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Fig. 2. Maximum Likelihood species tree from the concatenated 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 2. Maximum Likelihood species tree from the concatenated 50 % complete dataset consisting of 4561 loci. Values on the branch indicate Shimodaira Hasegawalike approximate likelihood ratio test and ultrafast bootstrap. Abbreviations as in Fig. 1.
UAV-based multispectral image data of a tree nursery, Eberswalde, Brandenburg, 2023 (Orthomosaics, DEMs, point clouds)
<p>This data set contains three multispectral surveys conducted with an unoccupied aerial vehicle (UAV DJI M300 RTK) of an oak tree nursery experiment</p> <ul> <li>Date of acquisition: 16.08.2023</li> <li>Location: Tree nursery, Eberswalde, Brandenburg, Germany</li> <li>UAV: DJI M300 RTK with active SAPOS connection</li> <li>Flight altitude above ground level: 30 m, 40 m, 60 m</li> <li>Image Overlap forward/side: 80 % / 80 %</li> <li>Camera: MicaSense Altum multispectral</li> <li>EPSG: 32632</li> </ul> <p>Data products: </p> <ul> <li>Orthomosaic multispectral (Resolution: 1.35 cm, 1.79 cm, 2.65 cm)</li> <li>Orthomosaic RGB</li> <li>Orthomosaic thermal LWIR in pseudo °C according to <a href="https://support.micasense.com/hc/en-us/articles/360022446473-Converting-Altum-Thermal-to-degrees-C-after-processing-in-Agisoft-or-Pix4D">Micasense</a> empirical formula</li> <li>DEM</li> <li>Dense point cloud RGB</li> <li>Spectral indices calculated: NDVI, NDRE</li> <li>Agisoft Report</li> </ul> <p><strong>Acknowledgment:</strong></p> <p><strong>Frank Becker</strong></p> <p>Landesbetrieb Forst Brandenburg</p> <p>Landeskompetenzzentrum Forst Eberswalde (LFE)</p>
August–September temperature reconstruction over the period 1792–2020 based on a tree-ring maximum latewood density
<p>We present a late summer (August–September) temperature reconstruction over the period<br> 1792–2020 based on a tree-ring maximum latewood density (MXD) chronology for the southern Tibetan Plateau (TP).<br> The reconstruction explained 66.2% of the variance in the instrumental temperature records during the calibration period<br> 1960–2020.</p>
Efficient genomics based ‘end-to-end’ selective tree breeding framework
Open the record for dataset details and reuse information.
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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QuCo: quartet-based co-estimation of species trees and gene trees
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Floristic monitoring of the 1,324 alignment tree bases of 15 streets in the district of Bercy, Paris, France, from 2009 to 2018
<p>Floristic monitoring of the 1,324 alignment tree bases of 15 streets in the district of Bercy, Paris, France, from 2009 to 2018.</p> <p>Nathalie Machon (CESCO, MNHN-CNRS-Sorbonne-Université)</p> <p>Data collectors : Noëlie Maurel, Marion Noualhaguet, Marion Dubois, Sébastien Julliard, Ambre Zéléla Bouvard, Paul Haenel, Florence Devers, Hélène Beaugeard, Gwendoline Chastel, laure Schneider-Maunoury and Mona Omar</p> <p>Centre d’Ecologie et des Sciences de la Conservation, Muséum national d’Histoire naturelle, 61 rue Buffon, 75005 Paris, nathalie.machon@mnhn.fr</p> <p>In cities, trees planted along streets host at their base a high number of spontaneous plants. Thus, they may provide shelters and corridors across the urban matrix.</p> <p>From 2009, we monitor urban tree bases in streets of Paris, France. Our objective is to follow the dynamics of these plant communities (Omar et al. 2018, 2019).</p> <p> </p> <p><strong>Study area and floristic inventories</strong></p> <p>The monitoring was performed in the 12th administrative district of Paris (Postal code: 75012; France; 48°50′26.91″N, 2°23′17.46″E),</p> <p>We monitored the 1,324 tree bases distributed along the 15 streets or avenues which contained at least 30 alignment trees in the district.</p> <p>Tree bases (TB) were for some of them covered by metal grills (grill/soil) to prevent soil compaction to preserve tree roots.</p> <p>The present file gives the list of all wild vascular plant taxa observed in each tree base, in May or June, each year from 2009 to 2018 except in 2013 because of a lack of observers. The taxonomic reference is the French Flora Reference TAXREF v8.0 (Gargominy et al., 2016).</p>
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1.
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1.
Data from: ASTRAL: genome-scale coalescent-based species tree estimation
<p>Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions.</p> <p>Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees.</p>
Supplementary data to article "From single trees to country-wide maps: Modeling mortality rates in Germany based on the Crown Condition Survey"
<p>This repository provides regression models and annual prediction rasters for tree mortality in Germany. </p> <p><strong>Regression models:</strong><br>Logistic regression models which predict tree mortality for the species (beech = Fagus sylvatica, <br>oak = Quercus petraea and robur, pine = Pinus sylvestris, spruce = Picea abies) and species <br>groups (OB = other broadleaves, OC = other conifers) based on observations of dead trees in the<br>German Crown Condition Survey (Waldzustandserhebung) and a set of environmental predictor <br>variables. The predictors come from the domains of climate (clim), site conditions (site, i.e. <br>topography, soil, land cover, deposition), tree age (age) and some models contain pairwise <br>interaction terms between predictors (inter). All models were fit in R and are represented as <br>objects of the class glm and stored in files of the type rds.</p> <p><strong>Prediction rasters:</strong><br>Spatial predictions of the mortality rate across Germany for each tree species and species group <br>and for each year from 1998 to 2022. The rasters have a spatial resolution of 100 m. Missing values<br>mark areas where the species/group does not occur. The mortality values are given as integers <br>between 0 (no mortality) and 10000 (100% mortality). The coordinate reference system is Lambert <br>Azimuthal Equal Area (LAEA; EPSG:3035). The rasters are provided in the file format GeoTIFF (tif).</p> <p>A detailed description of the data sources and analyses can be found in the following article.</p> <p><strong>Citation:</strong><br><em>Knapp, N., Wellbrock, N., Bielefeldt, J., Dühnelt, P., Hentschel, R., Bolte, A., 2024. </em><br><em>From single trees to country-wide maps: Modeling mortality rates in Germany based on the Crown Condition Survey.</em></p> <p><strong>Contact:</strong><br>nikolai.knapp@thuenen.de</p> <p> </p> <p> </p>
Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
<p><strong>Aim</strong>: Miombo woodlands form a characteristic vegetation type covering 2.7 million km<sup>2</sup> in southern and eastern Africa. Despite their wide geographical extent, their origin, floristic and spatial evolution through time remain understudied. To fill this gap, we studied the evolution of <em>Brachystegia</em> trees, one of the most representative genera of these woodlands (20 species), also represented in Guineo-Congolian rain forests (8 species).</p> <p><strong>Location</strong>: Tropical Africa, Guineo-Congolian forests and Zambezian savannahs.</p> <p><strong>Methods</strong>: We used a genome skimming approach to sequence the plastomes of 45 <em>Brachystegia</em> samples, covering 25 of the 29 existing species, and one outgroup (<em>Julbernardia paniculata</em>). The phylogeny of the plastomes was reconstructed and time-calibrated. We tested if the genetic divergence between lineages reflected taxonomic and/or geographic distances using Mantel tests. Finally, we inferred the evolutionary history of <em>Brachystegia</em> based on the age and spatial distribution of its lineages.</p> <p><strong>Results</strong>: Surprisingly, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Two main clades separate woodland and rain forest species, which diverged during the late Miocene-Pliocene (95% HPD = 2.78-8.59 Ma). In miombo woodlands, three subclades occur in parapatry along an East-West axis, ranging from Angola to East Africa. Their divergence started from the Plio-Pleistocene (95% HPD = 1.17-3.69 Ma). Divergence dates (TMRCA) within miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma).</p> <p><strong>Main Conclusions</strong>: <em>Brachystegia</em> plastomes appear unreliable to identify species, probably due to species introgression leading to recurrent chloroplast captures. However, they prove very informative for tracking the past dynamics of the genus, and suggest a historical westwards expansion of miombo <em>Brachystegia</em>, and possibly of miombo vegetation, during the Plio-Pleistocene. Further investigations using nuclear DNA are needed to assess the species tree as well as speciation and hybridisation events between species. </p>
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
<p>Whole genome duplication events are notably widespread in plants and this poses particular challenges for phylogenetic inference in allopolyploid lineages, i.e. lineages that result from the merging of two or more diverged genomes after interspecific hybridization. The nuclear genomes resulting from allopolyploidization contain homologous gene copies from different evolutionary origins called homoeologs, whose orthologs must be sorted out in order to reconstruct the evolutionary history of polyploid clades. In this study, we propose a methodological approach to resolve the phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which experienced some level of genome reshuffling and gene fractionation across their subgenomes. To illustrate our methodological framework, we applied it to a clade belonging to the model Brassicaceae plant family, the Brassiceae tribe, that experienced a mesohexaploidy event. The dataset analysed consists of both publically available genomic sequences and new transcriptomic data according to taxa. The present methodology requires a well-annotated reference genome, for which the identification of the parental subgenome fragments has been performed (e.g. Brassica rapa and Brassica oleracea). Focusing on fully retained genes (i.e., genes for which all homoeologous gene copies inherited from the parental lineages are still present in the reference genome), the method constructs multilabelled gene trees that allow subsequent assignment of each gene copy to its diploid parental lineage. Once the orthologous copies are identified, genes from the same parental origin are concatenated and tree-building methods are used to reconstruct the species tree. This method allows resolving the phylogenetic relationships (i) among extant species within a mesopolyploid clade, (ii) among the parental lineages of a mesopolyploid lineage, and (iii) between the parental lineages and closely related extant species. We report here the first well-resolved nuclear-based phylogeny of the Brassiceae tribe.</p>
Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
<p><span>The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.</span></p>
Files associated with: Migration-based simulations for Canadian trees show limited tracking of suitable climate under climate change
<p><strong>Aim</strong></p> <p>Species distribution models typically project climatically suitable habitat for trees in eastern North America to shift hundreds of kilometers this century. We simulated potential migration considering species' life history and traits for 10 tree species and their ability to track climatically suitable habitat.</p> <p><strong>Location</strong></p> <p>Eastern Canada, covering ~3.7 million km<sup>2</sup></p> <p><strong>Methods</strong></p> <p>We simulated migration-constrained range shifts through 2100 using a hybrid approach combining projections of climatically suitable habitat based on two Representative Concentration Pathways (RCP4.5, RCP8.5) for three time periods and two species distribution modelling approaches with process-based models parameterized using data related to <span>dispersal ability and generation time</span>. We developed a unique 'migration kernel' that uses seed dispersal traits and observed migration velocities to obtain kernel shape and dispersal probabilities. We then calculated lags between the migration-constrained range limits obtained through simulations and limits of climatically suitable habitat.</p> <p><strong>Results</strong></p> <p>All species demonstrated northward range shifts at the leading edge of their simulated distribution through 2100, but the magnitude and rate of that shift varied by species and time period. Climatically suitable habitat limits were found to be north of simulated distribution limits across both RCPs, with lags increasing through time. On average, the simulated distribution that remained within climatically suitable habitat showed higher decreases under RCP8.5 than RCP4.5, with large areas of the rear edge of the simulated distribution becoming partially or completely climatically unsuitable for many species.</p> <p><strong>Main conclusions</strong></p> <p><span>Climatically suitable habitat limits projected for 2100 far exceeded migration-constrained range limits for all 10 species, particularly for temperate species. This study underlines the limited extent to which species will track climate change via natural migration. Integrating observed migration velocities, seed dispersal and generation time with SDM outputs allows for more realistic evaluations of tree migration ability under climate change and may help orient forest conservation and restoration efforts.</span></p>
Forecasting 24-hour-averaged PM2.5concentration in the Aburrá Valley using tree-based ML models, global forecasts, and satellite information: Dataset
<p>Data necessary for the training and evaluating the 24-hourly-averaged PM2.5 forecast over 19 stations within the Aburrá Valley, Colombia, is included here.</p>
An Automated Method for Measuring Tree Rings Based on Super Resolution and Image Segmentation
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Data from: A trait-based root acquisition-defence-decomposition framework in angiosperm tree species
<p>Plants make trade-offs between root resource acquisition and defence ability, for adapting to the complex belowground environment. This includes forming partnerships with different types of root associating microorganisms, such as arbuscular mycorrhizal and ectomycorrhizal fungi. These trade-offs, by mediating root chemistry, exert legacy effects on nutrient release during decomposition, which may, in turn, affect the ability of new roots to re-acquire resources, thereby generating a feedback loop. However, the linkages at the basis of this potential feedback loop remain largely unquantified. Here, we propose a trait-based root 'acquisition-defence-decomposition' conceptual framework and test the strength of relevant linkages across 90 angiosperm tree species. We show that, at the plant species level, the root-fungal symbiosis gradient within the root economics space, root chemical defence (condensed tannins), and root decomposition rate are closely linked, providing support to this framework. Beyond the dichotomy between arbuscular mycorrhizal-dominated versus ectomycorrhizal-dominated systems, we suggest a continuous shift in feedback loops, from "high arbuscular mycorrhizal symbiosis-low defence-fast decomposition-inorganic nutrition" by evolutionarily ancient taxa to "high ectomycorrhizal symbiosis-high defence-slow decomposition-organic nutrition" by more modern taxa. This 'acquisition-defence-decomposition' framework provides solid foundation for testable hypotheses on the multidimensional linkages between species' belowground strategies and ecosystem nutrient cycling in evolutionary context.</p>
Enhancing High-Resolution Forest Stand Mean Height Mapping in China through an Individual Tree-Based Approach with Close-Range LiDAR Data
<p><span>We</span> have developed a tree-based approach to create spatially continuous forest stand mean height maps across China through integrating high-<span>point</span> density, high-precision close-range LiDAR data and multisource remote sensing data. The accuracy analysis of the arithmetic mean height (Ha) and the weighted mean height (Hw) demonstrates the feasibility of the proposed method. A practical framework for forestry investigation based on close-range LiDAR was proposed. The mean values of Ha and Hw are 13.3 ± 3.3 m 11.3 ± 2.9 m on pixel level, respectively. Validation based on LiDAR and field sample data shows that the RMSE values, range from 2.6 to 4.1 m for Ha and 2.9 to 4.3 m for Hw, respectively, indicating that our approach outperforms existing forest canopy height maps derived from area-based approaches. Hopefully, our methods and maps will serve as a foundation for estimating carbon storage, monitoring changes in forest structure, managing forest inventory, and assessing wildlife habitat availability. </p>
SKOS-based version of the open tree of life
<p>This is a <a href="https://www.w3.org/TR/skos-primer/">SKOS</a>-based representation of the data from :</p> <ul> <li>Open Tree of Life reference taxonomy version 3.6 <ul> <li>Version 3.6 draft 1 was generated on 18 September, 2023.</li> <li><a href="https://files.opentreeoflife.org/ott/ott3.6/ott3.6.tgz">Download</a></li> </ul> </li> </ul> <p>This SKOS representation was generated with the <a href="https://ontop-vkg.org/guide/cli.html#ontop-materialize">ontop tool </a>configuration files in <a href="https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology/tree/main/ontop_config/open-tree-of-life">here</a> .</p> <p><strong>Version note:</strong> In this version, OS undesired files were deleted.</p>
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.