Showing papers on "Species richness published in 2016"

Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity : relationship with gut microbiome richness and ecology [plus Supplementary data]

Abstract: Objective Individuals with obesity and type 2 diabetes differ from lean and healthy individuals in their abundance of certain gut microbial species and microbial gene richness. Abundance of Akkermansia muciniphila, a mucin-degrading bacterium, has been inversely associated with body fat mass and glucose intolerance in mice, but more evidence is needed in humans. The impact of diet and weight loss on this bacterial species is unknown. Our objective was to evaluate the association between faecal A. muciniphila abundance, faecal microbiome gene richness, diet, host characteristics, and their changes after calorie restriction (CR). Design The intervention consisted of a 6-week CR period followed by a 6-week weight stabilisation diet in overweight and obese adults (N=49, including 41 women). Faecal A. muciniphila abundance, faecal microbial gene richness, diet and bioclinical parameters were measured at baseline and after CR and weight stabilisation. Results At baseline A. muciniphila was inversely related to fasting glucose, waist-to-hip ratio and subcutaneous adipocyte diameter. Subjects with higher gene richness and A. muciniphila abundance exhibited the healthiest metabolic status, particularly in fasting plasma glucose, plasma triglycerides and body fat distribution. Individuals with higher baseline A. muciniphila displayed greater improvement in insulin sensitivity markers and other clinical parameters after CR. These participants also experienced a reduction in A. muciniphila abundance, but it remained significantly higher than in individuals with lower baseline abundance. A. muciniphila was associated with microbial species known to be related to health. Conclusions A. muciniphila is associated with a healthier metabolic status and better clinical outcomes after CR in overweight/obese adults. The interaction between gut microbiota ecology and A. muciniphila warrants further investigation. Trial registration number NCT01314690.

Species Diversity In Space And Time

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Integrative modelling reveals mechanisms linking productivity and plant species richness

Abstract: How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality

Abstract: Many experiments have shown that loss of biodiversity reduces the capacity of ecosystems to provide the multiple services on which humans depend. However, experiments necessarily simplify the complexity of natural ecosystems and will normally control for other important drivers of ecosystem functioning, such as the environment or land use. In addition, existing studies typically focus on the diversity of single trophic groups, neglecting the fact that biodiversity loss occurs across many taxa and that the functional effects of any trophic group may depend on the abundance and diversity of others. Here we report analysis of the relationships between the species richness and abundance of nine trophic groups, including 4,600 above- and below-ground taxa, and 14 ecosystem services and functions and with their simultaneous provision (or multifunctionality) in 150 grasslands. We show that high species richness in multiple trophic groups (multitrophic richness) had stronger positive effects on ecosystem services than richness in any individual trophic group; this includes plant species richness, the most widely used measure of biodiversity. On average, three trophic groups influenced each ecosystem service, with each trophic group influencing at least one service. Multitrophic richness was particularly beneficial for 'regulating' and 'cultural' services, and for multifunctionality, whereas a change in the total abundance of species or biomass in multiple trophic groups (the multitrophic abundance) positively affected supporting services. Multitrophic richness and abundance drove ecosystem functioning as strongly as abiotic conditions and land-use intensity, extending previous experimental results to real-world ecosystems. Primary producers, herbivorous insects and microbial decomposers seem to be particularly important drivers of ecosystem functioning, as shown by the strong and frequent positive associations of their richness or abundance with multiple ecosystem services. Our results show that multitrophic richness and abundance support ecosystem functioning, and demonstrate that a focus on single groups has led to researchers to greatly underestimate the functional importance of biodiversity.

Plant diversity patterns in neotropical dry forests and their conservation implications

Abstract: Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale.

Local biodiversity is higher inside than outside terrestrial protected areas worldwide

Abstract: Protected areas are widely considered essential for biodiversity conservation. However, few global studies have demonstrated that protection benefits a broad range of species. Here, using a new global biodiversity database with unprecedented geographic and taxonomic coverage, we compare four biodiversity measures at sites sampled in multiple land uses inside and outside protected areas. Globally, species richness is 10.6% higher and abundance 14.5% higher in samples taken inside protected areas compared with samples taken outside, but neither rarefaction-based richness nor endemicity differ significantly. Importantly, we show that the positive effects of protection are mostly attributable to differences in land use between protected and unprotected sites. Nonetheless, even within some human-dominated land uses, species richness and abundance are higher in protected sites. Our results reinforce the global importance of protected areas but suggest that protection does not consistently benefit species with small ranges or increase the variety of ecological niches.

Integrative modelling reveals mechanisms linking productivity and plant species richness

Abstract: How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology1. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns2, 3. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models4, 5, 6, 7. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis8, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

Climate velocity and the future global redistribution of marine biodiversity

Abstract: Ocean warming will cause widespread changes in species richness and assemblage composition over coming decades, with important implications for both conservation management and international ocean governance.

Ecology and evolution of plant diversity in the endangered campo rupestre: a neglected conservation priority

Abstract: Botanists, ecologists and evolutionary biologists are familiar with the astonishing species richness and endemism of the fynbos of the Cape Floristic Region and the ancient and unique flora of the kwongkan of south-western Australia. These regions represent old climatically-buffered infertile landscapes (OCBILs) that are the basis of a general hypothesis to explain their richness and endemism. However, few ecologists are familiar with the campo rupestre of central and eastern Brazil, an extremely old mountaintop ecosystem that is both a museum of ancient lineages and a cradle of continuing diversification of endemic lineages. Diversification of some lineages of campo rupestre pre-dates diversification of lowland cerrado, suggesting it may be the most ancient open vegetation in eastern South America. This vegetation comprises more than 5000 plant species, nearly 15 % of Brazil’s plant diversity, in an area corresponding to 0.78 % of its surface. Reviewing empirical data, we scrutinise five predictions of the OCBIL theory, and show that campo rupestre is fully comparable to and remarkably convergent with both fynbos and kwongkan, and fulfills the criteria for a classic OCBIL. The increasing threats to campo rupestre are compromising ecosystem services and we argue for the implementation of more effective conservation and restoration strategies.

Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition

Abstract: Nitrogen (N) deposition influences both above- and below-ground communities and influences ecosystem functioning. However it is not clear about direct or indirect interactions among plants, soils and microbes in response to nitrogen deposition. In this study, the responses of soil bacterial diversity to N enrichment were investigated at surface (0–10 cm) and sub-surface (10–20 cm) soils in a temperate steppe ecosystem. N addition (>120 kg N ha−1 yr−1) resulted in a significant shift in bacterial community composition and a decrease in bacterial OTU richness in surface soil, but the effect on the sub-surface layer was far less pronounced, even at the highest addition rate (240 kg N ha−1 yr−1). Bacterial OTU richness was significantly correlated with soil and plant characteristics. Hierarchical structural equation modeling showed that soil ammonium availability was responsible for the shift in bacterial richness, whereas the change in bacterial community composition was due to alterations in soil pH and plant composition. These results indicated that N fertilization directly affected soil bacterial richness but indirectly affected bacterial communities through soil acidification and plant community change, indicating distinct controls on soil bacterial diversity and community composition. Our results also suggest that N availability could be a good predictor for the loss of soil bacterial diversity under atmospheric nitrogen deposition.

Fish biodiversity and conservation in South America.

Abstract: The freshwater and marine fish faunas of South America are the most diverse on Earth, with current species richness estimates standing above 9100 species. In addition, over the last decade at least 100 species were described every year. There are currently about 5160 freshwater fish species, and the estimate for the freshwater fish fauna alone points to a final diversity between 8000 and 9000 species. South America also has c. 4000 species of marine fishes. The mega-diverse fish faunas of South America evolved over a period of >100 million years, with most lineages tracing origins to Gondwana and the adjacent Tethys Sea. This high diversity was in part maintained by escaping the mass extinctions and biotic turnovers associated with Cenozoic climate cooling, the formation of boreal and temperate zones at high latitudes and aridification in many places at equatorial latitudes. The fresh waters of the continent are divided into 13 basin complexes, large basins consolidated as a single unit plus historically connected adjacent coastal drainages, and smaller coastal basins grouped together on the basis of biogeographic criteria. Species diversity, endemism, noteworthy groups and state of knowledge of each basin complex are described. Marine habitats around South America, both coastal and oceanic, are also described in terms of fish diversity, endemism and state of knowledge. Because of extensive land use changes, hydroelectric damming, water divergence for irrigation, urbanization, sedimentation and overfishing 4-10% of all fish species in South America face some degree of extinction risk, mainly due to habitat loss and degradation. These figures suggest that the conservation status of South American freshwater fish faunas is better than in most other regions of the world, but the marine fishes are as threatened as elsewhere. Conserving the remarkable aquatic habitats and fishes of South America is a growing challenge in face of the rapid anthropogenic changes of the 21st century, and deserves attention from conservationists and policy makers.

Checklist of the native vascular plants of Mexico

Abstract: An updated inventory of the native vascular plants of Mexico records 23,314 species, distributed in 2,854 genera, 297 families, and 73 orders. The flora includes 1,039 species of ferns and lycophytes, 149 gymnosperms, and 22,126 angiosperms. On average, the number of synonyms per species is 1.3 (mode = 1). The number of species places Mexico as the country with the fourth largest floristic richness in the world, although among the non-insular countries, by its number of endemic species (about 50%) is second only surpassed by South Africa. The species distribution among higher taxonomic categories, and the richness and endemism values in the 32 states of Mexico are discussed. This compilation allows us to assess the flora's contribution to the overall Mexican biodiversity.

Cities are hotspots for threatened species

Abstract: Aim: Although urbanization impacts many species, there is little information on the patterns of occurrences of threatened species in urban relative to non-urban areas. By assessing the extent of the distribution of threatened species across all Australian cities, we aim to investigate the currently under-utilized opportunity that cities present for national biodiversity conservation. Location: Australian mainland, Tasmania and offshore islands. Methods: Distributions of Australia's 1643 legally protected terrestrial species (hereafter 'threatened species') were compiled. We assessed the extent to which they overlapped with 99 cities (ofmore than 10,000 people), with all non-urban areas, and with simulated 'dummy' cities which covered the same area and bioregion as the true cities but were non-urban. We analysed differences between animals and plants, and examined variability within these groups using species accumulation modelling. Threatened species richness of true versus dummy cities was analysed using generalized linear mixed-effects models. Results: Australian cities support substantially more nationally threatened animal and plant species than all other non-urban areas on a unit-area basis. Thirty per cent of threatened species were found to occur in cities. Distribution patterns differed between plants and animals: individual threatened plant species were generally found in fewer cities than threatened animal species, yet plants were more likely to have a greater proportion of their distribution in urban areas than animals. Individual cities tended to contain unique suites of threatened species, especially threatened plants. The analysis of true versus dummy cities demonstrated that, even after accounting for factors such as net primary productivity and distance to the coast, cities still consistently supported a greater number of threatened species. Main conclusions: This research highlights that Australian cities are important for the conservation of threatened species, and that the species assemblages of individual cities are relatively distinct. National conservation policy should recognize that cities play an integral role when planning for and managing threatened species.

Rare species contribute disproportionately to the functional structure of species assemblages

Abstract: There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions.

Structure and functioning of dryland ecosystems in a changing world.

Abstract: Understanding how drylands respond to ongoing environmental change is extremely important for global sustainability. In this review, we discuss how biotic attributes, climate, grazing pressure, land cover change, and nitrogen deposition affect the functioning of drylands at multiple spatial scales. Our synthesis highlights the importance of biotic attributes (e.g., species richness) in maintaining fundamental ecosystem processes such as primary productivity, illustrates how nitrogen deposition and grazing pressure are impacting ecosystem functioning in drylands worldwide, and highlights the importance of the traits of woody species as drivers of their expansion in former grasslands. We also emphasize the role of attributes such as species richness and abundance in controlling the responses of ecosystem functioning to climate change. This knowledge is essential to guide conservation and restoration efforts in drylands, as biotic attributes can be actively managed at the local scale to increase ecosystem re...

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

Abstract: Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

Abstract: Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.

Impact of forest management on species richness: global meta-analysis and economic trade-offs

Abstract: Forests managed for timber have an important role to play in conserving global biodiversity. We evaluated the most common timber production systems worldwide in terms of their impact on local species richness by conducting a categorical meta-analysis. We reviewed 287 published studies containing 1008 comparisons of species richness in managed and unmanaged forests and derived management, taxon and continent specific effect sizes. We show that in terms of local species richness loss, forest management types can be ranked, from best to worse, as follows: selection and retention systems, reduced impact logging, conventional selective logging, clear-cutting, agroforestry, timber plantations, fuelwood plantations. Next, we calculated the economic profitability in terms of the net present value of timber harvesting from 10 hypothetical wood-producing Forest Management Units (FMU) from around the globe. The ranking of management types is altered when the species loss per unit profit generated from the FMU is considered. This is due to differences in yield, timber species prices, rotation cycle length and production costs. We thus conclude that it would be erroneous to dismiss or prioritize timber production regimes, based solely on their ranking of alpha diversity impacts.

Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity.

Abstract: Global species extinction rates are orders of magnitude above the background rate documented in the fossil record. However, recent data syntheses have found mixed evidence for patterns of net species loss at local spatial scales. For example, two recent data meta-analyses have found that species richness is decreasing in some locations and is increasing in others. When these trends are combined, these papers argued there has been no net change in species richness, and suggested this pattern is globally representative of biodiversity change at local scales. Here we reanalyze results of these data syntheses and outline why this conclusion is unfounded. First, we show the datasets collated for these syntheses are spatially biased and not representative of the spatial distribution of species richness or the distribution of many primary drivers of biodiversity change. This casts doubt that their results are representative of global patterns. Second, we argue that detecting the trend in local species richness is very difficult with short time series and can lead to biased estimates of change. Reanalyses of the data detected a signal of study duration on biodiversity change, indicating net biodiversity loss is most apparent in studies of longer duration. Third, estimates of species richness change can be biased if species gains during post-disturbance recovery are included without also including species losses that occurred during the disturbance. Net species gains or losses should be assessed with respect to common baselines or reference communities. Ultimately, we need a globally coordinated effort to monitor biodiversity so that we can estimate and attribute human impacts as causes of biodiversity change. A combination of technologies will be needed to produce regularly updated global datasets of local biodiversity change to guide future policy. At this time the conclusion that there is no net change in local species richness is not the consensus state of knowledge.

Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

Abstract: Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg N⋅ha−1⋅y−1, we found a unimodal relationship; richness increased at low deposition levels and decreased above 8.7 and 13.4 kg N⋅ha−1⋅y−1 in open and closed-canopy vegetation, respectively. N deposition exceeded critical loads for loss of plant species richness in 24% of 15,136 sites examined nationwide. There were negative relationships between species richness and N deposition in 36% of 44 community gradients. Vulnerability to N deposition was consistently higher in more acidic soils whereas the moderating roles of temperature and precipitation varied across scales. We demonstrate here that negative relationships between N deposition and species richness are common, albeit not universal, and that fine-scale processes can moderate vegetation responses to N deposition. Our results highlight the importance of contingent factors when estimating ecosystem vulnerability to N deposition and suggest that N deposition is affecting species richness in forested and nonforested systems across much of the continental United States.

Ecosystem structure, function, and composition in rangelands are negatively affected by livestock grazing.

Abstract: Reports of positive or neutral effects of grazing on plant species richness have prompted calls for livestock grazing to be used as a tool for managing land for conservation. Grazing effects, however, are likely to vary among different response variables, types, and intensity of grazing, and across abiotic conditions. We aimed to examine how grazing affects ecosystem structure, function, and composition. We compiled a database of 7615 records reporting an effect of grazing by sheep and cattle on 278 biotic and abiotic response variables for published studies across Australia. Using these data, we derived three ecosystem measures based on structure, function, and composition, which were compared against six contrasts of grazing pressure, ranging from low to heavy, two different herbivores (sheep, cattle), and across three different climatic zones. Grazing reduced structure (by 35%), function (24%), and composition (10%). Structure and function (but not composition) declined more when grazed by sheep and cattle together than sheep alone. Grazing reduced plant biomass (40%), animal richness (15%), and plant and animal abundance, and plant and litter cover (25%), but had no effect on plant richness nor soil function. The negative effects of grazing on plant biomass, plant cover, and soil function were more pronounced in drier environments. Grazing effects on plant and animal richness and composition were constant, or even declined, with increasing aridity. Our study represents a comprehensive continental assessment of the implications of grazing for managing Australian rangelands. Grazing effects were largely negative, even at very low levels of grazing. Overall, our results suggest that livestock grazing in Australia is unlikely to produce positive outcomes for ecosystem structure, function, and composition or even as a blanket conservation tool unless reduction in specific response variables is an explicit management objective.

A healthy gastrointestinal microbiome is dependent on dietary diversity.

Abstract: Background Like all healthy ecosystems, richness of microbiota species characterizes the GI microbiome in healthy individuals. Conversely, a loss in species diversity is a common finding in several disease states. This biome is flooded with energy in the form of undigested and partially digested foods, and in some cases drugs and dietary supplements. Each microbiotic species in the biome transforms that energy into new molecules, which may signal messages to physiological systems of the host.

Species Richness: Estimation and Comparison

Abstract: On the basis of the sampling data from an assemblage, estimation of species richness (observed plus undetected) is statistically difficult especially for highly-diverse assemblages with many rare species. Simple counts of species richness in samples typically underestimate and strongly depend on sampling effort and sample completeness. There are two approaches to infer species richness and make fair comparisons among multiple assemblages based on possibly unequal-sampling effort and incomplete samples that miss many species. (1) An asymptotic approach: this approach compares the estimated asymptotes of species accumulation curves. It is based on statistical sampling-theory methods of estimating species richness. Both parametric and nonparametric methods are reviewed. We focus on the nonparametric estimators which are universally valid for all species abundance distributions. (2) A non-asymptotic approach: this approach compares the estimated species richnesses of standardized samples with a common finite sample size or sample completeness. It is based on the seamless sample-sizeand coverage-based rarefaction and extrapolation sampling curves. This approach aims to compare species richness estimates for equally-large or equallycomplete samples. These two approaches allow researchers to efficiently use all data to make robust and detailed inferences about species richness. Two R packages (SpadeR and iNEXT) are applied to rainforest tree data for illustration. Species richness (i.e., the number of species) is the simplest, most intuitive and most frequently used measure for characterizing the diversity of an assemblage (see Diversity measures). Species richness possesses intuitive mathematical properties, and features prominently in foundational models of community ecology. In biogeographic studies, species range maps and local and regional floras and faunas generally provide only species presence-absence information for each locality. For these studies, species richness thus becomes the only measure that can be used to quantify diversity. Even when species abundances are available,

Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level

Abstract: The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities.

The strong influence of collection bias on biodiversity knowledge shortfalls of Brazilian terrestrial biodiversity

Abstract: Aim The knowledge of biodiversity facets such as species composition, distribution and ecological niche is fundamental for the construction of biogeographic hypotheses and conservation strategies. However, the knowledge on these facets is affected by major shortfalls, which are even more pronounced in the tropics. This study aims to evaluate the effect of sampling bias and variation in collection effort on Linnean, Wallacean and Hutchinsonian shortfalls and diversity measures as species richness, endemism and beta-diversity. Location Brazil. Methods We have built a database with over 1.5 million records of arthropods, vertebrates and angiosperms of Brazil, based on specimens deposited in scientific collections and on the taxonomic literature. We used null models to test the collection bias regarding the proximity to access routes. We also tested the influence of sampling effort on diversity measures by regression models. To investigate the Wallacean shortfall, we modelled the geographic distribution of over 4000 species and compared their observed distribution with models. To quantify the Hutchinsonian shortfall, we used environmental Euclidean distance of the records to identify regions with poorly sampled environmental conditions. To estimate the Linnean shortfall, we measured the similarity of species composition between regions close to and far from access routes. Results We demonstrated that despite the differences in sampling effort, the strong collection bias affects all taxonomic groups equally, generating a pattern of spatially biased sampling effort. This collection pattern contributes greatly to the biodiversity knowledge shortfalls, which directly affects the knowledge on the distribution patterns of diversity. Main conclusions The knowledge on species richness, species composition and endemism in the Brazilian biodiversity is strongly biased spatially. Despite differences in sampling effort for each taxonomic group, roadside bias affected them equally. Species composition similarity decreased with the distance from access routes, suggesting collection surveys at sites far from roads could increase the probability of sampling new geographic records or new species.

Functional traits reveal the expansion and packing of ecological niche space underlying an elevational diversity gradient in passerine birds

Abstract: Variation in species richness across environmental gradients may be associated with an expanded volume or increased packing of ecological niche space. However, the relative importance of these alternative scenarios remains unknown, largely because standardized information on functional traits and their ecological relevance is lacking for major diversity gradients. Here, we combine data on morphological and ecological traits for 523 species of passerine birds distributed across an Andes-to-Amazon elevation gradient. We show that morphological traits capture substantial variation in species dietary (75%) and foraging niches (60%) when multiple independent trait dimensions are considered. Having established these relationships, we show that the 14-fold increase in species richness towards the lowlands is associated with both an increased volume and density of functional trait space. However, we find that increases in volume contribute little to changes in richness, with most (78%) lowland species occurring within the range of trait space occupied at high elevations. Taken together, our results suggest that high species richness is mainly associated with a denser occupation of functional trait space, implying an increased specialization or overlap of ecological niches, and supporting the view that niche packing is the dominant trend underlying gradients of increasing biodiversity towards the lowland tropics.

Sampling networks of ecological interactions

Abstract: Summary Sampling ecological interactions presents similar challenges, problems, potential biases, and constraints as sampling individuals and species in biodiversity inventories. Robust estimates of the actual number of interactions (links) within diversified ecological networks require adequate sampling effort that needs to be explicitly gauged. Yet we still lack a sampling theory explicitly focusing on ecological interactions. While the complete inventory of interactions is likely impossible, a robust characterization of its main patterns and metrics is probably realistic. We must acknowledge that a sizeable fraction of the maximum number of interactions Imax among, say, A animal species and P plant species (i.e., Imax = AP) is impossible to record due to forbidden links, i.e., life-history restrictions. Thus, the number of observed interactions I in robustly sampled networks is typically I << Imax, resulting in sparse interaction matrices with low connectance. Here I provide a review and outline a conceptual framework for interaction sampling by building an explicit analogue to individuals and species sampling, thus extending diversity-monitoring approaches to the characterization of complex networks of ecological interactions. Contrary to species inventories, a sizable fraction of non-observed pairwise interactions cannot be sampled, due to biological constraints that forbid their occurrence. Reasons for forbidden links are multiple but mainly stem from spatial and temporal uncoupling, size mismatches, and intrinsically low probabilities of interspecific encounter for most potential interactions of partner species. Adequately assessing the completeness of a network of ecological interactions thus needs knowledge of the natural history details embedded, so that forbidden links can be accounted for as a portion of the unobserved links when addressing sampling effort. Recent implementations of inference methods for unobserved species or for individual-based data can be combined with the assessment of forbidden links. This can help in estimating their relative importance, simply by the difference between the asymptotic estimate of interaction richness in a robustly-sampled assemblage and the maximum richness Imax of interactions. This is crucial to assess the rapid and devastating effects of defaunationdriven loss of key ecological interactions and the services they provide and the analogous losses related to interaction gains due to invasive species and biotic homogenization. This article is protected by copyright. All rights reserved.

Standardized Assessment of Biodiversity Trends in Tropical Forest Protected Areas: The End Is Not in Sight

Abstract: Extinction rates in the Anthropocene are three orders of magnitude higher than background and disproportionately occur in the tropics, home of half the world’s species. Despite global efforts to combat tropical species extinctions, lack of high-quality, objective information on tropical biodiversity has hampered quantitative evaluation of conservation strategies. In particular, the scarcity of population-level monitoring in tropical forests has stymied assessment of biodiversity outcomes, such as the status and trends of animal populations in protected areas. Here, we evaluate occupancy trends for 511 populations of terrestrial mammals and birds, representing 244 species from 15 tropical forest protected areas on three continents. For the first time to our knowledge, we use annual surveys from tropical forests worldwide that employ a standardized camera trapping protocol, and we compute data analytics that correct for imperfect detection. We found that occupancy declined in 22%, increased in 17%, and exhibited no change in 22% of populations during the last 3–8 years, while 39% of populations were detected too infrequently to assess occupancy changes. Despite extensive variability in occupancy trends, these 15 tropical protected areas have not exhibited systematic declines in biodiversity (i.e., occupancy, richness, or evenness) at the community level. Our results differ from reports of widespread biodiversity declines based on aggregated secondary data and expert opinion and suggest less extreme deterioration in tropical forest protected areas. We simultaneously fill an important conservation data gap and demonstrate the value of large-scale monitoring infrastructure and powerful analytics, which can be scaled to incorporate additional sites, ecosystems, and monitoring methods. In an era of catastrophic biodiversity loss, robust indicators produced from standardized monitoring infrastructure are critical to accurately assess population outcomes and identify conservation strategies that can avert biodiversity collapse.