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50 results for “old specimens”
Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen
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Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens
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Distribution. Much of mainland Australia except S Western Australia and W South Australia, also including Tiwi, Groote Eylandt, Fraser, and Moreton Is; two old specimens collected in Papua New Guinea (Central Province and National Capital District), but it has not been recorded again in this century in Emballonuridae
Distribution. Much of mainland Australia except S Western Australia and W South Australia, also including Tiwi, Groote Eylandt, Fraser, and Moreton Is; two old specimens collected in Papua New Guinea (Central Province and National Capital District), but it has not been recorded again in this century
Dataset from: Adding leaves to the Lepidoptera phylogeny: Capturing hundreds of nuclear genes from old museum specimens
<p>Museum collections around the world contain billions of specimens, including rare and extinct species. If their genetic information could be retrieved at a large scale, this would dramatically increase our knowledge of genetic and taxonomic diversity information, and support evolutionary, ecological and systematic studies. We here present a target enrichment kit for 2953 loci in 1753 orthologous nuclear genes + the barcoding region of cytochrome C oxidase 1, for Lepidoptera and demonstrate its utility to obtain a large number of nuclear loci from dry, pinned museum material collected from 1892 to 2017. We sequenced enriched libraries of 37 museum specimens across the order Lepidoptera, many from higher taxa not yet included in high-throughput molecular studies, showing that our kit can be used to generate comparable data across the order, and provides resolution both for shallower and deeper nodes. The filtered datasets (172 taxa, 234,464 amino acid positions and corresponding nucleotides from 1,835 CDS regions) were used to infer a phylogeny of Lepidoptera, which is largely congruent in topology to recent phylogenomic studies, but with the addition of some key taxa. <br> </p> <p>We furthermore present our TEnriAn (Target Enrichment Analysis) workflow for processing and combining target enrichment, transcriptomic and genomic data.<br> </p>
Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens
Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.
FIGURE 28 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 28. NJT tree (Kimura 2 parameter, built with MEGA6) for 10 species in the genus Lasiocampa based on sequence variation at COI. Sequence length of the holotype of Lasiocampa decolorata: 658bp. Width of triangles represent sample size, depth the genetic variation within the cluster. Source: DNA Barcode data from BOLD (Barcode of Life Database, cf. RATNASINGHAM & HEBERT 2007).
FIGURE 26 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 26. Morocco, Toubkal, Ait El Qad 2200–2600 m. Typical habitat of L. editae on the southern slopes of the High Atlas Mts. Here Dr. Revay collecting Coenonympha vaucheri, Berberia abdelkader and Hipparchia hansii, typical butterfly species associated with L. editae.
FIGURE 3 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 3. Lasiocampa editae sp. n. Genitalia slide Heterocera Nr. 19872 MWM "Morocco, High Atlas, Oukaimeden, NW slopes, 2,0–2,300 m, 11.–20. 08. 2012, G. Muller, E. Revay et al., BC ZSM Lep 76653, Museum Witt München". FIGURE 4. Lasiocampa staudingeri (BETHUNE-BAKER, 1885). Genitalia slide Heterocera Nr. 8691 MWM – Aedeagus mirror-inverted. "Coll. A. Seitz, Algerien, Lambessa, Coll. Th. Witt, München/Weiden".
Subspecies and Distribution. H. e. edwardsii Geoffroy Saint-Hilaire, 1818 — SE India and Sri Lanka. H. e. carnaticus Wroughton, 1921 — SW India (Karnatka). H. e. moerens Wroughton, 1915 — Bangladesh, Bhutan, C & NE India, and Nepal. H. e. montanus Bechthold, 1936 — Saudi Arabia to NW India. H. e. pallens Ryley, 1914 — W India (Gujarat). A few old museum specimens are reported from Peninsular Malaysia, whereit is said to have been introduced, butit has not been recorded there since the beginning of the 20" century. in Herpestidae
Subspecies and Distribution. H. e. edwardsii Geoffroy Saint-Hilaire, 1818 — SE India and Sri Lanka. H. e. carnaticus Wroughton, 1921 — SW India (Karnatka). H. e. moerens Wroughton, 1915 — Bangladesh, Bhutan, C & NE India, and Nepal. H. e. montanus Bechthold, 1936 — Saudi Arabia to NW India. H. e. pallens Ryley, 1914 — W India (Gujarat). A few old museum specimens are reported from Peninsular Malaysia, whereit is said to have been introduced, butit has not been recorded there since the beginning of the 20" century.
FIGURE. Distribution of Dicorynia. Physical map of the Amazonian region with all analyzed specimens of Dicorynia. A large amount of point overlays leading to reduced number of visible points is due to the large percentage of materials being old collections that rely only on the name of the municipality or similar. Source: NASA with modifications. Note that almost all specimens are contained in areas with less than 200 m high and the high elevations of the Guiana shield may represent a form of isolation between the two species. in A Taxonomic Revision of the Amazonian Genus Dicorynia (Fabaceae: Dialioideae)
FIGURE. Distribution of Dicorynia. Physical map of the Amazonian region with all analyzed specimens of Dicorynia. A large amount of point overlays leading to reduced number of visible points is due to the large percentage of materials being old collections that rely only on the name of the municipality or similar. Source: NASA with modifications. Note that almost all specimens are contained in areas with less than 200 m high and the high elevations of the Guiana shield may represent a form of isolation between the two species.
Distribution. Islands off peninsular Thailand (Koh Samui) and Peninsular Malaysia (Tioman, and Mapur); one old specimen from Mt Tahan, Pahang State, Malaysia, might also belong to this species, but no recent confirmation of this taxon on the Malay Peninsula cast doubts about the existence of such a continental population of Peninsular White-toothed Shrew. in Soricidae
Distribution. Islands off peninsular Thailand (Koh Samui) and Peninsular Malaysia (Tioman, and Mapur); one old specimen from Mt Tahan, Pahang State, Malaysia, might also belong to this species, but no recent confirmation of this taxon on the Malay Peninsula cast doubts about the existence of such a continental population of Peninsular White-toothed Shrew.
Supplementary material 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
Full information and metadata about the genomic and metagenomic samples : Explanation note: Detailed information about metadata, DNA quality and genomic/metagenomic results of fruit-body and EcM root tip samples.
Fig. 1 in Teratology in a Century-Old Museum Specimen of Kheper cupreus (Laporte de Castelnau, 1840) (Coleoptera: Scarabaeidae: Scarabaeinae) from Zimbabwe
Fig. 1. Head of Kheper cupreus. Teratological specimen: A) Dorsal view, B) Ventral view. Normal specimen: C) Dorsal view, D) Ventral view.
Fig. 2 in Teratology in a Century-Old Museum Specimen of Kheper cupreus (Laporte de Castelnau, 1840) (Coleoptera: Scarabaeidae: Scarabaeinae) from Zimbabwe
Fig. 2. Habitus of Kheper cupreus: A) Teratological specimen, B) Normal specimen from Opuwo, northern Namibia. Note the green tinge in the coloration of the teratological specimen from the hotter and lower Mazowe (Zimbabwe) compared to the black coloration in the specimen from the cooler highlands of northern Namibia.
The Effect of Non-invasive Bladder Stimulation Technique on Collecting Urine Specimen in Infants Under One Year Old
ClinicalTrials.gov study NCT05394454. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens
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Figure 4 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 4 Country repsentation of Juncus specimens in WRSL. Y-axis: number of herbarium labels analysed. The African collection deserves particular attention (98 sheets (4.5%)), including sets from South Africa (64 sheets). The Asian collection (96 sheets) is dominated by plants from India (59). The percentage of plants from North America is as high as 10%.
Figure 2 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 2 Origin of Juncus historically- and nomenclaturally-important specimens at WRSL according to country. Y-axis: number of herbarium sheets. Specimens most frequently originated from South Africa (42.3%). Juncus type specimens were collected by many distinguished botanists. Amongst these, the four individuals gathered 37.2% of Juncus specimens: C.F. Ecklon & C.L.P. Zeyher, C. Krauss and J.F. Drège.
Figure 1 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 1 Percentage of different categories of Juncus specimens. Types, original material and specimens collected from the original type localities, by the author of the name ("topotypes") at WRSL.
Data from: DNA barcodes from century-old type specimens using next generation sequencing
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain. The present study addresses this challenge by employing next generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164bp and 94bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories – high (164bp sequence), medium (94bp sequence), or low (no sequence). Ten specimens from each category were subsequently analyzed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458bp to 610bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
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OpenNeuro
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