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2,180 results for “Recombination”
Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta
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The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich
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Data from: The effect of parasite infection on the recombination rate of the yellow fever mosquito Aedes aegyti
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Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly
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Widespread recombination suppression facilitates plant sex chromosome evolution
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Evolution of novel mimicry polymorphisms through Haldane’s sieve and rare recombination
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Data for: Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko
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Breaking a species barrier by enabling hybrid recombination
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Data from: Asexual male production by ZW recombination in Artemia parthenogenetica
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Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
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Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes
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Environment dependent costs and benefits of recombination in independently evolved populations of Escherichia coli
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CO2 conversion in nonuniform discharges: disentangling dissociation and recombination mechanisms
<p>This archive contains supplementary data associated with the following publication:</p> <p>Title: CO2 Conversion in Nonuniform Discharges: Disentangling Dissociation and Recombination Mechanisms<br> Authors: A.J. Wolf, F.J.J. Peeters, P.W.C. Groen, W.A. Bongers, and M.C.M. van de Sanden<br> Journal: The Journal of Physical Chemistry C<br> Date of publication: July 14, 2020<br> DOI: https://dx.doi.org/10.1021/acs.jpcc.0c03637</p> <p>=====================================================================================<br> ABSTRACT<br> -------------------------------------------------------------------------------------<br> Motivated by environmental applications such as synthetic fuel synthesis, plasma-driven conversion shows promise for efficient and scalable gas-conversion of CO2 to CO. Both discharge contraction and turbulent transport have a significant impact on the plasma processing conditions, but are, nevertheless, poorly understood. This work combines experiments and modeling to investigate how these aspects influence the CO production and destruction mechanisms in the vortex-stabilized CO2 microwave plasma reactor. For this, a two-dimensional axisymmetric tubular chemical kinetics model of the reactor is developed, with careful consideration of the non-uniform nature of the plasma and the vortex-induced radial turbulent transport. Energy efficiency and conversion of the dissociation process show a good agreement with the numerical results over a broad pressure range from 80 - 600mbar. The occurrence of an energy efficiency peak between 100 - 200 mbar is associated with a discharge mode transition. The net CO production rate is inhibited at low pressure by the plasma temperature, while recombination of CO back to CO2 dominates at high pressure. Turbulence-induced cooling and dilution of plasma products limit the extent of the latter. The maxima in energy efficiency observed experimentally around 40% are related to limits imposed by production and recombination processes. Based on these insights, feasible approaches for optimization of the plasma dissociation process are discussed.<br> </p> <p>=====================================================================================<br> STRUCTURE AND CONTENT OF THE SUPPLEMENTARY DATA<br> -------------------------------------------------------------------------------------<br> The data and numerical code used to produce Figs. 6-16 in the publication are structured as listed below. The reactor model has been carried out in Wolfram Mathematica 11, as detailed in the publication. The code is available upon request by contacting the corresponding authors. The thermodynamics calculations regarding the quenching scenarios are carried out in python 3.7 using the thermodynamic equilibrium solver of the Cantera chemical kinetics library.</p> <p>DIRECTORY | DESCRIPTION<br> .\reactor_model | input files and simulation results used to produce Figs. 6 - 14<br> .\experimental | experimental data used in Fig 15<br> .\thermodynamics | thermodynamic calculations (python code and input file) used to produce Fig. 16<br> -------------------------------------------------------------------------------------</p> <p>=====================================================================================<br> TERMS OF USE<br> -------------------------------------------------------------------------------------<br> The data contained in this repository is published under a Creative Commons Attribution 4.0 license.</p>
Data from: Recombination rate variation shapes barriers to introgression across butterfly genomes
Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across the genome and between populations. Introgression can also erode species differences over time, but selection against introgression at certain loci acts to maintain post-mating species barriers. Theory predicts that species barriers made up of many loci throughout the genome should lead to a broad correlation between introgression and recombination rate, which determines the extent to which selection on deleterious foreign alleles will affect neutral alleles at physically linked loci. Here we describe the variation in genealogical relationships across the genome among three species of Heliconius butterflies: H. melpomene, H. cydno and H. timareta, using whole genomes of 92 individuals, and ask whether this variation can be explained by heterogeneous barriers to introgression. We find that species relationships vary predictably at the chromosomal scale. By quantifying recombination rate and admixture proportions, we then show that rates of introgression are predicted by variation in recombination rate. This implies that species barriers are highly polygenic, with selection acting against introgressed alleles across most of the genome. In addition, long chromosomes, which have lower recombination rates, produce stronger barriers on average than short chromosomes. Finally, we find a consistent difference between two species pairs on either side of the Andes, which suggests differences in the architecture of the species barriers. Our findings illustrate how the combined effects of hybridisation, recombination and natural selection, acting at multitudes of loci over long periods, can dramatically sculpt the phylogenetic relationships among species.
Recombination detection program (RDP4) results for ACMV and ACMBFV DNA-B
<p>A DNA-B multiple alignment (Zenodo record 3964979) was scanned with RDP4.100 (D. Martin et al. 2015). No events had statistical support from more than 4 of the 7 methods used to scan for signals of recombination.</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Recombination detection program (RDP4) results for EACMV-like DNA-B sequences (7 "species")
<p>A DNA-B multiple alignment (Zenodo record 3965023) was scanned with RDP4.97 (D. Martin et al. 2015). The input sequences belong to 7 “species”: CMMGV, EACMCV, EACMV, EACMKV, EACMMV, EACMZV, SACMV. Recombination breakpoints for events with statistical support from at least 5 of 7 methods were adjusted per the manual. These events were explicitly accepted, with the exception of one event which lost significance after adjustment of breakpoints. A CSV file with the results was exported and then saved a second time with Excel to normalize format (a comma in between every column).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Microbial Recombination with Population Structure
<p>This collection of data files contains, for each bacterial species:</p> <ol> <li>All raw genome sequence files.</li> <li>The core genome alignment obtained with REALPHY (this is the file with the .phy extension).</li> <li>A file with all SNP columns in the core genome alignment (the file name starts with columns_).</li> <li>A file listing all SNP types sorted from most to least common (the file name starts with snp_stats_)</li> <li>Two files containing the results of the pairwise analysis. First, a file with, for each pair, the histogram of SNP counts per alignment block (the file name ends in _histograms). And second, a file with the results of the mixture modeling (the file with the .pkl extension).</li> </ol> <p>In addition, for M. tuberculosis there is a subfolder with information about which strains have since been retracted from the database.</p> <p> </p> <p>The formats of these files are as follows:</p> <ol> <li>The raw genome sequence files are in FASTA format (.fasta or .fna).</li> <li>The core genome alignment is in PHYLIP multiple alignment format (.phy).</li> <li>The snp_stats file starts with a header line listing the total number of columns in the alignment with 1, 2, 3, and 4 different nucleotides. Each next line in the file corresponds to an observed SNP-type, sorted from most to least common. Each SNP line has the following columns:</li> </ol> <ol> <li>The total amount of genomic DNA associated with these SNP columns (associating each conserved alignment column to its closest SNP).</li> <li>The total number of occurrences of this SNP type.</li> <li>The number of strains sharing the minority allele.</li> <li>A bit-pattern describing the SNP type, with 1 for the strains sharing the minority allele, and zero for the others. The strains are sorted in the same order as in the PHYLIP alignment file.</li> <li>A list of all the strains sharing the minority allele.</li> </ol> <ol> <li>The columns_ file has one SNP per line, giving the position in the alignment plus the bit-pattern describing the SNP.</li> <li>The _histogram file contains, for each pair of strains, a histogram counting the number of 1Kb blocks with 0, 1, 2, etc SNPs. Note that these counts come from 1 kilobase sliding windows along the core genome alignment, sliding the window by 100 bases at a time, i.e. an alignment column will typically occur in 10 blocks.</li> <li>A pickle file with, for each pair, the results of the mixture modeling. Each line corresponds to a pair and has these fields: [spec1, spec2, div, Lpois, r_nomix, Lmix, rho, r, a, lam, mutpois, mutrecomb, cut] which correspond to:</li> </ol> <ol> <li>Name of strain 1.</li> <li>Name of strain 2.</li> <li>Their overall nucleotide divergence.</li> <li>The log-likelihood under a model assuming SNP counts form a simple Poisson distribution.</li> <li>The parameter of this fitted Poisson distribution.</li> <li>The log-likelihood of the mixture of a Poisson and negative binomial</li> <li>The fraction rho assigned to the Poisson part of the mixture.</li> <li>The parameter of the Poisson component.</li> <li>The exponent a of the negative binomial component.</li> <li>The second parameter (lambda) of the negative binomial.</li> <li>The estimated total number of mutations in the Poisson component.</li> <li>The estimated total number of mutations in the negative binomial component.</li> <li>The value at which the likelihood of negative poisson component starts exceeding the likelihood of the negative binomial component.</li> </ol> <p> </p> <p>In addition, for the human data we provide a PHYLIP multiple genome alignment and a file with all SNP columns.</p>
Data from: Beyond balancing selection: frequent mitochondrial recombination contributes to high female frequencies in gynodioecious Lobelia siphilitica L. (Campanulaceae)
(1) Gynodioecy is a sexual system where females and hermaphrodites co-occur. In most gynodioecious angiosperms, sex is determined by an interaction between mitochondrial male-sterility genes (CMS) that arise via recombination and nuclear restorer alleles that evolve to suppress them. In theory, gynodioecy occurs when multiple CMS types are maintained at equilibrium frequencies by balancing selection. However, some gynodioecious populations contain very high frequencies of females. High female frequencies are not expected under balancing selection, but could be explained by the repeated introduction of novel CMS types. (2) To test for balancing selection and/or the repeated introduction of novel CMS, we characterized cytoplasmic haplotypes from 61 populations of Lobelia siphilitica that vary widely in female frequency. (3) We confirmed that mitotype diversity and female frequency were positively correlated across populations, consistent with balancing selection. However, while low-female populations hosted mostly common mitotypes, high-female populations and female plants hosted mostly rare, recombinant mitotypes likely to carry novel CMS types. (4) Our results suggest that balancing selection maintains established CMS types across this species, but extreme female frequencies result from frequent invasion by novel CMS types. We conclude that balancing selection alone cannot account for extreme population sex-ratio variation within a gynodioecious species.
Data from: Loss of sexual recombination and segregation is associated with increased diversification in evening primroses
The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually-reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification rates (speciation minus extinction) in functionally asexual evening primrose lineages are roughly eight times faster than diversification rates in sexual lineages, largely due to higher speciation rates in asexual lineages. We further reject the hypothesis that a loss of recombination and segregation is irreversible because the transition rate from functional asexuality to sexuality is significantly greater than zero.and in fact exceeded the reverse rate. These results provide the first empirical evidence in support of the alternative theoretical prediction that asexual populations should instead diversify more rapidly than sexual populations because they are free from the homogenizing effects of sexual recombination and segregation. Although asexual reproduction may often constrain adaptive evolution, our results show that the loss of recombination and segregation need not be an evolutionary dead-end in terms of diversification of lineages.
Data from: Experimental evolution across different thermal regimes yields genetic divergence in recombination fraction but no divergence in temperature-associated plastic recombination
Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. The frequency of recombination in the model system Drosophila melanogaster has long been known to exhibit phenotypic plasticity in response to temperature. Here were use a panel of replicated experimental evolution populations of D. melanogaster to test whether variable environments favor enhanced plasticity in recombination rate in response to temperature. In contrast to expectation, we find no evidence for enhanced plasticity in recombination in the variable environment lines. Our data confirm a role of temperature in mediating recombination fraction in D. melanogaster, and indicate that recombination is genetically and plastically depressed under lower temperatures. Our data further suggest that the genetic architectures underlying plastic recombination and population-level variation in recombination rate are likely to be distinct.
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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)
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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.