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85 results for “Barcoding analysis”
FIGURES 61−66 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 61−66. Immature stages of South African Gracillariidae. 61, Caloptilia sp., larva on Cryptocarya transvaalensis (Lauraceae), Limpopo, Lekgalameetse N. R., A. & I. Sharp leg. 62, C. cataractias, larva on Rhynchosia minima (Fabaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 63, Macarostola noellineae, larva on Syzygium cordatum (Myrtaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 64, Ectropina spirostachydis sp. nov., larva on Spirostachys africana (Euphorbiaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 65, Cuphodes melanostola, mine on Euclea divinorum (Ebenaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 66, Conopomorphina ochnivora, Gauteng, Magaliesburg, on Ochna pretoriensis, (Ochnaceae), H. Staude leg.
FIGURES 58–60 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 58–60. Female genitalia of South African Gracillariidae. 58-59, Phyllocnistis magalismontani sp. nov., paratype: 58, lateral view; 59, signa. 60, P. allisonae sp. nov., holotype: ventral view. (All scale bar 190 μm).
FIGURES 56–57 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 56–57. Female genitalia of South African Gracillariidae. 56, Telamoptilia cordati sp. nov., paratype: ventral view. 57, Phyllonorycter pseudogrewiella sp. nov., holotype: lateral view. (All scale bar 190 μm).
FIGURES 44–46 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 44–46. Male genitalia of South African Gracillariidae. Phodoryctis tephrosiella sp. nov.: 44, holotype, ventral view; 45, phallus with bulbus ejaculatorius; 46, segment VIII in ventral view (ae: aedeagus; pb: phallobase; be: bulbus ejaculatorius). (All scale bars 190 μm).
FIGURES 25−30 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 25−30. Forewing pattern of South African Gracillariidae. 25, Leucocercops curatellifoliae sp. nov., Limpopo. 26, Phodoryctis tephrosiella sp. nov., Gauteng. 27, Telamoptilia cordati sp. nov., South Africa, Limpopo. 28, Telamoptilia sp., Madagascar. 29, Cameraria melhaniella sp. nov., Limpopo. 30, Phyllonorycter pseudogrewiella sp. nov., Limpopo.
FIGURES 13–18 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 13–18. Adults of South African Gracillariidae. 13, Cryptolectica capnodecta, Limpopo, Hoedspruit, A. & I. Sharp leg. 14, C. terminalina, Limpopo, Hoedspruit, A. & I. Sharp leg. 15, Dialectica pyramidota, Limpopo, Hoedspruit, A. & I. Sharp leg. 16, Amblyptila cynanchi, Western Cape, Knysna, S. Mecenero leg. 17, Leucocercops dasmophora, Gauteng, Tshwane, A. & I. Sharp leg. 18, L. curatellifoliae sp. nov. Limpopo, Hoedspruit, A. & I. Sharp leg.
FIGURES 32–34 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 32–34. Forewing pattern of the South African Phyllocnistinae. 32, Phyllocnistis magalismontani sp. nov., drawn by holotype; 33, P. allisonae sp. nov., holotype; 34, P. faureae, holotype.
FIGURE 31 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURE 31. Forewing pattern of the Afrotropical Phyllocnistinae. A, Phyllocnistis pharetrucha; B, P. saligna; C, P. magalismontani sp. nov.; D, P. faureae sp. nov.; E, P. loxosticha; F, P. citrella; G, P. allisonae sp. nov..
FIGURES 1−6 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 1−6. Adults of South African Gracillariidae. 1, Caloptilia sp., Limpopo, Lekgalameetse N. R., A. & I. Sharp leg. 2, Caloptilia rhusina, Western Cape, Robberg Nature Reserve, S. Mecenero leg. 3, Macarostola noellineae, Limpopo, Hoedspruit, A. & I. Sharp leg. 4, Caloptilia cataractias, Limpopo, Hoedspruit, leg. A. & I. Sharp. 5, Ectropina spirostachydis sp. nov., Limpopo, Hoedspruit, A. & I. Sharp leg. 6, Graphiocephala barbitias, Gauteng, Tshwane, A. Sharp leg.
FIGURES 7–12 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 7–12. Adults of South African Gracillariidae. 7, Semnocera procellaris, Limpopo, Hoedspruit, A. & I. Sharp leg. 8, Conopomorphina ochnivora, Gauteng, Magaliesburg, A. & I. Sharp leg. 9, C. aptata, Limpopo, Hoedspruit, A. & I. Sharp leg. 10, Cuphodes melanostola, Limpopo, Hoedspruit, A. & I. Sharp leg. 11, Acrocercops syzygiena, Gauteng, Tshwane, A. Sharp leg. 12, A. combreticola, Gauteng, Tshwane, A. Sharp leg.
Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi
<p><span>With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan).</span></p> <p><span>Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence.</span></p> <p><span>Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. </span></p> <p><span>Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.</span></p>
FIGURE 4. A in Pinellia hunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding
FIGURE 4. A classification tree of combined rbcL and matK data using neighbor-joining (NJ) and Bayesian of phylogenetic methods.
FIGURE 5 in Pinellia hunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding
FIGURE 5. Scatter plot of the first two axes from a detrended correspondence analysis (DCA) for 38 quantitative morphological variables (taxonomic characters) of 24 specimens (classification of 6 Pinellia species). The new species Pinellia hunanensis is circled, including its respective intraspecific variation.
FIGURE 2. Pinellia hunanensis—A in Pinellia hunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding
FIGURE 2. Pinellia hunanensis—A: habit; B: juvenile plant; C: leaf; D: inflorescence; E: spadix; F: infructescence; G: pistil; H: fruit; I: seed (Drawn after the holotype by Yitao Liu).
Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae
<p>Two datasets are provided to support the journal article (https://doi.org/10.1643/i2020112) by T. C. Grande and M. V. H. Wilson naming the new Bermuda fish species <em>Polymixia hollisterae</em>. The first dataset is for 2-D multivariate morphometric comparisons of selected specimens and species of the fish genus <em>Polymixia</em>. The file is in TPS format, as a plain text file, for use in the application MorphoJ. The data are for 27 specimens with pixel coordinates for 34 landmarks digitized in ImageJ and used to generate Fig. 13 in the referenced publication. The second dataset, published here courtesy of Dr. R. Eytan, is a mitochondrial DNA barcode sequence in fasta format for the second paratype specimen, a small juvenile of the new species. The specimen is only the third one known of the new species and the only one not from Bermuda. It was collected in the north-central Gulf of Mexico and is now deposited in the Harvard University MCZ fish collection as catalog number MCZ 174218. The fasta file can be used as input to the barcode identification function at boldsystems.org, although its original identification in BOLD was incorrect.</p>
Figure 2 in Not just cryptic, but a barcode bush: PTP re-analysis of global data for the bumblebee subgenus Bombus s. str. supports additional species (Apidae, genus Bombus)
Figure 2. Estimate of phylogeny from MrBayes for the fast-evolving COI gene of Bombus s. str. as a metric tree from the longest examples of sampled unique COI-barcode haplotypes (from data for 559 sequences from Williams, Brown, et al. 2012), combined with the Bayesian Poisson-tree-process (PTP) solution with spots showing the nodes with the highest support for coalescents of candidate species by maximum likelihood (outgroup B. vagans not shown). Values above the nodes are MrBayes Bayesian posterior probabilities, showing branch support for groups; values below the nodes are PTP maximum-likelihood support values that all daughter haplotypes are parts of a single species. The scale bar is calibrated in substitutions per nucleotide site. Each sample sequence is labelled with: the sequence length in number of nucleotides; a taxon name, often referring to a particular colour pattern; a code that consists of a specimen identifier from the project database and a sequence identifier; followed with its geographic origin. Lineages with high probabilities of representing one or more candidate species in the PTP results are shown with thick lines and the most recent common ancestor of each candidate species (the species' coalescent) is shown with a black spot. The branches within the candidate species are shown with thin lines.
Figure 1 in Not just cryptic, but a barcode bush: PTP re-analysis of global data for the bumblebee subgenus Bombus s. str. supports additional species (Apidae, genus Bombus)
Figure 1. Global distribution of sample sites for the samples of the subgenus Bombus s. str. with the 559 COI-barcode sequences from Williams, Brown, et al. (2012) that are re-analysed here (these bumblebees are not indigenous to sub-Saharan Africa, the Arabian peninsula, lowland India, Southeast Asia, Australia, or Central and South America). Spots are coloured to show the site elevation (scale in metres a.s.l. at left). Cartesian orthonormal projection, north at the top of the map.
FIGURE. DnaSP DNA polymorphism analysis - Nucleotide variability (Pi) comparison between Strobilanthes lupulina and S. glandulata. The window length and step size were set to 600bp and 200bp respectively. The most varying regions and the commonly used barcoding regions are listed against the base-pair differences found. in Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on the morphological and molecular evidences
FIGURE. DnaSP DNA polymorphism analysis - Nucleotide variability (Pi) comparison between Strobilanthes lupulina and S. glandulata. The window length and step size were set to 600bp and 200bp respectively. The most varying regions and the commonly used barcoding regions are listed against the base-pair differences found.
Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi
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Data from: Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species
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