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274 results for “plant phylogeny”
Figure 2 in The Halticini of the world (Insecta: Heteroptera: Miridae: Orthotylinae): generic reclassification, phylogeny, and host plant associations
Figure 2. Implied weighting phylogeny (k = 3). Unambiguous character optimizations are indicated by circles: filled circles indicate synapomorphies, white circles indicate homoplasies. Numbers above and below circles indicate character number and state, respectively. Large red numbers above branches indicate jackknife support (values below 50% not reported).
Fig. 4 in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 4. - Circular gene tree of RIPs. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The phylogenetic tree was constructed using the maximum-likelihood method with the amino acid substitution model WAG + R9, ultrafast bootstrapping approximation (UFBoot) with 1000 iterations and the SH-like approximate likelihood ratio test with 1000 iterations. The legend titled 'Order (outer ring)' outlines the coloured dots around the perimeter of the tree and represents the phylogenetic order from which each protein sequence originated. Proteins without a coloured dot belong to orders with less than ten proteins. The legend titled 'RIP domains (inner lines)' defines colours in the branches of the tree, each representing a RIP group, based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 2. - The number and type of RIPs within each plant order. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. Colours represent different RIP groups. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 6. Tile plot of the most conserved amino acids within RIP domains of each protein group. The Y axis depicts the amino acid and corresponding position within the pokeweed antiviral protein (protein databank: 1QCI), the X axis depicts the proteins groups. For the two pink-highlighted amino acids on the Y axis, different amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. The solid blue cells represent amino acids conserved at least 70% within each RIP group and with shared identity to the reference sequence 1QCI. Patterned blue cells represent amino acids conserved at least 70% within RIP groups but without identity to 1QCI. Any amino acid positions with 70% consensus in less than three protein groups were collapsed and shaded black.
Fig. 3 in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 3. - The number of RIPs within each plant species. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. Colours represent different RIP groups. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 1. - Physicochemical characteristics of different RIP groups. Values were calculated from the amino acid coding sequence of each protein in our dataset with the R package 'peptides' and presented on boxplot format. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. (A) molecular weight prediction; (B) theoretical net charge prediction; (C) Boman potential protein interaction index prediction; (D) aliphatic index prediction.
Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a in Phylogeny and domain architecture of plant ribosome inactivating proteins
Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. Colours indicate amino acids conserved in at least 70% of sequences. For the two pink-highlighted proteins, the black bolded amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. (A) Sequence alignment. RIP domain consensus: the consensus sequence generated from the multiple sequence alignment in Jalview excluding gaps; 1QCI: the amino acid sequence of pokeweed antiviral protein (protein databank: 1QCI). The third line denotes the similarity in the two sequences as determined by Clustal Omega. (B) The crystal structure of 1QCI visualized in UCSF ChimeraX in surface representation; (C) mesh representation; and (D) cartoon representation. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Data from: Plant-soil feedbacks from 30-year family-specific soil cultures: phylogeny, soil chemistry and plant life stage
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Data from: Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi
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Community composition of arctic root-associated fungi mirrors host plant phylogeny
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Data from: Phylogeny of Cecropieae (Urticaceae) and the evolution of an ant-plant mutualism
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Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
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Data from: Dated plant phylogenies resolve Neogene climate and landscape evolution in the Cape Floristic Region
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Data from: Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna
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Flower traits, habitat and phylogeny as predictors of pollinator service: a plant community perspective
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Data from: Abundance, origin and phylogeny of plants do not predict community-level patterns of pathogen diversity and infection
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data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models"
<p>The nucleotide, codon-degenerate and protein concatenated alignments of 83 chloroplast genes, with the respective character sets, in nexus format.</p>
Data from: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions
Plants are the primary producers of the terrestrial ecosystems that dominate much of the natural environment. Occurring approximately 480 MYA (Sanderson 2003; Kenrick et. al. 2012), the evolutionary transition of plants from an aquatic to a terrestrial environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors of land plants have a haplobiontic life cycle with a single haploid multicellular stage, whereas land plants, which include the bryophytes (liverworts, hornworts, and mosses) and tracheophytes (also called vascular plants, namely, lycopods, ferns, and seed plants), exhibit a marked alternation of generations with a diplobiontic life-cycle with both haploid and diploid multicellular stages and where the embryo remains attached to, and is nourished by, the gametophyte (Haig 2008). The interjection of a multicellular diploid phase into the land plant life cycle was an important adaptation that enabled long-distance dispersal via mitotic spores where water-borne male gametes have restricted motility in dry terrestrial environments. Despite the similarity among land-plant life-cycles, they differ in one significant aspect: in the three bryophyte groups, the haploid gametophytic stage is the dominant vegetative stage, whereas in vascular plants the diploid sporophyte dominates. A common assumption, and one implied by the tradition of referring to bryophytes as "lower plants" - in contrast to the "higher plants", the tracheophytes - is that the bryophytes and their life-cycle are primitive (Kato and Akiyama 2005). However, without a strong phylogenetic hypothesis of land-plant relationships, it is not clear which (if either) of the gametophyte or sporophyte was the dominant ancestral vegetative state present in the earliest land plants (Renzaglia et al. 2007; Qiu et al. 2012). Early land plants have a relatively poor fossil record with few intermediate forms (Kenrick and Crane 1997; Wellman et al. 2003; Clarke et al. 2011), so most of the evidence for early land plant evolution has been based upon the patterns of morphological change that are implied by phylogenetic trees of relationships among extant land plant and algal groups. In this context, several recent studies based on large molecular data sets have converged upon a phylogenetic solution to land plant origins wherein tracheophytes are derived from bryophyte ancestors (Karol et al. 2001; Qiu et al. 2006; Gao et al. 2010; Karol et al. 2010; Chang and Graham 2011). In this hypothesis, the three bryophyte groups, namely liverworts, mosses, and hornworts, diverged sequentially and form a paraphyletic group with the hornworts sister to the tracheophytes. This phylogeny supports an intuitively elegant evolutionary trajectory whereby plants increased in morphological complexity from single-celled algae to seed plants via bryophyte intermediates (Karol et al. 2001; McCourt et al. 2004). Specifically, it implies that the gametophyte-dominant bryophyte life-cycle was ancestral among land plants and that the complex modular growth form of the vascular plant sporophyte evolved from the simplistic bryophyte sporophyte that consists only of a single growth module (Kato and Akiyama 2005; Barthélémy and Caraglio 2007).
Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens
• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.
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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.