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77 results for “common garden”
Growth data for young of the year arctic grayling raised in a aquatic common garden at Toolik Field Station, summer 2017
Since 2009, the FISHSCAPE Project (Grant #1719267, 1417754, and 0902153), based at Toolik Field Station, has monitored physical, chemical, and biological parameters within three watersheds: The Kuparuk (including Toolik Lake and Toolik outlet stream); The Sagavanirktok (primarily Oksrukuyik Creek, but also including sections of the Ailish and Atigun Rivers and the Galbraith Lakes); and The Itkillik (primarily the I-Minus outlet stream, a tributary that that feeds into the Itkilik River). The goals are to understand and predict the adaptability and persistence of a key Arctic species, the Arctic grayling (Thymallus arcticus), to changing climate and hydrology. Research questions include: (1) Does landscape structure determine movement within and among watersheds; (2) do populations adapt to stream characteristics at local and regional scales; and (3) will the relative adaptability of populations determine their persistence under future climate change. To test ideas about local adaptation, we conducted an aquatic common garden experiment at Toolik Field Station, to investigate the genetic component of phenotypic variation among Arctic grayling populations on Alaska's North Slope. This file contains the growth data.
Survivorship data for young of the year Arctic grayling raised in an aquatic common garden at Toolik Field Station, summer 2017
Since 2009, the FISHSCAPE Project (grant # 1719267, 1417754, and 0902153), based at Toolik Field Station, has monitored physical, chemical, and biological parameters within three watersheds: The Kuparuk (including Toolik Lake and Toolik outlet stream); The Sagavanirktok (primarily Oksrukuyik Creek, but also including sections of the Ailish and Atigun Rivers and the Galbraith Lakes); and The Itkillik (primarily the I-Minus outlet stream, a tributary that that feeds into the Itkilik River). The goals are to understand and predict the adaptability and persistence of a key Arctic species, the Arctic grayling (Thymallus arcticus), to changing climate and hydrology. Research questions include: (1) Does landscape structure determine movement within and among watersheds; (2) do populations adapt to stream characteristics at local and regional scales; and (3) will the relative adaptability of populations determine their persistence under future climate change. To test ideas about local adaptation, we conducted an aquatic common garden experiment at Toolik Field Station, to investigate the genetic component of phenotypic variation among Arctic grayling populations on Alaska's North Slope. This file contains the survivorship data.
Eriophorum vaginatum leaf length 2015-2017 from 2014 common gardens established at Toolik Lake, Coldfoot, and Sagwon - Alaska
Data on Eriophorum vaginatum leaf length collected from common gardens established at Toolik Lake, Coldfoot, and Sagwon in 2014 with tussocks from Coldfoot, Toolik Lake, and Sagwon. Data collected during the growing seasons of 2015, 2016, and 2017
Contrasting plant adaptation strategies to latitude in the native and invasive range of Spartina alterniflora: geographic survey (2014) and Common garden (2015-2017)
We examined trait differences and evolution across geographic clines among continents of the intertidal grass Spartina alterniflora within its invasive and native ranges. Between September and November 2014, we sampled vegetative and reproductive traits in the field at 20 sites over 20° latitude in China (invasive range) and 28 sites over 17° latitude in the US (native range). We grew both Chinese and US plants in a greenhouse common garden for three years (2015 - 2017) to determine if differences in performance of S. alterniflora between the introduced and native ranges were due to genetic differences or differences in abiotic conditions.
Geographic variation of tree height of Pinus pinea L. gathered from common gardens in Europe
<p>This dataset collects individual georeferenced tree height data from <em>Pinus pinea </em>L. planted in common gardens in France and Spain, between years 1993 and 1997. The experimental design varies depending on the common garden, from a randomized complete to incomplete block design, RCB or RIB, respectively. The final dimensions of this database is 56,624 individual tree height measurements <em> </em>with 9 common gardens and 55 different provenances. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. </p>
Geographic variation of tree height of Pinus nigra Arn. gathered from common gardens in Europe
<p>This dataset collects individual georeferenced tree height data from <em>Pinus nigra</em> Arn. planted in common gardens in France, Germany and Spain, between years 1968 and 2009. The experimental design varies depending on the common garden, from a randomized complete to incomplete block design, RCB or RIB, respectively. The final dimension of the dataset is 194,642 individual tree height data measurements <em> </em>with 15 common gardens and 78 different provenances. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. </p> <p> </p>
Geographic variation of tree height of Pinus pinaster Aiton gathered from common gardens in Europe and North-Africa
<p>This dataset collects individual georeferenced tree height data from <em>Pinus pinaster</em> Aiton planted in common gardens in France, Morocco and Spain, between years 1966 and 1992. The experimental design varies depending on the common garden, from a randomized complete to incomplete block design, RCB or RIB, respectively. The final dimension of the dataset is 123,801 individual tree height data measurements <em> </em>with 14 common gardens and 182 different genetic units. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. </p>
Toolik Lake 2011 common garden leaf length phenology 2015-2016 Alaska
Data on Eriophorum vaginatum leaf length collected from a common garden established at Toolik Lake in 2011 with tussocks from No Name Creek, Coldfoot, Eagle Creek, Toolik Lake, Sagwon, and Prudhoe Bay. Data collected during the growing seasons of 2015 and 2016. Results published in Parker, T. C., J. Tang, M. B. Clark, M. M. Moody, and N. Fetcher. 2017. Ecotypic differences in the phenology of the tundra species Eriophorum vaginatum reflect sites of origin. Ecology and Evolution 7: 9775-9786. doi: 10.1002/ece3.3445
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>
From common gardens to candidate genes: Exploring local adaptation to climate in red spruce
<p><span>Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. </span></p> <p><span>In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association (GEA) methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure.</span></p> <p><span>This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two "modules" associated with different environmental gradients.</span></p> <p><span>This study nicely exemplifies the multivariate dimension of adaptation to climate in trees. </span></p>
Behavioural changes in the city: the common black garden ant defends aphids more aggressively in urban environments
<p>Data and R code to analyse changes in aphid and ant populations and behaviour along a gradient of urbanisation in Berlin, Germany. This release is associated to a publication in preparation and includes the updated R code used for publication:</p> <p>Gaber, H., Ruland, F, Jeschke, J. & Bernard-Verdier, M. (2024) Behavioural changes in the city: the common black garden ant defends aphids more aggressively in urban environments. <em>Ecology & Evolution</em> (publication details will soon be added)</p>
Figure 2 in Eriophyoid mites (Acari: Prostigmata) on common pear (Pyrus communis L.): species diversity and varietal attractiveness in the Fomin Botanical Garden (Kyiv, Ukraine)
Figure 2. Pear leaves damaged by the second and third generations of Eriophyes pyri (Academician Fomin Botanical Garden, 2020).
Figure 1 in Eriophyoid mites (Acari: Prostigmata) on common pear (Pyrus communis L.): species diversity and varietal attractiveness in the Fomin Botanical Garden (Kyiv, Ukraine)
Figure 1. Young pear leaves damaged by the first generation of Eriophyes pyri (Academician Fomin Botanical Garden,
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>
Data from: The city and forest bird flock together in a common garden: Genetic and environmental effects drive urban phenotypic divergence
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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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Data and code from: Parental care liberates juvenile growth: A common-garden test of the evolutionary benefits of care
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