Niche overlap estimates based on quantitative functional traits: a new family of non-parametric indices

Thermocline stratification favors phytoplankton spatial overlap and species diversity in a subtropical deep reservoir

Spatial segregation of species along opposing resource gradients is a major research topic in ecology as it enables the coexistence and maintenance of high diversity. Thermocline stratification causes heterogeneous resource distribution, however, the effect of thermocline stratification on phytoplankton dynamic in-depth profiles is still unclear. To understand the underlying mechanism behind the effects of thermocline stratification on phytoplankton species diversity in stratified lakes, the monthly changes in thermocline parameters, deep chlorophyll maxima (DCM) parameters, spatial overlap (SO) among major phytoplankton taxonomic groups, and phytoplankton species diversity were evaluated in Lake Qiandaohu in the Zhejiang Province of China from April 2017 to December 2018. Thermocline depth (TD) was significantly negatively related to thermocline strength (TS). The monthly air temperature was the main driver behind the thermocline and the seasonal thermal-stratification cycle was divided into two stratification stages. Significant linear relationships were observed between the DCM parameters (depth, concentration, and thickness) and TD during the strong stratification period. TD was significantly positively related to phytoplankton species diversity and the SO between Cryptophyta and Chlorophyta as well as between Cryptophyta and Bacillariophyta during weak stratification periods. Significant positive correlations were observed between SO and Shannon diversity during both periods. Structural equation modeling (SEM) showed that air temperature significantly decreased TD and increased species diversity by increasing SO during the strong stratification period. Strong stratification under warming favored the formation of shallower and thinner DCMs, leading to phytoplankton coexistence and maintenance of high species diversity through a preclusion of dominance. This study characterized the temporal dynamics of phytoplankton dynamic in-depth profiles in response to strong stratification from warming.

Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change

Determining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.

Quaternary megafauna extinctions altered body size distribution in tortoises

The late Quaternary is characterized by the extinction of many terrestrial megafauna, which included tortoises (Family: Testudinidae). However, limited information is available on how extinction shaped the phenotype of surviving taxa. Here, based on a global dataset of straight carapace length, we investigate the temporal variation, spatial distribution and evolution of tortoise body size over the past 23 million years, thereby capturing the effects of Quaternary extinctions in this clade. We found a significant change in body size distribution characterized by a reduction of both mean body size and maximum body size of extant tortoises relative to fossil taxa. This reduction of body size occurred earlier in mainland (Early Pleistocene 2.588-0.781 Ma) than in island tortoises (Late Pleistocene/Holocene 0.126-0 Ma). Despite contrasting body size patterns between fossil and extant taxa on a spatial scale, tortoise body size showed limited variation over time until this decline. Body size is a fundamental functional trait determining many aspects of species ecologies, with large tortoises playing key roles as ecosystem engineers. As such, the transition from larger sized to smaller sized classes indicated by our findings likely resulted in the homogenization of tortoises' ecological functions and diminished the role of tortoises in structuring the vegetation community.

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties

Microbe–microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM’s followed the Taylor’s power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.

Advancing biological invasion hypothesis testing using functional diversity indices

Pioneering investigations on the effects of introduced populations on community structure, ecosystem functioning and services have focused on the effects of invaders on taxonomic diversity. However, taxonomic-based diversity metrics overlook the heterogeneity of species roles within and among communities. As the homogenizing effects of biological invasions on community and ecosystem processes can be subtle, they may require the use of functional diversity indices to be properly evidenced. Starting from the listing of major functional diversity indices, alongside the presentation of their strengths and limitations, we focus on studies pertaining to the effects of invasive species on native communities and recipient ecosystems using functional diversity indices. By doing so, we reveal that functional diversity of the recipient community may strongly vary at the onset of the invasion process, while it stabilizes at intermediate and high levels of invasion. As functional changes occurring during the lag phase of an invasion have been poorly investigated, we show that it is still unknown whether there are consistent changes in functional diversity metrics that could indicate the end of the lag phase. Thus, we recommend providing information on the invasion stage under consideration when computing functional diversity metrics. For the existing literature, it is also surprising that very few studies explored the functional difference between organisms from the recipient communities and invaders of the same trophic levels, or assessed the effects of non-native organism establishment into a non-analogue versus an analogue community. By providing valuable tools for obtaining in-depth diagnostics of community structure and functioning, functional diversity indices can be applied for timely implementation of restoration plans and improved conservation strategies. To conclude, our work provides a first synthetic guide for their use in hypothesis testing in invasion biology.

Variations in Functional Richness and Assembly Mechanisms of the Subtropical Evergreen Broadleaved Forest Communities along Geographical and Environmental Gradients

Linking functional trait space and environmental conditions can help to understand how species fill the functional trait space when species increase along environmental gradients. Here, we examined the variations in functional richness (FRic) and their correlations with key environmental variables in forest communities along latitudinal, longitudinal, and elevational gradients, by measuring seven functional traits of woody plants in 250 forest plots of 0.04 ha across five locations in the subtropical evergreen broadleaved forests (SEBLF) of China. On this basis, we explored whether environmental filtering constrained the functional volume by using a null model approach. Results showed that FRic decreased with increasing elevation and latitude, while it increased with increasing longitude, mirroring the geographical gradients in species richness. FRic was significantly related to precipitation of driest quarter, soil pH, and total phosphorus. Negative SES.FRic was prevalent (83.2% of the communities) in most SEBLF communities and was negatively related to mean diurnal range. Our study suggested that the geographical variation in the functional space occupied by SEBLF communities was affected mainly by climate and soil conditions. The results of the null model revealed that niche packing was dominant in SEBLF communities, highlighting the importance of environmental filtering in defining functional volume within SEBLF communities.

Effects of Vertical Spatial Overlap on Phytoplankton Diversity under Experimentally Altered Lake Stratification Regimes

In phytoplankton communities, competitive exclusion might occur when functionally similar species are impeded from regulating their positions along light and nutrient gradients to reduce niche overlap. Greater spatial overlap (SO) between species due to water column mixing could thus promote competitive exclusion, reducing community taxonomic diversity. However, greater SO could also promote coexistence of functionally different taxa. Using data from a whole-lake experiment, we investigated the effects of SO and other relevant environmental factors on phytoplankton diversity across the water columns of lake basins with different thermocline manipulations. We estimated SO using an in situ fluorometer, and overall community diversity microscopically. Using structured equation models, we estimated directional relationships between phytoplankton diversity, SO, the lake physical structure and the zooplankton community. No significant effect of SO on phytoplankton taxonomic diversity was observed, but higher SO was associated with greater functional diversity. Change in lake physical structure and in the zooplankton community also affected diversity, with a negative response to increased top-down interactions. Overall, despite the fact that the alteration of water column stratification structure and top-down interactions were stronger drivers of phytoplankton diversity in our system, some effect of spatial overlap on the outcome of inferred competitive interactions were observable.

Fine-root traits in the global spectrum of plant form and function

Plant traits determine how individual plants cope with heterogeneous environments. Despite large variability in individual traits, trait coordination and trade-offs^1,2 result in some trait combinations being much more widespread than others, as revealed in the global spectrum of plant form and function (GSPFF³) and the root economics space (RES⁴) for aboveground and fine-root traits, respectively. Here we combine the traits that define both functional spaces. Our analysis confirms the major trends of the GSPFF and shows that the RES captures additional information. The four dimensions needed to explain the non-redundant information in the dataset can be summarized in an aboveground and a fine-root plane, corresponding to the GSPFF and the RES, respectively. Both planes display high levels of species aggregation, but the differentiation among growth forms, families and biomes is lower on the fine-root plane, which does not include any size-related trait, than on the aboveground plane. As a result, many species with similar fine-root syndromes display contrasting aboveground traits. This highlights the importance of including belowground organs to the GSPFF when exploring the interplay between different natural selection pressures and whole-plant trait integration.

Diel niche variation in mammals associated with expanded trait space

Mammalian life shows huge diversity, but most groups remain nocturnal in their activity pattern. A key unresolved question is whether mammal species that have diversified into different diel niches occupy unique regions of functional trait space. For 5,104 extant mammals we show here that daytime-active species (cathemeral or diurnal) evolved trait combinations along different gradients from those of nocturnal and crepuscular species. Hypervolumes of five major functional traits (body mass, litter size, diet, foraging strata, habitat breadth) reveal that 30% of diurnal trait space is unique, compared to 55% of nocturnal trait space. Almost half of trait space (44%) of species with apparently obligate diel niches is shared with those that can switch, suggesting that more species than currently realised may be somewhat flexible in their activity patterns. Increasingly, conservation measures have focused on protecting functionally unique species; for mammals, protecting functional distinctiveness requires a focus across diel niches.

Intraspecific trait variability and community assembly in hawkmoths (Lepidoptera: Sphingidae) across an elevational gradient in the eastern Himalayas, India

We investigated some aspects of hawkmoth community assembly at 13 elevations along a 200- to 2770-m transect in the eastern Himalayas, a little studied biodiversity hot spot of global importance. We measured the morphological traits of body mass, wing loading, and wing aspect ratio of 3,301 free-ranging individuals of 76 species without having to collect or even constrain them. We used these trait measurements and T-statistic metrics to assess the strength of intracommunity ("internal") and extra-community ("external") filters which determine the composition of communities vis-a-vis the regional pool of species.The trait distribution of constituent species turned out to be nonrandom subsets of the community-trait distribution, providing strong evidence for internal filtering in all elevational communities. The external filter metric was more ambiguous. However, the elevational dependence of many metrics including that of the internal filter provided evidence for external (i.e., environmental) filtering. On average, a species occupied as much as 50%-75% of the total community-trait space, yet the T-statistic metric for internal filter was sufficiently sensitive to detect a strong nonrandom structure in the trait distribution.We suggest that the change in T-statistic metrics along the environmental gradient may provide more clues to the process of community assembly than previously envisaged. A large, smoothly varying and well-sampled environmental span would make it easier to discern them. Developing T-statistics for combined analysis of multiple traits will perhaps provide a more accurate picture of internal/filtering and niche complementarity. Moths are a hyperdiverse taxon and a very important component of many ecosystems. Our technique for accurately measuring body and wing dimensions of free-ranging moths can generate trait database for a large number of individuals in a time- and resource-efficient manner for a variety of community assembly studies using this important taxon.

Empirical support for the biogeochemical niche hypothesis in forest trees

The possibility of using the elemental compositions of species as a tool to identify species/genotype niche remains to be tested at a global scale. We investigated relationships between the foliar elemental compositions (elementomes) of trees at a global scale with phylogeny, climate, N deposition and soil traits. We analysed foliar N, P, K, Ca, Mg and S concentrations in 23,962 trees of 227 species. Shared ancestry explained 60-94% of the total variance in foliar nutrient concentrations and ratios whereas current climate, atmospheric N deposition and soil type together explained 1-7%, consistent with the biogeochemical niche hypothesis which predicts that each species will have a specific need for and use of each bio-element. The remaining variance was explained by the avoidance of nutritional competition with other species and natural variability within species. The biogeochemical niche hypothesis is thus able to quantify species-specific tree niches and their shifts in response to environmental changes.

How many submerged macrophyte species are needed to improve water clarity and quality in Yangtze floodplain lakes?

Successful re-establishment and maintenance of submerged macrophytes is a pivotal problem for the restoration of shallow eutrophic lakes, since submerged macrophytes can facilitate a shift of lake ecosystems from a turbid water state to a clear water state through their structuring roles. However, little is known about the optimal number of macrophyte species (species richness) needed for the recovery of shallow eutrophic lakes. Here, we investigated 19 shallow eutrophic lakes along the mid-lower reaches of the Yangtze River to reveal the underlying interrelations among water clarity, water quality and species richness. Our results showed positive correlations of water nutrients (TN and TP) with K_d and Red/Blue light ratio, suggesting that bad water quality can significantly lower water clarity. The results of path analysis indicated that the underwater light climate directly affects morphological and physiological traits and species richness of submerged macrophytes. Changes in functional traits also affected significantly the species richness of submerged macrophytes. Moreover, the presence of submerged macrophytes not only had positive effects on the underwater light climate (water clarity), but also on water quality. Most importantly, the assemblage of three or more submerged macrophyte species can significantly improve water clarity in these sampled eutrophic lakes, but not water quality. Additionally, the basic species assemblage of Myriophyllum spicatum and Vallisneria natans can be used for restoration of submerged macrophytes in shallow eutrophic Yangtze floodplain lakes. It is concluded that species richness and species assemblage are critical for recovery of submerged macrophytes in shallow eutrophic lakes.

Environmental niche patterns of native and non-native fishes within an invaded African river system

To test ecological niche theory, this study investigated the spatial patterns and the environmental niches of native and non-native fishes within the invaded Great Fish River system, South Africa. For the native fishes, there were contrasting environmental niche breadths that varied from being small to being large and overlapped for most species, except minnows that were restricted to headwater tributaries. In addition, there was high niche overlap in habitat association among fishes with similar distribution. It was therefore inferred that habitat filtering-driven spatial organisation was important in explaining native species distribution patterns. In comparison, most non-native fishes were found to have broad environmental niches and these fishes showed high tolerance to environmental conditions, which generally supported the niche opportunity hypothesis. The proliferation of multiple non-native fishes in the mainstem section suggest that they form a functional assemblage that is probably facilitated by the anthropogenic modification of flow regimes through inter-basin water transfer. Based on the distribution patterns observed in the study, it was inferred that there was a likelihood of negative interactions between native and non-native fishes. Such effects are likely to be exacerbated by altered flow regime that was likely to have negative implications for native ichthyofauna.

Different "metabolomic niches" of the highly diverse tree species of the French Guiana rainforests

Tropical rainforests harbor a particularly high plant diversity. We hypothesize that potential causes underlying this high diversity should be linked to distinct overall functionality (defense and growth allocation, anti-stress mechanisms, reproduction) among the different sympatric taxa. In this study we tested the hypothesis of the existence of a metabolomic niche related to a species-specific differential use and allocation of metabolites. We tested this hypothesis by comparing leaf metabolomic profiles of 54 species in two rainforests of French Guiana. Species identity explained most of the variation in the metabolome, with a species-specific metabolomic profile across dry and wet seasons. In addition to this “homeostatic” species-specific metabolomic profile significantly linked to phylogenetic distances, also part of the variance (flexibility) of the metabolomic profile was explained by season within a single species. Our results support the hypothesis of the high diversity in tropical forest being related to a species-specific metabolomic niche and highlight ecometabolomics as a tool to identify this species functional diversity related and consistent with the ecological niche theory.

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.

Niche partitioning of sympatric penguins by leapfrog foraging appears to be resilient to climate change

Interspecific competition can drive niche partitioning along multidimensional axes, including allochrony. Competitor matching will arise where the phenology of sympatric species with similar ecological requirements responds to climate change at different rates such that allochrony is reduced. Our study quantifies the degree of niche segregation in foraging areas and depths that arises from allochrony in sympatric Adélie and chinstrap penguins and explores its resilience to climate change. Three-dimensional tracking data were sampled during all stages of the breeding season and were used to parameterise a behaviour-based model that quantified spatial overlap of foraging areas under different scenarios of allochrony. The foraging ranges of the two species were similar within breeding stages, but differences in their foraging ranges between stages, combined with the observed allochrony of 28 days, resulted in them leapfrogging each other through the breeding season such that they were exploiting different foraging locations on the same calendar dates. Allochrony reduced spatial overlap in the peripheral utilisation distribution of the two species by 54.0% over the entire breeding season, compared to a scenario where the two species bred synchronously. Analysis of long-term phenology data revealed that both species advanced their laying dates in relation to October air temperatures at the same rate, preserving allochrony and niche partitioning. However, if allochrony is reduced by just a single day, the spatial overlap of the core utilisation distribution increased by an average of 2.1% over the entire breeding season. Niche partitioning between the two species by allochrony appears to be resilient to climate change and so competitor matching cannot be implicated in the observed population declines of the two penguin species across the Western Antarctic Peninsula.

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.

Intraspecific and interspecific competition induces density-dependent habitat niche shifts in an endangered steppe bird

Interspecific competition is a dominant force in animal communities that induces niche shifts in ecological and evolutionary time. If competition occurs, niche expansion can be expected when the competitor disappears because resources previously inaccessible due to competitive constraints can then be exploited (i.e., ecological release). Here, we aimed to determine the potential effects of interspecific competition between the little bustard (Tetrax tetrax) and the great bustard (Otis tarda) using a multidimensional niche approach with habitat distribution data. We explored whether the degree of niche overlap between the species was a density‐dependent function of interspecific competition. We then looked for evidences of ecological release by comparing measures of niche breadth and position of the little bustard between allopatric and sympatric situations. Furthermore, we evaluated whether niche shifts could depend not only on the presence of great bustard but also on the density of little and great bustards. The habitat niches of these bustard species partially overlapped when co‐occurring, but we found no relationship between degree of overlap and great bustard density. In the presence of the competitor, little bustard's niche was displaced toward increased use of the species' primary habitat. Little bustard's niche breadth decreased proportionally with great bustard density in sympatric sites, in consistence with theory. Overall, our results suggest that density‐dependent variation in little bustard's niche is the outcome of interspecific competition with the great bustard. The use of computational tools like kernel density estimators to obtain multidimensional niches should bring novel insights on how species' ecological niches behave under the effects of interspecific competition in ecological communities.

Intraspecific leaf trait variability along a boreal-to-tropical community diversity gradient

Disentangling the mechanisms that shape community assembly across diversity gradients is a central matter in ecology. While many studies have explored community assembly through species average trait values, there is a growing understanding that intraspecific trait variation (ITV) can also play a critical role in species coexistence. Classic biodiversity theory hypothesizes that higher diversity at species-rich sites can arise from narrower niches relative to species-poor sites, which would be reflected in reduced ITV as species richness increases. To explore how ITV in woody plant communities changes with species richness, we compiled leaf trait data (leaf size and specific leaf area) in a total of 521 woody plant species from 21 forest communities that differed dramatically in species richness, ranging from boreal to tropical rainforests. At each forest, we assessed ITV as an estimate of species niche breadth and we quantified the degree of trait overlap among co-occurring species as a measure of species functional similarity. We found ITV was relatively invariant across the species richness gradient. In addition, we found that species functional similarity increased with diversity. Contrary to the expectation from classic biodiversity theory, our results rather suggest that neutral processes or equalizing mechanisms can be acting as potential drivers shaping community assembly in hyperdiverse forests.

Trait variation and functional diversity maintenance of understory herbaceous species coexisting along an elevational gradient in Yulong Mountain, Southwest China

Characterizing trait variation across different ecological scales in plant communities has been viewed as a way to gain insights into the mechanisms driving species coexistence. However, little is known about how changes in intraspecific and interspecific traits across sites influence species richness and community assembly, especially in understory herbaceous communities. Here we partitioned the variance of four functional traits (maximum height, leaf thickness, leaf area and specific leaf area) across four nested biological scales: individual, species, plot, and elevation to quantify the scale-dependent distributions of understory herbaceous trait variance. We also integrated the comparison of the trait variance ratios to null models to investigate the effects of different ecological processes on community assembly and functional diversity along a 1200-m elevational gradient in Yulong Mountain. We found interspecific trait variation was the main trait variation component for leaf traits, although intraspecific trait variation ranged from 10% to 28% of total variation. In particular, maximum height exhibited high plasticity, and intraspecific variation accounted for 44% of the total variation. Despite the fact that species composition varied across elevation and species richness decreased dramatically along the elevational gradient, there was little variance at our largest (elevation) scale in leaf traits and functional diversity remained constant along the elevational gradient, indicating that traits responded to smaller scale influences. External filtering was only observed at high elevations. However, strong internal filtering was detected along the entire elevational gradient in understory herbaceous communities, possibly due to competition. Our results provide evidence that species coexistence in understory herbaceous communities might be structured by differential niche-assembled processes. This approach -- integrating different biological scales of trait variation -- may provide a better understanding of the mechanisms involved in the structure of communities.

The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models

Null models exploring species co-occurrence and trait-based limiting similarity are increasingly used to explore the influence of competition on community assembly; however, assessments of common models have not thoroughly explored the influence of variation in matrix size on error rates, in spite of the fact that studies have explored community matrices that vary considerably in size. To determine how smaller matrices, which are of greatest concern, perform statistically, we generated biologically realistic presence-absence matrices ranging in size from 3–50 species and sites, as well as associated trait matrices. We examined co-occurrence tests using the C-Score statistic and independent swap algorithm. For trait-based limiting similarity null models, we used the mean nearest neighbour trait distance (NN) and the standard deviation of nearest neighbour distances (SDNN) as test statistics, and considered two common randomization algorithms: abundance independent trait shuffling (AITS), and abundance weighted trait shuffling (AWTS). Matrices as small as three × three resulted in acceptable type I error rates (p < 0.05) for both the co-occurrence and trait-based limiting similarity null models when exclusive p-values were used. The commonly used inclusive p-value (≤ or ≥, as opposed to exclusive p-values; < or >) was associated with increased type I error rates, particularly for matrices with fewer than eight species. Type I error rates increased for limiting similarity tests using the AWTS randomization scheme when community matrices contained more than 35 sites; a similar randomization used in null models of phylogenetic dispersion has previously been viewed as robust. Notwithstanding other potential deficiencies related to the use of small matrices to represent communities, the application of both classes of null model should be restricted to matrices with 10 or more species to avoid the possibility of type II errors. Additionally, researchers should restrict the use of the AWTS randomization to matrices with fewer than 35 sites to avoid type I errors when testing for trait-based limiting similarity. The AITS randomization scheme performed better in terms of type I error rates, and therefore may be more appropriate when considering systems for which traits are not clustered by abundance.

Plant functional traits suggest a change in novel ecological strategies for dominant species in the stages of forest succession

In forest succession, the ecological strategies of the dominant species that are based on functional traits are important in the determination of both the mechanisms and the potential directions of succession. Thirty-one plots were established in the Loess Plateau region of northern Shaanxi in China. Fifteen leaf traits were measured for the 31 dominant species that represented the six stages of succession, and the traits included four that were related to morphology, seven to stoichiometry and four to physiological ecology. The species from the different successional stages had different patterns of distribution of the traits, and different key traits predicted the turnover of the species during succession. The ash and the cellulose contents were key regulatory factors of species turnover in the early successional communities, and the trait niche forces in sugar and leaf dry mass content might become more important with the progression of succession. When only the three herb stages were considered, a progressive replacement of the ruderal by the competitive-ruderal species occurred in the intermediate stages of succession, which was followed by the stress-tolerant-competitive or the competitive-stress tolerant-ruderal strategists late in the succession. Thus, the different species that occurred in the different stages of succession shared different trait-based ecological strategies. Additionally, these differences occurred concomitantly with a shift toward competitive-stress tolerant-ruderal strategies.

Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis

A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans.

No species is an island: testing the effects of biotic interactions on models of avian niche occupation

Traditionally, the niche of a species is described as a hypothetical 3D space, constituted by well-known biotic interactions (e.g. predation, competition, trophic relationships, resource–consumer interactions, etc.) and various abiotic environmental factors. Species distribution models (SDMs), also called “niche models” and often used to predict wildlife distribution at landscape scale, are typically constructed using abiotic factors with biotic interactions generally been ignored. Here, we compared the goodness of fit of SDMs for red-backed shrike Lanius collurio in farmlands of Western Poland, using both the classical approach (modeled only on environmental variables) and the approach which included also other potentially associated bird species. The potential associations among species were derived from the relevant ecological literature and by a correlation matrix of occurrences. Our findings highlight the importance of including heterospecific interactions in improving our understanding of niche occupation for bird species. We suggest that suite of measures currently used to quantify realized species niches could be improved by also considering the occurrence of certain associated species. Then, an hypothetical “species 1” can use the occurrence of a successfully established individual of “species 2” as indicator or “trace” of the location of available suitable habitat to breed. We hypothesize this kind of biotic interaction as the “heterospecific trace effect” (HTE): an interaction based on the availability and use of “public information” provided by individuals from different species. Finally, we discuss about the incomes of biotic interactions for enhancing the predictive capacities on species distribution models.

Functional trait space and the latitudinal diversity gradient

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory.

The emergence and promise of functional biogeography

Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous distribution of traits. However, this is a challenge for the field of biogeography historically grounded on the species concept. Here we focus on the newly emergent field of functional biogeography: the study of the geographic distribution of trait diversity across organizational levels. We show how functional biogeography bridges species-based biogeography and earth science to provide ideas and tools to help explain gradients in multifaceted diversity (including species, functional, and phylogenetic diversities), predict ecosystem functioning and services worldwide, and infuse regional and global conservation programs with a functional basis. Although much recent progress has been made possible because of the rising of multiple data streams, new developments in ecoinformatics, and new methodological advances, future directions should provide a theoretical and comprehensive framework for the scaling of biotic interactions across trophic levels and its ecological implications.

Niche-habitat mechanisms and biotic interactions explain the coexistence and abundance of congeneric sandgrouse species

Ascertaining which niche processes allow coexistence between closely related species is of special interest in ecology. We quantified variations in the environmental niches and densities of two congeneric species, the pin-tailed and the black-bellied sandgrouse (Pterocles alchata and Pterocles orientalis) in allopatry and sympatry under similar abiotic, habitat and dispersal contexts to understand their coexistence. Using principal component analysis, we defined environmental gradients (niche dimensions) including abiotic, habitat and anthropogenic variables, and calculated niche breadth, position and overlap of both species in sympatry and allopatry. Additionally, sandgrouse density was modelled as a function of the niche dimensions and the density of the other species. We found evidence that each species occupies distinct environmental niches in sympatry and in allopatry. The black-bellied sandgrouse exploits a broader range of environmental conditions (wider niche breadth) while the pin-tailed sandgrouse reaches high densities where conditions seem to match its optimum. In sympatry, both species shift their niches to intermediate positions, indicating the importance of abiotic factors in setting coexistence areas. Environmental conditions determine regional densities of pin-tailed sandgrouse whereas biotic interactions explain the density of the black-bellied sandgrouse in areas with abiotic conditions similarly conducive for both species. Highly suitable areas for the pin-tailed sandgrouse fall beyond the upper thermal limit of the black-bellied sandgrouse, leading to niche segregation and low densities for the latter. Finally, local niche shift and expansion plus possible heterospecific aggregation allow the pin-tailed sandgrouse to thrive in a priori less favourable environments. This work provides insight into how different mechanisms allow species coexistence and how species densities vary in sympatry compared to allopatry as a result of environmental filtering and biotic interactions.

Sexual dimorphism dominates divergent host plant use in stick insect trophic morphology

BACKGROUND

Clear examples of ecological speciation exist, often involving divergence in trophic morphology. However, substantial variation also exists in how far the ecological speciation process proceeds, potentially linked to the number of ecological axes, traits, or genes subject to divergent selection. In addition, recent studies highlight how differentiation might occur between the sexes, rather than between populations. We examine variation in trophic morphology in two host-plant ecotypes of walking-stick insects (Timema cristinae), known to have diverged in morphological traits related to crypsis and predator avoidance, and to have reached an intermediate point in the ecological speciation process. Here we test how host plant use, sex, and rearing environment affect variation in trophic morphology in this species using traditional multivariate, novel kernel density based and Bayesian morphometric analyses.

RESULTS

Contrary to expectations, we find limited host-associated divergence in mandible shape. Instead, the main predictor of shape variation is sex, with secondary roles of population of origin and rearing environment.

CONCLUSION

Our results show that trophic morphology does not strongly contribute to host-adapted ecotype divergence in T. cristinae and that traits can respond to complex selection regimes by diverging along different intraspecific lines, thereby impeding progress toward speciation.

The return of the variance: intraspecific variability in community ecology

Despite being recognized as a promoter of diversity and a condition for local coexistence decades ago, the importance of intraspecific variance has been neglected over time in community ecology. Recently, there has been a new emphasis on intraspecific variability. Indeed, recent developments in trait-based community ecology have underlined the need to integrate variation at both the intraspecific as well as interspecific level. We introduce new T-statistics ('T' for trait), based on the comparison of intraspecific and interspecific variances of functional traits across organizational levels, to operationally incorporate intraspecific variability into community ecology theory. We show that a focus on the distribution of traits at local and regional scales combined with original analytical tools can provide unique insights into the primary forces structuring communities.

Individual-scale variation, species-scale differences: inference needed to understand diversity

As ecological data are usually analysed at a scale different from the one at which the process of interest operates, interpretations can be confusing and controversial. For example, hypothesised differences between species do not operate at the species level, but concern individuals responding to environmental variation, including competition with neighbours. Aggregated data from many individuals subject to spatio-temporal variation are used to produce species-level averages, which marginalise away the relevant (process-level) scale. Paradoxically, the higher the dimensionality, the more ways there are to differ, yet the more species appear the same. The aggregate becomes increasingly irrelevant and misleading. Standard analyses can make species look the same, reverse species rankings along niche axes, make the surprising prediction that a species decreases in abundance when a competitor is removed from a model, or simply preclude parameter estimation. Aggregation explains why niche differences hidden at the species level become apparent upon disaggregation to the individual level, why models suggest that individual-level variation has a minor impact on diversity when disaggregation shows it to be important, and why literature-based synthesis can be unfruitful. We show how to identify when aggregation is the problem, where it has caused controversy, and propose three ways to address it.

Spearfishing regulation benefits artisanal fisheries: the ReGS indicator and its application to a multiple-use Mediterranean marine protected area

The development of fishing efficiency coupled with an increase of fishing effort led to the overexploitation of numerous natural marine resources. In addition to this commercial pressure, the impact of recreational activities on fish assemblages remains barely known. Here we examined the impact of spearfishing limitation on resources in a marine protected area (MPA) and the benefit it provides for the local artisanal fishery through the use of a novel indicator. We analysed trends in the fish assemblage composition using artisanal fisheries data collected in the Bonifacio Strait Natural Reserve (BSNR), a Mediterranean MPA where the spearfishing activity has been forbidden over 15% of its area. Fish species were pooled into three response groups according to their target level by spearfishing. We developed the new flexible ReGS indicator reflecting shifts in species assemblages according to the relative abundance of each response group facing external pressure. The catch per unit effort (CPUE) increased by ca. 60% in the BSNR between 2000 and 2007, while the MPA was established in 1999. The gain of CPUE strongly depended on the considered response group: for the highly targeted group, the CPUE doubled while the CPUE of the untargeted group increased by only 15.5%. The ReGS value significantly increased from 0.31 to 0.45 (on a scale between 0 and 1) in the general perimeter of this MPA while it has reached a threshold of 0.43, considered as a reference point, in the area protected from spearfishing since 1982. Our results demonstrated that limiting recreational fishing by appropriate zoning in multiple-use MPAs represents a real benefit for artisanal fisheries. More generally we showed how our new indicator may reveal a wide range of impacts on coastal ecosystems such as global change or habitat degradation.

The spatial pattern of nitrogen cycling in the Adirondack Park, New York

Maps of canopy nitrogen obtained through analysis of high-resolution, hyperspectral, remotely sensed images now offer a powerful means to make landscape-scale to regional-scale estimates of forest N cycling and net primary production (NPP). Moreover, recent research has suggested that the spatial variability within maps of canopy N may be driven by environmental gradients in such features as historic forest disturbance, temperature, species composition, moisture, geology, and atmospheric N deposition. Using the wide variation in these six features found within the diverse forest ecosystems of the 2.5 million ha Adirondack Park, New York, USA, we examined linkages among environmental gradients and three measures of N cycling collected during the 2003 growing season: (1) field survey of canopy N, (2) field survey of soil C:N, and (3) canopy N measured through analysis of two 185 x 7.5 km Hyperion hyperspectral images. These three measures of N cycling strongly related to forest type but related poorly to all other environmental gradients. Further analysis revealed that the spatial pattern in N cycling appears to have distinct inter- and intraspecific components of variability. The interspecific component, or the proportional contribution of species functional traits to canopy biomass, explained 93% of spatial variability within the field canopy N survey and 37% of variability within the soil C:N survey. Residual analysis revealed that N deposition accounted for an additional 2% of variability in soil C:N, and N deposition and historical forest disturbance accounted for an additional 2.8% of variability in canopy N. Given our finding that 95.8% of the variability in the field canopy N survey could be attributed to variation in the physical environment, our research suggests that remotely sensed maps of canopy N may be useful not only to assess the spatial variability in N cycling and NPP, but also to unravel the relative importance of their multiple controlling factors.