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293 results for “context-dependence”

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zenodo44/100

Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis

This Zenodo archive is associated with the manuscript: Hernandez, D.J., Pohlmann, G.B., Afkhami, M.E. (2025) Gene family expansions provide molecular flexibility required for context-dependent species interactions. Ecology Letters. Abstract: As environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency – how species regulate interactions to match changing environments – is crucial. However, generalizable molecular mechanisms underpinning context-dependency remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for the first time that gene family expansions undergird context-dependent regulation of species interactions. Gene families expanded in mycorrhizal fungi-associating plants display up to 200% more context-dependent gene expression and double the genetic variation associated with mycorrhizal benefits to plant fitness. Moreover, we discover these gene family expansions arise primarily from tandem duplications with >2-times more tandem duplications genome-wide, indicating gene family expansions continuously supply genetic variation throughout plant evolution allowing fine-tuning of context-dependency in species interactions.

opencc-by-4.0Apr 2024View details →

zenodo44/100

Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors

Summary statistics for chromatin accessibility and gene expression quantitative trait loci (ca/eQTLs) from Matoba, N., Le, B.D., Valone, J.M. et al. Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors. Nat Neurosci (2024). https://doi.org/10.1038/s41593-024-01773-6

opencc-by-4.0Sep 2024View details →

dryad40/100

Context-dependent multimodal behaviour in a coral reef fish: Stage 1 & 2 total duration and count data in behaviour trials

Animals are expected to respond flexibly to changing circumstances, with multimodal signalling providing potential plasticity in social interactions. Whilst numerous studies have documented context-dependent behavioural trade-offs in terrestrial species, far less work has considered such decision-making in fish, especially in natural conditions. Coral reef ecosystems host 25% of all known marine species, making them hotbeds of competition and predation. We conducted experiments with wild Ambon damselfish (Pomacentrus amboinensis) to investigate context-dependent responses to a conspecific intruder; specifically, how nest defence is influenced by an elevated predation risk. We found that nest-defending male Ambon damselfish responded aggressively to a conspecific intruder, spending less time sheltering and more time interacting, as well as signalling both visually and acoustically. In the presence of a model predator compared to a model herbivore, males spent less time interacting with the intruder, with a tendency towards reduced investment in visual displays compensated for by an increase in acoustic signalling instead. We therefore provide ecologically valid evidence that the context experienced by an individual can affect its behavioural responses and multimodal displays towards conspecific threats.

opencc-zeroMar 2024View details →

dryad40/100

Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne Host range restriction peptidase (hrrP), whose product degrades target NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.

opencc-zeroApr 2022View details →

dryad40/100

Context-dependence in the symbiosis between Dictyostelium discoideum and Paraburkholderia

Symbiotic interactions change with environmental context. Measuring these context-dependent effects in hosts and symbionts is critical to determining the nature of symbiotic interactions. We investigated context-dependence in the symbiosis between social amoeba hosts and their inedible Paraburkholderia bacterial symbionts, where the context is the abundance of host food bacteria. Paraburkholderia have been shown to harm hosts dispersed to food-rich environments, but aid hosts dispersed to food-poor environments by allowing hosts to carry food bacteria. Through measuring symbiont density and host spore production, we show that this food context matters in three other ways. First, it matters for symbionts, who suffer a greater cost from competition with food bacteria in the food-rich context. Second, it matters for host-symbiont conflict, changing how symbiont density negatively impacts host spore production. Third, data-based simulations show that symbiosis often provides a long-term fitness advantage for hosts after rounds of growth and dispersal in variable food-contexts, especially when conditions are harsh with little food. These results show how food context can have many consequences for the Dictyostelium-Paraburkholderia symbiosis and that both sides can frequently benefit.

opencc-zeroApr 2022View details →

zenodo40/100

Data for: Context-dependent effects of glucocorticoids on the lizard gut microbiome

Data from: Context-dependent effects of glucocorticoids on the lizard gut microbiome (provisionally accepted, Molecular Ecology 2021)  Metadata is in Sheet 2. Address queries to kirstyjmacleod@gmail.com. Publication abstract: The vertebrate gut microbiota (bacterial, archaeal, and fungal communities of the gastrointestinal tract) can have profound effects on physiological processes of their hosts. Although relatively stable, changes in microbiome structure and composition occur due to changes in the environment, including exposure to stressors and associated increases in glucocorticoid hormones. Although a growing number of studies have linked stressor exposure to microbiome changes, few studies have experimentally explored the specific influence of glucocorticoids on the microbiome in wild animals, or across ecologically-important processes (e.g., reproductive stages). Here we tested the response of the gut microbiota of adult female Sceloporus undulatus across gestation to ecologically relevant elevations of a stress-relevant glucocorticoid hormone (CORT) in order to determine a) how experimentally elevated CORT influenced microbiome characteristics, and b) whether this relationship was dependent on reproductive context (i.e. whether females were gravid or not, and in those that were gravid, gestational stage). We show that the effects of CORT on gut microbiota are complex and depend on both gestational state and stage. CORT treatment altered microbial community membership and resulted in an increase in microbiome diversity in late-gestation females, and microbial community membership varied according to treatment. In non-gravid females, CORT treatment resulted in inter-individual variation in microbial communities, but this effect was not observed in late-gestation females.  Our results highlight the need for a more holistic understanding of the downstream physiological effects of glucocorticoids, as well as the importance of context (here, gestational state and stage) in interpreting stress effects in ecology.

opencc-by-4.0Aug 2021View details →

zenodo40/100

Context-dependent memory recall in HMD-based immersive virtual environments

Data represent result of an original VR-based experimental research, which studied human memory recollection in different visual environments. 92 students of psychology using head-mounted VR displays were introduced into a computer-generated virtual environment and asked to memorize presented lists of words. Afterwards, the number of accurate and false memory recollections were measured when participants were placed in the same, respectively different virtual environment.

opencc-by-4.0Mar 2021View details →

zenodo40/100

Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.

opengpl-3.0Jun 2023View details →

dryad40/100