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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.
Figure 8 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach
Figure 8. Obama maculipunctata sp. nov. in dorsal view. (A) Photograph of a live specimen (holotype MZUSP PL.1565). (B) Dorsal pattern of pigmentation of the holotype. (C) Eye pattern of a fixed specimen (paratype MZU PL.00197). (D) Photograph of monolobated eyes of a fixed specimen (paratype MZU PL.00197) in clove oil. (E) Photograph of trilobated eyes of a fixed specimen (paratype MZU PL.00197) in clove oil.
Figure 2 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach
Figure 2. Cratera ochra sp. nov., holotype, in dorsal view. (A) Photograph of the live specimen. (B) Dorsal pattern of pigmentation of the preserved specimen.
Figure 1. Bayesian phylogenetic tree inferred from the 640 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach
Figure 1. Bayesian phylogenetic tree inferred from the 640-bp of cytochrome c oxidase subunit I gene under GTR + I + G model of sequence evolution. The two new species are highlighted in light grey (Cratera ochra sp. nov.) and dark grey (Obama maculipunctata sp. nov.). Values indicate support for each node according to the maximum posterior probabilities>70% and bootstrap support values> 70%, respectively.
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.
Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon
<p>This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus <em>Calandrella</em>, with the description of a range-restricted African relic taxon" by Stervander <em>et al</em>. </p> <p>For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript. </p> <p><strong>Phylogenetic analyses</strong></p> <ol> <li>Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa</li> <li>BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml</li> <li>BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log</li> <li>BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees</li> <li>TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk</li> </ol> <p><strong>Species delimitation</strong></p> <ol> <li>Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk</li> <li>mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt</li> <li>mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt</li> <li>mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg</li> </ol>
Fig. 4 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 4. Amobia burnsi (Malloch, 1930), ♂, NSW, North Head, Sydney Harbour, 14 Feb. 1978, G. Daniels leg. (AM) A. Habitus, lateral view. B. Head, lateral view. C. Habitus, dorsal view. D. Head, dorsal view. E. Abdomen, dorsal view. F. Left wing, dorsal view. G. Head, anterior view. Scale bars: 1 mm.
Fig. 1 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 1. Maximum likelihood phylogenetic tree indicating the placement of Amobia among the global Miltogramminae, inferred from COI, CYTB, ND4 and EF1α sequence data. With the exception of the three newly sequenced Australian Amobia and Macronychia rubesca, data was acquired from Piwczyński et al. (2017). Node support values are shown for both maximum likelihood analysis (bootstrap support, 1000 iterations; in bold font) and Bayesian analysis (posterior probability, 40 million generations), 'NA' indicates nodes resolved that were not resolved by the Bayesian analysis. Branch length scale = 0.3 nucleotide substitutions per site (calculated by the GTR+G nucleotide substitution model).
Fig. 6 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 6. Amobia serpenta sp. nov., holotype, ♂, NT, Serpentine Gorge, West MacDonnell National Park, 13 Nov. 2017, Johnston, Wallman and Szpila leg. (ANIC). A. Habitus, lateral view. B. Head, lateral view. C. Habitus, dorsal view. D. Head, dorsal view. E. Abdomen, dorsal view. F. Left wing, dorsal view. G. Head, anterior view. Scale bars: 1 mm.
Fig. 3 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 3. Amobia auriceps (Baranov, 1935), male terminalia, QLD, Cairns, 1919, J.F. Illingworth leg. (BM). A. Epandrium, cerci, surstyli and phallus, posterior view. B. Epandrium, cerci, surstyli, phallus and pre-gonite, lateral view. Abbreviations: c = cercus; d = distal lobe of phallus; s = surstylus; p = pregonite. Scale bars: 100 µm.
Fig. 5 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 5. Amobia burnsi (Malloch, 1930), male terminalia, NT, 15 km N Katherine, 16 May 2005, R.W. Matthews leg (ANIC). A. Epandrium, cerci, surstyli and phallus, posterior view. B. Epandrium, cerci, surstyli, phallus and pre-gonite, lateral view. C. SEM image of epandrium, gonites, cerci and surstyli, posterior view. D. SEM image of epandrium, gonites, phallus, cerci and surstyli, lateral view. Abbreviations: c = cercus; d = distal lobe of phallus; s = surstylus; p = pre-gonite. Scale bars: 100 µm.
Fig. 2 in Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region
Fig. 2. Hyphessobrycon frickei Guimarães, Brito, Bragança, Katz & Ottoni sp. nov. (CICCAA 02388), 17.7 mm SL; jaw suspensory. A. Premaxillary. B. Maxilla. C. Dentary. Scale bar: 1 mm
Fig. 8 in Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region
Fig. 8. Topology of the ultrametric tree performed in BEAST ver. 1.8.4 including unique haplotypes summarizing the results of GMYC, bPTP and ABGD. Numbers above and below branches are posterior probability values. The star indicates the Hyphessobrycon copelandi clade.
Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach
<p>Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus <em>Quercus</em>). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analyzed inter- and intra-specific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models, and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with species distribution models and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.</p>
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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.