Integrating trait and phylogenetic distances to assess scale‐dependent community assembly processes

Biodiversity is structured by multiple mechanisms that are dependent, at least in part, on ecological similarities and differences among species. Integrating traits and phylogenies in diversity metrics may provide deeper insight into community assembly processes across spatial scales. However, different traits are influenced by processes at different spatial scales, and it is not clear how trait‐spatial scale mismatches skew our ability to detect assembly patterns. An additional complexity is how phylogenetic distances, which might capture unmeasured traits, reflect spatially dependent processes. Here we analyze a freshwater zooplankton dataset from 91 ponds and show that different traits are associated with processes at different spatial scales. We first assessed the response of individual traits to processes at both α‐ and β‐scales, and then quantified the power of different combinations of traits and phylogenetic distances to reveal environmental and spatial drivers of α‐ and β‐diversity. We found that explanatory power was maximised when we accounted for environmental and spatial drivers with single, but different traits for α‐ and β‐diversity. Using the most appropriate trait for each spatial scale outperformed phylogenetic information, but phylogenetic information outperformed the same traits when these were used at the wrong spatial scale, and all outperformed taxonomic analyses that ignore trait and phylogenetic information. We demonstrate that accounting for species’ similarities and differences provides important information about dominant assembly mechanisms at different spatial scales, and that phylogeny is especially useful when measured traits are uninformative at a given spatial scale or when there is lack of trait data. Our study also indicates, however, that trait‐scale mismatches among phylogenetically conserved traits may affect the performance of phylogenetic indices compared to indices that account only for the best single trait at each spatial scale.     

Mind the gap: scale‐dependent and dispersal‐mediated response to forest fragmentation

Species richness of habitat fragments is affected by spatial isolation. However, the scale of this phenomenon, and its interactions with the species’ seed dispersal potential has remained underexplored. By integrating seed trap and species distribution data, Koh et al., in this issue of the Journal of Vegetation Science, make a compelling case for scale‐dependent species’ responses to forest fragmentation.     

Species‐specific and temporal scale‐dependent responses of birds to drought

Global climate change is increasing the frequency and intensity of weather extremes, including severe droughts in many regions. Drought can impact organisms by inhibiting reproduction, reducing survival and abundance, and forcing range shifts. For birds, considering temporal scale by averaging drought‐related variables over different time lengths (i.e., temporal grains) captures different hydrologic attributes which may uniquely influence food supplies, vegetation greenness/structure, and other factors affecting populations. However, studies examining drought impacts on birds often assess a single temporal grain without considering that different species have different life histories that likely determine the temporal grain of their drought response. Furthermore, while drought is known to influence bird abundance and drive between‐year range shifts, less understood is whether it causes within‐range changes in species distributions. Our objectives were to (a) determine which temporal grain of drought (if any) is most related to bird presence/absence and whether this response is species specific; and (b) assess whether drought alters bird distributions by quantifying probability of local colonization and extinction as a function of drought intensity. We used North American Breeding Bird Survey data collected over 16 years, generalized linear mixed models, and dynamic occupancy models to meet these objectives. Different bird species responded to drought at different temporal grains, with most showing the strongest signal at annual or near‐annual grains. For all drought‐responsive species, increased drought intensity at any temporal grain always correlated with decreased occupancy. Additionally, colonization/extinction analyses indicated that one species, the dickcissel (Spiza americana), is more likely to colonize novel areas within the southern/core portion of its range during drought. Considering drought at different temporal grains, along with hydrologic attributes captured by each grain, may better reveal mechanisms behind drought impacts on birds and other organisms, and therefore improve understanding of how global climate change impacts species and the landscapes they inhabit.     

Self‐organised patchiness and scale‐dependent bio‐geomorphic feedbacks in aquatic river vegetation

Spatial self‐organisation of ecosystems is the process by which large‐scale ordered spatial patterns emerge from disordered initial conditions through local feedbacks between organisms and their environment. Such process is considered important for ecosystem functioning, providing increased productivity, resistance and resilience against environmental change. Although spatial self‐organisation has been found for an increasing number of ecosystems, it has never been shown so far for aquatic river vegetation. Here we explore the existence of spatial self‐organisation of freshwater macrophyte patches in a typical lowland river (Belgium), showing that the underlying mechanisms for pattern formation are scale‐dependent feedbacks between plant growth, water flow and local river bed erosion and sedimentation. The mapping of vegetation patches showed that the frequency distribution of patch sizes is governed by a power‐law function, suggesting that the patches are self‐organised. Scale‐dependent feedbacks, likely to lead to this self‐organised pattern, were demonstrated with a mimic experiment. Both positive and negative feedbacks on plants were confirmed by a transplantation experiment. Placing vegetation patch mimics in the river showed experimentally that on a short range (within and behind the mimics) flow reduction and increased sedimentation occurred, while on a larger range (next to patches) the flow was accelerated and decreased sedimentation took place. By transplanting macrophytes within, next to and further away from existing patches, it was proven that the conditions within the patches favoured the survival and growth of transplants (i.e. short‐range positive feedback), while the conditions just next to patches led to decreased survival and growth (i.e. long‐range negative feedback).     

Dispersal and diversity – unifying scale‐dependent relationships within the neutral theory

The response of species diversity to dispersal capability is inherently scale‐dependent: increasing dispersal capability is expected to increase diversity at the local scale, while decreasing diversity at the metacommunity scale. However, these expectations are based on model formulations that neglect dispersal limitation and species segregation at the local scale. We developed a unifying framework of dispersal–diversity relationships and tested the generality of these expectations. For this purpose we used a spatially‐explicit neutral model with various combinations of survey area (local scale) and landscape size (metacommunity scale). Simulations were conducted using landscapes of finite and of conceptually infinite size. We analyzed the scale‐dependence of dispersal‐diversity relationships for exponentially‐bounded versus fat‐tailed dispersal kernels, several levels of speciation rate and contrasting assumptions on recruitment at short dispersal distances. We found that the ratio of survey area to landscape size is a major determinant of dispersal–diversity relationships. With increasing survey‐to‐landscape area ratio the dispersal–diversity relationship switches from monotonically increasing through a U‐shaped pattern (with a local minimum) to a monotonically decreasing pattern. Therefore, we provide a continuous set of dispersal–diversity relationships, which contains the response shapes reported previously as extreme cases. We suggest the mean dispersal distance with the minimum of species diversity (minimizing dispersal distance) for a certain scenario as a key characteristic of dispersal–diversity relationships. We show that not only increasing mean dispersal distances, but also increasing variances of dispersal can enhance diversity at the local scale, given a diverse species pool at the metacommunity scale. In conclusion, the response of diversity to variations of dispersal capability at spatial scales of interest, e.g. conservation areas, can differ more widely than expected previously. Therefore, land use and conservation activities, which manipulate dispersal capability, need to consider the landscape context and potential species pools carefully.     

A sense of scale: Foraging cetaceans' use of scale‐dependent multimodal sensory systems

Research on cetacean foraging ecology is central to our understanding of their spatial and behavioral ecology. Yet, functional mechanisms by which cetaceans detect prey across different scales remain unclear. Here, I postulate that cetaceans utilize a scale‐dependent, multimodal sensory system to assess and increase prey encounters. I review the literature on cetacean sensory systems related to foraging ecology, and hypothesize the effective scales of each sensory modality to inform foraging opportunities. Next, I build two “scale‐of‐senses” schematics for the general groups of dolphins and baleen whales. These schematics illustrate the hypothetical interchange of sensory modalities used to locate and discriminate prey at spatial scales ranging from 0 m to 1,000 km: (1) vision, (2) audition (sound production and sound reception), (3) chemoreception, (4) magnetoreception, and somatosensory perception of (5) prey, or (6) oceanographic stimuli. The schematics illustrate how a cetacean may integrate sensory modalities to form an adaptive foraging landscape as a function of distance to prey. The scale‐of‐senses schematic is flexible, allowing for case‐specific application and enhancement with improved cetacean sensory data. The framework serves to improve our understanding of functional cetacean foraging ecology, and to develop new hypotheses, methods, and results regarding how cetaceans forage at multiple scales.     

Biodiversity change is scale‐dependent: an example from Dutch and UK hoverflies (Diptera,Syrphidae)

We test whether temporal change in species richness (ΔS [%]) is scale‐dependent, using data on hoverflies from the UK and the Netherlands. We analysed ΔS between pre‐1980 and post‐1980 periods using 5 grid resolutions (10×10, 20×20, 40×40, 80×80 and 160×160 km). We also tested the effect of data quality and of unequal survey periods on ΔS estimates, and checked for spatial autocorrelation of ΔS estimates. Using data from equal survey periods, we found significant increases in hoverfly species richness in the Netherlands at fine scales, but no significant change at coarser scales indicating a decrease in beta diversity. In the UK, ΔS was negative at fine scale, near zero at intermediate scales, and positive at coarse scales, indicating that the degree of spatial beta diversity increased between the time periods. The use of unequal survey periods (using longer periods in the past to compensate for lower survey intensity) tended to inflate past species richness, biasing ΔS estimates downwards. High data quality thresholds sometimes obscured dynamics by reducing sample size, but never reversed trends. There was little spatial autocorrelation of ΔS, implying that local drivers (land use change or environmental noise) are important in dynamics of hoverfly diversity. A second, sample agglomeration approach to measure scaling resulted in greater noise in ΔS, obscuring the NL pattern, while still showing strong evidence of fine‐scale richness loss in the UK. Our results indicate that explicit considerations of spatial (and temporal) scale are essential in studies documenting past biodiversity change, or projecting change into the future.     

Scale‐dependent processes of community assemblyin an African rift lake

1. Ecologists continue to debate whether the assembly of communities of species is more strongly influenced by dispersal limitations or niche‐based factors. Analytical approaches that account for both mechanisms can help to resolve controls of community assembly. 2. We compared littoral snail assemblages in Lake Tanganyika at three different spatial scales (5–25 m, 0.5–10 km and 0.5–27 km) to test whether spatial distance or environmental differences are better predictors of community similarity. 3. At the finest scale (5–25 m), snail assemblages shifted strongly with depth but not across similar lateral distances, indicating a stronger response to environmental gradients than dispersal opportunities. 4. At the two larger scales (0.5–27 km), both environmental similarity and shoreline distance between sites predicted assemblage similarity across sites. Additionally, canonical correspondence analysis revealed that snail abundances were significantly correlated with algal carbon‐to‐nitrogen ratio and wave energy. 5. Our results indicate that the factors governing assemblage structure are scale dependent; niche‐based mechanisms act across all spatial scales, whereas community similarity declines with distance only at larger spatial separations.     

Where movement happens: scale‐dependent landscape effects on genetic differentiation in the European tree frog

Functional connectivity among fragmented populations depends on the landscape matrix between occupied habitat patches and its effect on the frequency of animal movement and gene flow. The quantification of landscape effects on gene flow should therefore be scale‐dependent. Here, we explored the impact of different spatial scales in a landscape genetic analysis of the European tree frog Hyla arborea in a fragmented landscape in Switzerland. We examined the effects of landscape elements and geographic distance on genetic differentiation at three distance classes reflecting varying frequencies of tree frog movement. We calculated pairwise F_ST‐values and assembled 16 landscape elements within 1 km wide corridors between all pairs of tree frog breeding sites. Per distance class, we computed a multiple regression model with stepwise backward elimination and permutation testing. At distances of<2 km, only a larger river acted as a barrier to gene flow. At distances>2 km, geographic distance had a negative effect on gene flow as had landscape elements such as forests and roads. In general, hedgerows and various structure‐rich landscape elements positively affected gene flow. As we found distinct scale‐dependent landscape effects on gene flow, future landscape genetic studies should analyse the effects of landscape variables at different spatial dimensions relevant for the movement and dispersal of the study organisms. Corresponding studies should also carefully consider relevant correlations among the landscape elements tested and should preferentially replicate their analysis at the landscape‐level in order to avoid idiosyncratic results owing to the particular scale and landscape studied.     

Spatial heterogeneity and scale‐dependent habitat selection for two sympatric raptors in mixed‐grass prairie

Sympatric predators are predicted to partition resources, especially under conditions of food limitation. Spatial heterogeneity that influences prey availability might play an important role in the scales at which potential competitors select habitat. We assessed potential mechanisms for coexistence by examining the role of heterogeneity in resource partitioning between sympatric raptors overwintering in the southern Great Plains. We conducted surveys for wintering Red‐tailed hawk (Buteo jamaicensis) and Northern Harrier (Circus cyanea) at two state wildlife management areas in Oklahoma, USA. We used information from repeated distance sampling to project use locations in a GIS. We applied resource selection functions to model habitat selection at three scales and analyzed for niche partitioning using the outlying mean index. Habitat selection of the two predators was mediated by spatial heterogeneity. The two predators demonstrated significant fine‐scale discrimination in habitat selection in homogeneous landscapes, but were more sympatric in heterogeneous landscapes. Red‐tailed hawk used a variety of cover types in heterogeneous landscapes but specialized on riparian forest in homogeneous landscapes. Northern Harrier specialized on upland grasslands in homogeneous landscapes but selected more cover types in heterogeneous landscapes. Our study supports the growing body of evidence that landscapes can affect animal behaviors. In the system we studied, larger patches of primary land cover types were associated with greater allopatry in habitat selection between two potentially competing predators. Heterogeneity within the scale of raptor home ranges was associated with greater sympatry in use and less specialization in land cover types selected.     

Opportunistic records reveal Mediterranean reptiles’ scale‐dependent responses to anthropogenic land use

Although classified among the greatest threats to the world's biodiversity, the effects of land use and their scale dependency are left unexplored in many taxonomic groups. Reptiles are among the most data‐deficient vertebrates in this respect, although their ecological traits make them highly sensitive to habitat modifications. We tested whether land use gradients shape the distributions of Mediterranean reptiles at regional and local scales, and whether species’ ecological traits and phylogeny explain these patterns. Reptiles are generally rare and hard to survey through standardized protocols. We overcame these obstacles by modeling an original data set of 18164 opportunistic occurrence records for 14 reptile species with spatially‐explicit point process models incorporating known sources of sampling heterogeneity and spatially autocorrelated error. At a regional scale, reptiles favored open habitats and tended to avoid urban areas. At a local scale, the persistence of open habitats did better than forest resulting from land abandonment in maintaining reptiles within a heavily anthropogenic matrix. Contrary to our expectations, the absence of any clear trait or phylogenetic signals suggests that these responses are mediated by a complex interplay between species’ ecology and regional biogeographic history. These results demonstrate that reptile responses to land use are scale‐dependent and locally exacerbated when anthropogenic pressure is high. We further show that land abandonment is insufficient to preserve reptiles in the face of anthropogenic pressures unless patches of suitable habitat are effectively maintained. Eventually, our study further illustrates the effectiveness of volunteer‐based opportunistic sampling in testing hypotheses on the determinants of rare species’ distributions.     

A novel framework for disentangling the scale‐dependent influences of abiotic factors on alpine treeline position

Low‐temperature growth limitation largely determines alpine treeline position globally, but treeline elevation also varies locally at a range of scales in response to multiple biotic and abiotic factors. In this study, we conceptualise how variability in treeline elevation is related to abiotic factors that act as thermal modifiers, physiological stressors, or disturbance agents. We then present a novel analytical framework for quantifying how abiotic factors influence treeline elevation at different spatial scales using New Zealand Nothofagus treelines as a case study. We delineated Nothofagus treelines in a GIS, along which we extracted data for treeline elevation and eight abiotic explanatory variables at 54 000 points. Each location was classified at each of five spatial scales based on nested river catchments, ranging from large regional to small hillslope catchments. We used hierarchical linear models to partition the variation in both treeline elevation and the eight abiotic variables by spatial scale, and then quantified the relationships between these at each spatial scale in turn. Nothofagus treeline elevation varied from 800–1740 m a.s.l. across New Zealand. Abiotic factors explained 82% of the variation in treeline elevation at the largest (regional) scale and 44–52% of variation at the four finer scales. Broad‐scale variation in Nothofagus treeline elevation was strongly associated with thermal modifiers, consistent with the idea that treelines coincide with a temperature‐driven, physiological limit. However, much of the finer‐scale variation in treeline elevation was explained by a combination of thermal, physiological stress‐related, and disturbance variables operating at different spatial scales. The conceptual model and analytical methods developed here provide a general framework for understanding treeline variation at different spatial scales.     

Animal space use: distinguishing a two‐level superposition of scale‐specific walks from scale‐free Lévy walk

How to differentiate between scale‐free space use like Lévy walk and a two‐level scale‐specific process like composite random walk (mixture of intra‐ and inter‐patch habitat movement) is surrounded by controversy. Composite random walk may under some parameter conditions appear Lévy walk‐like from the perspective of the path’s distribution of step lengths due to superabundance of very long steps relative to the expectation from a classic (single‐level) random walk. However, a more explicit focus on the qualitative differences between studying movement at a high resolution mechanistic (behavioral) level and the more coarse‐grained statistical mechanical level may contribute to resolving both this and other issues related to scaling complexity. Specifically, a re‐sampling of a composite random walk at larger time lags than the micro‐level unit time step for the simulation makes a Lévy‐look‐alike step length distribution re‐shaping towards a Brownian motion‐like pattern. Conversely, a true Levy walk maintains its scaling characteristics upon re‐sampling. This result illustrates how a confusing pattern at the mechanistic level may be resolved by changing observational scale from the micro level to the coarser statistical mechanical meso‐ or macro‐scale. The instability of the composite random walk pattern under rescaling is a consequence of influence of the central limit theorem. I propose that a coarse‐graining test – studying simulated animal paths at a coarsened temporal scale by re‐sampling a series – should be routinely performed prior to comparing theoretical results with those patterns generated from GPS data describing animal movement paths. Fixes from terrestrial mammals are often collected at hourly intervals or larger, and such a priori coarse‐grained series may thus comply better with the statistical mechanical meso‐ or macro‐level of analysis than the behavioral mechanics observed at finer resolutions typically in the range of seconds and minutes. If fixes of real animals are collected at this high frequency, coarse graining both the simulated and real series is advised in order to bring the analysis into a temporal scale domain where analytical methods from statistical mechanics can be applied.     

Life stage‐dependent effects of experimental heat waves on an insect herbivore

1. Worldwide concern about the consequences of climate change has prompted efforts to understand and predict the responses of populations to changes in temperature. 2. A heat wave can adversely affect organisms, may affect different life stages differently, and could decrease populations. In this study, green peach aphid [Myzus persicae (Sulzer)] nymphs, reproductive adults, and late‐reproductive adults were exposed to a heat wave, defined as 5 °C above the control temperature regime for five consecutive days. 3. The negative effects of experimental warming on development, reproduction, and survival negatively affected population growth. Nymphs and reproductive adults were more severely impacted than late‐reproductive adults. 4. Experiments designed to mimic temperature regimes can assess the direct effects of climate change on individuals and populations. Our study highlights the importance of assessing the life stage‐specific responses to heat stress.     

Effect of detection heterogeneity in occupancy‐detection models: an experimental test of time‐to‐first‐detection methods

Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time‐to‐first‐detection (TTD) occupancy models have been proposed as a cost–effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validated the performance of occupancy‐detection models by creating a situation where occupancy is known, and model outputs can be compared with the truth. We tested the performance of TTD occupancy models in the face of detection heterogeneity using an experiment based on standard survey methods to monitor koala Phascolarctos cinereus populations in Australia. Known numbers of koala faecal pellets were placed under trees, and observers, uninformed as to which trees had pellets under them, carried out a TTD survey. We fitted five TTD occupancy models to the survey data, each making different assumptions about detectability, to evaluate how well each estimated the true occupancy status. Relative to the truth, all five models produced strongly biased estimates, overestimating detection probability and underestimating the number of occupied trees. Despite this, goodness‐of‐fit tests indicated that some models fitted the data well, with no evidence of model misfit. Hence, TTD occupancy models that appear to perform well with respect to the available data may be performing poorly. The reason for poor model performance was unaccounted for heterogeneity in detection probability, which is known to bias occupancy‐detection models. This poses a problem because unaccounted for heterogeneity could not be detected using goodness‐of‐fit tests and was only revealed because we knew the experimentally determined outcome. A challenge for occupancy‐detection models is to find ways to identify and mitigate the impacts of unobserved heterogeneity, which could unknowingly bias many models.     

The exchange hypothesis for the formation of chromatid aberrations: an experimental test using bleomycin

The association between bleomycin-induced chromatid aberrations and BUdR-label exchange between sister chromatids was investigated in order to evaluate Revell's exchange hypothesis for the formation of chromatid aberrations. The results of this study indicate that a larger than expected proportion of chromatid breaks can be accounted for by the exchange hypothesis though not all breaks are the result of incomplete exchange.     

Temporal scales of density‐dependent habitat selection in a large grazing herbivore

Habitat selection is a density‐dependent process, but little is known regarding how this relationship may vary across different temporal scales. Over long time scales, grazing shapes the structure, diversity and functioning of terrestrial ecosystems, and grazing‐induced changes in forage production over time are likely to affect the level of density dependence in habitat selection. In this fully‐replicated, landscape‐scale experiment, we investigated how density‐dependent habitat selection by a large grazing herbivore, sheep Ovis aries, develops over the time scale of a decade. We also address an often‐neglected challenge in habitat selection studies; namely, whether there is variation in use within a particular habitat or vegetation type and why. We found clear evidence of density dependence in habitat selection, with a wider use of habitats at high density. Despite a change in the standing biomass of high‐productivity vegetation at high herbivore density over the years, with herb biomass declining and graminoid biomass increasing, there was no clear evidence that these grazing‐induced changes in habitat over the years were strong enough to affect the level of density‐dependent habitat selection. The difference in selection for high versus low‐productivity habitats remained similar, despite annual fluctuations in the strength of selection. We found strong variation in selection within each vegetation type, even when vegetation types were mapped at a fine‐resolution scale. Our study shows that despite the interactive effects of herbivores and habitats, they are not always sufficiently strong enough to affect the level of density‐dependent habitat selection.     

An experimental test of density‐dependent selection on temperament traits of activity,boldness and sociability

Temperament traits are seen in many animal species, and recent evolutionary models predict that they could be maintained by heterogeneous selection. We tested this prediction by examining density‐dependent selection in juvenile common lizards Zootoca vivipara scored for activity, boldness and sociability at birth and at the age of 1 year. We measured three key life‐history traits (juvenile survival, body growth rate and reproduction) and quantified selection in experimental populations at five density levels ranging from low to high values. We observed consistent individual differences for all behaviours on the short term, but only for activity and one boldness measure across the first year of life. At low density, growth selection favoured more sociable lizards, whereas viability selection favoured less active individuals. A significant negative correlational selection on activity and boldness existed for body growth rate irrespective of density. Thus, behavioural traits were characterized by limited ontogenic consistency, and natural selection was heterogeneous between density treatments and fitness traits. This confirms that density‐dependent selection plays an important role in the maintenance of individual differences in exploration‐activity and sociability.     

Seagrass beds and intertidal invertebrates: an experimental test of the role of habitat structure

The majority of field experiments have been carried out on relatively small spatial and short temporal scales, but some of the most interesting ecological processes operate at much larger scales. However, large-scale experiments appropriate to the landscape, often have to be carried out with minimal plot replication and hence reduced statistical power. Here, we report the results of such a large scale, un-replicated field experiment on the Mondego estuary, Portugal, which nevertheless provides compelling evidence of the importance of habitat structure for invertebrate community composition and dynamics. In this estuary, seagrass beds have suffered a dramatic decline over the last 20 years, associated with changes in invertebrate assemblages. In addition, the most abundant species in the system, Hydrobia ulvae, displays distinctly different population structures in those sites. The aim of the field experiment was to test the hypothesis that these differences are related to enhanced survival of snails due to protection from avian or fish predators so that they can grow to larger body sizes in the more complex habitat provided by seagrass. We tested this hypothesis through a large-scale experiment using artificial seagrass beds over a 12-month period. Adult snail densities were higher in the artificial bed plots compared to controls. However, these differences emerged only slowly, related to snail growth rate. This suggests that protection from epibenthic predators can have a significant effect on population structure and hence biomass and productivity of key species in this system. However, the invertebrate assemblage in artificial seagrass plots and the natural seagrass bed, remained statistically separate by the end of the experiment. Handling editor: K. Martens