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opencc-zeroJun 2022View details →

Performance of akaike information criterion and bayesian information criterion in selecting partition models and mixture models

In molecular phylogenetics, partition models and mixture models provide different approaches to accommodating heterogeneity in genomic sequencing data. Both types of models generally give a superior fit to data than models that assume the process of sequence evolution is homogeneous across sites and lineages. The Akaike Information Criterion (AIC), an estimator of Kullback-Leibler divergence, and the Bayesian Information Criterion (BIC) are popular tools to select models in phylogenetics. Recent work suggests AIC should not be used for comparing mixture and partition models. In this work, we clarify that this difficulty is not fully explained by AIC misestimating the Kullback-Leibler divergence. We also investigate the performance of the AIC and BIC by comparing amongst mixture models and amongst partition models. We find that under non-standard conditions (i.e. when some edges have a small expected number of changes), AIC underestimates the expected Kullback-Leibler divergence. Under such conditions, AIC preferred the complex mixture models and BIC preferred the simpler mixture models. The mixture models selected by AIC had a better performance in estimating the edge length, while the simpler models selected by BIC performed better in estimating the base frequencies and substitution rate parameters. In contrast, AIC and BIC both prefer simpler partition models over more complex partition models under non-standard conditions, despite the fact that the more complex partition model was the generating model. We also investigated how mispartitioning (i.e. grouping sites that have not evolved under the same process) affects both the performance of partition models compared to mixture models and the model selection process. We found that as the level of mispartitioning increases, the bias of AIC in estimating the expected Kullback-Leibler divergence remains the same, and the branch lengths and evolutionary parameters estimated by partition models become less accurate. We recommend that researchers be cautious when using AIC and BIC to select among partition and mixture models; other alternatives, such as cross-validation and bootstrapping should be explored, but may suffer similar limitations.

opencc-by-4.0May 2022View details →

Dataset: A conflict between spatial selection and evidence accumulation in area LIP

This dataset (packaged as the zip file cdots_share.zip) accompanies the article titled "A conflict between spatial selection and evidence accumulation in area LIP" by JA Seideman, TR Stanford, and E Salinas, in Nature Communications (2022). The experimental results in the paper are based on behavioral and single-neuron data collected from two subjects during performance of visuomotor tasks, as described in the article. The trial-by-trial data arrays (matrices inside .mat files) included here are the basis for most analyses reported in the article.  In addition to the trial-wise data matrices, the dataset includes Matlab functions and scripts (*.m files) used to analyze the data and generate figures in the article. Instructions and specifics are detailed in the README file.

opencc-by-4.0Jun 2022View details →

Strategic selection of cryptocurrency investment portfolios based on discrete multi-criteria methods.

In recent years, cryptocurrencies have gone from an unknown plane to a protagonist one, with strategic investment in these assets becoming increasingly popular for organizations seeking to diversify their portfolios. However, cryptocurrencies carry a high risk due to their high volatility.  Based on the multi-criteria decision making theory, a decision support system was developed for the design of business investment portfolios in cryptocurrencies, starting from the definition of criteria based on historical data that characterize returns and risks in different ways, all this for short time windows of 7 and 15 days. Then, the importance of criteria was analyzed by various methods and their impact was evaluated assuming changes in stock prices. Finally, multi-criteria methods were applied for the design of cryptocurrency investment portfolios in the above-mentioned time windows. The developed system is applicable to companies of any size, since the studied methods provide bigger rationality and objectivity to the strategic decision-making process. The resulting method can be extended in the future to incorporate criteria that take advantage of information on the market capitalization of cryptocurrencies, as well as capturing investor sentiment or the expected shortfall of the investment.

opencc-by-4.0Jun 2022View details →

Selection against early flowering in geothermally heated soils is associated with pollen but not prey availability in a carnivorous plant

This data set includes data on flowering phenology, rosette diameters and fitness of the perennial herb Pinguicula vulgaris, as well as data on soil temperature and experimental treatment applied. The data was collected during the summer of 2020 in 287 plant individuals located in a sub-arctic geothermal area in Ölfus municipality in SW-Iceland, Hengill (64°03’N; 21°18’W, ~360 m.a.s.l.).

opencc-zeroJun 2022View details →

Cumulative cultural evolution and mechanisms for cultural selection in wild bird songs

Cumulative cultural evolution, the accumulation of sequential changes within a single socially learned behaviour that results in improved function, is prominent in humans and has been documented in experimental studies of captive animals and managed wild populations. Here, we provide evidence that cumulative cultural evolution has occurred in the learned songs of Savannah sparrows. In a first step, "click trains" replaced "high note clusters" over a period of three decades. We use mathematical modeling to show that this replacement is consistent with the action of selection, rather than drift or frequency-dependent learning biases. Generations later, young birds elaborated the "click train" song form by adding more clicks. We show that the new songs with more clicks elicit stronger behavioural responses from both males and females. Therefore, we suggest that a combination of social learning, innovation, and sexual selection favoring a specific discrete trait was followed by directional sexual selection that resulted in naturally occurring cumulative cultural evolution in the songs of this wild animal population.

opencc-zeroJun 2022View details →

Experimental test of selection against hybridization as a driver of avian signal divergence

Signal divergence may be pivotal in the generation and maintenance of new biodiversity by allowing closely related species to avoid some costs of co-occurrence. In birds, closely related, sympatric species are more divergent in their colour patterns than those that live apart, but the selective pressures driving this pattern remain unclear. Traditionally, signal divergence among sympatric species is thought to result from selection against hybridization, but broad evidence is lacking. Here, we conducted field experiments on naïve birds using spectrometer-matched, painted 3D-printed models to test whether selection against hybridization drives colour pattern divergence in the genus Poecile. To address selection for male colour pattern divergence without the influence of learning or the evolution of female discrimination in sympatry, we simulated secondary contact between Poecile species, and conducted mate choice experiments on naïve, allopatric females. We found that female black-capped chickadees (P. atricapillus) are equally likely to perform copulation solicitation displays to sympatric and allopatric heterospecific congeners when they are paired with conspecifics, but exhibit a strong preference for less divergent males when presented with paired heterospecific congeners. These results suggest that increased colour pattern divergence among sympatric species can reduce the likelihood of mixed mating in some contexts, and therefore should be favoured by selection against hybridization.

Data from: The burden of T. solium cysticercosis and selected neuropsychiatric disorders in Mocuba district, Zambézia province, Mozambique

This dataset is from a study that aimed to evaluate the association of the disease with selected neuropsychiatric disorders and/or symptoms (chronic headache, epileptic seizures/epilepsy and psychosis) in Mocuba district, Mozambique.

opencc-zeroJul 2022View details →

Data from: Selection on early survival does not explain germination rate clines in Mimulus cardinalis

Premise Many traits covary with environmental gradients to form phenotypic clines. While local adaptation to the environment can generate phenotypic clines, other nonadaptive processes may also. If local adaptation causes phenotypic clines, then the direction of genotypic selection on traits should shift from one end of the cline to the other. Traditionally genotypic selection on non-Gaussian traits like germination rate have been hampered because it is challenging to measure their genetic variance. Methods Here we used quantitative genetics and reciprocal transplants to test whether a previously discovered cline in germination rate showed additional signatures of adaptation in the scarlet monkeyflower (Mimulus cardinalis). We measured genotypic and population level covariation between germination rate and early survival, a component of fitness. We developed a novel discrete log-normal model to estimate genetic variance in germination rate. Results Contrary to our adaptive hypothesis, we found no evidence that genetic variation in germination rate contributed to variation in early survival. Across populations, southern populations in both gardens germinated earlier and survived more. Conclusions Southern populations have higher early survival but this is not caused by faster germination. This pattern is consistent with nonadaptive forces driving the phenotypic cline in germination rate, but future work will need to assess whether there is selection at other life stages. This statistical framework should help expand quantitative genetic analyses for other waiting-time traits.

Code and Data associated with "Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations"

Code and data sufficient to reproduce analyses in "Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations".

opencc-zeroJul 2022View details →

Data from: Bateman gradients reflect variation in sexual selection in a species with dynamic sex roles

Bateman gradients, the slope of the regression of reproductive success on mating success, are among the most commonly reported measures of sexual selection. They are particularly insightful in species with reversed sex roles, where females are expected to be under sexual selection. We measured Bateman gradients in replicate experimental populations of the spermatophore gift-giving bushcricket Kawanaphila nartee (Orthoptera: Tettigoniidae). In this species, the operational sex ratio (OSR) and thus the sex competing for mates varies depending on the availability of pollen food resources: under pollen-limited regimens females are more competitive, whereas under pollen-rich regimens males are more competitive. We maintained populations in enclosures with either limited or supplemented pollen, and calculated Bateman gradients for males and females under both conditions. Bateman gradients were significantly positive in males, and the slope was steeper in pollen-supplemented populations where the OSR was more male-biased. Bateman gradients for females were shallow and nonsignificant regardless of pollen availability. Our results show that the strength of sexual selection on males can depend on environmental context. The lack of significant gradients among females may reflect experimental limitations on our ability to estimate Bateman gradients in female K. nartee.

Code and Data associated with "Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with Escherichia coli"

Code and data sufficient to reproduce analyses in "Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with Escherichia coli".

opencc-by-4.0Dec 2021View details →

Precision synthesis of reducing-end thiol-modified cellulose enabled by enzyme selection

We provide here the underlying data of the publication "Precision synthesis of reducing-end thiol-modified cellulose enabled by enzyme selection". Please find the abstract below. Enzyme-catalyzed iterative β-1,4-glycosylation of β-glycosides is promising for bottom-up polymerization of reducing-end-modified cello-oligosaccharide chains. Self-assembly of the chains from solution yields crystalline nanocellulose materials with properties that are tunable by the glycoside group used. Cellulose chains with a reducing-end thiol group are of interest to install a controllable pattern of site-selective modifications into the nanocellulose material. Selection of the polymerizing enzyme (cellodextrin phosphorylase; CdP) was pursued here to enhance the synthetic precision of β-1-thio-glucose conversion to generate pure “1-thio-cellulose” (≥95%) unencumbered by plain (unlabeled) cellulose resulting from enzymatic side reactions. The CdP from Clostridium stercorarium (CsCdP) was 21 times more active on β-1-thio-glucose (0.17 U/mg; 45 °C) than the CdP from Clostridium cellulosi (CcCdP), and it lacked hydrolase activity, which is substantial in CcCdP, against the α-D-glucose 1-phosphate donor substrate. The combination of these enzyme properties indicated that CsCdP is a practical catalyst for 1-thio-cellulose synthesis directly from β-1-thio-glucose (8 h; 25 mol% yield) that does not require a second enzyme (cellobiose phosphorylase), which was essential when using the less selective CcCdP. The 1-thio-cellulose chains had an average degree of polymerization of &sim;10 and were assembled into highly crystalline cellulose II crystallinity material.

opencc-by-4.0Jan 2022View details →

VESPA ASL: VElocity and SPAtially Selective Arterial Spin Labeling

This repository contains the simulation code, in vivo data, preprocessing code, and analysis code used in the Magnetic Resonance in Medicine article titled "VESPA ASL: VElocity and SPAtially Selective Arterial Spin Labeling" (<a href="https://doi.org/10.1002/mrm.29159">https://doi.org/10.1002/mrm.29159</a>). Please cite this article and this repository (<a href="https://doi.org/10.5281/zenodo.6870683">https://doi.org/10.5281/zenodo.6870683</a>) if you use any of this code or data in your work. Software requirements: BASH, FSL6, and MATLAB (tested with MATLAB versions 2021a and 2021b; requires the Optimization Toolbox and the Statistics and Machine Learning Toolbox). Preprocessing steps tested on macOS 12.4 (Monterey) and 10.14 (Mojave). This updated version (V2.0) simplifies and streamlines the setup of command line and MATLAB paths, making it easier to re-run the preprocessing and analysis steps.

Southeast Brazil average temperature for selected stations (1985-2010)

Dataset with annual, summer, and winter average temperature for selected weather stations in Southeast Brazil for the period between 1985 and 2010. Information about station location, altitude, NDVI, and cloud cover is also available.

opencc-zeroAug 2022View details →

Size-selective harvesting affects the immunocompetence of guppies exposed to the parasite Gyrodactylus

Harvesting is typically positively size-selective, targeting large individuals. This is expected to lead to reduced average body size and earlier maturation, i.e., faster life histories. Such changes can also affect traits seemingly unrelated to harvesting, including immunocompetence. The pace-of-life syndrome predicts that faster life histories are correlated with decreased immunocompetence, i.e., a negative association between positively size-selective harvesting and immunocompetence. However, the energetic trade-off between early growth and immunocompetence suggests the opposite pattern. Here, we empirically evaluated these predictions using an experimental system consisting of the ectoparasite Gyrodactylus turnbulli and lines of guppies Poecilia reticulata that had been subjected to either positively, randomly, or negatively size-selective harvest. We followed the infection progression of individually infected fish for 15 days. We found significant differences between the harvested lines: fish from the negative size-selection lines had the highest parasite loads. During the early phase of the infection, parasite loads were the lowest in the positive-harvested lines, whereas the terminal loads were the lowest for the randomly harvested lines. These results agree with the predictions from the energetic trade-off hypothesis but contradict with the pace-of-life syndrome ones. To our knowledge, this is the first demonstration of the consequences of size-selective harvesting on immunocompetence.

opencc-by-4.0Aug 2022View details →

Bulk and critical material demand for selected 'Starter Kit' energy system models - dataset

This repository contains the data related to the Data in Brief article titled: Bulk and critical material demand for selected ‘Starter Kit’ energy system models. The data include the modeled mass of materials and their embodied emissions. A metadata file is also included to clarify the units, materials and scenario names.

opencc-by-4.0Jul 2017View details →

Aeolian saltation fieldwork: values for size-selective transport measurements

This excel spreadsheet (‘SizeSelectiveTransport.xlsx’) contains the following information on surface and airborne particle size distributions (PSDs) for size-selective saltation transport analyses at our six field sites (Jericoacoara, Rancho Guadalupe, Oceano N1, Oceano S1, Oceano N2, Oceano S2): <ul> <li>“d_lower_mm” – Lower limit diameter for each particle size bin [mm].</li> <li>“d_mid_mm” – Midpoint diameter for each particle size bin [mm].</li> <li>“d_upper_mm” – Upper limit diameter for each particle size bin [mm].</li> <li>“dVdlnd_bed” – Site-averaged non-dimensionalized volume fraction in each size bin for surface samples, \(\frac{dV_{bed}}{d\ln(d)}\).</li> </ul> The field measurements from which these values were calculated are described in Martin and Kok (2017). <ul> <li>“dVdlnd_air” – Site-averaged non-dimensionalized volume fraction in each size bin for airborne samples, \(\frac{dV_{air}}{d\ln(d)}\).</li> <li>Site-averaged non-dimensionalized volume fraction in each size bin for airborne samples, conditioned on each non-dimensionalized shear stress range, \(\frac{dV_{air}}{d\ln(d)}|_{\tau/\tau_{it}}\). Cases in which a PSD is lacking for a shear stress range are marked as “NaN”: <ul> <li>“dVdlnd_air_taunorm_below_10” – for \(\tau/\tau_{it} \leq 1.0\)</li> <li>“dVdlnd_air_taunorm_10_15” – for \(1.0 < \tau/\tau_{it} \leq 1.5\)</li> <li>“dVdlnd_air_taunorm_15_22” – for \(1.5 < \tau/\tau_{it} \leq 2.2\)</li> <li>“dVdlnd_air_taunorm_22_30” – for \(2.2 < \tau/\tau_{it} \leq 3.0\)</li> <li>“dVdlnd_air_taunorm_30_40” – for \(3.0 < \tau/\tau_{it} \leq 4.0\)</li> </ul> </li> <li>“f_bed” – Fraction of bed surface particles in size bin i, \(f_{bed,i}\). Fraction is computed only for bins with particle diameter d > 1.3 mm. Bins below this value are marked as “NaN”.</li> <li>“f_air_bar” – Mean fraction of airborne particles in size bin i, \(\langle f_{air,i} \rangle\). Fraction is computed only for bins with particle diameter d > 1.3 mm. Bins below this value are marked as “NaN”.</li> <li>“f_air_sigma” – Uncertainty on mean fraction of airborne particles in size bin i, \(\sigma_{\langle f_{air,i} \rangle}\). “NaN” values correspond to undefined values for f_air_bar.</li> </ul> The Matlab file (‘GrainSizeData.mat’) includes further raw data, including number-based size distributions for individual samples.

opencc-by-4.0Aug 2022View details →

METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS AND ITS DETERMINANTS OF RAW COW MILK CONTAMINATION IN SELECTED GAMO ZONE DISTRICT OF SOUTHERN ETHIOPIA

We conducted this study, titled "Methicillin-Resistant Staphylococcus aurous and its Determinants of Raw Cow Milk Contamination in a Selected Gamo Zone District of Southern Ethiopia," in order to disseminate our findings to the scientific community. The research has its own strengths, such as the work we did on milk quality and potential milk borne pathogens, as well as the determinants of contamination at the selling point, which is only on fresh milk after it has been checked for freshness. As a result, the authors initiated this research based on practical challenges encountered while providing professional support to various producers in the milk selling point. Because of the irrational use of antibiotics among human and animal health in the study area, this research aimed to estimate the microbial load, prevalence of methicillin resistant S. aurous (MRSA), and determinants of raw cow milk contamination at selling points. This could be a source of drug resistance development in Ethiopia and in the study area in particular. Furthermore, due to resource constraints, the study focuses on bacteriological analysis, risk factor association, and drug sensitivity testing, which can serve as baseline data for future characterization and intervention. Hoping that we authors are interested to publish our research output in your journal with your eminent support for the article gets published.

opencc-zeroAug 2022View details →

Data from: Evolutionary divergence via sexual selection acting on females in a species with sex role reversal

1. There is much evidence that sexual selection drives the evolutionary divergence of male sexual traits, but little is known of females. 2. Comparisons between neutral genetic divergence (FST) and phenotypic divergence (PST) among populations can reveal evolutionary responses to selection. 3. In the bushcricket Kawanaphila nartee, changes in floral food availability cause sex roles to shift from competitive females and choosy males to choosy females and competitive males midway through the breeding season. Males call to attract females, and female auditory spiracle size is under sexual selection. We ask whether selection on females can drive an evolutionary divergence in auditory spiracle size among populations. 4. We sampled 188 individuals from nine geographic locations and analysed 9,478 neutral SNP loci and two phenotypic characters to estimate FST and PST, respectively. 5. We found that PST for female auditory spiracle size far exceeded the global FST, suggesting that female auditory spiracle size is subject to strong directional selection. We relate differences in phenotypic traits to differences in geological and floristic characteristics among the sites. 6. Our data suggest that variation in sexual selection driven by variation in the floristic community on which this species feeds may contribute to the strength of directional selection acting on female K. nartee among populations. 7. Together, these findings indicate that divergence among populations can be driven by sexual selection acting on females, even when that selection is temporary and circumscribed.