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2,052 results for “tree species”
Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf
<p>Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf.</p> <p>Ludt, W.B., Jabado, R.W., Al Hameli, S.M., Freeman, L., Teruyama, G., Chakrabarty, P. & Al Dhaheri, S.S. (2020) Establishing a reference collection and DNA barcoding the coastal fishes of the United Arab Emirates. <em>Journal of the Ocean Science Foundation</em>, 35, 54–64.</p>
Figure 2 from: Yang Q, Jiang N, Tian C-M (2020) Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed. MycoKeys 69: 71-89. https://doi.org/10.3897/mycokeys.69.54012
Figure 2 Maximum parsimony phylogram of Gnomoniosis based on a combined matrix of ITS, tef1-α and tub2 genes. The MP and ML bootstrap support values above 50% are shown at the first and second position, respectively. Thickened branches represent posterior probabilities above 0.90 from BI. Scale bar: 80 nucleotide substitutions. Strains in this study are in blue and ex-type strains are in blod.
Figure 4 from: Yang Q, Jiang N, Tian C-M (2020) Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed. MycoKeys 69: 71-89. https://doi.org/10.3897/mycokeys.69.54012
Figure 4 Cryphognomonia pini on Pinus armandii (BJFC-S1725) A–C habit of ascomata on twigs D, E transverse section of ascomata F longitudinal section through ascomata G asci H, I ascospores. Scale bars: 2 mm (A); 500 μm (B–F); 10 μm (G–I).
Figure 1 from: Yang Q, Jiang N, Tian C-M (2020) Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed. MycoKeys 69: 71-89. https://doi.org/10.3897/mycokeys.69.54012
Figure 1 Maximum parsimony phylogram of Gnomoniaceae based on a combined matrix of ITS, LSU, tef1 and rpb2 genes. The MP and ML bootstrap support values above 50% are shown at the first and second position, respectively. Thickened branches represent posterior probabilities above 0.90 from BI. Scale bar: 80 nucleotide substitutions. Strains in this study are in blue and ex-type strains are in blod.
Figure 3 from: Yang Q, Jiang N, Tian C-M (2020) Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed. MycoKeys 69: 71-89. https://doi.org/10.3897/mycokeys.69.54012
Figure 3 Maximum parsimony phylogram of Plagiostoma based on a combined matrix of ITS, tef1-α and tub2 genes. The MP and ML bootstrap support values above 50% are shown at the first and second position, respectively. Thickened branches represent posterior probabilities above 0.90 from BI. Scale bar: 30 nucleotide substitutions. Strains in this study are in blue.
Supplementary material 2 from: Liu F, Marincowitz S, Chen S, Mbenoun M, Tsopelas P, Soulioti N, Wingfield MJ (2020) Novel species of Huntiella from naturally-occurring forest trees in Greece and South Africa. MycoKeys 69: 33-52. https://doi.org/10.3897/mycokeys.69.53205
Figure S2. ML tree of Huntiella species generated from the BT1 DNA sequence data
Supplementary material 3 from: Liu F, Marincowitz S, Chen S, Mbenoun M, Tsopelas P, Soulioti N, Wingfield MJ (2020) Novel species of Huntiella from naturally-occurring forest trees in Greece and South Africa. MycoKeys 69: 33-52. https://doi.org/10.3897/mycokeys.69.53205
Figure S3. ML tree of Huntiella species generated from the TEF-1α DNA sequence data
Figure 2 from: Liu F, Marincowitz S, Chen S, Mbenoun M, Tsopelas P, Soulioti N, Wingfield MJ (2020) Novel species of Huntiella from naturally-occurring forest trees in Greece and South Africa. MycoKeys 69: 33-52. https://doi.org/10.3897/mycokeys.69.53205
Figure 2 Micrographs of Huntiella hellenica sp. nov. (ex-holotype CMW 54800 = PPRI 27982) A culture grown on 2% MEA at 30 °C (optimum growth temperature) in the dark for 34 d B, C colony with ascomatal base embedded in mycelia with ascospore mass at the tip of ostiolar neck D–F young ascoma showing development of ostiolar neck and less-pigmented base G, H mature ascoma ornamented with spines I close-up of ascomatal wall showing spines J–L close up of ornament (spin-like) M, N Ostiolar hyphae O Ascospores P Ascospores covered with sheath appearing like a hat Q, R Germinating ascospores S Lageniform conidiogenous cell T Cylindrical-shape conidiogenous cell U Conidia in various shapes from diverse barrel-shaped to rectangular-shaped V rectangular-shaped conidia W chains of conidia. Scale bars: 1 mm (B, C); 50 µm (D–H); 10 µm (I–W).
Figure 5 from: Yang Q, Jiang N, Tian C-M (2020) Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed. MycoKeys 69: 71-89. https://doi.org/10.3897/mycokeys.69.54012
Figure 5 Gnomoniopsis xunwuensis on Castanopsis fissa (BJFC-S1688) A symptoms on leaves of host plant B the colony on PDAC conidiomata on PDAD, E conidiophores attached with condia F conidia. Scale bars: 500 μm (C); 20 μm (D–F).
Figure 3 from: Liu F, Marincowitz S, Chen S, Mbenoun M, Tsopelas P, Soulioti N, Wingfield MJ (2020) Novel species of Huntiella from naturally-occurring forest trees in Greece and South Africa. MycoKeys 69: 33-52. https://doi.org/10.3897/mycokeys.69.53205
Figure 3 Micrographs of Huntiella krugeri sp. nov. (ex-holotype CMW 36849 = CBS 131676 = PPRI 27952). A Culture grown on 2% MEA in the dark for 34 d B, C Conidiogenous cell D Conidia in various shapes E Chain of conidia in different shapes F Chain of rectangular-shaped conidia with top-end of club-shaped G, HAleurioconidia. Scale bars: 10 µm (B–H).
Figure 1 from: Liu F, Marincowitz S, Chen S, Mbenoun M, Tsopelas P, Soulioti N, Wingfield MJ (2020) Novel species of Huntiella from naturally-occurring forest trees in Greece and South Africa. MycoKeys 69: 33-52. https://doi.org/10.3897/mycokeys.69.53205
Figure 1 ML tree of Huntiella species generated from the combined DNA sequence data of ITS, BT1 and TEF-1α DNA. Sequences generated from this study are printed in bold type. Bold branches indicate posterior probabilities values ≥ 0.9. Bootstrap values and posterior probabilities values are presented above branches as ML/MP/BI. Bootstrap value < 50% or probabilities values < 0.9 are marked with *. Nodes lacking the support value are marked with -. Ceratocystis cercfabiensis (CMW 43029) represents the outgroup.
Supplementary material 1 from: Liu F, Marincowitz S, Chen S, Mbenoun M, Tsopelas P, Soulioti N, Wingfield MJ (2020) Novel species of Huntiella from naturally-occurring forest trees in Greece and South Africa. MycoKeys 69: 33-52. https://doi.org/10.3897/mycokeys.69.53205
Figure S1. ML tree of Huntiella species generated from the ITS DNA sequence data
Figure 6 from: Yang Q, Jiang N, Tian C-M (2020) Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed. MycoKeys 69: 71-89. https://doi.org/10.3897/mycokeys.69.54012
Figure 6 Plagiostoma populinum on Populus tomentosa (BJFC-S1724) A–C habit of conidiomata on twigs D transverse section through conidiomata E longitudinal section through conidiomata F, G conidiogenous cells attached with conidia H, I condia. Scale bars: 2 mm (A); 1 mm (B, C); 500 μm (D, E); 10 μm (F–I).
Fig. 55. Maximum likelihood tree inferred from ITS2 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. 55. Maximum likelihood tree inferred from ITS2 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); 3–4 = ABGD with initial partitions (IP); 5–7 = ABGD with recursive partitions (RP); 8 = GMYC yule analysis; 9 = GMYC coalescent analysis; 10 = bPTP with ML; 11 = 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.
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)
<p>Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World Treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting and poorly supported topologies among major clades. We showed that incomplete lineage sorting was present at all nodes that exhibited high levels of discordance, which was caused by extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology, and hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that species tree inference can be improved using a total-evidence and multi-faceted approach that utilizes the most amount of data and considers results from different analytical methods and datasets.</p>
Genomic characterization and curation of UCEs improves species tree reconstruction: Supplementary Material S1
<p>Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all datasets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.<br> </p>
Figure 6 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 6. Megaselia henrydisneyi female, details of abdomen. (A) Left cercus; (B) lobes at rear of sternum 8; (C) tergites 5–7. Scale bars: 0.1 mm.
Figure 5 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 5. Megaselia henrydisneyi male. (A) Frons (with bristles represented by their basal sockets only); (B) right face of hypopygium; (C) left face of hypopygium. Scale bars: 0.1 mm.
Figure 2 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 2. Megaselia crassipes male (synonym of M. basiturgida). (A) Left face of hypopygium; (B) posterior face of front tibia and basitarsus. Scale bar: 0.1 mm.
Figure 4 from: Casiraghi A, Espadaler X, Pérez Hidalgo N, Gómez K (2020) Two additions to the Iberian myrmecofauna: Crematogaster inermis Mayr, 1862, a newly established, tree-nesting species, and Trichomyrmex mayri (Forel, 1902), an emerging exotic species temporarily nesting in Spain (Hymenoptera, Formicidae). Journal of Hymenoptera Research 78: 57-68. https://doi.org/10.3897/jhr.78.51858
Figure 4 Crematogaster inermis. Worker head in frontal view, with abraded mandible denticles. (HW 1.125 mm) (Image X. Espadaler).
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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.