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26 results for “common garden experiments”
Climate Change Across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest: growth and enzyme activity traits of soil fungi isolated from CCASE in July 2017, grown under a common garden experiment in the laboratory that mimicked CCASE soil temperature treatments
Projections for the northeastern U.S. indicate that mean air temperatures will rise and snowfall will become less frequent, causing more frequent soil freezing. To test fungal responses to these combined chronic and extreme soil temperature changes, we conducted a laboratory-based common garden experiment with soil fungi that had been subjected to different combinations of growing season soil warming, winter soil freeze/thaw cycles, and ambient conditions for four years in the field. We found that fungi originating from field plots experiencing a combination of growing season warming and winter freeze/thaw cycles had inherently lower activity of acid phosphatase, but higher cellulase activity, that could not be reversed in the lab. In addition, fungi quickly adjusted their physiology to freeze/thaw cycles in the laboratory, reducing growth rate and potentially reducing their carbon use efficiency. Our findings suggest that less than four years of new soil temperature conditions in the field can lead to physiological shifts by some soil fungi, as well as irreversible loss or acquisition of extracellular enzyme activity traits by other fungi. These findings could explain field observations of shifting soil carbon and nutrient cycling under simulated climate change. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Datasets from: Adaptation of Mediterranean forest species to climate: lessons from common garden experiments
<p>We include information (raw Datasets) corresponding to the paper; Adaptation of Mediterranean forest species to climate: lessons from common garden experiments.</p> <p>Table Journal of Ecology Review.xls. Material used in the metaanalysis</p> <p>JoE Row data Common garden.xls. Raw data for survival and height used in the study. Multi-environment commong garden data for Pinus canariensis, P. halepensis, P. nigra, P. pinaster, Quercus ilex, and Q. suber.</p> <p>JoE Dataset4.xls. Data used for the analysis of local adaptation.</p> <p> </p>
Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes
<p>Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype-phenotype associations, it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulates traits. Here we assess lipid content, growth, weight, and length variation in full and hybrid F<sub>1</sub> crosses of deep and shallow water sympatric lake charr ecotypes reared for nine years in a common garden experiment. Redundancy analysis (RDA) and quantitative-trait-loci (QTL) genomic scans are used to identify associations between genotypes at 19,714 single nucleotide polymorphisms (SNPs) aligned to the lake charr genome and individual phenotypes to determine the role that genetic inheritance plays in ecotype phenotypic diversity. Lipid content, growth, length, and weight differed significantly among lake charr crosses throughout the experiment suggesting that pedigree plays a large role in lake charr development. Polygenic scores of 15 SNPs putatively associated with lipid content and/or condition factor indicated that ecotype distinguishing traits are polygenically regulated and additive. A QTL identified on chromosome 38 contained >200 genes, some of which were associated with lipid metabolism and growth, demonstrating the complex nature of ecotype diversity. The results of our common garden study further indicate that lake charr ecotypes observed in nature are pre-determined at birth and that ecotypes differ fundamentally in lipid metabolism and growth.</p>
Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks
<p>This release includes the different genomic datasets used in the article entitled "<em>Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks</em> " by Ramírez-Valiente et al.,</p> <p>File description:</p> <p><strong>Samples.xlsx</strong>: Description of individual and population codes used in the different analyses and genomic datasets.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_all_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus faginea</em> including all loci.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_neutral_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus faginea</em> excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_all_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus lusitanica </em>including all loci.</p> <p><strong>Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus lusitanica </em>excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_BAYESCAN.txt</strong>: Input file used to perform BAYESCAN analyses for <em>Quercus faginea</em>.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_BAYESCAN.txt</strong>: Input file used to perform BAYESCAN analyses for <em>Quercus lusitanica</em>.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_ARLEQUIN.arp</strong>: Input file used to perform ARLEQUIN analyses for <em>Quercus faginea</em>.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_ARLEQUIN.arp</strong>: Input file used to perform ARLEQUIN analyses for <em>Quercus lusitanica</em>.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_all_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus faginea</em> including all loci.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_neutral_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus faginea</em> excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_all_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus lusitanica </em>including all loci.</p> <p><strong>Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus lusitanica </em>excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_faginea_Greenhouse_DRIFTSEL.txt</strong>: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for <em>Quercus faginea </em>under common garden greenhouse experiments.</p> <p><strong>Quercus_faginea_Outdoor_DRIFTSEL.txt</strong>: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for <em>Quercus faginea</em> under common garden outdoor experiments.</p> <p><strong>Quercus_lusitanica_Greenhouse_DRIFTSEL.txt</strong>: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for <em>Quercus lusitanica </em>under common garden greenhouse experiments.</p>
Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes
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SNPs derived from a common garden experiment across the biogeographic range of <em>Kelletia kelletii</em>
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Common-garden experiment reveals clinal trends of bud phenology in black spruce populations from a latitudinal gradient in the boreal forest
<p>Climate warming is modifying the movement of air masses over Northern latitudes, producing warming and cooling events across the boreal regions. These new conditions changes may mismatch plant phenology from weather conditions, and affect the growing period of trees. Understanding the processes of local adaptation in bud phenology can help to predict the response of plants to these rapid and unexpected environmental changes.</p> <p>Our study monitored bud burst and bud set weekly during four growing seasons in black spruce [Picea mariana (Mill.) B.S.P.] saplings planted in a common garden and originating from five provenances representing the whole latitudinal distribution of the closed boreal forest in Quebec, Canada. We compared the variance in bud phenology among populations and years, and analyzed the relationships with the temperatures at the origin sites.</p> <p>Bud burst and bud set occurred in mid-May and mid-July, respectively, with a large variability among provenances and between the study years. A delayed bud phenology was observed in the provenances from warmer sites, with bud burst and bud set being 1.1 and 1.4 days later for every additional degree in mean annual temperature at the origin site, respectively. Populations with earlier bud bursts also showed earlier bud sets, thus the growing season was similar among provenances. The heritability of bud set was higher than that of bud burst, with estimates of 0.26 and 0.21, respectively. On average, variance in bud phenology among provenances reached 5.3%, which was higher than that within provenances (2.6%). The factor year explained 37.7-69.7% of the variance in bud phenology.</p> <p>Synthesis. Results demonstrate the plastic response of bud burst to changing temperatures and suggest the effects of endogenous factors on bud set. The earlier growth reactivation due to global warming occurring under higher frost risks in spring are expected to produce damage to the developing buds. Meanwhile, the ability of bud phenology to match the inter-annual variability in weather could help to cope with the changing environmental conditions expected in the future.</p>
Dataset: Acorn weight as determinant of germination in red and white oaks: evidences from a common-garden greenhouse experiment
<p>This repository contains the files associated with the following article:</p> <p>Sánchez-Montes de Oca EJ, EI Badano, LE Silva-Alvarado, J Flores, F Barragán-Torres & JA Flores-Cano. Acorn weight as determinant of germination in red and white oaks: evidences from a common-garden greenhouse experiment. Annals of Forest Science, 75, article 12. <a href="https://doi.org/10.1007/s13595-018-0693-y">https://doi.org/10.1007/s13595-018-0693-y</a></p> <p>Both datasets are provided in Microsoft Excel format. The first dataset (2015 data-Relationships acorn fresh weight-germination) contains information about the phylogenetic section to which each oak species included in the study belong to, the fresh weights of acorns after they were soaked and their respective germination responses (100 acorns per oak species). These data were used to assess whether acorn weight influences germination across and within species. The second dataset (2017 data-Relationships acorn dry-fresh weights) also contains the phylogenetic section to which each oak species belongs to, indicating the dry biomass of acorns, their fresh weight after soaking, and their percent water content (100 acorns per oak species). These data were used to assess how dry biomass of acorns influences their fresh weight and percent water content after soaking.</p>
Data from a drought experiment on saplings of Crataegus monogyna in a common garden setting with three provenances (Belgian, Swedish and Spanish)
<p><span>Data are from the common shrub <em>Crataegus monogyna</em> that experienced two summer droughts, each followed by rewatering. The experimental design consisted of a common garden with potted saplings from a local Belgian, a Swedish and a Spanish-Pyrenean provenance. We quantified the effects on growth and leaf phenology, focusing on the legacies in the year following the droughts. Responses were influenced by the severity of the drought and by its timing. </span></p>
data from a drought stress experiment on Cornus sanguineum in a common garden
<p>Data obtained from a drought stress experiment performed in 2021 on potted plants from the shrub species Cornus sanguineum in a common garden with two provenances, a local (Belgian) and a Pyrenean.</p>
Data from: An established plant invader may still benefit from increasing genetic diversity – Insights from artificial populations in a common garden experiment
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Trait data of Primula elatior from common garden experiments and field campaigns
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Common-garden experiment reveals clinal trends of bud phenology in black spruce populations from a latitudinal gradient in the boreal forest
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No evidence for early fitness penalty in glyphosate-resistant biotypes of Conyza canadensis: common garden experiments in the absence of glyphosate
<p>Strong selection from herbicides has led to the rapid evolution of herbicide-resistant weeds, greatly complicating weed management efforts worldwide. In particular, overreliance on glyphosate, the active ingredient in RoundUp®, has spurred the evolution of resistance to this herbicide in ≥40 species. Previously, we reported that <i>Conyza canadensis</i> (horseweed) has evolved extreme resistance to glyphosate, surviving at 40x the original 1x effective dosage. Here, we tested for underlying fitness effects of glyphosate resistance to better understand whether resistance could persist indefinitely in this self-pollinating, annual weed. We sampled seeds from a single maternal plant ("biotype") at each of 26 horseweed populations in Iowa, representing 9 susceptible biotypes (S), 8 with low-level resistance (LR), and 9 with extreme resistance (ER). In 2016 and 2017, we compared early growth rates and bolting dates of these biotypes in common garden experiments at two sites near Ames, Iowa. Nested ANOVAs showed that, as a group, ER biotypes attained similar or larger rosette size after 6 weeks compared to S or LR biotypes, which were similar to each other in size. Also, ER biotypes bolted 1-2 weeks earlier than S or LR biotypes. These fitness-related traits also varied among biotypes within the same resistance category, and time to bolting was inversely correlated with rosette size across all biotypes. Disease symptoms affected 40% of all plants in 2016 and 78% in 2017, so we did not attempt to measure lifetime fecundity. In both years, the frequency of disease symptoms was greatest in S biotypes and similar in LR vs. ER biotypes. Overall, our findings indicate there is no early growth penalty and possibly no lifetime fitness penalty associated with glyphosate resistance, including extremely strong resistance. We conclude that glyphosate resistance is likely to persist in horseweed populations, with or without continued selection pressure from exposure to glyphosate.</p>
Data from: A common garden experiment to evaluate the morphological distinction between two species of shooting star (Primula section Dodecatheon) native to Pennsylvania
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No evidence for early fitness penalty in glyphosate-resistant biotypes of Conyza canadensis: common garden experiments in the absence of glyphosate
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Data from: The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature
Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild 'home' environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50 km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.
Data from: A common-garden experiment to quantify evolutionary processes in copepods: the case of emamectin benzoate resistance in the parasitic sea louse Lepeophtheirus salmonis
Background:The development of pesticide resistance represents a global challenge to food production. Specifically for the Atlantic salmon aquaculture industry, parasitic sea lice and their developing resistance to delousing chemicals is challenging production. In this study, seventeen full sibling families, established from three strains of Lepeophtheirus salmonis displaying differing backgrounds in emamectin benzoate (EB) tolerance were produced and quantitatively compared under a common-garden experimental design. Lice surviving to the preadult stage were then exposed to EB and finally identified through the application of DNA parentage testing. Results: With the exception of two families (19 and 29%), survival from the infectious copepod to preadult stage was very similar among families (40-50%). In contrast, very large differences in survival following EB exposure were observed among the families (7.9-74%). Family survival post EB exposure was consistent with the EB tolerance characteristics of the strains from which they were established and no negative effect on infection success were detected in association with increased EB tolerance. Two of the lice families that displayed reduced sensitivity to EB were established from a commercial farm that had previously used this chemical. This demonstrates that resistant alleles were present on this farm even though the farm had not reported treatment failure. Conclusions: To our knowledge, this represents the first study where families of any multi-cellular parasite have been established and compared in performance under communal rearing conditions in a common-garden experiment. The system performed in a predictable manner and permitted, for the first time, elucidation of quantitative traits among sea lice families. While this experiment concentrated on, and provided a unique insight into EB sensitivity among lice families, the experimental design represents a novel methodology to experimentally address both resistance development and other evolutionary questions in parasitic copepods.
Supplementary material 1 from: Jagodziński AM, Dyderski MK, Horodecki P, Knight KS, Rawlik K, Szmyt J (2019) Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment. NeoBiota 46: 1-21. https://doi.org/10.3897/neobiota.46.30413
: Data type: measurement
Supplementary material 2 from: Jagodziński AM, Dyderski MK, Horodecki P, Knight KS, Rawlik K, Szmyt J (2019) Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment. NeoBiota 46: 1-21. https://doi.org/10.3897/neobiota.46.30413
: Data type: measurement
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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
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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.
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