturados, de modo que gradientes ocorrem dentro de outros gradientes. Portanto, relacoes entre variaveis especificas de cada sitio podem mascarar o panorama geral sobre os fatores que estruturam comunidades vegetais na Amazonia.

To ensure a sustainable food supply for the growing population, the challenge is to find agricultural systems that can meet production requirements within environmental constraints and demands. This study compares the impacts of winter wheat production on energy use, land use and 100 years Global Warming Potential (GWP100) under different arable farming systems and farming practices. Life cycle assessment was used to simulate the impacts of organic, conventional and integrated farming (IF) systems along the production chain from input production up to the farm gate. The IF system models were designed to combine the best practices from organic and conventional systems to reduce negative environmental impacts without significant yield reductions. An integrated system that used food waste digestate as a fertiliser, and utilised pesticides and no-tillage had the lowest energy use and GWP per functional unit of 1000 kg wheat output. When the impacts of some specific practices for reducing energy use and GWP were compared, the highest energy use reductions were achieved by replacing synthetic nitrogen fertilisers with anaerobically treated food waste or nitrogen fixing crops, increasing yields through crop breeding and using no-tillage instead of ploughing. The highest GWP reductions were achieved by using nitrification inhibitors, replacing synthetic nitrogen fertilisers and increasing yields. The major contributors to the uncertainty range of energy use were associated with machinery fuel use and the assumed crop yields. For GWP results, the main source of uncertainty related to the N2O emissions. In conclusion, farming systems that combine the best practices from organic and conventional systems have potential to reduce negative environmental impacts while maintaining yield levels.

Ecologists widely agree that species diversity consists of two components, richness (the number of species) and evenness (a measure of the equitability of the proportional abundances of those species). However, no consensus on an exact definition of evenness (or equitability) has emerged. Instead, numerous equitability indices have been used in the ecological literature, as different researchers have preferred indices with different mathematical properties. In this paper, I show that the phrase ‘species diversity consists of two independent components, richness and evenness’ logically leads to one particu­ lar definition of evenness (Evenness  Diversity/Richness). To facilitate accurate communication, I propose that the term ‘evenness’ be used only to refer to this phenomenon, and that other terms be used for the equitability indices that measure other things. Here I provide a review of popular equitability indices, explain what each measures in practice, and show how they relate to each other and to evenness itself. I also explore how the partitioning of diversity into richness and evenness components is related to the partitioning of diversity into alpha and beta components. Dissecting the indices makes it easier to see the conceptual differences among them. Such understanding is necessary to ensure that an appropriate index is chosen for the questions at hand, as well as to interpret the index values correctly and to assess when index values can and when they cannot be considered comparable.