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119 results for “mutation rate”
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
<p>Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of <i>de novo</i> mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (<i>Microcebus</i> <i>murinus</i>), we estimated the mutation rate to be 1.52 × 10<sup>–8</sup> (95% credible interval: 1.28 × 10<sup>−8</sup> to 1.78 × 10<sup>−8</sup>) mutations/site/generation, a rate among the highest calculated for a mammal. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG-sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false negative and false positive rate for our data and show that any point estimate of a <i>de novo </i>mutation rate should be considered with a large degree of uncertainty. To validate these observations, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which <i>de novo</i> mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution rate analyses for all species compared.</p>
Research data supporting article "Somatic mutation rates scale with lifespan across mammals"
<p>Data files supporting analyses described in the article "Somatic mutation rates scale with lifespan across mammals" (Cagan, Baez-Ortega et al., 2022).</p>
Wild pedigrees inform mutation rates and historic abundance in baleen whales
<p>Phylogeny-based estimates suggesting a low germline mutation rate (<em>μ</em>) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated <em>μ</em> directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of <em>μ</em> reduces previous genetic–based estimates of pre-exploitation whale abundance by 86% and suggests that <em>μ</em> cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate <em>μ</em> directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.</p>
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
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Wild pedigrees inform mutation rates and historic abundance in baleen whales
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Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
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Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama
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Quantifying influences on intragenomic mutation rate: data files
<p>Raw, intermediate and final datasets associated with the the paper "Quantifying influences on intragenomic mutation rate".</p> <p>Code will be made available at <a href="https://github.com/helmutsimon/ProbPolymorphism">https://github.com/helmutsimon/ProbPolymorphism</a>. Refer to README.md at this site.</p>
Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli
Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
Data from: Historical mutation rates predict susceptibility to radiation in Chernobyl birds
Extreme environmental perturbations are rare, but may have important evolutionary consequences. Responses to current perturbations may provide important information about the ability of living organisms to cope with similar conditions in the evolutionary past. Radioactive contamination from Chernobyl constitutes one such extreme perturbation, with significant but highly variable impact on local population density and mutation rates of different species of animals and plants. We explicitly tested the hypothesis that species with strong impacts of radiation on abundance were those with high rates of historical mutation accumulation as reflected by cytochrome b mitochondrial DNA base pair substitution rates during past environmental perturbations. Using a dataset of 32 species of birds we show higher historical mitochondrial substitution rates in species with the strongest negative impact of local levels of radiation on local population density. These effects were robust to different estimates of impact of radiation on abundance, weighting of estimates of abundance by sample size, statistical control for similarity in the response among species due to common phylogenetic descent, and effects of population size and longevity. Therefore, species that respond strongly to the impact of radiation from Chernobyl are also the species that in the past have been most susceptible to factors that have caused high substitution rates in mitochondrial DNA.
Data used for ECAL 2015 paper "Optimal Mutation Rate Control under Selection in Hamming Spaces"
<p>This dataset contains the evolved mutation rate control functions, obtained by following the methods described in the following paper, from which the means and standard deviations shown in the paper were calculated.</p> <p>Paper: Optimal Mutation Rate Control under Selection in Hamming Spaces, accepted for publication in Advances in Artificial Life, ECAL 2015: Proceedings of the Thirteenth European Conference on the Synthesis and Simulation of Living Systems.</p>
Data used for ALife 2016 paper "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes"
<p>The results files in this directory contain the evolved critical mutation rates, exponential or quadratic curves produced by curve-fitting using the given data in R, and biological data used for comparison in the following paper:</p> <p>Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes, accepted for publication in ALife 2016: Proceedings of the 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV)</p>
FIGURE 4. Tarsi I in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 4. Tarsi I (A-C), II (D-F), III (G-I), IV (J-L) for M. americanus specimen IZ-133812(105662)-7420 (left column), M. savannahensis sp. nov. specimen IZ-133799(105645)-7185 (median column), and M. sassafrasensis sp. nov. specimen IZ- 134535(105644)-7176 (right column).
FIGURE 12 in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 12. Close-up dorsal views of spermatopositors from, A, M. savannahensis sp. nov. (IZ-133799(105645)-7185) and, B, M. americanus (IZ-133812(105662)-7420), showing the lobus medialis (LM), lacinia dorsalis (LD), lobulus lateralis (LL), and digitus (D).
FIGURE 8. A in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 8. A, detail of anterior margin of gonostome and, B, of anal plate of M. savannahensis sp. nov. female specimen IZ- 133800(105646)-7223.
FIGURE 6 in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 6. Details of anal plate for males of, A, M. americanus specimen IZ-133812(105662)-7420, B, M. savannahensis sp. nov. specimen 105645-7185, C, M. savannahensis sp. nov. specimen IZ-133800(105646)-7221, and, D, M. sassafrasensis sp. nov. specimen IZ-134535(105644)-7176.
FIGURE 7. A in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 7. A, gonostome and ventral complex detail and, B, full ventral view of M. savannahensis sp. nov. male specimen IZ-133800(105646)-7214.
FIGURE 2. A in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 2. A, molecular phylogeny of Metasiro COI sequences, made ultrametric using a relaxed clock, showing the four putative species from the GMYC model (red clades above the dashed red line); B, lineage-through-time plot for Metasiro diversification, the red line indicating the inferred time of rapid within-species COI diversification resulting from a singlethreshold analysis. Time for all plots is expressed as the proportion of time since the present to the root. Specimens of M. americanus collected from the Apalachicola River region and Florida Caverns are colored by location.
FIGURE 1 in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 1. Unrooted phylogeny for all Metasiro COI sequences, found under parsimony in POY and showing parsimony branch lengths. Insets A, B, and C show the locations of unique nucleotides (smaller, lower triangles) and amino acids (larger, upper triangles) along the 769 bp COI fragment. The frequencies of corrected pairwise divergences are shown in inset D and are divided by the type of comparison: solid black for intraspecific distances, dashed black for interspecific distances, and dashed gray for distances among widespread populations of M. americanus in the Florida panhandle.
FIGURE 3 in Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates
FIGURE 3. Male specimens of Metasiro, showing dorsal (left column), lateral (middle), and ventral (right) views: A–C, M. americanus specimen IZ-133813(105663)-7436; D–F, M. savannahensis sp. nov. holotype, specimen IZ-133799(105645)- 7184; and G–I, M. sassafrasenesis sp. nov. holotype, specimen IZ-134535(105644)-7171.
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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.