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.
4,566
datasets available to search
ShareScore release 0.9.0
Dataset results
4,566 results for “marker”
FIG. 4 in Phylogeny of the genus Pinnixa White, 1846 (Crustacea, Brachyura, Pinnotheridae) and allies inferred from mitochondrial and nuclear molecular markers, with generic reassignment of twenty-one species
FIG. 4. — Reproduced thumbnail sketches of male gonopods and gonopodal plates on lost USNM specimens of Glassella faxoni (Rathbun, 1918) n. comb. (A-C), by R. H. Gore, 1978-1979; G. faxoni n. comb. (D), und Glassella vanderhorsti (Rathbun, 1922) n. comb.; (E, F) by D. L. Felder, 1979-1982. A, left gonopod, pleonal surface, paratype, USNM 23436; B, left gonopod, pleonal surface, holotype, USNM 7639; C, gonopods and gonopodal plate, pleonal surface, holotype USNM 7639; D, gonopods and gonopodal plate, pleonal surface, holotype, USNM 7639; E, gonopodal plate, pleonal surface, topotypic material, USNM 56903; F, gonopods and gonopodal plate, pleonal surface, topotypic material, USNM 56903.
FIG. 1 in Phylogeny of the genus Pinnixa White, 1846 (Crustacea, Brachyura, Pinnotheridae) and allies inferred from mitochondrial and nuclear molecular markers, with generic reassignment of twenty-one species
FIG. 1. — Phylogeny for species of superfamily Pinnotheroidea De Haan, 1833, emphasis on genus Pinnixa White, 1846 s.l. inferred from Randomized Accelerated Maximum Likelihood (RAxML) analysis of a 1445 bp long fragment concatenated from the mitochondrial complex 16S/tRNA-Leu/ NADH1 (776 bp), the mitochondrial 12S rRNA gene (340 bp) and the nuclear gene for the histone 3 subunit (327 bp). Bootstrap support values are shown at the nodes when higher than 50%. Collection number follows the species name to identify samples. For samples in the subfamily Pinnixinae Števčić, 2005, abbreviations indicating geographic origin are defined in "Materials and Methods". Species name combinations as shown are prior to revisions in present paper. Abbreviations as in Material and Methods.
FIG. 2 in Phylogeny of the genus Pinnixa White, 1846 (Crustacea, Brachyura, Pinnotheridae) and allies inferred from mitochondrial and nuclear molecular markers, with generic reassignment of twenty-one species
FIG. 2. — Morphological characters of the type species of Pinnixa White, 1846 s.s., P. cylindrica (Say, 1818), along with those for five molecularly segregated genera formerly treated in Pinnixa s.l.: A-D, Pinnixa cylindrica: A, male dorsal view; B, male cheliped; C, third maxilliped (adapted from Rathbun 1918:160 fig. 99a); D, male pleon; E-G: Glassella costaricana (Wicksten, 1982): E, female holotype dorsal view; F, female cheliped; G, third maxilliped (adapted from Campos & Wicksten 1997: fig. 1, fig. 2c, a, with permission from Allen Press); H, I, Glassella faxoni (Rathbun, 1918) n. comb.: H, third maxilliped; I, male pleon (adapted from Rathbun 1918:133 fig. 77b, a); J-M: Rathbunixa sayana (Stimpson, 1960) n. comb.: J, male dorsal view; K, male cheliped; L, third maxilliped; M, male pleon (L, M adapted from Rathbun 1918:158 fig. 98a, b); N-Q: Sayixa monodactyla (Say, 1818) n. comb., male (ULLZ 8713, Fort Pierce, FL, USA); N, dorsal view; O, cheliped; P, third maxilliped; Q, pleon; R, T, U, Scleroplax granulata Rathbun, 1893; R, female carapace and pereopods 2-5; T, third maxilliped; U, male pleon (R, T adapted from Campos 2006:fig. 1a-c, with permission from Magnolia Press; U, adapted from Rathbun 1918:171 fig. 109a); S, Scleroplax littoralis (Holmes, 1894) n. comb., female and male chelipeds (adapted from Rathbun 1918:146 fig. 89a, b); V-Y, Tubicolixa chaetopterana (Stimpson, 1860) n. comb.: V, male dorsal view; W, female and male chelipeds; X, third maxilliped; Y, male pleon (X, Y, adapted from Rathbun 1918:152 fig. 94a, b).
Data for "Accurate Estimation of Marker-Associated Genetic Variance and Heritability in Complex Trait Analyses"
<p>This data is associated with the manuscript titled "Accurate Estimation of Marker-Associated Genetic Variance and Heritability in Complex Trait Analyses".</p> <p>9 files are contained. These files contain the summary statistics from the linear mixed model analyses in the simulations</p> <p>data_fig1a - all data for recreating Figure 1A</p> <p>data_fig1b - all data for recreating Figure 1B</p> <p>data_fig1c - all data for recreating Figure 1C</p> <p>data_fig1d - all data for recreating Figure 1D</p> <p>data_fig1e - all data for recreating Figure 1E</p> <p>data_fig1f - all data for recreating Figure 1F</p> <p>data_fig2 - all data for recreating Figure 2</p> <p>data_fig3 - all data for recreating Figure 3</p> <p>data_fig4 - all data for recreating Figure 4</p>
Data from: Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers
Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, Cinachyra Sollas, 1886, Cinachyrella Wilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers
<p>Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received infuences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds difer considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African infuence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confrm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.</p>
Optical topography of rough surfaces using vortex localization of fluorescent markers_experimental dataset
<p>This file contains the raw unprocessed experimental data for the results published in Petr Schovánek et al., Optical topography of rough surfaces using vortex localization of fluorescent markers, Optics Letters Vol. 45, Issue 16, pp. 4468-4471 (2020).</p>
Increased immune marker variance in a population of invasive birds
<p>Immunity and parasites have been linked to the success of invasive species. Especially lower parasite burden in invasive populations has been suggested to enable a general downregulation of immune investment (Enemy Release and Evolution of Increased Competitive Ability Hypotheses). Simultaneously, keeping high immune competence towards potentially newly acquired parasites in the invasive range is essential to allow population growth. To investigate the variation of immune effectors of invasive species, we compared the mean and variance of multiple immune effectors in the context of parasite prevalence in an invasive and a native Egyptian goose (Alopochen aegyptiacus) population. Three of ten immune effectors measured showed higher variance in the invasive population. Mean levels were higher in the invasive population for three effectors but lower for eosinophil granulocytes. Parasite prevalence depended on the parasite taxa investigated. We suggest that variation of specific immune effectors, which may be important for invasion success, may lead to higher variance and enable invasive species to reduce the overall physiological cost of immunity while maintaining the ability to efficiently defend against novel parasites encountered.</p>
Genomic SSR and EST-SSR markers for phylogenetic and pedigree reconstruction: A comparison in sea buckthorn
<p>Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non-model species. We identified SSRs from expressed sequence tags (EST-SSRs) and whole genome sequences (gSSRs), by analyzing the transcriptome and genome of the Mongolian sea buckthorn (<i>Hippophae rhamnoides</i> subsp. <i>Mongolica</i>) cultivar 'Sunny'<i>.</i> Using the same number of loci, EST-SSRs showed higher transferability to <i>Hippophae </i>than gSSRs, and phylogenetic trees based on EST-SSRs demonstrated higher resolution for classifying <i>Hippophae </i>species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST-SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST-SSRs and gSSRs would provide insight into the trade-off between differentiation and polymorphism in marker selection for breeding programs.</p>
Reappraising plastid markers of the red algae for phylogenetic community ecology in the gnomic era
<p>Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for phylogenetic community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of the phycological community has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). As a proof-of-concept study, we leverage this resource to develop and apply a phylogenomic strategy to seek candidate plastid markers that best capture the identity of component species in an eDNA metabarcoding study. We ranked the core plastid genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies and found that the most widely used marker, <i>rbc</i>L,<i> </i>is not necessarily the optimal marker, while more informative markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of these, <i>rpoC1</i>, for a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the <i>rpoC1</i> primers will be useful to the phycological community for eDNA metabarcoding of the red algae.</p>
Data from: Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery
Premise of the study: We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. Methods and Results: A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus. Conclusions: This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.
Data from: Diversification at high latitudes: speciation of buntings in the genus Plectrophenax inferred from mitochondrial and nuclear markers
High-latitude diversification is a process characterized by speciation and extinction due to climatically driven vicariance and dispersal events. McKay's buntings (Plectrophenax hyperboreus) are high-latitude island endemic songbirds, and their global range is restricted to Beringia. Snow buntings (P. nivalis), their closest relatives, are distributed throughout the Holarctic, breeding in available habitat surrounding the island range of McKay's buntings. We sequenced 1123 base pairs of mitochondrial DNA for 40 individuals of each species and analyzed a total of 913 AFLPs for 57 individuals. Both marker types suggested weak but significant genetic differentiation. Analysis of sequence data indicated divergence occurring when the current breeding range of McKay's buntings was a hill on the Beringian steppe (~18,400 to ~73,700 years before present), suggesting that snow buntings were restricted to lower latitudes by ice sheets. Ancestral effective population size estimates indicate a founder event in McKay's buntings followed by an expansion and then a reduction in effective size. Rising sea levels and asymmetric hybridization from McKay's buntings into the postglacially-colonizing population of snow buntings could account for this reduction. Reproductive isolation is likely maintained through differential arrival dates on breeding grounds and the high breeding density of McKay's buntings. This recent, high-latitude divergence best fits a model of founder event speciation driven by vicariance and oscillations in habitat due to climate change.
Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
Data from: Does GST underestimate genetic differentiation from marker data?
The widely applied genetic differentiation statistics FST and GST have recently been criticized for underestimating differentiation when applied to highly polymorphic markers such as microsatellites. New statistics claimed to be unaffected by marker polymorphisms have been proposed and advocated to replace the traditional FST and GST. This study shows that GST gives accurate estimates and underestimates of differentiation when demographic factors are more and less important than mutations, respectively. In the former case, all markers, regardless of diversity (HS), have the same GST value in expectation and thus give replicated estimates of differentiation. In the latter case, markers of higher HS have lower GST values, resulting in a negative, roughly linear correlation between GST and HS across loci. I propose that the correlation coefficient between GST and HS across loci, rGH, can be used to distinguish the two cases and to detect mutational effects on GST. A highly negative and significant rGH, when coupled with highly variable GST values among loci, would reveal that marker GST values are affected substantially by mutations and marker diversity, underestimate population differentiation, and are not comparable among studies, species and markers. Simulated and empirical data sets are used to check the power and statistical behaviour, and to demonstrate the usefulness of the correlation analysis.
Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps
<p>Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data. Concatenation analyses consistently place Mymaridae and Trichogrammatidae sister to remaining Chalcidoidea. However, our coalescent analyses provide a different hypothesis with a grouping of (Mymaridae (((Trichogrammatidae, Eulophidae), (Encyrtidae, Aphelinidae)), remaining Chalcidoidea)). This hypothesis complicates our hypothesis of egg parasitism as being ancestral in Chalcidoidea. At the deeper nodes, the results uncovered a wide spectrum of gene discordance in the transcriptomic markers and identified a strong signal of functional bias in genes supporting alternative phylogenies. The basal nodes of the phylogeny are thus strongly influenced by biased support from different functional gene complexes. Shallower nodes showed similar gene discordance, but without strong functional bias. Understanding and identifying mechanisms that result in gene tree discordance may be beneficial and even essential for sorting out backbone relationships, especially for groups that have undergone extremely rapid radiation.</p>
Data from: De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing.
Recent developments in sequencing technologies and bioinformatics analyses provide an unprecedented opportunity for cost and time effective high quality microsatellite marker discovery in non-model organisms for which no genomic information is available. Here, we use shotgun pyrosequencing of a microsatellite-enriched library to develop, for the first time, microsatellite markers for Alnus glutinosa, a keystone tree species of European riparian woodland communities. From a total of 17,855 short sequences, we identified 590 perfect microsatellites from which 392 had designed primers. A subset of 48 loci were tested for amplification, twelve of which were polymorphic in A. glutinosa. These twelve loci were successfully co-amplified in a single multiplex PCR experiment and validated for population genetics applications. In addition, ten and eight of these microsatellites were found to be transferable to the related A. incana and A. cordata species. The developed multiplex of 12 microsatellite markers therefore provides new opportunities for experimental evolutionary and forest genetics research in Alnus.
Data from: Identifying genetic markers for a range of phylogenetic utility–from species to family level
Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
Figure 1 from: Merkhan M, Mohammad J, Fathi Z, Younis Z, Mahmood S, Mohammed M (2021) Silent hyperlipidaemia modulated vascular endothelial markers. Pharmacia 68(2): 479-484. https://doi.org/10.3897/pharmacia.68.e67959
Figure 1 Lipid profile is higher in patient group compared to healthy individuals. LDL=low density lipoprotein, VLDL= very low-density lipoprotein. Data expressed as mean±SD, *p<0.001.
Figure 2 from: Merkhan M, Mohammad J, Fathi Z, Younis Z, Mahmood S, Mohammed M (2021) Silent hyperlipidaemia modulated vascular endothelial markers. Pharmacia 68(2): 479-484. https://doi.org/10.3897/pharmacia.68.e67959
Figure 2 Hyperlipidaemia associated with modulation of vascular endothelial markers. Comparison between result analysed from serum of healthy and patient group indicated that Hyperlipidaemia reduced arylesterase (AE) and nitric oxide (NO) together with increase peroxidae (PO), arginase (AG), metalloendopeptidase (MEP), myeloperoxidase (MPO), and peroxynitrite (PN). Data expressed as mean±SD, *p<0.001.
New set of microsatellite markers for the great-billed seed-finch (Sporophila maximiliani – Passeriformes: Thraupidae): tools for inspection and conservation
<p>The Thraupidae family is one of the most wanted by bird breeders in Brazil due to its diverse, colorful and melodious singers as representatives. The Great-billed Seed-finch, Sporophila maximiliani, is the only representative of the genus Sporophila considered critically endangered in Brazil. Due to the demands of environmental agencies and of conservation programs, there is a need to increase the number of molecular markers available for the genus and specially for S.maximiliani. Therefore, this work aimed to provide a new set of microsatellite markers for S. maximiliani in order to help bird breeders and environmental agencies on fulfilling its demands as well as contributing with extra genetics tools for conservation programs of the Great-billed Seed-finch. Of the 30 markers developed, 25 successfully amplified and 22 were polymorphic. Annealing temperature varied from 52 to 64°C, number of alleles from two to 13 and the medium allele richness was 7.25 and medium expected and observed heterozygosity was, respectively, 0.812 and 0.661. The identity estimate was 8.54x10 -27 and all the other probabilities of non-exclusion (sib-identity, parent pair and first-parent) were <0.001, indicating that this set of microsatellite markers have high genetic variability and high power of individual genetic differentiation for S.maximiliani. Therefore, this work increases the options of molecular markers to be used on inspection for environmental agencies and for conservation programs on analyzing genetic variability and population studies for the Great-billed Seed-finch.</p>
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.