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96 results for “interacting phenotypes”
Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients
<p><em>Background:</em></p> <p>Understanding the mechanisms by which genes control and regulate complex quantitative traits during periods of fluctuating resources remains a challenging and uncertain task in photosynthesis studies. Most studies have focused on the structure of photosynthesis, the photosynthetic response under stress, or the genetic mechanisms involved in photosynthetic effects and neglected the interactive genetic mechanism that governs various traits through significant quantitative trait loci (QTLs). Results In this study, we have developed a differential dynamic system that enables the identification of QTLs based on the photosynthetic phenotypic and genotypic data under varying levels of light intensity gradients. The framework not only allows for the assessment of the direct effects of QTLs on phenotypes but also captures how they influence interactions among phenotypes as light intensities change. We have analyzed the genetic effects and genetic variance, visualized the genetic network associated with photosynthesis interactions, and validated the effectiveness and stability of the DDS framework. Pivotal QTLs were identified individually to uncover the process and pattern of interaction. Through functional annotation, we made an intriguing discovery that seemingly unimportant QTLs can still have significant genetic effects on phenotypic changes through their regulation with other QTLs. Conclusions This finding emphasizes the significance of considering the interactive genetic architecture when seeking to understand the genetic interaction mechanism of photosynthesis in natural populations of woody plants. Moreover, our research provides a novel framework that can be extended to explore the interactive genetic architecture among organisms, contributing to a deeper understanding of stress resistance mechanisms in woody plants.</p>
Resource manipulation reveals interactive phenotype-dependent foraging in free-ranging lizards
<p>Recent evidence suggests that individuals differ in foraging tactics and this variation is often linked to an individual's behavioural type (BT). Yet, while foraging typically comprises a series of search and handling steps, empirical investigations have rarely considered BT-dependent effects across multiple stages of the foraging process, particularly in natural settings.</p> <p>In our long-term sleepy lizard (Tiliqua rugosa) study system, individuals exhibit behavioural consistency in boldness (measured as an individual's willingness to approach a novel food item in the presence of a threat) and aggressiveness (measured as an individual's response to an 'attack' by a conspecific dummy). These BTs are only weakly correlated and have previously been shown to have interactive effects on lizard space use and movement, suggesting that they could also affect lizard foraging performance, particularly in their search behaviour for food.</p> <p>To investigate how lizards' BTs affect their foraging process in the wild, we supplemented food in 123 patches across a 120-ha study site with three food abundance treatments (high, low, and no-food-controls). Patches were replenished twice a week over the species' entire spring activity season and feeding behaviours were quantified with camera traps at these patches. We tracked lizards using GPS to determine their home range (HR) size and repeatedly assayed their aggressiveness and boldness in designated assays.</p> <p>We hypothesised that bolder lizards would be more efficient foragers while aggressive ones would be less attentive to the quality of foraging patches. We found an interactive BT effect on overall foraging performance. Individuals that were both bold and aggressive ate the highest number of food items from the foraging array. Further dissection of the foraging process showed that aggressive lizards in general ate the fewest food items in part because they visited foraging patches less regularly, and because they discriminated less between high and low-quality patches when revisiting them. Bolder lizards, in contrast, ate more tomatoes because they visited foraging patches more regularly, and ate a higher proportion of the available tomatoes at patches during visits.</p> <p>Our study demonstrates that BTs can interact to affect different search and handling components of the foraging process, leading to within-population variation in foraging success. Given that individual differences in foraging and movement will influence social and ecological interactions, our results highlight the potential role of BT's in shaping individual fitness strategies and population dynamics.</p>
Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)
<p><span><strong>Premise</strong>:</span><span> Island systems have long served as a model for evolutionary processes due to their unique species interactions. Many studies of the evolution of species interactions on islands have focused on endemic taxa. Fewer studies have focused on how antagonistic and mutualistic interactions shape the phenotypic divergence of widespread non-endemic species living on island populations. </span></p> <p><span><strong>Methods</strong>:</span><span> We used the widespread plant <em>Tribulus</em> <em>cistoides</em> (Zygophyllaceae) to test phenotypic divergence in traits that mediate antagonistic interactions with vertebrate granivores (birds) and mutualistic interactions with pollinators and how this is explained by bioclimatic variables. We used both herbarium specimens and field-collected samples to compare phenotypic divergence between continental and island populations. </span></p> <p><span><strong>Results</strong>:</span><span> Fruits from island populations were larger than on continents, but the presence of lower spines on mericarps was lower on islands. The presence of spines was largely explained by environmental variation among islands. Petal length was on average 9% smaller on island than continental populations, an effect that was especially accentuated on the Galápagos Islands. </span></p> <p><span><strong>Conclusions</strong>:</span><span> <em>Tribulus</em> <em>cistoides</em> exhibits phenotypic divergence between island and continental habitats for antagonistic traits (seed defence) and mutualistic traits (floral traits). Further, the evolution of phenotypic traits that mediate antagonistic and mutualistic interactions depended on the abiotic characteristics of specific islands. This study shows the potential of using a combination of herbarium and field samples for comparative studies on a globally distributed species to test phenotypic divergence on island habitats.</span></p>
Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients
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Resource manipulation reveals interactive phenotype-dependent foraging in free-ranging lizards
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Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)
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Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics
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Phenotypic and genotypic divergence of plant-herbivore interactions along an urbanization gradient
<p class="MsoNormal"><span>Urban environments provide challenging conditions for species survival, including increased temperatures, drought, and pollution. Species can deal with these conditions through evolution across generations or the immediate expression of phenotypic plasticity. The resulting phenotypic changes are key to the performance of species and their interactions with other species in the community. We here document patterns of herbivory in <em>Arabidopsis thaliana</em> along a rural-urban gradient, and tested the genetic background and ecological consequences of traits related to herbivore resistance. Aphid densities increased with urbanization levels along the gradient while plant size did not change. Offspring of urban mothers, raised under common garden conditions, were larger and had a decreased trichome density and seed set but a higher caterpillar (<em>Pieris brassicae</em>) tolerance. In contrast, no urban evolution was detected for defenses against aphids (<em>Myzus persicae</em>). Aphids reduced seed set more strongly in urban offspring, but this effect disappeared in second-generation plants. In general, urban adaptations as expressed in size and caterpillar tolerance were found, but these adaptations were associated with smaller inflorescences. The maternal effect on the response of seed set to aphid feeding demonstrates the relevance of intergenerational plasticity as a direct ecological consequence of herbivory. Our study demonstrates that the urban environment interacts with the plant's genotype and the extended phenotype as determined by ecological interactions.</span></p>
Interactive Heatmap of all Disease Phenolog Behavioural Phenotypes
<p><span><span>An interactive clustermap of behavioural tracking data for a panel of 25 <em>C. elegans</em> disease model phenologs (associated with the linked published paper). This is a static html file that can be opened in a browser and zoomed in for a detailed inspect of how the various strains differ from the control (N2). Mousing over the heatmap shows the name of features at each position so that a more intutive conclusion of the data, i.e., 'Strain A is slow' or 'Strain B is more curved', can be reached.</span></span><span></span></p>
Data from: Virulence phenotypes result from interactions between pathogen ploidy and genetic background
<p>Studying fungal virulence is often challenging and frequently depends on many contexts, including host immune status and pathogen genetic background. However, the role of ploidy has often been overlooked when studying virulence in eukaryotic pathogens. Since fungal pathogens, including the human opportunistic pathogen <i>Candida albicans</i>, can display extensive ploidy variation, assessing how ploidy impacts virulence has important clinical relevance. As an opportunistic pathogen, <i>C. albicans</i> causes non-lethal, superficial infections in healthy individuals, but life-threatening bloodstream infections in individuals with compromised immune function. Here, we determined how both ploidy and genetic background of <i>C. albicans</i> impacts virulence phenotypes in healthy and immunocompromised nematode hosts by characterizing virulence phenotypes in four near-isogenic diploid and tetraploid pairs of strains, which included both laboratory and clinical genetic backgrounds. We found that <i>C. albicans</i> infections decreased host survival and negatively impacted host reproduction, and we leveraged these two measures to survey both lethal and non-lethal virulence phenotypes across the multiple <i>C. albicans</i> strains. In this study, we found that regardless of pathogen ploidy or genetic background, immunocompromised hosts were susceptible to fungal infection compared to healthy hosts. Furthermore, for each host context, we found a significant interaction between <i>C. albicans</i> genetic background and ploidy on virulence phenotypes, but no global differences between diploid and tetraploid pathogens were observed.</p>
Helminth-associated changes in host immune phenotype connect top-down and bottom-up interactions during co-infection
<p>Within-host parasite interactions can be mediated by the host and changes in host phenotypes often serve as indicators of the presence or intensity of parasite interactions.</p> <p>Parasites like helminths induce a range of physiological, morphological, and immunological changes in hosts that can drive bottom-up (resource-mediated) or top-down (immune-mediated) interactions with co-infecting parasites. Although top-down and bottom-up interactions are typically studied in isolation, the diverse phenotypic changes induced by parasite infection may serve as a useful tool for understanding if, and when, these processes act in concert.</p> <p>Using an anthelmintic treatment study of African buffalo (Syncerus caffer), we tracked changes in host immunological and morphological phenotypes during helminth-coccidia co-infection to investigate their role in driving independent and combinatorial bottom-up and top-down parasite interactions. We also examined repercussions for host fitness.</p> <p>Clearance of a blood-sucking helminth, Haemonchus, from the host gastrointestinal tract induced a systemic Th2 immune phenotype, while clearance of a tissue-feeding helminth, Cooperia, induced a systemic Th1 phenotype. Furthermore, the Haemonchus-associated systemic Th2 immune phenotype drove simultaneous top-down and bottom-up effects that increased coccidia shedding by changing the immunological and morphological landscapes of the intestine.</p> <p>Higher coccidia shedding was associated with lower host body condition, a lower chance of pregnancy, and older age at first pregnancy, suggesting that coccidia infection imposed significant condition and reproductive costs on the host.</p> <p>Our findings suggest that top-down and bottom-up interactions may commonly co-occur and that tracking key host phenotypes that change in response to infection can help uncover complex pathways by which parasites interact.</p>
Obesity Risk in African American Women is Determined by a Diet-by-phenotype Interaction
ClinicalTrials.gov study NCT03499509. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE)
ClinicalTrials.gov study NCT01142947. IPD Sharing: NO. Countries: 1. Publications: 1.
Helminth-associated changes in host immune phenotype connect top-down and bottom-up interactions during co-infection
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Phenotypic plasticity, heritability, and genotype-by-environment interactions in an insect dispersal polymorphism
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Data from: Virulence phenotypes result from interactions between pathogen ploidy and genetic background
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Phenotypic and genotypic divergence of plant-herbivore interactions along an urbanization gradient
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Data from: Interacting phenotypic plasticities: Do male and female responses to the sociosexual environment interact to determine fitness?
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Data from: Complex interactions between local adaptation, phenotypic plasticity, and sex affect vulnerability to warming in a widespread marine copepod
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Data from: Cannibalism as an interacting phenotype: pre-cannibalistic aggression is influenced by social partners in the endangered Socorro isopod (Thermosphaeroma thermophilum)
Models for the evolution of cannibalism highlight the importance of asymmetries between individuals in initiating cannibalistic attacks. Studies may include measures of body size but typically group individuals into size/age classes or compare populations. Such broad comparisons may obscure the details of interactions that ultimately determine how socially contingent characteristics evolve. We propose that understanding cannibalism is facilitated by using an interacting phenotypes perspective that includes the influences of the phenotype of a social partner on the behaviour of a focal individual and focuses on variation in individual pairwise interactions. We investigated how relative body size, a composite trait between a focal individual and its social partner, and the sex of the partners influenced precannibalistic aggression in the endangered Socorro isopod, Thermosphaeroma thermophilum. We also investigated whether differences in mating interest among males and females influenced cannibalism in mixed sex pairs. We studied these questions in three populations that differ markedly in range of body size and opportunities for interactions among individuals. We found that relative body size influences the probability of and latency to attack. We observed differences in the likelihood of and latency to attack based on both an individual's sex and the sex of its partner but found no evidence of sexual conflict. The instigation of precannibalistic aggression in these isopods is therefore a property of both an individual and its social partner. Our results suggest that interacting phenotype models would be improved by incorporating a new conditional ψ, which describes the strength of a social partner's influence on focal behaviour.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.