cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qrfj6qbm
title: A spatially aware likelihood test to detect sweeps from haplotype distributions

description: The inference of positive selection in genomes is a problem of great
 interest in evolutionary genomics. By identifying putative regions of the
 genome that contain adaptive mutations, we are able to learn about the
 biology of organisms and their evolutionary history. Here we introduce a
 composite likelihood method that identifies recently completed or ongoing
 positive selection by searching for extreme distortions in the spatial
 distribution of the haplotype frequency spectrum along the genome relative
 to the genome-wide expectation taken as neutrality. Furthermore, the
 method simultaneously infers two parameters of the sweep: the number of
 sweeping haplotypes and the “width” of the sweep, which is related to the
 strength and timing of selection. We demonstrate that this method
 outperforms the leading haplotype-based selection statistics, though
 strong signals in low-recombination regions merit extra scrutiny. As a
 positive control, we apply it to two well-studied human populations from
 the 1000 Genomes Project and examine haplotype frequency spectrum patterns
 at the LCT and MHC loci. We also apply it to a data set of brown rats
 sampled in NYC and identify genes related to olfactory perception. To
 facilitate use of this method, we have implemented it in user-friendly
 open source software.
description: These data comprise all files pertaining to power simulations and
 real data analysis examples for the saltiLASSI method for detecting
 selective sweeps in population genomic data.
description: power_sims.tar.gz - Contains all scripts necessary for performing
 simulations and evaluating power for all statistics in the
 manuscript NYC_rats.tar - contains the raw results from
 running the saltiLASSI method on the NYC brown rats data set
 TGP_humans.tar - contains the raw results, matched demographic
 simulations, and processing scripts for the CEU and YRI data set
 scripts.tar - contains scripts for processing and plotting
 results from both the human and rats data analyses
DOI: 10.5061/dryad.s4mw6m97m
title: Chemical screening in an estrogen receptor transactivation assay with metabolic competence

description: The U.S. EPA continues to utilize high-throughput screening data to
 evaluate potential biological effects of endocrine active substances
 without the use of animal testing. Determining the scope and need for in
 vitro metabolism in high-throughput assays requires the generation of
 larger data sets that assess the impact of xenobiotic transformations on
 toxicity-related endpoints. The objective of the current study was to
 screen a set of 768 ToxCast chemicals in the VM7Luc estrogen receptor
 transactivation assay (ERTA) using the Alginate Immobilization of
 Metabolic Enzymes (AIME) hepatic metabolism method. Chemicals were
 screened with or without metabolism to identify estrogenic effects and
 metabolism-dependent changes in bioactivity. Based on estrogenic hit
 calls, 85 chemicals were active in both assay modes, 16 chemicals were
 only active without metabolism, and 27 chemicals were only active with
 metabolism. Using a novel metabolism curve shift method that evaluates the
 shift in concentration-response curves, 29 of these estrogenic chemicals
 were identified as bioactivated and 59 were bioinactivated. Human
 biotransformation routes and associated metabolites were predicted in
 silico across the chemicals to mechanistically characterize possible
 transformation-related ERTA effects. Overall, the study profiled novel
 chemicals associated with metabolism-dependent changes in ERTA
 bioactivity, and suggested routes of biotransformation and putative
 metabolites responsible for the observed estrogenic effects. The data
 demonstrate a range of metabolism-dependent effects across a diverse
 chemical library and highlight the need to evaluate the role of intrinsic
 xenobiotic metabolism in endocrine and other toxicity-related health
 effects.
description: This is an original dataset generated at the U.S. EPA. Data was
 analyzed with the ToxCast Pipeline and deposited for release in invitroDB
 accessible via the U.S. EPA CompTox Chemicals Dashboard.
DOI: 10.7280/d1n10j
title: Surface CO2 variability from the stratosphere, or not

description: Fluctuations in atmospheric CO2 can be measured with great precision and
 are used to identify human-driven sources as well as natural cycles of
 ocean and land carbon.  One source of variability is the
 stratosphere, where the influx of aged CO2-depleted air can produce
 fluctuations at the surface.  This process has been speculated a
 potential source of interannual variability (IAV) in CO2 that might
 obscure the quantification of other sources of IAV.  Given the
 recent success in demonstrating that the stratospheric influx of N2O- and
 chlorofluorocarbon-depleted air is a dominant source of their surface IAV
 in the southern hemisphere, we here apply the same model and measurement
 analysis to CO2.  Using chemistry-transport modeling or scaling
 of the observed N2O variability, we find that the stratosphere-driven
 surface variability in CO2 is at most 10% of the observed IAV and is not
 an important source.  Diagnosing the amplitude of the CO2 annual
 cycle and its increase from 1985 to 2021 through the annual variance gives
 rates similar to traditional methods in the northern hemisphere (BRW,
 MLO), but can identify the emergence of small trends (0.08 ppm per decade)
 in the southern hemisphere (SMO, CGO).
description: The observational data used for this work are taken from the
 public NOAA data archives as described in the manuscript.  These are
 <em><strong>not</strong> </em>archived here, find
 them at the referenced sites below. Dlugokencky, E.J., Crotwell, A.M., Mund, J.W.,
 Crotwell, M.J., and Thoning, K.W.: Atmospheric Nitrous Oxide Dry Air Mole
 Fractions from the NOAA GML Carbon Cycle Cooperative Global Air Sampling
 Network, 1997-2020, Version: 2021-07-30, doi: 10.15138/53g1-x417,
 2021b. Dlugokencky, E.J., Mund, J.W., Crotwell, A.M.,
 Crotwell, M.J., and Thoning, K.W.: Atmospheric Carbon Dioxide Dry Air Mole
 Fractions from the NOAA GML Carbon Cycle Cooperative Global Air Sampling
 Network, 1968-2020, Version: 2021-07-30, doi: 10.15138/wkgj-f215,
 2021a. The modeled data are from 28-year simulations of
 the UCI CTM using ECMWF IFS Cy38r1 forecasts and simulating N2O-like and
 CO2-like tracers as described in the text.
description: Text:<br>       Prather_surfCO2var_v2_readme.txt is the
 readme file Folders:
 <strong>Analysis-matlab</strong>:  Analysis files
 combining matlab scripts and data.
 <strong>Figs&Data-main</strong>:  Copies of 
 the figures in the revised paper, as .png & .eps, along with .dat
 files containing the plotted values
 <strong>Figs&Data-aux</strong>:   Additional
 raw data created during the analysis, provided as .png, .eps, and/or .dat
 files.
DOI: 10.25338/b86057
title: Novel fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

description: Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp.
 fragariae, poses a significant threat to strawberry (Fragaria x ananassa)
 production in many parts of the world. This pathogen causes wilting,
 collapse, and death in susceptible genotypes. We previously identified a
 dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of
 the pathogen, and hypothesized that gene-for-gene resistance to Fusarium
 wilt was widespread in strawberry. To explore this, a genetically diverse
 collection of heirloom and modern cultivars and octoploid ecotypes were
 screened for resistance to Fusarium wilt races 1 and 2. Here we show that
 resistance to both races is widespread in natural and domesticated
 populations and that resistance to race 1 is conferred by partially to
 completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found
 on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying
 genes have not yet been cloned and functionally characterized; however,
 plausible candidates were identified that encode pattern recognition
 receptor or other proteins known to confer gene-for-gene resistance in
 plants. High-throughput genotyping assays for SNPs in linkage
 disequilibrium with FW1-FW5 were developed to facilitate marker-assisted
 selection and accelerate the development of race 1 resistant cultivars.
 This study laid the foundation for identifying the genes encoded by
 FW1-FW5, in addition to exploring the genetics of resistance to race 2 and
 other races of the pathogen, as a precaution to averting a Fusarium wilt
 pandemic.
description: This data submission contains phenotypic data, genotypic data,
 and scripts used for the generation of genetic maps in Pincot et al.
 (2022) "Novel Fusarium Wilt Resistance Genes Uncovered in Natural and
 Cultivated Strawberry Populations are Found on Three Non-Homoeologous
 Chromosomes". Please reference the readme.txt file
 for further details.
DOI: 10.5061/dryad.pzgmsbcnk
title: Data from: Selection bias in mutation accumulation

description: Mutation accumulation (MA) experiments, in which de
 novo mutations are sampled and subsequently characterized, are an
 essential tool in understanding the processes underlying evolution. In
 microbial populations, MA protocols typically involve a period of
 population growth between severe bottlenecks, such that a single
 individual can form a visible colony. While it has long been appreciated
 that the action of positive selection during this growth phase cannot be
 eliminated, it is typically assumed to be negligible. Here, we quantify
 the effect of both positive and negative selection in MA studies,
 demonstrating that selective effects can substantially bias the
 distribution of fitness effects (DFE) and mutation rates estimated from
 typical MA protocols in microbes. We then present a simple correction for
 this bias which applies to both beneficial and deleterious mutations, and
 can be used to correct the observed DFE in multiple environments. We use
 simulated MA experiments to illustrate the extent to which the MA-inferred
 DFE differs from the underlying true DFE, and demonstrate that the
 proposed correction accurately reconstructs the true DFE over a wide range
 of scenarios; we also provide an example of these corrections applied to
 experimental data. These results highlight that positive selection during
 microbial MA experiments is in fact not negligible, but can be corrected
 to gain a more accurate understanding of fundamental evolutionary
 parameters.
description: Simulation data from simulation of mutation accumulation
 protocols and the action of selection in biasing the observed
 results.
DOI: 10.5061/dryad.2ngf1vhpp
title: Data from: A generalized distribution interpolated between the exponential and power law distributions and applied to pill bug (Armadillidium vulgare) walking data

description: The walking pattern of an organism is typically designated as either a
 Lévy walk or a Brownian walk based on whether the frequency distribution
 of its linear step lengths follows a power law distribution or an
 exponential distribution. However, there are many cases where actual data
 cannot be classified into either of these categories. In this paper, we
 propose a general distribution that includes the power law and exponential
 distributions as special cases. This distribution has two parameters: one
 parameter represents the exponent, similar to the power law and
 exponential distributions, and the other is a shape parameter representing
 the shape of the distribution. By introducing this distribution, an
 intermediate distribution model can be interpolated between the power law
 and exponential distributions. In this study, the proposed distribution
 was fitted to the frequency distribution of the step length calculated
 from the walking data of pill bugs. The autocorrelation coefficients were
 also calculated from the time-series data of the step length, and the
 relationship between the shape parameter and time dependency was
 investigated. The results indicate that individuals whose step length
 frequency distributions are closer to the power law distribution have
 stronger time dependence. C++ program for parameter estimation of
 generalized distributions and source code for statistical
 analysis using R.
description: The programs for the parameter estimation and autocorrelation
 coefficient calculation described above were developed using C++. The
 compiler was MinGW 8.1.0 64-bit for C++. The Qt library (Qt version Qt
 5.15.2 MinGW 64-bit) was also used for development.
 The Wilcoxon's rank sum test was used to test the difference
 in the means. For all analyses, the statistical significance was set at
 p &lt; 0.01. The following analyses were performed using the R 3.6.1
 statistical software unless otherwise specified. We used the R packages of
 exactRankTests version 0.8.31 for the Wilcoxon rank sum test. The
 operating system used was Windows 10.
description: The data shown in 'sample_length_time_series_data.csv'
 is the walking data of a pill bug.<br> The values represent time
 series data of step length. For more information about step length, please
 refer to the literature
 (https://www.biorxiv.org/content/10.1101/2021.11.29.470497v1).
DOI: 10.5061/dryad.n8pk0p2wv
title: Habitat and not topographic heterogeneity constrains the range sizes of African mammals

description: Aim: The extinction risks of species are influenced by their geographical
 range sizes, as species with smaller ranges are more likely to go extinct
 following disturbance events. Theoretically, heterogeneous landscapes can
 maintain small-ranged species, because they facilitate the coexistence of
 taxa that are each constrained to distinct abiotic conditions. However, we
 do not fully understand whether this process is more attributable to
 variation in habitat types (habitat heterogeneity) or physical elevations
 (topographic heterogeneity) across landscapes. Here, we compare the
 influences of habitat versus topographic heterogeneity on mammalian range
 sizes in Africa. Location: Africa. Taxon: Mammalia.
 Methods: We built a phylogenetic generalized least squares model to
 predict the range sizes of 1033 mammalian species from their functional
 traits and abiotic conditions. We assessed how the performance of the
 model changed when we incorporated measures of the local habitat and,
 separately, topographic heterogeneity that species experience. Results:
 Habitat and topographic heterogeneity are weakly correlated across Africa
 (ρ = 0.14). Habitat heterogeneity is inversely related
 to range size (model coefficient = −0.88). Incorporating
 habitat heterogeneity significantly decreased the model's AICc,
 increased its likelihood and increased the proportion of variance that is
 explained in the range sizes of species. Conversely, topographic
 heterogeneity is not significantly related to range size and had no impact
 on the model's AICc, likelihood or predictive performance. This
 contrast between habitat and topographic heterogeneity is particularly
 prevalent in carnivorous mammalian clades. Results at multiple spatial
 resolutions differed minimally. Main Conclusions: Our findings advance
 ecological theory by demonstrating that a landscape's variation in
 habitats, and not in elevations, relates inversely with mammalian range
 size and therefore facilitates the coexistence of small-ranged mammals.
 Conservation efforts in regions of high habitat heterogeneity will be
 critical to prevent extinctions in Africa's biodiverse mammalian
 species.
DOI: 10.5061/dryad.2jm63xsqq
title: Possible link between brain size and flight mode in birds: Does soaring ease the energetic cost of the brain?

description: Elucidating determinants of interspecies variation in brain size has been
 a long-standing challenge in cognitive and evolutionary ecology. As the
 brain is an energetically expensive organ, energetic tradeoffs among
 organs are considered to play a key role in brain size evolution. This
 study examined the tradeoff between the brain and locomotion in birds by
 testing the relationship between brain size, flight modes with different
 energetic costs (flapping and soaring), and migratory behavior, using
 published data on the whole-brain mass of 2,242 species. According to
 comparative analyses considering phylogeny and body mass, soarers, who can
 gain kinetic energy from wind shear or thermals and consequently save
 flight costs, have larger brains than flappers among migratory birds.
 Meanwhile, the brain size difference was not consistent in residents, and
 the size variation appeared much larger than that in migrants. In
 addition, the brain size of migratory birds was smaller than that of
 resident birds among flappers, whereas this property was not significant
 in soarers. Although further research is needed to draw a definitive
 conclusion, these findings provide further support for the energetic
 tradeoff of the brain with flight and migratory movements in birds and
 advance the idea that a locomotion mode with lower energetic cost could be
 a driver of encephalization during the evolution of the brain.
description: <b>Datafile
 </b><b>S1</b> Dataset of whole-brain mass and body mass
 used for the comparative analyses (N = 2,242 species). <b>Datafile S2
 </b>Estimated phylogenetic tree of all species used for the
 comparative analyses of the brain size (N = 2,242 species listed in
 Datafile S1). <b>Datafile S3</b>
 Dataset of total developmental duration (sum of incubation and fledging
 durations) and body mass used for the comparative analyses (N = 3,347
 species).
DOI: 10.5061/dryad.wm37pvmpf
title: Areal (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots

description: One of the characteristic aspects of odour sensing in humans is the
 activation of olfactory receptors in a slightly different manner to
 different enantiomers. Here, we focused on whether plants showed
 enantiomer-specific responses similar to that in humans. We exposed
 Arabidopsis seedlings to methanol (control) and (+)- or (−)-borneol, and
 found that only (+)-borneol reduced the root length. Furthermore, the
 root-tip width was more increased upon (+)-borneol exposure than upon
 (−)-borneol exposure. In addition, root-hair formation was observed near
 the root tip in response to (+)-borneol. Auxin signalling was strongly
 reduced in the root tip following exposure to (+)-borneol, but was
 detected following exposure to (−)-borneol and methanol. Similarly, in the
 root tip, the activity of Cyclin B1:1 was detected on exposure to
 (−)-borneol and methanol, but not on exposure to (+)-borneol, indicating
 that (+)-borneol inhibits the meristematic activity in the root. These
 results partially explain (+)-borneol-specific reduction in the root
 length of Arabidopsis. Our results indicate the presence of a sensing
 system specific for (+)-borneol in Arabidopsis.
description: <em>Exposure of aboveground parts
 of Arabidopsis seedlings to airborne borneol</em> One seed was
 placed on the surface of 0.8% agar (9 mL) containing 1X Murashige and
 Skoog salt mixture and 1× Gamborg’s vitamin solution (Sigma-Aldrich, St.
 Louis, MO, USA) filled in a Bioramo centrifuge tube II VIO-15BN (15 mL:
 120 mm long) (AS ONE Corporation, Osaka, Japan). The pH of the mixture was
 adjusted to 5.9 with KOH. The depth of the agar was approximately 75 mm in
 the tube. The remaining
 volume (volatile exposure area) in the tube was 7.6 cm3.
 Three days after
 germination, the seedlings were treated with one of the borneol
 enantiomers for 4 days. We diluted
 (-) and (+)-borneol in methanol to obtain 5 and 25 mM solutions and added
 20 µL of the solution into a moist piece of cotton wool (&gt;1
 cm<sup>3</sup>) hung in the uppermost part of the exposed
 area. The amount of the impregnated compound was 15.4 and 77.0 µg,
 respectively. The concentration was determined from a pilot test of
 various borneol concentrations. At lower concentrations, we did not
 identify any characteristic morphological changes in the root tips. At
 higher concentrations, leaf chlorosis occurred. Twenty micro-litres of
 methanol was used as the control.
DOI: 10.5061/dryad.18931zczk
title: Data from: Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves

description: Understanding the resilience of temperate reefs to climate change requires
 exploring the recovery capacity of their habitat-forming species from
 recurrent marine heatwaves (MHWs). Here, we show that, in a Mediterranean
 highly enforced Marine Protected Area established more than 40 years ago,
 habitat-forming octocoral populations that were firstly affected by a
 severe MHW in 2003 have not recovered after 15 years. Contrarily, they
 have followed collapse trajectories that have brought them to the brink of
 local ecological extinction. Since 2003, impacted populations of the red
 gorgonian Paramuricea clavata (Risso, 1826) and the red
 coral Corallium rubrum (Linnaeus, 1758) have followed
 different trends in terms of size structure, but a similar progressive
 reduction in density and biomass. Concurrently, recurrent MHWs were
 observed in the area during the 2003-2018 study period, which may have
 hindered populations recovery. The studied octocorals play a unique
 habitat-forming role in the coralligenous assemblages (i.e., reefs endemic
 to the Mediterranean Sea home to approximately 10% of its species).
 Therefore, our results underpin the great risk that recurrent MHWs pose
 for the long-term integrity and functioning of these emblematic temperate
 reefs.
description: The demographic data included in the repository is the raw
 data used for this study. It was obtained by conducting a long-term
 monitoring (2003-2018) of 4 <em>Paramuricea
 clavata </em>populations and 1 <em>Corallium
 rubrum </em>population that were firstly impacted by the marine
 heatwave occurred in Scandola Marine Protected Area en 2003.
description: The dataset contains the Raw data and the annotated code to
 create all the Figures and Statistical analysis included in the associated
 manuscript.