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Independent avian epigenetic clocks for aging and development
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Data and coding files for: Within population plastic responses to combined thermal-nutritional stress differ from those in response to single stressors, and are genetically independent across traits in both males and females
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Do animal personality components independently evolve and develop in response to environmental complexity?
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Photoperiod controls wing polyphenism in a water strider independently of insulin receptor signaling
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Extended Lissamphibia: A tale of character non-independence, analytical parameters, and islands of trees
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Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat
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A migratory sparrow has personality in winter that is independent of other traits
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Web Archive of Independent News Sites on Turkish Affairs derivatives
<p>Derivatives of the <a href="https://archive-it.org/collections/12911">Web Archive of Independent News Sites on Turkish Affairs</a> collection from the <a href="https://archive-it.org/home/IvyPlus">Ivy Plus Libraries Confederation</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a> and <a href="https://cloud.archivesunleashed.org/">Archives Unleashed Cloud</a>.</p> <p>The <strong>ivy-12911-parquet.tar.gz</strong> derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/datathon-nyc/parquet_pandas_stonewall.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Word processor files<br> </li> </ul> <p>The <strong>ivy-12911-auk.tar.gz </strong>derivatives<strong> </strong>are the <a href="https://cloud.archivesunleashed.org/derivatives">standard set of web archive derivatives</a> produced by the Archives Unleashed Cloud.</p> <ul> <li><strong>Gephi </strong>file, which can be loaded into <a href="https://gephi.org/">Gephi</a>. It will have basic characteristics already computed and a basic layout.</li> <li><strong>Raw Network</strong> file, which can also be loaded into <a href="https://gephi.org/">Gephi</a>. You will have to use that network program to lay it out yourself.</li> <li><strong>Full text</strong> file. In it, each website within the web archive collection will have its full text presented on one line, along with information around when it was crawled, the name of the domain, and the full URL of the content.</li> <li><strong>Domains count</strong> file. A text file containing the frequency count of domains captured within your web archive.</li> </ul>
Independent Documentary Filmmakers from China, Hong Kong, and Taiwan Web Archive collection derivatives
<p>Web archive derivatives of the <a href="https://archive-it.org/collections/12172">Literary Authors from Europe and Eurasia Web Archive</a> collection from the <a href="https://archive-it.org/home/IvyPlus">Ivy Plus Libraries Confederation</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a> and <a href="https://cloud.archivesunleashed.org/">Archives Unleashed Cloud</a>.</p> <p>The <strong>ivy-12126-parquet.tar.gz</strong> derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/datathon-nyc/parquet_pandas_stonewall.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Word processor files<br> </li> </ul> <p>The <strong>ivy-12126-auk.tar.gz </strong>derivatives<strong> </strong>are the <a href="https://cloud.archivesunleashed.org/derivatives">standard set of web archive derivatives</a> produced by the Archives Unleashed Cloud.</p> <ul> <li><strong>Gephi </strong>file, which can be loaded into <a href="https://gephi.org/">Gephi</a>. It will have basic characteristics already computed and a basic layout.</li> <li><strong>Raw Network</strong> file, which can also be loaded into <a href="https://gephi.org/">Gephi</a>. You will have to use that network program to lay it out yourself.</li> <li><strong>Full text</strong> file. In it, each website within the web archive collection will have its full text presented on one line, along with information around when it was crawled, the name of the domain, and the full URL of the content.</li> <li><strong>Domains count</strong> file. A text file containing the frequency count of domains captured within your web archive.</li> </ul>
Data from: Distinct cold tolerance traits independently vary across genotypes in Drosophila melanogaster
The ability to cope with low temperature is a critical adaptation in thermally variable environments. Cold hardiness is comprised of several traits, including minimum temperatures for growth and activity, ability to survive severe cold, and ability to recover normal function after cold subsides. Across species, these traits are correlated and share physiological mechanisms, suggesting they were shaped by shared evolutionary processes. However, the extent cold hardiness traits and their associated mechanisms covary within populations has not been assessed. We measured five cold hardiness traits – critical thermal minimum (CTmin), chill coma recovery (CCR), acute and chronic cold tolerance, and cold-induced changes in locomotor behavior – along with cold-induced expression of two genes with known roles in cold hardiness (<i>Heat Shock Protein 70</i> and <i>Frost</i>) – across 12 lines of <i>D. melanogaster</i> derived from a single population. We observed significant genetic variation in all traits, but few correlated across genotypes, and these correlations were sex-dependent. Further, cold-induced gene expression varied by genotype, but there was no evidence supporting our hypothesis that cold-hardy lines would have either higher baseline expression or induction of stress genes. These results suggest cold hardiness traits possess unique mechanisms and may have the capacity to evolve independently.
Independent evolutionary changes in fine-root traits among main clades during the diversification of seed plants
<p><b>Rationale</b>: Changes in fine-root morphology are typically associated with transitions from the ancestral arbuscular mycorrhizal (AM) to the alternative ectomycorrhizal (ECM) or non-mycorrhizal (NM) associations. However, the modifications in root morphology may also coincide with new modifications in leaf hydraulics and growth habit during angiosperm diversification. These hypotheses have not been evaluated concurrently, which limits our understanding of the causes of fine-root evolution.</p> <p><b>Methods</b>: To explore the evolution of fine-root systems, we assembled a 600+ species database to reconstruct historical changes in seed plants over time. We utilize ancestral reconstruction approaches together with phylogenetically informed comparative analyses to test whether changes in fine-root traits were most strongly associated with mycorrhizal affiliation, leaf hydraulics or growth form.</p> <p><b>Key Results</b>: Our findings show significant shifts in root diameter, specific root length and root tissue density as angiosperms diversified, largely independent from leaf changes or mycorrhizal affiliation. Growth form was the only factor associated with fine-root traits in statistical models including mycorrhizal association and leaf venation, suggesting substantial modifications in fine-root morphology during transitions from woody to non-woody habits.</p> <p><b>Conclusion</b>: Divergences in fine-root systems were crucial in the evolution of seed plant lineages, with important implications for ecological processes in terrestrial ecosystems.</p>
Data from: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription
<p>One of the widely used applications of the popular Cre-loxP method for targeted recombination is the permanent activation of marker genes, such as reporter genes or antibiotic resistance genes, by excision of a preceding transcriptional stop signal. The STOP cassette consists of three identical SV40-derived poly(A) signal repeats and is flanked by two loxP sites. We found that in addition to complete loxP-mediated recombination, limiting levels of the Cre recombinase also cause incomplete recombination of the STOP cassette. Partial recombination leads to the loss of only one or two of the three identical poly(A) repeats with recombination breakpoints always precisely matching the end/start of each poly(A) signal repeat without any relevant similarity to the canonical or known cryptic loxP sequences, suggesting that this type of Cre-mediated recombination is loxP-independent. Incomplete deletion of the STOP cassette results in partial read-through transcription, explaining at least some of the variability often observed in marker gene expression from an otherwise identical locus.</p>
Multiple phenotypes conferred by a single insect symbiont are independent
<p>Many microbial symbionts have multiple phenotypic consequences for their animal hosts. However, the ways in which different symbiont-mediated phenotypes combine to affect fitness are not well understood. We investigated whether there are correlations between different symbiont-mediated phenotypes. We used the symbiont <i>Spiroplasma</i>, a striking example of a bacterial symbiont conferring diverse phenotypes on insect hosts. We took 11 strains of <i>Spiroplasma</i> infecting pea aphids (<i>Acyrthosiphon pisum</i>)<i> </i>and assessed their ability to provide protection against the fungal pathogen <i>Pandora neoaphidis</i> and the parasitoids <i>Aphidius ervi</i> and <i>Praon volucre</i>. We also assessed effects on male offspring production for five of the <i>Spiroplasma </i>strains. All but one of the <i>Spiroplasma</i> strains provided very strong protection against the parasitoid <i>P. volucre</i>. As previously reported, variable protection against <i>P. neoaphidis</i> and <i>A. ervi</i> was also present; male-killing was likewise a variable phenotype. We find no evidence of any correlation, positive or negative, between the different phenotypes, nor was there any evidence of an effect of symbiont phylogeny on protective phenotype. We conclude that multiple symbiont-mediated phenotypes can evolve independently from one another without trade-offs between them.</p>
The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes
<p>Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties<i> </i>within <i>Erythroxylum coca</i> Lam., and Colombian and Trujillo varieties within<i> E. novogranatense </i>(D.Morris) Hieron.) but our understanding of their wild progenitor(s) and origins remains rudimentary. In this study we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species <i>E. gracilipes</i>; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant.</p>
Datasets: thermal plasticity is independent of environmental history in an intertidal seaweed
<p><span><span><span><span><span><span><span><span><span><span><span>Organisms inhabiting the intertidal zonehave been used to study natural ecophysiological responses and adaptations to thermal stress because these organisms are routinely exposed to high-temperature conditions for hours at a time. While intertidal organisms may be inherently better at withstanding temperature stress due to regular exposure and acclimation, they could be more vulnerable to temperature stress, already living near the edge of their thermal limits. Strong gradients in thermal stress across the intertidal zone present an opportunity to test whether thermal tolerance is a plastic or canalized trait in intertidal organisms. Here, we studied the intertidal pool-dwelling calcified alga, <i>Ellisolandia elongata</i>, under near-future temperature regimes, and the dependence of its thermal acclimatization response on environmental history. Two timescales of environmental history were tested during this experiment. The intertidal pool of origin was representative of long-term environmental history over the alga's life (including settlement and development), while the pool it was transplanted into accounted for recent environmental history (acclimation over many months). Unexpectedly, neither long-term nor short-term environmental history, nor ambient conditions, affected photosynthetic rates in <i>E. elongata</i>. Individuals were plastic in their photosynthetic response to laboratory temperature treatments (mean 13.2°C, 15.7°C, and 17.7°C). Further, replicate ramets from the same individual were not always consistent in their photosynthetic performance from one experimental time point to another or between treatments, and exhibited no clear trend in variability over experimental time. High variability in climate change responses between individuals may indicate the potential for resilience to future conditions, and thus may play a compensatory role at the population or species level over time.</span></span></span></span></span></span></span></span></span></span></span></p>
Dataset - Calorie restriction improves metabolic state independently of gut microbiome composition
<p>This dataset contains the supplementary information for the paper: <em>Calorie restriction improves metabolic state independently of gut microbiome composition</em>.</p>
C4 photosynthesis and the economic spectra of leaf and root traits independently influence growth rates in grasses
<p>Photosynthetic pathway is an important cause of growth rate variation between species, such that the enhanced carbon uptake of C<sub>4</sub> species leads to faster growth than their C<sub>3</sub> counterparts. Leaf traits that promote rapid resource acquisition may further enhance the growth capacity of C<sub>4</sub> species. However, how root economic traits interact with leaf traits, and the different growth strategies adopted by plants with C<sub>3</sub> and C<sub>4</sub> photosynthetic pathways is unclear. Plant economic traits could interact with, or act independently of, photosynthetic pathway in influencing growth rate, or C<sub>3</sub> and C<sub>4</sub> species could segregate out along a common growth rate-trait relationship.</p> <p>We measured leaf and root traits on 100+ grass species grown from seeds in a controlled, common environment to compare with relative growth rates (RGR) during the initial phase of rapid growth, controlling for phylogeny and allometric effects.</p> <p>Photosynthetic pathway acts independently to leaf and root functional traits in causing fast growth. Using C<sub>4</sub> photosynthesis, plants can achieve faster growth than their C<sub>3</sub> counterparts (by an average 0.04 g g<sup>-1</sup> day<sup>-1</sup>) for a given suite of functional trait values, with lower investments of leaf and root nitrogen. Leaf and root traits had an additive effect on RGR, with plants achieving fast growth by possessing resource-acquisitive leaf traits (high specific leaf area and low leaf dry matter content) or root traits (high specific root length and area, and low root diameter), but having both leads to an even faster growth rate (by up to 0.06 g g-1 day-1). C<sub>4</sub> photosynthesis can provide a greater relative increase in RGR for plants with a 'slow' ecological strategy than in those with fast growth. However, aboveground and belowground strategies are not coordinated, so that species can have any combination of 'slow' or 'fast' leaf and root traits.</p> <p>Synthesis: C<sub>4</sub> photosynthesis increases growth rate for a given combination of economic traits, and significantly alters plant nitrogen economy in the leaves and roots. However, leaf and root economic traits act independently to further enhance growth. The fast growth of C<sub>4</sub> grasses promotes a competitive advantage under hot, sunny conditions.</p>
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Juvenile rank acquisition is associated with fitness independent of adult rank
<p>Social rank has been identified as a significant determinant of fitness in a variety of species. The importance of social rank suggests that the process by which juveniles come to establish their position in the social hierarchy is a critical component of development. Here, we use the highly predictable process of rank acquisition in spotted hyenas to study the consequences of variation in rank acquisition in early life. In spotted hyenas, rank is 'inherited' through a learning process called 'maternal rank inheritance.' This pattern is highly predictable: ~80% of juveniles acquire the exact rank predicted by the rules of maternal rank inheritance. This predictable nature of rank acquisition in these societies allows the process of rank acquisition to be studied independently from the ultimate rank that each juvenile attains. In this study, we use Elo-deviance scores, a novel application of the Elo-rating method, to calculate each juvenile's deviation from expected pattern of maternal rank inheritance during development. Despite variability in rank acquisition among juveniles, most of these juveniles come to attain the exact rank expected of them according to the rules of maternal rank inheritance. Nevertheless, we find that transient variation in rank acquisition in early life is associated with long term fitness consequences for these individuals: juveniles 'underperforming' their expected ranks show reduced survival and lower lifetime reproductive success than better-performing peers, and this relationship is independent of both maternal rank and rank achieved in adulthood. We also find that multiple sources of early life adversity have cumulative, but not compounding, effects on fitness. Future work is needed to determine variation in rank acquisition directly affects fitness, or if some other variable, such as maternal investment or juvenile condition, causes variation in both of these outcomes.</p>
Independent losses of the Hypoxia-Inducible Factor (HIF) pathway within Crustacea
<p>Metazoans respond to hypoxic stress via the Hypoxia Inducible Factor (HIF) pathway, a mechanism thought to be extremely conserved due to its importance in monitoring cellular oxygen levels and regulating responses to hypoxia. However, recent work revealed that key members of the HIF pathway have been lost in specific lineages (a tardigrade and a copepod), suggesting alternative mechanisms have evolved but are still undescribed. Using genomic and transcriptomic data from 70 different species across 12 major crustacean groups, we assessed the degree to which the gene <i>HIF</i><i>a</i>, the master regulator of the HIF pathway, was conserved. Mining of protein domains, followed by phylogenetic analyses of gene families, uncovered group-level losses of <i>HIF</i><i>a</i>, including one across three orders within Cirripedia, and in three orders within Copepoda. For these groups, additional assessment showed losses of HIF repression machinery (EGLN, VHL). These results suggest the existence of alternative mechanisms for cellular response to low oxygen, and highlight these taxa as models useful for probing these evolutionary outcomes.</p>
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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.