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95 results for “tree reconstruction”
Data from: Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
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Newick trees for "Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus"
<p>Newick format within-patient phylogenetic trees for a Barrett's Esophagus WGS dataset</p>
Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The mole salamanders (family Ambystomatidae) are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny and which ones yield phylogenetically inaccurate reconstructions. To shed light on this conflict, we present the first multi-locus DNA sequence-based phylogenetic study of the Ambystomatidae. We utilized a range of analyses, including coalescent-based methods of species-tree estimation that account for incomplete lineage sorting within a locus and concordance-based methods that estimate the number of sampled loci that support a particular clade. We repeated these analyses with the removal of individual loci to determine if any locus has a disproportionate effect on our phylogenetic results. Collectively, these results robustly resolved many deep and relatively shallow clades within Ambystoma, including the placement of A. gracile and A. talpoideum as the sister clade to a clade containing all remaining ambystomatids, and the placement of A. maculatum as the sister lineage to all remaining ambystomatids excluding A. gracile and A. talpoideum. Both Bayesian coalescent and concordance methods produced similar results, highlighting strongly supported branches in the species tree. Furthermore, coalescent-based analyses that excluded loci produced overlapping species-tree posterior distributions, suggesting that no particular locus – including mtDNA – disproportionately contributed to our species-tree estimates. Overall, our phylogenetic estimates have greater similarity with previous allozyme and mitochondrial sequence-based phylogenetic estimates. However, intermediate depths of divergence in the ambystomatid species tree remain unresolved, potentially highlighting a region of rapid species radiation or a hard polytomy, which limits our ability to comment on previous morphologically-based taxonomic groups.
Mesophication in temperate Europe: a dendrochronological reconstruction of tree succession and fires in a mixed deciduous stand in Białowieża Forest / supporting data
<p>The attached data was gathered to investigate the successional changes in Bialowieza Forest mixed-deciduous stands by reconstructing the long-term tree population dynamics (tree-ring data). Traces of fires were documented from a 43ha area to explore whether fire was involved in shaping the succession of this habitat.</p>
Data from: Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica
Background. Cloud forest, characterized by a persistent, frequent or seasonal low-level cloud cover and a fragmented distribution, is one of the most threatened habitats especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods. Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate the ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results. Bayesian trees retrieved Cyathea, Alsophila, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in the Mesoamerican cloud forests are recent, from the Neogene to the Quaternary. Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the four most significant variables or elevation. For elevational shifts we found repeated changes from low to high elevations. Conclusions. Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recently from their ancestors.
FIGURE 3. The Maximum Likelihood tree reconstructed from 16S in Inter- and intra-island divergence in Odorrana ishikawae (Anura, Ranidae) of the Ryukyu Archipelago of Japan, with description of a new species
FIGURE 3. The Maximum Likelihood tree reconstructed from 16S and sequence divergence data. The most parsimonious tree has the same topology.
FIGURE 4. Bayesian posterior probability tree was reconstructed from 16S in A new species of Kaloula (Amphibia: Anura: Microhylidae) from southern Guangxi, China
FIGURE 4. Bayesian posterior probability tree was reconstructed from 16S ribosomal RNA mitochondrial gene sequences with Metaphrynella pollicaris, Metaphrynella sundana and Phrynella pulchra as outgroups. Maximum-likelihood tree produced near-identical topology. Two reliability indices are given on nodes: the Bayesian posterior probabilities/the maximum likelihood bootstrap percentages. Symbol (*) indicates nodes with good bootstrap supports for ML (>80%) inferences and Bayesian posterior probabilities (BPP> 95%), and symbol (-) represents that node values are less than 60%.
FIGURE 1. Maximum likelihood tree reconstructed from tef1 in Trichoderma orarium (Hypocreales): a new species from Taiwan
FIGURE 1. Maximum likelihood tree reconstructed from tef1 sequences. The newly described species is displayed in blue bold. We indicated bootstrap values at the nodes based on 1000 replicates only exceeding 50%. Bar scale represents 0.01 substitutions per nucleotide position. T. inhamatum and T. bannaense were used as outgroup. The tef1 sequence accession numbers are provided in parentheses following the strain numbers. "T" denotes type strains.
Supplementary material 1 from: Erdélyi A, Hartdégen J, Malatinszky Á, Vadász C (2023) Historical reconstruction of the invasions of four non-native tree species at local scale: a detective work on Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo. One Ecosystem 8: e108683. https://doi.org/10.3897/oneeco.8.e108683
Derived data of Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo from the National Forestry Database and its archives.
A Dataset of Reconstructed Carotid Bifurcation Lumen and Plaque Models with Centerline Tree and Simulated Hemodynamics
<p><code>carotid_bifurcation_database.zip</code> contains 79 cases of left and right-side carotid bifurcations (152 inner wall models). For each case, inner wall (lumen) and plaque models were extracted from computed tomography angiography (CTA) scans. The models were segmented, reconstructed, and a centerline tree was created for each geometry using the <a href="https://github.com/PepeEulzer/CarotidAnalyzer">CarotidAnalyzer</a> pipeline. The geometries include varying degrees of internal carotid stenosis. Bifurcations with 100% stenosis were omitted, as the vessel is not discernible in the scan.</p> <p><code>carotid_flow_database.zip</code> contains hemodynamic flow simulations of the above models. Fluid data (velocity, pressure) and surface data (wall shear stress) are given in seperate files for each case. For each field, a systolic and diastolic time step are provided.</p> <p><strong>Further information regarding the extraction pipeline and flow simulations can be obtained from the following publications:<br></strong>P. Eulzer, F. von Deylen, W.-C. Hsu, R. Wickenhöfer, C. M. Klingner, and K. Lawonn (2023), A Fully Integrated Pipeline for Visual Carotid Morphology Analysis. Computer Graphics Forum, 42(3): 25-37. <a href="https://doi.org/10.1111/cgf.14808">https://doi.org/10.1111/cgf.14808</a></p> <p>Kevin Richter, Tristan Probst, Anna Hundertmark, Pepe Eulzer, and Kai Lawonn (2024), Longitudinal wall shear stress evaluation using centerline projection approach in the numerical simulations of the patient-based carotid artery. Computer Methods in Biomechanics and Biomedical Engineering, 27(3): 347-364. <a href="https://doi.org/10.1080/10255842.2023.2185478">https://doi.org/10.1080/10255842.2023.2185478</a></p> <p>P. Eulzer, K. Richter, A. Hundertmark, R. Wickenhöfer, C. M. Klingner, and K. Lawonn (2024), Instantaneous Visual Analysis of Blood Flow in Stenoses Using Morphological Similarity. Computer Graphics Forum 43(3): in print. <a href="https://doi.org/10.1111/cgf.15081">https://doi.org/10.1111/cgf.15081</a></p>
Point clouds and QSM for 598 individually scanned tree branches to support "Terrestrial laser scanning to reconstruct branch architecture from harvested branches"
<p>A collection of 598 harvested branches scanned in high resolution using terrestrial LiDAR. Branches were collected from GEM forest plots in Malaysia, Australia and Brazil.</p> <p>Branch nomenclature is <em>PLOT</em>-<em>TREE</em>-B<em>N</em><S or SH> where <em>PLOT </em>codes can be found in the manuscript, <em>N</em> refers to the sample number of branch harvested from a tree, and S and SH refer to sun or shade branch respectivetly.</p> <p>For each branch there are 3 files: </p> <ul> <li>Unfiltered point clouds (raw_pc) are clipped from the original data only and have had no post processing applied</li> <li>Filtered point clouds (filtered_pc) have been filtered according to the steps in the manuscript</li> <li>QSMs were produced using <em>treegraph </em>(<a href="https://doi.org/10.5281/zenodo.5226212">https://doi.org/10.5281/zenodo.5226212</a>)</li> </ul> <p>Polygon File Format (.ply) files can be viewed in software such as CloudCompare.</p> <p>Full details of methods can be found in: Wilkes, P., Shenkin, A., Disney, M., Malhi, Y., Bentley, L. P., & Vicari, M. B. (2021). Terrestrial laser scanning to reconstruct branch architecture from harvested branches. <em>Methods in Ecology and Evolution</em>, 12, 2487–2500. <a href="https://doi.org/10.1111/2041-210X.13709">https://doi.org/10.1111/2041-210X.13709</a></p>
Figure 3. COI–28S concatenated maximum-likelihood tree reconstructed using GARLI 2.0 in Unmasking Aurelia species in the Mediterranean Sea: an integrative morphometric and molecular approach
Figure 3. COI–28S concatenated maximum-likelihood tree reconstructed using GARLI 2.0. Numbers adjacent to nodes show the bootstrap support values. The scale indicates the number of substitutions per site. Reference sequences from GenBank are in bold.
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S in Lysobacter humi sp. nov., isolated from soil
Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S rRNA gene sequences of strains FJY8T and related taxa. Numbers at branch nodes present bootstrap values (>50 %) obtained as percentages of 1000 replicates. Filled circles indicate the corresponding nodes recovered by using the maximum-parsimony algorithm. Bar, 0.02 substitutions per nucleotide position.
FIGURE 7. Phylogenetic trees reconstructed using the mtDNA 16S in Johnius sasakii, a new species of croaker (Perciformes: Sciaenidae) with a key to Johnius from East Malaysia, Borneo
FIGURE 7. Phylogenetic trees reconstructed using the mtDNA 16S genes of five Johnius (Johnius) species. Values above the branches are respective bootstrap values from 5000 replications for the Neighbour-Joining (NJ) and Maximum-Likelihood (ML) analyses. Bar indicates genetic distances of 0.02.
A 440-Year Reconstruction of Heavy Precipitation in California from Blue Oak Tree Rings
<p>The .xlxs file contains the instrumental and paleoclimate data used in the article by Howard, Stahle, & Dettinger titled "A 440-year reconstruction of heavy precipitation in California from blue oak tree rings." </p>
Data from: Using ultraconserved elements to reconstruct the termite tree of life
<p><span>The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting </span><span>50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of <em>Cryptocercus</em>, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted <em>in silico</em> between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: </span><span><a href="https://github.com/oist/TER-UCE-DB/"><span>https://github.com/oist/TER-UCE-DB/</span></a></span><span>.</span></p>
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 in A new species of nurse-frog (Aromobatidae, Allobates) from the Madeira River basin with a small geographic range
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 bp fragment of the mitochondrial 16S rDNA sampled from six Allobates bacurau paratypes and other cryptically colored species of Allobates distributed in Brazil and across cis-Andean South America. Clade labels indicate bootstrap support values estimated from 5000 bootstrap replicates (only support values>80% are shown). Basal clades with low bootstrap support should not be considered to reflect the true evolutionary history between taxa. Locations described in parentheses indicate sequence samples obtained from voucher specimens that did not proceed from the species type locality.
FIGURE 3. Phylogenetic reconstruction for 30 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 3. Phylogenetic reconstruction for 30 specimens of Leptogomphus and three outgroup taxa using the combined COI+ITS dataset. The best Maximum Likelihood tree is shown, with posterior probabilities from the Bayesian Inference analysis also depicted on the branches. Bootstrap values and posterior probabilities are shown if less than 100 or 1.0 respectively. RMNH collection codes are shown for each specimen, as well as the sex of the specimen and an indication of where it was collected.
Visualizing reconstructed tree models
<p>Visualization on how a point cloud is created by a terrestrial laser scanner, and how a reconstructed quantitative structure model can be visualized in various ways. The visualization can be a cylinder model as shown in previous videos, but it can also be converted to a more continuous Bézier surface. The video also shows how the tree model can be augmented with non-intersecting leaves by sampling a certain distribution based on the branching structure. Both the branches and the leaves can be textured either for realism or something totally different.</p> <p>This animation was produced by the Inverse Problems research group in the Department of Mathematics at Tampere University of Technology (http://math.tut.fi/inversegroup).</p> <p>Animation created using Blender (http://www.blender.org).</p> <p>Music:<br> "Vanes" by Kevin MacLeod (http://incompetech.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p> <p>Textures:<br> "Bark 0007"<br> xoio (xoio.de)</p> <p>"Cherry Leaf"<br> BrianHanson2nd (deviantart.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p> <p>The animation builds upon but does not directly feature the "Prunus avium - Cherry Tree" point cloud data by Jan Hackenberg (http://www.simpletree.uni-freiburg.de/openData.html) shared under the Creative Commons - Attribution-NonCommercial-ShareAlike 4.0 International license<br> http://creativecommons.org/licenses/by-nc-sa/4.0/</p>
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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.