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88 results for “phylogenetic datasets”
Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>This archive contains the code and datasets generated in the associated manuscript: "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits". We provide instructions, environments and scripts to reproduce the presented analyses.</p>
Dataset for "Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process"
<p>Contains all simulation scripts, simulated data, and supplemental materials</p>
A Taxonomic Information System for Nereididae (Annelida): morphological datasets supporting description, interactive identification and phylogenetic analysis of the family
<p>Nereididae (Polychaeta)–A DELTA database of genera, and Australian species</p><p>Robin S. Wilson1,2 , Christopher J. Glasby3,4 , Torkild Bakken5</p><p> </p><p>1 Sciences Department, Museums Victoria Research Institute, Museums Victoria, GPO Box 666 Melbourne, Victoria 3001, Australia</p><p>2 The University of Melbourne, Melbourne, Victoria 3010, Australia</p><p>3 Museum and Art Gallery Northern Territory, PO Box 4646, Darwin NT 0801, Australia</p><p>4 Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia</p><p>5 Norwegian University of Science and Technology, NTNU University Museum, NO-7491 Trondheim, Norway</p><p> </p><p>Corresponding author: Robin S. Wilson (<a href="mailto:rwilson@museum.vic.gov.au">rwilson@museum.vic.gov.au</a>)</p><p>Scope</p><p>This Nereididae (Annelida) Delta database is the work of Robin Wilson, Torkild Bakken & Chris Glasby and was used to generate sections of Wilson et al. (2023a). Status of genera and nominal subfamily placements follow WoRMS <a href="https://www.marinespecies.org/polychaeta/">https://www.marinespecies.org/polychaeta/</a>.</p><p>The version distributed here includes only Nereididae genera and is part of the Wilson et al. (2023b) Zenodo repository which also includes other outputs: Nexus files as .nex and natural language output of taxon descriptions and character lists as .rtf files. </p><p>Updates including fixes to any errors found, and including new taxa and new taxonomic revisions, will be uploaded to Zenodo as new versions (the doi above will resolve to the most recent version). We intend that future versions will include all Nereididae species known from Australia; and all Nereididae species known from bathyal-abyssal depths (~2,000 m and deeper).</p><p>This repository contains an interactive key using the Delta Intkey software version by the Atlas of Living Australia (2014) <strong>but not yet that of Dallwitz (2020)</strong>.</p><p>References</p><p>Atlas of Living Australia (2014) Open-delta. A Java port of the Delta - DEscription Language for TAxonomy suite of applications into Java. Available from: https://github.com/AtlasOfLivingAustralia/open-delta (July 12, 2023).</p><p>Dallwitz MJ (2020) Installing and running the programs of the DELTA System. Reports, Division of Entomology CSIRO Australia. Available from: https://www.delta-intkey.com/www/programs.htm (January 31, 2023).</p><p>Wilson RS, Glasby CJ, Bakken T (2023a) The Nereididae (Annelida) – diagnoses, descriptions, and a key to the genera. ZooKeys 1182: 35–134. <a href="https://doi.org/10.3897/zookeys.1182.104258">https://doi.org/10.3897/zookeys.1182.104258</a></p><p>Wilson RS, Bakken T, Glasby CJ (2023b) A Taxonomic Information System for Nereididae (Annelida): morphological datasets supporting description, interactive identification and phylogenetic analysis of the family. <a href="https://doi.org/10.5281/zenodo.7776745">https://doi.org/10.5281/zenodo.7776745</a></p>
Data from: One tree to link them all: a phylogenetic dataset for the European Tetrapoda
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Evaluating the performance of probabilistic algorithms for phylogenetic analysis of big morphological datasets: a simulation study
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Dataset for co-phylogenetic analysis of Cicadas and their symbionts
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Cambrian comb jellies from Utah illuminate the early evolution of nervous and sensory systems in ctenophores - Phylogenetic dataset
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Reproductive barriers and genomic hotspots of adaptation during allopatric species divergence: datasets for all phylogenetic reconstructions represented in Fig 2
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Datasets for phylogenetic analyses of Pavlomulina ranunculiformis
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Datasets used in "Fast phylogenetic inference from typing data"
<p>Real datasets used in the paper "<a href="https://doi.org/10.1186/s13015-017-0119-7">Fast phylogenetic inference from typing data</a>", by João A Carriço, Maxime Crochemore, Alexandre P Francisco, Solon P Pissis, Bruno Ribeiro-Gonçalves, and Cátia Vaz, Algorithms for Molecular Biology 13 (1), 1-14, 2018. Check the paper for more information on the datasets.</p>
Dataset: Plant-plant facilitation increases with reduced phylogenetic relatedness along an elevation gradient
<p>Environmental conditions can modify the intensity and sign of ecological interactions. The stress gradient hypothesis (SGH) predicts that facilitation becomes more important than competition under stressful conditions. To properly test this hypothesis, it is necessary to account for all (not a subset of) interactions occurring in the communities and consider that species do not interact at random but following a specific pattern. We aim to assess elevational changes in facilitation, in terms of species richness, frequency and intensity of the interaction as a function of the evolutionary relatedness between nurses and their associated species. We sampled nurse and their facilitated plant species in two 1000-2000 m. elevation gradients in Mediterranean Chile where low temperature imposes a mortality filter on seedlings. We first estimated the relative importance of facilitation as a mechanism adding new species to communities distributed along these gradients. We then tested whether the frequency and intensity of facilitation increases with elevation, taking into account the evolutionary relatedness of the nurse species and the facilitated species.</p> <p>We found that nurses increase the species richness of the community by up to 35%. Facilitative interactions are more frequent than competitive interactions (56% vs. 44%) and facilitation intensity increased with elevation for interactions involving distantly related lineages. Our results highlight the importance of including an evolutionary dimension in the study of facilitation to have a clearer picture of the mechanisms enabling species to coexist and survive under stressful conditions. This knowledge is especially relevant to conserve vulnerable and threatened communities facing new climate scenarios, such as those located in Mediterranean-type ecosystems.</p>
Generalized hidden Markov models for phylogenetic comparative datasets
<ol> <li class="JamesManuscriptBody">Hidden Markov models (HMM) have emerged as an important tool for understanding the evolution of characters that take on discrete states. Their flexibility and biological sensibility make them appealing for many phylogenetic comparative applications.</li> <li class="JamesManuscriptBody">Previously available packages placed unnecessary limits on the number of observed and hidden states that can be considered when estimating transition rates and inferring ancestral states on a phylogeny.</li> <li class="JamesManuscriptBody">To address these issues, we expanded the capabilities of the R package corHMM to handle <i>n</i>-state and <i>n</i>-character problems and provide users with a streamlined set of functions to create custom HMMs for any biological question of arbitrary complexity.</li> <li class="JamesManuscriptBody">We show that increasing the number of observed states increases the accuracy of ancestral state reconstruction. We also explore the conditions for when an HMM is most effective, finding that an HMM is an appropriate model when the degree of rate heterogeneity is moderate to high.</li> <li class="JamesManuscriptBody">Finally, we demonstrate the importance of these generalizations by reconstructing the phyllotaxy of the ancestral angiosperm flower. Partially contradicting previous results, we find the most likely state to be a whorled perianth, whorled androecium, whorled gynoecium. The difference between our analysis and previous studies was that our modeling explicitly allowed for the correlated evolution of several flower characters.</li> </ol>
Data from: A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets
It has been proposed that supertree approaches should be applied to large multilocus sequence datasets to achieve computational tractability. Large datasets such as those derived from phylogenomics studies can be broken into many locus-specific tree searches and the resulting trees can be stitched together via a supertree method. Using simulated data, workers have reported that they can rapidly construct a supertree that is comparable to the results of heuristic tree search on the entire dataset. To test this assertion with organismal data, we compared tree length under the parsimony criterion and computational time for twenty multilocus datasets using supertree (SuperFine and SuperTriplets) and supermatrix (heuristic search in TNT) approaches. Tree length and computational times were compared among methods using the Wilcoxon matched-pairs signed rank test. Supermatrix searches produce significantly shorter trees than either supertree approach (SuperFine or SuperTriplets; p < 0.0002 in both cases). Moreover, the processing time of supermatrix search was significantly lower than SuperFine+locus-specific search (p < 0.01) but roughly equivalent to that of SuperTriplets+locus-specific search (p > 0.4, not significant). In conclusion, we show by using real rather than simulated data, that there is no basis, either in time tractability or tree length, for use of supertrees over heuristic tree search using a supermatrix for phylogenomics.
The mitochondrial genome datasets of phylogenetic analysis from the subfamily Coelidiinae
<p>58 leafhopper and 5 treehoppers species were selected to participate in the phylogenetic tree construction after the removal of unverified, lacks the accurate scientific name, and repeated species sequences. Phylogenetic analysis was performed using alignments of the 13 PCGs of leafhopper with the other complete or near complete genomes of the treehopper species. The two species of Cosmoscarta bispecularis (KP064511) and Tettigades auropilosa (KM000129) (Yan & Zu, 2019) were used as the outgroup.</p>
Aligned LSU dataset and phylogenetic relationships of Tylopilus glutinosus
<p><i>Tylopilus glutinosus</i> from Bangladesh is described and illustrated based on morphology along with molecular data. This species is characterized by its caespitose habitat, a purple pileus that becomes very viscid when wet, unchanging context, an ixotrichodermial pileipellis with the outer layer consisting of 3–4 cylindrical cells and the inner layer composed of filamentous hyphae, broadly fusoid to fusoid basidiospores, and putative association with <i>Shorea robusta</i>. Morphologically, this species resembles <i>T. plumbeoviolaceoides</i> and <i>T. plumbeoviolaceus</i>. However, some distinctive macro- and microscopic features along with geographical distribution and host preference can be used to separate them from each other. Furthermore, DNA sequence of the nuclear ribosomal large subunit (nrLSU) analysis undoubtedly placed them in different lineages or clades within <i>Tylopilus</i>. Detailed morphological descriptions, illustrations of the new species, and its comparison with the related taxa of <i>Tylopilus</i> are also provided with phylogenetic placement.</p>
Data from: Assessing among-lineage variability in phylogenetic imputation of functional trait datasets
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Data from: A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets
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Data from: Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices
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Data from: Decisive datasets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects
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Dataset: Plant-plant facilitation increases with reduced phylogenetic relatedness along an elevation gradient
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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.