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94 results for “evolutionary biology”
Simulation systems for: "Pore formation in complex biological membranes: torn between evolutionary needs"
<p>Simulation systems for the publication:</p> <div> <div> <div> <p>Leonhard J. Starke, Christoph Allolio, and Jochen S. Hub, <em>Pore formation in complex biological membranes: torn between evolutionary needs</em>, BioRxiv (2024), doi: <a href="https://doi.org/10.1101/2024.05.06.592649">10.1101/2024.05.06.592649</a></p> <p>Required software:<br>GROMACS Chain Coordinate, a modified GROMACS variant for pore formation across membranes or stalk formation between membranes: <a href="https://gitlab.com/cbjh/gromacs-chain-coordinate">https://gitlab.com/cbjh/gromacs-chain-coordinate</a></p> <p>See README_small.sh and README_large.sh files for instructions on how to run pulling simulations for inducing pores in the provided complex membrane models.</p> </div> </div> </div>
Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology
<p>The evolution of resistance to antibiotics provides a timely and relevant topic for teaching undergraduate students evolutionary biology. Here, we present a module incorporating modified sequencing data from eight antibiotic resistant pathogen outbreaks in hospital settings with bioinformatics and phylogenetic analyses. This module uses whole genome sequencing data from hospital outbreaks investigated by the Centers for Disease Control and Prevention to provide examples of antibiotic resistance spread. Students work in groups to analyze outbreak data to identify the bacterial species and antibiotic resistance genes, to infer a phylogenetic tree examining relatedness among isolates, and to determine a possible source of the outbreak. Students then compile their results in individual reports and provide recommendations for preventing the further spread of antibiotic resistant organisms. In addition to providing genomic outbreak data, we include a teaching concepts guide discussing three integral components of the module: how evolutionary biology concepts of natural selection and competition impact antibiotic resistance; outbreak investigation information to aid in phylogenetic analysis and creation of recommendations; and instructions for the bioinformatics protocol. Completion of this module provides students an opportunity to think critically about the evolution of resistance, practice bioinformatics techniques, and relate evolutionary biology to current events.</p>
Ecology and Evolutionary Biology Field Trip at the Coweeta Hydrologic Laboratory (Watershed 18) in 2004: Aquatic Invertebrates (Adult) data
As part of an educational project, we intend to conduct a short "bioblitz" that will focus on 4 major groups of organisms: (1) vertebrates, especially birds and salamanders; (2) the local flora, especially fungi, trees, and any herbaceous species present this early; (3) aquatic invertebrates; (4) terrestrial invertebrates. Data will be compared to available lists of taxa from Coweeta and Great Smoky Mountains National Park.
Basic list of international academic societies related to ecology and evolutionary biology.
<p>List of international societies related to ecology, evolutionary biology or whole-organism biology. The list is based on the table from Lagisz et al. (2023) (top 16 societies), appended with additional societies from internet searches, personal communication and societies associated with journals listed in SCImago under Ecology, Evolution, Behaviour and Systematics category. Alternative society names (usually in a non-English language) are not shown. Abbreviated society names (non-unique) usually match the official abbreviated society names (English or nn-English), but if abbreviation was not found on the website it was made up from the English society name. In the "Extract" column, "Yes" indicates active societies with individual membership.</p>
RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology
<p>This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology</p>
Figure 1. A, B, solitary A. pacificus web, a in Notes on the biology of Anelosimus pacificus Levi, 1963 (Theridiidae, Araneae)-evidence for an evolutionary reversal to a less social state
Figure 1. A, B, solitary A. pacificus web, a flimsy tangle of silk lines with conspicuous globules of glue throughout; C, web of the subsocial A. may Agnarsson, 2005, a typical Anelosimus 'basket' web with dense silk sheet containing living and dead leaves, and aerial threads above, without visible glue; D, the bright white A. pacificus egg sac. All webs have been dusted with corn starch to enhance the visibility of the silk lines.
FIG. 6. — Conohyus olujici n in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 6. — Conohyus olujici n. sp. (HPM-GP 10771), right mandibular fragment with m1-m3; A, labial view; B, lingual view; C, occlusal view. Scale bars: 2 cm.
FIG. 5. — Conohyus olujici n in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 5. — Conohyus olujici n. sp. (HPM-GP 10770), right mandibular fragment with p4-m3; A, labial view; B, occlusal view. Scale bars: 2 cm.
FIG. 11. — Log10 in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 11. — Log10 ratio diagrams; A, log10 ratio diagram of length (M1) on selected hyotheres and tetraconodonts, Hyotherium meissneri STD; B, log10 ratio diagram of width (M3) on selected hyotheres and tetraconodonts, Hyotherium meissneri STD. Abbreviations: Cheu, Conohyus huenermanni; Colu, Conohyus olujici n. sp.; CsimG, Conohyus simorrensis Göriach; CsimP, Conohyus simorrensis Paşalar; Csin, Conohyus sindiensis; Cstein, Conohyus steinheimensis; Hsha, Hyotherium shangwangense; Pcru, Parachleuastochoerus crusafonti; Psp, Parachleuastochoerus sp. Rudabánya.
FIG. 4. — Conohyus olujici n in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 4. — Conohyus olujici n. sp. (HPM-GP 10769), female mandible fragment with right canine, right i2, roots preserved of right i1, right i3 and left i1, left mandibular fragment with broken p3; A, labial view; B, occlusal view. Scale bar: 2 cm.
FIG. 3. — Conohyus olujici n in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 3. — Conohyus olujici n. sp. (HPM-GP 10768), left p4-m3 (plausibly the same individual as the holotype); A, labial view; B, lingual view; C, occlusal view. Scale bars: 2 cm.
FIG. 10 in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 10. — Bivariate plots; A, mandibular p3 basal length vs. width on selected hyotheres and tetraconodonts; B, mandibular p4 basal length vs. width on selected hyotheres and tetraconodonts; C, mandibular m2 basal length vs. width on selected hyotheres and tetraconodonts; D, mandibular m3 basal length vs. width on selected hyotheres and tetraconodonts. Abbreviations: Cheu, Conohyus hunermanni; Colu, Conohyus olujici n. sp.; CsimG, Conohyus simorrensis Göriach; CsimP, Conohyus simorrensis Paşalar; Csin, Conohyus sindiensis; Cstein, Conohyus steinheimensis; Hmei, Hyotherium meissneri; Hsha, Hyotherium shangwangense; Pcru, Parachleuastochoerus crusafonti; Psp, Parachleuastochoerus sp. Rudabánya.
FIG. 8. — Conohyus olujici n in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 8. — Conohyus olujici n. sp. (HPM-GP 10773), left mandibular fragment with broken m1 and m2; A, labial view; B, lingual view; C, occlusal view. Scale bar: 2 cm.
FIG. 2. — Conohyus olujici n in A contribution to the evolutionary biology of Conohyus olujici n. sp. (Mammalia, Suidae, Tetraconodontinae) from the early Miocene of Lučane, Croatia
FIG. 2. — Conohyus olujici n. sp., holotype (HPM-GP 10767), male right mandible fragment with canine, broken p2 and complete p3-m3; A, labial view; B, lingual view; C, occlusal view. Scale bars: 4 cm.
Figures 53–58 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 53–58. Stereoscan photographs of Pimplinae. Figs 53, 54, mesopleuron; 53, Dolichomitus annulicornis; 54, Pimpla azteca. Figs 55–58, propodeum, dorsal; 55, Xanthopimpla aurita; 56, Echthromorpha atrata; 57, Lissopimpla excelsa; 58, Zatypota percontatoria.
Figures 87–90 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 87–90. Hind end of mesosoma with hind legs and metasoma dis-articulated; 87, Neotheronia mellosa; 88, Pimpla sumichrasti; 89, Scambus annulatus; 90, Dolichomitus annuicornis.
Figures 41–46 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 41–46. Stereoscan photographs of Pimplinae. Fig. 41, Sinarachna pallipes, head, posterior. Fig. 42, Dreisbachia avivae, mandible. Figs 43–46, Head, lateral; 43, Dolichomitus irritator, 44, Zaglyptus simonis; 45, Echthromorpha atrata; 46, Hymenoepimecis bicolor.
Figures 71–76 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 71–76. Stereoscan photographs of Pimplinae. Figs 71, 72, tergites II—IV, dorsal; 71, Polysphincta tuberosa; 72, Zatypota petronae. Figs 73–75, apex of ovipositor; 73, Liotryphon crassiseta; 74, Endromopoda detrita; 75, Dolichomitus imperator. Fig. 76, Zatypota petronae, ovipositor entire.
Figures 23–28 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 23–28. Stereoscan photographs of Pimplinae, head, anterior; 23, Ephialtes manifestator; 24, Paraperithous gnathaulax; 25, Xanthephialtes oculatus; 26, Schizopyga frigida; 27, Theronia melanocera ♀; 28, Theronia melanocera ♂.
Figures 47–52 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 47–52. Stereoscan photographs of Pimplinae, pronotum, lateral; 47, Dolichomitus irritator; 48, Pimpla azteca; 49, Schizopyga frigida; 50, Clistopyga calixtoi; 51, Hymenoepimecis bicolor; 52, Acrodactyla degener.
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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.