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430 results for “phylogenetic relations”
FIGURE 1. Maximum Likelihood tree showing phylogenetic relationships among 124 in New insights on the systematics and reproductive behaviour in tree frogs of the genus Feihyla, with description of a new related genus from Asia (Anura, Rhacophoridae)
FIGURE 1. Maximum Likelihood tree showing phylogenetic relationships among 124 representative taxa from all recognised genera of the subfamily Rhacophorinae. Relationships are inferred based on 1,937 bp of mitochondrial (12SrRNA, tRNAVAL, 16SrRNA) and nuclear (RHO and RAG1) genes. Numbers above and below the branches indicate Bayesian Posterior Probabilities and RAxML bootstrap support values, respectively.
Data from: Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives
Premise of the study: Species limits of the emerging model organism Setaria viridis (tribe Paniceae, subtribe Cenchrinae) are not well defined. It is thought to be related to S. adhaerens, S. faberi, S. verticillata, and S. verticilliformis and in North America occurs with the morphologically similar S. pumila. An integrated approach was taken to evaluate its variation and relationships with the other taxa. Methods: Statistical morphology, flow cytometry, molecular phylogenetics, and growth experiments were employed to examine the group's physical variation, polyploidy, evolutionary relationships, and drought ecology, respectively. Key results: Setaria viridis contributed one genome to the tetraploids S. faberi, S. verticillata, and S. verticilliformis; the other genome of the latter two was contributed by S. adhaerens. Setaria pumila is unrelated. Morphologically, S. viridis is most similar to S. faberi, but all tested accessions of S. viridis were diploid, whereas those of S. faberi were all tetraploid. Principal component analysis of 70 morphological characters consistently separated S. viridis from S. faberi, largely by spikelet characters. The diagnostic morphological characters are not affected by watering. Setaria faberi is far more sensitive to drought, in terms of mortality and morphological stunting, than S. viridis or S. pumila. Conclusions: Setaria viridis is a diploid species and has contributed to several polyploid derivatives. The most morphologically similar of the polyploids is S. faberi, which differs in spikelet features, phylogenetics, genome size, and ecological response to drought. Researchers using field-collected S. viridis as a model organism will benefit from the clear delimitation provided in this study.
Data from: Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets
The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic spacer for 619 individuals representing ca. 354 species. The plastid rpoC1 gene (ca. 2600 bp) was sequenced for 84 selected species and combined in a more limited analysis with the other data sets to provide greater resolution. In a well-resolved, supported consensus, most clades were present in more than one individual analysis. All the currently recognized minor genera of "core" Maxillariinae (Anthosiphon, Chrysocycnis, Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium) are embedded within a polyphyletic Maxillaria s.l. Our results support the recognition of a more restricted Maxillaria, of some previously published segregate genera (Brasiliorchis, Camaridium, Christensonella, Heterotaxis, Ornithidium, Sauvetrea), and of several novel clades at the generic level. These revised monophyletic generic concepts should minimize further nomenclatural changes, encourage monographic studies, and facilitate more focused analyses of character evolution within Maxillariinae.
Data from: Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent
The origin of the fungal wheat pathogen Phaeosphaeria nodorum remains unclear despite earlier intensive global population genetic and phylogeographical studies. We sequenced 1,683 bp distributed across three loci in 355 globally distributed Phaeosphaeria isolates, including 74 collected in Iran near the center of origin of wheat. We identified nine phylogenetically distinct clades, including two previously unknown species tentatively named P1 and P2 collected in Iran. Coalescent analysis indicates that P1 and P2 are sister species of P. nodorum and the other Phaeosphaeria species identified in our analysis. Two species, P. nodorum and P. avenaria f. sp. tritici 1 (Pat1), comprised ∼85% of the sampled isolates, making them the dominant wheat-infecting pathogens within the species complex. We designed a PCR-RFLP assay to distinguish P. nodorum from Pat1. Approximately 4% of P. nodorum and Pat1 isolates showed evidence of hybridization. Measures of private allelic richness at SSR and sequence loci suggest that the center of origin of P. nodorum coincides with its host in the Fertile Crescent. We hypothesize that the origin of this species complex is also in the Fertile Crescent, with four species out of nine found exclusively in the Iranian collections.
FIGURE 2 in A new species of Typhlocharis Dieck, 1869 (Coleoptera: Carabidae: Anillini) from South Spain, with notes on the phylogenetic value of sexually related characters and the presence of stridulatory organ (pars stridens) in the genus
FIGURE 2. Abdomen (ventral view) of female and male, showing the median tubercle, the foveae, the chaetotaxy of the last segment and the "belt" of scaly microsculpture (shaded in grey).
FIGURE 4 in A new species of Typhlocharis Dieck, 1869 (Coleoptera: Carabidae: Anillini) from South Spain, with notes on the phylogenetic value of sexually related characters and the presence of stridulatory organ (pars stridens) in the genus
FIGURE 4. Pattern of microreticulation in the vertex region of T. monastica (a) and T. farinosae (b) showing the differences between species with and without pars stridens. (Modified from Zaballos & Wrase 1998, Zaballos & Ruíz-Tapiador 1997).
FIGURE 3 in A new species of Typhlocharis Dieck, 1869 (Coleoptera: Carabidae: Anillini) from South Spain, with notes on the phylogenetic value of sexually related characters and the presence of stridulatory organ (pars stridens) in the genus
FIGURE 3. Aedeagus in lateral and dorsal view, parameres in lateral view (a). Female genitalia in ventral view (b).
FIGURE 5 in The phylogenetic position of Aphrissa (Lepidoptera: Pieridae: Coliadinae) within its relatives the ancient American Catopsilias
FIGURE 5. Cladogram obtained to Aphrissa and its relatives under implied weights for K values of 1–10 (L=81, CI=61, RI=67). Numbers above branches indicate the characters and numbers below the branches indicate character states and branch support (bootstrap values). Black circles are apomorphies (synapomorphies or autapomorphies), white circles are homoplasies.
FIGURE 4 in The phylogenetic position of Aphrissa (Lepidoptera: Pieridae: Coliadinae) within its relatives the ancient American Catopsilias
FIGURE 4. Female genitalia of Aphrissa statira in dorsal view. Numbers indicate character and character state (23.1).
FIGURE 2 in The phylogenetic position of Aphrissa (Lepidoptera: Pieridae: Coliadinae) within its relatives the ancient American Catopsilias
FIGURE 2. Male genitalia of Anteos clorinde. Numbers indicate character and character state (13.0, 14.0, 15.1, and 16.1).
FIGURE 3 in The phylogenetic position of Aphrissa (Lepidoptera: Pieridae: Coliadinae) within its relatives the ancient American Catopsilias
FIGURE 3. Male genitalia of Phoebis argante. Numbers indicate character and character state (17.1 and 20.1).
FIGURE 1 in The phylogenetic position of Aphrissa (Lepidoptera: Pieridae: Coliadinae) within its relatives the ancient American Catopsilias
FIGURE 1. Apex shape of the forewings of Aphrissa and related genera. Numbers indicate character and character state.
FIGURE 13 in A fully web-illustrated morphological phylogenetic study of relationships among oak gall wasps and their closest relatives (Hymenoptera: Cynipidae).
FIGURE 13. Hypopygium: a Liebelia magna, b Cynips conspicua. Metasoma, male, lateral view: c Cynips.
FIGURE 12 in A fully web-illustrated morphological phylogenetic study of relationships among oak gall wasps and their closest relatives (Hymenoptera: Cynipidae).
FIGURE 12. Petiole: a Diplolepis triforma, b Neuroterus numismalis parth. gen., c Andricus quercusfoliata, d Biorhiza mellea.
FIGURE 6 in A fully web-illustrated morphological phylogenetic study of relationships among oak gall wasps and their closest relatives (Hymenoptera: Cynipidae).
FIGURE 6. Mesopleuron, lateral view: a Pediaspis aceris parth. gen., b Neuroterus numismalis parth. gen.
FIGURE 2 in A fully web-illustrated morphological phylogenetic study of relationships among oak gall wasps and their closest relatives (Hymenoptera: Cynipidae).
FIGURE 2. Pronotum, anterior view: a Phanacis phoenixopodos, b Trigonaspis gibbera, c Trichagalma serratae.
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm.
FIGURE. SEM images of the studied Coelastrella strains: (A) SYKOA Ch-045-09. (B) SYKOA Ch-047-11. (C) SYKOA Ch-072-17. (D) IRK-A 173. (E) IRK-A 2. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. SEM images of the studied Coelastrella strains: (A) SYKOA Ch-045-09. (B) SYKOA Ch-047-11. (C) SYKOA Ch-072-17. (D) IRK-A 173. (E) IRK-A 2. Scale bar: 10μm.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.