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.

3,878

datasets available to search

ShareScore release 0.9.0

Dataset results

3,878 results for “Molecular Data”

Learn how ShareScore rates datasets ↗

dryad28/100

Data from: Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos) and black bears (U. americanus) derived from genome sequences

We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25X for each species. A total of 1.4 billion 100-bp paired-end reads was assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the three species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately one million base pairs of ultra-conserved elements (UCE) in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

opencc-zeroDec 2012View details →

dryad28/100

Data from: Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.

opencc-zeroDec 2014View details →

dryad28/100

Data from: Application of a novel molecular method to age free-living wild Bechstein's bats

The age profile of populations fundamentally affects their conservation status. Yet age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes which have previously shown age-associated changes in humans and laboratory mice. All CpG sites from the tested genes showed a significant relationship between DNA methylation and age, both individually and in combination (multiple linear regression R2=0.58, p<0.001). Despite slight approximation around estimates, the approach is sufficiently precise to place animals into practically useful age cohorts. This method is of considerable practical benefit as it can reliably age individual bats. It is also much faster than traditional capture-mark-recapture techniques, with the potential to collect information on the age structure of an entire colony from a single sampling session to better inform conservation actions for Bechstein's bats. By identifying three genes where DNA methylation correlates with age across distantly related species, this study also suggests that the technique can potentially be applied across a wide range of mammals.

opencc-zeroDec 2017View details →

dryad28/100

Data from: Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks

Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone.

opencc-zeroDec 2015View details →

dryad28/100

Data from: Molecular and morphological data reveal three new tribes within the Scirpo-Caricoid Clade (Cyperoideae, Cyperaceae)

The circumscription of the circumboreal tribe Scirpeae has been contentious since the earliest infrafamilial classifications of the Cyperaceae (>100 genera, ~5,500 species). Molecular phylogenetic studies place Scirpeae in a strongly supported clade with the enigmatic genus Khaosokia and tribes Cariceae, Dulichieae, and Sumatroscirpeae, a lineage comprising more than 40% of all Cyperaceae species. This lineage was previously known as the Cariceae-Dulicheae-Scirpeae ("CDS") clade. Here we informally characterise it as the "Scirpo-Caricoid Clade". Previous phylogenetic and phylogenomic studies of the Scirpo-Caricoid Clade have shown Scirpeae to be paraphyletic, forming four distinct lineages that are successive sisters to a Cariceae + Sumatroscirpeae clade, thus confirming decade old suspicions that the modern circumscription of Scirpeae is unnatural. Using a total-evidence phylogenetic analysis incorporating three plastid markers (matK, ndhF, rps16), two nuclear ribosomal markers (ETS-1f, ITS), and 64 morphological characters, this study confirms the paraphyly of Scirpeae, the isolated phylogenetic position of Khaosokia, and identifies morphological synapomorphies for seven monophyletic lineages that are here recognized as tribes. Our new classification places for the first time all genera of the Scirpo-Caricoid Clade into natural tribes that are identifiable using morphological and embryological characters. Three new tribes are proposed: Calliscirpeae trib. nov., Khaosokieae trib. nov. and Trichophoreae trib. nov. Diagnoses for all tribes of the Scirpo-Caricoid Clade, an identification key to all currently recognized Cyperaceae tribes, and identification keys for all genera of the Scirpo-Caricoid Clade are provided.

Find research datasets worth reusing

Dataset results

Data from: Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos) and black bears (U. americanus) derived from genome sequences

Data from: Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

Data from: Application of a novel molecular method to age free-living wild Bechstein's bats

Data from: Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks

Data from: Molecular and morphological data reveal three new tribes within the Scirpo-Caricoid Clade (Cyperoideae, Cyperaceae)

Supplementary material 2 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 151-154 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 147-150 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 143-146 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 131-134 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 139-142 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 75-78 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 7- 8 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 70-74 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 101-106 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 43- 44 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 52-57 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 35- 36 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 3- 4 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Figures 107-112 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052

Understand access before you commit

Allen Brain Atlas

Annotated Behaviour and Observability Dataset (ABODe)

DANDI Archive for NWB datasets

International Brain Laboratory public data

OpenNeuro

Your academic CV and NIH biosketch