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.
226
datasets available to search
ShareScore release 0.9.0
Dataset results
226 results for “phylogenetic reconstruction”
Supporting Data: ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology-informed phylogenetic methods
<p>This dataset contains all scripts and data for reproducing the analyses of the paper. The README files contain additional information.</p>
Accuracy of phylogenetic reconstructions from continuous characters analyzed under parsimony and its parametric correlates
<p>Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyze this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, the ability of continuous characters to accurately infer relationships is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analyzed by parsimony. We sampled 100 empirical trees to simulate 9,000 matrices, each containing between 25 and 50 taxa and 50 and 150 continuous characters evolving under three evolutionary processes: Brownian-Motion (BM), Ornstein-Uhlenbeck (OU) and Early-Burst (EB) with variable parametrizations. Our cladogram comparisons revealed that continuous character matrices, when discretized objectively and analyzed by parsimony in TNT, carry phylogenetic signals to infer species relationships, regardless of the evolutionary models and parameterization schemes. Interestingly, implementing Equal Weighting (EW) or Implied Weighting (IW) with varying penalization strengths against homoplasies did not affect cladogram reconstructions on the basis of continuous characters. Finally, the accuracy of continuous characters in resolving species relationships is skewed toward apical nodes of the recovered trees. Our findings provide general insights of the utility of quantitative traits in cladistics and demonstrate that their effectiveness in estimating shallower nodes is independent of the underlying evolutionary model, parameters and weighting schemes.</p>
Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Above node numbers indicate posterior probability. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %. Area enclosed by dashed lines is enlarged on Fig. 2.
→ Fig. 2. Representative skeletal elements of ornithosuchid archosaur Dynamosuchus collisensis gen. et sp. nov. (CAPPA/UFSM 0248) from Janner outcrop, Carnian, Late Triassic. A. Selected skull bones in left lateral view. B. Reconstruction of the skull. C. Skull in ventral view. D. Left quadrate and quadratojugal in posterodorsal view. E. Parabasisphenoid in left lateral view. F. Neural arch of an anterior cervical vertebra in anterior view. G. Centrum of a cervical vertebra in left lateral view. H. Right osteoderm in dorsal view. I. Neural arch of an anterior dorsal vertebra in left lateral view. J. Left ilium in lateral view. L. Right humerus in anterior view. M. Right forearm in medial view. N. Left manus in dorsal view. O. Right (reversed) pubis in lateral view. P. Left femur in anterior view. Q. Left fibula in lateral view. Some unpreserved portions are modified from Baczko et al. in press, for the reconstruction of the skeleton of CAPPA/UFSM 0248 (preserved elements indicated in orange) (K). Scale bars 20 mm. in The first ornithosuchid from Brazil and its macroevolutionary and phylogenetic implications for Late Triassic faunas in Gondwana
→ Fig. 2. Representative skeletal elements of ornithosuchid archosaur Dynamosuchus collisensis gen. et sp. nov. (CAPPA/UFSM 0248) from Janner outcrop, Carnian, Late Triassic. A. Selected skull bones in left lateral view. B. Reconstruction of the skull. C. Skull in ventral view. D. Left quadrate and quadratojugal in posterodorsal view. E. Parabasisphenoid in left lateral view. F. Neural arch of an anterior cervical vertebra in anterior view. G. Centrum of a cervical vertebra in left lateral view. H. Right osteoderm in dorsal view. I. Neural arch of an anterior dorsal vertebra in left lateral view. J. Left ilium in lateral view. L. Right humerus in anterior view. M. Right forearm in medial view. N. Left manus in dorsal view. O. Right (reversed) pubis in lateral view. P. Left femur in anterior view. Q. Left fibula in lateral view. Some unpreserved portions are modified from Baczko et al. in press, for the reconstruction of the skeleton of CAPPA/UFSM 0248 (preserved elements indicated in orange) (K). Scale bars 20 mm.
Fig. 4. Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter
Fig. 4. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain NH33 with closely related species. Bootstrap values (>50%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 3. Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter
Fig. 3. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain NH19 with closely related species. Bootstrap values (>50%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 2. Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter
Fig. 2. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strains NH20 and YP416 with closely related species. Bootstrap values (>50%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 3. A Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of two unrecorded yeast species in the order Filobasidiales
Fig. 3. A Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the rela- tionships of strain PG1-1-10C with closely related species. Bootstrap values (>70%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 2. A Neighbor-joining phylogenetic tree reconstructed from a in Isolation and characterization of two unrecorded yeast species in the order Filobasidiales
Fig. 2. A Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relation- ships of strains GW1-3 with closely related species. Bootstrap values (>70%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 3. A neighbor-joining phylogenetic tree reconstructed from a in Description of unrecorded wild yeasts from soil in Republic of Korea under cold conditions
Fig. 3. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain PG3-4-10C with closely related species. Bootstrap values (>70%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position.
Fig. 2. A neighbor-joining phylogenetic tree reconstructed from a in Description of unrecorded wild yeasts from soil in Republic of Korea under cold conditions
Fig. 2. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain CY-9-10C with closely related species. Bootstrap values (>70%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.02 substitutions per nucleotide position.
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.
Text-fig. 2: Reconstruction of Protothymallus elongatus (KRAMBERGER, 1885) based on NHMV-1883, SMMGD-SaT 173, and UL-V2. in Revision Of The Cyprinids From The Early Oligocene Of The České Středohoří Mountains, And The Phylogenetic Relationships Of Protothymallus Laube, 1901 (Teleostei, Cyprinidae, Gobioninae)
Text-fig. 2: Reconstruction of Protothymallus elongatus (KRAMBERGER, 1885) based on NHMV-1883, SMMGD-SaT 173, and UL-V2.
FIGURE 16. M. costocoracoideus. Reconstruction for Neusticosaurus 1 in Soft-tissue anatomy of the Plesiosaur pectoral girdle inferred from basal Eosauropterygia taxa and the extant phylogenetic bracket
FIGURE 16. M. costocoracoideus. Reconstruction for Neusticosaurus 1 in anterior view, 2 in ventral view, 3 in lateral view, 4 fleshed-out muscle reconstruction and 5 complete skeletal reconstruction in lateral view. Reconstruction for Ceresiosaurus 6 in anterior view, 7 in ventral view, 8 in lateral view, 9 fleshed-out muscle reconstruction and 10 complete skeletal reconstruction in lateral view. Reconstruction for Rhomaleosaurus 11 in anterior view, 12 in ventral view, 13 in lateral view, 14 fleshed-out muscle reconstruction and 15 complete skeletal reconstruction in lateral view.
FIGURE 5. M. subcoracoscapularis. Reconstruction for Neusticosaurus 1 in Soft-tissue anatomy of the Plesiosaur pectoral girdle inferred from basal Eosauropterygia taxa and the extant phylogenetic bracket
FIGURE 5. M. subcoracoscapularis. Reconstruction for Neusticosaurus 1 in anterior view, 2 in ventral view, 3 in lateral view, 4 in fleshed-out muscle reconstruction and 5 complete skeletal reconstruction in lateral view. Reconstruction for Ceresiosaurus 6 in anterior view, 7 in ventral view, 8 in lateral view, 9 fleshed-out muscle reconstruction and 10 complete skeletal reconstruction in lateral view. Reconstruction for Rhomaleosaurus 11 in anterior view, 12 in ventral view, 13 in lateral view, 14 fleshed-out muscle reconstruction and 15 complete skeletal reconstruction in lateral view.
Fig. 3a-c in New Tools for Phylogenetic reconstruction using character state trees
Fig. 3a-c: A CST with the same structure as the one of fig. 1. The paths to the root of the states D (3a) and G (3b) are accentuated, as well as the elements of the set SDG (fig. 3c, see eq. 1).
Fig. 1 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 1 (from LORENZ 1941): Resulting tree out of a species/characters-matrix of 48 mainly behavioural characters from twenty Anatid species (in fact, this graphic is matrix and tree in one).
Fig. 4a-b in New Tools for Phylogenetic reconstruction using character state trees
Fig. 4a-b: (a) Cladogram for five species (the tips T1 to T5) and the character which is coded in fig. 2b as CST. The inner nodes of the cladogram are hypothetical species. Their character state is reconstructed by the algorithm described in the text. Prominent branches denote an evolutionary step (a change of state). (b) Bifurcation of a cladogram with the character coded in fig. 3.
Fig. 2a-c in New Tools for Phylogenetic reconstruction using character state trees
Fig. 2a-c: The same character state tree with Camin – Sokal (a) and Matrioshka (b) coding, and (c) as a combination of three subcharacters (factors), each one with two states.
Fig. 1 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 1: Evolution of the ovipositor and the ootheca of Dictyoptera (Insecta) as an example of a relatively complex character state tree (based on data of GRIMALDI & ENGEL 2005 and EHRMANN 2002). Each node of the tree corresponds to an observed character state.
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.