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15,702 results for “history”
Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)
<p>Abstract</p> <p>Premise of the Study</p> <p>Diatoms are one of the most species‐rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole‐genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well.</p> <p>Methods</p> <p>We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species.</p> <p>Key Results</p> <p>Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks‐based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.</p> <p>Conclusions</p> <p>Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity.</p>
Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples
<p>Beast v. 2.6.3 input (<em>.xml</em>) files and output (<em>.log</em> and <em>.trees</em>) files for phylogenetic analyses of rails, used to determined the evolutionary history of the Galápagos Rail <em>Laterallus spilonota</em>. There are two main datasets: coding sequences of the mitochondrial genome ('mtCDS'), partitioned per codon position, and a two mitochondrial/one nuclear marker dataset ('2mt1nc'). For each of the datasets, separate runs have been made in which the fossil calibration of Rallidae is applied to the stem of the present-day family ('calRallidaeStem') or the crown node ('calRallidaeCrown), and finally all runs have been replicated with three different starting seeds ('seed_NNNNNNNNN', with the different seeds 123456789, 456789123, and 789123456).</p> <p>We provide raw output (<em>.log</em> and <em>.raw.trees</em>) as well as maximum clade credibility ('mcc') trees (<em>.mcc.trees</em>), calculated after discarding 10% of the trees as burn-in, using median ('heights_median') or mean ('heights_mean') node heights as estimated node age.</p> <p>The runs used for Table 1 (and Figure 2) in the accompanying paper are:</p> <ul> <li>Dataset mtCDS, Rallidae calibration of stem: seed 123456789</li> <li>Dataset mtCDS, Rallidae calibration of crown: seed 456789123 </li> <li>Dataset 2mt1nc, Rallidae calibration of stem: seed 789123456</li> <li>Dataset 2mt1nc, Rallidae calibration of crown: seed 123456789</li> </ul> <p>This version of the data includes <em>Pellornis mikkelseni</em> among the fossils making up the calibration distribution for crown Gruiformes. In a previous version of this data deposit, that data point was represented by <em>Messelornis cristata </em>(see accompanying paper).</p>
Data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history''
<p><em>Eva Bons, Christine Leemann, Karin J. Metzner, Roland R. Regoes</em></p> <p>This repository contains all the data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history'</p> <p>See the readme after unpacking the .zip for a description of the files</p>
FIG. 6. — Couverture d in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 6. — Couverture d'un article de Naturae (Rascle et al. 2017), revue numérique en flux continu lancée en 2017 et distribuée sur http://sciencepress.mnhn.fr. Les articles sont maintenant dotés d'une couverture individuelle, adaptée à leur contenu. Les articles qui ne comportent pas de figures auront une couverture générique, annuelle/Cover of an article by Naturae (Rascle et al. 2017), a digital journal launched in 2017 and published in a continuous stream on http://scien- cepress.mnhn.fr. The cover of each issue is now adapted to its content. Issues that do not have figures are assigned a generic cover image that changes anually.
FIG. 11 in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 11. — Tableaux transmis par notre partenaire PLAZI chargé du développement d'une procédure de conversion des articles des périodiques en XML. Cet extrait montre sous quelle forme les données originales publiées pourront être présentées – sous formes de graphes par exemple – et seront distribuées – les bases de données de la recherche recevant plus rapidement, et de manière plus systématique, les données des articles que lors de leur saisie manuelle/Tables generated by our partner Plazi, responsible for the development of a procedure for converting journal articles into XML. This excerpt shows the forms in which original published data can be presented – in the form of graphs, for example – and distributed to the research databases in a faster and more systematical way then entering data manually.
FIG. 10 in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 10. — Publication sur différentes plateformes d'un article paru récemment dans EJT (Carvalho & Kury 2018) et qui a servi à faire des tests de conversion en XML: A, B, l'article original, paru sur le site d'EJT (A) et sur celui des Publications scientifiques du Muséum (B); C, le même article, sur la plateforme 'Treatment Bank' de Plazi (http://plazi.org); D, E, enfin, l'article est automatiquement soumis aux bases de données du Biodiversity Literature Repositery (D) et du Global Biodiversity Information Facility (GBIF) (E)/Cross-platform publication of an article published recently by EJT (Carvalho & Kury 2018) and used to make conver- sion tests in XML: A, B, original article, published on the EJT website (A) and that of the Muséum Science Press (B); C, the same article, on the Plazi platform 'Treatment Bank' (http://plazi.org); D, E, appropriate elements of the article are finally fed to the Biodiversity Literature Repository (D) and the Global Biodiversity Information Facility (GBIF) (E).
FIG. 9. — Capture d in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 9. — Capture d'écran des nouvelles pages des périodiques en flux continu sur le site des Publications scientifiques du Muséum (http://sciencepress.mnhn.fr). Les articles publiés jusqu'en 2017 apparaissent également sur cette page/Screenshot of the new pages for the periodical streams on the Muséum Science Press website (http://sciencepress.mnhn.fr). Articles published until 2017 also appear on this page.
FIG. 3 in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 3. — Le modèle de couverture des revues a été revu lors du passage au format A4 et à l'impression numérique (jusque-là, les périodiques étaient imprimés avec une technique d'impression offset). L'utilisation du format A4 permet de maximiser la taille des planches, une demande récurrente de la part des auteurs, qui passent ainsi à 175 mm de large au lieu des 145 mm de la précédente maquette. L'utilisation d'encres spécifiques (nuance pantone) n'étant plus possible, les couvertures durent être imprimées en quadrichromie, ouvrant de nouvelles possibilités, notamment pour les volumes thématiques. Les revues conservent bien sûr leurs couleurs respectives/The cover template for the journals was redesigned when they switched to A4 format and digital printing (until then, the periodicals were printed with in offset). The use of the A4 format allows for maximimized plate dimensions, a recurring request from the authors, now 175 mm wide instead of 145 mm in the previous format. As the use of specific inks (Pantone shades) is no longer possible, the covers are now printed in four-colour process (CMYK), opening up new possibilities, especially for thematic issues. Each journal however, has retained its respective colour.
FIG. 7. — Captures d in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 7. — Captures d'écran des sites web des publications de 1999 (en haut) et de 2004 (en bas), ce dernier ayant perduré jusqu'à la fin de l'année 2013. En mai 2015, le nouveau site des Publications scientifiques était en ligne/Screenshots of the Science Press websites from 1999 (top) and 2004 (bottom); the latter was operational until late 2013. In May 2015, the current version of the of the Science Press website was launched.
FIG. 5 in 1802-2018: 220 ans d'histoire des périodiques au Muséum 1802-2018: a 220-year history of the Muséum periodicals
FIG. 5. — Couvertures de deux numéros d'EJT édités exceptionnellement en version papier/Covers of two issues of EJT published exceptionally in paper version.
Perceptual history propagates down to early levels of sensory analysis
<p>One function of perceptual systems is to construct and maintain a reliable representation of the environment. A useful strategy intrinsic to modern “Bayesian” theories of perception is to take advantage of the relative stability of the input and use perceptual history (priors) to predict current perception. This strategy is efficient but can lead to stimuli being biased toward perceptual history, clearly revealed in a phenomenon known as serial dependence. However, it is still unclear whether serial dependence biases sensory encoding or only perceptual decisions. We leveraged on the “surround tilt illusion”—where tilted flanking stimuli strongly bias perceived orientation—to measure its influence on the pattern of serial dependence, which is typically maximal for similar orientations of past and present stimuli. Maximal serial dependence for a neutral stimulus preceded by an illusory one occurred when the perceived, not the physical, orientations of the two stimuli matched, suggesting that the priors biasing current perception incorporate the effect of the illusion. However, maximal serial dependence of illusory stimuli induced by neutral stimuli occurred when their physical (not perceived) orientations were matched, suggesting that priors interact with incoming sensory signals before they are biased by flanking stimuli. The evidence suggests that priors are high-level constructs incorporating contextual information, which interact directly with early sensory signals, not with highly processed perceptual representations.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Jairo Mora Prendas, <a href="https://orcid.org/0000-0002-6195-935X">https://orcid.org/0000-0002-6195-935X</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach
<p>Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus <em>Quercus</em>). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analyzed inter- and intra-specific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models, and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with species distribution models and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.</p>
Image 10 in Robust Trapdoor Tarantula Haploclastus validus Pocock, 1899: notes on taxonomy, distribution and natural history (Araneae: Theraphosidae: Thrigmopoeinae)
Image 10. Habitat destruction at Aarey Milk Colony for removal of soil for brick making. Note the exposed burrow due to this practice in the inset
Image 3 in Robust Trapdoor Tarantula Haploclastus validus Pocock, 1899: notes on taxonomy, distribution and natural history (Araneae: Theraphosidae: Thrigmopoeinae)
Image 3. Haploclastus validus female from Aarey Milk Colony (Mumbai, Maharashtra) depicting coloration in life. Not collected
Figures 8–11. 8 in Robust Trapdoor Tarantula Haploclastus validus Pocock, 1899: notes on taxonomy, distribution and natural history (Araneae: Theraphosidae: Thrigmopoeinae)
Figures 8–11. 8 - Spermathecae; 9 - Male palp, prolateral view; 10 - Male palp, retrolateral view; 11 - Male palp, ventral view (scale 1mm)
Figures 1–7. 1 in Robust Trapdoor Tarantula Haploclastus validus Pocock, 1899: notes on taxonomy, distribution and natural history (Araneae: Theraphosidae: Thrigmopoeinae)
Figures 1–7. 1 - Dorsal view of spider, scale 0.5mm; 2 - Eye, scale 1mm; 3 - Sternum, maxillae, labium, scale 0.5mm; 4 - Chelicerae, scale 1mm; 5 - Chelicerae teeth, scale 1mm; 6 - Maxillae, scale 1mm; 7 - Spinnerets, scale 1mm
Time spent in distinct life-history stages has sex-specific effects on reproductive fitness in wild Atlantic salmon
<p><span>In species with complex life cycles, life history theory predicts that fitness is affected by conditions encountered in previous life history stages. Here, we use a four-year pedigree to investigate if time spent in two distinct life history stages has sex-specific reproductive fitness consequences in anadromous Atlantic salmon (<i>Salmo salar</i>). We determined the amount of years spent in fresh water as juveniles (freshwater age, FW, measured in years), and years spent in the marine environment as adults (sea age, SW, measured in sea winters) on 264 sexually mature adults collected on a river spawning ground. We then estimated reproductive fitness as the number of offspring (reproductive success) and the number of mates (mating success) using genetic parentage analysis (>5000 offspring). Sea age is significantly and positively correlated with reproductive and mating success of both sexes whereby older and larger individuals gained the highest reproductive fitness benefits (females: 62.2% increase in offspring/SW and 34.8% increase in mate number/SW; males: 201.9% offspring/SW and 60.3% mates/SW). Younger freshwater age was significantly related to older sea age and thus increased reproductive fitness, but only among females (females: -33.9% offspring/FW and -32.4% mates/FW). This result implies that females can obtain higher reproductive fitness by transitioning to the marine environment earlier. In contrast, male mating and reproductive success was unaffected by freshwater age and more males returned at a younger age than females despite the reproductive fitness advantage of later sea age maturation. Our results show that the timing of transitions between juvenile and adult phases has a sex-specific consequence on female reproductive fitness, demonstrating a life-history trade-off between maturation and reproduction in wild Atlantic salmon.</span></p>
FIGURES 3 – 8 in A new species of Stasimopus from the Eastern Cape Province of South Africa (Araneae, Mygalomorphae, Ctenizidae), with notes on its natural history
FIGURES 3 – 8. Stasimopus mandelai sp. nov., holotype male (MY 557). 3, left leg I, retrolateral aspect; 4, left leg I, prolateral aspect; 5, pedipalp, patella to bulb, retrolateral aspect; 6, pedipalp, distal portion, ventral aspect. Paratype male (MY 559). 7, leg I, retrolateral aspect; 8, pedipalp, retrolateral aspect (box showing enlarged view of palpal organ). Scale bars for legs = 2.0 mm; for pedipalps = 1.0 mm.
FIGURES 1 – 2 in A new species of Stasimopus from the Eastern Cape Province of South Africa (Araneae, Mygalomorphae, Ctenizidae), with notes on its natural history
FIGURES 1 – 2. Stasimopus mandelai sp. nov., live habitus images. 1, female; 2, holotype male. Scale bars = 5.0 mm.
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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.