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132 results for “human evolution”
Deep splicing plasticity of the human adenovirus type 5 transcriptome as a driver of virus evolution nanopore data 48hpi
<p>Adenovirus infected MRC5 cells direct RNA sequencing of the mRNA using nanopore. From the paper Deep splicing plasticity of the human adenovirus type 5 transcriptome as a driver of virus evolution. Both the uncorrected fastq files and the lordec corrected files together with the normalised illumina data used to correct the nanpore data are here.</p>
Evolution of FDA Guidelines on Control of Nitrosamine Impurities in Human Drugs – A Comparative Analysis of September 2024 Revisions
<p>Nitrosamine impurities have become a significant concern in the pharmaceutical industry due to their carcinogenic potential. In response, the U.S. Food and Drug Administration (FDA) has continuously updated its guidelines to ensure the safety and efficacy of drug products. This review article provides a comprehensive analysis of the evolution of FDA guidelines on the control of nitrosamine impurities, with a particular focus on the September 2024 revisions. By comparing the latest guidance with previous versions, this article highlights key changes, including the expanded focus on Nitrosamine Drug Substance-Related Impurities (NDSRIs), updated risk assessment strategies, and the introduction of new Acceptable Intake (AI) limits. The analysis underscores the FDA's commitment to enhancing drug safety through rigorous control measures and global harmonization efforts.</p>
Evolution of a mosquito's hatching behavior to match its human-provided habitat
<p>A subspecies of the yellow fever mosquito, <em>Aedes aegypti</em>, has recently evolved to specialize in biting and living alongside humans. It prefers human odor and breeds in human-provided artificial containers rather than the forest tree holes of its ancestors. Here, we report one way this human specialist has adapted to the distinct ecology of human environments. While eggs of the ancestral subspecies rarely hatch in pure water, those of the derived human-specialist do so readily. We trace this novel behavior to a shift in how eggs respond to dissolved oxygen, low levels of which may signal food abundance. Moreover, we show that while tree holes are consistently low in dissolved oxygen, artificial containers often have much higher levels. There is thus a concordance between the hatching behavior of each subspecies and the aquatic habitat it uses in the wild. We find this behavioral variation is heritable, with both maternal and zygotic effects. The zygotic effect depends on dissolved oxygen concentration (i.e., GxE), pointing to potential changes in oxygen-sensitive circuits. Together, our results suggest that a shift in hatching response contributed to the pernicious success of this human-specialist mosquito and illustrate how animals may rapidly adapt to human-driven changes in the environment.</p>
Complete numerical solutions for "Inference of ecological and social drivers of human brain-size evolution" by Mauricio González-Forero and Andy Gardner
<p>This zip file contains the complete numerical solutions across the parameter sweep over the P parameters for the six cases considered.</p> <p>/1RatioForm/ -> solutions for power competence.<br> /2DiffForm/ -> solutions for exponential competence.</p> <p>/1RatioForm/1BenchmarkFromSimpleInitialGuess -> solution for the step 1 of initialization (section 5 of the SI).<br> /1RatioForm/2Benchmark/ -> solution for the step 2 of the initialization (section 5 of the SI).<br> /1RatioForm/3AdditiveCoop/ -> solutions across the P parameter combinations for additive cooperation.<br> /1RatioForm/4MultCoop/ -> solutions across the P parameter combinations for multiplicative cooperation.<br> /1RatioForm/5SubMultCoop/ -> solutions across the P parameter combinations for submultiplicative cooperation.</p> <p>The contents of /2DiffForm/ are analogous.</p> <p>The P vector is written in these files in the order (etas,etac,etaC,etag), where<br> etas -> P1<br> etac -> P3<br> etaC -> P2<br> etag -> P4</p> <p>The files 1runNotesACMC.pdf and 2runNotesSC.pdf contain the tree structure of the parameter sweep, specifying which parameter combination was used as the resident and which combinations converged to an uninvadable strategy (those with a checkmark).</p> <p>The file 3runNotesMaternalCareOptimization.pdf contains the 10 parameter combinations that yielded the best adult fit, which then were subject to variation in the parameter phi to find the combination that yielded the best ontogenetic fit.</p> <p>The file 4runNotesDuplicates.pdf gives the parameter combinations that were not run because they are equivalent to other parameter combinations.</p> <p>Running [T,N1,run,Tshort,N1short,runShort]=etaCombinations in Matlab and typing run.seed{i}.parallel{:} gives the "next" parameter combinations from parameter combination i (where i is a number 1,2,...) for PC-AC, EC-MC, PC-SC, and EC-SC. The meaning of "next" is explained in step 4 of the parameter sweep (section 5 of the SI). Typing runShort.seed{i}.parallel{:} gives the "next" parameter combinations from parameter combination i for PC-MC and EC-AC.</p> <p>The terminal folders contain the solutions and have the following files:<br> brainNashDeep.m -> the master file launching the iteration of best responses.<br> brainMainDeep.m -> the file launching one iteration solving the optimal control problem to find best response.<br> brainMainTestRunDeep.m -> runs a test to check if there are infeasibility warnings.<br> brainContinuous.m -> specifies the dynamic constraints.<br> brainEndpoint.m -> specifies the terminal constraints.<br> parameters.m -> specifies the parameter values and rescales them to rescale units as specified in section 5 of the SI.<br> getSolution.m -> extracts solution.<br> plots.m -> plots solutions over best response iterations.<br> brainPlot.m -> plots solution of a given best response iteration.<br> guessDeep.mat -> initial guess and resident used.<br> solutionNashDeep.mat -> solutions over best response iterations.<br> solutionDeep.mat -> solution of last best response iteration.</p> <p> </p>
Human-specific tandem repeat expansion and differential gene expression during primate evolution
<p>THIS DATASET IS PART OF THE FOLLOWING STUDY:<br> <a href="https://www.pnas.org/content/early/2019/10/22/1912175116">https://www.pnas.org/content/early/2019/10/22/1912175116</a></p> <p> </p> <p>THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:<br> <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056</a></p> <p><br> ORIGINAL UPLOAD: 09/06/2019</p> <p>UPDATES: 10/28/2019; 01/27/2020</p> <p>DESCRIPTION: Contigs were assembled using Phased-SV (<a href="https://www.nature.com/articles/s41467-018-08148-z">Chaisson et al, Nature Communications 2019</a>) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified 21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in <a href="https://science.sciencemag.org/content/360/6393/eaar6343">Kronenberg et al, Science 2018</a>. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.</p>
Text-fig. 5. Dorsal view of endocranium of 93 mm human fetus. Derivatives of the teniform cartilages blue. con: orbitonasal commissure; lp: parietal lamina; oc: orbital cartilage; rco: remnants of orbitoparietal commissure. (Modified from Reinbach 1963; cf. Bersch and Reinbach 1970.) in Cartilago Teniformis And Its Derivatives: Additional Information On The Basic Composition And Evolution Of The Skull
Text-fig. 5. Dorsal view of endocranium of 93 mm human fetus. Derivatives of the teniform cartilages blue. con: orbitonasal commissure; lp: parietal lamina; oc: orbital cartilage; rco: remnants of orbitoparietal commissure. (Modified from Reinbach 1963; cf. Bersch and Reinbach 1970.)
Mammalian Evolution of Human cis-regulatory Elements and Transcription Factor Binding Sites
<p>Code and data associated with the manuscript entitled "Mammalian Evolution of Human cis-regulatory Elements and Transcription Factor Binding Sites "</p>
Evolution of a mosquito’s hatching behavior to match its human-provided habitat
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In search of the genetic variants of human sex ratio at birth: Was Fisher wrong about sex ratio evolution?
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An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans
<p>Dizygotic twinning, the simultaneous birth of siblings when multiple ova are released, is an evolutionary paradox. Twin bearing mothers often have elevated fitness<sup>1-5</sup>; but despite twinning being heritable<sup>6</sup>, twin births only occur at low frequencies in human populations<sup>7</sup>. We resolve this paradox by showing that twinning and non-twinning are not competing strategies, instead dizygotic twinning is the outcome of an adaptive conditional ovulatory strategy of switching from single to double ovulation with increasing age. This conditional strategy when coupled with the well-known decline in fertility as women age, maximizes reproductive success and explains the increase and subsequent decrease in twinning rate with maternal age that is observed across human populations<sup>8-10</sup>.<span> We show that the most successful ovulatory strategy would be to always double ovulate as an insurance against early fetal loss, but to never bear twins. This finding supports the hypothesis that twinning is a byproduct of selection for double ovulation rather than twinning.</span></p>
Biomechanics of the human thumb and the evolution of dexterity
<p>Systematic tool production and use is one of humanity<span>'</span>s defining characteristics, possibly originating as early as >3 million years ago.<span class="reference-citation-wrapper"><span></span><span class="citation-view-wrapper"><span class="citation-container"><span class="original"><span>1<span>–</span>3</span></span></span></span><span></span></span> Although heightened manual dexterity is considered to be intrinsically intertwined with tool use and manufacture, and critical for human evolution, its role in the emergence of early culture remains unclear. Most previous research on this question exclusively relied on direct morphological comparisons between early hominin and modern human skeletal elements, assuming that the degree of a species<span>'</span> dexterity depends on its similarity with the modern human form. Here, we develop a new approach to investigate the efficiency of thumb opposition, a fundamental component of manual dexterity, in several species of fossil hominins. Our work for the first time takes into account soft tissue as well as bone anatomy, integrating virtual modeling of <span>musculus opponens pollicis</span> and its interaction with three-dimensional bone shape form. Results indicate that a fundamental aspect of efficient thumb opposition appeared approximately 2 million years ago, possibly associated with our own genus <span>Homo</span>, and did not characterize <span>Australopithecus</span>, the earliest proposed stone tool maker. This was true also of the late <span>Australopithecus</span> species, <span>Australopithecus sediba</span>, previously found to exhibit human-like thumb proportions. In contrast, later <span>Homo</span> species, including the small-brained <span>H.<span> </span>naledi</span>, show high levels of thumb opposition dexterity, highlighting the increasing importance of cultural processes and manual dexterity in later human evolution.</p>
Evaluating refugia in recent human evolution in Africa: Supplementary information
<p><em>Homo sapiens</em> have adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late Pleistocene <em>Homo sapiens</em> populations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world where <em>Homo sapiens</em> have clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130-10 thousand years ago). We present two alternate models suggesting that between 27-66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome, and ecotone distributions within these refugial zones.</p>
Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway
<p>Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; i.e. Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F<sub>ST</sub> between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbour-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F<sub>ST</sub>) between marine and brackish sprat is larger in the comparison Norway- Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, i.e., 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.</p>
Data and code from: Viral outbreak dynamics and evolution in wildlife at the interface with humans
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Biomechanics of the human thumb and the evolution of dexterity
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An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans
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Data from: Human-driven evolution of insect color
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Evaluating refugia in recent human evolution in Africa: Supplementary information
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Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway
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Data from: Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the U.S., have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In contemplating future management actions for this species should major Snake River dams ever be removed (as many have proposed), it will be important to understand whether evolution is at least partially responsible for this life-history change. We hypothesized that if this trait is genetically based, parents who migrated to sea as subyearlings should produce faster-growing offspring that would be more likely to reach a size threshold to migrate to sea in their first year. We tested this with phenotypic data for over 2600 juvenile SRFCS that were genetically matched to parents of hatchery and natural origin. Three lines of evidence supported our hypothesis: 1) the animal model estimated substantial heritability for juvenile growth rate for three consecutive cohorts; 2) linear modeling showed an association between juvenile life history of parents and offspring growth rate; and 3) faster-growing juveniles migrated at greater speeds, as expected if they were more likely to be heading to sea. Surprisingly, we also found that parents reared a full year in a hatchery produced the fastest-growing offspring of all—apparently an example of cross-generational plasticity associated with artificial propagation. We suggest that SRFCS is an example of a potentially large class of species that can be considered to be "anthro-evolutionary"—signifying those whose evolutionary trajectories have been profoundly shaped by altered selective regimes in human-dominated landscapes.
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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.