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4,144 results for “ITS barcode”
Predation patterns on the tundra – genetic barcoding of scats from two sympatric fox species
<p>In the Arctic tundra, climate-induced emergence of the red fox (Vulpes vulpes), a competitor to the Arctic fox (Vulpes lagopus), is predicted to influence predation patterns of both fox mesopredators. In this study, we i) identified predator species from scats through an established barcoding approach, and ii) explored the use of a cheap, quick barcoding method of fox feces (n = 103). We investigated differences in diet between the red fox (predicted generalist predator) and Arctic fox (predicted specialist predator) over two years with varying prey abundance. We amplified short DNA fragments (< 200 bp) from small rodents, birds and hares. For both predators, there was a high frequency of occurrence of rodents (38 - 69 %) identifying them as primary prey species and birds as secondary prey species (13-31%). This demonstrates the strength of a straightforward DNA barcoding method for dietary analyses in sympatric fox predators, with species-level resolution of prey. Barcoding is a promising tool for future dietary studies, however a few methodological improvements, along with extended sampling, are needed for a more complete assessment of fox predation patterns. Integrating high-resolution dietary analyses has great potential to enhance our understanding of predation patterns in Arctic tundra communities.</p>
FIGURE 3 in Triplax sulphuricollis Reitter, 1887 from the Hyrcanian forests of Iran recognized as a valid species by morphology and barcoding (Coleoptera: Erotylidae)
FIGURE 3. Localities of sampled specimens of Triplax collaris (Schaller, 1783) and T. sulphuricollis Reitter, 1887 examined in this study. The Hyrcanian forest in northern Iran and Azerbaijan is depicted by a dark green line.
FIGURE 2 in Triplax sulphuricollis Reitter, 1887 from the Hyrcanian forests of Iran recognized as a valid species by morphology and barcoding (Coleoptera: Erotylidae)
FIGURE 2. (a) Dorsal view and (b) ventral view of Triplax collaris (Schaller, 1783) (Austria, Neusiedler See, 05.05.1989, leg. Dries, col H. Bussler) (c) Dorsal view of male Triplax sulphuricollis (Iran, Chalandar, 36.94225°, 51.64551°, 30.06.2014, leg. S. Thorn) with characteristic orange-yellow antennal club and linear punctation in depressed rows on elytra, (d) ventral view, (e) male genitalia and (f) female genitalia.
FIGURE 1 in Triplax sulphuricollis Reitter, 1887 from the Hyrcanian forests of Iran recognized as a valid species by morphology and barcoding (Coleoptera: Erotylidae)
FIGURE 1. Neighbor-joining tree based on COI barcodes of Triplax sulphuricollis Reitter, 1887 and its presumed sister species, Triplax collaris (Schaller, 1783), created in BOLD. Genbank accession numbers age given along with species names.
FIGURES 20–25 in New or little-known taxa of Anurophorinae (Collembola) with anal spines from East Asia with notes on DNA barcode
FIGURES 20–25. Distal part of abdomen in genera with four anal spines on Abd.V: 20–21, Tetracanthella, T. wahlgreni (20) and T. stebaevae (21); 22–23, Blissia, B. glabra, after Rusek (1985) (22) and B. robusta (23); 24, Sibiracanthella (S. rara), 25, Dimorphacanthella (D. mediaseta). Anterior row of setae notated as a1, Md, a3, Mdl. s—s-seta. Most of lateral setae not shown.
FIGURES 6–10 in New or little-known taxa of Anurophorinae (Collembola) with anal spines from East Asia with notes on DNA barcode
FIGURES 6–10. Sahacanthella saoriae sp. nov.: 6, PAO and ocelli; 7, medial conical protuberance, lateral view; 8, Abd.IV– VI; 9, distal part of tibiotarsus 3; 10, Ant.3, lateral view, variability shown. Md—dorsal macroseta, s—s-seta.
FIGURES 17–19 in New or little-known taxa of Anurophorinae (Collembola) with anal spines from East Asia with notes on DNA barcode
FIGURES 17–19. Distal part of abdomen in Octodonthophora ornata: 17–18, common variant with 9 spines, latero-dorsal (17) and latero-ventral (18) views; 19, small male with 8 spines, latero-dorsal views, most of lateral setae not shown. For the abbreviations see the text.
FIGURES 11–16 in New or little-known taxa of Anurophorinae (Collembola) with anal spines from East Asia with notes on DNA barcode
FIGURES 11–16. Octodonthophora ornata: 11, chaetotaxy of body tergites; 12. PAO and ocelli; 13, appearance and macrochaetotaxy; 14, furca; 15, Abd.IV–VI, dorsal view; 16, Th.II. Abbreviations as in Figs 1–5.
FIGURES 1–5 in New or little-known taxa of Anurophorinae (Collembola) with anal spines from East Asia with notes on DNA barcode
FIGURES 1–5. Sahacanthella kele (1, 4) and S. saoriae sp. nov. (2, 3, 5): 1–2, chaetotaxy of body tergites; 3–4, distal part of furca in individuals with the least number of setae on dens, variation (3) shown, lateral view; 5, furca, posterior view. Mdl, Ml—dorso-lateral and lateral macroseta, s, ms—s-setae and ms-seta.
Supplementary material 1 from: Skowron Volponi MA, Volponi P (2017) A new species of wasp-mimicking clearwing moth from Peninsular Malaysia with DNA barcode and behavioural notes (Lepidoptera, Sesiidae). ZooKeys 692: 129-139. https://doi.org/10.3897/zookeys.692.13587
Video of Pyrophleps ellawi in natural habitat : Explanation note: Supplementary video from the wild shows the behaviour and authentic postures of Pyrophleps ellawi. High resolution video available from Vimeo on: https://vimeo.com/230445159
Supplementary material 2 from: Skowron Volponi MA, Volponi P (2017) A new species of wasp-mimicking clearwing moth from Peninsular Malaysia with DNA barcode and behavioural notes (Lepidoptera, Sesiidae). ZooKeys 692: 129-139. https://doi.org/10.3897/zookeys.692.13587
Multiple alignment of barcode sequences : Explanation note: Multiple alignment of barcode sequences of the following species: Pyrophleps ellawi, P. vitripennis, Heterosphecia pahangensis (3 specimens), H. bantanakai, H. tawonoides, Aschistophleps longipoda.
Supplementary material 1 from: Estupiñán RA, Ferrari SF, Gonçalves EC, Barbosa MSR, Vallinoto M, Schneider MPC (2016) Evaluating the diversity of Neotropical anurans using DNA barcodes. ZooKeys 637: 89-106. https://doi.org/10.3897/zookeys.637.8637
Data on the specimens examined in the present study : Explanation note: Please note that some of the sequences used in the study are incompletely referenced in the GenBank barcode database because they lack some data and we are unable to rectify this because the samples were collected too long ago (1980s or before) for the missing data to be found.
Supplementary material 1 from: Raupach MJ, Hannig K, Morinière J, Hendrich L (2016) A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. ZooKeys 592: 121-141. https://doi.org/10.3897/zookeys.592.8316
Barcode analysis using the BOLD workbench : Explanation note: Molecular distances based on the Kimura 2-parameter model of the analyzed specimens of the analyzed species of the genera Asaphidion, Bembidion, Ocys and Sinechostictus. Divergence values were calculated for all studied sequences, using the Nearest Neighbour Summary implemented in the Barcode Gap Analysis tool provided by the Barcode of Life Data System (BOLD). Align sequencing option: BOLD aligner (amino acid based HMM), ambiguous base/gap handling: pairwise deletion. ISD = intraspecific distance. BINs are based on the barcode analysis from 01-02-2016. Asterisks indicate species not recorded from Germany. Species with intraspecific maximum pairwise distances >2.2% and species pairs with interspecific distances <2.2% are marked in bold. Country codes: A = Austria, B = Belgium, CZ = Czech Republic, D = Germany, F = France, I = Italy, S = Sweden and SLO = Slovenia.
Supplementary material 2 from: Raupach MJ, Hannig K, Morinière J, Hendrich L (2016) A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. ZooKeys 592: 121-141. https://doi.org/10.3897/zookeys.592.8316
Neighbor joining topology : Explanation note: Neighbor joining topology of all analyzed carabid beetles based on Kimura 2-parameter distances. Specimens are classified using ID numbers from BOLD and species name. Numbers next to nodes represent non-parametric bootstrap values (1,000 replicates, in %).
Supplementary material 2 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Uncorrected P-Distance : Explanation note: Uncorrected P-Distance between the 66 analyzed specimens.
Supplementary material 1 from: Raupach MJ, Radulovici AE (2015) Looking back on a decade of barcoding crustaceans. ZooKeys 539: 53-81. https://doi.org/10.3897/zookeys.539.6530
A decade of DNA barcoding of crustaceans: input file: Explanation note: Raw data related to 164 publications on crustacean barcoding as retrieved from Web of Science: bibliography, citations, habitat type, geographical area, BOLD use.
Supplementary material 2 from: Hogendoorn K, Stevens M, Leijs R (2015) DNA barcoding of euryglossine bees and the description of new species of Euhesma Michener (Hymenoptera, Colletidae, Euryglossinae). ZooKeys 520: 41-59. https://doi.org/10.3897/zookeys.520.6185
Phylogenetic relationships of euryglossine species based on CO1 sequence data: Explanation note: tree based on CO1 sequence data.
Supplementary material 6 from: Rozo-Lopez P, Mengual X (2015) Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology. ZooKeys 513: 39-64. https://doi.org/10.3897/zookeys.513.9561
NJ tree based on 1,292 sequences of Neotropical mosquitoes: Explanation note: Original Neighbour-Joining tree of the barcoding sequences of mosquito species listed for the Neotropics, based on Tamura-Nei genetic distances (.tre).
Supplementary material 2 from: Rozo-Lopez P, Mengual X (2015) Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology. ZooKeys 513: 39-64. https://doi.org/10.3897/zookeys.513.9561
COI mosquito sequences downloaded from NCBI and BOLD: Explanation note: Sequences from NCBI and BOLD. Sequences downloaded between December 2013 and February 2014 for all identified species with a minimum length of 480 bp of COI barcoding region, no stop codons and possible alignment among the majority of the sequences. Total of 1,159 sequences. In blue: Additional species sequences from other geographic areas for those Neotropical groups without available sequences from the Neotropics.
Supplementary material 1 from: Wesener T, Voigtländer K, Decker P, Oeyen JF, Spelda J, Lindner N (2015) First results of the German Barcode of Life (GBOL) – Myriapoda project: Cryptic lineages in German Stenotaenia linearis (Koch, 1835) (Chilopoda, Geophilomorpha). In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 15-29. https://doi.org/10.3897/zookeys.510.8852
Table. Estimates of Evolutionary Divergence between Sequences: Explanation note: The number of base differences per site from between sequences are shown. The analysis involved 45 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All ambiguous positions were removed for each sequence pair. There were a total of 658 positions in the final dataset. Evolutionary analyses were conducted in MEGA6.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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