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.
50
datasets available to search
ShareScore release 0.9.0
Dataset results
50 results for “old specimens”
Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi
<p>Natural history collections are important data repositories, but different chemical treatments of specimens can influence morphological measurements and DNA extraction, complicating taxonomic and conservation decisions dependent upon these data. One such example is the Bay Springs Salamander (<i>Plethodon ainsworthi</i>), the only United States amphibian categorized as Extinct by the IUCN.<i> </i>Recent research has proposed that <i>P. ainsworthi </i>is an invalid taxon, arguing that the 55-year-old type specimens' morphological distinctiveness from syntopic <i>P. mississippi</i> is a preservation artifact. To address this controversy, we tested for morphological changes across five experimental treatments in proxy <i>P. shermani</i> specimens, and we re-examined the datasets used to support the invalidity of <i>P. ainsworthi</i>. We also tested recently developed DNA extraction techniques on the putatively formalin-fixed <i>P. ainsworthi</i> holotype. We used Bayesian models to demonstrate that preservation method can differentially bias morphological measurements, with most methods causing lower estimates of mass and modestly higher estimates of snout-vent-length:head width ratio. These results are broadly consistent with previous studies of other vertebrates, but inconsistent with the hypothesis that <i>P. ainsworthi </i>type specimens are actually poorly preserved <i>P. mississippi</i>. Attempts to extract DNA from the <i>P. ainsworthi</i> holotype unfortunately proved unsuccessful, preventing conclusive resolution of its status and emphasizing the limitations of promising new methods. Nonetheless, we tentatively recommend continued recognition of <i>P. ainsworthi</i> as a valid but possibly extinct taxon. More generally, we invite all authors who study preserved specimens to recognize and report how certain chemical treatments might impact their results.</p>
FIGURE 27 in Taxonomy 2.0: Sequencing of old type specimens supports the description of two new species of the Lasiocampa decolorata group from Morocco (Lepidoptera, Lasiocampidae)
FIGURE 27. Morocco, High Atlas, Oukaimeden, Tisrafene south facing slopes, 2,800–3,000m.
Distribution. Borneo. Said to occur on Sumatra, but this is based only on two old museum specimens. in Herpestidae
Distribution. Borneo. Said to occur on Sumatra, but this is based only on two old museum specimens.
FIGURE 9. Fossil larva BUB 4436, specimen 7. A. Overview dorsal side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 9. Fossil larva BUB 4436, specimen 7. A. Overview dorsal side. B. Colour-marked version of B. C. Ventral side. D. Close-up on thorax; arrows point to claws. E. Close-up trunk end. F. Close-up on head. Abbreviations: ad = abdomen; at = antenna; fe = femur; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax.
Fig. 1 – Specimen SNHMB.G 8109, Kachin amber. A – Dorsal view. B in A modern type of ant-like stone beetle larva preserved in 99-million-year-old Kachin amber (Coleoptera: Staphylinidae, Scydmaeninae)
Fig. 1 – Specimen SNHMB.G 8109, Kachin amber. A – Dorsal view. B – Colour-marked version of A. Abbreviations: 1t = trunk appendage 1 ("front leg"); a2 = abdomen segment 2; at = antenna; cl = claw; fe = femur; hc = head capsule; mt = metathorax; mx = maxilla; pt = prothorax; te = trunk end; ti = tibio-tarsus.
Figure 2 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Figure 2 - Impact of maximum obtained DNA concentration and number of Illumina HiSeq reads on the size of all scaffolds (A, B) and largest nuclear rDNA scaffold (C, D). Regular straight lines and dotted lines indicate linear and better fitting logarithmic relationships, respectively.
Figure 1 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Figure 1 - Effect of specimen age on the recovery of reads in the Illumina HiSeq run. Closed circles, 'old' fruit-bodies; shaded circles, 'regular' fruit-bodies; open circles, 'unsequenced' fruit-bodies; shaded triangles, ectomycorrhizal root tips representing unique rare lineages; open triangles, 'unsequenced' ectomycorrhizal root tips.
Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi
Open the record for dataset details and reuse information.
Data from: DNA barcodes from century-old type specimens using next generation sequencing
Open the record for dataset details and reuse information.
Figure 3 from: Proćków J, Faltyn-Parzymska A, Jarzembowski P, Proćków M, Jakubska-Busse A (2020) How many type specimens can be stored in old lesser-known herbaria with turbulent histories? – A Juncus case study reveals their importance in taxonomy and biodiversity research. PhytoKeys 153: 85-110. https://doi.org/10.3897/phytokeys.153.50735
Figure 3 Collectors' names. Y-axis: number of herbarium labels analysed.
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.