Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
35
datasets available to search
ShareScore release 0.9.0
Dataset results
35 results for “tree species composition”
Data and code from "Water availability is a stronger driver of soil microbial processing of organic nitrogen than tree species composition"
<p>#### Data description<br> Data from large scale, long-term tree diversity experiment in southwestern France (<a href="https://sites.google.com/view/orpheeexperiment/home">ORPHEE</a>), additionally manipulating water contraint. Variables presented are soil nitrogen cycling rates measured using isotope pool dilutions.</p> <p>Companion paper is found here:</p> <p>Maxwell TL, Augusto L, Tian Y, Wanek W & Fanin N (2023). Water availability is a stronger driver of soil microbial processing of organic nitrogen than tree species composition. <em>European Journal of Soil Science</em>. <a href="https://doi.org/10.1111/ejss.13350">https://doi.org/10.1111/ejss.13350</a></p> <p>#### Metadata<br> Soil sampling: July 2020<br> Maxwell_ShortComm_Data.csv data description</p> <p>ID: unique identifier per sample<br> Block: numbered 1-6. Blocks 1,3,6 are control (unirrigated), Blocks, 2,4,5 are irrigated<br> Plot: numbered plot according to the ORPHEE design. Plot 1 = BP, Plot 5 = PP, Plot 9 = BP_PP<br> Espece: species ID. BP = pure birch (<em>Betula pendula</em>), PP = pure pine (<em>Pinus pinaster</em>), BP_PP (50% mixed birch-pine)<br> Rep: sample replicate, 3 replicates per plot<br> Sample name: long unique identifier per sample. Concatenation of Block, Plot, and Espece<br> PD: gross protein depolymerization rates (micrograms nitrogen per grams dry soil per day = µg N g-1 d-1)<br> AAU: gross free amino acid uptake rates (µg N g-1 d-1)<br> Cmicrobial_ug_g: microbial biomass carbon (µg C g-1)<br> Nmicrobial_ug_g: microbial biomass nitrogen (µg N g-1)<br> MRT_FAA_hrs: mean residence time of free amino acids (hours)<br> FAA_ugN_g: free amino acids (µg N g-1)<br> Moisture_percent: soil moisture percent (%)<br> N_nonfumige_ug_g: nitrogen from non fumigated soils, i.e. extractable N (µg N g-1)<br> C_nonfumige_ug_g: nitrogen from non fumigated soils, i.e. extractableC (µg C g-1)</p>
Fig. 3 in Regional uniqueness of tree species composition and response to forest loss and climate change
Fig. 3 | Response of tree species to climate change across biomes. The median absolute latitude and median elevation shift among species, fraction of lost and gained species, and change in taxonomic and phylogenetic composition under climate change were computed for each forest ecoregion. The boxplots show statistics for n = 239 ecoregions for Tropical Moist Broadleaf Forests, n = 14 ecoregions for Tropical Coniferous Forests, n = 55 ecoregions for Tropical Dry Broadleaf Forests, n = 26 ecoregions for Boreal Forests, n = 91 ecoregions for Temperate Broadleaf Forests, n = 49 ecoregions for Temperate Conifer Forests and n = 61 ecoregions for Mediterranean Forests. The center line of the boxplots shows the median, the box limits the quartiles, the whiskers 1.5 times the interquartile range, and the points the outliers.Changes are computed between predicted distributions with climate variables for 1981-2010 and climate projections for 2071-2100 under climate change scenario SSP 5.85. Changes in composition are computed as the Euclidean distance between scaled NMDS and evoPCA values computed at the ecoregion level. Source data are provided as a Source Data file.
Fig. 2 in Regional uniqueness of tree species composition and response to forest loss and climate change
Fig. 2 | Species occupancy range distribution and loss. a Distributions of species occupancy range sizes globally (gray) and constrained to forests (at least 10% tree cover, color) for species in each forest biome. b Boxplot of relative range reduction across species in each forest biome with the center line showing the median, the box limits the quartiles, the whiskers 1.5 times the interquartile range, and the points the outliers. The distributions and boxplots are computed for n = 6810 species for Tropical Moist Broadleaf Forests, n = 588 species for Tropical Coniferous Forests, n = 1101 species for Tropical Dry Broadleaf Forests, n = 54 species for Boreal Forests, n = 1744 species for Temperate Broadleaf Forests, n = 178 species for Temperate Conifer Forests and n = 580 species for Mediterranean Forests. c Global map of median species range size constrained to forests, created with QGIS110. The gray base map corresponds to all areas for which model predictors were available. d Plot of species' median latitude against range size constrained to forests, colored by point density, where red indicates the highest density. Source data are provided as a Source Data file.
Fig. 1 in Regional uniqueness of tree species composition and response to forest loss and climate change
Fig. 1 | Gradients in taxonomic and phylogenetic composition show a near- a, c. Scatter plot of taxonomic and phylogenetic ordinations in environmental unique biodiversity signature of every single location on the planet. Taxonomic space, a 2-dimensional space made up of the 2 first axes of a PCA of the environcomposition is represented by a 3-axis non-metric dimensional scaling (NMDS) and mental variables used for species distribution modeling: mean annual temperature phylogenetic beta-diversity is represented by the 3 first axes of a phylogenetic (MAT), temperature seasonality (T season), annual precipitation (Annual P), preordination (evoPCA). Both the taxonomic and phylogenetic ordinations are com- cipitation seasonality (P season), growing season length (GSL), net primary proputed on the global community matrix derived from the modeled distributions of ductivity (NPP),silt content (Silt),coarse fragments (CF),and soil pH (pH).b, d. Map n = 10,590 tree species sampled at a resolution of 100 km, resulting in n = 12,548 of taxonomic and phylogenetic ordinations in geographical space. Source data are sites. The 3 axes of each ordination are mapped to red, green, and blue with provided as a Source Data file. The maps were created with QGIS110 and the gray minimum and maximum values corresponding to the 10th and 90th percentiles. base map corresponds to all areas for which model predictors were available.
Data from: Do temperate tree species diversity and identity influence soil microbial community function and composition?
Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. The present study investigates inter-trophic links between tree diversity and soil microbial community function and composition.We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM) and tree identity. The site was a 4-yr-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles (CLPP) and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroRespTM system, respectively. The relationship between tree species richness and glucose induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration (BR)), with higher biomass (glucose induced respiration (GIR)), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity – leaf habit) affected soil microbial community respiration, biomass and composition. For the first time, we identified functional traits related to life history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.
Diversity, species coexistence, and functional composition patterns in subtropical Atlantic Forests invaded by non-native trees
<ol> <li>Biological invasions are a major environmental challenge today. Interactions between invasive and native species can significantly shape community structures, influencing co-existence, diversity, and functional composition of species. The subtropical Atlantic forest in southern Brazil, a recognized biodiversity hotspot, provides a unique setting to study these interactions, given its vulnerability to alien tree invasions. </li> <li>Our study sought to elucidate the impacts of such invasions on this fragile ecosystem by addressing key questions: 1) How are tree community diversity patterns affected by the abundance of invading alien tree species? 2) What are the patterns of coexistence between native and alien invasive trees? 3) Is the functional composition of the forests altered by the abundance of invasive trees?</li> <li>To address these questions, we compiled data on the abundance and functional traits of native and invasive trees. We determined the diversity patterns and functional composition of plots with different degrees of invasion. These data were analyzed using Generalized Linear Mixed Models, Principal Component Analysis, and a coexistence index.</li> <li>In plots with a higher abundance of invasive trees, there was a significant decrease in the taxonomic and functional richness of native species. Furthermore, we observed that invasive alien trees coexisted with native species, and as the abundance of invasive trees increased, the native community weighted mean (CWM) of the leaf area and specific leaf area decreased.</li> <li>In conclusion, within the subtropical Atlantic forest areas of southern Brazil, our findings highlight that the abundance of invasive trees adversely affects the taxonomic and functional richness of native species. Furthermore, while invasive alien trees were found to coexist with native species, increased invasive abundance corresponded to a reduction in the leaf area and the specific leaf area of the native community.</li> </ol>
Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay
<p>Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear.</p> <p>To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality, and chemical or physical defense mechanisms. After one and four years of decay, we assessed the richness and composition of wood-inhabiting fungi using amplicon sequencing and determined the proportional wood density loss.</p> <p>Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% yr<sup>-1</sup> for the subsequent three years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7-24.8% yr<sup>-1</sup>) and subsequent years (0-11.3% yr<sup>-</sup><sup>1</sup>). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood-inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after four years of exposure in the field, where fungal communities dominated by brown-rot and white-rot Basidiomycetes were linked to higher wood decomposition rate.</p> <p><em>Synthesis.</em> Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor-made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; Initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.</p>
Not all trees can make a forest: tree species composition and competition control forest encroachment in a tropical savanna
<p>Forest encroachment into savannas is a widespread phenomenon, the rate of which may depend on soil conditions, species composition, or changes in stand structure. As savanna specialist trees are replaced by generalist species, rates of stand development may increase. Because generalists can persist in forests, they are likely to grow more quickly and survive longer in dense stands, compared to savanna specialists. Furthermore, the faster growth rates of generalists may allow them to overtop and outcompete savanna specialists, causing rapid species turnover.</p> <p>We measured growth and survival of 6147 individuals of 112 species of savanna and generalist tree species over a period of 10 years in an ecological reserve in Assis, São Paulo State, Brazil. We modeled growth and mortality as a function of soil texture and nutrients, tree size, competitive neighborhood, and membership in savanna or generalist (species which can persist in forests and savannas) functional groups.</p> <p>Tree growth and survival was strongly influenced by competition, as estimated by the basal area of trees taller than a focal tree. At the stand level, savanna species are unable to contribute basal area growth in closed stands, while generalist species continue to increase in basal area even at high stand basal area. This phenomenon is driven by differences in growth and mortality. Generalists grew faster than savanna species, both in height and diameter. This difference in growth rates led to savanna species becoming suppressed more rapidly than generalists. When suppressed, savanna species were more than twice as likely to die than were generalists. Soils had inconsistent and mostly weak effects which were difficult to separate from gradients of stand structure.</p> <p>Synthesis: We demonstrate that the presence of generalist trees accelerates rates of basal area accumulation due to their greater growth rates and tolerance of shading. Generalists outcompete savanna trees by growing faster in the open and overtopping savanna specialists. Due to the slow growth and high mortality of savanna species in the shade, they are unable to form closed-canopy stands. Accounting for differences among functional types and development of vegetation structure is critical for modeling forest encroachment.</p>
Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species - Sampling Raw Data
<p>Sampling Raw Data for the manuscript "<strong>Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species </strong>" </p> <p>R Code for producing the sunburst plots from the data obtained by classyFire</p> <p> </p>
Data for: Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests
<p><span>Declining biodiversity is a global challenge to sustainability and resilience of ecosystems facing multiple novel stressors, including climate change and invasive pests-pathogens. Northern hardwood forests (NHF) of the Great Lakes region have experienced declines in canopy tree diversity since European colonization, with current tree regeneration patterns in some areas suggesting perpetuation of this trend. However, regional (10<sup>6</sup> ha) patterns and possible causes are underexplored. To address this information gap, we used data from 141 managed NHF stands, Michigan, USA to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand-level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6 – 7 species and <3 effective common species); however, some species contributing to sapling diversity are unlikely to contribute to future canopy diversity (<em>Fraxinus americana </em>and<em> Fagus grandifolia</em>, insect/pathogen limited; <em>Ostrya virginiana, </em>small maximum size). For the 11 most common species, conspecific canopy density (+, significant for 11 seedlings, 11 species) and stand basal area (-, saplings, 3 species) were the most consistent drivers of density, with less consistent effects for deer use, site quality, and substrate. Patterns of relative density by size class among the 18 species present on > 10 % of sites were consistent with theories of establishment or recruitment limitations due to deer browsing, deep shade, or limited suitable substrate. For seven species (including e.g., <em>Tsuga canadensis</em><span>, </span><em>Betula alleghaniensis, Populus grandidentata, Tilia americana</em><span>)</span>, relative abundance was lowest in the seedling layer and increased in larger size classes, <span>suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (<em>Acer saccharum, Quercus rubra.</em>), patterns of reduced sapling relative abundance compared to seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g., <em>F</em></span><em>agu<span>s grandifolia, Ostrya virginiana, Pinus strobus</span></em><span>) had highest relative density for saplings suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most abundant for </span><em>Acer rubrum </em><span>and </span><em>Prunus </em><span>spp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and for F. Americana, consistent with recent pest-related canopy mortality. Our results</span> suggest sustained low diversity and shifting composition are being driven by limited local seed availability, deep shading, limited seedling establishment substrate, and abundant deer. Management aimed at overcoming these specific limitations may be necessary to promote future NHF resilience.</span></p>
Data from: Incomplete recovery of tree community composition and rare species after 120 years of tropical forest succession in Panama
<p>Determining how fully tropical forests regenerating on abandoned land recover characteristics of old-growth forests is increasingly important for understanding their role in conserving rare species and maintaining ecosystem services. Despite this, our understanding of forest structure and community composition recovery throughout succession is incomplete, as many tropical chronosequences do not extend beyond the first 50 years of succession. Here, we examined trajectories of forest recovery across eight 1-hectare plots in middle and later stages of forest succession (40 – 120 years) and five 1-hectare old-growth plots, in the Barro Colorado Nature Monument (BCNM), Panama. We first verified that forest age had a greater effect than edaphic or topographic variation on forest structure, diversity and composition and then corroborated results from smaller plots censused 20 years previously. Tree species diversity (but not species richness) and forest structure had fully recovered to old-growth levels by 40 and 90 years, respectively. However, rare species were missing, and old-growth specialists were in low abundance, in the mid- and late secondary forest plots, leading to incomplete recovery of species composition even by 120 years into succession. We also found evidence that dominance early in succession by a long-lived pioneer led to altered forest structure and delayed recovery of species diversity and composition well past a century after land abandonment. Our results illustrate the critical importance of old-growth and old secondary forests for biodiversity conservation, given that recovery of community composition may take several centuries, particularly when a long-lived pioneer dominates in early succession.</p>
Data from: Incomplete recovery of tree community composition and rare species after 120 years of tropical forest succession in Panama
Open the record for dataset details and reuse information.
Data from: Do temperate tree species diversity and identity influence soil microbial community function and composition?
Open the record for dataset details and reuse information.
Data for: Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests
Open the record for dataset details and reuse information.
Edaphic effects on forest structure and tree species composition in three seasonally dry tropical forest types in Cambodia
Open the record for dataset details and reuse information.
Integrated effects of neighborhood composition and resource levels on growth of a dominant tree species in a tropical forest
Open the record for dataset details and reuse information.
Diversity, species coexistence, and functional composition patterns in subtropical Atlantic Forests invaded by non-native trees
Open the record for dataset details and reuse information.
Data from: Effects of frugivore species pool and seed size on the diversity and functional composition of frugivores visiting fruiting trees
Open the record for dataset details and reuse information.
Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites
Open the record for dataset details and reuse information.
Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.