Biology subjects

Chase, J. M.

Publications and source records attributed to Chase, J. M..

12 recordsLinked to original sources

bioRxiv2025

Land use influences on freshwater biodiversity

Land-use change is a major driver of biodiversity loss, but most generalizations about its effects come from terrestrial ecosystems. In freshwater systems, impacts are often indirect, driven by changes in the surrounding landscape that alter flow, chemistry, and connectivity. Using species-level abundance data from 163 studies across 6 biological groups, we examined how urban, agricultural, and forestry land uses affect freshwater biodiversity at local and regional scales. All three land-use types reduced species richness and altered relative abundance structure compared to natural vegetation, with urban systems showing the strongest and most consistent declines. Only urbanization was associated with biotic homogenization, particularly among abundant species. Biodiversity responses to land-use change also varied with latitude and taxonomic group: tropical assemblages tended to differentiate across sites, while homogenization was more common at higher latitudes. Macroinvertebrates and fish showed the strongest overall declines. These findings challenge assumptions of generality across ecosystems and highlight the need to explicitly incorporate freshwater biodiversity into global change research and policy.

ecology↗

bioRxiv2025

Disturbance interacts with dispersal and niche breadth to shape scale-dependent diversity change in metacommunities

Disturbances influence the maintenance of diversity in important, but complex, ways across spatial and temporal scales. Although disturbance effects on diversity are known to be scale-dependent and taxon-specific, there is little mechanistic understanding of the processes that influence the observed context-dependency. Here, we take a theoretical approach based on metacommunity theory to examine the interaction between metacommunity processes and disturbance in shaping diversity patterns across spatial scales. We find that disturbance shapes diversity at local and regional scales in ways which can lead to either homogenization (decreases in {beta}-diversity) or differentiation (increases in {beta}-diversity). How it does so depend on the spatial extent of the disturbance in the landscape, the dispersal rates and niche breadth of species in the metacommunity, and whether diversity is measured immediately following disturbance or during recovery.We show that high dispersal jointly promotes the rapid recovery of local diversity and the loss of regional diversity, resulting in decreases in {beta}-diversity. Niche breath buffers against diversity loss at both scales during disturbance, but interacts with dispersal to drive transient diversity loss at the regional scale after disturbance. Our results suggest that particular processes in metacommunities interact with disturbance and leave behind distinct signatures of diversity change across scales that can be used to better parse observed patterns of diversity change in empirical systems.

ecology↗

bioRxiv2024

Geometric and demographic effects explain contrasting fragmentation-biodiversity relationships across scales

There is consensus that habitat loss is a major driver of biodiversity loss, while the effects of fragmentation, given a constant total habitat amount, are still debated. Here, we use a process-based metacommunity model to show how strongly scale- and context-dependent fragmentation-biodiversity relationships can emerge from the interplay of two types of fragmentation effects - geometric and demographic. Geometric effects arise from the spatial distribution of species and landscape modification, whereas demographic effects reflect long-term changes in species demographic rates following landscape modification. We introduce a novel approach to partitioning these two types of effects and assess how key ecological processes and factors, such as dispersal, habitat heterogeneity, and edge effects, influence geometric, demographic, and net fragmentation effects across spatial scales. We conclude that the framework of geometric and demographic effects can reconcile previous apparently conflicting results and hopefully unlock and advance the debate on biodiversity change in modified landscapes.

ecology↗

bioRxiv2023

The interacting effects of climate and land-use/land-cover changes on ecological communities

Human activities continue to create land-use/land-cover (LULC) change across the Earths surface, and together with climate change, are major drivers of changes in biodiversity through time. However, the impacts of these spatiotemporally variable drivers on biodiversity change can be complex. We examined the effects of interactions between climate and LULC change on bird communities across the continental United States over nearly three decades. We analyzed temperature and precipitation data alongside data on tree-canopy, cropland, urban, and surface-water cover to understand how climate/LULC-change interactions influence species richness and abundance. Our results revealed stable or increasing trends in species richness, but a decline in overall abundance primarily from common species and a consequent increase in aspects of evenness of communities. We found that areas experiencing warming and drying climates exhibited increased species richness and slower declines in abundance. However, impacts of LULC change had contrasting effects on richness and abundance. Areas that experienced increasing tree-canopy cover over time had increasing trends in species richness, but exacerbated declines in abundance. On the other hand, areas with increasing cropland had moderated abundance declines, but more declining trends in richness. Finally, we found that the effects of climate/LULC-change interactions varied across the range of each pressure. While some interactions support a dominant role of climate change in structuring communities, others indicate that LULC change can mitigate or exacerbate the impact of climate change on biodiversity. Overall, our results highlight the importance of considering the direction and magnitude of each driver when assessing how climate and LULC interactions shape ecological communities.

ecology↗

bioRxiv2023

Disentangling non-random structure from random placement when estimating β-diversity through space or time

There is considerable interest in understanding patterns of {beta}-diversity that measure the amount of change in species composition through space or time. Most hypotheses for {beta}-diversity evoke nonrandom processes that generate spatial and temporal within species aggregation; however, {beta}-diversity can also be driven by random sampling processes. Here, we describe a framework based on rarefaction curves that quantifies the non-random contribution of species compositional differences across samples to {beta}-diversity. We isolate the effect of within-species spatial or temporal aggregation on beta-diversity using a coverage standardized metric of {beta}-diversity ({beta}C). We demonstrate the utility of our framework using simulations and an empirical case study examining variation in avian species composition through space and time in engineered versus natural riparian areas. The primary strengths of our approach are that it provides an intuitive visual null model for expected patterns of biodiversity under random sampling that allows integrating analyses across -, {gamma}-, and {beta}-scales. Importantly, the method can accommodate comparisons between communities with different species pool sizes, and can be used to examine species turnover both within and between meta-communities. Open Research statement: all code and data used in this manuscript are available at the following link: https://github.com/MoBiodiv/beta_concept

ecology↗

bioRxiv2023

Widespread reductions in body size are paired with stable assemblage biomass.

Biotic responses to global change include directional shifts in organismal traits. Body size, an integrative trait that determines demographic rates and ecosystem functions, is often thought to be shrinking in the Anthropocene. Here, we assess the prevalence of body size change in six taxon groups across 5,032 assemblage time-series spanning 1960-2020. Using the Price equation to partition this change into within-species body size versus compositional changes, we detect prevailing decreases in body size through time. Change in assemblage composition contributes more to body size changes than within-species trends, but both components show substantial variation in magnitude and direction. The biomass of assemblages remains remarkably stable as decreases in body size trade-off with increases in abundance. One-Sentence SummaryVariable within-species and compositional trends combine into shrinking body size, abundance increases and stable biomass.

ecology↗

bioRxiv2022

The recovery of biodiversity and species composition after agricultural abandonment across spatial scales

O_LIHuman impacts have led to dramatic biodiversity change which can be highly scale-dependent across space and time. A primary means to manage these changes is via passive (here, the removal of disturbance) or active (management interventions) ecological restoration. The recovery of biodiversity, following the removal of disturbance is often incomplete relative to some kind of reference target. The magnitude of recovery of ecological systems following disturbance depend on the landscape matrix, as well as the temporal and spatial scales at which biodiversity is measured. C_LIO_LIWe measured the recovery of biodiversity and species composition over 27 years in 17 temperate grasslands abandoned after agriculture at different points in time, collectively forming a chronosequence since abandonment from one to eighty years. We compare these abandoned sites with known agricultural land-use histories to never-disturbed sites as relative benchmarks. We specifically measured aspects of diversity at the local plot-scale (-scale, 0.5m2) and site-scale ({gamma}-scale, 10m2), as well as the within-site heterogeneity ({beta}-diversity) and among-site variation in species composition (turnover and nestedness). C_LIO_LIAt our -scale, sites recovering after agricultural abandonment only had 70% of the plant species richness (and [~]30% of the evenness), compared to never-ploughed sites. Within-site {beta}-diversity recovered following agricultural abandonment to around 90% after 80 years. This effect, however, was not enough to lead to recovery at our {gamma}-scale. Richness in recovering sites was [~]65% of that in remnant never-ploughed sites. The presence of species characteristic of the never disturbed sites increased in the recovering sites through time. Forb and legume cover declines in years since abandonment, relative to graminoid cover across sites. C_LIO_LISynthesis. We found that, during the 80 years after agricultural abandonment, old-fields did not recover to the level of biodiversity in remnant never-ploughed sites at any scale. {beta}-diversity recovered more than -scale or {gamma}-scales. Plant species composition recovered, but not completely, over time, and some species groups increased their cover more than others. Patterns of ecological recovery in degraded ecosystems across space and long time-scales can inform effective, targeted active restoration interventions and perhaps, lead to better outcomes. C_LI

ecology↗

bioRxiv2020

Resolving the species pool dependence of beta-diversity using coverage-based rarefaction

Understanding how species are non-randomly distributed in space, as well as how the resulting spatial structure of diversity responds to ecological, biogeographic and anthropogenic drivers is a critical piece of the biodiversity puzzle. However, most metrics that quantify the spatial structure of diversity (i.e., community differentiation), such as Whittakers classical {beta}-diversity metric are influenced by sampling effects. As a result, these measures are influenced by species pool size, species abundance distributions and numbers of individuals. Null models have been proposed to evaluate the degree of differentiation among communities due to spatial structuring relative to that expected from sampling effects. However, to date, these null models do not accommodate the influence of sample completeness (i.e. the proportion of the species pool in the sample). Here, we develop an approach that makes use of individual- and coverage-based rarefaction and extrapolation. Using spatially explicit simulations, we show that our derived metric, {beta}C, captures changes in intraspecific aggregation independently of changes in the species pool size. We then provide two case studies examining spatial structure in forest plots spanning latitudinal gradients: (1) a re-analysis of the "Gentry" plot dataset, and (2) comparing a high diversity plot in Barro Colorado Island, Panama with a low diversity plot in Harvard Forest, Massachusetts, USA. We find no evidence for systematic changes in spatial structure with latitude in these datasets. As it is rooted in biodiversity sampling theory and explicitly controls for sample completeness, our approach represents an important advance over existing null models for spatial aggregation. Potential applications of the approach range from better descriptors of biogeographic diversity patterns to the consolidation of local and regional diversity trends in the current biodiversity crisis. Open research statementThe novel code for the calculation of {beta}C can be found in supplementary material S4. Empirical data sets utilized for this research are as follows: Phillips & Miller (2002), Orwig et al. (2015), Condit et al. (2019). Our research repository including the novel code is also available at https://github.com/t-engel/betaC and will be uploaded to Zenodo upon acceptance of this manuscript.

ecology↗

bioRxiv2019

A multiscale framework for disentangling the roles of evenness, density and aggregation on diversity gradients

Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes changes in species diversity into three components of community structure: the species abundance distribution (SAD), the total community abundance, and the within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that ant species richness decreased along the elevational gradient because of changes in the SAD and in spatial aggregation, but not because of changes in the number of individuals. Specifically, with increasing elevation, species evenness was lower and species were less aggregated. These results do not support the more-individuals hypothesis; alternative hypotheses are required to explain why evenness and aggregation decrease with elevation. Our extension of MoB has the potential to elucidate the drivers of diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients.

ecology↗

bioRxiv2018

The geometry of habitat fragmentation: effects of distribution patterns on short-term species persistence

Land-use changes cause habitat loss and fragmentation and are thus important drivers of anthropogenic biodiversity change. However, there is an ongoing debate about how fragmentation per se affects biodiversity in a given amount of habitat. We illustrate why it is important to distinguish two different aspects of fragmentation to resolve this debate: (i) geometric fragmentation effects, which exclusively arise from the spatial distributions of species and habitat fragments, and (ii) demographic fragmentation effects due to reduced fragment size, increased isolation, or edge effects. While most empirical studies are primarily interested in quantifying demographic fragmentation effects, geometric effects are typically invoked only as post-hoc explanations of biodiversity responses to fragmentation per se. Here, we present an approach to quantify geometric fragmentation effects on species persistence probability. We illustrate this approach using spatial simulations where we systematically varied the initial abundances and distribution patterns (i.e. random, aggregated, and regular) of species as well as habitat amount and fragmentation per se. As expected, we found no geometric fragmentation effects when species were randomly distributed. However, when species were aggregated, we found positive effects of fragmentation per se on persistence probability for a large range of scenarios. For regular species distributions, we found weakly negative geometric effects. These findings are independent of the ecological mechanisms which generate non-random species distributions. Our study helps to reconcile seemingly contradictory results of previous fragmentation studies. Since intraspecific aggregation is a ubiquitous pattern in nature, our findings imply widespread positive geometric fragmentation effects. This expectation is supported by many studies that find positive effects of fragmentation per se on species occurrences and diversity after controlling for habitat amount. We outline how to disentangle geometric and demographic effects of fragmentation, which is critical for predicting the response of biodiversity to landscape change.

ecology↗

bioRxiv2018

A framework for dissecting ecological mechanisms underlying the island species-area relationship

The relationship between an islands size and the number of species on that island--the island species-area relationship (ISAR)--is one of the most well-known patterns in biogeography, and forms the basis for understanding biodiversity loss in response to habitat loss and fragmentation. Nevertheless, there is contention about exactly how to estimate the ISAR, and the influence of the three primary ecological mechanisms--random sampling, disproportionate effects, and heterogeneity-- that drive it. Key to this contention is that estimates of the ISAR are often confounded by sampling and estimates of measures (i.e., island-level species richness) that are not diagnostic of potential mechanisms. Here, we advocate a sampling-explicit approach for disentangling the possible ecological mechanisms underlying the ISAR using parameters derived from individual-based rarefaction curves estimated across spatial scales. If the parameters derived from rarefaction curves at each spatial scale show no relationship with island area, we cannot reject the hypothesis that ISARs result only from random sampling. However, if the derived metrics change with island area, we can reject random sampling as the only operating mechanism, and infer that effects beyond sampling (i.e., disproportionate effects and/or heterogeneity) are also operating. Finally, if parameters indicative of within-island spatial variation in species composition (i.e., {beta}-diversity) increase with island area, we can conclude that intra-island compositional heterogeneity plays a role in driving the ISAR. We illustrate this approach using representative case studies, including oceanic islands, natural island-like patches, and habitat fragments from formerly continuous habitat, illustrating several combinations of underlying mechanisms. This approach will offer insight into the role of sampling and other processes that underpin the ISAR, providing a more complete understanding of how, and some indication of why, patterns of biodiversity respond to gradients in island area.

ecology↗

bioRxiv2017

mobsim: An R package for the simulation and measurement of biodiversity across spatial scales

1. Estimating biodiversity and its changes in space and time poses serious methodological challenges. First, there has been a long debate on how to quantify biodiversity, and second, measurements of biodiversity change are scale-dependent. Therefore comparisons of biodiversity metrics between communities are ideally carried out across scales. Simulation can be used to study the utility of biodiversity metrics across scales, but most approaches are system specific and plagued by large parameter spaces and therefore cumbersome to use and interpret. However, realistic spatial biodiversity patterns can be generated without reference to ecological processes, which suggests a simple simulation framework could provide an important tool for ecologists.\n\n2. Here, we present the R package mobsim that allows users to simulate the abundances and the spatial distribution of individuals of different species. Users can define key properties of communities, including the total numbers of individuals and species, the relative abundance distribution, and the degree of spatial aggregation. Furthermore, the package provides functions that derive biodiversity patterns from simulated communities, or from observed data, as well as functions that simulate different sampling designs.\n\n3. We show several example applications of the package. First, we illustrate how species rarefaction and accumulation curves can be used to disentangle changes in the fundamental biodiversity components: (i) total abundance, (ii) relative abundance distribution, (iii) and species aggregation. Second, we demonstrate how mobsim can be used to assess the performance of species-richness estimators. The latter indicates how spatial aggregation challenges classical non-spatial species-richness estimators.\n\n4. mobsim allows the simulation and analysis of a large range of biodiversity scenarios and sampling designs in an efficient and comprehensive way. The simplicity and control provided by the package can also make it a useful didactic tool. The combination of controlled simulations and their analysis will facilitate a more rigorous interpretation of real world data that exhibit sampling effects and scale-dependence.

ecology↗