Time is of the essence: A general framework for uncovering temporal structures of communities

Ecological communities are inherently dynamic: species constantly turn over within years, months, weeks or even days. These temporal shifts in community composition determine essential aspects of species interactions and how energy, nutrients, information, diseases and perturbations 'flow' through systems. Yet, our understanding of community structure has relied heavily on static analyses not designed to capture critical features of this dynamic temporal dimension of communities. Here, we propose a conceptual and methodological framework for quantifying and analysing this temporal dimension. Conceptually, we split the temporal structure into two definitive features, sequence and duration, and review how they are linked to key concepts in ecology. We then outline how we can capture these definitive features using perspectives and tools from temporal graph theory. We demonstrate how we can easily integrate ongoing research on phenology into this framework and highlight what new opportunities arise from this approach to answer fundamental questions in community ecology. As climate change reshuffles ecological communities worldwide, quantifying the temporal organization of communities is imperative to resolve the fundamental processes that shape natural ecosystems and predict how these systems may change in the future.

Eurasian beaver - A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter

There is increasing awareness of the ecosystem engineering services provided by recovering populations of Eurasian beaver. By modifying aquatic environments, this species has a significant, positive influence on biodiversity. Beaver activity affects not only aquatic ecosystems but also terrestrial habitats and organisms. Our study compares and evaluates the species richness and activity of terrestrial mammals in winter at beaver ponds (N = 65) and randomly-selected reference sites along nearby watercourses unmodified by beavers (N = 65) in Poland (central Europe). Mammal assemblages were investigated near pond/watercourse edges, and also at some distance from them. The species richness of mammal and numbers of their tracks were respectively 25% and 33% greater on the beaver than on the reference sites. The higher species richness on beaver sites extended to areas 40-60 m distant from ponds, devoid any signs of beaver activity. Twenty-three mammal species were recorded on beaver sites (mean species richness 3.8 ± 1.6 SD), and 20 on reference ones (3.0 ± 1.5 SD). The numbers of tracks of grey wolf, least weasel and European polecat were higher on beaver than reference sites. Mammal species richness and activity were related to the existence of beaver ponds, but were also correlated with the numbers of snags and coverage of grass, bramble and coniferous saplings in neighbouring terrestrial habitats. Large and small carnivores occurred more frequently and were more active on beaver sites. The frequencies of occurrence of mesocarnivores, mesoherbivores and small herbivores were correlated with habitat characteristics, regardless of whether beavers were present or not. Our results highlight the fact that both pond creation and the habitat changes resulting from the presence of beavers rearrange the occurrence and activity of the terrestrial mammal assemblage.

Functional Responses Shape Node and Network Level Properties of a Simplified Boreal Food Web

Ecological communities are fundamentally connected through a network of trophic interactions that are often complex and difficult to model. Substantial variation exists in the nature and magnitude of these interactions across various predators and prey and through time. However, the empirical data needed to characterize these relationships are difficult to obtain in natural systems, even for relatively simple food webs. Consequently, prey-dependent relationships and specifically the hyperbolic form (Holling’s Type II), in which prey consumption increases with prey density but ultimately becomes saturated or limited by the time spent handling prey, are most widely used albeit often without knowledge of their appropriateness. Here, we investigate the sensitivity of a simplified food web model for a natural, boreal system in the Kluane region of the Yukon, Canada to the type of functional response used. Intensive study of this community has permitted best-fit functional response relationships to be determined, which comprise linear (type I), hyperbolic (type II), sigmoidal (type III), prey- and ratio-dependent relationships, and inverse relationships where kill rates of alternate prey are driven by densities of the focal prey. We compare node- and network-level properties for a food web where interaction strengths are estimated using best-fit functional responses to one where interaction strengths are estimated exclusively using prey-dependent hyperbolic functional responses. We show that hyperbolic functional responses alone fail to capture important ecological interactions such as prey switching, surplus killing and caching, and predator interference, that in turn affect estimates of cumulative kill rates, vulnerability of prey, generality of predators, and connectance. Exclusive use of hyperbolic functional responses also affected trends observed in these metrics over time and underestimated annual variation in several metrics, which is important given that interaction strengths are typically estimated over relatively short time periods. Our findings highlight the need for more comprehensive research aimed at characterizing functional response relationships when modeling predator-prey interactions and food web structure and function, as we work toward a mechanistic understanding linking food web structure and community dynamics in natural systems.

Habitat Associations of Overwintering Bats in Managed Pine Forest Landscapes

Research Highlights: Seasonal variation in environmental conditions coinciding with reproductive and energetic demands might result in seasonal differences in species-specific habitat use. We studied a winter assemblage of insectivorous bats and found that species acted as habitat generalists during winter compared to expectations based on the summer active season. Background and Objectives: In temperate regions, seasonal fluctuations in resource availability might restructure local bat assemblages. Initially perceived to only hibernate or migrate to avoid adverse winter conditions, temperate insectivorous bats appear to also employ intermediate overwintering strategies, as a growing body of literature suggests that winter activity is quite prevalent and even common in some lower latitude areas. However, to date, most studies have exclusively assessed habitat associations during summer. Because habitat use during summer is strongly influenced by reproduction, we hypothesized that habitat associations might differ during the non-reproductive winter period. We used acoustic monitoring to assess the habitat associations of bats across a managed pine landscape in the southeastern United States. Materials and Methods: During the winters of 2018 and 2019, we deployed acoustic detectors at 72 unique locations to monitor bat activity and characterized vegetation conditions at two scales (microhabitat and landscape). We used linear mixed models to characterize species-specific activity patterns associated with different vegetation conditions. Results: We found little evidence of different activity patterns during winter. The activity of three species (hoary bat: Lasiurus cinereus; southeastern myotis: Myotis austroriparius; and tricolored bat: Perimyotis subflavus) was not related to vegetation variables and only modest relationships were evident for four other species/groups (big brown bat: Eptesicus fuscus; eastern red bat: L. borealis; Seminole bat: L. seminolus; evening bat: Nycticeius humeralis; and Brazilian free-tailed bat: Tadarida brasiliensis). Conclusions: During winter, the bats in our study were active across the landscape in various cover types, suggesting that they do not exhibit the same habitat associations as in summer. Therefore, seasonal differences in distributions and habitat associations of bat populations need to be considered so that effective management strategies can be devised that help conserve bats year round.

Balancing food acquisition and predation risk drives demographic changes in snowshoe hare population cycles

Snowshoe hare cycles are one of the most prominent phenomena in ecology. Experimental studies point to predation as the dominant driving factor, but previous experiments combining food supplementation and predator removal produced unexplained multiplicative effects on density. We examined the potential interactive effects of food limitation and predation in causing hare cycles using an individual-based food-supplementation experiment over-winter across three cycle phases that naturally varied in predation risk. Supplementation doubled over-winter survival with the largest effects occurring in the late increase phase. Although the proximate cause of mortality was predation, supplemented hares significantly decreased foraging time and selected for conifer habitat, potentially reducing their predation risk. Supplemented hares also lost less body mass which resulted in the production of larger leverets. Our results establish a mechanistic link between how foraging time, mass loss and predation risk affect survival and reproduction, potentially driving demographic changes associated with hare cycles.

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.

Integrating plant stoichiometry and feeding experiments: state-dependent forage choice and its implications on body mass

Intraspecific feeding choices comprise a large portion of herbivore foraging decisions. Plant resource quality is heterogeneously distributed, affected by nutrient availability and growing conditions. Herbivores navigate landscapes, foraging not only according to food qualities, but also energetic and nutritional demands. We test three non-exclusive foraging hypotheses using the snowshoe hare (Lepus americanus): (1) herbivore feeding choices and body conditions respond to intraspecific plant quality variation; (2) high energetic demands mitigate feeding responses; and (3) feeding responses are inflated when nutritional demands are high. We measured black spruce (Picea mariana) nitrogen, phosphorus and terpene compositions, as indicators of quality, within a snowshoe hare trapping grid and found plant growing conditions to explain spruce quality variation (R² < 0.36). We then offered two qualities of spruce (H1) from the trapping grid to hares in cafeteria-style experiments and measured their feeding and body condition responses (n = 75). We proxied energetic demands (H2) with ambient temperature and coat insulation (% white coat) and nutritional demands (H3) with the spruce quality (nitrogen and phosphorus content) in home ranges. Hares with the strongest preference for high-quality spruce lost on average 2.2% less weight than hares who ate the least high-quality spruce relative to low-quality spruce. The results supported our energetic predictions as follows: hares in colder temperatures and with less-insulative coats (lower % white) consumed more spruce and were less selective towards high-quality spruce. Collectively, we found variation in plant growing conditions within herbivore home ranges substantial enough to affect herbivore body conditions, but energetic stats mediate plant-herbivore interactions.

Plant breeding systems influence the seasonal dynamics of plant-pollinator networks in a subtropical forest

Temporal dynamics of plant-pollinator interactions inform the mechanisms of community assembly and stability. However, most studies on the dynamics of pollination networks do not consider plant reproductive traits thus offering poor understanding of the mechanism of how networks maintain stable structure under seasonal changes in flower community. We studied seasonal dynamics of pollination networks in a subtropical monsoon forest in China with a clear rainy season (April-September) and dry season (October-March) over 2 consecutive years. We constructed dioecy-ignored networks (combining visitations to dioecious male and female plants by ignoring the difference between dioecious and hermaphroditic plants) and dioecy-considered networks (excluding those visitations that only occurred either on dioecious male or female plants) for eight sampling sessions for each season. Although flower richness and flower abundance were higher in the rainy season than in the dry season, no pronounced seasonal difference was found in network specialization, nestedness and modularity for both networks. There were only significant differences in plant community robustness and pollinator specialization between seasons for dioecy-considered networks but not for dioecy-ignored networks. Furthermore, we found the flower abundance of dioecious and hermaphrodite plants mostly showed trade-off variation between rainy and dry seasons. Our results suggest various plant reproductive traits affect the temporal dynamics of pollination networks, which should be considered for conservation of plant-pollinator interactions in forest communities.

Seasonal variation in UVA light drives hormonal and behavioural changes in a marine annelid via a ciliary opsin

The right timing of animal physiology and behaviour ensures the stability of populations and ecosystems. To predict anthropogenic impacts on these timings, more insight is needed into the interplay between environment and molecular timing mechanisms. This is particularly true in marine environments. Using high-resolution, long-term daylight measurements from a habitat of the marine annelid Platynereis dumerilii, we found that temporal changes in ultraviolet A (UVA)/deep violet intensities, more than longer wavelengths, can provide annual time information, which differs from annual changes in the photoperiod. We developed experimental set-ups that resemble natural daylight illumination conditions, and automated, quantifiable behavioural tracking. Experimental reduction of UVA/deep violet light (approximately 370-430 nm) under a long photoperiod (16 h light and 8 h dark) significantly decreased locomotor activities, comparable to the decrease caused by a short photoperiod (8 h light and 16 h dark). In contrast, altering UVA/deep violet light intensities did not cause differences in locomotor levels under a short photoperiod. This modulation of locomotion by UVA/deep violet light under a long photoperiod requires c-opsin1, a UVA/deep violet sensor employing Gi signalling. C-opsin1 also regulates the levels of rate-limiting enzymes for monogenic amine synthesis and of several neurohormones, including pigment-dispersing factor, vasotocin (vasopressin/oxytocin) and neuropeptide Y. Our analyses indicate a complex inteplay between UVA/deep violet light intensities and photoperiod as indicators of annual time.

Decoupling the effects of food and density on life-history plasticity of wild animals using field experiments: Insights from the steward who sits in the shadow of its tail, the North American red squirrel

Long-term studies of wild animals provide the opportunity to investigate how phenotypic plasticity is used to cope with environmental fluctuations and how the relationships between phenotypes and fitness can be dependent upon the ecological context. Many previous studies have only investigated life-history plasticity in response to changes in temperature, yet wild animals often experience multiple environmental fluctuations simultaneously. This requires field experiments to decouple which ecological factor induces plasticity in fitness-relevant traits to better understand their population-level responses to those environmental fluctuations. For the past 32 years, we have conducted a long-term integrative study of individually marked North American red squirrels Tamiasciurus hudsonicus Erxleben in the Yukon, Canada. We have used multi-year field experiments to examine the physiological and life-history responses of individual red squirrels to fluctuations in food abundance and conspecific density. Our long-term observational study and field experiments show that squirrels can anticipate increases in food availability and density, thereby decoupling the usual pattern where animals respond to, rather than anticipate, an ecological change. As in many other study systems, ecological factors that can induce plasticity (such as food and density) covary. However, our field experiments that manipulate food availability and social cues of density (frequency of territorial vocalizations) indicate that increases in social (acoustic) cues of density in the absence of additional food can induce similar life-history plasticity, as does experimental food supplementation. Changes in the levels of metabolic hormones (glucocorticoids) in response to variation in food and density are one mechanism that seems to induce this adaptive life-history plasticity. Although we have not yet investigated the energetic response of squirrels to elevated density or its association with life-history plasticity, energetics research in red squirrels has overturned several standard pillars of knowledge in physiological ecology. We show how a tractable model species combined with integrative studies can reveal how animals cope with resource fluctuations through life-history plasticity.

Seasonal food webs with migrations: multi-season models reveal indirect species interactions in the Canadian Arctic tundra

Models incorporating seasonality are necessary to fully assess the impact of global warming on Arctic communities. Seasonal migrations are a key component of Arctic food webs that still elude current theories predicting a single community equilibrium. We develop a multi-season model of predator-prey dynamics using a hybrid dynamical systems framework applied to a simplified tundra food web (lemming-fox-goose-owl). Hybrid systems models can accommodate multiple equilibria, which is a basic requirement for modelling food webs whose topology changes with season. We demonstrate that our model can generate multi-annual cycling in lemming dynamics, solely from a combined effect of seasonality and state-dependent behaviour. We compare our multi-season model to a static model of the predator-prey community dynamics and study the interactions between species. Interestingly, including seasonality reveals indirect interactions between migrants and residents not captured by the static model. Further, we find that the direction and magnitude of interactions between two species are not necessarily accurate using only summer time-series. Our study demonstrates the need for the development of multi-season models and provides the tools to analyse them. Integrating seasonality in food web modelling is a vital step to improve predictions about the impacts of climate change on ecosystem functioning. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Monitoring the Efficiency of Rhazya stricta L. Plants in Phytoremediation of Heavy Metal-Contaminated Soil

Heavy metal-contaminated soil constitutes many environmental concerns. The toxic nature of heavy metals poses serious threats to human health and the ecosystem. Decontamination of the polluted soil by phytoremediation is of fundamental importance. Vegetation is an appealing and cost-effective green technology for the large-scale phytoremediation of polluted soils. In this paper, a greenhouse experiment was carried out to test the potential of Rhazya stricta as a heavy metal phytoremediator in polluted soil. Plants were grown for three months in pots filled with soils treated with the heavy metals Cd, Pb, Cu, and Zn at rates of 10, 50, and 100 mg/kg. The bioaccumulation factor (BCF) and translocation factor (TF) were calculated to detect the ability of R. stricta to accumulate and transfer heavy metals from soil to plant organs. The results showed that under increasing levels of soil pollution, the bioconcentration of Cd and Zn heavy metals showed the highest values in plant roots followed by leaves, whereas in the case of Pb and Cu, roots showed the highest values followed by stems. Heavy metals accumulation was higher in roots than in stems and leaves. The BCF of Zn reached the highest values in roots and stems for 10 mg/kg soil treatment, followed by the BCFs of Cd, Cu, and Pb. The TF for the different heavy metal pollutants' concentrations was less than unity, suggesting that the plants remediate pollutants by phytostabilization. The TF values ranged from higher to lower were in the order Zn > Cu > Cd > Pb. The rapid growth of R. stricta and its tolerance of heavy metals, as well as its ability to absorb and accumulate metals within the plant, recommends its use in the phytoremediation of slightly polluted soils in arid lands by limiting the heavy metals transport.

Whither mammalian ecology?

The critical agenda for mammalian ecologists over this century is to obtain a synthetic and predictive understanding of the factors that limit the distribution and abundance of mammals on Earth. During the last 100 years, a start has been made on this agenda, but only a start. Most mammal species have been described, but there still are tropical areas of undisclosed species richness. We have been measuring changes in distribution and abundance of many common mammals during the last century, and this monitoring agenda has become more critical as climate change has accelerated and habitat destruction has increased with human population growth. There are a small number of factors that can limit the distribution and abundance of mammals: weather, predation, food supplies, disease, and social behavior. Weather limits distribution and abundance mostly in an indirect manner by affecting food supplies, disease, and predation in the short term and habitat composition and structure in the longer term. A good starting point for all studies of mammals is to define them within a well-structured trophic web, and then quantify the major linkages within that web. We still are far from having data on enough model systems to develop a complete theory and understanding of how food webs are structured and constrained as climate shifts and humans disturb habitats. We have many of the bits and pieces for some of our major ecosystems but a poor understanding of the links and the resilience of our mammalian communities to changes in trophic webs driven by climate change and human disturbances.

From winter to summer and back: Lessons from the parameterization of a seasonal food web model for the Białowieża forest

Dynamic food web models describe how species abundances change over time as a function of trophic and life-history parameters. They are essential to predicting the response of ecosystems to perturbations. However, they are notoriously difficult to parameterize, so that most models rely heavily either on allometric scaling of parameters or inverse estimation of biomass flows. The allometric approach makes species of comparable body mass have near-identical parameters which can generate extinctions within a trophic level. The biomass flow approach is more precise, but is restricted to steady-states, which is not appropriate for time-varying environments. Adequately parameterizing large food webs of temperate and arctic environments requires dealing both with many species of similar sizes and a strongly seasonal environment. Inspired by the rich empirical knowledge on the vertebrate food web of the Białowieża forest, we parameterize a bipartite food web model comprising 21 predators and 124 prey species. Our model is a non-autonomous coupled ordinary differential equations system that allows for seasonality in life-history and predation parameters. Birth and death rates, seasonal descriptions of diet for each species, food requirements and biomass information are combined into a seasonal parameterization of a dynamic food web model. Food web seasonality is implemented with time-varying intrinsic growth rate and interaction parameters, while predation is modelled with both type I and type II functional responses. All our model variants allow for >80% persistence in spite of massive apparent competition, and a quantitative match to observed (seasonal) biomasses. We also identify trade-offs between maximizing persistence, reproducing observed biomasses, and ensuring model robustness to sampling errors. Although multi-annual cycles are expected with type II functional responses, they are here prevented by a strong predator self-regulation. We discuss these results and possible improvements on the model. We provide a general workflow to parameterize dynamic food web models in seasonal environments, based on a real case study. This may help to better predict how biodiverse food webs respond to changing environments.

Drought alters the trophic role of an opportunistic generalist in an aquatic ecosystem

Abiotic change can alter species interactions by modifying species' trophic roles, but this has not been well studied. Until now, bromeliad-dwelling tipulid larvae were thought to positively affect other macroinvertebrates via a facilitative processing chain. However, under drought, we found the opposite. We performed two microcosm experiments in which we factorially manipulated water level and predation by tipulids, and measured the effects on mosquito and chironomid larvae. The experiments differed in whether high water was contrasted with low or no water, allowing us to distinguish between the effects of desiccation stress (no water) and increased encounter rates due to compression of habitat or reductions in prey mobility (low and no water). We also included a caged tipulid treatment to measure any non-consumptive effects. As well as directly reducing prey survival, reductions in water level indirectly decreased chironomid and mosquito survival by altering the trophic role of tipulids. Our results suggest that increased encounter rates with prey led to tipulids becoming predatory under simulated drought, as tipulids consumed prey under both low and no water. When water level was high, tipulids exerted negative non-consumptive effects on prey survival. Because opportunistic predators are common throughout aquatic ecosystems, the effects of drought on the trophic roles of species may be widespread. Such restructuring of food webs should be considered when attempting to predict the ecological effects of environmental change.

Understanding Evolutionary Impacts of Seasonality: An Introduction to the Symposium

Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging. Here, we have identified four important research questions with the goal of advancing our understanding of evolutionary impacts of seasonality. First, we ask how characteristics of environments and species will determine which adaptive response occurs. Relevant characteristics include costs and limits of plasticity, predictability, and reliability of cues, and grain of environmental variation relative to generation time. A second important question is how phenological shifts will amplify or ameliorate selection on physiological hardiness. Shifts in phenology can preserve the thermal niche despite shifts in climate, but may fail to completely conserve the niche or may even expose life stages to conditions that cause mortality. Considering distinct environmental sensitivities of life history stages will be key to refining models that forecast susceptibility to climate change. Third, we must identify critical physiological phenotypes that underlie seasonal adaptation and work toward understanding the genetic architectures of these responses. These architectures are key for predicting evolutionary responses. Pleiotropic genes that regulate multiple responses to changing seasons may facilitate coordination among functionally related traits, or conversely may constrain the expression of optimal phenotypes. Finally, we must advance our understanding of how changes in seasonal fluctuations are impacting ecological interaction networks. We should move beyond simple dyadic interactions, such as predator prey dynamics, and understand how these interactions scale up to affect ecological interaction networks. As global climate change alters many aspects of seasonal variability, including extreme events and changes in mean conditions, organisms must respond appropriately or go extinct. The outcome of adaptation to seasonality will determine responses to climate change.