Biology subjects

Stepney, S.

Publications and source records attributed to Stepney, S..

4 recordsLinked to original sources

bioRxiv2026

Short and long-term consequences of Habitat Transformation for Biodiversity

Humans have dramatically altered the Earths surface and the distributions of species, but coherent patterns distinguishing cause from effect are hard to discern. Community composition and ecosystem function can change as rapidly as local land-use, and we lack robust principles to understand the outcomes of these changes. This hampers assessments of ecosystem collapse or robustness. Here we create theoretical ecosystems using a community assembly framework in which we manipulate environmental filtering via both the local land-use and species traits. This isolates the impacts of environmental filtering into land-use, land-use change, and species trait diversity, allowing us to extract clear patterns and relationships. First, we identify the paradox of maladaptation. We find that better land-use adaptation reduces species richness in the habitat but increases species abundance and ecosystem complexity. Increasing diversity amongst species traits reduces species richness via a similar mechanism. Additionally, whilst over long time scales there is very little effect of land-use change, on very short time scales there is a predominantly negative effect on richness. Together, this highlights the need for careful facilitation and management of land-use change in the face of an ever-changing world. Author SummaryHumans have dramatically altered the Earths surface, primarily through land-use change and changing where species are and where they can go. This has resulted in extinctions, immigration, and, most of all, variation in where species end up. Here, we use simulations to compare how habitat, habitat change, and species adaptations create variation in outcomes due to land-use change. First, we show that while adaptation is good for individual species, it also reduces the overall diversity (number of species) of the ecosystem; similarly, well-adapted species out-perform and exclude less well-adapted species, also lowering the resulting diversity of the ecosystem. Secondly, we find that habitat change has different short- and long-term consequences. Habitat change can create dramatic declines on short time scales due to the different pressures experienced by species based on which species they eat (trophic level). But, on long time scales it has very little effect on diversity, as communities acquire new species adapted to the new conditions. We conclude that short-term declines in diversity due to recent or ongoing habitat change could be eased by helping well-adapted species to immigrate to form ecological communities in the new environment.

ecology↗

bioRxiv2025

TORCphysics: A physical model of DNA-topology-controlled gene expression

DNA superhelicity and transcription are intimately related because changes to DNA topology can influence gene expression and vice versa. Information is transferred through the modulation of local DNA torsional stress, where the expression of one gene may influence the superhelical level of neighbouring genes, either promoting or repressing their expression. In this work, we introduce a one-dimensional physical model that simulates supercoiling-mediated regulation. This TORCphysics model takes as input a genome architecture represented either by a plasmid or by a linear DNA sequence with ends constrained under specific biological conditions, and computes the molecules output. Our findings demonstrate that the expression profiles of genes are directly influenced by the gene circuit design, including gene location, the positions of topological barriers, promoter sequences, and topoisomerase activity. The novelty that TORCphysics offers is versatility, where users can define distinct activity models for different types of proteins and protein binding sites. The aim of this research is to establish a flexible framework for developing physical simulations of gene circuits to deepen our comprehension of the intricate mechanisms involved in gene regulation.

biophysics↗

bioRxiv2023

Increased dispersal explains increasing local diversity with global biodiversity declines

The narrative of biodiversity decline in response to human impacts is overly simplistic because different biodiversity metrics show different trajectories at different spatial scales. It is also debated whether human-caused biodiversity changes lead to subsequent, accelerating change (cascades) in ecological communities, or alternatively build increasingly robust community networks with decreasing extinction rates and reduced invasibility. Mechanistic approaches are needed that simultaneously reconcile different metrics of biodiversity change, and explore the robustness of communities to further change. We develop a trophically-structured, mainland-archipelago metacommunity model of community assembly. Varying the parameters across model simulations shows that local alpha diversity (the number of species per island) and regional gamma diversity (the total number of species in the archipelago) depend on both the rate of extirpation per island and on the rate of dispersal between islands within the archipelago. In particular, local diversity increases with increased dispersal and heterogeneity between islands, but regional diversity declines because the islands become biotically similar and local one-island and few-island species are excluded (homogenisation, or reduced beta diversity). This mirrors changes observed empirically: real islands have gained species (increased local and island-scale community diversity) with increased human-assisted transfers of species, but global diversity has declined with the loss of endemic species. However, biological invasions may be self-limiting. High-dispersal, high local-diversity model communities become resistant to subsequent invasions, generating robust species-community networks unless dispersal is extremely high. A mixed-up world is likely to lose many species, but the resulting ecological communities may nonetheless be relatively robust. Significance StatementBiodiversity is commonly regarded as threatened due to human impacts, but biodiversity metrics at different scales produce contradictory results. A framework is needed that can reproduce and connect these results across scales and address whether biodiversity change will inexorably accelerate following perturbation or become self-limiting as new ecological communities form. We address this challenge by constructing size-structured model communities using a mainland/island paradigm and tracking diversity at different scales. Our simulations reproduce the literatures discrepancy across scales and provide new insight. Ecological communities (islands) gain species with increasing (human-assisted) dispersal, but global diversity declines with the consequent loss of endemic species. Communities also become less invasible as dispersal increases, suggesting that human-mediated dispersal favours robust communities that resist subsequent change.

ecology↗

bioRxiv2021

Nothing in evolution makes sense except in the light of parasites

Parasitism emerges readily in models and laboratory experiments of RNA world and would lead to extinction unless prevented by compartmentalisation or spatial patterning. Modelling replication as an active computational process opens up many degrees of freedom that are exploited to meet environmental challenges, and to modify the evolutionary process itself. Here we use automata chemistry models and spatial RNA world models to study the emergence of parasitism and the complexity that evolves in response. The system is initialised with a hand-designed replicator that copies other replicators with a small chance of point mutation. Almost immediately, short parasites arise; these are copied more quickly, and so have an evolutionary advantage. The replicators also become shorter, and so are replicated faster; they evolve a mechanism to slow down replication, which reduces the difference of replication rate of replicators and parasites. They also evolve explicit mechanisms to discriminate copies of self from parasites; these mechanisms become increasingly complex. New parasite species continually arise from mutated replicators, rather than from evolving parasite lineages. Evolution itself evolves, eg by effectively increasing point mutation rates, and by generating novel emergent mutational operators. Thus, parasitism drives the evolution of complex replicators and complex ecosystems.

evolutionary biology↗