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203 results for “rates of evolution”
Data from: Tetrapod vocal evolution reveals faster rates and higher-pitched sounds for mammals
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Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity
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Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
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Data from: Modeling the evolution of rates of continuous trait evolution
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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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Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation
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Data: Female-limited responses in remating rate and mating duration in the experimental evolution of a beetle Callosobruchus chinensis
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Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
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High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms
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Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation
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Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle ( Leptinotarsa decemlineata, Say)
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Cosmic Rates of Black Hole Mergers and Pair-Instability Supernovae from Chemically Homogeneous Binary Evolution
<p>Data products and files to reproduce the results from du Buisson et al. (2020).</p> <p><strong>MESA Calculations</strong></p> <p>This work included the calculation of large grids of binary models with the MESA code version 11701. The template used for these calculations is included (template.tar.xz), to model any specific system the files inlist_extra and inlist_extra_sj must be updated with the necessary initial parameters.</p> <p>The resulting data from all simulations is also included in the files named Z*.tar.xz, where the "*" should be replaced for the specific value of log10(Z) for that set of simulations. Data is included in folders with a naming format of logM1_massratio_periodindays, so for instance the folder named 2.100_1.000_2.800 contains a simulation performed for a primary of mass 10^(2.1) Msun, a mass ratio of unity, and an initial orbital period of 2.8 days (note that all simulations are done for a mass ratio of unity). Each folder is a full MESA work directory, including the necessary input files and source code to rerun the simulation. The data files included in each folder are:</p> <ol> <li>LOGS1/history.data.s: A MESA history file containing information of the primary every 5 steps of the simulation. This file has been processed from the original MESA output to reduce its size.</li> <li>binary_history.data.s: Similar to the previous one but containing information of the binary system itself</li> <li>last_profile_1.data.s: MESA profile file containing the interior structure of the star at the end of the simulation. These files are only stored for systems that deplete central carbon, or become pair unstable. This file has also been post-processed to reduce its size, mostly by removing redundant columns and reducing the reported precision.</li> <li>out.txt.s: The last 100 lines of the terminal output from the simulation, useful to quickly glance the outcome.</li> </ol> <p><strong>Summary data tables for the MESA simulations</strong></p> <p>Data tables summarizing the outcome of all simulations are included in the file data_tables.tar.xz. Each of the files contained in that archive have the results from one metallicity, with the name indicating the value of log10(Z). Each row in the files represents one simulation, and the data provided in the different columns is:</p> <ol> <li>"log10(M_1i)(Msun)", "qratio(M_2i/M_1i)", "P_i(days)", "metallicity": The initial parameters of the simulation.</li> <li>"result": A string indicating the outcome of the system (see the header of the data files for a list of outcomes). In particular when the outcome is "double_BH", "PISN", "PPISN", the following columns indicate information at the terminal point of the simulation. For all other outcomes, most of the following columns are empty.</li> <li>had_contact: Specifies whether the system undergoes a contact phase (see header in the data files for allowed values).</li> <li>"M_1f(Msun)", "M_2f(Msun)", "P_f(days)": Final orbital parameters.</li> <li>"merge_time(Gyr)": Time to merge from the system assuming the system forms a binary black hole with masses and period given by the M_1f, M_2f and P_f values.</li> <li>"Kerr_param_1", "Kerr_param_2": Black hole spin assuming all angular momentum and mass is conserved at collapse.</li> <li>For the values listed in 4,5 and 6, we also provide values with an added "wpi" description, these indicate the expected results when including pair and pulsational pair instability supernovae, as described in the paper.</li> <li>"he_core_mass_1": Mass coordinate in Msun of the uppermost layer of the star with a mass fraction of hydrogen < 0.01. Any other arbitrary cut can be computed using the profile data.</li> <li>"c_core_mass_1": Mass coordinate in Msun of the uppermost layer of the star with a mass fraction of helium < 0.01.</li> <li>"total_mass_h1_1", "total_mass_he4_1": Total mass of hydrogen and helium at the end of the simulation</li> <li>The remaining columns contain the same information as points 8,9,10 for the secondary. Since all our simulations have q=1 they're actually redundant.</li> </ol> <p><strong>Montecarlo Simulations</strong></p> <p>Using the results of the MESA calculations, Montecarlo simulations were performed that sample the relevant distribution functions and the cosmic star formation history. The code used to perform these calculations is included in the archive montecarlo_code.tar.xz, and it includes a readme.txt file with instructions on how to use it. The outcome of these Montecarlo simulations is included in the files:</p> <ol> <li>fiducial.tar.xz</li> <li>sfr_c1.tar.xz</li> <li>sfr_c2.tar.xz</li> <li>sfr_c3.tar.xz</li> <li>sfr_c4.tar.xz</li> </ol> <p>The first file contains the information on our standard choice of SFR history, including simulations with no kicks, and with and without PPISN. The other four files correspond to each of the cases of SFR variations that we considered in the paper. Each of these archives contain three files:</p> <ol> <li>direct.txt: Information for systems that form BHs through direct collapse</li> <li>PISN.txt: Sampled systems which undergo PISN.</li> <li>PPISN.txt: Systems that fall in the range where we expect PPISN to occur. Information is provided assuming both direct collapse and PPISN mass loss, so the effect of PPISNe can be distinguished.</li> <li>volume.txt: Comoving value for the simulation. All the formed BHs and PISN listed can be assumed to be a complete sample of a box of this size through cosmic time (formed by the CHE channel of course, we don't include our evolutionary channels here).</li> </ol> <p>The data contained for these systems is</p> <ol> <li>"M1i[Msun]", "Pi[days]", "Z", "z_b": Initial primary mass (same as secondary), orbital period in days, metallicity and birth redshift. We assume the time between birth and formation of the binary black hole or PISN event is negligible.</li> <li>"M1f[Msun]", "Pf[days]": For the case of BH formation, these indicate the mass of the black hole formed by the primary (which is equal to the secondary) and the orbital period at BBH formation. For the case of systems undergoing PISN, they represent instead the properties at the onset of the PISN.</li> <li>"spin": Spin of each BH. We assume the spin is aligned with the orbit. Not included for PISN systems.</li> <li>"z_m": Redshift at which the BBH would merge from GW emission. Not included for PISN systems.</li> <li>"t_d[Gyr]": The delay time between BBH formation and merger due to GW emission. Not included for PISN systems.</li> <li>"p_*": Detection probability for the source assuming a random orientation of the source in the sky with respect to the detector. This includes "O1", "O2" and "O3" for LIGO's first observing runs, as well as "F" for LIGO's design sensitivity. "ET" is used for the detection probability for the Einstein telescope. Not included for PISN systems. Also, for the different studies of SFR variations we only considered LIGO at full design sensitivity and ET.</li> <li>All quantities denoted with "_pp" indicate variations to the previous values in the case we consider pulsational pair instability supernovae, as described in the paper.</li> </ol> <p>The Montecarlo simulations with kicks are not included, but can be recomputed using the source code provided.</p>
Variation in the strength of allometry drives rates of evolution in primate brain shape - Supplementary Material
<p>Large brains are a defining feature of primates, as is a clear allometric trend</p> <p>between body mass and brain size. However, important questions on the</p> <p>macroevolution of brain shape in primates remain unanswered. Here we</p> <p>address two: (i), does the relationship between the brain size and its shape</p> <p>follow allometric trends and (ii), is this relationship consistent over evolutionary</p> <p>time? We employ three-dimensional geometric morphometrics and</p> <p>phylogenetic comparative methods to answer these questions, based on a</p> <p>large sample representing 151 species and most primate families. We found</p> <p>two distinct trends regarding the relationship between brain shape and</p> <p>brain size. Hominoidea and Cercopithecinae showed significant evolutionary</p> <p>allometry, whereas no allometric trends were discernible for Strepsirrhini,</p> <p>Colobinae or Platyrrhini. Furthermore,we found that in the taxa characterized</p> <p>by significant allometry, brain shape evolution accelerated, whereas for taxa in</p> <p>which such allometrywas absent, the evolution of brain shape decelerated.We</p> <p>conclude that although primates in general are typically described as largebrained,</p> <p>strong allometric effects on brain shape are largely confined to the</p> <p>order's representatives that display more complex behavioural repertoires.</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.
Stellar evolution tracks comparing turbulent pressure driven mass loss and the de Jager mass-loss rates
<p>The uploaded files provide a series of stellar evolution tracks with initial masses from 16 to 20 <span class="math-tex">\(M_\odot\)</span>. The two sets of tracks compare the evolution of stars evolved on the red supergiant branch with the Kee et al. turbulent pressure driven mass-loss rates to stars that instead use the de Jager mass-loss rates.</p>
Data from: What makes a leaf tough? Patterns of correlated evolution between leaf toughness traits and demographic rates among 197 shade-tolerant woody species in a neotropical forest
Slow-growing juveniles of shade-tolerant plant species are predicted to have tough leaves because of the high cost of leaf replacement in shade relative to potential carbon gain. We assessed the degree of correlated evolution among eight traits associated with leaf toughness and their relationships with growth and mortality rates of 197 tree and shrub species from the understory of the 50-hectare forest dynamics plot on Barro Colorado Island, Panama. Path analysis with phylogenetically independent contrasts revealed that leaves attained material toughness (resistance to fracture per unit fracture area) through increases in tissue density, percent cellulose per unit dry mass, and vein fracture toughness. Lamina density and cellulose content evolved independently, and thus represent different paths to material toughness. Structural toughness (resistance to fracture per unit fracture length) depended on material toughness and lamina thickness. Mortality rates of individuals 1-10 cm in stem diameter were negatively correlated with material toughness and lamina density, but were independent of structural toughness and cell wall fiber contents. Leaf toughness traits were uncorrelated with relative growth rates. These results imply that material toughness enhances resistance to natural enemies, which increases survival and offsets the biomass allocation cost of producing tough leaves in the shaded understory.
Data from: Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (Proteaceae)
Background: Hotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a major contributor to these patterns. We constructed the first near-complete phylogeny of Banksia (Proteaceae) to test whether diversification rates have differed between lineages confined to the southwest Australian hotspot and those found throughout southern, eastern and northern Australia. We then tested for variation in diversification rates among the bioclimatic zones within the southwest hotspot itself. Results: Although Banksia species richness in the southwest is ten times that of the rest of the continent, we find little evidence for more rapid diversification in the southwest, although this result is inconclusive. However, we find firmer support for substantial rate variation within the southwest hotspot, with more rapid diversification in the semi-arid heaths and shrublands, compared to the high-rainfall forests. Most of the Banksia diversity of the southwest appears to be generated in the heaths and shrublands, with a high migration rate out of this zone boosting diversity of the adjacent forest zone. Conclusions: The geographic pattern of diversification in Banksia appears more complex than can be characterized by a simple hotspot vs. non-hotspot comparison, but in general, these findings contrast with the view that the high diversity of Mediterranean hotspots is underpinned by rapid radiations. Steady accumulation of species at unexceptional rates, but over long periods of time, may also have contributed substantially to the great botanical richness of these regions.
Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid 'background' rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent.
Data from: Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds
Birds are the most diverse living tetrapod group and are a model of large-scale adaptive radiation. Neontological studies suggest a radiation within the avian crown group, long after the origin of flight. However, deep time patterns of bird evolution remain obscure because only limited fossil data have been considered. We analyse cladogenesis and limb evolution on the entire tree of Mesozoic theropods, documenting the dinosaur–bird transition and immediate origins of powered flight. Mesozoic birds inherited constraints on forelimb evolution from non-flying ancestors, and species diversification rates did not accelerate in the earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit both phenotypic release of the hindlimb and increased diversification rates, unparalleled in magnitude at any other time in the first 155 Myr of theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group birds was enabled by restructuring of the terrestrial locomotor module, which represents a key innovation. Our results suggest two phases of radiation in Avialae: with the Cretaceous diversification overwritten by extinctions of stem-group birds at the Cretaceous–Palaeogene boundary, and subsequent diversification of the crown group. Our findings illustrate the importance of fossil data for understanding the macroevolutionary processes generating modern biodiversity.
Data from: Rate of resistance evolution and polymorphism in long- and short-lived hosts
Recent theoretical work has shown that long-lived hosts are expected to evolve higher equilibrium levels of disease resistance than shorter-lived hosts, but questions of how longevity affects the rate of resistance evolution and the maintenance of polymorphism remain unanswered. Conventional wisdom suggests that adaptive evolution should occur more slowly in long-lived organisms than in short-lived organisms. However, the opposite may be true for the evolution of disease-resistance traits where exposure to disease, and therefore the strength of selection for resistance increases with longevity. In a single locus model of innate resistance to a frequency-dependent, sterilizing disease, longer-lived hosts evolved resistance more rapidly than short-lived hosts. Moreover, resistance in long-lived hosts could only be polymorphic for more costly and more extreme resistance levels than short-lived hosts. The increased rate of evolution occurred in spite of longer generation times because longer-lived hosts had both a longer period of exposure to disease as well as higher disease prevalence. Qualitatively similar results were found when the model was extended to mortality-inducing diseases, or to density-dependent transmission modes. Our study shows that the evolutionary dynamics of host resistance is determined by more than just levels of resistance and cost but is highly sensitive to the life history traits of the host.
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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.