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29 results for “venom evolution”
Proteo-transcriptomic characterization of the venom from the endoparasitoid wasp Pimpla turionellae with aspects on its biology and evolution
<p>Within mega-diverse Hymenoptera non-aculeate parasitic wasps represent 75 % of all hymenopteran species. Their ovipositor dual-functionally injects venom and employs eggs into (endoparasitoids) or onto (ectoparasitoids) diverse host species. Few endoparasitoid wasps such as <em>Pimpla turionellae</em> paralyze the host and suppress its immune responses, such as encapsulation and melanization, to guarantee their offspring’s survival. In our proteo-transcriptomic analysis we shed new light on the venom biology of the endoparasitoid <em>Pimpla turionealle</em>.</p> <p>All additional data is made available here, such as the transcriptome assembly file, CDS prediction and all proteome data files including the raw data. All alignments to train HMMsearch and JACKHMMERsearch are stored here as well and the alignments of identified venom proteins (known and novel).</p> <p>The readme file gives further explanation/information.</p>
Evolution of venom production in marine predatory snails
<p>This repository contains the following datasets:</p> <ul> <li><strong>annotations.zip</strong>: includes two files per species. The "species_code_annot.tsv" file (e.g., CI_annot.tsv) includes the blast hits to Uniprot/SwissProt (_sp), gastropod genomes (_gastr), Cdd (_cdd), Pfam (_pfam), ToxProt (_tox), and Conoserver (_cono); the output of SignalP and of ConoPrec. The "species_code_topGO.tsv" file (e.g., CI_topGO.tsv) corresponds the GO annotations in a format compatible with TopGO.</li> <li><strong>assemblies.zip</strong>: includes the nucleotide coding sequences as "species_code_cds.fasta" (e.g., CI_cds.fasta) and the predicted amino acid sequences as "species_code.faa" (e.g., CI.faa) in fasta format.</li> <li><strong>expression_matrices.zip</strong>: includes the final, quality-filtered expression matrices in TPM for each species separately as "species_code_tpm.tsv" (e.g., CI_tpm.tsv). The multi-species expression matrices based on the random-selection method ("multispecies_tpm_random.tsv") and mean method ("multispecies_tpm_mean.tsv") are provided.</li> <li><strong>tissue_specific_gene_sets.zip</strong>: includes the list of tissue-specific genes for each species as "species_code_fc2_tb.tsv" (e.g., CI_fc2_tb.tsv). The column "tissue1" corresponds to the tissue with the highest TPM value ("tpm1"), therefore the tissue to which that gene is specific, while "tissue2" correspond to the tissue with the second-highest TPM values ("tpm2"). "FC" is the fold-change.</li> <li><strong>orthologer_output</strong>: includes the orthogroup assigment as outputted by the software OrthoLoger. Specifically, "path2proteome_orthogroups.txt" corresponds to the orthogroup assignment for all genes assigned to an orthogroup, while "path2proteome_stats.txt" list some statistic parameters (e.g., size of the orthogroups etc.).</li> <li><strong>CAGEE_output</strong>: includes the output from the software CAGEE as reported in the manual (https://github.com/hahnlab/CAGEE/blob/main/docs/manual/cagee_manual.md#Installation). The results for both, a gene expression matrix based on the random-selection method and the mean-based method are reported in separate folders. Within each folder are reported the results for the gland, salivary glands, and oesophagus separately. Additionally, the ultrametric species tree and the sigma tree, both in in Newick format, are provided.</li> </ul> <p> </p>
FIGURE 7 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 7. Tooth specializations (grooves and serrations) in the Anguimorpha. A. Estesia mongoliensis (IGM 3/196), with arrows pointing to tooth grooves and flanges on the anterior and posterior carinae of a dentary tooth. B. Dentary tooth of Heloderma suspectum (AMNH R-71082). C. Dentary tooth of Tylosaurus proriger (AMNH FR 1543). D. Dentary tooth of Varanus komodoensis (AMNH R-37909). Not to scale.
FIGURE 11 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 11. Character evolution of tooth specializations in the Anguimorpha. The labels on the branches indicate the origination of derived states as optimized on the tree (ACCTRAN optimization). Clades in black are those with specializations (derived states) on the marginal teeth. Clades in gray are those that show the plesiomorphic state of the corresponding characters: Character 429 – root-to-tip grooves in marginal teeth: (0) absent; (1) present, at anterior carina; (2) present, at anterior and posterior carinae. Character 430 – serrations on marginal teeth: (0) absent; (1) present.
FIGURE 10 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 10. The strict consensus tree of the morphology-only analysis. The clade in grey shade is the Monstersauria.
FIGURE 6 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 6. The mandible of IGM 3/196 in dorsal and ventral views. Scale bar = 10 mm; abbreviations are listed in appendix 6.
FIGURE 9 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 9. The strict consensus tree of the combined analysis of morphological and molecular data. Support values are labeled beneath branches. The number written before the slash is bootstrap value; the number written after the slash is Bremer support. Only bootstrap values above 50% are listed, so some branches show only Bremer support values.
FIGURE 3. A in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 3. A. Skull of IGM 3/196 in dorsal and ventral view (scale bar = 10 mm). B. Line drawings of the skull of IGM 3/196 in dorsal and ventral view (scale bar =10 mm). Abbreviations are listed in appendix 6.
Figure 7 in The evolution of venom-delivery systems in snakes
Figure 7. Most parsimonious reconstructions of the evolution of fang character states, with characters ordered, in the context of the phylogenies of (A) Cadle (1988) and (B) Kraus & Brown (1998). The Kraus & Brown tree is an example of just one of seven equally parsimonious reconstructions. U, ungrooved; G, grooved; and T, tubular.
Figure 6 in The evolution of venom-delivery systems in snakes
Figure 6. Most parsimonious recontruction of the evolution of the position of attachment of the pterygoideus within the context of the hypotheses of (A) Cadle (1988) and (B) Kraus & Brown (1998). A, anterior attachment near the posterior maxillary teeth, on the posterior end of the maxilla; P, anterior attachment on the ectopterygoid (i.e. posterior).
Figure 4 in The evolution of venom-delivery systems in snakes
Figure 4. Most parsimonious reconstruction of the evolution of venom glands and Duvernoy's glands in the context of (A) Cadle's (1988) and (B) Kraus & Brown's (1998) phylogeny. X, Duvernoy's gland and venom gland absent; D, Duvernoy's gland present; VV, venom gland of viperid type present; VE, venom gland of elapid type present; VA, venom gland of atractaspidid type present.
Data from: Phylogenomic reclassification of the world's most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using sequence-capture phylogenomics, we instead show convincingly that atracines are sister to actinopodids, and that hexathelids are non-monophyletic. Three new mygalomorph lineages are elevated to the family level, and a revised circumscription of the family Hexathelidae is presented. Re-writing this phylogenetic story has major implications for how we study venom evolution in these spiders, and potentially genuine consequences for antivenom development and bite treatment research. More generally, our research provides a textbook example of the applied importance of modern phylogenomic research.
FIGURE 8 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 8. Postcrania of Estesia mongoliensis (IGM 3/760). Scale bar = 10 mm.
FIGURE 2 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 2. Lateral view of IGM 3/196. Scale bar = 10 mm.
Figure 2 in The evolution of venom-delivery systems in snakes
Figure 2. Relationships among colubroid snakes proposed by Cadle (1988).
Figure 3 in The evolution of venom-delivery systems in snakes
Figure 3. Relationships among colubroid snakes proposed by Kraus & Brown (1998).
Figure 1 in The evolution of venom-delivery systems in snakes
Figure 1. Phylogenetic relationships among living snakes (Pough et al., 2001).
Data from: Island biogeography and competition drive rapid venom complexity evolution across rattlesnakes
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Data from: Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution
Open the record for dataset details and reuse information.
Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid 'background' rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent.
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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.