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2,052 results for “tree species”
Data from: Trans-species predictors of tree leaf mass
Tree leaf mass is a small, highly variable, but critical, component of forest ecosystems. Estimating leaf mass on standing trees with models is challenging because leaf mass varies both within and between tree species and at different locations and points in time. Typically, models for estimating tree leaf mass are species-specific, empirical models that predict intra-specific variation from stem diameter at breast height (DBH). Such models are highly limited in their application because there are many other factors beyond tree girth and species that cause leaf mass to vary and because such models provide no way to predict leaf mass for species for which data are not available. We conducted destructive sampling of 17 different species in Michigan, covering multiple life history traits and sizes, to investigate the potential for using a single, 'trans-species' model for predicting leaf mass for all the trees in our study. Our results show the most important predictors of tree leaf mass are DBH, five-year basal area increment, crown class, and competition index, none of which are species specific. Species-specific variation could be captured by leaf longevity and shade tolerance and wood specific gravity was a statistically significant, but marginally-important predictor. Together, these variables describing tree size, life-history traits, and competitive environment were able to allow us to develop a generalized leaf mass model applicable to a diverse set of species, without having to develop species-specific equations.
Data from: Near infrared spectroscopy (NIRS) predicts non-structural carbohydrate concentrations in different tissue types of a broad range of tree species
1. The allocation of non-structural carbohydrates (NSCs) to reserves constitutes an important physiological mechanism associated with tree growth and survival. However, procedures for measuring NSC in plant tissue are expensive and time-consuming. Near-infrared spectroscopy (NIRS) is a high-throughput technology that has the potential to infer the concentration of organic constituents for a large number of samples in a rapid and inexpensive way based on empirical calibrations with chemical analysis. 2. The main objectives of this study were (i) to develop a general NSC concentration calibration that integrates various forms of variation such as tree species and tissue types and (ii) to identify characteristic spectral regions associated with NSC molecules. In total, 180 samples from different tree organs (root, stem, branch, leaf) belonging to 73 tree species from tropical and temperate biomes were analysed. Statistical relationships between NSC concentration and NIRS spectra were assessed using partial least squares regression (PLSR) and a variable selection procedure (competitive adaptive reweighted sampling, CARS), in order to identify key wavelengths. 3. Parsimonious and accurate calibration models were obtained for total NSC (r2 of 0·91, RMSE of 1·34% in external validation), followed by starch (r2 = 0·85 and RMSE = 1·20%) and sugars (r2 = 0·82 and RMSE = 1·10%). Key wavelengths coincided among these models and were mainly located in the 1740–1800, 2100–2300 and 2410–2490 nm spectral regions. 4. This study demonstrates the ability of general calibration model to infer NSC concentrations across species and tissue types in a rapid and cost-effective way. The estimation of NSC in plants using NIRS therefore serves as a tool for functional biodiversity research, in particular for the study of the growth–survival trade-off and its implications in response to changing environmental conditions, including growth limitation and mortality.
Data from: Colonization and extinction dynamics among the plant species at tree bases in Paris (France)
1. In cities, trees growing along streets could play an important ecological role for spontaneous plants that grow at their bases. For example, these trees could represent corridors that allow species to move in the urban matrix by potentially connecting large green spaces (e.g., parks, gardens, etc.) We considered sets of urban trees in 15 streets as metapopulations for 15 plant species. Our objective was to determine the factors influencing the dynamics of colonization and extinction of populations based on the distance of the streets from green spaces and the biological traits of each species. 2. The species in 1,324 tree bases of the Bercy district of Paris were surveyed annually from 2009 to 2015. For each species and each street, we used SPOMSIM software to identify the best-fit metapopulation model: the propagule rain model (PRM), Levins model (LM), and the PRM and LM with a fixed extinction or a rescue effect. 3. The results demonstrated that the species more often conformed to the PRM in streets near green spaces, which suggested that green spaces could act as the sources for the populations in those streets. Species with seeds with long-term persistence more often conformed to the PRM, indicating that a soil seed bank helps species invade entire streets. Finally, a higher percentage of species with a short height conformed to models with a rescue effect, which indicated that those species resisted the effects of weeding by the city technical services more often than taller species. 4. Synthesis and applications. This study showed how the biological traits of species and the geography of the district determine the dynamics of the plants in the streets, and the results may provide important information for biodiversity management in cities.
Data from: Novel forests maintain ecosystem processes after the decline of native tree species
The positive relationship between species diversity (richness and evenness) and critical ecosystem functions, such as productivity, carbon storage, and nutrient cycling, is often used to predict the consequences of extinction. At regional scales, however, plant species richness is mostly increasing rather than decreasing because successful plant species introductions far outnumber extinctions. If these regional increases in richness lead to local increases in diversity, a reasonable prediction is that productivity, carbon storage, and nutrient cycling will increase following invasion, yet this prediction has rarely been tested empirically. We tested this prediction in novel forest communities dominated by introduced species (~ 90% basal area) in lowland Hawaiian rainforests by comparing their functionality to that of native forests. We conducted our comparison along a natural gradient of increasing nitrogen availability, allowing for a more detailed examination of the role of plant functional trait differences (specifically, N2-fixation) in driving possible changes to ecosystem function. Hawai'i is emblematic of regional patterns of species change; it has much higher regional plant richness than it did historically, due to > 1000 plant species introductions and only ~ 71 known plant extinctions--resulting in an approximately 100% increase in richness. At local scales, we found that novel forests had significantly higher tree species richness and higher diversity of dominant tree species. We further found that aboveground biomass, productivity, nutrient turnover (as measured by soil-available and litter-cycled nitrogen and phosphorus), and belowground carbon storage either did not differ significantly or were significantly greater in novel relative to native forests. We found that the addition of introduced N2-fixing tree species on N-limited substrates had the strongest effect on ecosystem function--a pattern found by previous empirical tests. Our results support empirical predictions of the functional effects of diversity, but they also suggest basic ecosystem processes will continue even after dramatic losses of native species diversity if simple functional roles are provided by introduced species. Because large portions of the Earth's surface are undergoing similar transitions from native to novel ecosystems, our results are likely to be broadly applicable.
Data from: Incorporating the disease triangle framework for testing the effect of soil-borne pathogens on tree species diversity
1. The enemies-induced Janzen-Connell (JC) effect, a classic model invoking conspecific negative density dependence (CNDD) and distance dependence, is a primary biodiversity maintenance hypothesis. Yet, conflicting evidence for the JC effect leads to disagreement about its role in maintaining forest diversity. 2. We focus this review on soil-borne pathogens, which are the primary agent inducing the JC effect in many forest ecosystems. Although the test of the pathogen-induced JC effect in ecology critically rests on the seedling mortality caused by soil pathogens, what has not been explicitly explored in the early literature but has increasingly received attention is the long-recognized fact that the environment can alter virulence of pathogens and host susceptibility (and thus pathogen-host interactions), as predicted by the classic disease triangle framework enlightened by pathology research in agricultural systems. 3. Here, following the disease triangle framework we review evidence on how the pathogen-induced JC effect may be contingent on context (e.g., environmental conditions, pathogen inoculum load, and genetic divergence in host and pathogen populations). The reviewed evidence reveals and clarifies the conditions where pathogens may or may not cause disease to hosts, thus contributing to reconciling the inconsistent results about the pathogen-induced JC effect in the literature. The context-dependence of the disease triangle predicts that the pathogen-induced JC effect would change under global change. 4. Gaining insights from evidence that the pathogen-induced JC effect is context-dependent, we suggest that future tests on the JC hypothesis be conducted under the framework of disease triangle, and we stress the necessity by controlling the effect of context factors on plant-pathogen interactions when testing for the JC effect. We conclude the review by proposing three lines of future research for testing the importance of the JC effect in maintaining global forest tree species diversity, with a particular emphasis on testing the effect of global warming on the strength of pathogen-host interactions for better predicting changes of forest biodiversity under climate change.
Fig. 1 in First record of Metapolystoma (Monogenea: Polystomatidae) from Boophis tree frogs in Madagascar, with the description of five new species
Fig. 1. Map of Madagascar showing parasite type localities and distribution areas of hosts.
DENTRO Tree Matrix: dataset behind DENTRO - a Tree Species Selection Guide for Agroforestry
<p><strong>As a choice has to be made on whether a tree species matches the conditions of an agroforestry project in terms of e.g. soil characteristics and objectives, this dataset can support the tree species selection process.</strong></p> <p>This dataset, called <strong>‘’DENTRO Tree Matrix’’ (EN)</strong> or <strong>‘’DENTRO Bomenmatrix’’ (NL)</strong>, contains information about how tree species match certain relevant parameters varying from abiotic conditions (e.g. soil, weather, light, etc.), animals, objectives (e.g. wood/fruit/nut production and ecological function), and feasibility (e.g. disease risks and planting material availability).</p> <p>In recent years, a growing interest in agroforestry systems has been observed in Belgium and the Netherlands. Therefore, it is important to pay sufficient attention to the tree species selection process as this plays a major role in whether the agroforestry project is successful or not. Also in terms of climate change, it is important to select a tree species that both fits the farmer’s field conditions and can handle well with the extreme weather conditions occurring in the region in which the plot is located. This is why the DENTRO Tree Matrix also includes parameters such as strong wind, drought, frost, heat waves, and floods.</p> <p>The objective of the DENTRO Tree Matrix is to offer knowledge about commonly planted tree species in temperate regions (with a focus on Belgium and The Netherlands), so the right choices considering e.g. field and weather conditions can be made by the end user (farmers, advisors, ...).</p> <p>The DENTRO Tree Matrix also serves as a back-end dataset behind a set of decision support and/or tree species selection tools (currently (<strong>BETULA, AgroforesTreeAdvice, and DENTRO</strong>). </p> <p>The use of BETULA (a), DENTRO (a) and AgroforesTreeAdvice (b) is free, and these tools can be accessed through the following links:</p> <p>(a) <a href="https://www.agroforestryvlaanderen.be/en/agroforestry-planner-2">https://www.agroforestryvlaanderen.be/en/agroforestry-planner-2</a> </p> <p>(b) <a href="https://agroforestreeadvice.sk8.inrae.fr/">AgroforesTreeAdvice (inrae.fr)</a></p> <p>The background info sheet can be read here: <a href="https://www.agroforestryvlaanderen.be/nl/nieuws/boomsoortenselectie-waarmee-rekening-houden">Boomsoortenselectie: waarmee rekening houden? - Agroforestry (agroforestryvlaanderen.be)</a> (currently in Dutch).</p> <p>More info? Contact us through info@agroforestryvlaanderen.be </p>
Water use partitioning of native and non-native tree species in riparian ecosystems under contrasting climatic conditions
<p>We aimed at evaluating water-source partitioning between native and non-native tree species coexisting in central Spain floodplains; determining the dependency on drought stress of such water-sources-use; and assessing if the reliance on deeper water sources relates with physiological and growth performance. We assessed water-uptake depth, leaf functional traits related to physiological performance and growth of native (<em>Populus alba</em>) and non-native trees <em>(Ailanthus altissima, Robinia pseudoacacia</em>) coexisting in riparian forests under different drought conditions (drier, intermediate and wetter). We analyzed δ<sup>2</sup>H and δ<sup>18</sup>O isotopes in xylem water and in soil water from top, mid and deep soil depths and determined the contribution of each water source to plant xylem water. Leaf traits related with resource use and secondary growth were assessed for each species.</p>
Supplementary Material-Tree Cover Improved the Species Diversity of Understory Spontaneous Herbs in a Small City
<p>A table of trait data for all species identified in the study "Tree Cover Improved the Species Diversity of Understory Spontaneous Herbs in a Small City"</p>
Fig 21 from: Collins N, Coronado González IM, Govaerts BVA (2019) Oecanthus mhatreae sp. nov. (Gryllidae: Oecanthinae): A new species of tree cricket from Mexico, with an irregular song pattern and unique chirp-like trill configuration. Journal of Orthoptera Research 28(2): 137-143. https://doi.org/10.3897/jor.28.33781
Fig 21 Graph comparing chirps per minute at given temperatures.
Fig 20 from: Collins N, Coronado González IM, Govaerts BVA (2019) Oecanthus mhatreae sp. nov. (Gryllidae: Oecanthinae): A new species of tree cricket from Mexico, with an irregular song pattern and unique chirp-like trill configuration. Journal of Orthoptera Research 28(2): 137-143. https://doi.org/10.3897/jor.28.33781
Fig 20 Oecanthus mhatreaesp. nov. males chirping in various temperatures.
Fig 10 from: Collins N, Coronado González IM, Govaerts BVA (2019) Oecanthus mhatreae sp. nov. (Gryllidae: Oecanthinae): A new species of tree cricket from Mexico, with an irregular song pattern and unique chirp-like trill configuration. Journal of Orthoptera Research 28(2): 137-143. https://doi.org/10.3897/jor.28.33781
Fig 10 Adult female coloring and ovipositor length (on non-native Ruta graveolens L.).
LiDAR data for tree species classification
<p>The zip file contains two datasets in csv table format to be used for tree species classification uasing lidar features.</p> <p>For each dataset there are two files. The first file (e.g. dataset_1_training_test.csv) contains training and test samples: each column refer to a lidar feature, and one column with the label coresponding to the tree species. The sceond file contains unlabeled data (e.g. dataset_1_unlabeled_set.csv).</p>
Individual encounters with neighbors are disproportionate between tree species and through life stages in a temperate mixed forest
<p>Here is data for the paper "Individual encounters with neighbors are disproportionate between tree species and through life stages in a temperate mixed forest" by Chinatsu Homma et al.</p> <p>Metadata for each ordered data is provided in “Readme.pdf”;</p> <ul> <li>01Seedlings.csv</li> <li>02Saplings2x2.csv</li> <li>02SaplingsFloodPlain.csv</li> <li>03Poles.csv</li> <li>04Adults.csv</li> <li>spCode.csv: Correspondence table between species name and species code.</li> <li>universal_color.csv: Colour code for drawing figures.</li> </ul>
Supplementary materials of inferred species trees from 32 datasets
<p>This repository contains the results of the inferred species trees from 32 datasets. In total 32 files are stored where the files with the prefix "Aln12_cds" are the results based on the 1st and 2nd position codon nucleotide datasets, the files with the prefix "Backtrans_cds" are the results based on the codon-level nucleotide datasets, the files with the prefix "Pure_cds" are the results based on the raw nucleotide datasets while the files with the prefix "Taper_cds" are the results based on the TAPER-masked nucleotide datasets. The suffixal numbers 0,10,20,30,40,50,60,70 represent the 8 branch filtering cutoffs for each one of the four multiple sequence alignment (MSA) datatypes. The caption for each plot is as follows.</p> <p>Phylogenetic inference of 470 angiosperms species | The colored strips denote the affliation at order level or the ANA grade for each angiosperm species. The branch colors of the cladogram represent the inferred coalescent units and the local posterior probability (LPP) is marked on the internal nodes.</p>
Figure 1 from: Pacheco da Silva VC, Kaydan MB, Germain J-F, Malausa T, Botton M (2016) Three new species of mealybug (Hemiptera, Coccomorpha, Pseudococcidae) on persimmon fruit trees (Diospyros kaki) in southern Brazil. ZooKeys 584: 61-82. https://doi.org/10.3897/zookeys.584.8065
Figure 1 - Anisococcus granarae Pacheco da Silva & Kaydan, sp. n. Live adult female.
Figure 2 from: Pacheco da Silva VC, Kaydan MB, Germain J-F, Malausa T, Botton M (2016) Three new species of mealybug (Hemiptera, Coccomorpha, Pseudococcidae) on persimmon fruit trees (Diospyros kaki) in southern Brazil. ZooKeys 584: 61-82. https://doi.org/10.3897/zookeys.584.8065
Figure 2 - Adult female Anisococcus granarae Pacheco da Silva & Kaydan, sp. n. Holotype.
Figure 3 from: Pacheco da Silva VC, Kaydan MB, Germain J-F, Malausa T, Botton M (2016) Three new species of mealybug (Hemiptera, Coccomorpha, Pseudococcidae) on persimmon fruit trees (Diospyros kaki) in southern Brazil. ZooKeys 584: 61-82. https://doi.org/10.3897/zookeys.584.8065
Figure 3 - Adult female Ferrisia kaki Kaydan & Pacheco da Silva, sp. n. Holotype.
Figure 5 from: Pacheco da Silva VC, Kaydan MB, Germain J-F, Malausa T, Botton M (2016) Three new species of mealybug (Hemiptera, Coccomorpha, Pseudococcidae) on persimmon fruit trees (Diospyros kaki) in southern Brazil. ZooKeys 584: 61-82. https://doi.org/10.3897/zookeys.584.8065
Figure 5 - Adult female Pseudococcus rosangelae Pacheco da Silva & Kaydan, sp. n. Holotype.
Figure 1 in Species complexes of leaf-inhabiting mites on Prunus laurocerasus L. (Rosaceae) trees in Ordu, Turkey
Figure 1. Eleven sampled areas in Ordu, Turkey (Black Sea Region) during the 2015 and 2016.
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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)
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.