SEARCH · Search bioRxiv

Results for “Preprint”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

bioRxiv2017

Cooperation And Liaison Between Universities And Editors (CLUE): Recommendations On Best Practice

Journals and research institutions have common interests regarding the trustworthiness of research publications but their specific roles and responsibilities differ. These draft recommendations aim to address issues surrounding cooperation and liaison between journals and institutions about possible and actual problems with reported research. The proposals will be discussed at various meetings including the World Conference on Research Integrity in May 2017. We will also consider comments and suggestions posted on this preprint.\n\nThe main recommendations are that: O_LINational registers of individuals or departments responsible for research integrity at institutions should be created.\nC_LIO_LIInstitutions should develop mechanisms for assessing the validity of research reports that are independent from processes to determine whether individual researchers have committed misconduct.\nC_LIO_LIEssential research data and peer review records should be retained for at least 10 years.\nC_LIO_LIWhile journals should normally raise concerns with authors in the first instance, they also need criteria to determine when to contact the institution before, or at the same time as, alerting the authors in cases of suspected data fabrication or falsification to prevent the destruction of evidence.\nC_LIO_LIAnonymous or pseudonymous allegations made to journals or institutions should be judged on their merit and not dismissed automatically.\nC_LIO_LIInstitutions should release relevant sections of reports of research trustworthiness or misconduct investigations to all journals that have published research that was the subject of the investigation.\nC_LI

scientific communication and education↗

bioRxiv2017

Parallel radiations of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100033). Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of lake Pebas, and closure of the Panama Isthmus on two clades of trees (Cremastosperma, c. 31 spp.; and Mosannona, c. 14 spp.; both Annonaceae) found in humid forest distributed across the transition zones between the Andes and Western (lowland) Amazonia and between Central and South America. We inferred phylogenies based on c. 80% of recognised species of each clade using plastid and nuclear encoded sequence markers, revealing similar patterns of geographically restricted clades. Using molecular dating we showed that diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. In apparent contradiction of high dispersal abilities of rainforest trees, Cremastosperma clades within Amazonia are also geographically restricted, with a southern/montane clade that appears to have diversified along the foothills of the Andes sister to one of more northern/lowland species that diversified in a region once inundated by lake Pebas. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma. Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrasts with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees.

evolutionary biology↗

bioRxiv2017

Using Connectivity To Identify Climatic Drivers Of Local Adaptation

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100034). Despite being able to conclusively demonstrate local adaptation, we are still often unable to objectively determine the climatic drivers of local adaptation. Given the rapid rate of global change, understanding the climatic drivers of local adaptation is vital. Not only will this tell us which climate axes matter most to population fitness, but such knowledge is critical to inform management strategies such as translocation and targeted gene flow. While simple assessments of geographic trait variation are useful, geographic variation (and its associations with environment) may represent plastic, rather than evolved, differences. Additionally, the vast number of trait-environment combinations makes it difficult to determine which aspects of the environment populations adapt to. Here we argue that by incorporating a measure of landscape connectivity as a proxy for gene flow, we can differentiate between trait-environment relationships underpinned by genetic differences versus those that reflect phenotypic plasticity. By doing so, we can rapidly shorten the list of trait-environment combinations that may be of adaptive significance. We demonstrate how this reasoning can be applied using data on geographic trait variation in a lizard species from Australia's Wet Tropics rainforest. Our analysis reveals an overwhelming signal of local adaptation for the traits and environmental variables we investigated. Our analysis also allows us to rank environmental variables by the degree to which they appear to be driving local adaptation. Although encouraging, methodological issues remain: we point to these issue in the hope that the community can rapidly hone the methods we sketch here. The promise is a rapid and general approach to identifying the environmental drivers of local adaptation.

evolutionary biology↗

bioRxiv2017

Renewed diversification following Miocene landscape turnover in a Neotropical butterfly radiation

\"This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100032)\"\n\nThe Neotropical region has experienced a dynamic landscape evolution throughout the Miocene, with the large wetland Pebas occupying western Amazonia until 11-8 my ago and continuous uplift of the Andes mountains along the western edge of South America. Although the complex dynamics between the Andes and Amazonia may have strongly affected the trajectory of Neotropical biodiversity, there is little evidence for such an influence from time-calibrated phylogenies of groups that diversified during this period. Here, we generate one of the most comprehensive time-calibrated molecular phylogenies of a group of Neotropical insects: the butterfly tribe Ithomiini. Our tree includes 340 species (87% of extant species), spanning 26 million years of diversification in the Neotropics. We investigate temporal and spatial patterns of diversification, focusing on the influence of Miocene landscape tranformations on the dynamics of speciation, extinction and biotic interchanges at the Amazonia/Andes interface. We find that Ithomiini likely began diversifying at the interface between the Andes and the Amazonia around 26.4 my ago. Five subtribes with a very low extant diversity started diversifying early in western Amazonia, but a rapid decrease in diversification rate due to increased extinction rate between 20 and 10 my ago suggests a negative impact of the Pebas wetland system on these early lineages. By contrast, the clade containing the five most species-rich subtribes (85% of extant species) was characterized by a high, positive net diversification rate. This clade diversified exclusively in the Central Andes from 20 to 10 my ago. After the demise of the Pebas system (11-8 my ago), we found a sudden increase of interchanges with the Northern Andes and Amazonia, followed by local diversification, which led to a substantial renewal of diversification. In general, ecological turnovers throughout the Miocene strongly determined the dynamics of speciation, and extinction and interchanges, and appear as a key driving force shaping the regions current extraordinary biodiversity.

evolutionary biology↗

bioRxiv2017

Pleistocene climate change and the formation of regional species pools

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100053). Despite the description of bioregions dates back from the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We use a network approach to identify regional and sub-regional faunas of European Carabus beetles, and analyse the effects of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration of Carabus faunas occurred during the Pleistocene. Our results show how extreme recent historical events -such as Pleistocene climate cooling, rather than just deep-time evolutionary processes, can profoundly modify the composition and structure of geographic species pools.

ecology↗

bioRxiv2017

Identification And Evolutionary Analysis Of Eight Non-Coding Genomic Elements Regulating Neurodevelopmental Genes

Many non-coding regulatory elements conserved in vertebrates regulate the expression of genes involved in development and play an important role in the evolution of morphology through the rewiring of developmental gene networks. Available biological datasets allow the identification of non-coding regulatory elements with high confidence; furthermore, chromatin conformation data can be used to confirm enhancer-promoter interactions in specific tissue types and developmental stages. We have devised an analysis pipeline that integrates datasets about gene expression, enhancer activity, chromatin accessibility, epigenetic marks, and Hi-C contact frequencies in various brain tissues and developmental stages, leading to the identification of eight non-coding elements that might regulate the expression of three genes with important roles in brain development in vertebrates. We have then performed comparative sequence and microsynteny analyses in order to reconstruct the evolutionary history of the regulatory landscape around these genes; we observe a general pattern of ancient regulatory elements conserved across most vertebrate lineages, together with younger elements that appear to be mammal and primate innovations. This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100035)

evolutionary biology↗

bioRxiv2017

Trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100039). The efficiency of plant resistance to fungal pathogen populations is expected to decrease over time, due to its evolution with an increase in the frequency of virulent or highly aggressive strains. This dynamics may differ depending on the scale investigated (annual or pluriannual), particularly for annual crop pathogens with both sexual and asexual reproduction cycles. We assessed this time-scale effect, by comparing aggressiveness changes in a local Zymoseptoria tritici population over an eight-month cropping season and a six-year period of wheat monoculture. We collected two pairs of subpopulations to represent the annual and pluriannual scales: from leaf lesions at the beginning and end of a single annual epidemic, and from crop debris at the beginning and end of a six-year period. We assessed two aggressiveness traits - latent period and lesion size - on sympatric and allopatric host varieties. A trend toward decreased latent period concomitant with a significant loss of variability was established during the course of the annual epidemic, but not over the six-year period. Furthermore, a significant cultivar effect (sympatric vs. allopatric) on the average aggressiveness of the isolates revealed host adaptation, arguing that the observed patterns could result from selection. We thus provide an experimental body of evidence of an epidemiological trade-off between the intra- and inter-annual scales in the evolution of aggressiveness in a local plant pathogen population. More aggressive isolates were collected from upper leaves, on which disease severity is usually lower than on the lower part of the plants left in the field as crop debris after harvest. We suggest that these isolates play little role in sexual reproduction, due to an Allee effect (difficulty finding mates at low pathogen densities), particularly as the upper parts of the plant are removed from the field, explaining the lack of transmission of increases in aggressiveness between epidemics.

epidemiology↗

bioRxiv2017

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100046). The recent Ebola virus (EBOV) outbreak in West Africa witnessed considerable efforts to obtain viral genomic data as the epidemic was unfolding. If such data can be deployed in real-time, molecular epidemiological investigations could play a role in complementing contact tracing undertaken by public health agencies. Analysing the EBOV genomes accumulated to date can also deliver insights into epidemic dynamics. Such analyses have been shown that metapopulation dynamics were critical for EBOV dispersal between rural and urban areas during the epidemic, but the implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events (between administrative areas >250 km apart) were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, urban areas - specifically those encompassing the three capital cities and their suburbs - were critical in attracting and further disseminating the virus: preventing viral lineage movement to all three simultaneously would have contained epidemic size by two-thirds. Using continuous phylogeographic reconstructions we estimate a distance kernel for EBOV spread and reveal considerable heterogeneity in dispersal velocity through time. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions.

epidemiology↗

bioRxiv2017

Maternal X chromosome upregulation in both sexes initiates dosage compensation evolution

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100044).\n\nSex chromosomes have repeatedly evolved from a pair of autosomes1. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced Y gene expression and eventual Y gene loss. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes. A diverse set of dosage compensating mechanisms that alleviates these negative effects has been described in animals2-4. However, the early steps in the evolution of dosage compensation remain unknown and dosage compensation is poorly understood in plants5. Here we show a novel dosage compensation mechanism in the evolutionarily young XY sex determination system of the plant Silene latifolia. Genomic imprinting results in higher expression from the maternal X chromosome in both males and females. This compensates for reduced Y expression in males but results in X overexpression in females and may be detrimental. It could represent a transient early stage in the evolution of dosage compensation. Our finding has striking resemblance to the first stage proposed by Ohno for the evolution of X inactivation in mammals.

evolutionary biology↗

bioRxiv2017

Natural selection on plasticity of thermal traits in a highly seasonal environment

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100048). For ectothermic species with broad geographical distributions, latitudinal/altitudinal variation in environmental temperatures (averages and extremes) are expected to shape the evolution of physiological tolerances and the acclimation capacity (i.e., degree of phenotypic plasticity) of natural populations. This can create geographical gradients of selection in which environments with greater thermal variability (e.g., seasonality) tend to favour individuals that maximize performance across a broader range of temperatures compared to more stable environments. Although thermal acclimation capacity plays a fundamental role in this context, it is unknown whether natural selection targets this trait in natural populations. Here we addressed such an important gap in our knowledge by measuring survival, through mark recapture integrated into an information-theoretic approach, as a function of the plasticity of critical thermal limits for activity, behavioural thermal preference and the thermal sensitivity of metabolism in the northernmost population of the four-eyed frog Pleurodema thaul. Overall, our results indicate that thermal acclimation in this population is not being targeted by directional selection, although there might be signals of selection on individual traits. According to the most supported models, survival decreased in individuals with less tolerance to cold when cold-acclimated (probably because daily low extremes are frequent during the cooler periods of the year) and increased with body size. However, in both cases, the directional selection estimates were non-significant.

evolutionary biology↗

bioRxiv2019

Oligomerization of the antimalarial drug target PfATP4 is essential for parasite survival

Withdrawal StatementThe authors have withdrawn their manuscript owing to further investigations on PfATP4 that have revealed that the main conclusion of the preprint that PfATP4 forms oligomers is incorrect. Initial cryogenic electron microscopy observations showed a large detergent belt that surrounds monomers of PfATP4, which could have affected migration of the molecule on blue-native polyacrylamide gels. This gave an incorrect impression of the molecule to be in a dimeric or oligomeric state. Authors regret this error in interpreting the data. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

biochemistry↗

bioRxiv2019

Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein.

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a pleiotropic neuropeptide hormone functioning in the central nervous system and peripheral tissues. The PACAP receptor PAC1R, which belongs to the class B G-protein-coupled receptors (GPCRs), is a drug target for mental disorders and dry eye syndrome. Here we present a cryo-electron microscopy structure of human PAC1R bound to PACAP and an engineered Gs heterotrimer. The structure revealed that TM1 plays an essential role in PACAP recognition. The ECD (extracellular domain) of PAC1R tilts by ~40{degrees} as compared to that of the glucagon-like peptide-1 receptor (GLP1R), and thus does not cover the peptide ligand. A functional analysis demonstrated that the PAC1R-ECD functions as an affinity trap and is not required for receptor activation, whereas the GLP1R-ECD plays an indispensable role in receptor activation, illuminating the functional diversity of the ECDs in the class B GPCRs. Our structural information will facilitate the design and improvement of better PAC1R agonists for clinical applications. This article is a preprint version and has not been certified by peer review.

molecular biology↗

bioRxiv2020

Diverse genetic origins of medieval steppe nomad conquerors - a response to Mikheyev et al. (2019)

Recently, Mikheyev et al. (2019) have produced a preprint study describing the genomes of nine Khazars archeologically dated from the 7th to the 9th centuries found in the Rostov county in modern-day Russia. Skull morphology indicated a mix of "Caucasoid" and "Mongoloid" shapes. The authors compared the samples to ancient and contemporary samples to study the genetic makeup of the Khazars and their genetic legacy and addressed the question of the relationships between the Khazar and Ashkenazic Jews. A careful examination reveals grave concerns regarding all the aspects of the study from the identification of the "Khazar" samples, the choice of environment for ancient DNA sequencing, and the analyses. The authors did not disclose the data used in their study, and their methodology is incoherent. We demonstrate that their analyses yield nonsensical results and argue that none of the claims made in this study are supported by the data unequivocally. Provided the destruction of the bone samples and the irreproducibility of the analyses, even by the forgivable standards of the field, this study is irreplicable, wasteful, and misleading.

genomics↗

bioRxiv2020

Protein evolution is structure dependent and non-homogeneous across the tree of life

MotivationProtein sequence evolution is a complex process that varies among-sites within proteins and across the tree of life. Comparisons of evolutionary rate matrices for specific taxa ( clade-specific models) have the potential to reveal this variation and provide information about the underlying reasons for those changes. To study changes in patterns of protein sequence evolution we estimated and compared clade-specific models in a way that acknowledged variation within proteins due to structure. ResultsClade-specific model fit was able to correctly classify proteins from four specific groups (vertebrates, plants, oomycetes, and yeasts) more than 70% of the time. This was true whether we used mixture models that incorporate relative solvent accessibility or simple models that treat sites as homogeneous. Thus, protein evolution is non-homogeneous over the tree of life. However, a small number of dimensions could explain the differences among models (for mixture models ~50% of the variance reflected relative solvent accessibility and ~25% reflected clade). Relaxed purifying selection in taxa with lower long-term effective population sizes appears to explain much of the among clade variance. Relaxed selection on solvent-exposed sites was correlated with changes in amino acid side-chain volume; other differences among models were more complex. Beyond the information they reveal about protein evolution, our clade-specific models also represent tools for phylogenomic inference. AvailabilityModel files are available from https://github.com/ebraun68/clade_specific_prot_models. Contactebraun68@ufl.edu Supplementary informationSupplementary data are appended to this preprint.

evolutionary biology↗

bioRxiv2020

BIP4COVID19: Releasing impact metrics data for articles relevant to COVID-19

Since the beginning of the 2019-20 coronavirus pandemic, a large number of relevant articles has been published or become available in preprint servers. These articles, along with earlier related literature, compose a valuable knowledge base affecting contemporary research studies, or even government actions to limit the spread of the disease and treatment decisions taken by physicians. However, the number of such articles is increasing at an intense rate making the exploration of the relevant literature and the identification of useful knowledge in it challenging. In this work, we describe BIP4COVID19, an open dataset compiled to facilitate the coronavirus-related literature exploration, by providing various indicators of scientific impact for the relevant articles. Additionally, we provide a publicly accessible Web interface on top of our data, allowing the exploration of the publications based on the computed indicators.

scientific communication and education↗

bioRxiv2020

Open Access and Altmetrics in the pandemic age: Forescast analysis on COVID-19 related literature

We present an analysis on the uptake of open access on COVID-19 related literature as well as the social media attention they gather when compared with non OA papers. We use a dataset of publications curated by Dimensions and analyze articles and preprints. Our sample includes 11,686 publications of which 67.5% are openly accessible. OA publications tend to receive the largest share of social media attention as measured by the Altmetric Attention Score. 37.6% of OA publications are bronze, which means toll journals are providing free access. MedRxiv contributes to 36.3% of documents in repositories but papers in BiorXiv exhibit on average higher AAS. We predict the growth of COVID-19 literature in the following 30 days estimating ARIMA models for the overall publications set, OA vs. non OA and by location of the document (repository vs. journal). We estimate that COVID-19 publications will double in the next 20 days, but non OA publications will grow at a higher rate than OA publications. We conclude by discussing the implications of such findings on the dissemination and communication of research findings to mitigate the coronavirus outbreak.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

The UCSC SARS-CoV-2 Genome Browser

BackgroundResearchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into "annotation tracks" where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis. ResultsThe UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day. ConclusionsWe invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at genome-www@soe.ucsc.edu with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.

genomics↗

bioRxiv2020

Neural Correlates of Value Are Intrinsically History Dependent

The authors have withdrawn their manuscript since they no longer stand by the results reported in this preprint. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

neuroscience↗