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404 results for “DNA taxonomy”
Density-dependent effects of exotic brook trout on aquatic communities in mountain lakes revealed by environmental DNA and morphological taxonomy
Invasion of non-native fishes threatens freshwater biodiversity worldwide. Yet, detailed estimates of population demography for invasive species, that estimate population size and body size of the invasive species, are rarely integrated in evaluating aquatic community responses. Our study capitalized on detailed brook trout population demographic data collected for a replicated whole lake ecosystem experiment involving experimental harvesting of exotic brook trout in nine mountain lakes. We applied environmental DNA (eDNA) metabarcoding and morphological taxonomy to examine the response of crustacean zooplankton and macroinvertebrate communities to gradients in brook trout effective density and lake elevation. Density-dependent effects of brook trout on crustacean zooplankton and macroinvertebrate communities were detected even decades after their first introductions (between 1926 and 1980). However, they were moderated by environmental factors such as elevation, lake maximum depth and dissolved organic carbon. Elevation was important in structuring crustacean zooplankton and macroinvertebrate community composition. While there were differences in explanatory variables when describing communities characterized by eDNA metabarcoding and morphological taxonomy, the principal environmental factors that structured the communities were similar. Our paper highlights persisting density-dependent impacts of exotic trout on invertebrate communities even decades after first introduction, and it considers the conservation implications for lake restoration.
Figures 60–65 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 60–65. Heterolepisma cooloola sp. nov. holotype ♀ (60) presternum, prothoracic sternum and PI; (61) mesothoracic sternum and PII; (62) apex of mesothoracic sternum; (63) metathoracic sternum and PIII; (64) apex of metathoracic sternum; (65) pretarsus of PIII. Scale bars = 0.1 mm.
Figures 24–31 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 24–31. Heterolepisma coorongooba sp. nov. holotype ♀ (24) presternum, prothoracic sternum and PI; (25) mesothoracic sternum; (26) metathoracic sternum and PIII; (27) urotergite III; (28) idem, sublateral comb; (29) idem, submedial comb; (30) urotergite IX, infralateral combs; (31) urotergite X. Scale bars = 0.1 mm.
Figures 15–23 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 15–23. Heterolepisma coorongooba sp. nov. holotype ♀ (15) left lateral, anterior and posterior margins of pronotum; (16) idem, detail of left anterior trichobothrial area; (17) idem, detail of right posterior trichobothrial area; (18) idem, left posterior comb of pronotum; (19) lateral margin of mesonotum; (20) idem, trichobothrial areas of right side; (21) idem, left posterior comb of mesonotum; (22) lateral margin of metanotum; (23) idem, trichobothrial areas of left side. Scale bars = 0.1 mm.
Figures 7–14 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 7–14. Heterolepisma sclerophylla Smith and Heterolepisma coorongooba sp. nov. (7) Heterolepisma sclerophylla Smith, holotype ♀, medial section of pronotal collar. (8–14) Heterolepisma coorongooba sp. nov. holotype ♀ (8) medial section of pronotal collar; (9) lateral bristlecomb of urotergite III and adjacent scale; (10) head; (11) scape, pedicel and basal interval of flagellum, from above; (12) antenna, most distal surviving annuli; (13) maxilla, only larger setae of palp illustrated; (14) labium, setae of palp not strong so not illustrated. Scale bars = 0.1 mm.
Figures 32–36 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 32–36. Heterolepisma coorongooba sp. nov. holotype ♀, unless otherwise indicated by specimen number (32) urosternite III; (33) idem, posterior comb; (34) coxites VIII and IX, ovipositor and styli; (35) coxite IX, paramere and penis (K.260993); (36) paramere (K.260993). Scale bars = 0.1 mm.
Figures 78–85 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 78–85. Heterolepisma cooloola sp. nov. holotype ♀ unless otherwise indicated by specimen number (78) stylet IX (QM 207012); (79) apex of anterior gonapophysis; (80) apex of posterior gonapophysis; (81) bases of terminal filaments; (82) most distal surviving divisions of cerci; (83) most distal surviving divisions of median filament; (84) coxites IX, styli and penis of male (QM 207012); (85) paramere. Scale bars = 0.1 mm.
Figures 49–59 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 49–59. Heterolepisma cooloola sp. nov. holotype ♀ (49) labium, only large setae of palp illustrated; (50) idem, ultimate article of palp; (51) pronotum; (52) idem, right margin; (53) idem, detail of right anterior trichobothrial area; (54) idem, detail of left posterior trichobothrial area; (55) lateral margin of mesonotum; (56) idem, posterior trichobothrial area; (57) idem, anterior trichobothrial area; (58) idem, right posterior comb; (59) lateral margin of metanotum. Scale bars = 0.1 mm.
Figure 4 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 4. BI tree for concatenated COI and 28S genes. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figure 3 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 3. BI tree for nuclear gene 28S. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figure 5 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 5. Scatterplot of principal component analysis 1. Members of lineages are indicated by a ⅔ confidence interval ellipse.
Figures 38–48 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 38–48. Heterolepisma cooloola sp. nov. holotype ♀, unless indicated otherwise by specimen number(38) habitus (K.377754); (39) posterior comb of pronotum with scale; (40) head; (41) scape, pedicel and basal intervals of flagellum, from above; (42) idem, from below; (43) antenna, most distal surviving interval; (44) mandible; (45) idem, detail of molar and incisor regions; (46) maxilla, only larger setae of palp illustrated; (47) idem, lacinia and galea (QM 207012); (48) ultimate article of maxillary palp of ♂ (QM 207012). Scale bars = 0.1 mm unless otherwise indicated.
Figures 66–77 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 66–77. Heterolepisma cooloola sp. nov. holotype ♀, unless otherwise indicated by specimen number (66) urotergite IV; (67) urotergite V, right lateral comb; (68) idem, left sublateral comb; (69) idem, left submedial comb; (70) right side of urotergite VIII (K.261189); (71) infralateral comb of urotergite IX; (72) urotergite X; (73) urotergite X of paratype (QM 207012); (74) urosternite IV; (75) posterior comb of urosternite V; (76) urosternites VII, VIII, IX and ovipositor; (77) base of stylus VII. Scale bars = 0.1 mm.
Figure 2 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 2. BI trees for mitochondrial genes 16S and COI. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively.Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figs 30–35 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Figs 30–35. Variation of the male palps, left palps, prolateral views. 30–33. Loxosceles tolantongo sp. nov. 30–32. Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo (type locality). 33. 500 m west of the entrance No. 5 to the Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo. 34–35. Loxosceles jaca Gertsch & Ennik, 1983. 2.5 km north of Jacala de Ledezma, Municipality of Jacala de Ledezma, Hidalgo. Scale bars = 0.5 mm.
Fig. 56 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 56. Maximum likelihood tree inferred from the concatenated matrix (CO1 + ITS2) of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–5 = ABGD with recursive partitions (RP); 6 = GMYC yule analysis; 7 = GMYC coalescent analysis; 8 bPTP with ML; 9 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
Figs 20–25 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Figs 20–25. Loxosceles tolantongo sp. nov., ♂ holotype (CNAN-T01317). 20–22. Left palp, prolateral, dorsal and retrolateral views, respectively. 23–25. Detail of the bulb and embolus, retrolateral, dorsal and apical views, respectively. Scale bars: 20–22 = 0.5 mm; 23–25 = 0.2 mm.
Fig. 54 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 54. Maximum likelihood tree inferred from CO1 gene of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–6 = ABGD with recursive partitions (RP); 7 = GMYC yule analysis; 8 = GMYC coalescent analysis; 9 = bPTP with ML; 10 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers on branches correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
Figure 1 in Evaluation of the taxonomy of Helix cincta (Muller, 1774) and Helix nucula (Mousson, 1854); insights using mitochondrial DNA sequence data
Figure 1. Map showing the localities of samples used in the present study representing the morphologically defined species and the distribution of Helix cincta (dash line, light grey) and Helix nucula (continuous line, dark grey).
Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
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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.