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FIGURE 2 in Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.
FIGURE 2. Hemigrapha asteriscus (G 00292584, syntype). a. Herbarium material. b–d. Appearance of ascostromata on host surface. c, d. Ascostromata in the water. e–j. Section of ascostroma. h. Asci with hamathecial tissues. i–m. Asci. n, o. Ascospores. Scale bars: a = 20 mm, b–d = 500 μm, e–g = 50 μm, h–o = 5 μm.
FIGURE 1 in Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.
FIGURE 1. Maximum likelihood phylogenetic tree generated by RAxML (GTR+G model) based on analysis of combined LSU and SSU sequence data. ML values (>50 %) resulting from 1000 bootstrap replicates and Bayesian posterior probabilities greater than 0.80 are given at the nodes. The strain numbers are noted after the species names. The tree is rooted to Dendrographa decolorans (DUKE 0047570).
FIGURE 3 in Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.
FIGURE 3. Inocyclus psychotriae (K 180637, lectotype). a, b. Herbarium material. c, d. Ascostromata on leaves. E. Squash mount of dark brown to black ascostromata. f, g. Hand section of ascostroma (Note: the peridium without apical cells). h–l. Ascospores immersed in KOH. m–q. Asci with ascospores immersed in KOH. Scale bars: c =500 μm, d = 200 μm, e = 100 μm, f = 50 μm, g = 20 μm, h–l = 5 μm, m–q = 10 μm.
FIGURE 5 in Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.
FIGURE 5. Parmularia styracis (S F21306). A. Herbarium material. B. Appearance of ascostromata on upper of leaf surface. c, e, f. Black shield-like ascostroma. d. Dark brown ascostroma wall. G. Sections of ascostroma showing multi-locules. H. Wall cells of ascostroma. i, j. Asci with ascospores. K. Pseudoparaphyses with brown swollen apices. l–n. Immature hyaline ascospores. Scale bars: b =10 mm, c =1 mm, d = 5 μm, e, f = 500 μm, g=100 μm, h = 50 μm, i–k = 10 μm, l–n = 10 μm.
FIGURES 9–15 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURES 9–15. Tetrasporangial anatomy of the holotype of Sporolithon indopacificum (L 3964509). 9. Scanning electron micrograph (SEM) showing two tetra/bisporangial sori in surface view (arrowheads) (scale bar = 200 μm). 10. SEM showing a magnified view of several tetra/bisporangial chambers in surface view. Note the open, unoccluded pores (P), intact pore plugs (p) and the rosette cells surrounding the pores (scale bar = 15 μm). 11. Transverse section through two contiguously fused protuberances showing an extensive sorus (arrowheads) (scale bar = 300 μm). 12. Vertical section through the edge of a raised sorus (S) showing tetra/bisporangial chambers with floors (black arrowhead) that are flush with the surrounding vegetative surface (white arrowhead) (scale bar = 50 μm). 13. Vertical section through the edge of a raised sorus (S) showing tetra/bisporangial chambers with floors (black arrowhead) that are sunken below the surrounding vegetative surface (white arrowhead) (scale bar = 50 μm). 14. Vertical section through a sorus showing several tightly abutting, longitudinally elliptical tetra/bisporangial chambers bearing mostly uncleaved sporangia (t) borne on a single stalk cell (black arrowheads). Note the sporangial chamber pore plugs (white arrowheads), a 'T'-shaped divided tetrasporangium (T) and the sterile paraphyses of elongate cells (arrow) between two adjacent tetra/bisporangial chambers (scale bar = 50 μm). 15. Magnified view through a sorus showing three tetra/bisporangial chambers, one of which bears a zonately arranged bisporangium (B). Note the sporangial chamber pore plugs (white arrowheads) and the layer of elongate cells at the base of the sporangial chambers (black arrowheads) (scale bar = 30 μm).
FIGURES 3–8 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURES 3–8. Vegetative anatomy of the holotype of Sporolithon indopacificum (L 3964509). 3. Holotype specimen showing lumpy growth form with swollen, crowded protuberances (scale bar = 10 mm). 4. Magnified view of the protuberances showing their contiguously fused nature and numerous superficial sori (white arrowheads) scattered across the protuberances. Note that sori are often abraded or shed from the surface (black arrowheads) (scale bar = 2 mm). 5. Vertical section showing layers of S. indopacificum crusts (L) overgrowing itself in a superimposed manner (scale bar = 200 μm). 6. Vertical section through the monomerous thallus showing the epithallus (arrowhead) and a predominantly thick cortex (C) subtended by a thin medulla (M) (scale bar = 100 μm). 7. Vertical section of the ventral region of the thallus showing a plumose medulla (M) and cortical filaments (C) joined primarily by secondary pit connections (arrowheads) (scale bar = 50 μm). 8. Vertical section of the dorsal region of the thallus showing a single layer of flared epithallial cells (arrow) subtended by a layer of subepithallial initials (i). Note the layer of senescent epithallial cells (e) being shed, the primary pit connections between adjacent cortical filaments (black arrowheads) and a single, rare cell fusion (white arrowhead) (scale bar = 20 μm).
FIGURE 1 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURE 1. Phylogram of Sporolithon species inferred by maximum likelihood analysis of psbA sequences; Heydrichia species were the outgroup; sequences identified by GenBank accession number. Bolded scientific names are type specimens, topotype specimens, or specimens linked to type specimens by DNA sequence. Bootstrap support values (in %) are provided for nodes where> 50%. Scale bar refers to substitutions per site.
FIGURE 2 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURE 2. Phylogram of Sporolithon species inferred by maximum likelihood analysis of rbcL sequences; Heydrichia species were the outgroup; sequences identified by GenBank accession number. Bolded scientific names are type specimens, topotype specimens, or specimens linked to type specimens by DNA sequence. Bootstrap support values (in %) are provided for nodes where> 50%. Scale bar refers to substitutions per site.
FIGURE 3 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 3. Bayesian maximum clade reliability trees based on combined nuclear At103 and chloroplast rps16, trnL-F datasets for Dracaena, Sansevieria, and selected outgroups. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP. Long branches were shortened by half their length (indicated by \\).
FIGURE 2 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 2. Bayesian maximum clade credibility trees based on nuclear At103 (A) and chloroplast rps16, trnL-F (B) datasets for Dracaena and Sansevieria. Outgroups were trimmed from the Figure. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP.
FIGURE 1 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 1. Representative morphological diversity in the dracaenoid genera, Dracaena and Sansevieria. A, Dracaena draco subsp. draco, Spain, Canary Islands, Tenerife, Icod de los Vinos; B, D. konaensis, origin: USA, Hawai'i, Big Island, Kona coast, in cultivation at Kew (Acc. No. 2008-239); C, D. arborea, Gabon, Woleu-Ntem Rd, Mitzic to Njole; D, D. laxissima, São Tomé and Príncipe, São Nicolau; E, D. goldieana, origin: Gabon, in cultivation at Kew (Acc. No. 1990-2300); F, D. aubryana, Gabon, Woleu-Ntem Rd Mitzic to Njole; G, Sansevieria frequens, Kenya, Laikipia District, Ngare Ndare Farm (type locality); H, S. aethiopica, Namibia, 74 km from Windhoek, on road to Walvis Bay; I, S. fischeri, Kenya, Munda, 18.9 km NE of Mwatate on Taveta road; J, S. pinguicula, Kenya, by Kowi airstrip, north bank of Tiva Lugga; K, S. ascendens, Kenya, Coast Province, Kwale District, around base of Taru Hill (type locality); L, S. kirkii var. pulchra, in cultivation (private collection, Miami, FL). Photographs by A, L. Mucina; B, I. Willey; C, E–F, T.H.J. Damen; D, J.J.F.E. de Wilde; G-K, L. E. Newton; L, S. Zona.
FIGURE 2 in Bipolaris omanensis, a novel saprobic species of Bipolaris from Oman based on morphology and sequence data
FIGURE 2. Bipolaris omanensis (SQUCC 13828) a–e Conidiophores. f–i Conidia. j–l Conidiophore with conidia under scanning electron microscope. Scale bars a, b, d, f, j, i = 25 μm, Scale bar of b applies to b–c. Scale bar of d applies to d–e, Scale bar of f applies to f–i, Scale bar of j applies to j–k.
FIGURE 1 in Bipolaris omanensis, a novel saprobic species of Bipolaris from Oman based on morphology and sequence data
FIGURE 1. Phylogram generated from maximum likelihood analysis (ML) of combined ITS and GAPD sequence data of species of Bipolaris. ML bootstrap support values ≥50 % and ML bootstrap support values ≥50 % are given at the nodes (ML/MP). The new isolates are in red and the tree is rooted with Curvularia lunata (CBS 157.34) and Curvularia subpapendorfii (CBS 656.74). The scale bar represents the expected number of changes per site.
miRNA sequencing raw data_cgmuro
Open the record for dataset details and reuse information.
Fastqc reports of sequencing data from Coccomyxa elongata SAG 216-3b
<p>Here we provide access to the fastqc files of the corresponding PacBio Hifi, ONT, Hi-C and RNAseq data that were used to generate a high-quality chromosome-scale genome assembly and annotation for the freshwater alga <em>Coccomyxa elongata </em>SAG 216-3b.</p>
FIGURE 1. A–B. Veltheimia capensis. A in Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data
FIGURE 1. A–B. Veltheimia capensis. A. Flowering plant in situ. B. Plant in fruit, also showing the papery tunic at the exposed part of the bulb. C–F. Veltheimia bracteata. C. Yellow form in cultivation. D. Common colour form. E. Striated leaved form from Baviaanskloof. F. Whole plant showing the globose bulb and fleshy scales. Photographs: A, B: L. Mucina; C: J. Sampson; D: T. Dold; E: G. Schafer; F: N. Barker.
FIGURE 2 in Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data
FIGURE 2. Specimen distribution of species of Veltheimia. Red dots = known localities of V. bracteata, blue triangles = known locations of V. capensis (based on data from the BODATSA database of the National Herbarium, South Africa, http://posa.sanbi.org/). The inserted frame shows the Bayesian Inference phylogeny of the combined chloroplast non-coding data set (numbers shown below the branches indicate Posterior Probability values, the number above the red branch is the parsimony Bootstrap Support value). The branch with the thick red line indicates the "bracteata clade". Numbers preceding sample names link to specimens listed in Table 1, and are also (where the locality is known) indicated on the map. The Median Joining Network (MJN) is shown overlaid on the distribution to indicate the location of the samples (and haplotypes) used in the MJN analysis. The numbers in parentheses next to the lines linking the haplotypes indicate the number of mutational differences between the haplotypes, and the solid black circle indicate an un-sampled or hypothesised missing haplotype.
Associated data for "Optimisation strategies for directed evolution without sequencing"
<p>Associated publication available at https://www.biorxiv.org/content/10.1101/2024.03.18.585521v1. Code for visualisation available at https://github.com/nesou2/direvo_sim (PLOS_figures/PLOS_figures.ipynb).</p>
Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
Data from: A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability
1. Combining several crop species and associated agricultural practices in a crop sequence has the potential to control weed abundance while promoting weed diversity in arable fields. However, how the variability of environmental conditions that arise from crop sequences affects weed diversity and abundance remains poorly understood, with most studies to-date simply opposing weed communities in monoculture and in crop rotation. Here, we describe crop sequences along gradients of disturbance and resource variability using a crop functional trait and associated agricultural practices. We tested the hypothesis that variability of disturbances reduces weed abundance while variability of resources promotes weed diversity. 2. We used functional Hill's numbers to compute crop sequence functional diversity based on sowing date, herbicide spectrum and crop height - these are the respective proxies of disturbance timings, disturbance types and light availability. Using a large-scale weed monitoring database, we assessed crop sequence diversity for 1045 crop sequences of five consecutive cropping seasons. We computed weed richness and abundance at pluri-annual (pool of weeds observed across five cropping seasons) and annual (pool of weeds observed during a winter cereal cropping season preceded by five cropping seasons) scales. We also accounted for herbicide and tillage intensities to test whether management intensity affects the response of weed diversity and abundance to crop sequence diversity. 3. At the pluri-annual scale, weed richness increased with the diversity of crop height and sowing date while weed abundance decreased with sowing date diversity. Annual weed richness decreased with sowing date diversity while annual weed abundance poorly relied on crop sequence diversity. 4. Synthesis and applications. This study establishes a scientific basis for designing crop sequences according to specific weed management goals. We show that farmers may enhance arable weed diversity on a pluri-annual scale by sequentially sowing crop species that differ in their competitive ability and sowing date. They may also achieve a better control of weed abundance by increasing the diversity of crop sowing dates across the crop sequence.
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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)
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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.