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.
40
datasets available to search
ShareScore release 0.9.0
Dataset results
40 results for “Tree distance”
INTERPNT Software for Mapping Trees Using Distance Measurements
The INTERPNT method can be used to produce accurate maps of trees based solely on tree diameter and tree-to-tree distance measurements. For additional details on the technique please see the published paper (Boose, E. R., E. F. Boose and A. L. Lezberg. 1998. A practical method for mapping trees using distance measurements. Ecology 79: 819-827). Additional information is contained in the documentation that accompanies the program. The Abstract from the paper is reproduced below. "Accurate maps of the locations of trees are useful for many ecological studies but are often difficult to obtain with traditional surveying methods because the trees hinder line of sight measurements. An alternative method, inspired by earlier work of F. Rohlf and J. Archie, is presented. This "Interpoint method" is based solely on tree diameter and tree-to-tree distance measurements. A computer performs the necessary triangulation and detects gross errors. The Interpoint method was used to map trees in seven long-term study plots at the Harvard Forest, ranging from 0.25 ha (200 trees) to 0.80 ha (889 trees). The question of accumulation of error was addressed though a computer simulation designed to model field conditions as closely as possible. The simulation showed that the technique is highly accurate and that errors accumulate quite slowly if measurements are made with reasonable care (e.g., average predicted location errors after 1,000 trees and after 10,000 trees were 9 cm and 15 cm, respectively, for measurement errors comparable to field conditions; similar values were obtained in an independent survey of one of the field plots). The technique requires only measuring tapes, a computer, and two or three field personnel. Previous field experience is not required. The Interpoint method is a good choice for mapping trees where a high level of accuracy is desired, especially where expensive surveying equipment and trained personnel are not available."
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
Data from: Assisted migration of cloud forest trees: Unearthing the effects of climatic transfer distance
Open the record for dataset details and reuse information.
Do natural enemies mediate conspecific negative distance- and density-dependence of trees? A meta-analysis of exclusion experiments
<p>Conspecific negative distance- and density-dependence is believed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. Plant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their general effects at different plant life stages are still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides, or exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that conspecific negative distance- and density-dependence was more common at the seedling stage. Only 30% of studies showed significant conspecific negative distance- and density-dependence. Among those studies, applying fungicides significantly reduced the effect of conspecific negative distance -dependent mortality. Excluding large mammals reduced the effect of conspecifics, but with only marginal significance (p < 0.1). Our study confirms that plant pathogens have a significant impact on distance -dependent mortality and suggests that the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals, respectively, appear to weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types, and assess how global change may affect natural enemies and thus influence the strength of conspecific distance- and density-dependence.</p>
Data from: Seed survival in tropical pioneer trees is unrelated to conspecific distance but linked to fungal infection
Open the record for dataset details and reuse information.
Do natural enemies mediate conspecific negative distance- and density-dependence of trees? A meta-analysis of exclusion experiments
Open the record for dataset details and reuse information.
Data from: Fruit traits of pioneer trees structure seed dispersal across distances on tropical deforested landscapes: implications for restoration
<ol> <li>Pioneer trees with fleshy fruits are typically planted in restoration projects to attract frugivores as a mean to increase dispersal and accelerate forest regeneration. However, differences in fruit traits of pioneer trees can potentially influence dispersal and their restoration outcomes.</li> <li>Here we investigated the effects of bird and plant traits, and distance to forest fragments, on the seed rain using a tree-planting experiment replicated in 12 deforested sites in Brazil. Factors were fruit traits of pioneer trees (wind-dispersed, bird-dispersed with lipids or with carbohydrates, and controls) and distance (10, 50, 300 m) from forest fragments.</li> <li>We found that density and richness of birds and seeds decreased exponentially with distance from fragments, yet these effects were minor compared to the effects of fruit traits on the structure of the seed rain.</li> <li>Overall, plots with fleshy-fruited pioneers attracted much greater bird activity and seed dispersal than plots with wind-dispersal pioneers and the controls. For instance, plots with carbohydrate-rich fruits received more than twice the average species richness and density of birds and seeds of plots with lipid-rich pioneer trees, surpassing wind-dispersed pioneers by more than 80%, and controls by over 90%. Furthermore, the fruit trait treatments resulted in morphological shifts in the average traits of visiting birds. Significant differences in bill gape and flight capacities (wing-loading) were associated with the differences in the seed rain associated with each treatments.</li> <li> <i>Synthesis and applications</i>. Understanding how trait-matching processes mediating mutualistic seed dispersal by frugivores interact with distance-dependent dispersal limitation on deforested tropical landscapes is critical for improving forest restoration efforts. This is especially relevant in the context of applied nucleation. As shown here, avian seed dispersal can thus be manipulated in restoration projects in order to increase connectivity and speed up forest recovery and the provision of the multiple ecosystem services that follow forest succession.</li> </ol>
Critical seed transfer distances for selected tree species in eastern North America
<p>Forest planting events present key opportunities to enhance forest adaptation and growth through the selection of appropriate growing materials (seeds and seedlings). Critical to such efforts is knowledge of the climatic distance that seed sources can be moved before significant growth forfeitures are incurred. These limits, referred to here as critical seed transfer distances (CSTD), can be used to identify a potential seed procurement region for any given planting site and can readily incorporate climate change projections. We assembled provenance trial data from a variety of sources and employed transfer functions to derive CSTDs for five major tree species in eastern North America. Calculated transfer limits were large, indicating that seed sources could be moved significant climatic distances before height growth was less than 90 percent relative to that of the local seed source. These broad relationships would allow considerable flexibility in resulting seed transfer systems; however, given the significant uncertainty surrounding climate change – particularly in the location and timing of extreme weather events – prudent application of seed transfer limits may be appropriate. Synthesis: We assembled and analyzed a significant amount of provenance data to derive novel information on seed movement limits for five tree species in eastern North America. This information will support forest managers in ongoing efforts to incorporate climate change into forest regeneration operations.</p>
Data from: Does long distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape
Tropical trees often display long distance pollen dispersal, even in highly fragmented landscapes. Understanding how patterns of spatial isolation influence gene flow and interact with background patterns of fine scale spatial genetic structure are critical for evaluating the genetic consequences of habitat fragmentation. In the endangered tropical timber tree Dysoxylum malabaricum (Meliaceae) we apply eleven microsatellite markers with paternity and parentage analysis to directly estimate contemporary gene flow across a large area (216 km2) in a highly fragmented agro-forest landscape. A comparison of genetic diversity and genetic structure in adult and juvenile life stages indicates an increase of differentiation and fine-scale spatial genetic structure (FSGS) over time. Paternity analysis and parentage analysis demonstrate high genetic connectivity across the landscape by pollen dispersal. A comparison between mother trees in forest patches with low and high densities of adult trees shows that the frequency of short distance mating increases, as does average kinship among mates in low density stands. We interpret this as an early warning sign of potentially negative genetic consequences of forest fragmentation. Single isolated trees, in contrast, frequently receive heterogeneous pollen from distances exceeding five kilometres. We discuss the processes leading to the observed patterns of gene flow and the implications of this for conservation management of D. malabaricum and tropical trees more generally.
Data from: Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging
The natural regeneration of tree species depends on seed and pollen dispersal. To assess if limited dispersal could be critical for the sustainability of selective logging practices, we performed parentage analyses in two Central African legume canopy species displaying contrasted floral and fruit traits: Distemonanthus benthamianus and Erythrophleum suaveolens. We also developed new tools linking forward dispersal kernels with backward migration rates to better characterize long-distance dispersal. Much longer pollen dispersal in D. benthamianus (mean distance dp=700m, mp=52% immigration rate in 6 km2 plot, s=7% selfing rate) than in E. suaveolens (dp=294m, mp=22% in 2 km2 plot, s=20%) might reflect different insect pollinators. At a local scale, secondary seed dispersal by vertebrates led to larger seed dispersal distances in the barochorous E. suaveolens (ds=175m) than in the wind-dispersed D. benthamianus (ds=71m). Yet, seed dispersal appeared much more fat-tailed in the latter species (15-25% seeds dispersing >500m), putatively due to storm winds (papery pods). The reproductive success was correlated to trunk diameter in E. suaveolens and crown dominance in D. benthamianus. Contrary to D. benthamianus, E. suaveolens underwent significant assortative mating, increasing further the already high inbreeding of its juveniles due to selfing, which seems offset by strong inbreeding depression. To achieve sustainable exploitation, seed and pollen dispersal distances did not appear limiting, but the natural regeneration of E. suaveolens might become insufficient if all trees above the minimum legal cutting diameter were exploited. This highlights the importance of assessing the diameter structure of reproductive trees for logged species.
Data from: Biogeographic variation of distance-dependent effects in an invasive tree species
1.Plant pathogens and herbivores can maintain forest diversity by reducing survival of tree seedlings close to conspecifics. However, how biogeographic variation in these natural enemies affects such distance‐dependent processes is unknown. Because invasive plants escape ecologically important enemies when introduced to a new range, distance‐dependent mortality may differ between their native and introduced ranges. 2. Here, we test whether the invasive tree Triadica sebifera escaped distance‐dependent mortality when introduced to the US from China, and examine the roles of natural enemies in native and introduced ranges. In both US and China, we performed field surveys along with field and greenhouse experiments with field collected soils and soil sterilization treatments. 3. In field surveys and the field experiment, insect damage on T. sebifera seedlings decreased with distance to conspecific trees in the native range (China) but damage was low at all distances in the introduced range (US). In the greenhouse experiment testing the effects of soil pathogens, T. sebifera seedling mortality decreased with soil distance from conspecific trees in both ranges but distance‐independent mortality was higher in native range soils. 4. Our findings indicate that both insect herbivores and the soil biota contribute to distance‐ dependent effects on T. sebifera in its native range. They suggest, however, that plants may more readily escape herbivore than soil biota distance‐dependent effects when introduced to a new range and so herbivores, rather than soil pathogens, contribute more strongly to biogeographic variation in distance‐dependent effects. These results highlight the importance of considering species biogeographic variation in distance‐dependent effects and teasing apart the roles that different natural enemies play when studying species coexistence, community diversity, and biological invasions.
Data from: Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae)
Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tumors. We identify patterns of pollen-mediated gene flow within natural populations of F. picrosperma and estimate genetic parameters and genetic structure between adult and juvenile groups using microsatellite markers. Our results show pollination events occur over much shorter distances than reported for tropical canopy species. At least 63 % of seeds are sired by male trees located within 30 m of the mother. On average, 27 % of the local male population contributed to successful reproduction of F. picrosperma with most fathers siring a single seed, however, the contributions to reproduction were uneven. Larger male trees with more flowers had gre ater reproductive success than those with less flowers (P < 0.05). There were comparatively low levels of genetic variation across the species (HE = 0.405 for adult trees and 0.379 for juveniles) and we found no loss of genetic diversity between adult and juvenile trees. Short distance pollen flow and low genetic diversity is theoretically a prelude to genetic impoverishment, however F. picrosperma has persisted through multiple significant climatic oscillations. Nevertheless, the remaining low genetic diversity is of concern for domestication programs which require maximal genetic diversity to facilitate efficient selective breeding and genetic improvement of this commercially significant species.
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 in Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 individuals of G. locorojo from eight "localities" on three continents. See Appendix A for specimen source data.
WGSUniFrac experiment1 tree pairwise distance matrix
<p>Pairwise distance matrix generated from filtered nodes of gg_13_5 99_otus tree from Greengenes.</p>
Bioclimatic, soil, terrain, distance to Native American settlement, and historical tree taxon relative abundance data at 8-km resolution for the northeastern United States
<p><span>Researchers have debated impacts of past Native American land use on forests including upon tree species composition in northeastern United States (US), with estimates of impacts ranging from local to regional extent. This study examines tree relative abundances in the </span><span>northeastern US </span><span>(approx. 420,000 km2) </span><span>to assess whether Native Americans influenced geographic distributions of 18 tree taxa prior to Euro-American settlement. </span><span>We used boosted regression trees to model abundance patterns and to assess the importance of distance-based proxies of Native American land use versus environmental variables. We trained models that included and excluded distance-based proxies. Abundance estimates from original land survey records (1650-1850 CE) were acquired for taxa at 8 km spatial resolution, and related to Native American settlement locations (1500-1800 CE) and 27 environmental variables. </span><span>When evaluated upon test data, regional-scale models of relative abundance that included distance-based proxies performed only slightly better than models that excluded them, with mean improvements in RMSE of 0.1 percentage points. Models suggest that Native American land use modestly altered the relative abundance of taxa locally, extending no more than 50 km from settlement. Models also suggest slight increases near settlement of a few percentage points in relative abundance for fire-tolerant and/or dietary taxa (e.g. oak, hickory, and pine), and for early-successional taxa (e.g. ash). </span><span>Past</span><span> Native American land use had no detectable effect on forest composition across a regional extent, but increased the abundance of fire-tolerant, shade-intolerant, and nut-producing trees locally.</span></p> <p><span>The Excel-format (.xlsx) dataset here provides the training and testing data for the BRT models in this publication. It contains relative abundances of the 18 tree taxa expressed as a fraction of total number of trees. It also provides bioclimatic (e.g. annual temperature, annual preciptation), soil (e.g. pH, percent sand), terrain (e.g. slope), and Native American (e.g. distance to settlement) variables developed from multiple sources. A column also indicates whether an observation was part of the training data or the test data. See the publication and its Supporting Information for full details on the acquisition and processing of these data, as well as the original providers of the data. If using these data, please </span><span>cite both this dataset's corresponding article, as well as the original providers of the data.</span></p> <p>Also provided are ascii-format (.asc) gridded data layers that were used for making spatial predictions of taxon relative abundances from BRT models.</p> <p>The original creators/providers of the relative abundance, bioclimatic, soil, terrain, and Native American data or layers used for creating the gridded data in this study are:</p> <p><span>Abel, T. (2016). The Iroquoian occupations of Northern New York: A summary of current research. Ontario Archaeology, 96, 65–75. </span></p> <p><span>CIFAS. (2017). Map Of First Nations in New Brunswick. Comitas Institute for Anthropological Study. <a href="http://cifas.us/first-nations-maps/">http://cifas.us/first-nations-maps/</a> </span></p> <p><span>Grumet, R. S. (1995). Historic Contact: Indian People and Colonists in Today's Northeastern United States in the Sixteenth through Eighteenth Centuries. University of Oklahoma Press.</span></p> <p><span>Jordan, K. A. (2013). Incorporation and colonization: Postcolumbian Iroquois satellite communities and processes of indigenous autonomy. American Anthropologist, 115(1), 29–43.</span></p> <p><span>Milner, G. R., & Chaplin, G. (2010). Eastern North American population at ca. A.D. 1500. American Antiquity, 75(4), 707–726.</span></p> <p><span>NASA. (2000). SRTM 90m Digital Elevation Database v4.1. <a href="https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/">https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/</a> </span></p> <p><span>O'Donnell, M. S., & Ignizio, D. A. (2012). Bioclimatic Predictors for Supporting Ecological Applications in the Conterminous United States (Data Series 691; p. 10). U.S. Geological Survey. <a href="https://www.sciencebase.gov/catalog/item/4fe0f9f4e4b05d4ed81d9392">https://www.sciencebase.gov/catalog/item/4fe0f9f4e4b05d4ed81d9392</a> </span></p> <p><span>Paciorek, C. J., Goring, S. J., Thurman, A. L., Cogbill, C. V., Williams, J. W., Mladenoff, D. J., Peters, J. A., Zhu, J., & McLachlan, J. S. (2016). Statistically-estimated tree composition for the northeastern United States at the time of Euro-American settlement. PLoS ONE, 11(2), e0150087. <a href="https://doi.org/10.1371/journal.pone.0150087">https://doi.org/10.1371/journal.pone.0150087</a> </span></p> <p><span>Peters, M. P., Iverson, L. R., Prasad, A. M., & Matthews, S. N. (2013). Integrating Fine-scale Soil Data into Species Distribution Models: Preparing Soil Survey Geographic (SSURGO) Data from Multiple Counties (General Technical Report NRS-122; p. 70). U.S. Forest Service. <a href="https://www.fs.usda.gov/treesearch/pubs/45308">https://www.fs.usda.gov/treesearch/pubs/45308</a> </span></p>
Data from: Fruit traits of pioneer trees structure seed dispersal across distances on tropical deforested landscapes: implications for restoration
Open the record for dataset details and reuse information.
Data from: Does long distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape
Open the record for dataset details and reuse information.
Data from: Distance-dependent seed‒seedling transition in the tree Castanopsis sclerophylla is altered by fragment size
Open the record for dataset details and reuse information.
Data from: Persistence of long-distance, insect-mediated pollen movement for a tropical canopy tree species in remnant forest patches in an urban landscape
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.