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.
200
datasets available to search
ShareScore release 0.7.1
Dataset results
200 results for “species delineation”
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Figure 2. Salopella australis displaying parallel parent axes dichotomising into much shorter daughter axes that are terminated with elongate sporangia, delineated with a in Early land plants from the Lower Devonian of central Victoria, Australia, including a new species of Salopella
Figure 2. Salopella australis displaying parallel parent axes dichotomising into much shorter daughter axes that are terminated with elongate sporangia, delineated with a constriction just above dark sporogeneous region. All from Wilson Creek Shale on Frenchmans Spur track, 10 km west of Matlock. A, erect parent axes parallel to each other, dichotomising into two elongate sporangia from Wilson Creek Shale. Re-photographed here; originally published in Tims and Chambers (1984: pl. 32, fig. 4) and Tims (1980: fig. 4.1.9). Specimen NMV P50014. B, forked dichotomy terminated by sporangia from Wilson Creek Shale. And to the right hand side of the forked axis is another long axis, which based on its orientation may also be part of the same plant. Constriction at arrow, lower arrow at dichotomy and double arrow at two aligned axes. Specimen NMV P33219. C, close-up of fructification in A, sporangia barely extend beyond the confines of their subtending axes, with slight constriction present above sporogeneous region (at arrow). Specimen NMV P50014. D, E, holotype, part and counterpart. On part, constriction at arrow in sporangium. On counterpart, both parent axes are parallel to each other (at dotted arrow). Re-photographed here, originally published in Tims and Chambers (1984: pl. 32, figs. 1, 2). Specimens NMV P50008.1 and NMV P50008.2, respectively. F, Gen. et sp. indet. – short daughter axes terminated in elongate sporangia. The cortex may be absent from subtending axes, with only the central line visible. The lack of cortex prevents assigning to S. australis as width of subtending axis to sporangial width is required. Originally photographed by Tims (1980: fig. 4.1.13). Specimen NMV P50010.2. G, S. australis, with two short daughter axes, with constriction at arrow of the sporangium, which is the same width as its subtending axis. Specimen NMV P202886.
Fig. 1 in Comparative molecular and morphological species delineation of Halammohydra Remane, 1927 (Hydrozoa)-with the description of four new species
Fig. 1 Phylogenetic tree of all three genes concatenated with support values of BI/ML (posterior probability/bootstrap value). Nodes with an * have a support of 100/100. Some clusters are collapsed. Sum-
Fig. 5 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 5. Phylogenetic tree based on analysis of mitochondrial COI sequences of the Sarcocystidae including the new Sarcocystis sp. examined in this study (black symbols). Other taxa of the Apicomplexa served as root. Evolutionary history was inferred by the Maximum Likelihood (ML) method based on the TamuraNei model, whereby 619 positions were included in the final data set. All positions with less than 95% site coverage were eliminated; that is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. Bootstrap percentages (1000 iterations) are shown next to branches. COI sequences E357-13 and E120-13 (not shown in the tree) are available at GenBank (MN732561 and MN732562, respectively).
Fig. 2 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 2. Ultrastructure of S. scandentiborneensis sp. nov. Note, due to ethanol-fixation some ultrastructural details are poorly resolved (e.g. membranes). A) Longitudinal section through the same sample as in Fig. 1C, showing a gross view of the sarcocyst and its villous protrusions (VP) that are sectioned in different orientations. The inset shows a cross section through various VP that reveals the arrangement of microtubules in their inner core; while in this case 16 microtubules are visible (asterisks), sections through more apical portions of the VP showed lower numbers. B) Longitudinal section through the fingerlike VPs that appear to be anchored in the ground substance (arrow) by microtubules (asterisks) that extend into each protrusion; note the electron-dense, U-shaped structure at each tip of the protrusions (arrowheads) and the apparently serrated surface of the VP (flat arrowheads). The inset shows a higher magnification of the apical part of a single VP with the typical U-shaped apex (asterisk), which appears to be connected with the host cell through an electronlucent contact zone (white arrowheads); interestingly, the protrusion appears fenestrated (also visible in the main image) possessing thorn-like structures (black arrows; the white arrow indicates a crosssectional view) that could be responsible for the serration visible at lower magnification. CZ, cystozoites; HC, host cell; VP, villous protrusion.
Fig. 1 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 1. Light microscopy of Sarcocystis scandentiborneensis sp. nov. A and B, Haematoxylin & Eosinstained histological sections of striated musculature; C and D, Richardson's dye-stained 1.0 μm thin sections of sarcocysts. A) Tissue section of laryngeal muscle with various sarcocysts in cross section (asterisks), indicating a relatively high density of cysts in this part of musculature. B) Longitudinal section through a sarcocyst, showing a cigar-shaped appearance; however, isolated native sarcocysts, which were not available, may look different. C) Part of a longitudinal section through the tip of a sarcocyst, note the very thin ground substance (arrows) and the fine septae extending into the interior of the cyst (arrowheads); cystozoites (CZ) were loosely scattered within chambers while metrocytes were rarely seen, indicating maturity of the cyst; bars indicate the variable thickness of the cyst wall: the wall was thinner in regions where the villous protrusions were bent (right bar); note that the intense staining at the interface between host cell (HC) and parasite is part of the host cell. D) Cross-section through a sarcocyst showing cystozoites and the cyst wall (bar) including its thin ground substance (arrows).
Fig. 4 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 4. Mapping (to the Toxoplasma gondii reference molecule M97703) of frequencies (%) of base pair changes observed in sequence comparisons of nu clear 18S rDNA within the new Sarcocystis sp. from treeshrews (intraspecific variation: isolates E364–13 versus E357–13) and between the new species and Sarcocystis zuoi and/or S. clethrionomyelaphis (interspecific variation: E364–13 versus S. zuoi/clethrionomyelaphis). Results were combined for the two latter species to simplify the graph. Here, 87.2% of 2118 alignment positions showed moderate to high levels of consistency, while sections of ambiguous alignment did not relate to the species under investigation. Due to gaps in the alignment, not all of the observed nt changes could be mapped to a homologous position of the reference molecule (i.e., 7 out of 24 bp changes in intraspecific comparison; 33 out of 74 bp changes in interspecific comparison), in which case the position of each nt relative to the helix was inferred from neighboring nt for which such position was known. Gaps were mainly due to insertions in helices V2, V4, and V9 rendering E357-13/E364-13 longer than the sequence of T. gondii. The percentage of parsimony-informative (pi) bp changes per helix is shown for helices V1, V2, V4, V7, and V9 above each column. Also shown is the ratio of transitions versus transversions (Ti/Tv) for selected helices.
Figure 7 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 7. The phylogeny most strongly supported by our electrophoretic data. Note that C. reimanni and C. novaeguineae could not be separated electrophoretically, but we retain them as separate on the basis of morphological evidence (Philippen & Grossman, 1990; Rhodin, 1994a). The symbols + show the progressive development of robusticity in both the skull and triturating surfaces.
Figure 6 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 6. The best-supported phylogeny for the Chelodina prior to the present electrophoretic study (Burbidge et al., 1974; Rhodin & Mittermeier, 1976; Georges & Adams, 1992; Rhodin, 1994a,b). The root was chosen on the basis of evidence presented by Georges & Adams (1992), Seddon et al. (1997) and Georges et al. (1998). This phylogeny serves as the working hypotheses against which to compare our data. Only those taxa we regard to be species are included.
Figure 2 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 2. Principal co-ordinates analysis applied to a matrix of Roger's D genetic distances between all individuals of Chelodina expansa. The plot shows a degree of differentiation between coastal Queensland forms (Albert River in the south to Fitzroy–Dawson River in the north, including Fraser Island) (O) and those of the Murray-Darling system (•), but these differences have not moved to fixation at any locus (45 loci).
Figure 3 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 3. Principal co-ordinates analysis applied to a matrix of Roger's D genetic distances between all individuals of Chelodina rugosa (Queensland form) (O), C. rugosa (Northern Territory form) (Z), C. siebenrocki (•), Chelodina burrungandjii (O) and an undescribed form from the Kimberley plateau of Western Australia (Ɨ). A hybrid between Chelodina burrungandjii and C. rugosa (Northern Territory form) is included (). Three groups are evident. Chelodina burrungandjii and the undescribed form from the Kimberley plateau are undifferentiated and probably represent a single taxon. Chelodina seibenrocki and the Queensland form of C. rugosa are undifferentiated, and also probably represent a single taxon. The Northern Territory form of C. rugosa represents the third group. These three groups differ each by only one fixed difference.
GapA, RecA and DnaX sequences used for species delineation and phylogenetic analysis
<p>Survey of soft rot Pectobacteriaceae along a river stream highlights various ecological behaviour among species: GapA, RecA and DnaX sequences used for species delineation and phylogenetic analysis (fasta file format).</p>
Data from: When less is more and more is less: the impact of sampling effort on species delineation
Taxonomy is the very first step of most biodiversity studies, but how confident can we be in the taxonomic-systematic exercise? One may hypothesise that the more material, the better the taxonomic delineation, because the more accurate the description of morphological variability. As rarefaction curves assess the degree of knowledge on taxonomic diversity through sampling effort, we aim to test the impact of sampling effort on species delineation by subsampling a given assemblage. To do so, we use an abundant and morphologically diverse conodont fossil record. Within the assemblage, we first recognize four well established morphospecies but about 80% of the specimens share diagnostic characters of these morphospecies. We quantify these diagnostic characters on the sample using geometric morphometrics, and assess the number of morphometric groups, i.e. morphospecies, using ordination and cluster analyses. Then we gradually subsample the assemblage in two ways (randomly and by mimicking taxonomist work) and redo the 'ordination + clustering' protocol to appraise the evolution of the number of clusters related to sampling effort. We observe the number of delineated morphospecies decreasing when increasing the number of specimens, whatever the subsampling method, resulting mostly in less morphospecies than expected. Such rather counter-intuitive influence of sampling effort on species delineation highlights the complexity of taxonomical work. This indicates that new morphotaxa should not be erected based on small samples, and encourages researchers to largely illustrate, measure, and quantitatively compare their material to better constrain the morphological variability of a clade, and so to better characterize and delineate morphospecies. --
Data from: Delineating seagrass species in the genera Halodule and Halophila from Tanzanian coastal waters using ITS and rbcL DNA barcoding
<p>The seagrass species in <em>Halodule</em> and <em>Halophila</em> may for several reasons be considered as taxonomic complexes. They show close evolutionary relationships, morphological plasticity, and share similar features making misidentifications likely when morphological identification is applied. In Tanzanian coastal waters, there is some uncertainty about the identity of members of <em>Halodule</em>, particularly the existence of <em>Halodule wrightii</em> and the species composition of the <em>Halophila ovalis</em> complex. This study used morphology as well as internal transcribed spacer (ITS1 and ITS2) and ribulose-bisphosphate carboxylase (rbcL) DNA barcoding to identify species of <em>Halodule</em> and <em>Halophila</em>. Seagrass samples were collected during low spring tides, from Tanzania's coastal waters of Tanga, Dar es Salaam, Mtwara, Mafia Island, and Unguja Island, from August 2020 to February 2022. Morphological diagnosis, phylogenetic analysis, and evolutionary divergences inferred from the ITS gene supported the identification of five species, namely <em>Halophila ovalis</em>, <em>H. minor,</em> and <em>H. stipulacea</em>, with the first two forming the <em>H. ovalis</em> complex; as well as <em>Halodule uninervis</em> and <em>H. pinifolia</em>. It is the first time that <em>H. pinifolia</em> is reported in Tanzania. This is the first study reporting the delineation of seagrass species in East African coastal waters using DNA barcoding coupled with morphology.</p>
Comparative molecular and morphological species delineation of Halammohydra Remane, 1927 (Hydrozoa) – with description of four new species
<p><span>Whereas most cnidarians are macrofaunal, a few microscopic lineages have evolved and some of them inhabit marine sediments. The meiofaunal genus with the most species is <em>Halammohydra</em>, comprising nine nominal species. Species are described with high intraspecific variability in e.g., number of tentacles and statocysts and the shape and length of tentacles and body, complicating morphological identification to species level. Additionally, there is not much molecular data available. This study aims to revise already described species with morphological and molecular methods, as well as, to delineate potential new species answering questions about their geographical distribution. For this, specimens were sampled at 16 locations in the Northwest Atlantic and two localities in the East Atlantic, documented with light microscopy and fixed individually for sequencing (16S, 18S and CO1). Herewith morphological characters were linked to a specific sequence, enabling testing of character variation within one molecular phylogenetic group. Phylogenetic analyses were conducted (Bayesian Interference and Maximum Likelihood) in combination with species delimitation tests (ABGD, GMYC and bPTP). Four already described species were identified in the data sets, and all of these were found at multiple localities. Four new species are described. Overall, the combined molecular and morphological data acquisition revealed multiple new species and a high degree of sympatry in <em>Halammohydra</em>. This, together with the confirmed excessive intraspecific variation in morphological traits, underlines the necessity of molecular sequencing for taxonomy and species identification of <em>Halammohydra</em>. </span></p>
Data from: Delineating seagrass species in the genera Halodule and Halophila from Tanzanian coastal waters using ITS and rbcL DNA barcoding
Open the record for dataset details and reuse information.
Data from: When less is more and more is less: the impact of sampling effort on species delineation
Open the record for dataset details and reuse information.
Comparative molecular and morphological species delineation of Halammohydra Remane, 1927 (Hydrozoa) – with description of four new species
Open the record for dataset details and reuse information.
Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock
Open the record for dataset details and reuse information.
FIGURE 8. Branch containing Desmognathus quadramaculatus, D. marmoratus and D in Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades
FIGURE 8. Branch containing Desmognathus quadramaculatus, D. marmoratus and D. folkertsi pruned from Bayesian majority-rule consensus phylogram, diamonds represent posterior probabilities> 0.90. Numbers following species names in parenthesis represent population sample numbers.
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.