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.
68
datasets available to search
ShareScore release 0.7.1
Dataset results
68 results for “taxon sampling”
Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics
1. The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. 2. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway-Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of 1) the number of taxa included in the regional phylogeny; 2) random vs. targeted sampling of species to assemble the regional species pool; 3) including only species from specific clades rather than broad sampling; 4) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and 5) using phylograms compared to chronograms. 3. We found that including more taxa in a study increases the likelihood of observing significantly non-random phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. 4. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.
Fig. 3 in Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA
Fig. 3. Concatenated mitochondrial and nuclear SSU-rDNA tree inferred from an alignment of 2333 included characters. Most likely ML tree is shown; the BI tree was the same for well-supported nodes. Node support is as in Fig 1.
Fig. 2 in Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA
Fig. 2. Nuclear SSU-rDNA tree inferred from an alignment of 1543 included characters. The most likely ML tree is shown; the BI tree was the same for well-supported nodes. Node support is as in Fig 1.
Fig. 1 in Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA
Fig. 1. Mitochondrial SSU-rDNA tree inferred from an alignment of 790 included characters. The most likely ML tree is shown; the BI tree was the same for well-supported nodes. Node support is shown as: ML bootstraps/BI posterior probability. Values ≤ 50 are shown as "-".
Taxon sampling and inferred community phylogenies: R replication code and data.
<p>1 ) Code for simulating community phylogenies:</p> <p>community_simulations_creation.R</p> <p>[taxon].gene</p> <p>[taxon].phy</p> <p>[taxon].RAxML_bestTree.tre</p> <p>[taxon].Simulate.A.Community.pl</p> <p>[taxon].Simulate.B.Community.pl</p> <p>[taxon].Simulate.C.Community.pl</p> <p>[taxon].Simulate.D.Community.pl</p> <p> </p> <p>2) R code for creating and comparing phylogenetic diversity metrics:</p> <p>simulated_metric_calculation_and_comparison.R</p> <p>empirical_metric_calculation_and_comparison.R</p> <p> </p> <p>3) R code and data for statistical analyses:</p> <p>simulated_data_analysis.R</p> <p>empirical_data_analysis.R</p> <p>simulated_interval_individual_lme_data.csv</p> <p>simulated_summary_interval_individual_lme_data.csv</p> <p>empirical_interval_individual_lme_data.csv</p> <p>empirical_summary_interval_lme_data.csv</p> <p> </p>
Fig. 24 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 24. Tlacuatzin canescens, photographed by Gerardo Ceballos in March 1995 at the ChamelaCuixmala Biosphere Reserve, Jalisco, Mexico. Specimens from southern populations (especially topotypical material from Oaxaca) are markedly grayer than this individual.
Fig. 12 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 12. Bivariate comparison of two dental proportions discussed in the text, with illustrated examples of contrasting morphologies. Closed curves delimit sets of taxa assigned to alternative states of character 57. Taxon labels: 1, Caluromys lanatus; 2, Caluromys philander; 3, Caluromysiops irrupta; 4, Chironectes minimus; 5, Didelphis albiventris; 6, Didelphis marsupialis; 7, Didelphis virginiana; 8, Glironia venusta; 9, Gracilinanus microtarsus; 10, Lestodelphys halli; 11, Lutreolina crassicaudata; 12, Marmosa canescens; 13, Marmosa lepida; 14, Marmosa mexicana; 15, Marmosa murina; 16, Marmosa robinsoni; 17, Marmosa rubra; 18, Marmosops impavidus; 19, Marmosops incanus; 20, Marmosops noctivagus; 21, Marmosops parvidens; 22, Marmosops pinheiroi; 23, Metachirus nudicaudatus; 24, Micoureus demerarae; 25, Micoureus paraguayanus; 26, Micoureus regina; 27, Monodelphis adusta; 28, Monodelphis brevicaudata; 29, Monodelphis emiliae; 30, Monodelphis theresa; 31, Philander frenata; 32, Philander mcilhennyi; 33, Philander opossum; 34, Thylamys pallidior; 35, Thylamys venustus. Other labels: MC, metacrista; PC, postprotocrista.
Fig. 20 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 20. Strict consensus of 18 maximumlikelihood trees under the bestfit model of IRBP sequence evolution, rooted to be consistent with our assumption of ingroup (didelphine) monophyly (see text). Bootstrap support values are shown below each branch. Outgroup taxa are indicated with asterisks.
Fig. 9 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 9. Oblique ventrolateral view of left ear region in Marmosops impavidus (A, MUSM 13284) and Philander mcilhennyi (B, MUSM 13299) illustrating taxonomic differences in ectotympanic suspension. Whereas the ectotympanic (ect) is suspended from the skull by attachments both to the petrosal (pet) and to the malleus (mal) in Marmosops, the ectotympanic of Philander is suspended only from the malleus (there is no attachment to the petrosal). Other abbreviations: als, alisphenoid; pro, promontorium; rtp, rostral tympanic process (of petrosal); sq, squamosal.
Fig. 2 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 2. Ventral view of rhinarium in Thylamys pallidior (A, UMMZ 156349) and Marmosa robinsoni (B, UMMZ 117236). Only a single groove is present on the ventral margin of the rhinarium to either side of the median sulcus in T. pallidior, whereas two ventrolateral grooves are present in M. robinsoni. Scale bars = 2 mm.
Fig. 5 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 5. Palatal morphology of Thylamys venustus (AMNH 261254) illustrating nomenclature for fenestrae and foramina described in the text. The maxillary dentition (C–M4) provides convenient landmarks for defining the size and position of palatal perforations. Abbreviations: if, incisive foramen; m, maxillary fenestra; mp, maxillopalatine fenestra; p, palatine fenestra; plpf, posterolateral palatal foramen.
Fig. 15 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 15. Occlusal views of right dp3 and m1 illustrating taxonomic differences in trigonid morphology of the deciduous tooth. Top, Marmosa murina (MUSM 15297) with a distinctly tricuspid (complete) dp3 trigonid. Bottom, Marmosops impavidus (MUSM 13286) with a bicuspid (incomplete) dp3 trigonid.
Fig. 16 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 16. Lingual views of right m2 and m3 illustrating taxonomic differences in entoconid size. Top, Thylamys pallidior (AMNH 262405) with a large entoconid (arrow). Bottom, Monodelphis adusta (AMNH 272781) with an indistinct entoconid (arrow).
Fig. 7 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 7. Oblique dorsolateral view of the left orbit in Thylamys venustus (A, AMNH 263562) and Monodelphis adusta (B, AMNH 272695) illustrating taxonomic differences in sutural patterns. In Thylamys (and most other didelphids), the maxillary (max) and alisphenoid (als) bones are separated by the palatine (pal), but the alisphenoid extends anteriorly across the palatine to contact the maxillary in Monodelphis. Other osteological abbreviations: fr, frontal; hp, hamular process of pterygoid; ju, jugal; la, lacrimal; par, parietal; sq, squamosal.
Fig. 11 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 11. Unworn premaxillary dentitions of Marmosops pinheiroi (A, AMNH 267341) and Lutreolina crassicaudata (B, AMNH 210422) illustrating taxonomic differences in the shape of the incisor crowns. In Marmosops and many other small didelphines, the crowns of I2–I5 are symmetrically rhomboidal, with subequal anterior (mesial) and posterior (distal) cutting edges that converge to form a sharp central apex; a distinct posterior corner (distostyle) is always present on I5. By contrast, in Lutreolina (and certain other taxa), the crowns of I2–I5 are conspicuously asymmetrical, with longer anterior than posterior cutting edges; a distinct distostyle is usually absent on I5. Scale bars = 1 mm.
Fig. 6 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 6. Ventral midcranial view of Caluromys philander (A, AMNH 267002) and Micoureus demerarae (B, AMNH 266428) illustrating taxonomic differences in palatal morphology. In caluromyines the posterior palate slopes gently ventrally, and the palatal margin is arched (concave posteriorly) without strongly projecting lateral corners; the internal nares (in) are very broad. In didelphines, however, the posterior palate is abruptly inflected ventrally and the palatal margin is moreorless straight with projecting lateral corners (arrows in lower panel); the internal nares are narrow.
Fig. 1 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 1. Strict consensus of 18 equally mostparsimonious trees resulting from a heuristic analysis of IRBP sequences by Jansa and Voss (2000). For simplicity, placental outgroups and nondidelphid marsupial ingroup taxa (Caenolestes, Dromiciops, Echymipera, Phascogale, Pseudochirops, Vombatus) are not shown. Alphabetic labels (A, B, C, etc.) serve to identify clades for which formal taxon names are either unavailable or confusing due to conflicting usages.
Fig. 4 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 4. Ventral view of rostrum in Marmosa rubra (A, MVZ 153280) and Monodelphis brevicaudata (B, AMNH 257203) illustrating taxonomic differences in premaxillary morphology. A broad, shelflike rostral process (rp) extends the suture between right and left bones well anterior to the incisors in M. rubra, but the premaxillae form only narrow alveolar rims anterior to I1 in M. brevicaudata, where the left and right bones are separated by a small tissuefilled gap (not a distinct suture).
Fig. 10 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 10. Posterior and lateral views of the occipital region in Lestodelphys halli (A, B, UWZM 22422) and Metachirus nudicaudatus (C, D, AMNH 267009). In Lestodelphys the dorsal margin of the foramen magnum (fm) is formed by the excoccipitals (exo) and the supraoccipital (sup), but in adult specimens of Metachirus the right and left exocciptals are joined to exclude the supraoccipital from the dorsal margin of the foramen. Another conspicuous taxonomic difference illustrated in these views concerns the parocciptal process (pp), which is a small, inconspicuous bony mass adnate to the pars mastoideus (mas) of the petrosal in Lestodelphys. By contrast, the paroccipital process of Metachirus is much larger and projects almost straight ventrally. Other abbreviations: als, alisphenoid tympanic wing; par, parietal; sq, squamosal.
Fig. 22 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 22. Alternative resolutions of the ''other Marmosa'' + Micoureus clade based on parsimony analysis of the combined (nonmolecular + IRBP2) data. Among the 34 equally mostparsimonious trees whose strict consensus is illustrated in figure 21, resolution A is represented by 10 trees, B by 4 trees, C by 10 trees, D by 6 trees, and E by 4 trees.
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.