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.
353
datasets available to search
ShareScore release 0.9.0
Dataset results
353 results for “Molecular markers”
FIGURE 12 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 12. Austinixa artankeri sp. nov.; A, male, cw 8.9 mm, Panama Caribbean (UF 18950, photograph from A. Anker); B, ovigerous female, cw 6.8 mm, Panama Caribbean (ULLZ 13336); C, female, Panama Caribbean (ULLZ 13334). Austinixa roblesi sp. nov.; D, male, cw 9.2 mm, Belize (ULLZ 12114); E, ovigerous female, cw 7.8 mm, Panama Caribbean (ULLZ 13335); F, ovigerous female, cw 11.1 mm, Belize (ULLZ 12114). Austinixa cuestai sp. nov.; G, male, cw 7.7 mm, Panama Pacific (USNM1552956); H, male, cw 11.1 mm, Panama Pacific (USNM 1552956); I, female, cw 8.5 mm, Panama Pacific (USNM 1552957); J, ovigerous female, cw 10.7 mm, Panama Pacific (USNM 1552958) (photographs from J. Scioli).
FIGURE 8 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 8. Austinixa roblesi sp. nov.; A, B, D–G, male paratype, cw 9.0 mm (USNM 1558340); C, H, I, male holotype, cw 9.9 mm (USNM 1558341); both from Dangriga, Belize. A, carapace, chelipeds, and right ambulatory appendages, dorsal; B, carapace frontal region, from anterior; C. third maxilliped, external; D, right chela, internal, setae not shown; E, right pereopod 4, dorsal; F, right pereopod 5, dorsal; G, male pleon; H, left first gonopod tip, pleonal surface; I left first gonopod tip, sternal surface. Scale bars = 1.0 mm.
FIGURE 4 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 4. Austinixa artankeri sp. nov.; male holotype, cw 7.6 mm (USNM 1558334), Bocas del Toro, Caribbean coast of Panama. A, carapace and right appendages, dorsal; B, carapace frontal region, from anterior; C, left third maxilliped, external; D, right chela, internal; E, right pereopod 2, dorsal; F, right pereopod 3, dorsal; G, right pereopod 4, dorsal; H, right pereopod 4 setae not shown, dorsal; I, right pereopod 4, ventral; J. right pereopod 5, dorsal. Scale bars = 1.0 mm.
FIGURE 7 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 7. Austinixa cuestai sp. nov.; A–C, male paratype, cw 8.3 mm (ULLZ 5566); D–F ovigerous female paratype, cw 8.3 mm (ULLZ 5566); both from Nagualapa, Pacific coast of Nicaragua. A, male pleon; B, left first gonopod, sternal surface; C, left first gonopod tip, pleonal surface; D, right cheliped, internal; E, right cheliped, external; F, female pleon. Scale bars = 1.0 mm (A, B, D–F), 0.5 mm (C).
FIGURE 11 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 11. Austinixa felipensis; A–C, male, cw 12.3 mm (ULLZ 5556); D–F, female cw 10.6 mm, both from San Felipe, Baja California, Mexico. A, male pleon; B, right first gonopod, sternal surface; C, right first gonopod tip, pleonal surface; D, left chela, external; E, left chela, internal. Scale bars = 1.0 mm (A, B, D–F), 0.5 mm (C).
FIGURE 9 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 9. Austinixa roblesi sp. nov.; A–D, ovigerous female paratype, cw 9.8 mm (USNM 1558340); E, ovigerous female paratype, cw 9.4 mm (ULLZ 12115); F, female paratype, cw 6.6 mm (ULLZ 13143); all from Dangriga, Belize. A, carapace, dorsal; B, enlarged right side of carapace, dorsal; C, carapace frontal region, from anterior; D, right chela, internal; E, left chela, dorsal, F, female pleon. Scale bars = 1.5 mm (A), 1.0 mm (B–F).
FIGURE 5 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 5. Austinixa artankeri sp. nov.; A, male paratype, cw 7.3 mm (UF 18916); B, male paratype, cw 8.5 mm (ULLZ 13732); C, D, male paratype, cw 6.2 mm (ULLZ 13731); E, ovigerous female paratype, cw 8.5 mm (UF 18928); F, female paratype, cw 8.8 mm (UF 18950); G, ovigerous female paratype, cw 9.0 mm (USNM 1558331); H, ovigerous female paratype, cw 5.8 mm (ULLZ 13644), all from Bocas del Toro, Caribbean coast of Panama. A, right chela, internal, setae not shown; B, male pleon; C, D, left first gonopod, pleonal surface, entire and enlarged tip; E, right chela, internal, setae not shown; left chela, internal, setae not shown. Scale bars = 1.0 mm (A, B, E–H), 0.5 mm (C), 0.25 mm (D).
FIGURE 3 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 3. Distribution of the species of Austinixa Heard & Manning, 1997. In most cases, latitudinal ranges are shown. For A. cristata, the latitudinal range shown corresponds to the distribution on the Atlantic coast only. Specific locations are shown for records of A. cristata in the Gulf of Mexico, as well as for A. bragantina and three undescribed species (symbols as shown in legend). Only A. bragantina and A. leptodactyla were not included in the present phylogenetic analyses.
FIGURE 2 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 2. Phylogeny of Pinnotheroidea, with emphasis on Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of concatenated 1415 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 complex (705 bp), the mitochondrial 12S rRNA gene (293 bp) and nuclear histone 3 subunit (328 bp). Maximum Likelihood (ML) bootstrap, Bayesian (BAY) posterior probabilities and maximum parsimony (MP) bootstrap values are shown, in order ML/BAY/MP. "–" indicates a value lower than 50%. When all three values are the same, only one number is shown. If values are lower than 50% for all three, no number is shown. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations). Modified from Palacios Theil et al. (2016) and generic assignments of some species of Pinnixa updated according to Palacios Theil & Felder (2020)
FIGURE 1 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 1. Consensus tree for Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of 821 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 gene complex. Bootstrap values higher than 50% indicated at internal nodes. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations).
Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.
................................................................................................................................................. Fig. 3. SDSPAGE analysis of total bacterial protein extracts of the four roe deer isolates as well as other Bartonella species. Extracts of total bacterial protein were separated by SDSPAGE and stained with Coomassie brilliant blue. Lanes: M, molecular mass markers; 1, R1T; 2, R3; 3, R4; 4, R6; 5, Bartonella henselae; 6, Bartonella quintana; 7, Bartonella bacilliformis; 8, Bartonella elizabethae; 9, Bartonella clarridgeiae; 10, Bartonella alsatica; 11, Bartonella tribocorum; 12, Bartonella grahamii. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 3. SDSPAGE analysis of total bacterial protein extracts of the four roe deer isolates as well as other Bartonella species. Extracts of total bacterial protein were separated by SDSPAGE and stained with Coomassie brilliant blue. Lanes: M, molecular mass markers; 1, R1T; 2, R3; 3, R4; 4, R6; 5, Bartonella henselae; 6, Bartonella quintana; 7, Bartonella bacilliformis; 8, Bartonella elizabethae; 9, Bartonella clarridgeiae; 10, Bartonella alsatica; 11, Bartonella tribocorum; 12, Bartonella grahamii.
Data from: Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers
An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.
Data from: Is telomere length a molecular marker of past thermal stress in wild fish?
Telomeres protect eukaryotic chromosomes; variation in telomere length has been linked (primarily in homoeothermic animals) to variation in stress, cellular ageing and disease risk. Moreover, telomeres have been suggested to function as biomarker for quantifying past environmental stress, but studies in wild animals remain rare. Environmental stress, such as extreme environmental temperatures in poikilothermic animals, may result in oxidative stress that accelerates telomere attrition. However, growth, which may depend on temperature, can also contribute to telomere attrition. To test for associations between multitissue telomere length and past water temperature while accounting for the previous individual growth, we used quantitative PCR to analyse samples from 112 young-of-the-year brown trout from 10 natural rivers with average water temperature differences of up to 6°C (and an absolute maximum of 23°C). We found negative associations between relative telomere length (RTL) and both average river temperature and individual body size. We found no indication of RTL–temperature association differences among six tissues, but we did find indications for differences among the tissues for associations between RTL and body size; size trends, albeit nonsignificant in their differences, were strongest in muscle and weakest in fin. Although causal relationships among temperature, growth, oxidative stress, and cross-sectional telomere length remain largely unknown, our results indicate that telomere-length variation in a poikilothermic wild animal is associated with both past temperature and growth.
Data from: Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq
We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina® reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script to estimate the ascertainment bias in SNP detection considering the pooling and sampling effects on the probability of not detecting an existing polymorphism. Gene Ontology (GO) and transposable element (TE) search analyses were applied to both data sets. The RADseq and the mRNAseq assemblies represented 0.1% and 0.6% of the genome, respectively. Genome complexity reduction resulted in 17% of the RADseq contigs potentially coding for proteins. This rate was doubled in the mRNAseq data set, suggesting that RADseq also explores noncoding low-repeat regions. The two methods gave very similar GO-slim profiles. As expected, the two assemblies were poor in TE-like sequences (<4% of contigs length). We identified 17,348 single nucleotide polymorphisms (SNPs) in the RADseq data set and 5,714 simple sequence repeats (SSRs) in the transcriptome. A subset of 282 SNPs was validated using the Fluidigm genotyping technology, giving a conversion rate of 50.4%, falling within the expected range for conifers. Increasing sample size had the greatest effect for ascertainment bias reduction. These results validated the utility of the RADseq approach for highly complex genomes such as conifers.
Data from: Multilocus microsatellite markers for molecular typing of Candida tropicalis isolates
Background: Candida tropicalis is considered to be the leading pathogen causing nosocomial fungemia and hepatosplenic fungal infections in patients with cancer, particularly those with leukemia. Microsatellite-based typing methods using sets of genetic markers have been developed and reported for population structure analysis of C. albicans, C. glabrata, and C. parapsilosis, but no studies have been published for genetic analysis of C. tropicalis. The objective of this study was to develop new microsatellite loci that have the ability to distinguish among C. tropicalis isolates. Results: DNA sequences containing over 10 bi- or tri-nucleotide repeats were selected from the C. tropicalis genome database. Thirty PCR primers sets specific for the microsatellite loci were designed and tested using eight clinically independent isolates. According to the amplification efficiency, specificity, and observed polymorphisms, eight markers were selected for further population structure analysis and molecular typing. Sixty-five independent C. tropicalis isolates were genotyped using these 8 markers. Based on these analyses, six microsatellite loci were confirmed, although two loci were found to be with unstable flanking areas. The six polymorphic loci displayed 4–22 alleles and 7–27 genotypes. The discriminatory power of the six loci ranged from 0.70 to 0.95. Genotyping results obtained by microsatellite analysis were compared to PCR-fingerprinting and multi-locus sequence typing (MLST). The comparisons showed that microsatellite analysis and MLST had the similar discriminatory power for C. tropicalis, which were more powerful than PCR-fingerprinting. Conclusions: This is the first attempt to develop new microsatellite loci for C. tropicalis. These newly developed markers will be a valuable resource for the differentiation of C. tropicalis isolates. More C. tropicalis isolates will need to be sequenced and analyzed in order to fully show the potential of these newly developed microsatellite markers.
Data from: Recurrent hybridisation events between Primula vulgaris, P. veris and P. elatior (Primulaceae, Ericales) challenge the species boundaries: Using molecular markers to re‐evaluate morphological identifications
Three Primula species, Primula vulgaris, P. veris and P. elatior, have been objects of fascination for gardeners and botanists over several centuries. The species are able to hybridise, and where they co-occur, hybrids are commonly found. In Denmark, Møns Klint on the island of Møn and Købelev Skov on Lolland are examples of localities where all three species occur and where the hybrids P. ×digenea, the hybrid between P. vulgaris and P. elatior, and P. ×polyantha, the hybrid between P. veris and P. vulgaris, can also be found. To investigate relations between the species and their hybrids, 168 specimens from 10 geographical locations were sampled for genetic analysis using DNA markers and identified based on morphological traits, primarily inflorescense structure, the size, shape, colour and markings of corolla and leaf basis, leaf blade texture and hairiness. After identifying species-specific SNPs in the internal transcribed spacer sequence, these were used to resolve species and hybrid boundaries and status through a cleaved amplified polymorphic sequence assay. Polymorphisms in the chloroplast trnL sequence were used as a high-throughput marker and used to determine the maternal parent of hybrids. Ten simple sequence repeat markers were applied to obtain further insight into the genetic makeup of the accessions using Structure and Introgress, providing information of genetic variability within and between populations. Data analyses indicated that backcrossing of P. ×digenea hybrids with parental species has occurred, and that many of the P. ×digenea found in the study were later-generation hybrids rather than F1s. Analyses of P. ×polyantha specimens show mostly the expected pattern for primary hybrids but indications of P. veris ancestry of a P. vulgaris plant was discovered. Our results further indicate that some of the specimens initially identified as P. elatior include P. vulgaris among their progenitors and thus challenge currently accepted species boundaries.
Systematic Identification of Needlefish (Belonidae) Species using Molecular Genetic and Morphological Markers in the Mediterranean and Black Seas
<p><span>In this study, we aimed to clarify the taxonomic status of Belonidae species distributed in the Mediterranean Sea and the Black Sea by conducting detailed genetic and morphological markers. A total of 550 needlefish samples were caught between January 2022 and January 2024.<span> </span>The data set used in the study contains a total of 171 sequences for the <em>COI</em> gene and 120 sequences for the <em>12s rRNA</em> gene from different Belonidae species, including data from GenBank. Systematic analysis of needlefish species was investigated by using sequencing of mtDNA <em>COI</em> and <em>12s rRNA</em> gene regions and morphological characters in the Turkish Marine Waters. A separate analysis of the two mitochondrial genes supported by morphological characters revealed that each species is grouped within itself. The genetic and morphological analyses showed that <em>Belone belone acus</em> and <em>Belone belone euxini</em> which are considered as the subspecies of <em>Belone belone</em> are not subspecies of the genus <em>Belone</em> and should be considered at the species level, <em>Belone belone</em>.<span> </span><em>Belone svetovidovi</em> is also considerably different from <em>Belone belone</em> and should be considered as a different species. <em>T. acus imperialis</em>, which is thought to be distributed in the Mediterranean Sea, is not a subspecies of <em>Tylosorus acus and should be revised as Tylosorus imperialis </em><span>which genetically </span>differs from<em> Tylosorus acus </em>and also other<em> Tylosorus </em><span>species</span><em> </em>at the species level<em>. </em></span></p>
Molecular and biochemical markers of oxidative stress in skeletal muscle
<p>Dataset of experimental animal study involved high-intensity interval training and molecular aspects of skeletal muscle.</p>
FIGURE 6 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 6. STRUCTURE analysis of L. rigidum populations (A: the relationship between k and Delta k; the grouping based on k=18 (top) and k=17 (below) (The population code is according to Table 1).
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.