One sixth of Amazonian tree diversity is dependent on river floodplains

Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.

Mapping density, diversity and species-richness of the Amazon tree flora

Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.

Bait attractiveness changes community metrics in dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae)

Species relative abundance (SRA) is an essential attribute of biotic communities, which can provide an accurate description of community structure. However, the sampling method used may have a direct influence on SRA quantification, since the use of attractants (e.g., baits, light, and pheromones) can introduce additional sources of variation in trap performance. We tested how sampling aided by baits affect community data and therefore alter derived metrics. We tested our hypothesis on dung beetles using data from flight interception traps (FITs) as a baseline to evaluate baited pitfall trap performance. Our objective was to assess the effect of bait attractiveness on estimates of SRA and assemblage metrics when sampled by pitfall traps baited with human feces.Dung beetles were sampled at three terra firme primary forest sites in the Brazilian Amazon. To achieve our objective, we (i) identified species with variable levels of attraction to pitfall baited with human feces; (ii) assessed differences in SRA; and (iii) assessed the effect of bait on the most commonly used diversity metrics derived from relative abundance (Shannon and Simpson indices). We identified species less and highly attracted to the baits used, because most attracted species showed greater relative abundances within baited pitfall traps samples compared with our baseline. Assemblages sampled by baited pitfall traps tend to show lower diversity and higher dominance than those sampled by unbaited FITs. Our findings suggest that for ecological questions focused on species relative abundance, baited pitfall traps may lead to inaccurate conclusions regarding assemblage structure. Although tested on dung beetles, we suggest that the same effect could be observed for other insect taxa that are also sampled with baited traps. We highlight a need for further studies on other groups to elucidate any potential effects of using baits.

High rates of mercury biomagnification in fish from Amazonian floodplain-lake food webs

Despite a global phase out of some point sources, mercury (Hg) remains elevated in aquatic food webs, posing health risks for fish-eating consumers. Many tropical regions have fast growing organisms, potentially short food chains, and few industrial point sources, suggesting low Hg baselines and low rates of trophic magnification with limited risk to people. Nevertheless, insufficient work on food-web Hg has been undertaken in the tropics and fish consumption is high in some regions. We studied Hg concentrations in fishes from floodplain lakes of the Juruá River, Amazonas, Brazil with three objectives: 1) determine rates of Hg trophic magnification, 2) assess whether Hg concentrations are high enough to impact humans eating fish, and 3) determine whether there are seasonal differences in fish Hg concentrations. A total of 377 fish-muscle samples were collected from 12 floodplain lakes during the low-water (September 2018) and falling-water (June 2019) seasons and analysed for total Hg and stable nitrogen (N) isotopes. The average trophic magnification factor (increase per trophic level) was 10.1 in the low-water season and 5.4 in the falling-water season, both well above the global average for freshwaters. This high rate of trophic magnification, coupled with higher-than-expected Hg concentrations in herbivorous species, led to high concentrations (up to 17.6 ng/g dry weight) in predatory pirarucu and piranha. Nearly 70% of all samples had Hg concentrations above the recommended human-consumption guidelines. Average concentrations were 42% higher in the low-water season than the falling-water season, but differences varied by species. Since Hg concentrations are higher than expected and fish consumption in this region is high, future research should focus on Hg exposure for human populations here and in other tropical-rainforest regions, even in the absence of local point sources of Hg.

NEOTROPICAL FRESHWATER FISHES: A dataset of occurrence and abundance of freshwater fishes in the Neotropics

The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications.

Human-wildlife conflicts with crocodilians, cetaceans and otters in the tropics and subtropics

Conservation of freshwater biodiversity and management of human-wildlife conflicts are major conservation challenges globally. Human-wildlife conflict occurs due to attacks on people, depredation of fisheries, damage to fishing equipment and entanglement in nets. Here we review the current literature on conflicts with tropical and subtropical crocodilians, cetaceans and otters in freshwater and brackish habitats. We also present a new multispecies case study of conflicts with four freshwater predators in the Western Amazon: black caiman (Melanosuchus niger), giant otter (Pteronura brasiliensis), boto (Inia geoffrensis) and tucuxi (Sotalia fluviatilis). Documented conflicts occur with 34 crocodilian, cetacean and otter species. Of the species reviewed in this study, 37.5% had conflicts frequently documented in the literature, with the saltwater crocodile (Crocodylus porosus) the most studied species. We found conflict severity had a positive relationship with species body mass, and a negative relationship with IUCN Red List status. In the Amazonian case study, we found that the black caiman was ranked as the greatest ‘problem’ followed by the boto, giant otter and tucuxi. There was a significant difference between the responses of local fishers when each of the four species were found entangled in nets. We make recommendations for future research, based on the findings of the review and Amazon case study, including the need to standardise data collection.

Community-based conservation with formal protection provides large collateral benefits to Amazonian migratory waterbirds

Populations of migratory waterbirds are facing dramatic declines worldwide due to illegal hunting, habitat loss and climate change. Conservation strategies to reverse these trends are imperative, especially in tropical developing countries, which almost invariably allocate insufficient levels of investment for environmental protection. Here, we compared the effectiveness of sustainable-use Protected Areas (PAs) and Community-based Conservation (CBC) arrangements for the conservation of migratory waterbirds that breed on seasonal riverine sandy beaches in Brazilian Amazonia. We modeled local population responses of four migratory waterbird species on 155 beaches along a ~1,600 km section of a major tributary of the Amazon, as a function of community enforcement, official protection status, human pressure and landscape features. We show that 21 community-protected beaches within the study area host more than 80% of all sampled birds. Black Skimmers showed the most dramatic response, with breeding numbers 135-fold larger in CBC arrangements compared to beaches with no official protection status. The same pattern was observed for nesting Large-Billed and Yellow-Billed Terns. For the Near Threatened Orinoco Goose, PA status was the strongest predictor of local population size. These dramatic results demonstrate the value of protected refugia, achieved through the concerted action of participating local communities, to support breeding populations of key waterbird species. This highly-effective and low-cost conservation model can potentially be replicated in other regions of the developing world experiencing increasingly intensive exploitation of riverine natural resources.

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data.

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Extinction filters mediate the global effects of habitat fragmentation on animals

Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity—affected by avoidance of habitat edges—should be driven by historical exposure to, and therefore species’ evolutionary responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world’s tropical forests.

Zooming into plant-flower visitor networks: an individual trait-based approach

Understanding how ecological communities are structured is a major goal in ecology. Ecological networks representing interaction patterns among species have become a powerful tool to capture the mechanisms underlying plant-animal assemblages. However, these networks largely do not account for inter-individual variability and thus may be limiting our development of a clear mechanistic understanding of community structure. In this study, we develop a new individual-trait based approach to examine the importance of individual plant and pollinator functional size traits (pollinator thorax width and plant nectar holder depth) in mutualistic networks. We performed hierarchical cluster analyses to group interacting individuals into classes, according to their similarity in functional size. We then compared the structure of bee-flower networks where nodes represented either species identity or trait sets. The individual trait-based network was almost twice as nested as its species-based equivalent and it had a more symmetric linkage pattern resulting from of a high degree of size-matching. In conclusion, we show that by constructing individual trait-based networks we can reveal important patterns otherwise difficult to observe in species-based networks and thus improve our understanding of community structure. We therefore recommend using both trait-based and species-based approaches together to develop a clearer understanding of the properties of ecological networks.

Coarse- and fine-scale patterns of distribution and habitat selection places an Amazonian floodplain curassow in double jeopardy

Patterns of habitat selection are influenced by local productivity, resource availability, and predation risk. Species have taken millions of years to hone the macro- and micro-habitats they occupy, but these may now overlap with contemporary human threats within natural species ranges. Wattled Curassow (Crax globulosa), an endemic galliform species of the western Amazon, is threatened by both hunting and habitat loss, and is restricted to white-water floodplain forests of major Amazonian rivers. In this study conducted along the Juruá River, Amazonas, Brazil, we quantified the ranging ecology and fine-scale patterns of habitat selection of the species. We estimated the home range size of C. globulosa using conventional VHF telemetry. To estimate patterns of habitat selection, we used geo-locations of day ranges to examine the extent and intensity of use across the floodplain, which were then compared to a high-resolution flood map of the study area. We captured two females and one male, which we monitored for 13 months between September 2014 and September 2015. Average home range size was 283 ha, based on the 95% aLoCoH estimator. Wattled Curassows selected areas of prolonged flood pulses (six to eight months/year) and had a consistent tendency to be near open water, usually in close proximity to river banks and lakes, especially during the dry season. Amazonian floodplains are densely settled, and the small portions of floodplain habitat used by Wattled Curassows are both the most accessible to hunters and most vulnerable to deforestation. As a result, the geographic and ecological distribution of Wattled Curassows places them at much higher extinction risk at multiple spatial scales, highlighting the need to consider habitat preferences within their conservation strategy.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Multitrophic diversity effects of network degradation

Predicting the functional consequences of biodiversity loss in realistic, multitrophic communities remains a challenge. No existing biodiversity–ecosystem function study to date has simultaneously incorporated information on species traits, network topology, and extinction across multiple trophic levels, while all three factors are independently understood as critical drivers of post‐extinction network structure and function. We fill this gap by comparing the functional consequences of simulated species loss both within (monotrophic) and across (bitrophic) trophic levels, in an ecological interaction network estimated from spatially explicit field data on tropical fecal detritus producer and consumers (mammals and dung beetles). We simulated trait‐ordered beetle and mammal extinction separately (monotrophic extinction) and the coextinction of beetles following mammal loss (bitrophic extinction), according to network structure. We also compared the diversity effects of bitrophic extinction models using a standard monotrophic function (the daily production or consumption of fecal detritus) and a unique bitrophic functional metric (the proportion of daily detritus production that is consumed). We found similar mono‐ and bitrophic diversity effects, regardless of which species traits were used to drive extinctions, yet divergent predictions when different measures of function were used. The inclusion of information on network structure had little apparent effect on the qualitative relationship between diversity and function. These results contribute to our growing understanding of the functional consequences of biodiversity from real systems and underscore the importance of species traits and realistic functional metrics to assessments of the ecosystem impacts of network degradation through species loss.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

BIOFRAG - a new database for analyzing BIOdiversity responses to forest FRAGmentation

Habitat fragmentation studies have produced complex results that are challenging to synthesize. Inconsistencies among studies may result from variation in the choice of landscape metrics and response variables, which is often compounded by a lack of key statistical or methodological information. Collating primary datasets on biodiversity responses to fragmentation in a consistent and flexible database permits simple data retrieval for subsequent analyses. We present a relational database that links such field data to taxonomic nomenclature, spatial and temporal plot attributes, and environmental characteristics. Field assessments include measurements of the response(s) (e.g., presence, abundance, ground cover) of one or more species linked to plots in fragments within a partially forested landscape. The database currently holds 9830 unique species recorded in plots of 58 unique landscapes in six of eight realms: mammals 315, birds 1286, herptiles 460, insects 4521, spiders 204, other arthropods 85, gastropods 70, annelids 8, platyhelminthes 4, Onychophora 2, vascular plants 2112, nonvascular plants and lichens 320, and fungi 449. Three landscapes were sampled as long-term time series (>10 years). Seven hundred and eleven species are found in two or more landscapes. Consolidating the substantial amount of primary data available on biodiversity responses to fragmentation in the context of land-use change and natural disturbances is an essential part of understanding the effects of increasing anthropogenic pressures on land. The consistent format of this database facilitates testing of generalizations concerning biologic responses to fragmentation across diverse systems and taxa. It also allows the re-examination of existing datasets with alternative landscape metrics and robust statistical methods, for example, helping to address pseudo-replication problems. The database can thus help researchers in producing broad syntheses of the effects of land use. The database is dynamic and inclusive, and contributions from individual and large-scale data-collection efforts are welcome.

Size-energy relationships in ecological communities

Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights into mechanisms underlying local size-energy relationships and has important implications for predicting species interactions and for understanding the structure and dynamics of ecological communities.

A Stereospecific Synthesis of (±)-Abscisic Acid

A convenient separation of (E)- and (Z)-3-methylpent-2-enedioic acids was devised, and it was shown that with acetyl chloride or thionyl chloride the (Z)-acid yields the cyclic anhydride while the (E)-acid forms 6-chloro-4-methylpyran-2-one. The chloropyranone by conventional chemistry gave 4-methyl-6-(2′-oxopropyl)pyran-2-one which condensed with 4-methylpent-3-en-2-one in the presence of pyrrolidine, yielding 4-methyl-6-(2′,6′,6′-trimethyl-4′-oxocyclohex-2′-enyl)pyran-2-one. Oxidation with selenium dioxide or t-butyl chromate then gave 6-(1′-hydroxy-2′,6′,6′-trimethyl-4′-oxotyclohex-2′-enyl)-4-methylpyran-2-one, which on reduction by lithium aluminium hydride and reoxidation afforded (±)-abscisic acid stereospecifically.