cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ncjsxkt11
title: A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

description: Underrepresentation of non-European populations hinders growth of global
 precision medicine. Resources such as imputation reference panels that
 match the study population are necessary to find low-frequency variants
 with substantial effects. We created a reference panel consisting of
 14,393 whole-genome sequences including more than 11,000 Asian
 individuals. Genome-wide association studies were conducted using the
 reference panel and a population-specific genotype array of 72K subjects
 for eight phenotypes. This panel yields improved imputation accuracy of
 rare and low-frequency variants within East Asian populations compared
 with the largest reference panel. Thirty-nine previously unidentified
 associations were found, and more than half of the variants were
 East-Asian-specific. We discovered genes with rare protein-altering
 variants, including LTBP1 for height and GPR75 for body mass index, as
 well as putative regulatory mechanisms for rare noncoding variants with
 cell-type-specific effects. We suggest this data set will add to the
 potential value of Asian precision medicine.
description: De-identified Korean Genome and Epidemiology Study data, which
 includes three cohorts (City cohort, N = 58,700; Rural cohort, N = 8,105;
 and Ansung Ansan Community cohort, N = 5,493) were received from the Korea
 National Institute of Health, Korea Disease Control and Prevention Agency.
 All data were generated with the Korean Biobank Array and preprocessed
 according to the Korea Biobank Array Project analysis protocol. We imputed
 genotypes with the NARD2 reference panel. Haplotypes of the input
 genotypes were phased by BEAGLE v5.0 using impute = false, ap = true, and
 gp = true options. We then performed imputation of the phased genotypes by
 Minimac4 using the NARD2 reference panel with ‘allTypedSites’ and
 ‘ignoreDuplicates’ options. We selected variants with R2Est &gt;= 0.3,
 Hardy–Weinberg equilibrium P value &gt;= 1e-6, and variant missing
 rate &lt; 0.1. Phenotype data were provided by the
 Korea National Institute of Health, Korea Disease Control and Prevention
 Agency. For all quantitative phenotypes, we performed normalization for
 males and females separately and merged the normalized values afterwards.
 We first inversely normalized each phenotype, then used linear regression
 with age, age2, and the first five genotype principal components. The
 residuals were standardized to a normal distribution. We excluded samples
 from individuals taking antihypertensive medication and from individuals
 taking diabetes medication. DM was defined if at least one of the
 following criteria was met: 1) record of diabetic medication; 2) HbA1c
 &gt;= 6.5%; 3) fasting blood glucose level &gt;= 126 mg/dL. HTN
 was defined if at least one of the following criteria was met: 1) record
 of antihypertensive medication; 2) SBP &gt;= 140 mmHg; 3) DBP
 &gt;= 90 mmHg.
DOI: 10.5061/dryad.r2280gbj3
title: X chromosome drive is constrained by sexual selection and influences ornament evolution

description: Experimental evolution provides an integrative method for revealing
 complex interactions among evolutionary processes. One such interaction
 involves sex-linked selfish genetic elements and sexual selection.
 X-linked segregation distorters, a type of selfish genetic element,
 influence sperm transmission to increase in frequency and consequently
 alter the population sex ratio and the opportunity for sexual selection,
 while sexual selection may impact the spread of X-linked distorters. Here
 we manipulated sexual selection by controlling female mating opportunities
 and the presence of a distorting X chromosome in experimental lines of the
 stalk-eyed fly, Teleopsis dalmanni , over 11 generations . We find that
 removal of sexual selection leads to an increase in the frequency of the
 X-linked distorter and sex ratio across generations and that
 post-copulatory sexual selection alone is sufficient to limit the
 frequency of distorters. In addition, we find that male eyestalk length, a
 trait under pre-copulatory sexual selection, evolves in response to
 changes in the strength of sexual selection with the magnitude of the
 response dependent on X chromosome type and the frequency of distorting X
 chromosomes. These results reveal how a selfish X can interact with sexual
 selection to influence the evolution of sexually selected traits in
 multiple ways.
description: Please see the README document and the accompanying published
 article: Paczolt Kimberly A., Welsh Gabrielle T. and Wilkinson Gerald S.
 2023 X chromosome drive is constrained by sexual selection and influences
 ornament evolutionProc. R. Soc. B.290:20230929.20230929  DOI:
 http://doi.org/10.1098/rspb.2023.0929
DOI: 10.5061/dryad.msbcc2g3x
title: Determinants of spring migration departure dates in a New World sparrow: weather variables reign supreme

description: Numerous factors influence the timing of spring migration in birds, yet
 the relative importance of intrinsic and extrinsic variables on migration
 initiation remains unclear. To test for interactions among weather,
 migration distance, parasitism, and physiology in determining spring
 departure date, we used the Dark-eyed Junco (Junco hyemalis) as a model
 migratory species known to harbor diverse and common haemosporidian
 parasites. Prior to spring migration departure from their wintering
 grounds in Indiana, USA, we quantified the intrinsic variables of fat,
 body condition (i.e., mass~tarsus residuals), physiological stress (i.e.,
 ratio of heterophils to lymphocytes), cellular immunity (i.e., leukocyte
 composition and total count), migration distance (i.e., distance to the
 breeding grounds) using stable isotopes of hydrogen from feathers, and
 haemosporidian parasite intensity. We then attached nanotags to determine
 the timing of spring migration departure date using the Motus Wildlife
 Tracking System. We used additive Cox proportional hazard mixed models to
 test how risk of spring migratory departure was predicted by the combined
 intrinsic measures, along with meteorological predictors on the evening of
 departure (i.e., average wind speed and direction, relative humidity, and
 temperature). Model comparisons found that the best predictor of spring
 departure date was average nightly wind direction and a principal
 component combining relative humidity and temperature. Juncos were more
 likely to depart for spring migration on nights with largely southwestern
 winds and on warmer and drier evenings (relative to cooler and more humid
 evenings). Our results indicate that weather conditions at take-off are
 more critical to departure decisions than the measured physiological and
 parasitism variables.
description: # Determinants of spring migration departure dates in a New World sparrow:
 weather variables reign supreme --- This dataset is used to analyze the
 determinants of spring migration departure timing in dark-eyed juncos ##
 Description of the Data and file structure Each row corresponds to an
 individual bird ("Band") and the days between release and
 departure ("ddiff" variable) alongside weather variables,
 physiological variables, and additional factors (including ordinal date of
 departure, "doy"). Variable definitions are provided in the meta
 tab of the XLSX. Missing values (i.e., blood smears not readable) are
 indicated as NA. We also include the R script for conducting the primary
 analyses.
DOI: 10.5061/dryad.2ngf1vhv3
title: Data from: Humidity stress and its consequences for male pre- and post-copulatory fitness traits in an insect

description: Global declines in insect abundance are of significant concern. While
 there is evidence that climate change is contributing to insect declines,
 we know little of the direct mechanisms responsible for these declines.
 Male fertility is compromised by increasing temperatures, and the thermal
 limit to fertility has been implicated as an important factor in the
 response of insects to climate change. However, climate change is
 affecting both temperature and hydric conditions, and the effects of water
 availability on male fertility have rarely been considered. Here we
 exposed male crickets Teleogryllus oceanicus to either low- or
 high-humidity environments while holding temperature constant. We measured
 water loss and the expression of both pre- and post-mating reproductive
 traits. Males exposed to a low-humidity environment lost more water than
 males exposed to a high-humidity environment. A male’s cuticular
 hydrocarbon profile (CHC) did not affect the amount of water lost, and
 males did not adjust the composition of their CHC profiles in response to
 hydric conditions. Males exposed to a low-humidity environment were less
 likely to produce courtship song or produced songs of low quality. Their
 spermatophores failed to evacuate and their ejaculates contained sperm of
 reduced viability. The detrimental effects of low humidity on male
 reproductive traits will compromise male fertility and population
 persistence. We argue that limits to insect fertility based on temperature
 alone are likely to underestimate the true effects of climate change on
 insect persistence, and that the explicit incorporation of water
 regulation into our modelling will yield more accurate predictions of the
 effects of climate change on insect declines.
DOI: 10.5061/dryad.5mkkwh7bq
title: Low- and high-intensity fire in the riparian savanna: demographic impacts in an avian model species and implications for ecological fire management

description: Climate change is driving changes in fire frequency and intensity, making
 it more urgent for conservation managers to understand how species and
 ecosystems respond. In tropical monsoonal savannas – Earth’s most
 fire-prone landscapes – ecological fire management aims to prevent intense
 wildfires late in the dry season through prescribed low-intensity burns
 early in the dry season. Riparian habitats embedded within tropical
 savannas represent critical refuges for biodiversity, yet are particularly
 fire-sensitive. Better understanding of the impact of fire – including
 prescribed burns – on riparian habitats is therefore key but requires
 long-term detailed post-fire monitoring of species’ demographic rates, as
 effects may persist and/or be delayed. We analyse impacts of (prescribed)
 low-intensity and (prescribed but escaped) high-intensity fire in northern
 Australian riparian and adjacent savanna habitat. We quantify multi-year
 impacts on density, survival, reproduction and dispersal of an Endangered
 riparian bird, the western purple-crowned fairy-wren (Malurus coronatus
 coronatus), in a well-studied individually-marked population. Following
 low-intensity fire, bird density was reduced by &gt;20% in burnt
 compared to adjacent unburnt riparian habitat for ≥2.5 years. This was a
 result of reduced breeding success and recruitment for two years
 immediately following fire, rather than mortality or dispersal of adults.
 In contrast, high-intensity fire (in a dry year) resulted in a sharp
 decline in population density by 50% 2–8 months after fire, with no signs
 of recovery after 2.5 years. The decline in density was due to post-fire
 adult mortality, rather than dispersal. Breeding success of the (few)
 remaining individuals was low but not detectably lower than in unburnt
 areas, likely because breeding success was poor overall due to prevailing
 dry conditions. Synthesis and applications. Even if there is no or very
 low mortality during fire, and no movement of birds away from burnt areas,
 both low- and high-intensity fire in the riparian zone reduce population
 density. However, the mechanism by which this occurs, and recovery time,
 differs with fire intensity. To minimise impacts of fire on riparian zones
 in tropical savannas, we suggest employing low-intensity prescribed burns
 under optimal conditions shortly after the breeding season.
DOI: 10.5061/dryad.mpg4f4r54
title: Data from: Dominant species determine grazing effects on the stability of herbaceous community production at multiple scales in drylands

description: Sustainable provision of critical ecosystem services in drylands is
 reliant on their stability under anthropogenic disturbances. Livestock
 grazing and shrub encroachment are the primary drivers of disturbance that
 impact their biodiversity and production dynamics. However, the effects of
 grazing on the stability at multiple scales, particularly following the
 transition from grass-dominated to shrub-encroached drylands, is still
 largely unexplored. Here, we conducted comparable sheep-grazing
 experiments in two types of drylands (grass-dominated vs. shrub-encroached
 grasslands) on the Mongolia Plateau to explore the effects of grazing and
 shrub encroachment on biodiversity and stability at multiple scales. We
 examined how grazing affected the temporal stability of aboveground
 biomass in herbaceous communities in both grass-dominated and
 shrub-encroached grasslands, through two potential mechanisms: insurance
 effects and changes in the population-level stability of individual
 species. We found that an increase in sheep grazing intensity had
 significant and negative effects on insurance effects by decreasing both
 species asynchrony and spatial asynchrony but it had no effects on
 population stability, consequently leading to reductions in herbaceous
 community stability of the grasslands. However, grazing-increased
 insurance effects canceled out grazing-decreased population stability,
 contributing to no changes in the community stability of shrub-encroached
 grasslands. Likely, because grazing-induced reductions in the relative
 abundance of the dominant species were more noticeable in shrub-encroached
 grasslands than that of in grasslands. Moreover, the grazing-decreased
 abundance of dominant species was directly correlated to increases in
 insurance effects in shrub-encroached grasslands but not in grasslands,
 despite the positive relationships between population stability and the
 relative abundance of the dominant species in both grass-dominated and
 shrub-encroached drylands.  Synthesis and applications. Our
 results indicate that grazing can decrease the stability of herbaceous
 production in drylands, but this negative effect is attenuated with the
 transition from grasslands to shrub-encroached grasslands, suggesting that
 grazing effects on herbaceous community stability can be altered by shrub
 encroachment in drylands. Furthermore, the stability of dominant grasses
 plays a crucial role in stabilizing herbaceous communities, and should be
 considered in promoting sustainable ecosystem functioning and services in
 drylands.
DOI: 10.5061/dryad.9zw3r22kf
title: Shear experiment datas for laumontite and mixed gouges at different temperatures and pore pressures

description: Laumontite is a common and potentially frictionally-unstable hydrothermal
 alteration product present in deep faults of the Gonghe EGS reservoir. We
 characterize the friction-stability characteristics of synthetic
 laumontite gouge under in situ reservoir conditions. The gouge is
 frictionally strong (μ=0.73–0.98) with quartz/laumontite mixtures (1:1)
 generally less strong (μ=0.73–0.78) with both largely independent of
 temperature but increasing with elevated pore pressure. The pure gouge and
 mixture are strongly velocity-weakening over a broad range in temperatures
 (~90–220℃) and excess pore pressures (0–90MPa) relevant to the Gonghe
 stimulation. Microearthquakes (MEQs) observed during stimulation are
 confined to within the broad depth range of inferred frictional
 instability – although fluid overpressures are also limited to this
 region. The observation that laumontite mixtures are frictionally unstable
 over a broad range of pressures and especially temperatures representative
 of EGS reservoirs and insensitive to the proportion of the coexisting
 mineral phase suggests its presence is a strong indicator of potential
 seismic hazard – and thus worthy of careful consideration.
DOI: 10.5061/dryad.w0vt4b8xd
title: Colony-level coral demographic data from Japan & Australia (2016-2019)

description: The persistent exposure of coral communities to more variable abiotic
 regimes is assumed to augment their resilience to future climatic
 variability. Yet, while the determinants of coral population resilience
 across species remain unknown, we are unable to predict the winners and
 losers across reef ecosystems exposed to increasingly variable conditions.
 Using annual surveys of 3171 coral individuals across Australia and Japan
 (2016-2019), we explored spatial variation across the short- and long-term
 dynamics of competitive, stress-tolerant, and weedy assemblages to
 evaluate how thermal variability mediates the structural composition of
 coral communities. Here this dataset contains the raw colony-level data
 collected during these annual surveys, detailing the size, survival, and
 recruitment of coral colonies within a series of permenant plots arranged
 throughout the reef communities of Okinawa, Kochi (both Japan), the
 Solitary Islands Marine Park, and Heron Island (both Australia). This data
 set facilitates the comparison of coral population dynamics between
 tropical and subtropical ecoregions and between different taxonomic and
 morpho-functional groups.
description: For methodological details please see Cant <em>et
 al</em>. (2023) Coral assemblages at higher latitudes favour
 short-term potential over long-term
 performance. <em>Ecology.</em>
description: The raw data is provided as a csv file arranged in a stacked
 format with each row detailing the demographic transitions recorded for an
 individual colony across a single annual interval
 (<em>i.e</em>., 2016 to 2017). The first 11 columns of the
 dataset outline each colonies associated metadata such as location
 (Country, ecoregion etc.), colony identity (e.g. Plot number), taxonomy
 (to species level where possible), and life history classification
 (<strong>LHS</strong>). The remaining columns then describe
 each colonies recorded demographic transitions as follows:
 <em>time.t = </em>'Starting year of
 corresponding annual interval'
 <em>Fragment.t = '</em>was the colony a product
 of fragmentation during the previous year' (Yes/No/NA)
 <em>Bleaching.t = '</em>Bleaching state at
 time <em>t</em>'
 (None/Slight/Moderate/Severe/NA) <em>Size.t =
 '</em>Colony size recorded at time <em>t</em>'
 (is NA if colony recruited between
 time <em>t </em>and <em>t+1</em>)
 <em>time.t1 = '</em>Ending year of corresponding
 annual interval' <em>No.frag.t1
 =</em><em> '</em>Number of fragments produced by
 colony between time <em>t </em>and
 time <em>t+1</em>'
 <em>Bleaching.t1 = '</em>Bleaching state at
 time <em>t+1'
 </em>(None/Slight/Moderate/Severe/NA)
 <em>Size.t1 = </em>Colony size recorded at time
 <em>t+1</em>' (is NA if colony died between
 time<em> t </em>and<em> t+1</em>)
 <em>Fragment .t1 = '</em>was the colony a
 product of fragmentation between time <em>t</em> and time
 <em>t+1</em>'  (Yes/No/NA)
 <em>Recruit.t1 = </em>'was the colony a product
 of fragmentation between time <em>t </em>and time
 <em>t+1</em>' (Yes/No/NA)
DOI: 10.7291/d1n68m
title: The rapid rise of severe marine heat wave systems

description: We introduce a new methodology to study marine heat waves (MHWs), extreme
 events in the sea surface temperature (SST) of the global ocean. Motivated
 by previously large and impactful MHWs and by the theoretical expectation
 that the dominant heating processes coherently affect large regions of the
 ocean, we introduce a methodology from computer vision to construct marine
 heat wave systems (MWHSs) – the collation of SST extrema in dimensions of
 area and time. We identify 649,475 MHWSs in the 37 year period (1983–2019)
 of daily SST records and find that the duration tdur (days),
 maximum area Amax (km2), and total ‘volume’ VMHWS (days
 km2) for the majority of MHWSs are well-described by power-law
 distributions: tdur^-3,  Amax^−2 and VMHWS^−2 . These
 characteristics confirm SST extrema exhibit strong spatial coherence that
 defines the formation and evolution of MHWs. Furthermore, the most severe
 MHWSs deviate from these power-laws and are the dominant manifestation of
 MHWs: extrema in ocean heating are driven by the ∼200 systems with the
 largest area and duration. We further demonstrate that the previously
 purported rise in the incidence of MHW events over the past decade is only
 significant in these severe systems. A change point analysis reveals a
 rapid increase in days under a severe MHW in most regions of the global
 ocean over the period of 2000–2005. Understanding the origin and impacts
 of MHWs in the current and future ocean, therefore, should focus on the
 production and evolution of the largest-scale and longest-duration heating
 phenomena.
description: See https://iopscience.iop.org/article/10.1088/2752-5295/accd0e and https://zenodo.org/badge/latestdoi/262816104.
description: netCDF viewer SQL viewer
 table viewer
DOI: 10.5061/dryad.t4b8gtj6t
title: Data from: Accelerated high-throughput imaging and phenotyping system for small organisms

description: Studying the complex web of interactions in biological communities
 requires large multifactorial experiments with sufficient statistical
 power. Automation tools reduce the time and labor associated with setup,
 data collection, and analysis in experiments that untangle these webs. We
 developed tools for high-throughput experimentation (HTE) in duckweeds,
 small aquatic plants that are amenable to autonomous experimental
 preparation and image-based phenotyping. We showcase the abilities of our
 HTE system in a study with 6,000 experimental units grown across 2,000
 treatments. These automated tools facilitated the collection and analysis
 of time-resolved growth data, which revealed finer dynamics of
 plant-microbe interactions across environmental gradients. Altogether, our
 HTE system can run experiments with up to 11,520 experimental units and
 can be adapted for other small organisms.
description: # Title of Dataset: Data from: Accelerated high-throughput imaging and
 phenotyping system for small organisms --- This dataset contains the
 phenotypic data from an experiment in which the growth of one clonal
 genotype of the duckweed Lemna minor was measured across ten nitrogen
 concentrations for ten days, in both the presence and absence of microbes.
 ## Description of the Data and file structure The .csv file contains the
 following data: block: temporal block (range 1-4) daycol: day of the
 experiment (range 0-10) nitr_N: nitrogen treatment level in mg/L (range
 0-45) inoc: inoculated (l+) or not inoculated (l-) with microbes isolated
 from field-collected duckweeds from the same site as the focal duckweed
 genotype edge: whether the well is at the edge (TRUE) or in the interior
 (FALSE) of the well plate well: The ID of the individual well in the
 96-well plate plate_number: A unique ID for each 96-well plate (range
 1-16) sqmm: The area in square millimeters of duckweed fronds in the well
 green_per_arr: The greenness intensity of duckweed fronds in the well,
 calculated as G/(R+G+B), where R, G, B are the red, green, and blue values
 for each pixel, which each range from 0 to 255 Missing data is coded as
 NA. ## Sharing/access Information Data was derived from original images of
 experimental plates. The paper describes the MATLAB imaging processing
 tool that we developed to extract duckweed frond area and other phenotypes
 (e.g., greenness) from the original images.