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.
48
datasets available to search
ShareScore release 0.9.0
Dataset results
48 results for “phylogeny reconstruction”
Training data for 'Preparing genomic data for phylogeny reconstruction' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network training 'Preparing genomic data for phylogeny reconstruction'. There are four nucleotide sequences from chromosome 5 of four strains of S. cerevisiae. The GenBank annotated sequenced were produced using 'funannotate predict annotation' (Galaxy Version 1.8.9+galaxy2) on the nucleotide sequences sequences. References: DOI: 10.1126/science.274.5287.546; DOI: 10.1126/science.1189015; DOI: 10.1016/j.cell.2016.08.020</p>
URL list for downloading training data for 'Maximum Likelihood Phylogeny Reconstruction'' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network (GTN) training 'Maximum Likelihood Phylogeny Reconstruction'. It is a list of Zenodo URL pointers to a dataset of 173 amino acid alignments of orthologs found in chromosome 5 of four strains of S. cerevisiae. Original sequence data (https://zenodo.org/record/6610704) was processed in Galaxy following GTN 'Preparing genomic data for phylogeny reconstruction' training (10.48546/workflowhub.workflow.359.1) to generate alignments of orthologs.</p>
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.
Fig. 7. MAXENT reconstruction for clade I in Fig. 11. Left G1s in Tuerkayana latens, a New Species of Land Crab from French Polynesia, with a Discussion on the Phylogeny of the Genus (Crustacea: Decapoda: Brachyura: Gecarcinidae)
Fig. 7. MAXENT reconstruction for clade I (A) and clade III (B) of Amphibalanus amphitrite in the world representing current distribution models.
Fig. 7. Tommotiid Camenella reticulosa Conway Morris, 1990 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 7. Tommotiid Camenella reticulosa Conway Morris, 1990, from lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia. A. Sellate sclerite (dextral), SAMP 43181, Bunyeroo 4; dorsal view showing narrow lateral lobes and wide sella with reduced, possibly abraded ornament. B. Mitral sclerite (dextral), SAMP 43182, MMF 0.0; B1, oblique view of deformed oblicate and accrescent sides showing wide through and disturbed radial ornament; B2, oblique view of plicate and decrescent sides showing normal placation, a pointed apex and deep internal cavity.
Fig. 9 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 9. Tommotiid Dailyatia sp., probable C−type sclerite, SAMP 43187 from MMF 0.0, lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia. A. Oblique apertural view showing asymmetric twist. B. Side view showing open coiling through almost a full whorl.
Fig. 6. Tommotiid Camenella reticulosa Conway Morris, 1990 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 6. Tommotiid Camenella reticulosa Conway Morris, 1990 from lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia, sellate sclerites. A. SAMP 43177 (sinistral), MMF 0.0; internal view of sclerite with damaged apex. B. SAMP 43178 (Dextral),Wilkawillina Q; B1, internal view of large specimen with apex removed by co−marginal breakage showing well developed duplicature; B2, Detail of duplicature showing minor co−marginal with nodose ornament and fine co−marginal and radial striae. C. SAMP 43179 (sinistral), Wilkawillina S; C1, side view of specimen with preserved apex viewed from the large lobe; C2, detail of lateral flank of large lobe with co−marginal ribs ornamented by nodes and superimposed reticulation. D. SAMP 43180 (Dextral), MMF 0.0; internal view of specimen with small lobe damaged showing cavity under duplicature of the large lobe.
Fig. 5. Tommotiid Camenella reticulosa Conway Morris, 1990 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 5. Tommotiid Camenella reticulosa Conway Morris, 1990 from lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia, sellate sclerites. A. SAMP 43172 (dextral), Wilkawillina Q; A1, dorsal view of specimen with large and small lobe strongly inclined and ornament of wide co−marginal ribs; A2, oblique dorsal view showing unequal height of the lobes; A3, detail of ornament on small lobe showing wide co−marginal ribs with nodes and superimposed reticulation and fine growth striae between the ribs. B. SAMP 43173 (dextral), MMF 0.0; B1, side view (from small lobe) of specimen with narrow and densely spaced co−marginal ribs showing tightly coiled apex; B2, oblique dorsal view showing deep sella, radial rib on large lobe overhanging the sella and faint radial folds on both large and small lobe. C. SAMP 43174 (sinistral), MMF 0.0; dorsal view of small specimen showing maximum inclination of large and small lobes. D. SAMP 43175 (dextral), MMF 0.0; D1, side view (from large lobe) of specimen with intermediate development of co−marginal ribs showing tightly coiled apex; D2, oblique dorsal view showing unequal development of lobes and relatively narrow sella. E. SAMP 43176 (sinistral), Wilkawillina Q; dorsal view of large specimen with damaged small lobe, radial folds on large lobe and wide sella without co−marginal ornament (abrasion?).
Fig. 4. Tommotiid Camenella reticulosa Conway Morris, 1990 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 4. Tommotiid Camenella reticulosa Conway Morris, 1990 from lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia, mitral sclerites. A. SAMP 43170 (sinistral), Wilkawillina S; A1, apertural view of large specimen showing deep apertural cavity and angular deflection of radial ribs on plicate side which is developed into a lip projecting under the accrescent side (on left in the picture); A2, view from accrescent side showing strong curvature of the specimen and aperture; A3, apical view showing initial equal development of radial ribs on plicate and obplicate (lowermost in picture) sides, development of the plicate side into a projecting lip and faint co−marginal ornament on the internal surface of the sclerite; A4, detail of apex showing circular perforation (breakage?) and subdued ornament. B. SAMP 43171 (sinistral), MMF 0.0; B1, apertural view of specimen showing deep apertural cavity, deflection of radial ribs on plicate side and growth disturbances on plicate and obplicate sides following damage and/or growth retardation at 2/3 of final sclerite length; B2, detail of growth disturbances on internal surface of obplicate side; B3, detail apex showing smoothly rounded apex without perforations.
Fig. 2. Tommotiid Camenella reticulosa Conway Morris, 1990 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 2. Tommotiid Camenella reticulosa Conway Morris, 1990, from lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia explanation of terminology. A, B. Sellate sclerites. A. SAMP 43172 (dextral), Wilkawillina Q, in dorsal view. B. SAMP 43178 (dextral),Wilkawinnina Q, in ventral view. C. Mitral sclerite, SAMP 43167 (sinistral), MMF 0.0, in apical view.
Fig. 3. Tommotiid Camenella reticulosa Conway Morris, 1990 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 3. Tommotiid Camenella reticulosa Conway Morris, 1990 from lower Cambrian Hawker Group, Flinders Ranges, Arrowie Basin, South Australia, mitral sclerites. A. SAMP 43164 (sinistral), Wilkawillina S; oblicate/accrescent view of sclerite showing wide radial ribs. B. SAMP 43165 (sinistral), MMF 0.0; obplicate/accrescent view of specimen with deep radial folds. C. SAMP 43166 (sinistral), Wilkawillina Q; C1, obplicate/ accrescent view of specimen with pointed apex; C2, decrescent view showing strong curvature of the aperture; C3, detail of shell ornament on accrescent side showing co−marginal ribs capped by nodes and a superimposed reticulation; C4, detail of smoothly rounded apex showing a circular depression. D. SAMP 43167 (sinistral), MMF 0.0; D1, oblique obplicate/accrescent view of small specimen; D2, apical view showing the almost equal development of radial ribs on plicate (lowermost in picture) and obplicate sides. E. SAMP 43168 (sinistral), MMF 0.0; oblique obplicate/accrescent view of specimen with minimal helical twist. F. SAMP 43169 (dextral), Bunyeroo 4b; F1, oblique apical/obplicate/decrescent view of abraded specimen with strong helical twist; F2, oblique apical/plicate/decrescent view showing angular deflection of strongly developed radial ribs on plicate side.
Fig. 1 in The tommotiid Camenella reticulosa from the early Cambrian of South Australia: Morphology, scleritome reconstruction, and phylogeny
Fig. 1. Simplified locality map showing sample localities within the Wilkawillina Limestone that yielded Camenella at Bunyeroo Gorge, Wilkawillina Gorge and the MMF section in the central Flinders Ranges (A). The regional context of all localities within South Australia is also depicted (B, C).
Figure 9. Mapped and reconstructed soldier head shapes positioned across a Termitidae phylogeny. Nodes a–g in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 9. Mapped and reconstructed soldier head shapes positioned across a Termitidae phylogeny. Nodes a–g are referred to in the text.
UnFATE: A comprehensive probe set and bioinformatics pipeline for phylogeny reconstruction and multilocus barcoding of filamentous ascomycetes (Ascomycota, Pezizomycotina)
Open the record for dataset details and reuse information.
Multivariate mapping of ontogeny, taphonomy, and phylogeny to reconstruct problematic fossil taxa
<p>Exceptionally preserved fossils of soft-bodied organisms provide unique evidence of evolutionary history, but they are often contentious; different approaches frequently produce radically different reconstructions of taxa and their affinities. Conflict arises due to difficulties in disentangling the three non-independent factors that underlie all morphological variation within and between fossils: ontogeny, taphonomy, and phylogeny. Comparative data from extant organisms can be extremely powerful in this context, but is often difficult to apply given the multidimensionality of anatomical variation. Here we present a multivariate ordination method using discrete morphological character data from modern taxa at different ontogenetic and taphonomic stages (semaphoront and 'semataphonts'). Analysing multiple axes of morphological variation simultaneously allows us to visualise character combinations that are likely to exist in fossil specimens at intersecting stages of growth and decay, and thus constrain interpretation of fossils. Application to early vertebrates finds variation in fossil specimens to be accounted for by all three axes: primarily decay in <em>Mayomyzon</em>, ontogeny in <em>Priscomyzon</em>, and phylogeny in 'euphaneropoids' and <em>Palaeospondylus</em>. Our demonstration of empirical multifactorial variation underscores the need for multivariate approaches to fossil interpretation, especially non-biomineralized taxa. As such, this conceptual approach provides a new method for resolving enigmatic taxa throughout the fossil record.</p>
FIGURE 5 Ancestral state reconstructions. A. Whorl count. B. Body length. C in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 5 Ancestral state reconstructions. A. Whorl count. B. Body length. C. Altitude.
Data from: How many characters are needed to reconstruct a phylogeny?
Open the record for dataset details and reuse information.
Reconstructing the phylogeny and evolutionary history of freshwater fishes (Nemacheilidae) across Eurasia since early Eocene
Open the record for dataset details and reuse information.
Multivariate mapping of ontogeny, taphonomy, and phylogeny to reconstruct problematic fossil taxa
Open the record for dataset details and reuse information.
Data from: The evolution of skull and body shape in Triturus newts reconstructed from 3D morphometric data and phylogeny
To explore the relationship between morphological change and species diversification, we reconstructed the evolutionary changes in skull size, skull shape, and body elongation in a monophyletic group of eight species that make up salamander genus Triturus. Their well-studied phylogenetic relationships and the marked difference in ecological preferences among five species groups makes this genus an excellent model system for the study of morphological evolution. The study involved three-dimensional imagery of the skull and the number of trunk vertebrae, in material that represents the morphological, spatial, and molecular diversity of the genus. Morphological change largely followed the pattern of descent. The reconstruction of ancestral skull shape indicated that morphological change was mostly confined to two episodes, corresponding to the ancestral lineage that all crested newts have in common and the Triturus dobrogicus lineage. When corrected for common descent, evolution of skull shape was correlated to change in skull size. Also, skull size and shape, as well as body shape, as inferred from the number of trunk vertebrae, were correlated, indicating a marked impact of species' ecological preferences on morphological evolution, accompanied by a series of niche shifts, with the most pronounced one in the T. dobrogicus lineage. The presence of phylogenetic signal and correlated evolutionary changes in skull and body shape suggested complex interplay of niche shifts, natural selection, and constraints by a common developmental system
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.