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66 results for “growth phenotypes”
Shifting environmental predictors of phenotypes under climate change: A case study of growth in high latitude seabirds
<p>Climate change is altering species' traits across the globe. To predict future trait changes and understand the consequences of those changes, we need to know the environmental drivers of phenotypic change. In the present study, we use multi-decadal long datasets to determine periods of within-year environmental variation that predict growth of three seabird species. We evaluate whether these periods changed over time and use them to predict future growth under climate change. We find that predictions of trait change could be improved by considering that 1) the timing of environmental factors used to predict traits (predictive-environmental features) can change over time, and 2) the type of predictive-environmental features can change over time. We find evidence of changes in the timing of environmental predictors in all populations studied and evidence for a change in the type of predictor in the studied Arctic murre population. Environmental models of growth predict that warming conditions will decrease growth rates and bird body sizes in two species (black-legged kittiwakem <em>Rissa</em> <em>tridactyla</em>, and glaucous-winged gullm <em>Larus</em> <em>glaucescens</em>), but not the third (thick-billed murrem <em>Uria</em> <em>lomvia</em>). Consequently, climate change is likely to decrease fledging rates in the gulls and kittiwakes. Further, we find that ice-cover historically predicted murre chick growth well, but no longer does – instead air temperature is now a better predictor of murre growth. Our study highlights a need to investigate whether environmental determinants of trait variation commonly shift in a changing climate and whether such changes have implications for adaptation to novel environments.</p>
Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
<p>This dataset supports the article "Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth", which is under minor revision in Journal of Experimental Botany. The study addresses the combined effects of and plant population origin, drought and heat stress on plant growth, plant morphology and the leaf metabolome. The data were assessed in Northern and Southern European individuals of <em>Cakile maritma</em> (See Rocket). An R-script containing all statistical analyses that have been implemented with these data is also provided.</p>
Data from: Testing the evolutionary potential of an alpine plant: Phenotypic plasticity in response to growth temperature outweighs parental environmental effects and other genetic causes of variation
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Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
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Shifting environmental predictors of phenotypes under climate change: A case study of growth in high latitude seabirds
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Data from: Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon
<p>Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50–70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.</p>
Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?
<p>Pathways through which phenotypic variation among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. <span>To address</span> biological complexity below the species level<span>, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr <i>Salvelinus namaycush</i> ecotypes in Rush Lake, USA. </span>A rapid phenotypic shift in body and head shape was found within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (ages 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing changes in growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.</p>
Adaptive effects of parental and developmental environments on offspring survival, growth, and phenotype
<p><span>Phenotypic adjustments to environmental variation are particularly relevant to cope with putative environmental mismatches often imposed by natal dispersal.</span></p> <p><span>We used an inter-generational cross-transplant field-based experiment to evaluate the morphological and physiological effects of parental and post-settlement water flow environments on the orange-fin anemonefish <em>Amphiprion chrysopterus</em> through ontogeny (at pre- and post-settlement stages).</span></p> <p><span>Offspring born from parents under high water flow had an 18% higher caudal fin aspect ratio (</span><span>a compound measure of shape) at the pre-settlement stage, 10% slower growth after settlement, and 55% lower survival after settlement compared to offspring from low-water-flow parents. At the pre-settlement stage, caudal fin length was determined by parental caudal fin length. At the post-settlement stage, fish survived equally well with similar phenotypes in both high- and low-developmental-flow environments. However, results suggest potential developmental phenotypic plasticity in caudal fin length, which increases more under low water flow during development. After settlement growth was the only morphological or physiological trait that was associated with parental water flow, which was lower from parents under high flow, as was survival.</span></p> <p><span>These results give important insights into the parental contribution, both genetic and non-genetic, in determining early offspring phenotype and subsequent growth and survival. Our results also suggest that offspring may possess the flexibility </span><span>to cope with a wide range of local environments including those different from their parents. Overall, the findings of this study show the fitness consequences of living in different environments and the likely trade-offs between parental and offspring fitness in a wild population.</span></p>
Fluid flow drives phenotypic heterogeneity in bacterial growth and adhesion on surfaces
<p>Raw data for the study reported by Hubert et al., Nature Communications 2024 (accepted).</p> <p>Each of the 4 folders within the archive, denoted 'Ulow', 'Low', 'Med', and 'High' contains 3 sets of raw experimental data, each corresponding to an experiment performed in the 'Ulow', 'Low', 'Med', and 'High' shear stress regime, in accordance with the folders' names.</p> <p>Each of these data sets is bundled into a single .avi video, consisting of raw images recorded at a 1/60 Hz acquisition frequency (i.e., 1 image per minute).</p> <p>The folder 'Supplementary_Software'contains Matlab and Python scripts used to treat the raw data, with a raw data sample. The file 'HOWTO_use_the_scripts.txt' explains how to use the scripts.</p> <p>Except for this HOWTO file, the files inside the various subfolders of folder 'Supplementary_Software' are not listed in the file tree below. Only the subfolders are listed.</p> <p>./<br>├── README_data_sets_and_treatment_scripts.txt (this file)<br>├── Ulow/<br> | ├── Ulow_set1.avi<br> | ├── Ulow_set2.avi<br> | └── Ulow_set3.avi<br>├── Low/<br> | ├── Low_set1.avi<br> | ├── Low_set2.avi<br> | └── Low_set3.avi<br>├── Med/<br> | ├── Med_set1.avi<br> | ├── Med_set2.avi<br> | └── Med_set3.avi<br>└── High/<br> | ├── High_set1.avi<br> | ├── High_set2.avi<br> | └── High_set3.avi<br>└── Supplementary_Software/<br> ├── HOWTO_use_the_scripts.txt<br> ├── step1_matlab/ <br> | ├── Pos0_100_every_1000/ <br> | ├── matlab_image_processing/ <br> | ├── images_treated_20201120_220854/ <br> | └── Outputs/<br> └── step2_python/<br> └── Outputs/</p> <p> </p> <p> </p>
Zea mays MAGIC RIL population - growth chamber phenotyping data
<p>MIAPPE compliant ISA-tab files of 197 recombinant inbred lines of two different maize (Zea mays) populations including indepth phenotyping of the fourth leaf at later stages of development.</p>
Data and code from: Phenotypic memory drives population growth and extinction risk in a noisy environment
<p>Random environmental fluctuations pose major threats to wild populations. As patterns of environmental noise are themselves altered by global change, there is growing need to identify general mechanisms underlying their effects on population dynamics. This notably requires understanding and predicting population responses to the color of environmental noise, i.e. its temporal autocorrelation pattern. Here, we show experimentally that environmental autocorrelation has a large influence on population dynamics and extinction rates, which can be predicted accurately provided that a memory of past environment is accounted for. We exposed near to 1000 lines of the microalgae <em>Dunaliella salina</em> to randomly fluctuating salinity, with autocorrelation ranging from negative to highly positive. We found lower population growth, and twice as many extinctions, under lower autocorrelation. These responses closely matched predictions based on a tolerance curve with environmental memory, showing that non-genetic inheritance can be a major driver of population dynamics in randomly fluctuating environments. </p>
Data and code from: Phenotypic memory drives population growth and extinction risk in a noisy environment
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Effect of parental phenotype on dispersal, growth and maturation of offspring in wild masu salmon
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Data from: Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon
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Adaptive effects of parental and developmental environments on offspring survival, growth, and phenotype
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Data from: Bacterial and fungal growth on fungal necromass and its diverse components: shared profiles and divergent constraints revealed by high-throughput phenotyping
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Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?
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Data from: Gene expression in the phenotypically plastic Arctic charr (Salvelinus alpinus): a focus on growth and ossification at early stages of development
Gene expression during development shapes the phenotypes of individuals. Although embryonic gene expression can have lasting effects on developmental trajectories, few studies consider the role of maternal effects, such as egg size, on gene expression. Using qPCR, we characterize relative expression of 14 growth and/or skeletal promoting genes across embryonic development in Arctic charr (Salvelinus alpinus). We test to what extent their relative expression is correlated with egg size and size at early life‐stages within the study population. We predict smaller individuals to have higher expression of growth and skeletal promoting genes, due to less maternal resources (i.e., yolk) and prioritization of energy toward ossification. We found expression levels to vary across developmental stages and only three genes (Mmp9, Star, and Sgk1) correlated with individual size at a given developmental stage. Contrary to our hypothesis, expression of Mmp9 and Star showed a non‐linear relationship with size (at post fertilization and hatching, respectively), whilst Sgk1 was higher in larger embryos at hatching. Interestingly, these genes are also associated with craniofacial divergence of Arctic charr morphs. Our results indicate that early life‐stage variation in gene expression, concomitant to maternal effects, can influence developmental plasticity and potentially the evolution of resource polymorphism in fishes.
Data from: Variable effects on growth and defence traits for plant ecotypic differentiation and phenotypic plasticity along elevation gradients
Along ecological gradients, phenotypic differentiation can arise through natural selection on trait diversity and magnitude, and environment-driven plastic changes. The magnitude of ecotypic differentiation versus phenotypic plasticity can vary depending on the traits under study. Using reciprocal transplant-common gardens along steep elevation gradients, we evaluated patterns of ecotypic differentiation and phenotypic plasticity of several growth and defence-related traits for two coexisting but unrelated plant species, Cardamine pratensis and Plantago major. For both species, we observed ecotypic differentiation accompanied by plasticity in growth related traits. Plants grew faster and produced more biomass when placed at low elevation. In contrast, we observed fixed ecotypic differentiation for defence and resistance traits. Generally, low elevation ecotypes produced higher chemical defences regardless of the growing elevation. Yet, some plasticity was observed for specific compounds, such as indole glucosinolates. The results of this study may suggest that ecotypic differentiation in defence traits is maintained by costs of chemical defence production, while plasticity in growth traits is regulated by temperature driven growth response maximization.
Data from: A novel phenotype combining primary ovarian insufficiency growth retardation and pilomatricomas with MCM8 mutation
<p><b>Context</b>: Primary Ovarian insufficiency (POI) affects 1% of women under 40 years and leads most often to definitive infertility with adverse health outcomes. Very recently, genes involved in DNA repair have been shown to cause POI. </p> <p><b>Objective</b>: To identify the cause of a familial POI in a consanguineous Turkish family.</p> <p><b>Design:</b> Exome sequencing was performed in the proposita and her mother. Chromosomal breaks were studied in lymphoblastoid cell lines treated with Mitomycin (MMC).</p> <p><b>Setting and patients:</b> The proposita presented intra-uterine and post-natal growth retardation, multiple pilomatricomas in childhood and primary amenorrhea. She was treated with growth hormone (GH) from 14 to 18 years.</p> <p><b>Results:</b> We identified a novel nonsense mutation in exon 9 of the minichromosome maintenance complex component 8 gene (<i>MCM8)</i> NM_001281522.1: c.925C>T/p.R309* yielding a truncated protein devoid of the 531 C-terminal residues. </p> <p>The mutation was homozygous in the daughter and heterozygous in the mother. MMC induced DNA breaks and aberrant metaphases in the patient's lymphoblastoid cells. The mother's cells had intermediate but significantly higher chromosomal breaks compared to a control.</p> <p><b>Conclusion</b>: We describe a novel phenotype of syndromic POI related to a novel truncating <i>MCM8</i> mutation. We show for the first time that spontaneous tumors (pilomatricomas) are associated with <i>MCM8</i> genetic defect making the screening of this gene necessary before starting GH therapy in POI with short stature, especially in a familial or consanguineous context. Appropriate familial monitoring in the long term is necessary and fertility preservation should be considered in heterozygous siblings to avoid rapid follicular atresia.</p>
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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)
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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.