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.
198
datasets available to search
ShareScore release 0.9.0
Dataset results
198 results for “Character states”
Data from: Predicting the ancestral character changes in a tree is typically easier than predicting the root state
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rate become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, depending on the tree and branch length distribution, reconstructing these changes (i.e. reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony-based and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification.
Data from: Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages
A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models. Here we introduce a new stochastic character mapping algorithm that overcomes these limitations, and apply it to study mating system evolution over a time-calibrated phylogeny of the plant family Onagraceae. Utilizing a hidden state SSE model we tested the association of the loss of self-incompatibility with shifts in diversification rates. Confirming long standing theory, we found that self-compatible lineages have higher extinction rates and lower net diversification rates compared to self-incompatible lineages. Furthermore, these results provide empirical evidence for the "senescing" diversification rates predicted in highly selfing lineages: our mapped character histories show that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in negative net diversification. Lineages that have long been self-compatible such as Fuchsia and Clarkia are in a previously unrecognized and ongoing evolutionary decline. Our results demonstrate that stochastic character mapping of SSE models is a powerful tool for examining the timing and nature of both character state transitions and shifts in diversification rates over the phylogeny.
Text-fig. 13: Cladogram showing the systematic position of Protothymallus within the Gobioninae, (for the character states see Tab. 1 and text). 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. 13: Cladogram showing the systematic position of Protothymallus within the Gobioninae, (for the character states see Tab. 1 and text).
TABLE 3. Character state matrix derived from Table 1 in A description of Promanodes serafini gen. et sp. nov. from Baltic amber, with a review of related New Zealand Promanus Sharp, 1877 (Coleoptera: Trogossitidae)
<p><b>TABLE 3.</b> Character state matrix derived from Table 1.</p><table><tbody><tr><th>Taxon/Character</th><th>0 12345</th></tr></tbody><tbody><tr><th><i>Lophocateres</i></th><td>0 0 0 100</td></tr><tr><th><i>Grynocharis</i></th><td>200101</td></tr><tr><th><i>Promanus</i></th><td>101011</td></tr><tr><th><i>Promanodes</i></th><td>0 11011</td></tr></tbody></table>
Figure 3. Cranial character states. A in The phylogeny and taxonomy of Hippopotamidae (Mammalia: Artiodactyla): a review based on morphology and cladistic analysis
Figure 3. Cranial character states. A, lateral view of a Hexaprotodon liberiensis skull. B, Lateral view of a Hippopotamus amphibius skull. C, lateral view of a Hex. mingoz skull. D, three dorsal views of the braincase (from bottom to top: in Hex. harvardi, in Hex. mingoz, in Hip. amphibius). E, four schematic anterior views of the left orbit (from right to left: in Hex. protamphibius, in Hex. harvardi, in Hip. gorgops, in Hex. sivalensis).
Fig. 32. Character 18. Fore wing ulnar cell 3, states 0 and 1 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 32. Character 18. Fore wing ulnar cell 3, states 0 and 1: (0) angled to radial cell; (1) substantially parallel to radial cell.
Data from: Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages
Open the record for dataset details and reuse information.
Data from: Standard sister clade comparison fails when testing derived character states
Open the record for dataset details and reuse information.
Data from: Predicting the ancestral character changes in a tree is typically easier than predicting the root state
Open the record for dataset details and reuse information.
FIGURE 2 in A new species of Sphenomorphus (Squamata: Scincidae) from Phu Quoc Island Vietnam with a discussion of biogeography and character state evolution in the S stellatus group
FIGURE 2. Head scale nomenclature and their positional relationship and size illustrated by the adult female Sphenomorphus phuquocensis sp. nov. ZMMU R-11518 (SVL = 60.8 mm) from the type locality of Phu Quoc National Park, Vietnam. A) dorsal view and B) right lateral view. Terminology is adapted from Taylor (1935). AL = anterior loreal, Cs = chinshield; F = frontal, Fn = frontonasal, Fp = frontoparietal, IL = infralabial, Ip = interparietal, M = mental, N = nasal, NU = nuchal, P = parietal, Pf = prefrontal, PL = posterior loreal, Pm = postmental, Pr = preocular, Prs = presubocular, PT = primary temporal, Psl = postsupralabial, R = rostral, SL = supralabial, So = supraocular, ST = secondary temporal, TT = tertiary temporal, UPT = upper pretemporal, LPT = lower pretemporal, * = superciliary and # = postsubocular. Illustration by NAP.
FIGURE 8 in A new species of Sphenomorphus (Squamata: Scincidae) from Phu Quoc Island Vietnam with a discussion of biogeography and character state evolution in the S stellatus group
FIGURE 8. SCM analysis inferring the probability of the ancestral condition of the dorsal pattern at each node in the BEAST maximum clade credibility tree.
FIGURE 4 in A new species of Sphenomorphus (Squamata: Scincidae) from Phu Quoc Island Vietnam with a discussion of biogeography and character state evolution in the S stellatus group
FIGURE 4. Discriminant function analysis showing the separation of Sphenomorphus annamiticus, S. perylangensis, and S. phuquocensis sp. nov.
FIGURE 1 in A new species of Sphenomorphus (Squamata: Scincidae) from Phu Quoc Island Vietnam with a discussion of biogeography and character state evolution in the S stellatus group
FIGURE 1. Known distribution and localities for Sphenomorphus annamiticus, S. praesignis, S. phuquocensis sp. nov., S. preylangensis, and S. stellatus. Stars represent type localities. Peninsular Malaysia: 1 = Bukit Larut, Perak; 2 = Cameron Highlands, Pahang; 3 = Fraser's Hill, Pahang; 4 = Genting Highlands, Pahang; 5 = Gunung Tahan, Pahang; 6 = Gunung Lawit, Terengganu; 7 = Gunung Tebu, Terengganu. Thailand: 8 = Khao Wang Hip, Nakon Si Thammarat Province; 9 = Khao Soi Dao Wildlife Sanctuary, Chantaburi Province; 24 = Phu Wiang, Khon Kean Province. Cambodia: 10 = Chum Noab, Koh Kong Province; 11 = Bokor National Park, Kampot Province; 21 = Phnom Chi, Prey Lang Wildlife Sanctuary, Kampong Thom Province. Vietnam: 12 = Ma Da, Dong Nai Province; 13 = Cat Tien, Dong Nai Province; Dalat, Annam, Lam Dong Province; 15 = Thac Nham, Kon Tum Province; 16 = Buon Luoi Village, Gia Lai Province; 17 = Tram Lap Village, Gia Lai Province; 18–20 = Mang Canh Village and vicinity, Kon Tum Province; 22 = Phuc-Son, Annam (now Phuoc Son District, Quang Nam Province); 23 = K Bang, Gia Lai Province; 25 = Phu Quoc Island, Kien Giang Province.
FIGURE 7 in A new species of Sphenomorphus (Squamata: Scincidae) from Phu Quoc Island Vietnam with a discussion of biogeography and character state evolution in the S stellatus group
FIGURE 7. Ancestral ranges recovered by the DIVALIKE+J model (tree) of that analysis for species of the Sphenomorphus stellatus group.
FIGURES 1–11. Dendrothrips. Head and pronotum 1–5 in Character state variation within Dendrothrips (Thysanoptera: Thripidae) with a revision of the species from China
FIGURES 1–11. Dendrothrips. Head and pronotum 1–5: (1) latimaculatus; (2) diaspora; (3) ornatus; (4) minowai; (5) homalii. Head and thorax of magnoliae 6–7: (6) female; (7) male. (8) Head of octosparsus sp. n. Pronotum 9–11: (9) jeanneli; (10) octosparsus sp. n.; (11) stannardi.
text-fig. 41. Articulated pubes of two theropods in anterior view, illustrating different states of character 182. A, Herrerasaurus ischigualastensis', redrawn from Novas (1993). B, unnamed compsognathine from the Lower Cretaceous of Brazil; SMNK 2349 Pal. Scale bars represent 50 mm (a) and 10 mm (b). in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 41. Articulated pubes of two theropods in anterior view, illustrating different states of character 182. A, Herrerasaurus ischigualastensis', redrawn from Novas (1993). B, unnamed compsognathine from the Lower Cretaceous of Brazil; SMNK 2349 Pal. Scale bars represent 50 mm (a) and 10 mm (b).
Figure 2 in Geometric and traditional morphometrics for the assessment of character state identity: multivariate statistical analyses of character variation in the genus Arrenurus (Acari, Hydrachnidia, Arrenuridae)
Figure 2. Species of Arrenurus (Megaluracarus) included in the morphometric analyses, with cauda in posterior view: (A) Arrenurus anae; (B) Arrenurus colitus; (C) Arrenurus neoexpansus; (D) Arrenurus zitavus; (E) Arrenurus maya; (F) Arrenurus catoi; (G) Arrenurus tabascoensis; (H) Arrenurus anitahoffmannae; (I) Arrenurus urbanus; (J) Arrenurus olmeca; (K) Arrenurus costeroae. The pairs of ventroglandularia V1, V2, and V3 in (F) are indicated with arrows pointing at gland openings and setae insertions. Scale bars: 100 µm.
Figure 36. Character 74 and its postulated states. A3–A5 in Morphology-based phylogenetic analysis and classification of the family Rhinocryptidae (Aves: Passeriformes)
Figure 36. Character 74 and its postulated states. A3–A5 elements, dorsal surface, configuration: A, complete, not reduced – 74.0; B, A3 vestigial, A4 and A5 reduced – 74.1; C, A3 vestigial, A4 and A5 absent – 74.2. Stippled areas are cartilaginous tissue, non-stippled areas are calcified structures. A1/B1 elements are indicated. Syringes of (A) Myornis senilis (QCAZ 3724), (B) Eleoscytalopus indigoticus (MCP 2044), and (C) Merulaxis ater (MCP 2001) in dorsal view. Scale bars = 2 mm.
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.