Biology subjects

Beckerman, A. P.

Publications and source records attributed to Beckerman, A. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Vertebrates do not display consistent declines in abundance or stability with contemporary range or realized climate niche centrality

The abundant-centre (ACH) and stable-centre hypotheses (SCH) predict population abundance and stability decline with increasing distances from a species' range and multivariate climate niche centres. ACH and SCH are widely held assumptions underpinning many ecological and conservation applications, with range and climate centrality often assumed to reflect suitability. However, empirical support that abundance (distance-abundance) and stability (distance-variability) decline away from range and climate centres is mixed and hampered by radically different climate centrality assumptions. Here, we test distance-abundance relationships in >5000 vertebrate species and distance-variability relationships in >1000 vertebrate species across their realized geographic and climate niche spaces. We found no vertebrate taxa display consistent declines in abundance or stability with increasing distances from range centres or realized climate (niche) centres modelled from species' breeding ranges, native ranges or contemporary occurrences. Distance-abundance and distance-variability relationships were weak and inconsistent across taxa irrespective of centrality metric, modelling approach, climate variables, abundance metric or dataset. Contemporary vertebrate abundance patterns, therefore, are often decoupled from position in contemporary range and realized climate space, challenging a central assumption of core-periphery models. Broadly, our study indicates that frequently used range and climate centrality metrics may be weak predictors of vertebrate abundance patterns in contemporary landscapes and biological forecasting or climate change applications should be cautious of their unvalidated use.

ecology↗

bioRxiv2026

Temporal resolution reshapes dynamics of inferred community structure and extinction selectivity across the Permian-Triassic mass extinction

The Permian-Triassic mass extinction fundamentally restructured ecosystems, yet it remains unresolved whether ecological collapse unfolded gradually or in discrete steps, and how extinction selectivity varied with environmental change. Here, we analyse marine food webs from Meishan (China) at high temporal resolution. We show that trophic structure destabilised prior to peak biodiversity loss, followed by a structural tipping point during the extinction interval when the community became less robust to secondary extinctions. Extinction selectivity shifted substantially across the study interval. During the extinction interval, extinction was concentrated at lower trophic levels, propagating upwards from benthic herbivores to higher-level consumers. Although coarse resolution preserves temporal trends in trophic structure and extinction selectivity, it obscures abrupt transitions, sequential extinction dynamics, and critical shifts in ecological organisation. We demonstrate that temporal resolution governs inference of extinction dynamics, with important implications for reconstructing past ecological crises and interpreting ecosystem responses to rapid environmental change.

paleontology↗

bioRxiv2026

Adaptation to free-living drives loss of beneficial endosymbiosis through metabolic trade-offs

Symbioses are widespread (1) and underpin the function of diverse ecosystems (2-6), but their evolutionary stability is challenging to explain (7,8). Fitness trade-offs between contrasting intracellular and extracellular niches could act to stabilise endosymbioses because adaptation to either niche is predicted to reduce fitness in the alternate niche, thus reinforcing symbiosis (8,9). Here, we experimentally evolved four diverse Chlorella green algal endosymbionts of Paramecium bursaria to free-living conditions supplying either an amino acid, as provisioned by hosts (10,11), or nitrate, as available in freshwater (12), as the sole nitrogen source. Experimental algal populations adapted to free-living environments, generally increasing in population density and cellular chlorophyll content over time. In one of the four endosymbiont strains, adaptation to the nitrate free-living environment, but not the amino acid environments, drove the loss of fitness benefits to the host in reconstituted symbioses. This loss was not associated with reduced ability to grow on host-provisioned amino acids, nor lost ability to release the sugars provisioned to the host (10,13). Genome sequencing of evolved algal lines revealed genomic divergence between nitrate-adapted and amino acid-adapted lines, affecting genes involved with metabolic organisation and intracellular resource transport. Untargeted metabolomic profiling further showed extensive changes to membrane remodelling and turnover in N-evolved lines. Together, our data support a role for metabolic trade-offs driving divergence between contrasting intracellular and extracellular niches, with nitrogen as a key environmental axis driving divergence. Fitness trade-offs may, therefore, be a general, simple mechanism acting to reinforce symbiosis, contributing to evolutionary stability.

evolutionary biology↗

bioRxiv2026

No global collapse of food webs across the Permian-Triassic Mass Extinction

The Permian-Triassic mass extinction (PTME), the Earths most severe biotic crisis associated with extreme environmental perturbations, eliminated >80% of marine species1. However, whether it triggered a globally pervasive top-down collapse of marine food webs, and whether recovery proceeded through bottom-up reassembly, remain unresolved2-4. Here we reconstruct spatially explicit metacommunity food webs from seven regions spanning equatorial to high latitudes to test how extinction dynamics and ecosystem reorganization varied geographically. By integrating estimates of community structure and species interactions, we provide direct inference on trophic disruption across the PTME. Despite catastrophic species loss and flattening of the latitudinal diversity gradient5, trophic collapse was not globally uniform, and higher trophic levels were not globally truncated. Instead, extinction selectivity was spatially heterogenous and tracked environmental severity. Benthic, low-motility herbivores with limited respiratory capacity were disproportionately lost, consistent with intensified warming, deoxygenation and disruption of primary productivity under elevated pCO2. Mid-to high-latitude communities became top-heavy and structurally complex, whereas tropical systems remained bottom-heavy and less robust to secondary extinction. These results demonstrate that trophic disruption and recovery were geographically structured, mediated by environmental forcing, species traits and pre-extinction food-web architecture, with implications for predicting marine ecosystem responses to ongoing climate change.

paleontology↗

bioRxiv2025

Reintroductions backfire by destabilising food webs and triggering further extinction cascades

Conservation interventions like reintroduction are considered vital to bending the curve of biodiversity loss1, with the potential for multiplicative benefits that not only reduce extinction pressure on the reintroduced species, but also restore wider community dynamics and ecosystem functions2,3. Its growing popularity reflects these perceived benefits4. Reintroduction success is usually judged only by the survival of the released species4, but there is no guarantee that the wider community will recover. Using simulated food webs, we show that reintroductions can frequently have unintended negative consequences: triggering extinction cascades, reducing biomass, and destabilising communities. These perverse impacts are unlikely to be detected as reintroduction success is often measured solely by the ability for reintroduced species to survive - which our models suggest is likely - introducing a risk that conservation action superficially appears successful but is actually further depleting our ecosystems.

ecology↗

bioRxiv2025

Metabolomic profiling of glyphosate resistance evolution in green alga Chlamydomonas reinhardtii

The widespread use of glyphosate has led to a rapid increase in glyphosate resistant weeds at a considerable cost to agriculture. Furthermore, agricultural run-off means non-target, natural ecosystems are also affected. Resistance may arise both through mutations to target enzyme EPSPS in the shikimate pathway generating insensitivity to glyphosate and through non-target site mutations regulating the dose of glyphosate reaching the shikimate pathway. Either mechanism may trade-off against normal cell functioning. Here, using experimental evolution of replicated Chlamydomonas reinhardtii populations facing glyphosate, we reveal the metabolomic fingerprint of both glyphosate action and emerging resistance by applying untargeted metabolomic screens throughout the course of resistance evolution. Furthermore, this allows us to evaluate potential underlying molecular mechanisms and fitness costs. We find evidence of build-up of shikimate pathway metabolites, a characteristic signal of glyphosate action, that subsides but does not disappear as resistance evolves, suggesting a fitness trade-off. Concurrent with this is evidence of cell wide disruption of the amino acid pool, that stabilises as resistance evolves. We also found evidence of effects of glyphosate on membrane lipids and increased levels of reactive oxygen species persisting after resistance had evolved. This suggests a considerable effect of the recently described secondary effect of glyphosate: oxidative damage. These data highlight several metabolic processes disrupted by and persisting with the evolution of resistance to glyphosate and may provide a template for enhancing predictions of population and ecosystem effects.

evolutionary biology↗

bioRxiv2025

Biodiversity temporal trends are reshaping food web structure and redundancy in riverine ecosystems

Biodiversity temporal changes are expected to profoundly impact ecosystem functioning and stability, yet large-scale empirical evidence remains limited. Bridging this gap requires aligning biodiversity temporal trends with food web theory and Biodiversity-Ecosystem Functioning research, both of which provide strong predictions about the ecological consequences of biodiversity loss. Most insights on those consequences currently rely on spatial comparisons of ecological communities, assuming they reflect temporal trends--a space-for-time substitution. Here, we analyze biodiversity and food web time series from over 400 riverine fish communities across France (1995-2018) to evaluate how biodiversity temporal trends reshape food web structure and community functioning. We examine relationships among species richness, community biomass, and three key food web metrics: connectance, weighted average trophic level, and trophic pathway redundancy. We also test the space-for-time hypothesis using spatial gradients and a theoretical food web model. Our structural equation models and robustness analysis reveal that declines in species richness strongly correlate with reduced community biomass, with top trophic-level species playing a disproportionate role in food web changes. Declining biomass is associated with the loss of top trophic levels and decreased connectance, while temporal changes in species richness negatively correlates with changes in connectance. Both biomass and species richness declines reduce trophic pathway redundancy, suggesting that biodiversity loss weakens community robustness to future perturbations. Our findings align with food web theory and Biodiversity-Ecosystem Functioning research, support the validity of space-for-time approaches for basic food web metrics, and demonstrate the relevance of food web metrics as indicators of ecosystem function and fragility. SignificanceRates of biodiversity loss raise urgent concerns about ecosystem functioning and stability, yet how biodiversity trends directly impact these critical processes remains unclear. For instance, food web & Biodiversity-Ecosystem Functioning research has delivered strong predictions about the ecological consequences of biodiversity loss but lack of empirical assessment. Using an extensive dataset of riverine fish communities, we link biodiversity trends to temporal changes in food web structure. We demonstrate that temporal changes in species richness and community biomass consistently associate with altered food web structure. We found that declining biodiversity reduces trophic pathway redundancy, likely increasing ecosystem vulnerability to perturbations. Our findings suggest that food web structure metrics could serve as valuable indicators for monitoring ecosystem health and guiding conservation strategies.

ecology↗

bioRxiv2024

Response diversity is a major driver of temporal stability in complex food webs

Global change constitutes a major threat to biodiversity and ecosystem functioning which can materialise in the temporal stability of ecological communities. However, the majority of research on stability has focused on single trophic level communities and has not yet integrated classic theory about species richness and food web structure with more recent theory centred on response diversity and stochasticity. Using a stochastic, bioenergenetic food web model, we integrate these multiple bodies of theory to reveal that response diversity is a major driver of community stability. Moreover, our integrated theory reveals that positive stability-richness relationships emerge only in the presence of response diversity. In contrast to previous work, food web structure is only a secondary driver of community stability, but interacts with response diversity to determine the sign of the stability-richness relationship. Our study reveals identifiable pathways by which food web structure and response diversity drive community stability, and raises concerns about how the loss of response diversity (biotic homogenisation) may lead to a breakdown of community stability.

ecology↗

bioRxiv2024

EcologicalNetworksDynamics.jl: A Julia package to simulate the temporal dynamics of complex ecological networks

O_LISpecies interactions play a crucial role in shaping biodiversity, species coexistence, population dynamics, community stability and ecosystem functioning. Our understanding of the role of the diversity of species interactions driving these species, community and ecosystem features is limited because current approaches often focus only on trophic interactions. This is why a new modelling framework that includes a greater diversity of interactions between species is crucially needed. C_LIO_LIWe developed a modular, user-friendly, and extensible Julia package that delivers the core functionality of the bio-energetic food web model. Moreover, it embeds several ecological interaction types alongside the capacity to manipulate external drivers of ecological dynamics like temperature. These new features represent important processes known to influence biodiversity, coexistence, functioning and stability in natural communities. Specifically, they include: a) an explicit multiple nutrient intake model for producers, b) competition among producers, c) temperature dependence implemented via the Boltzmann-Arhennius rule, and d) the ability to model several non-trophic interactions including competition for space, plant facilitation, predator interference and refuge provisioning. C_LIO_LIThe inclusion of the various features provides users with the ability to ask questions about multiple simultaneous processes and stressor impacts, and thus develop theory relevant to real world scenarios facing complex ecological communities in the Anthropocene. It will allow researchers to quantify the relative importance of different mechanisms to stability and functioning of complex communities. C_LIO_LIThe package was build for theoreticians seeking to explore the effects of different types of species interactions on the dynamics of complex ecological communities, but also for empiricists seeking to confront their empirical findings with theoretical expectations. The package provides a straightforward framework to model explicitly complex ecological communities or provide tools to generate those communities from few parameters. C_LI

ecology↗

bioRxiv2024

Glyphosate resistance evolution to lethal and sublethal doses in chemostat populations of model organism Chlamydomonas reinhardtii

Herbicide resistant weeds are an increasing economic and ecological problem world-wide. Evolutionary theory and insight from experiments testing this theory are now a central part of solving resistance problems. More specifically, experimental evolution, where populations are allowed to evolve under specific conditions, can offer substantial insights into the trade-offs that govern the pace at which resistance arises. Here we leverage the green alga Chlamydomonas reinhardtii facing glyphosate as a model plant system to evaluate such theory, monitoring the level of evolved resistance and associated fitness costs throughout the course of adaptation. On a gradient of lethal and sub-lethal doses of glyphosate, we found evidence for evolved resistance from standing genetic variation but limited evidence for classic growth rate trade-offs that are expected to affect the pace of resistance evolution.

evolutionary biology↗

bioRxiv2024

Evidence for a trade-off between glyphosate resistance and anti-grazer defence in green alga Chlamydomonas reinhardtii

O_LIThe widespread and persistent use of herbicides has both selected for dramatically increased levels of herbicide resistance in the weed populations they were designed to control, and increased contamination of non-target ecosystems. C_LIO_LIExperimental evolution using microbes offers the opportunity to explore basic evolutionary theory, including testing for the existence of intrinsic and extrinsic fitness trade-offs, connecting them to the patterns observed in both natural and agricultural populations. C_LIO_LIWe used green alga Chlamydomonas reinhardtii adapted to high and moderate levels of glyphosate to test for an extrinsic cost to glyphosate resistance in the form of a trade-off with clumping, the inducible anti-grazer defence deployed against gape-limited micrograzers. Through exposing the algae to freshwater rotifer Brachionus calyciflorus as well as their isolated info-chemicals, we test whether glyphosate resistance affects ability to deploy defences as well as ability to withstand grazing compared to control populations. C_LIO_LIWe find an increase in variation rather than uni-directional effect of glyphosate treatment, with treated populations exhibiting both lower and higher degree of anti-grazer defence compared to controls. Furthermore, our data suggests there are at least three different glyphosate resistant phenotypes present, with two conferring different extrinsic costs in the form of tradeoff with anti-grazer defence. C_LIO_LIOur study indicates that extrinsic costs to glyphosate resistance may be context dependent in this system, possibly only being present at particular stages in the adaptation process or with particular resistance mechanisms. C_LI

ecology↗

bioRxiv2024

A framework for reconstructing ancient food webs using functional trait data

O_LIFood webs provide quantitative insights into the structure and dynamics of ecological communities. Previous work has shown their utility in understanding community responses to modern and ancient perturbations, including anthropogenic change and mass extinctions. However, few ancient food webs have been reconstructed due to difficulties assessing trophic interactions amongst extinct species derived from an incomplete fossil record. C_LIO_LIWe present and assess the Paleo Food web Inference Model (PFIM). PFIM uses functional trait data--predictive of interactions in modern ecosystems and commonly available for fossil organisms--to reconstruct ancient food webs. We test the model by (i) applying it to four modern ecosystems with empirical constrained food webs to directly compare PFIM-constructed networks to their empirical counterparts, (ii) by carefully comparing discrepancies between PFIM-inferred and empirical webs in one of those systems, and (iii) by comparing networks describing feasible trophic interactions ("feasible webs") with networks to which we superimpose characteristic interaction distributions derived from modern theory ("realized webs"). As a proof of concept, we then apply the method to faunal data from two Cambrian fossil deposits to reconstruct ancient trophic systems. C_LIO_LIPFIM-inferred feasible food webs successfully predict [~]70% of trophic interactions across four modern systems. Furthermore, inferred food webs with enforced interaction distributions (i.e., realized webs) accurately predict [~]90% of interactions. Comparisons with a global database of trophic interactions and other food web models, suggest that under sampling of empirical webs accounts for up to 21% of the remaining differences between PFIM and empirical food webs. C_LIO_LIFood webs can be reasonably approximated by inferring trophic interactions based upon life habit traits. This study provides the foundation to use trait-based inference models across the fossil record to examine ancient food webs and community evolution. C_LI

paleontology↗

bioRxiv2022

Overconfidence undermines global wildlife abundance trends

In the face of rapid global change and an uncertain fate for biodiversity, it is vital to quantify trends in wild populations. These trends are typically estimated from abundance time series for suites of species across large geographic and temporal scales. Such data implicitly contain phylogenetic, spatial, and temporal structure which, if not properly accounted for, may obscure the true magnitude and direction of biodiversity change. Here, using a novel statistical framework to simultaneously account for all three of these structures, we show that the majority of current abundance trends estimates among 10 high-profile datasets, representing millions of abundance observations, are likely unreliable or incorrect. Our new approach suggests that previous models are too simplistic, incorrectly estimating global abundance trends and often dramatically underestimating uncertainty, an aspect that is critical when translating global assessments into policy outcomes. Further, our approach also results in substantial improvements in abundance forecasting accuracy. Whilst our results do not improve the outlook for biodiversity, our framework does allow us to make more robust estimates of global wildlife abundance trends, which is critical for developing policy to protect our biosphere.

ecology↗

bioRxiv2022

Innovation and elaboration on the avian tree of life

1Widely documented, megaevolutionary jumps in phenotypic diversity continue to perplex researchers because it remains unclear whether these dramatic changes can emerge from microevolutionary processes. Here we tackle this question using new approaches for modeling multivariate traits to evaluate the magnitude and distribution of elaboration and innovation in the evolution of bird beaks. We find that elaboration, evolution along the major axis of phenotypic change, is common at both macro- and megaevo-lutionary scales whereas innovation, evolution away from the major axis of phenotypic change, is more prominent at megaevolutionary scales. Indeed, the major axis of phenotypic change among species beak shapes at megaevolutionary scales is an emergent property of innovation across clades. Our analyses suggest that the reorientation of phenotypes via innovation is a ubiquitous route for divergence that can arise through gradual change alone, opening up new avenues for evolution to explore.

evolutionary biology↗

bioRxiv2022

Extinction cascades, community collapse, and recovery across a Mesozoic hyperthermal event

Biotic interactions and community structure are seldom examined in mass extinction studies but must be considered if we are to truly understand extinction and recovery dynamics at the ecosystem scale. Here, we model shallow marine food web structure across the Toarcian extinction event in the Cleveland Basin, UK using a trait-based inferential modelling framework. First, we subjected our pre-extinction community to extinction cascade simulations in order to identify the nature of extinction selectivity and dynamics. Second, we tracked the pattern and duration of the recovery of ecosystem structure and function following the extinction event. In agreement with postulated scenarios, we found that primary extinctions targeted towards infaunal and epifaunal benthic guilds reproduced the empirical post-extinction community. These results are consistent with geochemical and lithological evidence of an anoxia/dysoxia kill mechanism for this extinction event. Structural and functional metrics show that the extinction event caused a switch from a diverse, stable community with high levels of functional redundancy to a less diverse, more densely connected, and less stable community of generalists. Ecological recovery appears to have lagged behind the recovery of biodiversity, with most metrics only beginning to return to pre-extinction levels [~]7 million years after the extinction event. This protracted pattern supports the theory of delayed benthic ecosystem recovery following mass extinctions even in the face of seemingly recovering taxonomic diversity.

paleontology↗

bioRxiv2022

Mesostats - A multiplexed, low-cost, do-it-yourself continuous culturing system for experimental evolution of mesocosms

Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions in the lab. Experimental evolution in chemostats (i.e. continuous flow through cultures) has recently gained increased interest as it allows tighter control of selective pressures compared to static batch cultures, with a growing number of efforts to develop systems that are easier and cheaper to construct. This protocol describes the design and construction of a multiplexed chemostat array (dubbed "mesostats") designed for cultivation of algae in 16 concurrent populations, specifically intended for studying adaptation to herbicides. We also present control data from several experiments run on the system to show replicability, data illustrating the effects of common issues like leaks, contamination and clumps, and outline possible modifications and adaptations of the system for future research.

evolutionary biology↗

bioRxiv2021

Stabilizing selection shapes variation in phenotypic plasticity

The adaptive nature of phenotypic plasticity is widely documented in natural populations. However, little is known about the evolutionary forces that shape genetic variation in plasticity within populations. Here we empirically address this issue by testing the hypothesis that stabilizing selection shapes genetic variation in the anti-predator developmental plasticity of Daphnia pulex. The anti-predator morphological defense is characterized by pedestal and spikes that grow on the back of the Daphnia neck following exposure to predator cure. We characterized variation in this plasticity using a novel, high-throughput phenotyping method that describes the entire dorsal shape amongst >100 D. pulex strains originating from a natural population in the UK. We found low genetic diversity for morphological defenses among genetically diverse clones upon predation risk exposure. The strongest reduction in genetic variation was observed in areas of greatest phenotypic plasticity, which we interpret as evidence of stabilizing selection. By assessing among-clone variance in clonally related, field derived strains, we contrasted mutational variation (Vm) to standing variation (Vg). We found that Vg/Vm is lowest in areas of greatest plasticity. These data strongly suggest that stabilizing selection operates directly on phenotypic plasticity, providing a rare glimpse into the evolution of fitness related traits in natural populations.

evolutionary biology↗

bioRxiv2020

Niche-based processes and neutrality influence patterns of indirect interactions in mutualistic networks

Indirect interactions are central to ecological and evolutionary dynamics in pollination communities, yet we have little understanding about the processes determining patterns of indirect interactions, such as those between pollinators through shared flowering plants. Instead, research has concentrated on the processes responsible for direct interactions and whole-network structures. This is partly due to a lack of appropriate tools for characterising indirect interaction structures, because traditional network metrics discard much of this information. The recent development of tools for counting motifs (subnetworks depicting interactions between a small number of species) in bipartite networks enable detailed analysis of indirect interaction patterns. Here we generate plant-hummingbird pollination networks based on three major assembly processes - neutral effects (species interacting in proportion to abundance), morphological matching and phenological overlap - and evaluate the motifs associated with each one. We find that different processes produce networks with significantly different patterns of indirect interactions. Neutral effects tend to produce densely-connected motifs, with short indirect interaction chains, and motifs where many specialists interact indirectly through a single generalist. Conversely, niche-based processes (morphology and phenology) produced motifs with a core of interacting generalists, supported by peripheral specialists. These results have important implications for understanding the processes determining indirect interaction structures.

ecology↗