Biology subjects

Andersen, A. N.

Publications and source records attributed to Andersen, A. N..

6 recordsLinked to original sources

bioRxiv2026

The nightshift lowdown: can ants buffer climate change through shifts in vertical and temporal activity?

Temperature fluctuations across space and time create a multidimensional thermal landscape within which organisms are exposed to local climates while conducting their daily activities. Tropical species are considered to be particularly sensitive to climate change, with narrow thermal safety margins - the buffer between operative and lethal temperatures. In tropical rainforests, however, species can hypothetically mediate thermal exposure via activity over two local thermal dimensions: vertical (ground-canopy) and temporal (day-night). Such spatiotemporal flexibility could protect species from elevated temperatures and improve thermal safety margins, but this mechanism has not been previously investigated. We test this hypothesis using rainforest ants at a warm lowland and cool upland site (100, 1200 m a.s.l.) in the Australian Wet Tropics. At lowland and upland sites, we quantified microclimate, foraging activity, community composition, and thermal ecology of ants across vertical and temporal dimensions. To assess spatiotemporal flexibility as a climate change mitigation strategy, we calculated thermal safety margins (TSM) as the difference between a species upper thermal limit (CTmax) and mean activity temperature (Te). For each species in each of their spatiotemporal niches (ground-arboreal-day-night) we test whether shifting activity to cooler niches increases TSM using the hottest niches (arboreal and/or daytime) as a baseline. At both lowland and upland sites, ant species were highly stratified vertically, but the large majority (77 - 87.5%) were active both day and night, indicating widespread temporal generalisation. Shifting activity to cooler parts of the thermal landscape substantially improved TSMs: in the lowlands, species with arboreal diurnal foraging increased their TSM by an average of 4.4 {degrees}C ({+/-} 1.7 SE) by shifting to the ground and 6.7 {degrees}C ({+/-} 1.63 SE) by shifting to nocturnal foraging. Improvements were more modest in the uplands: arboreal diurnal foragers increased TSM by 2.1 {degrees}C ({+/-} 2.07 SE) and 2 {degrees}C ({+/-} 0.28 SE) for ground and nocturnal shifts respectively. We therefore demonstrate that foraging niche flexibility is an important climate-change mitigation trait and is most beneficial in the lowlands. Lowland diurnal canopy specialists, however, are most at risk. This represents a large proportion of tropical rainforest biodiversity, supporting previous hypotheses of lowland biotic attrition under climate change.

ecology↗

bioRxiv2025

Perturbational fitness analysis of CRISPR screens uncovers information-theoretic relation between gene function and selection

Despite major advances in genetic screening technology, a formal approach for quantifying gene function remains underdeveloped, thereby limiting the utility of these techniques in deciphering the complex behavior of human cells. In this study, we leverage information theory with a perturbational analysis of replicator dynamics to characterize functional drivers of selection in pooled CRISPR screens. Our approach challenges established methods for CRISPR screen analysis, while offering additional insight into selection dynamics through the Kullback-Leibler divergence (DKL) and cumulants of the fitness distribution. By modeling fluctuations in gene-fitness effects as a linear response to environmental perturbations, we derive a geometric measure for genomic information content based on a second-order approximation of the DKL. Our analysis reveals that functional information--encoded (or shared) between genes--can be quantified by analyzing the directions corresponding to maximal conditional selection within the space of decomposed gene-environment interactions. This geometric representation offers several advantages for the functional analysis of the human genome and its network architecture. Moreover, by constraining the space to cell-type-specific fluctuations, we uncover developmental and tissue-specific functional signatures. These findings represent significant progress in the dynamic analysis of gene function and in the functional wiring of the human genome.

systems biology↗

bioRxiv2025

The economic strategies of superorganisms

The leaf economics spectrum links strategies of plant investment in resource-acquiring leaves to overall fitness. We test whether an economic spectrum can also explain variation in ecological strategies of ant species across environmental gradients, where colony investment in workers is analogous to plant investment in leaves. A fast return of resource investment was associated with large colonies of smaller, less robust, short-lived workers with low nitrogen:phosphorus ratios. Slow resource payback was associated with small colonies of densely built, energetically conservative and longer-lived workers with high nitrogen:phosphorus ratios. Species representing the entire economic continuum co-occurred in all communities. Phylogenetic analyses suggest genus level conservation of core investment templates. These results unify studies of plants and ants, suggesting common economic principles apply across the tree of life.

ecology↗

bioRxiv2024

Genome-wide profiling of the hierarchical control of autophagy dynamics using deep learning

Recycling of cellular components through autophagy maintains homeostasis in dynamic nutrient environments, and its dysregulation is linked to several human disorders. Although extensive research has characterized the core mechanisms of autophagy, limited insight into its systems-wide dynamic control has hampered predictive modeling and effective in vivo manipulation. In this study, we mapped the genetic network that controls both the dynamic activation and inactivation of autophagy during nitrogen changes, using a combination of time-resolved high-content imaging, deep learning, and latent feature analysis. This approach generated a comprehensive genome-wide profiling repository, termed AutoDRY, categorizing 5919 mutants based on their nutrient response kinetics and differential contributions to autophagosome formation and clearance. Integrating these profiles with functional and genetic network data unveiled a hierarchical and multi-layered control of autophagy, identifying new regulatory aspects of the core machinery and established nutrient-sensing pathways. By leveraging multi-omics resources and explainable machine learning to predict genetic perturbation effects and infer new regulatory mechanisms, we identified the retrograde pathway as a pivotal, time-varying autophagy modulator through transcriptional tuning of core genes. By charting the systems-wide dynamical control of autophagy, we have laid the groundwork for connecting the complexity of genome-wide influences with specific core mechanisms. This represents a significant advancement in studying complex genetic phenotypes, guides functional genomics of dynamic cellular processes in any organism, and provides a powerful starting point for hypothesis-based research on autophagy.

systems biology↗

bioRxiv2021

Kel1 is a phosphorylation-regulated noise suppressor of the pheromone signaling pathway

Mechanisms have evolved that allow cells to detect signals and generate an appropriate response. The accuracy of these responses relies on the ability of cells to discriminate between signal and noise. How cells filter noise in signaling pathways is not well understood. Here, we analyze noise suppression in the yeast pheromone signaling pathway and show that the poorly characterized protein Kel1 serves as a major noise suppressor and prevents cell death. At the molecular level, Kel1 prevents spontaneous activation of the pheromone response by inhibiting membrane recruitment of Ste5 and Far1. Only a hypophosphorylated form of Kel1 suppresses signaling, reduces noise and prevents pheromone-associated cell death, and our data indicate that the MAPK Fus3 contributes to Kel1 phosphorylation. Taken together, Kel1 serves as a phospho-regulated suppressor of the pheromone pathway to reduce noise, inhibit spontaneous activation of the pathway, regulate mating efficiency, and to prevent pheromone-associated cell death.

cell biology↗

bioRxiv2020

Indigenous plants promote insect biodiversity in urban greenspaces

The contribution of urban greenspaces to support biodiversity and provide benefits for people is increasingly recognised. However, ongoing management practices still favour (1) vegetation oversimplification, often limiting greenspaces to lawns and tree canopy rather than multi-layered vegetation that includes under and midstorey; and (2) the use of nonnative plant species. These practices likely hinder the potential of greenspaces to sustain indigenous biodiversity, particularly for taxa like insects, that rely on plants for food and habitat. Yet, little is known about which plant species may maximise positive outcomes for taxonomically and functionally diverse insect communities in urban greenspaces. Additionally, while urban environments are expected to experience high rates of introductions, quantitative assessments of the relative occupancy of indigenous vs. introduced insect species in greenspace are rare - hindering understanding of how greenspace management may promote indigenous biodiversity while limiting the establishment of introduced insects. Using a hierarchically replicated study design across 15 public parks, we recorded occurrence data from 552 insect species on 133 plant species - differing in planting design element (lawn, midstorey and tree canopy), midstorey growth form (forbs, lilioids, graminoids and shrubs) and origin (nonnative, native and indigenous) - to assess: (1) the relative contributions of indigenous and introduced insect species and (2) which plant species sustained the highest number of indigenous insects. Our data indicates that the insect community was predominately composed of indigenous rather than introduced species. Our findings further highlight the core role of multi-layered vegetation in sustaining high insect biodiversity in urban areas, with indigenous midstorey and canopy representing key elements to maintain rich and functionally diverse indigenous insect communities. Intriguingly, graminoids supported the highest indigenous insect richness across all studied growth forms by plant origin groups. Taken together, our study emphasise the opportunity posed by indigenous understory and midstorey plants, particularly indigenous graminoids in our study area, to promote indigenous insect biodiversity in urban greenspaces. Our work provides a blueprint and stimulus for built-environment professionals to incorporate into their practice plant species palettes that foster a larger presence of indigenous over regionally native or nonnative plant species, whilst incorporating a broader mixture of midstorey growth forms.

ecology↗