Integrating spatial and temporal approaches to understanding species richness

Environmental variables drive spatial patterns of trophic diversity in mammals

Understanding environmental drivers of species diversity has become increasingly important under climate change. Different trophic groups (predators, omnivores and herbivores) interact with their environments in fundamentally different ways and may therefore be influenced by different environmental drivers. Using random forest models, we identified drivers of terrestrial mammals' total and proportional species richness within trophic groups at a global scale. Precipitation seasonality was the most important predictor of richness for all trophic groups. Richness peaked at intermediate precipitation seasonality, indicating that moderate levels of environmental heterogeneity promote mammal richness. Gross primary production (GPP) was the most important correlate of the relative contribution of each trophic group to total species richness. The strong relationship with GPP demonstrates that basal-level resource availability influences how diversity is structured among trophic groups. Our findings suggest that environmental characteristics that influence resource temporal variability and abundance are important predictors of terrestrial mammal richness at a global scale.

User-centered visual explorer of in-process comparison in spatiotemporal space

Abstract

We propose a user-centered visual explorer (UcVE) for progressive comparing multiple visualization units in spatiotemporal space. We create unique unit visualization with the customizable aggregated view based on the visual metaphor of flower bursts. Each visualization unit is encoded with the abstraction of spatiotemporal properties. To reduce user cognition load, UcVE allows users to visualize, save, and track in-the-process exploration results. In coordination of storage sequence and block tracking views, UcVE can facilitate comparison with multiple visualization units concurrently, selected from historical and current exploration results. UcVE offers a flexible geo-based layout, with aggregation functions and temporal views of the timeline with categorized events, to maximize the user's exploration capabilities. Finally, we demonstrate the usefulness by using COVID-19 datasets, case studies with different user scenarios, and expert feedback.

Graphical abstract

The Effects of Multi-Scale Climate Variability on Biodiversity Patterns of Chinese Evergreen Broad-Leaved Woody Plants: Growth Form Matters

Large-scale patterns of species diversity are thought to be linked to contemporary climate variability and Quaternary glacial–interglacial climate change. For plants, growth forms integrate traits related to competition or migration capacity, which determine their abilities to deal with the climate variability they face. Evergreen broad-leaved woody plants (EBWPs) are major components of numerous biomes in the subtropical and tropical regions. Hence, incorporating phylogenetic (temporal) and biogeographic (spatial) approaches, we assessed the relative importance of short- and long-term climate variability for biodiversity patterns of different growth forms (i.e., tree, shrub, liana, and bamboo) in EBWPs. We used a dated phylogeny and the distribution records for 6,265 EBWP species which are naturally occurred in China, and computed the corrected weighted endemism, standardized phylogenetic diversity and net relatedness index for the four growth forms, respectively. Ordinary least squares linear regressions, spatial error simultaneous autoregressive models, partial regression and hierarchical variation partitioning were employed to estimate the explanatory power of contemporary climate variability and climate-change velocity from the Last Glacial Maximum to the present. Our results showed that short- and long-term climate variability play complementary role in the biogeographic patterns of Chinese EBWPs. The former had larger effects, but the legacy effects of past climate changes were also remarkable. There were also differences in the effects of historical and current climate among the four growth forms, which support growth forms as a critical plant trait in predicting vegetation response to climate change. Compared to the glacial-interglacial climate fluctuation, seasonality as a unique feature of mid-latitude monsoon climate played a dominant role in the diversification and distribution of EBWP species at the macroscale. The results indicated that the relative importance of climate variability at different temporal scales may relate to distinct mechanisms. To understand effects of future climate change on species distribution more thoroughly, climate conditions in different time scales should be incorporated.

Dynamic social learning in temporally and spatially variable environments

Cultural evolution is partly driven by the strategies individuals use to learn behaviour from others. Previous experiments on strategic learning let groups of participants engage in repeated rounds of a learning task and analysed how choices are affected by individual payoffs and the choices of group members. While groups in such experiments are fixed, natural populations are dynamic, characterized by overlapping generations, frequent migrations and different levels of experience. We present a preregistered laboratory experiment with 237 mostly German participants including migration, differences in expertise and both spatial and temporal variation in optimal behaviour. We used simulation and multi-level computational learning models including time-varying parameters to investigate adaptive time dynamics in learning. Confirming theoretical predictions, individuals relied more on (conformist) social learning after spatial compared with temporal changes. After both types of change, they biased decisions towards more experienced group members. While rates of social learning rapidly declined in rounds following migration, individuals remained conformist to group-typical behaviour. These learning dynamics can be explained as adaptive responses to different informational environments. Summarizing, we provide empirical insights and introduce modelling tools that hopefully can be applied to dynamic social learning in other systems.

Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and consists mostly of repeated static analyses. Here we propose a novel analytical framework to assess metacommunity processes using path analyses of spatial and temporal diversity turnovers. We detail the principles and practical aspects of this framework and apply it to simulated datasets to illustrate its ability to decipher the respective contributions of entangled drivers of metacommunity dynamics. We then apply it to four empirical datasets. Empirical results support the view that metacommunity dynamics may be generally shaped by multiple ecological processes acting in concert, with environmental filtering being variable across both space and time. These results reinforce our call to go beyond static analyses of metacommunities that are blind to the temporal part of environmental variability.

Spatial and temporal variations of aridity shape dung beetle assemblages towards the Sahara desert

Background

Assemblage responses to environmental gradients are key to understand the general principles behind the assembly and functioning of communities. The spatially and temporally uneven distribution of water availability in drylands creates strong aridity gradients. While the effects of spatial variations of aridity are relatively well known, the influence of the highly-unpredictable seasonal and inter-annual precipitations on dryland communities has been seldom addressed.

Aims

Here, we study the seasonal and inter-annual responses of dung beetle (Coleoptera, Scarabaeidae) communities to the variations of water availability along a semiarid region of the Mediterranean.

Methods

We surveyed a 400 km linear transect along a strong aridity gradient from the Mediterranean coast to the Sahara (Eastern Morocco), during four sampling campaigns: two in the wet season and two in the dry season. We measured species richness, abundance and evenness. Variations in community composition between sites, seasons and years were assessed through beta diversity partitioning of dissimiliarity metrics based on species occurrences and abundances. The effects of climate, soil, vegetation and dung availability were evaluated using Spearman-rank correlations, general linear regressions and partial least-squares generalized linear regressions for community structure, and non-metric multi-dimensional scaling, Permutational Analysis of Variance (PERMANOVA) and distance-based RDA variation partitioning for compositional variations.

Results

Dung beetle abundance and species richness showed large seasonal variations, but remained relatively similar between years. Indeed, aridity and its interaction with season and year were the strongest correlates of variations in species richness and composition. Increasing aridity resulted in decreasing species richness and an ordered replacement of species, namely the substitution of the Mediterranean fauna by desert assemblages dominated by saprophagous and generalist species both in space towards the Sahara and in the dry season.

Discussion

Our study shows that aridity determines composition in dung beetle communities, filtering species both in space and time. Besides the expected decrease in species richness, such environmental filtering promotes a shift towards generalist and saprophagous species in arid conditions, probably related to changes in resource quality along the transect and through the year. Our results highlight the importance of considering the effects of the highly-unpredictable seasonal and inter-annual variations in precipitation when studying dryland communities.

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

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

Temporal changes in bird functional diversity across the United States

Global changes are modifying the structure of species assemblages, but the generality of resulting diversity patterns and of their drivers is poorly understood. Any such changes can be detected and explained by comparing temporal trends in taxonomic and functional diversity over broad spatial extents. In this study, we addressed three complementary questions: How did bird taxonomic and functional diversity change over the past 40 years in the conterminous United States? Are these trends non-linear? Can temporal variations in functional diversity be explained by broad-scale changes in climate and vegetation productivity? We quantified changes in taxonomic and functional diversity for 807 bird assemblages over the past four decades (1970-2011) considering a suite of 16 ecological traits for 435 species. We found increases in local bird species richness and taxonomic equitability that plateaued in the early 2000's while total abundance declined over the whole period. Functional richness, the total range of traits in an assemblage, increased due to the rising prevalence of species with atypical life-history strategies and under-represented habitat or trophic preferences. However, these species did not trigger major changes in the functional composition of bird assemblages. Inter-annual variations in climate and primary productivity explained the richness of bird life-history traits in local assemblages, suggesting that these traits are influenced by broad-scale environmental factors, while others respond more to more local drivers. Our results highlight that a comparative analysis of the multiple facets of functional diversity can raise novel insights on processes underlying temporal trends in biodiversity.

Species Turnover through Time: Colonization and Extinction Dynamics across Metacommunities

Island biogeography and metacommunity theory often use equilibrium assumptions to predict local diversity, yet nonequilibrium dynamics are common in nature. In nonequilibrium communities, local diversity fluctuates through time as the relative importance of colonization and extinction change. Here, we test the prevalence and causes of nonequilibrium dynamics in metacommunities of mites associated with rubber trees distributed over large spatial (>1,000 km) and temporal (>30-60 generations) scales in Brazil. We measured colonization and extinction rates to test species turnover and nonequilibrium dynamics over a growing season. Mite metacommunities exhibited nonequilibrium dynamics for most months of the year, and these dynamics tracked climatic conditions. Monthly shifts in temperature of more than 1°C resulted in nonequilibrium dynamics, as did mean temperatures outside of two critical ranges. Nonequilibrium dynamics were caused by a change in colonization with temperature change and changes in both colonization and extinction with absolute temperature. Species turnover showed different trends; high relative humidity increased both colonization and extinction rates, increasing turnover but not nonequilibrium dynamics. Our study illustrates that testing nonequilibrium dynamics can provide new insights into the drivers of colonization, extinction, and diversity fluctuations in metacommunities.

Psychometrics and Assessment of an Empathy Distance Gradient

Research has indicated declining empathy within specific professions and social structures. Few psychometric instruments have addressed empathy within the context of psychological distance/relatedness to other individuals and even to other species, relationships that can be important contributors to psychological well-being and health. We developed and tested the Empathy Gradient Questionnaire (EGQ), which contains five subscales (i.e., Family, Friend, Peer, Distant Other, and Species Empathy) representing increasing psycho-spatial distances. We used LISREL to factor validate the five-factor structure of the EGQ, and we evaluated levels of empathy among a sample of n = 161 individuals, aged 18 to 60+. The EGQ was shown to have high subscale (0.80-0.89) and overall internal consistencies (0.94). The factor pattern and structural equation models showed five latent factors explaining 69.8% of variance for all variables (goodness-of-fit index [GFI] = 0.98, adjusted goodness-of-fit index [AGFI] = 0.98, standardized root mean square residual [SRMR] = 0.06, comparative fit index [CFI] = 0.92). There were no significant effects for age, gender, or race on overall empathy or for each of the five subscales. A decreasing gradient was noted for Friend to Species Empathies.

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

Community ecology in a changing environment: Perspectives from the Quaternary

Community ecology and paleoecology are both concerned with the composition and structure of biotic assemblages but are largely disconnected. Community ecology focuses on existing species assemblages and recently has begun to integrate history (phylogeny and continental or intercontinental dispersal) to constrain community processes. This division has left a "missing middle": Ecological and environmental processes occurring on timescales from decades to millennia are not yet fully incorporated into community ecology. Quaternary paleoecology has a wealth of data documenting ecological dynamics at these timescales, and both fields can benefit from greater interaction and articulation. We discuss ecological insights revealed by Quaternary terrestrial records, suggest foundations for bridging between the disciplines, and identify topics where the disciplines can engage to mutual benefit.

An empirical evaluation of four variants of a universal species-area relationship

The Maximum Entropy Theory of Ecology (METE) predicts a universal species–area relationship (SAR) that can be fully characterized using only the total abundance (N) and species richness (S) at a single spatial scale. This theory has shown promise for characterizing scale dependence in the SAR. However, there are currently four different approaches to applying METE to predict the SAR and it is unclear which approach should be used due to a lack of empirical comparison. Specifically, METE can be applied recursively or non-recursively and can use either a theoretical or observed species-abundance distribution (SAD). We compared the four different combinations of approaches using empirical data from 16 datasets containing over 1000 species and 300,000 individual trees and herbs. In general, METE accurately downscaled the SAR (R² > 0.94), but the recursive approach consistently under-predicted richness. METE’s accuracy did not depend strongly on using the observed or predicted SAD. This suggests that the best approach to scaling diversity using METE is to use a combination of non-recursive scaling and the theoretical abundance distribution, which allows predictions to be made across a broad range of spatial scales with only knowledge of the species richness and total abundance at a single scale.

The effect of positive interactions on temporal turnover of community composition along an environmental gradient

It has been demonstrated that the interplay between negative and positive interactions simultaneously shapes community structure and composition. However, few studies have attempted to examine the effect of facilitation on compositional changes in communities through time. Additionally, due to the difficulties in collecting the long-term data, it would be useful to indicate the rate of temporal turnover using a readily obtainable metric. Using an individual-based model incorporating plant strategies, we examined the role of facilitation on the temporal turnover of communities located at different positions along an environmental gradient for three model scenarios: CM without facilitation; CFM-U, a unimodal relationship between facilitation and environmental severity; and CFM-L, a positively linear relationship between facilitation and environmental severity. Our results demonstrated that facilitation could increase, decrease or have no remarkable effect on temporal turnover. The specific outcome depended on the location of the focal community across the environmental gradient and the model employed. Compared with CM, the inclusion of positive interactions (i.e. CFM-U and CFM-L), at intermediate environmental stress levels (such as S = 0.7 and 0.8) resulted in lower Bray-Curtis similarity values; at other severity levels, facilitation slowed down (such as S = 0.3 and 0.4 at low to medium stress levels, and S = 0.9 at high stress levels) or had only a subtle effect (such as at S = 0.1) on temporal turnover. We also found that the coefficient of variation (CV) in species abundances and the rate of temporal variability showed a significant quadratic relationship. Our theoretical analysis contributes to the understanding of factors driving temporal turnover in biotic communities, and presents a potential metric (i.e. CV in species abundances) assessing the consequences of ongoing environmental change on community structure.

Assessing paleo-biodiversity using low proxy influx

We developed an algorithm to improve richness assessment based on paleoecological series, considering sample features such as their temporal resolutions or their volumes. Our new method can be applied to both high- and low-count size proxies, i.e. pollen and plant macroremain records, respectively. While pollen generally abounds in sediments, plant macroremains are generally rare, thus leading to difficulties to compute paleo-biodiversity indices. Our approach uses resampled macroremain influxes that enable the computation of the rarefaction index for the low influx records. The raw counts are resampled to a constant resolution and sample volume by interpolating initial sample ages at a constant time interval using the age∼depth model. Then, the contribution of initial counts and volume to each interpolated sample is determined by calculating a proportion matrix that is in turn used to obtain regularly spaced time series of pollen and macroremain influx. We applied this algorithm to sedimentary data from a subalpine lake situated in the European Alps. The reconstructed total floristic richness at the study site increased gradually when both pollen and macroremain records indicated a decrease in relative abundances of shrubs and an increase in trees from 11,000 to 7,000 cal BP. This points to an ecosystem change that favored trees against shrubs, whereas herb abundance remained stable. Since 6,000 cal BP, local richness decreased based on plant macroremains, while pollen-based richness was stable. The reconstructed richness and evenness are interrelated confirming the difficulty to distinguish these two aspects for the studies in paleo-biodiversity. The present study shows that low-influx bio-proxy records (here macroremains) can be used to reconstruct stand diversity and address ecological issues. These developments on macroremain and pollen records may contribute to bridge the gap between paleoecology and biodiversity studies.

A meta-analysis of changes in bacterial and archaeal communities with time

Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species–time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and ‘macro'-bial communities alike.

Reversal in the relationship between species richness and turnover in a phytoplankton community

Negative relationships between species richness and the rate of compositional turnover are common, suggesting that diverse communities have greater stability than depauperate ones; however, the mechanistic basis for this pattern is still widely debated. Species richness and turnover can covary either because they are mechanistically linked or because they share common environmental drivers. Few empirical studies have combined long-term changes in community composition with multiple drivers of environmental change, and so little is known about how the underlying mechanisms of species coexistence interact with changes in the mean and variability of environmental conditions. Here, we use a 33 year long time series (1976-2008) of phytoplankton community composition from Lake Zurich, to examine how environmental variation influences the relationship between richness and annual turnover. We find that the relationship between richness and annual turnover reverses midway through the time series (1992-1993), leading to a hump-shaped relationship between species richness and annual turnover. Using structural equation modeling we show that annual turnover and diversity are independently associated with different drivers of environmental change. Furthermore, we find that the observed annual sequences of community assembly give rise to rates of species accumulation that are more heterogeneous through time than expected by chance, likely owing to a high proportion of species showing significant autocorrelation and to strong positive covariation in the occurrences of species.

An automated platform for phytoplankton ecology and aquatic ecosystem monitoring

High quality monitoring data are vital for tracking and understanding the causes of ecosystem change. We present a potentially powerful approach for phytoplankton and aquatic ecosystem monitoring, based on integration of scanning flow-cytometry for the characterization and counting of algal cells with multiparametric vertical water profiling. This approach affords high-frequency data on phytoplankton abundance, functional traits and diversity, coupled with the characterization of environmental conditions for growth over the vertical structure of a deep water body. Data from a pilot study revealed effects of an environmental disturbance event on the phytoplankton community in Lake Lugano (Switzerland), characterized by a reduction in cytometry-based functional diversity and by a period of cyanobacterial dominance. These changes were missed by traditional limnological methods, employed in parallel to high-frequency monitoring. Modeling of phytoplankton functional diversity revealed the importance of integrated spatiotemporal data, including circadian time-lags and variability over the water column, to understand the drivers of diversity and dynamic processes. The approach described represents progress toward an automated and trait-based analysis of phytoplankton natural communities. Streamlining of high-frequency measurements may represent a resource for understanding, modeling and managing aquatic ecosystems under impact of environmental change, yielding insight into processes governing phytoplankton community resistance and resilience.

Can unified theories of biodiversity explain mammalian macroecological patterns?

The idea of a unifying theory of biodiversity linking the diverse array of macroecological patterns into a common theoretical framework is very appealing. We explore this idea to examine currently proposed unified theories of biodiversity (UTBs) and their predictions. Synthesizing the literature on the macroecological patterns of mammals, we critically evaluate the evidence to support these theories. We find general qualitative support for the UTBs' predictions within mammals, but rigorous testing is hampered by the types of data typically collected in studies of mammals. In particular, abundance is rarely estimated for entire mammalian communities or of individual species in multiple locations, reflecting the logistical challenges of studying wild mammal populations. By contrast, there are numerous macroecological patterns (especially allometric scaling relationships) that are extremely well characterized for mammals, but which fall outside the scope of current UTBs. We consider how these theories might be extended to explain mammalian biodiversity patterns more generally. Specifically, we suggest that UTBs need to incorporate the dimensions of geographical space, species' traits and time to reconcile theory with pattern.

Biological diversity in a changing world

From the pioneering explorations of Joseph Banks (later a President of the Royal Society), to the present day, a great deal has been learnt about the extent, distribution and stability of biological diversity in the world. We now know that diverse life can be found even in the most inhospitable places. We have also learned that biological diversity changes through time over both large and small temporal scales. These natural changes track environmental conditions, and reflect ecological and evolutionary processes. However, anthropogenic activities, including overexploitation, habitat loss and climate change, are currently causing profound transformations in ecosystems and unprecedented loss of biological diversity. This series of papers considers temporal variation in biological diversity, examines the extent of human-related change relative to underlying natural change and builds on these insights to develop tools and policies to help guide us towards a sustainable future.