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189 results for “DNA specimens”
Figure 3 from: Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K (2018) Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). ZooKeys 746: 105-121. https://doi.org/10.3897/zookeys.746.13502
Figure 3 - Determination of the threshold genetic distance for species identification. False positive (grey) and false negative (black) identification error rates summed across a range of distance thresholds from 0.01 to 1.9 %. The cumulative error plot indicates the transition between intraspecific and interspecific distances, the genetic distance corresponding to the least cumulative error (1.51 %) showing the appropriate threshold value for the dataset.
Figure 1 from: Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K (2018) Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). ZooKeys 746: 105-121. https://doi.org/10.3897/zookeys.746.13502
Figure 1 - Evaluation of barcode gap in the dataset. Boxplot of the interspecific (inter) and intraspecific genetic (intra) distances, indicating the existence of a barcode gap, i.e., interspecific distance is larger than intraspecific distance. The median is indicated by the horizontal line and the range as the vertical dashed lines and outliers by bold vertical lines.
Supplementary material 1 from: Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G (2019) PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 53: 73-91. https://doi.org/10.3897/mycokeys.53.34761
: Data type: measurement
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 (CO1) 551 bp sequence analyses. (2) Phylogenetic analysis based on maximum likelihood algorithm with the sample codes, GenBank or BOLD accession numbers and sample sites shown. Bootstrap percentages are shown at the tree nodes. (3) Haplotype network with the haplotypes labelled as H1 to H9. The circle size is proportional to the number of samples, and different sample sites are represented by different colours. Small white circle represents median vector which is the hypothesized or missing haplotype. Each dash on the line symbolizes one mutational step.
Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques
A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.
Multiple mitochondrial haplotypes within individual specimens affect biodiversity estimation by DNA metabarcoding
<p>In the global action for biodiversity conservation, the most urgent need is to delimit and identify species. DNA barcoding and metabarcoding based on molecular markers have been increasingly used in species delimitation and species diversity assessment, respectively, owing to their advantages of standardization and high throughput. The molecular markers used in these methods for animals are mainly derived from mitochondrial DNA. The principle involved is that inter-specific genetic distances are greater than intra-specific genetic distances. However, if multiple mitochondrial haplotypes exist within individual specimens and the divergence between these haplotypes is greater than the assumed maximum intra-specific divergence, the species delimitation and species diversity assessment may be affected. In our recent studies, a widespread phenomenon of multiple mitochondrial haplotypes within individual specimens was discovered in fig wasps (Hymenoptera, Insecta), having negative impact on DNA barcoding and metabarcoding. In this study, we expanded the taxa to include up to 480 specimens from 82 species, 66 genera, 45 families, and 13 orders of Insecta and Arachnida. By high-throughput sequencing of mitochondrial <i>cox1</i> fragments within individual specimens, we studied the pattern of multiple mitochondrial haplotypes within individual specimens. Three DNA metabarcoding strategies, one of which was simulated, were applied. The results revealed that multiple mitochondrial haplotypes within individual specimens could lead to an overestimation of species diversity by metabarcoding. Simultaneously, we found that the infection with intracellular endosymbiotic bacteria <i>Wolbachia</i> was significantly negatively related with this effect. These results suggest that additional attention should be paid to the interference of multiple mitochondrial haplotypes within individual specimens on the results of DNA metabarcoding in species diversity assessment of animals.</p>
Supplementary material 1 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Reconstructed micro-CT scan of C.559479
Figure 4 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure 4 Phylogenetic relationships of C.559479 based on maximum likelihood analysis of the reduced 16S rRNA dataset. More distant outgroups have been removed and the topology rooted on Philine scabra + P. indistincta. Numbers near nodes refer to bootstrap percentages above 70%. The scale bar indicates 0.05 changes per site. Sequences are identified by accession number and species name or informal designation recorded in GenBank except those labelled P. quadripartita for which the species names have been changed for reasons outlined in the text. Accessions with an sp. number designation followed by a space and "TO" with a one or two digit designation refer to sequences from Oskars et al. (2015). Note that this article refers to the undescribed species in alphabetical rather than numerical order so that sp. 4 in GenBank is identified as sp. D in Oskars et al. (2015).
Supplementary material 2 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure S1. Image from the reconstructed micro-CT scan of C.559479
Figure 3 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure 3 C.559479, outer surface of gizzard plates from the micro-CT reconstruction A paired plate, left B unpaired plate C paired plate, right. Scale bar: 2 mm (A–C).
Figure 2 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure 2 Micro-CT reconstruction images of C.559479 A ventral view of the shell B–D three perspectives from the reconstruction. Scale bar: 5 mm (A–D).
Figure 3 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 3 - DNA concentration (log10 transformed) for specimens in the time series study that yielded or failed to yield a successful DNA barcode sequence arranged by A body size B year collected. Successes (filled circles) and failures (while circles) partitioned into destructive (red) and nondestructive (blue) DNA extraction methods.
Figure 2 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 2 - Sequencing success for the time series study of 31 spider species frequently collected in the Netherlands. Data for each species arranged horizontally along a time axis (year of collection). Small circles represent standard destructive extraction; outer circle represents nondestructive extraction. Red small circle and blue outer circle indicate successful sequencing, unfilled circles represent failed attempts; half-filled circle indicates mixed success among multiple specimens for that species and year. Solid horizontal lines extend from the present to the oldest successful DNA barcode based on destructive extraction for each species; where nondestructive extraction yielded successful DNA barcode from older specimens, this is indicated by a dashed line. Data are arranged according to a neighbour joining tree (A) or by species body size (B). Spider families and major lineages (Orbiculariae and 'RTA' clade) are indicated in A. AGE Agelenidae AMA Amaurobiidae ARA Araneidae CLU Clubionidae COR Corinnidae LIN Linyphiidae LYC Lycosidae PHI Philodromidae PIS Pisauridae SAL Salticidae THD Theridiidae THO Thomisidae ZOR Zoridae.
Figure 1 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 1 - A Sequencing success profile for specimens included in this study. Data are species attempted, all specimens in the study including the time series, and fresh specimens collected in 2010 or later. Success expressed as a percentage appears on the blue (success) portion of each bar B Sequencing success rates for fresh (collected 2010 or later) and older specimens grouped by decade. Data given for all extractions regardless of method, and also partitioned into destructive and nondestructive extraction methods. Total number of specimens attempted and the subset of specimens attempted using nondestructive extraction given in parentheses. Note that the relatively high success rate for nondestructive extractions of specimens from the 1960s is based on two successes out of four attempts.
Figure 5 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 5 - DNA barcode sequencing success for fresh specimens (collected 2010 or later). A Specimen body size not significantly different for successful vs. failed DNA barcode sequencing attempts (one-way ANOVA, F (1, 216) = 1.45, p = 0.230). Boxes are 25–75% quartiles bisected by the median, whisker lines drawn to the largest/smallest data point less than 1.5 times the box height, outliers less than 3 times the box height shown as circles, more than 3 shown as stars. B Most of the fresh specimens included in this study belonged to one of two clades: Orbiculariae (ORB) or the 'RTA' clade (RTA); only a handful of specimens represented older phylogenetic branches, such as haplogyne (HAP) spiders; no mygalomorph spiders were included; success expressed as a percentage appears on or above each bar. Success rate for Orbiculariae vs. 'RTA' clade specimens not significantly different (χ2 = 2.18, d.f. = 2, N = 220, p = 0.337).
Figure 4 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 4 - A DNA concentration (log10 transformed) for specimens in the time series study that yielded or failed to yield a successful DNA barcode sequence ranked by DNA concentration; symbols as in Figure 3 B Box plot showing difference in DNA concentration for specimens extracted using both destructive and nondestructive methods; species arranged by size (Araneus quadratus, Tegenaria atrica, and Dolomedes plantarius excluded). Sample size in parentheses, boxes are 25–75% quartiles bisected by the median, whisker lines indicate minimum/maximum values (where n > 4).
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.
Supplementary material 2 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099
Species names, code numbers and collecting data
Supplementary material 1 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099
Identity of Argyria lacteella (Fabricius) revised
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