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2,052 results for “tree species”
Figure 1 from: Zumstein P, Bruelheide H, Fichtner A, Schuldt A, Staab M, Härdtle W, Zhou H, Assmann T (2021) What shapes ground beetle assemblages in a tree species-rich subtropical forest? In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 907-927. https://doi.org/10.3897/zookeys.1044.63803
Figure 1 Relationships between ground beetle abundance and canopy cover (A), herb cover (B) and pH-value of the soil (C). Black lines indicate significant relationships at p < 0.05 obtained from mixed-effects models (keeping other significant predictors fixed at their means) with grey areas indicating the 95% confidence intervals. Points represent observed values per trap. Note that some traps had similar abundance and predictor values. The fixed-effects explained 22% of the variation in ground beetle abundance.
FIGURE 3 in Mimosa sobralii (Fabaceae, Mimosoideae), a new tree species endemic to the southern Brazilian highland slopes
FIGURE 3. Distribution of Mimosa sobralii and Mimosa bifurca in South America.
SimPhy configuration scripts for simulations reported in the study titled: Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs
<p>Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number of loci available for analysis. The question we seek to answer in this study is: What happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two large biological data sets, we show that running such methods on data with paralogs can still provide accurate results. We use multiple different methods, some of which are based directly on the multispecies coalescent (MSC) model, and some of which have been proven to be statistically consistent under it. We also treat the paralogous loci in multiple ways: from explicitly denoting them as paralogs, to randomly selecting one copy per species. In all cases the inferred species trees are as accurate as equivalent analyses using single-copy orthologs. Our results have significant implications for the use of ILS-aware phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci. This will greatly increase the amount of data that can be used for phylogenetic inference.</p>
FIGURE 7. Maximum likelihood phylogenetic tree inferred from a in Three uncharted endemicearthworm species of the genus Eutyphoeus (Oligochaeta Octochaetidae) from Mizoram, India
FIGURE 7. Maximum likelihood phylogenetic tree inferred from a dataset of 609 positions.
FIGURE 3 in A new tree species of Schinopsis (Anacardiaceae) from Paraguay and Bolivia
FIGURE 3. Distribution map of S. boqueronensis in South America.
Figure 9 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 9 Sporothrix cryptarchum sp. nov. (CBS 147934) a ascoma b ascomatal base c, d ostiolar hyphae e ascospores f asci g conidiogenous cell with an inflated cluster of denticles at the apex h conidia i globose conidia arising on long conidiophore j globose conidia arising directly from hyphae k fourteen-day-old culture on MEA. Scale bars: 100 μm (a), 25 μm (b–d), 10 μm (e), 25 μm (f, g), 10 μm (h, i), 5 μm (j).
Figure 8 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 8 Sporothrix resoviensis sp. nov. (CBS 147927) a ascoma b, c ostiolar hyphae d ascospores e–g conidiogenous cell with an inflated cluster of denticles at the apex h conidia i fourteen-day-old culture on MEA. Scale bars: 250 μm (a), 25 μm (b, c), 10 μm (d), 25 μm (e), 10 μm (f–h).
Figure 7 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 7 Sporothrix fraxini sp. nov. (CBS 147936) a ascoma b ascomatal base c ostiolar hyphae d ascospores e conidiogenous cell with an inflated cluster of denticles at the apex f conidia g fourteen-day-old culture on MEA. Scale bars: 100 μm (a), 50 μm (b), 25 μm (c), 10 μm (d–f).
Figure 5 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 5 Phylogram obtained from Maximum Likelihood (ML) analyses of the combined βT and CAL sequences of the Sporothrix spp. Sequences obtained during this study are presented in bold type. The Bootstrap values ≥ 75% for ML and Maximum Parsimony (MP) analyses are presented at nodes as follows: ML/MP. Bold branches indicate posterior probabilities values ≥ 0.95 obtained from Bayesian Inference (BI) analyses. * Bootstrap values <75%. The tree is drawn to scale (see bar) with branch length measured in the number of substitutions per site. Graphilbum fragrans represent the outgroup.
Figure 6 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 6 Sporothrix cracoviensis sp. nov. (CBS 147942) a ascoma b ascomatal base c ostiolar hyphae d ascospores e, f conidiogenous cell with an inflated cluster of denticles at the apex g conidiogenous cells arising directly from hyphae h conidia i fourteen-day-old culture on MEA. Scale bars: 50 μm (a, b), 25 μm (c), 10 μm (d–h).
Figure 4 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 4 Phylogram obtained from Maximum Likelihood (ML) analyses of TEF1-α data for the Sporothrix spp. Sequences obtained during this study are presented in bold type. The Bootstrap values ≥ 75% for ML and Maximum Parsimony (MP) analyses are presented at nodes as follows: ML/MP. Bold branches indicate posterior probabilities values ≥ 0.95 obtained from Bayesian Inference (BI) analyses. * Bootstrap values <75%. The tree is drawn to scale (see bar) with branch length measured in the number of substitutions per site. Graphilbum fragrans represent the outgroup.
Figure 2 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 2 Phylogram obtained from Maximum Likelihood (ML) analyses of βT data for the Sporothrix spp. Sequences obtained during this study are presented in bold type. The Bootstrap values ≥ 75% for ML and Maximum Parsimony (MP) analyses are presented at nodes as follows: ML/MP. Bold branches indicate posterior probabilities values ≥ 0.95 obtained from Bayesian Inference (BI) analyses. * Bootstrap values <75%. The tree is drawn to scale (see bar) with branch length measured in the number of substitutions per site. Graphilbum fragrans represent the outgroup.
Figure 3 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 3 Phylogram obtained from Maximum Likelihood (ML) analyses of CAL data for the Sporothrix spp. Sequences obtained during this study are presented in bold type. The Bootstrap values ≥ 75% for ML and Maximum Parsimony (MP) analyses are presented at nodes as follows: ML/MP. Bold branches indicate posterior probabilities values ≥ 0.95 obtained from Bayesian Inference (BI) analyses. * Bootstrap values <75%. The tree is drawn to scale (see bar) with branch length measured in the number of substitutions per site. Graphilbum fragrans represent the outgroup.
Figure 11 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 11 Sporothrix cavum sp. nov. (CBS 147943) a–c conidiogenous cell with an inflated cluster of denticles at the apex and below apex d conidiogenous cells arising directly from hyphae e conidia f fourteen-day-old culture on MEA. Scale bars: 10 μm (a), 25 μm (b), 10 μm (c–e).
Figure 10 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 10 Sporothrix undulata sp. nov. (CBS 147929) a ascoma b ascomatal base c ostiolar hyphae d asci e ascospores f–h globose conidia arising on long conidiophore or directly from hyphae i globose conidia j conidiogenous cell with an inflated cluster of denticles at the apex k conidia l–m fourteen-day-old culture on MEA (left- pigmented CBS 147929, right – white KFL404DB16bRJCU). Scale bars: 100 μm (a), 25 μm (b–d), 10 μm (e), 25 μm (f), 10 μm (g, h), 5 μm (i), 10 μm (j), 5 μm (k).
Figure 1 from: Ostafińska A, Jankowiak R, Bilański P, Solheim H, Wingfield MJ (2021) Six new species of Sporothrix from hardwood trees in Poland. MycoKeys 82: 1-32. https://doi.org/10.3897/mycokeys.82.66603
Figure 1 Phylogram obtained from Maximum Likelihood (ML) analyses of the ITS1-5.8S-ITS2 data for the Sporothrix spp. Sequences obtained during this study are presented in bold type. The Bootstrap values ≥ 75% for ML and Maximum Parsimony (MP) analyses are presented at nodes as follows: ML/MP. Bold branches indicate posterior probabilities values ≥ 0.95 obtained from Bayesian Inference (BI) analyses. * Bootstrap values <75%. The tree is drawn to scale (see bar) with branch length measured in the number of substitutions per site. Graphilbum fragrans represent the outgroup.
Figure 6. A reference tree produced with 58 in Taxonomy and phylogeny of the genus Liotesba Scheerpeltz (Coleoptera: Staphylinidae: Staphylininae: Xantholinini) with descriptions of four new species
Figure 6. A reference tree produced with 58 characters.
Fig. 2 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia
Fig. 2. Clustering of populations in morphospace as inferred from the first three principal components of the PCA analysis (A–C; E–G) and the discriminant analysis of principal components (D, H).
Fig. 6 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia
Fig. 6. Dorsal and ventral images of Rentapia flavomaculata, new species, paratype UMTZC 1404 (A, B) from Sungai Bubu, Terengganu, Malaysia and BBM 7252 (C, D) from Kota Tinggi, Johor, Malaysia.
FIG. 3. The tree resulting from a in Three New Species of Musseromys (Muridae, Rodentia), the Endemic Philippine Tree Mouse from Luzon Island
FIG. 3. The tree resulting from a maximum-likelihood analysis of the cytochrome b gene from Phloeomys Division species under the best-fitting model (GTR+I+Γ4). Numbers at nodes indicate maximum-likelihood (above the line) bootstrap support. Terminal taxa are identified by species name and a unique alphanumeric identifier (either FMNH catalog number or Genbank accession number). Trees are rooted with Rattus norvegicus (Genbank number X14848) and with three species of gerbil: Meriones unguiculatus (AF119264), Gerbillus nigeriae (AJ430555), and Gerbilliscus guineae (AJ430562) as outgroups (not shown). Black and gray branches indicate elevational range reconstructed using parsimony optimization (see Molecular Genetic Methods), where black and grey indicate lowland and montane distributions, respectively.
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.