Measuring biodiversity to explain community assembly: a unified approach

Intercontinental trends in functional and phylogenetic structure of stream fish assemblages

Understanding of community assembly has been improved by phylogenetic and trait-based approaches, yet there is little consensus regarding the relative importance of alternative mechanisms and few studies have been done at large geographic and phylogenetic scales. Here, we use phylogenetic and trait dispersion approaches to determine the relative contribution of limiting similarity and environmental filtering to community assembly of stream fishes at an intercontinental scale. We sampled stream fishes from five zoogeographic regions. Analysis of traits associated with habitat use, feeding, or both resulted in more occurrences of trait underdispersion than overdispersion regardless of spatial scale or species pool. Our results suggest that environmental filtering and, to a lesser extent, species interactions were important mechanisms of community assembly for fishes inhabiting small, low-gradient streams in all five regions. However, a large proportion of the trait dispersion values were no different from random. This suggests that stochastic factors or opposing assembly mechanisms also influenced stream fish assemblages and their trait dispersion patterns. Local assemblages tended to have lower functional diversity in microhabitats with high water velocity, shallow water depth, and homogeneous substrates lacking structural complexity, lending support for the stress-dominance hypothesis. A high prevalence of functional underdispersion coupled with phylogenetic underdispersion could reflect phylogenetic niche conservatism and/or stabilizing selection. These findings imply that environmental filtering of stream fish assemblages is not only deterministic, but also influences assemblage structure in a fairly consistent manner worldwide.

Assessing the utility of conserving evolutionary history

It is often claimed that conserving evolutionary history is more efficient than species-based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human-centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile. Most - but not all - arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity-ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.

Trait probability density (TPD): measuring functional diversity across scales based on TPD with R

Functional diversity (FD) has the potential to address many ecological questions, from impacts of global change on biodiversity to ecological restoration. There are several methods estimating the different components of FD. However, most of these methods can only be computed at limited spatial scales and cannot account for intraspecific trait variability (ITV), despite its significant contribution to FD. Trait probability density (TPD) functions (which explicitly account for ITV) reflect the probabilistic nature of niches. By doing so, the TPD approach reconciles existing methods for estimating FD within a unifying framework, allowing FD to be partitioned seamlessly across multiple scales (from individuals to species, and from local to global scales), and accounting for ITV. We present methods to estimate TPD functions at different spatial scales and probabilistic implementations of several FD concepts, including the primary components of FD (functional richness, evenness, and divergence), functional redundancy, functional rarity, and solutions to decompose beta FD into nested and unique components. The TPD framework has the potential to unify and expand analyses of functional ecology across scales, capturing the probabilistic and multidimensional nature of FD. The R package TPD (https://CRAN.R-project.org/package=TPD) will allow users to achieve more comparative results across regions and case studies.

Reconciling the concepts and measures of diversity, rarity and originality in ecology and evolution

The concept of biological diversity, or biodiversity, is at the core of evolutionary and ecological studies. Many indices of biodiversity have been developed in the last four decades, with species being one of the central units of these indices. However, evolutionary and ecological studies need a precise description of species' characteristics to best quantify inter-species diversity, as species are not equivalent and exchangeable. One of the first concepts characterizing species in biodiversity studies was abundance-based rarity. Abundance-based rarity was then complemented by trait- and phylo-based rarity, called species' trait-based and phylogenetic originalities, respectively. Originality, which is a property of an individual species, represents a species' contribution to the overall diversity of a reference set of species. Originality can also be defined as the rarity of a species' characteristics such as the state of a functional trait, which is often assumed to be represented by the position of the species on a phylogenetic tree. We review and compare various approaches for measuring originality, rarity and diversity and demonstrate that (i) even if attempts to bridge these concepts do exist, only a few ecological and evolutionary studies have tried to combine them all in the past two decades; (ii) phylo- and trait-based diversity indices can be written as a function of species rarity and originality measures in several ways; and (iii) there is a need for the joint use of these three types of indices to understand community assembly processes and species' roles in ecosystem functioning in order to protect biodiversity efficiently.

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

PREMISE

At the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high alpine flora in the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.

METHODS

We used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assessed whether maximum elevation explains phylogenetic structure. To evaluate similarities between summits, we quantified phylogenetic turnover, taking into consideration microhabitats (talus vs. meadows).

RESULTS

We found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely not different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: overdispersion degraded as elevation increased. Between summits, we found high phylogenetic turnover driven by greater niche heterogeneity on summits with alpine meadows.

CONCLUSIONS

Our results provide further evidence that stochastic processes may also play an important role in the assembly of vascular plant communities in high alpine habitats at regional scales. However, order-specific patterns suggest that adaptations are still important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important in disentangling the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

Mapping Soil Biodiversity in Europe and the Netherlands

Soil is fundamental for the functioning of terrestrial ecosystems, but our knowledge about soil organisms and the habitat they provide (shortly: Soil biodiversity) is poorly developed. For instance, the European Atlas of Soil Biodiversity and the Global Soil Biodiversity Atlas contain maps with rather coarse information on soil biodiversity. This paper presents a methodology to map soil biodiversity with limited data and models. Two issues were addressed. First, the lack of consensus to quantify the soil biodiversity function and second, the limited data to represent large areas. For the later issue, we applied a digital soil mapping (DSM) approach at the scale of the Netherlands and Europe. Data of five groups of soil organisms (earthworms, enchytraeids, micro-arthropods, nematodes, and micro-organisms) in the Netherlands were linked to soil habitat predictors (chemical soil attributes) in a regression analysis. High-resolution maps with soil characteristics were then used together with a model for the soil biodiversity function with equal weights for each group of organisms. To predict soil biodiversity at the scale of Europe, data for soil biological (earthworms and bacteria) and chemical (pH, soil organic matter, and nutrient content) attributes were used in a soil biodiversity model. Differential weights were assigned to the soil attributes after consulting a group of scientists. The issue of reducing uncertainty in soil biodiversity modelling and mapping by the use of data from biological soil attributes is discussed. Considering the importance of soil biodiversity to support the delivery of ecosystem services, the ability to create maps illustrating an aggregate measure of soil biodiversity is a key to future environmental policymaking, optimizing land use, and land management decision support taking into account the loss and gains on soil biodiversity.

Land-sparing agriculture sustains higher levels of avian functional diversity than land sharing

The ecological impacts of meeting rising demands for food production can potentially be mitigated by two competing land-use strategies: off-setting natural habitats through intensification of existing farmland (land sparing), or elevating biodiversity within the agricultural matrix via the integration of "wildlife-friendly" habitat features (land sharing). However, a key unanswered question is whether sparing or sharing farming would best conserve functional diversity, which can promote ecosystem stability and resilience to future land-use change. Focusing on bird communities in tropical cloud forests of the Colombian Andes, we test the performance of each strategy in conserving functional diversity. We show that multiple components of avian functional diversity in farmland are positively related to the proximity and extent of natural forest. Using landscape and community simulations, we also show that land-sparing agriculture conserves greater functional diversity and predicts higher abundance of species supplying key ecological functions than land sharing, with sharing becoming progressively inferior with increasing isolation from remnant forest. These results suggest low-intensity agriculture is likely to conserve little functional diversity unless large blocks of adjacent natural habitat are protected, consistent with land sparing. To ensure the retention of functionally diverse ecosystems, we urgently need to implement mechanisms for increasing farmland productivity whilst protecting spared land.

Ecological filtering in scrub fragments restructures the taxonomic and functional composition of native bee assemblages

Predicting the long-term consequences of habitat alteration for the preservation of biodiversity and ecosystem function requires an understanding of how ecological filters drive taxonomic and functional biodiversity loss. Here, we test a set of predictions concerning the role of ecological filters in restructuring native bee assemblages inhabiting fragmented coastal sage scrub ecosystems in southern California, USA. In 2011 and 2012, we collected native bees in scrub habitat belonging to two treatment categories: large natural reserves and small habitat fragments embedded in an urban landscape. We compared bee assemblages in reserve and fragment sites with respect to their taxonomic and functional alpha diversity, beta diversity, assemblage composition, and mean geographical range size estimated via distribution maps compiled for this study from digitized specimen records. We found multiple lines of evidence that ecological filtering drove bee diversity loss in fragments: a disproportionate loss of functional diversity relative to taxonomic diversity, shifts in assemblage composition driven largely by the preferential extirpation of reserve-associated indicator species, and disproportionate loss of range-restricted species. However, we found no evidence of taxonomic or functional homogenization across fragment bee assemblages, suggesting that filtering was not sufficiently strong to cause a subset of functional traits (and their associated species) to dominate assemblages in fragments. Our results suggest that ecological filtering altered bee assemblages in habitat fragments, even when such fragments contained well-preserved native plant assemblages, underscoring the importance of preserving large areas of natural habitat for the conservation of bees (especially range-restricted taxa) and their associated ecological functions.

Different roles for geography, energy and environment in determining three facets of freshwater molluscan beta diversity at broad spatial scales

Current understanding of different facets of beta diversity and their underlying determinants remains limited at broad scales in the freshwater realm. We examined the geographical patterns and spatial congruence of three beta diversity facets of freshwater molluscs across all of China, and evaluated the relative importance of environmental and spatial factors underlying the observed patterns. Taxonomic (β-TD), functional (β-FD) and phylogenetic (β-PD) beta diversity were calculated for 212 drainage basins belonging to 10 hydrographic regions using compiled occurrence data of 313 molluscan species. Geographical patterns of the three diversity facets were visualized on maps and pairwise spatial congruence among them was evaluated using regression on distance matrices. Variation partitioning and multivariate regression trees were used to assess the relative importance of different factors underlying beta diversity patterns. Beta diversity maps revealed that geographical patterns of β-TD and β-PD showed strong spatial clustering and were well matched with hydrographic regions' boundaries, while β-FD showed only moderate spatial aggregation. The three facets were only moderately congruent, with over 60% of the variation in one facet remaining unexplained by any other facet. Remarkably, all diversity facets were best explained by the spatial factors with considerable unique effects. Environmental filtering associated with energy gradients also made a large contribution, while habitat availability only explained minor fractions of the variation in beta diversity. At the national scale, β-TD and β-PD were more strongly related to spatial processes, whereas β-FD was more strongly associated with energy gradients. Our results suggested that, for freshwater organisms with low dispersal capacity, dispersal processes may override environmental filtering in driving geographical diversity patterns. However, different ecological drivers were important for each diversity facet. Importantly, rather weak spatial congruence among the different diversity facets stresses the need to incorporate functional and phylogenetic facets into the development of conservation planning.

An ordination approach to explore similarities among communities

Analysis of similarities among communities can help to decipher the biogeographical, evolutionary, and ecological factors that drive local diversity. Recent indices of similarity among communities incorporate not only information on species presence and abundance but also information on how similar species are in their traits and how closely related they are in terms of taxonomy or phylogeny. Towards this aim, trait-based, taxonomic or phylogenetic similarities among species have been defined and bounded between 0 (species are maximally distinct) and 1 (species are similar). A required property for an index of similarity between two communities is that it must provide minimum similarity (0) where communities have maximally distinct species, as well as maximum similarity (1) where communities are equivalent in their trait, taxonomic or phylogenetic compositions. Here, I developed a new ordination methodology that conforms to the requirement: double similarity principal component analysis (DSPCA). DSPCA summarizes multidimensional trait-based, taxonomic or phylogenetic similarities among communities into orthogonal axes. The species that drive each similarity pattern can be identified together with their traits or with their taxonomic or phylogenetic positions. I applied this methodology to theoretical examples and to empirical data sets on bird and bat communities to illustrate key properties of DSPCA. I compared the results obtained with DSPCA with those provided by related approaches. Theoretical and empirical case studies highlight the following additional properties of DSPCA: (i) axes are orthogonal and identify independent (dis)similarity patterns between communities; (ii) the more functionally, taxonomically or phylogenetically similar communities are, the closer they are on an axis; (iii) the coordinate of a species on an axis expresses how representative the species is of the pattern identified by the axis; and (iv) a species is representative of x communities if the functional, taxonomic or phylogenetic characteristics of this species are very common within each of these x communities. DSPCA is an efficient approach to visualize functional, taxonomic and phylogenetic similarities between communities. It is also a useful alternative to recent methods dedicated to phylogenetic diversity patterns. It will be an asset for all studies that aim to compare functional, taxonomic, genetic and phylogenetic diversity.

Univariate Community Assembly Analysis (UniCAA): Combining hierarchical models with null models to test the influence of spatially restricted dispersal, environmental filtering, and stochasticity on community assembly

Identifying the influence of stochastic processes and of deterministic processes, such as dispersal of individuals of different species and trait-based environmental filtering, has long been a challenge in studies of community assembly. Here, we present the Univariate Community Assembly Analysis (UniCAA) and test its ability to address three hypotheses: species occurrences within communities are (a) limited by spatially restricted dispersal; (b) environmentally filtered; or (c) the outcome of stochasticity-so that as community size decreases-species that are common outside a local community have a disproportionately higher probability of occurrence than rare species. The comparison with a null model allows assessing if the influence of each of the three processes differs from what one would expect under a purely stochastic distribution of species. We tested the framework by simulating "empirical" metacommunities under 15 scenarios that differed with respect to the strengths of spatially restricted dispersal (restricted vs. not restricted); habitat isolation (low, intermediate, and high immigration rates); and environmental filtering (strong, intermediate, and no filtering). Through these tests, we found that UniCAA rarely produced false positives for the influence of the three processes, yielding a type-I error rate ≤5%. The type-II error rate, that is, production of false negatives, was also acceptable and within the typical cutoff (20%). We demonstrate that the UniCAA provides a flexible framework for retrieving the processes behind community assembly and propose avenues for future developments of the framework.

Historical biogeography of fishes from coastal basins of Maranhão State, northeastern Brazil

ABSTRACT The Amazonian ichthyofauna is one of the most diverse in the world, yet fishes from the adjacent coastal basins of Maranhão State in Northeastern Brazil remain poorly known. We use phylogeographic, community phylogenetic and phylogenetic beta diversity methods to study the biogeographic history of fishes from the coastal basins of Maranhão State. We report a total of 160 fish species from the basins of the Maranhão region, representing a 93% increase over results of previous studies. All the fish species assemblages from Maranhão are polyphyletic, with only a few putative sister species pairs inhabiting the region. The modern watershed divides among Maranhão basins do not form substantial barriers to dispersal for freshwater fish species, and are more effectively modelled as biogeographic islands than as biogeographic provinces. In combination these results suggest that the Maranhão ichthyofauna was assembled under the influence of several macroevolutionary (extinction, dispersal) and landscape evolution processes, during the Miocene and Pliocene, as well as by the modern ecological characteristics of the region. The results indicate that the distinctive geological and climatic conditions and history of Northeastern Brazil strongly constrained the formation of aquatic faunas in coastal basins of Maranhão State.

Change in fish functional diversity and assembly rules in the course of tidal marsh restoration

Functional trait theory provides a mechanistic framework to understand change in community composition and community assembly through time and space. Despite this, trait-based approaches have seldom been used in ecological restoration. Succession theory predicts that habitat complexity and resource availability will increase with restoration time, leading to increased functional dissimilarity among coexisting species. However, in the case of tidal marsh restoration, it is not clear whether reestablishing the harsh abiotic conditions typical of estuaries will initiate successional trajectories. We investigated monotonic changes in the functional structure of fish communities and shifts in assembly mechanisms, with tidal restoration time. A five-level gradient of ‘intertidal habitat naturalness’ was constructed from a set of artificialized (dyked), restored (with different ages) and natural intertidal sites, and used as a surrogate for restoration progress. The fish ecophases were described using ten functional traits related to food acquisition and swimming ability. The trends in six functional dimensions (identity, richness, evenness, dispersion, originality and specialization) were investigated along the naturalness gradient. Consistenly with succession theory, functional specialization, dispersion and, less markedly, richness increased with intertidal naturalness meaning that restored and natural intertidal habitats supplied fish with specific foraging and dwelling conditions absent from dyked marshes. Community assembly patterns varied with respect to traits and differed at both ends of the naturalness gradient. Dyked marshes were more affected by trait convergence possibly due to limiting resources. Environmental filtering was detected all along the naturalness gradient although the traits affected varied depending on the naturalness level of habitats. Environmental filtering tended to decrease in restored and natural intertidal habitats. Increased naturalness restored the attractivity of benthic habitats as feeding or settling grounds, promoted shelter-seeking vs. free-swimming strategists and favoured ecophases with carnivorous diets, feeding on microinvertebrates and benthic low-mobility macroinvertebrates. Approaches based on functional trait diversity have the potential to question and refine the theoretical frame of ecological restoration and to assist managers in their efforts to restore tidal wetlands.

Consequences of shade management on the taxonomic patterns and functional diversity of termites (Blattodea: Termitidae) in cocoa agroforestry systems

Termites have gained importance as major pests in cocoa agroforests. Proper identification of termite species and knowledge on their functional diversity are the first steps in developing environmentally compatible management strategies. We tested the hypothesis that patterns of termite species richness in different cocoa agroforests is related to responses by termite functional groups to changes in shade management. We compared termite assemblages under five cocoa agroforestry systems in Cameroon to assess the impact of shade on termite taxonomic and functional group diversity. Sampling was done using a modified standardized transect method. Two 30 × 30 m quadrates each divided into three transects were laid in four farms at each site. Termites sampled were identified and grouped according to habitats, functional groups, and feeding habits. Sixty-nine termite species in 33 genera and five subfamilies under two families were sampled. Termitidae was the most dominant family and Rhinotermitidae the least dominant with few species. Termite species richness decreased significantly from the heavy shaded cocoa agroforests (44 species) to the full sun (11 species). Functional group pattern differed significantly in all the cocoa agroforests and within each agroforestry system and dominated by wood and litter feeder species. Many species belonging to this group were responsible to most damages on cocoa trees. Both the richness of termite pests and marketable yield followed a quadratic curve and were found to be lowest and highest in plots with shade cover above 40%. The simulated optimal shade levels for low termite infestations and marketable yield overlapped between 45% and 65% indicating that cocoa agroforestry systems with around 55% shade cover may be optimal to balance termite infestations and marketable yield. Shade maintenance in cocoa agroforests is valuable in reducing termite pest species and conserving soil feeding termites which provide beneficial ecosystem services.

Towards an eco-evolutionary understanding of endemism hotspots and refugia

BACKGROUND

Refugia are island-like habitats that are linked to long-term environmental stability and, as a result, high endemism. Conservation of refugia and endemism hotspots should be based on a deep ecological and evolutionary understanding of their functioning, which remains limited. Although functional traits can provide such insights, a corresponding, coherent framework is lacking.

PROPOSED FRAMEWORK

Plant communities in refugia and endemism hotspots should, due to long-term environmental stability, display unique functional characteristics linked to distinct phylogenetic patterns. Therefore, such communities should be characterized by a functional signature that exhibits: (1) distinct values and combinations of traits, (2) higher functional diversity and (3) a prevalence of similar traits belonging to more distantly related lineages inside, compared to outside, of endemism hotspots and refugia. While the limited functional trait data available from refugia and endemism hotspots do not allow these predictions to be tested rigorously, three potential applications of the functional signature in biogeography and conservation planning are highlighted. Firstly, it allows the functional characteristics of endemism hotspots and refugia to be identified. Secondly, the strength of the functional signature can be compared among these entities, and with the surrounding landscape, to provide an estimate of the capacity of endemism hotspots and refugia to buffer environmental changes. Finally, the pattern of the functional signature can reveal ecological and evolutionary processes driving community assembly and functioning, which can assist in predicting the effect of environmental changes (e.g. climate, land-use) on communities in endemism hotspots and refugia.

CONCLUSION

The proposed functional signature concept allows the systematic integration of plant functional traits and phylogeny into the study of endemism hotspots and refugia, but more data on functional traits in these entities are urgently needed. Overcoming this limitation would facilitate rigorous testing of the proposed predictions for the functional signature, advancing the eco-evolutionary understanding of endemism hotspots and refugia.

Divergent trends in functional and phylogenetic structure in reptile communities across Africa

Despite extensive research on ecological community compositions, general patterns across large-scale environmental gradients have remained unclear. A widely used explanatory model is the stress dominance hypothesis (SDH), predicting that the relative influence of environmental filtering is greater in stressful habitats while competition is more important in benign environments. Here, we test the SDH using African squamates as a model system to facilitate general predictions on community structures amidst changing global environments. For the first time we investigate changes in functional, phylogenetic and species diversity across continental, environmental gradients within a multidimensional, phylogenetically informed approach. Results suggest that phylogenetic patterns of African squamates were likely shaped by clade-specific biogeographic histories, whereas functional structure reflects SDH predictions. We further detected significant structuring at both local and regional spatial scales, emphasizing the impact of regional-historical processes on local assemblages, and the need for broad conceptual frameworks to detect general patterns of community composition.

The biogeographic drivers of reptile diversity are poorly understood relative to other animal groups. Here, using a dataset of distributions of African squamates, the authors show that environmental filtering explains diversity in stressful habitats while competition explains diversity in benign habitats.

Past is prologue: host community assembly and the risk of infectious disease over time

Infectious disease risk is often influenced by host diversity, but the causes are unresolved. Changes in diversity are associated with changes in community structure, particularly during community assembly; therefore, by incorporating change over time, host community assembly may provide a framework to resolve causation. In turn, community assembly can be driven by many processes, including resource enrichment. To test the hypothesis that community assembly causally links host diversity to future disease, we experimentally manipulated host diversity and resource supply to hosts, then allowed communities to assemble for 2 years (surveyed 2012-2014). Initially, host diversity increased disease. Subsequently, host diversity did not directly alter disease. However, host diversity determined the trajectory of host community assembly, altering colonisation by exotic host species and richness-independent host phylogenetic diversity, which together reversed the initial increase in disease. Ultimately, incorporating the temporal dimension of community assembly revealed novel mechanisms linking host diversity to future disease.

Elevational and Possible Bushmeat Exploitation Effects on Dung Beetle (Scarabaeidae: Scarabaeinae) Communities on Mount Cameroon, West Central Africa

Dung beetle species richness and abundance on Mt Cameroon were investigated to evaluate the effects of elevation. Surveys were done at five different elevations on the southwest facing slope from 216 to 2,102 m above sea level near the tree line at intervals of ~500 m. In total, 27 species and 1,886 specimens were collected during the study. No linear relationship between either species richness or beetle abundance and elevation was found with an expected highest diversity and abundance at low elevation and the lowest diversity and abundance at high elevation. Instead, both the highest diversity and abundance were discovered at the middle elevation (914-1,012 m) with 22 species and 48% of the total catch. The highest diversity indices (Shannon and Simpson) were found at the second lowest elevation (522-625 m). The lowest diversity found at the highest elevation (1,974-2,101 m) included only two species and represented only 4% of the beetles sampled. Unexpected low diversity and abundance at the lowest elevation are hypothesized to be due at least in part to the effects of bushmeat hunting in the more accessible lower elevations and the concomitant effects on dung beetles that mainly utilize mammal dung. The most similar faunas based on Morisita-Horn paired comparisons were those at the two highest and the two lowest elevations while the most dissimilar were the middle compared with the highest elevation. Faunas appear to be divided into high and low elevation communities with a boundary or division at c.1,500-1,750 m elevation.

Increased anthropogenic disturbance and aridity reduce phylogenetic and functional diversity of ant communities in Caatinga dry forest

Anthropogenic disturbance and climate change are major threats to biodiversity. The Brazilian Caatinga is the world's largest and most diverse type of seasonally dry tropical forest. It is also one of the most threatened, but remains poorly studied. Here, we analyzed the individual and combined effects of anthropogenic disturbance (three types: livestock grazing, wood extraction, and miscellaneous use of forest resources) and increasing aridity on taxonomic, phylogenetic and functional ant diversity in the Caatinga. We found no aridity and disturbance effects on taxonomic diversity. In spite of this, functional diversity, and to a lesser extent phylogenetic diversity, decreased with increased levels of disturbance and aridity. These effects depended on disturbance type: livestock grazing and miscellaneous resource use, but not wood extraction, deterministically filtered both components of diversity. Interestingly, disturbance and aridity interacted to shape biodiversity responses. While aridity sometimes intensified the negative effects of disturbance, the greatest declines in biodiversity were in the wettest areas. Our results imply that anthropogenic disturbance and aridity interact in complex ways to endanger biodiversity in seasonally dry tropical forests. Given global climate change, neotropical semi-arid areas are habitats of concern, and our findings suggest Caatinga conservation policies must prioritize protection of the wettest areas, where biodiversity loss stands to be the greatest. Given the major ecological relevance of ants, declines in both ant phylogenetic and functional diversity might have downstream effects on ecosystem processes, insect populations, and plant populations.

Prioritizing phylogenetic diversity captures functional diversity unreliably

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the “phylogenetic gambit”. Here, we empirically test this gambit using data on ecologically relevant traits from >15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy.

An ongoing conservation question is if we can maintain functional diversity by optimizing for preservation of phylogenetic diversity. Here, Mazel et al. show that functional diversity increases with phylogenetic diversity in some clades but not others, and thus could be a risky conservation strategy.

Effects of patch size and basal area on avian taxonomic and functional diversity in pine forests: Implication for the influence of habitat quality on the species-area relationship

Relationships between avian diversity and habitat area are assumed to be positive; however, often little attention has given to how these relationships can be influenced by the habitat structure or quality. In addition, other components of biodiversity, such as functional diversity, are often overlooked in assessing habitat patch value. In the Sandhills Ecoregion of Georgia, USA, we investigated the relationship between avian species richness and functional diversity, forest basal area, and patch size in pine forests using basal area as a surrogate for overstory structure which in turn impacts vegetation structure and determines habitat quality within a patch. We conducted bird surveys in planted mature pine stands, during breeding season of 2011. We used three classes of stand basal area (BA): OS, overstocked (BA ≥ 23 m2/ha); FS, fully/densely stocked (13.8 m2/ha ≤ BA < 23 m2/ha); and MS, moderately stocked (2.3 m2/ha ≤ BA < 13.8 m2/ha). MS patches showed more structural diversity due to higher herbaceous vegetation cover than other two pine stocking classes of patches. Total species richness and functional richness increased with the size of MS patches, whereas functional divergence decreased with the size of OS patches (p < 0.05). Functional richness tended to be lower than expected as the size of OS patches increased. Greater richness of pine-grassland species was also found at MS patches. Percent cover of MS patches within a landscape influenced positively the richness of pine-grassland species (p < 0.05). Our results suggest that (a) avian species-habitat area relationship can be affected by habitat quality (structural diversity) and varies depending on diversity indices considered, and (b) it is important to maintain moderate or low levels of pine basal area and to preserve large-sized patches of the level of basal area to enhance both taxonomic and functional diversity in managed pine forests.

Bird diversity and dissimilarity show contrasting patterns along heavy metal pollution gradients in the Urals, Russia

The effects of industrial pollution on bird diversity have been widely studied using traditional diversity measures, which assume all species to be equivalent. We compared species richness and Shannon index with distance-based measures of taxonomic, functional, and phylogenetic diversity (the abundance-weighted mean nearest taxon distances), which describe within-community dissimilarity at terminal branches. Analysis of dissimilarity can shed light on the processes underlying community assembly, i.e., environmental filtering decreases dissimilarity whereas competitive exclusion increases it. In the 2-year study near Karabash and Revda copper smelters in Russia, point counts of nesting birds and habitat descriptions were taken at 10 sites (40 plots) along each pollution gradient. The abundance and diversity of birds showed good repeatability in both regions. The total density of birds, number of species per plot, and Shannon diversity decreased at high toxic load in both regions. The taxonomic, functional, and phylogenetic nearest taxon distances showed the same pattern within regions. Species dissimilarity within communities increased with pollution in Karabash (due to loss of functionally similar species), but did not change in Revda (due to mass replacement of forest species by species of open habitats). Pollution-induced changes in bird communities near Karabash were greater due to the stronger deterioration of the forest ecosystems and less favorable natural conditions (more arid climate, lower diversity and vitality of the tree stand and understorey) compared to Revda. This study emphasizes the need for a multi-level approach to the analysis of bird communities using traditional indices of diversity, functional, taxonomic, or phylogenetic distances between species and environmental variables.

Phytoregionalisation of the Andean páramo

Background

The páramo is a high-elevation biogeographical province in the northern Andes, known for its great biodiversity and ecosystem services. Because there have been very few biogeographic studies encompassing the entire province to date, this study aimed at conducting a phytogeographical regionalisation of the páramo. Specifically, (1) clustering analyses were conducted to identify the main phytogeographical units in the three altitudinal belts: sub-páramo, mid-páramo and super-páramo, and examine their diagnostic flora, (2) an ordination complemented the geo-climatic characterization of the obtained units and (3) a hierarchical classification transformation was obtained to evaluate the relationships between units.

Methods

The study area included the entire Andean páramo range in northern Peru, Ecuador, Colombia and Venezuela. The analyses were based on 1,647 phytosociological plots from the VegPáramo database. The K-means non-hierarchical clustering technique was used to obtain clusters identifiable as phytogeographical units, and the Ochiai fidelity index was calculated to identify their diagnostic species. A principal component analysis was conducted to obtain the geo-climatic characterization of each unit. Finally, the relationships between clusters were traced using a hierarchical plot-based classification.

Results

Fifteen clusters were obtained, 13 natural and two artificial, of which two represented the sub-páramo, nine the mid-páramo and four the super-páramo. Even though data representativeness was a potential limitation to segregate certain sub-páramo and super-páramo units, the overall bioregionalisation was robust and represented important latitudinal, altitudinal and climatic gradients.

Discussion

This study is the first to bioregionalise the páramo province based on a substantial widely distributed biological dataset, and therefore provides important novel scientific insight on its biogeography. The obtained phytogeographical units can be used to support further research on the páramo at smaller scale and on the humid Neotropical high-elevation ecosystems at broader-scale. Finally, several units were highlighted in our results as particularly worthy of further scientific and conservation focus.

Trait and phylogenetic diversity provide insights into community assembly of reef-associated shrimps (Palaemonidae) at different spatial scales across the Chagos Archipelago

Coral reefs are the most biodiverse marine ecosystem and one of the most threatened by global climate change impacts. The vast majority of diversity on reefs is comprised of small invertebrates that live within the reef structure, termed the cryptofauna. This component of biodiversity is hugely understudied, and many species remain undescribed. This study represents a rare analysis of assembly processes structuring a distinct group of cryptofauna, the Palaemonidae, in the Chagos Archipelago, a reef ecosystem under minimal direct human impacts in the central Indian Ocean. The Palaemonidae are a diverse group of Caridae (infraorder of shrimps) that inhabit many different niches on coral reefs and are of particular interest because of their varied habitat associations. Phylogenetic and trait diversity and phylogenetic signal were used to infer likely drivers of community structure. The mechanisms driving palaemonid community assembly and maintenance in the Chagos Archipelago showed distinct spatial patterns. At local scales, among coral colonies and among reefs fringing individual atolls, significant trait, and phylogenetic clustering patterns suggest environmental filtering may be a dominant ecological process driving Palaemonidae community structure, although local competition through equalizing mechanisms may also play a role in shaping the local community structure. Importantly, we also tested the robustness of phylogenetic diversity to changes in evolutionary information as multi‐gene phylogenies are resource intensive and for large families, such as the Palaemonidae, are often incomplete. These tests demonstrated a very modest impact on phylogenetic community structure, with only one of the four genes (PEPCK gene) in the phylogeny affecting phylogenetic diversity patterns, which provides useful information for future studies on large families with incomplete phylogenies. These findings contribute to our limited knowledge of this component of biodiversity in a marine locality as close to undisturbed by humans as can be found. It also provides a rare evaluation of phylogenetic diversity methods.

Traits Without Borders: Integrating Functional Diversity Across Scales

Owing to the conceptual complexity of functional diversity (FD), a multitude of different methods are available for measuring it, with most being operational at only a small range of spatial scales. This causes uncertainty in ecological interpretations and limits the potential to generalize findings across studies or compare patterns across scales. We solve this problem by providing a unified framework expanding on and integrating existing approaches. The framework, based on trait probability density (TPD), is the first to fully implement the Hutchinsonian concept of the niche as a probabilistic hypervolume in estimating FD. This novel approach could revolutionize FD-based research by allowing quantification of the various FD components from organismal to macroecological scales, and allowing seamless transitions between scales.

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

Although spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scales, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic turnover across phylogenetic scales, accounting for covariation with environmental differences. We compared phylogenetic turnover, at the species- and individual-level, within and between five successional stages, representing woody plant communities in a subtropical forest chronosequence. We decomposed turnover at different phylogenetic depths and assessed its covariation with between-plot abiotic differences. Phylogenetic turnover between stages was low relative to species turnover and was not explained by abiotic differences. However, within the late-successional stages, there was high presence-/absence-based turnover (clustering) that occurred deep in the phylogeny and covaried with environmental differentiation. Our results support a deterministic model of community assembly where (i) phylogenetic composition is constrained through successional time, but (ii) toward late succession, species sorting into preferred habitats according to niche traits that are conserved deep in phylogeny, becomes increasingly important.

The effects of restoring logged tropical forests on avian phylogenetic and functional diversity

Selective logging is the most prevalent land-use change in the tropics. Despite the resulting degradation of forest structure, selectively logged forests still harbor a substantial amount of biodiversity leading to suggestions that their protection is the next best alternative to conserving primary, old-growth forests. Restoring carbon stocks under Reducing Emissions from Deforestation and Forest Degradation (REDD+) schemes is a potential method for obtaining funding to protect logged forests, via enrichment planting and liberation cutting of vines. This study investigates the impacts of restoring logged forests in Borneo on avian phylogenetic diversity, the total evolutionary history shared across all species within a community, and on functional diversity, with important implications for the protection of evolutionarily unique species and the provision of many ecosystem services. Overall and understorey avifaunal communities were studied using point count and mist netting surveys, respectively. Restoration caused a significant loss in phylogenetic diversity and MPD (mean pairwise distance) leaving an overall bird community of less total evolutionary history and more closely related species compared to unlogged forests, while the understorey bird community had MNTD (mean nearest taxon distance) that returned toward the lower levels found in a primary forest, indicating more closely related species pairs. The overall bird community experienced a significant loss of functional strategies and species with more specialized traits in restored forests compared to that of unlogged forests, which led to functional clustering in the community. Restoration also led to a reduction in functional richness and thus niches occupied in the understorey bird community compared to unlogged forests. While there are additional benefits of restoration for forest regeneration, carbon sequestration, future timber harvests, and potentially reduced threat of forest conversion, this must be weighed against the apparent loss of phylogenetic and functional diversity from unlogged forest levels, making the biodiversity-friendliness of carbon sequestration schemes questionable under future REDD+ agreements. To reduce perverse biodiversity outcomes, it is important to focus restoration only on the most degraded areas or at reduced intensity where breaks between regimes are incorporated.