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.
351
datasets available to search
ShareScore release 0.9.0
Dataset results
351 results for “gene tree”
FIGURE 129 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 129. Distribution of L. williamsoni (black square) and L. sp. cf williamsoni (red triangle).
Supplementary phylogenetic trees of Babesia bigemina based on partial sequences of both genes Rap-1a and gp45, with SH-aLRT support values (%), aBayes support, and ultrafast bootstrap support (%).
Open the record for dataset details and reuse information.
Data from: Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L.
Several well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here, we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step, highly discordant genes within genomic blocks (putative paralogs) are identified and excluded from the data set and, in the second step, blocks of linked genes are grouped according to their hybrid history. Existing multispecies coalescent software can then be applied to recover the principal tree(s) that make up the species tree/network without violating the underlying model. The potential of the approach is evaluated on simulated data derived from a species network composed of nine species, of which one is of hybrid origin, and displaying a single-gene duplication that leads to paralogous comparisons. We apply our method to an empirical set of 12 genes from 7 species sampled in the plant genus Medicago that display phylogenetic discordance. We identify the causes of the discordance and demonstrate that the Medicago orbicularis lineage experienced an episode of ancient hybridization. Our results show promise as a new way to explore phylogenetic sequence data that can significantly improve species tree inference in presence of hybridization and undetected paralogy or other causes leading to extremely discordant gene trees.
Data from: A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels
Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology–diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.
Figure 1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 1. Locality map.
Data from: Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life
Open the record for dataset details and reuse information.
Data from: Gene tree discordance causes apparent substitution rate variation
Open the record for dataset details and reuse information.
Data from: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
Open the record for dataset details and reuse information.
Data from: Coestimating reticulate phylogenies and gene trees from multilocus sequence data
Open the record for dataset details and reuse information.
Data from: Baculovirus-induced tree-top disease: how extended is the role of egt as a gene for the extended phenotype?
Open the record for dataset details and reuse information.
Data from: TreeFix: statistically informed gene tree error correction using species trees
Open the record for dataset details and reuse information.
Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
Open the record for dataset details and reuse information.
Data from: Incongruence of mitochondrial and nuclear gene trees in the carabid beetles Ohomopterus
Open the record for dataset details and reuse information.
Data from: Robustness to divergence time underestimation when inferring species trees from estimated gene trees
Open the record for dataset details and reuse information.
Estimating accurate gene trees in the presence of intra-locus recombination: A simulation study
Open the record for dataset details and reuse information.
Data from: SimPhy: phylogenomic simulation of gene, locus and species trees
Open the record for dataset details and reuse information.
Data from: Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees
Open the record for dataset details and reuse information.
Data from: Complete genome sequences provide a case study for the evaluation of gene-tree thinking
Open the record for dataset details and reuse information.
Data from: Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L.
Open the record for dataset details and reuse information.
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)
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.