Biology subjects

Yates, L. A.

Publications and source records attributed to Yates, L. A..

13 recordsLinked to original sources

bioRxiv2026

Interactions between thermal and nutritional stress reveal cryptic adaptive potential

Predicting whether populations can adapt fast enough to persist under global change requires understanding how adaptive potential changes with the environment. Theory predicts that cryptic genetic variation hidden under benign conditions may be released under stress, but empirical tests are rare and typically manipulate single stressors in isolation, which is not realistic under global change. Using a quantitative genetic breeding design with Drosophila melanogaster, we quantified additive genetic variance in fitness (female productivity) across combinations of temperature and nutritional stress. We found that nutritional stress increased genetic variance at cold and hot margins. Temperature and diet also interacted to shape which genotypes performed best: nutritional stress weakened genetic correlations across temperatures at the hot margin, whereas genetic correlations across diets strengthened at the cold margin. Adaptive potential is therefore environment-dependent and multidimensional, meaning single stressor experiments are likely to systematically misrepresent adaptive capacity under realistic global change scenarios.

evolutionary biology↗

bioRxiv2026

Rapid reversible RNA isoform switching during loss and recovery of turgor in Arabidopsis thaliana

Plant genes can each produce multiple RNA isoforms, but little is known about when and how they are produced, or their functions. We conducted a detailed time course analysis of rapid changes in abundance of RNA isoforms in response to transient water deficit in Arabidopsis thaliana seedlings. We identified 95,104 transcripts in total, 21,935 of which were differentially expressed. Strikingly, 1,258 differentially expressed genes were identified only by means of RNA isoform analysis and would have been missed by conventional analysis. Several hundred genes exhibited a very rapid and reversible switch in the most abundant RNA isoform, with timings corresponding to defined changes in seedling water potential. In most cases it is predicted that RNA isoform switching would generate new protein products. Many of these genes encoded proteins of RNA metabolism and splicing, while others potentially function more directly in the response to water deficit. We propose a model in which very rapid RNA processing mechanisms come into play within minutes of imposition of the stress, changing the RNA isoform population including RNAs that encode components of the RNA processing apparatus itself. These changes together with subsequent changes in transcription facilitate further changes in the RNA isoform population as part of the stress and recovery responses. More broadly we propose that responses to abiotic stress involve substantial changes in gene function through the production of RNA isoforms, and we present a detailed approach to identifying such genome-wide RNA isoform switching.

plant biology↗

bioRxiv2026

Trait - climate relations in Themeda triandra: a widely distributed C4 grass and crop wild relative

O_LIQuantifying relationships between traits and climate using plants collected from diverse climatic origins, grown under common conditions, potentially provides valuable insights into climate adaptation. C_LIO_LIWe report on fifteen accessions of kangaroo grass (Themeda triandra), a C4 species distributed across Australia, Asia, the Middle East and Africa from the Andropogoneae clade of grasses that is vital to global agriculture. Plants were grown to maturity in glasshouses under two thermal regimes, with ample water supplied. Numerous physiological, "economic" and developmental traits were characterised. C_LIO_LIAs expected, plants grown at 20{degrees}C maxima had lower photosynthetic rates (Asat) and dark respiration rates, reduced leaf expansion, and delayed flowering compared with plants grown at 30{degrees}C. However, surprisingly few traits varied with climate-of-origin: accessions from colder climates had higher Asat alongside lower leaf mass per area, but only when grown at 20{degrees}C; flowering time showed the strongest correlation with site climate, with plants from wetter, warmer or less variable climates taking longer to flower. C_LIO_LIOur findings highlight remarkable phenotypic flexibility in key traits of T. triandra; this flexibility is likely key to its wide distribution. The strong relationship between flowering time and climate-of-origin underscores the importance of reproductive phenology as an adaptive trait. C_LI

ecology↗

bioRxiv2025

Conserved strategies underpin the replicated evoluton of aridity tolerance in trees

Predicting forest responses to climate change requires a detailed understanding of trait-environment coordination. Adaptation to environment comprises both conserved and labile components of trait variation. However, few studies explore the decomposition of trait-environment relationships in a rigorous phylogenetic framework. Combining a revised phylogeny with trait, climate and soil data to achieve unprecedented species coverage ([~]85%), we identified patterns of replicated evolution that allowed the evergreen tree genus, Eucalyptus, to rapidly radiate across Australia in response to aridification. Eucalypts from arid regions are short, produce dense wood, and have small, physically robust leaves with high nitrogen content, promoting hydraulic safety and economies in photosynthetic water use. Phylogenetic modelling reveals strong niche conservatism, with adaptation to aridity occurring primarily via clade-level divergences, followed by phylogenetically independent adjustments to local conditions. Ancestral state reconstructions accounting for trends in the paleoclimate record indicate that transitions in aridity tolerance are associated with distinct signals of environmental filtering and directional selection on functional trait variation. However, astonishing repeatability of trait changes in different clades reveals a narrow optimal solution to water availability, opening a path to predict future species distributions from phylogenetically structured trait data and signalling major implications for functional and species diversity under progressive climate change.

evolutionary biology↗

bioRxiv2024

Shape-constrained, changepoint additive models for time series omics data with cpam

Time series omics experiments are critical for the study of a wide range of biological processes such as cell differentiation and developmental programs or responses to pathogens and environmental cues. While statistical tools for differential analysis across static conditions have matured, comparable comprehensive methodology is lacking for time series data. Here, we introduce cpam, a novel time series method and user-friendly software that performs temporal differential analysis of omics data for case-only or case-control time series, incorporating quantification uncertainty. Powerful features of cpam include changepoint detection and shape-constrained temporal trend estimation to allocate omics data into similar clusters. Performance evaluation shows that cpam outperforms existing time series methods in terms of control of the false discovery rate versus power to detect temporal changes and accurate changepoint estimation. In particular, we find that trend-based models provide superior performance compared to pairwise comparisons, even with as few as six time points. The software provides an interactive interface with modern customizable visualisations, offering both graphical and statistical insight into complex molecular processes. Application to published transcriptome data illustrates RNA isoform-level modelling together with high resolution clustering during human embryogenesis and the identification of 910 novel genes differentially expressed in response to excess light in Arabidopsis. This method has the potential for application to a range of omics data, including single-cell analyses via pseudobulked data, providing the analytical power to reveal complex temporal patterns of gene expression in any biological system.

bioinformatics↗

bioRxiv2023

Tree species richness and evenness affect forest biomass differently across biogeographic regions

The relationship between tree species diversity, measures of forest structure, and forest biomass has long been debated, with local- or continental-scale studies often finding contrasting results. Given the importance of forests as global carbon sinks, understanding the characteristics that underpin biomass accumulation is thus a critical component of mitigating climate change. Here we present a global analysis of 11,400 forest plots, sourced from scientific publications and forest inventories, to investigate the association of forest basal area (used as a proxy for biomass) with stem density and measures of tree species diversity (richness and evenness). We used generalised additive models to account for the confounding effects of climate and spatial signal and we modelled the density, climate, and diversity effects both globally and for each biogeographic region. Stem density showed a strong positive association with basal area across all biogeographic regions, while the effect of species richness varied. In the Palearctic, Nearctic, and Neotropical biogeographic regions, basal area was positively associated with species richness, although this was only detectable for lower values of basal area. In the Ethiopian and Oriental biogeographic regions there was no relationship between richness and basal area, while in the Australian biogeographic regions it was negative. The weak-to-no association between species evenness and basal area in all bioregions other than Australia suggests that the overall correlation emerges from processes operating at more local scales. Our results highlight the importance of accounting for biogeographic processes when evaluating strategies to mitigate climate change and support nature conservation.

ecology↗

bioRxiv2023

Land use change drives major loss of Southeast Asian biodiversity

Southeast Asia is highly biodiverse and currently experiences among the highest rates of tropical deforestation globally, but impacts on biodiversity are not well synthesized. We use Bayesian multi-level modeling to meta-analyse 831 pairwise comparisons of biodiversity in sites subject to human land use change and anthropogenic forest disturbance (for example in plantations or logged forest) versus undisturbed sites. After controlling for hierarchical dependences, we show that biodiversity is a fifth lower in sites with these land-use changes (95% credible interval= 16-28%, mean = 22%). This reduction was greater when land use change/anthropogenic forest disturbances were high-intensity (34% reduction in biodiversity) compared to low-intensity (18% reduction), and effects were consistent across biogeographic regions and taxa. Oil-palm plantations lead to the greatest reduction in biodiversity (39%, CI 27-48%), and agroforests the least (24%, CI 10-37%). We also find that biodiversity is reduced in young secondary forest by 26% (CI 4-42%) compared to undisturbed forest, but there is no reduction in biodiversity for intermediate or mature-aged secondary forest (although species composition is potentially altered). Overall, our study provides the clearest evidence yet of the substantial detrimental impact of land-use change and anthropogenic forest disturbance on the biodiversity of Southeast Asia.

ecology↗

bioRxiv2023

Phosphoregulation of the Rad51 auxiliary factor Swi5-Sfr1

Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks, the most severe form of DNA damage. The Rad51 protein is central to HR, but multiple auxiliary factors regulate its activity. The heterodimeric Swi5-Sfr1 complex is one such factor. It was previously shown that two sites within the intrinsically disordered domain of Sfr1 are critical for the interaction with Rad51. Here, we show that phosphorylation of five residues within this domain regulates the interaction of Swi5-Sfr1 with Rad51. Biochemical reconstitutions demonstrated that a phosphomimetic mutant version of Swi5-Sfr1 is defective in both the physical and functional interaction with Rad51. This translated to a defect in DNA repair, with the phosphomimetic mutant yeast strain phenocopying the previously established interaction mutant. Interestingly, a strain in which Sfr1 phosphorylation was blocked also displayed sensitivity to DNA damage. Taken together, we propose that controlled phosphorylation of Sfr1 is important for the role of Swi5-Sfr1 in promoting Rad51-dependent DNA repair.

biochemistry↗

bioRxiv2022

A DNA damage-induced phosphorylation circuit enhances Mec1ATR-Ddc2ATRIP recruitment to Replication Protein A.

The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 senses single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA-damage induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modelling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signalling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/521831v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@139e23corg.highwire.dtl.DTLVardef@133d6e6org.highwire.dtl.DTLVardef@6198b5org.highwire.dtl.DTLVardef@1709a73_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIRfa1-S178 phosphorylation promotes Ddc2 recruitment and Ddc2-RPA complexes modulate RPA-ssDNA behaviour. C_LIO_LIDdc2 phosphorylation enhances Mec1-Ddc2 recruitment and is important for the DNA damage checkpoint in yeast. C_LIO_LIStructure of a Ddc2:RPA complex shows phosphorylation-dependent higher order assemblies stabilised by Zn2+. C_LIO_LIWe propose a Mec1-Ddc2 recruitment strategy that allows fast accumulation of Mec1-Ddc2 through DNA damage-induced phosphorylation and promotes autophosphorylation. C_LI

biochemistry↗

bioRxiv2022

Multi-Response Phylogenetic Mixed Models: Concepts andApplication

The scale and resolution of trait databases and molecular phylogenies is increasing rapidly. These resources permit many open questions in comparative biology to be addressed with the right statistical tools. Multi-response (MR) phylogenetic mixed models (PMM) offer great potential for multivariate analyses of trait evolution. While flexible and powerful, these methods are not often employed by researchers in ecology and evolution, reflecting a specialised and technical literature that creates barriers to usage for many biologists. Here we present a practical and accessible guide to MR-PMM. We begin with a review of single-response (SR) PMM to introduce key concepts and outline the limitations of this approach for characterizing patterns of trait co-evolution. We emphasise MR-PMM as a preferable approach to analyses involving multiple species traits, due to the explicit decomposition of trait covariance across levels in the model hierarchy. We discuss multilevel distributional models, meta-analyses, multivariate models of evolution, and extensions to non-Gaussian response traits. We highlight techniques for causal inference using precision matrices, as well as advanced topics including prior specification and latent factor models. Using simulated data and visual examples, we discuss interpretation, prediction, and model validation. We implement many of the techniques discussed in example analyses of plant functional traits to demonstrate the general utility of MR-PMM in handling complex real world datasets. Finally, we discuss the emerging synthesis of comparative techniques made possible by MR-PMM, highlight strengths and weaknesses, and offer practical recommendations to analysts. To complement this material, we provide extensive online tutorials including side-by-side model implementations in two popular R packages, MCMCglmm and brms.

evolutionary biology↗

bioRxiv2021

Roadkill islands: carnivore extinction shifts seasonal use of roadside carrion by generalist avian scavenger

O_LIGlobal road networks facilitate habitat modification and are integral to human expansion. Many animals, particularly scavengers, use roads as they provide a reliable source of food, such as carrion left after vehicle collisions. Tasmania is often cited as the roadkill capital of Australia, with the isolated offshore islands in the Bass Strait experiencing similar, if not higher, levels of roadkill. However, native mammalian predators on the islands are extirpated, meaning the remaining scavengers are likely to experience lower interference competition. C_LIO_LIIn this study, we use a naturally occurring experiment to examine how the loss of mammalian carnivores within a community impacts roadside foraging behaviour by avian scavengers. C_LIO_LIWe monitored the locations of roadkill and forest ravens (Corvus tasmanicus), an abundant scavenger species, on eight road transects across the Tasmanian mainland (high scavenging competition) and the Bass Strait islands (low scavenging competition). We represented raven observations as one-dimensional point patterns, using hierarchical Bayesian models to investigate the dependence of raven spatial intensity on habitat, season, distance to roadkill and route location. C_LIO_LIWe found that roadkill carcasses were a strong predictor of raven presence along road networks. The effect of roadkill was amplified on roads on the Bass Strait islands, where roadside carrion was a predictor of raven presence across the entire year. In contrast, ravens were more often associated with roadkill on Tasmanian mainland roads in the autumn, when other resources were low. This suggests that in the absence of competing mammalian scavengers, ravens choose to feed on roadside carrion throughout the year, even in seasons when other resources are available. This low interference competition could be disproportionately benefiting forest ravens, leading to augmented raven populations and changes to the vertebrate community structure. C_LIO_LIOur study provides evidence that scavengers modify their behaviour in response to reduced scavenger species diversity, potentially triggering trophic shifts and highlighting the importance of conserving or reintroducing carnivores within ecosystems. C_LI

ecology↗

bioRxiv2021

Spatial pattern analysis of line-segment data in ecology

O_LIThe spatial analysis of linear features (lines and curves) is a challenging and rarely attempted problem in ecology. Existing methods are typically expressed in abstract mathematical formalism, making it difficult to assess their relevance and transferability into an ecological setting. A set of concrete and accessible tools is needed. C_LIO_LIWe develop a new method to analyse the spatial patterning of line-segment data. It is based on a generalisation of Ripleys K-function and includes an analogue of the transformed L-function, together with estimators and theoretical expectation values. We introduce a class of line-segment processes, related to the Boolean model, which we use in conjunction with Monte-Carlo methods and information criteria to generate and compare candidate models. We demonstrate the utility of our method using fallen tree (dead log) data collected from two one-hectare Australian tall eucalypt forest plots. C_LIO_LIComparing six line-segment models, we find for both plots that the distribution of fallen logs is best explained by plot-level spatial heterogeneity. The use of non-uniform distributions to model dead-log orientation on the forest floor improves model performance in one of the two sites. Our case study highlights the challenges of model comparison in spatial-pattern analysis, where Monte-Carlo approaches based on the discrepancy of simulated summary functions can generate a different ranking of models than that of information criteria. C_LIO_LIThese methods are of a general nature and are applicable to any line-segment data. In the context of forest ecology, the integration of fallen logs as linear structural features in a landscape with the point locations of living trees, and a quantification of their interactions, will yield new insights into the functional and structural role of tree fall in forest communities and their enduring post-mortem ecological legacy as spatially distributed decomposing logs. C_LI

ecology↗

bioRxiv2019

Structure of nucleotide-bound Tel1ATM reveals the molecular basis of inhibition and structural rationale for disease mutations

SUMMARYYeast Tel1 and its highly conserved human orthologue ATM are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia (A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Using cryo electron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Our structure reveals molecular details of key residues surrounding the nucleotide binding site and provides a structural and molecular basis for its intrinsically low basal activity. We show that the catalytic residues are in a productive conformation for catalysis, but the PIKK-regulatory domain-Insert (PRD-I) restricts peptide-substrate access and the N-lobe is in an open conformation, thus explaining the requirement for Tel1 activation. Structural comparisons with other PIKKs suggest a conserved and common allosteric activation mechanism. Our work also provides a structural rationale for many mutations found in A-T and cancer.

biophysics↗