cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.612jm6430
title: SimBit: A high performance, flexible and easy-to-use population genetic simulator

description: SimBit is a general purpose, high performance forward-in-time population
 genetics simulator. SimBit can simulate a wide variety of selection
 scenarios (any selection and dominance coefficients variation, any
 epistatic interaction, any spatial and temporal changes of selection
 scenario, etc.), demographic scenarios (any changes in patch sizes,
 migration rates, realistic demography dependent on fecundity, hard vs.
 soft selection, exponential vs logistic growth, gametic or zygotic
 dispersion, etc.) and mating systems (cloning and selfing rates,
 hermaphrodites or males and females). SimBit can also track QTLs (with
 hyperdimensional phenotypes, explicit fitness landscape, plasticity,
 developmental noise, etc.). Finally, SimBit can simulate multiple species
 with their ecological relationships. SimBit comes with a R wrapper that
 simplifies the management of an entire research project from the creation
 of a grid of parameters and corresponding inputs, running simulations and
 gathering outputs for analysis. SimBit’s performance was extensively
 benchmarked in comparison to SLiM, Nemo and SFS_CODE, varying population
 size, recombination rate, mutation rate, and the number of loci. I also
 reproduced simulations from previous papers, benchmarked QTLs and
 coalescent tree recording techniques. SimBit was most often the highest
 performing programs with the only notable exception of SLiM outperforming
 SimBit in scenarios with few loci and low genetic diversity.
description: See README.md
description: Description details of the simulated scenario are found in the
 paper and appendix A.
DOI: 10.15468/dl.2gnz3m
title: Occurrence Download

description: A dataset containing 723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Ginkgo biloba"
 ]
}

 The dataset includes 723 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002796-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3ffbg79hk
title: Data from: Selection for functional performance in the evolution of cuticle hardening mechanisms in insects

description: Calcified tissues have repeatedly evolved in many animal lineages and show
 a tremendous diversity of forms and functions. The cuticle of many insects
 is enriched with elements other than Calcium, a strategy of hardening that
 is taxonomically widespread but apparently poorly variable among clades.
 Here, we investigate the evolutionary potential of the enrichment with
 metals in insect cuticle at different biological levels. We combined
 experimental evidence of Zinc content variation in the mandibles of a
 target species (Chorthippus cazurroi) with phylogenetic comparative
 analyses among grasshopper species. We found that mandibular Zinc content
 was repeatable among related individuals and was associated with an
 indicator of fitness, so there was potential for adaptive variation. Among
 species, Zinc enrichment evolved as a consequence of environmental and
 dietary influences on the physical function of the jaw (cutting and
 chewing), suggesting a role of natural selection in environmental fit.
 However, there were also important within and transgenerational
 environmental sources of similarity among individuals. These environmental
 influences, along with the tight relationship with biomechanics, may limit
 the potential for diversification of this hardening mechanism. This work
 provides novel insights into the diversification of biological structures
 and the link between evolutionary capacity and intra and interspecific
 variation.
description: We measured Zinc content and strengths of grasshopper mandibles,
 by means of scanning electron microscope and calibrated multifocus
 pictures. We used biological and ecological information obtained from
 field and experimental data on the grasshopper species inhabiting the
 Cantabrian Mountains (NW Spain).
description: The different datasets of the study can be found in separate
 sheets. An informative title on sheet content has been given to each
 sheet. In tables, column names refer to the variable measured (and the
 unit of measurement).
DOI: 10.5061/dryad.j9kd51cbr
title: Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

description: Although we are currently experiencing worldwide biodiversity loss, local
 species richness does not always decline under anthropogenic pressure.
 This conservation paradox may also apply in protected areas but has not
 yet received conclusive evidence in marine ecosystems. Here, we survey
 fish assemblages in six Mediterranean no-take reserves and their adjacent
 fishing grounds using environmental DNA (eDNA) while controlling for
 environmental conditions. We detect less fish species in marine reserves
 than in nearby fished areas. The paradoxical gradient in species richness
 is accompanied by a marked change in fish species composition under
 different managements. This dissimilarity is mainly driven by species that
 are often overlooked by classical visual surveys but detected with eDNA:
 cryptobenthic, pelagic and rare fishes. These results do not negate the
 importance of reserves in protecting biodiversity but shed new light on
 how under-represented species groups can positively react to fishing
 pressure and how conservation efforts can shape regional biodiversity
 patterns.
description: 30 L of seawater were collected along 2 km transects and filtered
 using 0.20-µM filtration capsules. Environmental DNA was extracted and
 amplified by PCR with the fish-specific primer pair teleo targeting a 70
 bp fragment at the end of the mitochondrial DNA 12S rRNA gene. PCR
 reactions were carried out in 12 replicates per sample and unique tags
 were given to each sample. A paired-end sequencing (2x125 bp) was carried
 out on a MiSeq (Illumina, San Diego, CA, USA).<br>  
description: Runs_b Compressed file containing the
 compressed forward and reverse sequence files of runs 5 through
 7. corr_tag File making the link
 between the sequence files and sample information.
 column 1: run code<br> column 2: run type<br> column
 3: project name<br> column 4: sample name (lab identifier, starts
 with "SPY")<br> column 5: sample name with PCR replicate
 number<br> column 6: tag name = position on plate<br> column
 7: tag sequence<br> column 8: forward primer sequence<br>
 column 9: reverse primer sequence
 corr_field File making the link between the
 sample laboratory ID and the sample (field) metadata. <br> Assigning
 the field ID allows to run the analyses on
 https://github.com/eboulanger/MEDeDNA--reserves column
 1: sample lab code<br> column 2: sample field code<br> column
 3: sampling date<br> column 4: longitude coordinate of the transect
 center<br> column 5: latitude coordinate of the transect
 center
DOI: 10.5061/dryad.0cfxpnw1q
title: Spatiotemporal variation in drivers of parasitism in a wild wood mouse population

description: Host-parasite interactions in nature are driven by a range of factors
 across several ecological scales, so observed relationships are often
 context-dependent. Importantly, if these factors vary across space and
 time, practical sampling limitations can limit or bias inferences, and the
 relative importance of different drivers can be hard to discern. Here we
 ask to what degree environmental, host, and within-host influences on
 parasitism are shaped by spatiotemporal variation. We use a replicated,
 longitudinal dataset of nearly 1000 individual wood mice (Apodemus
 sylvaticus) encompassing 6 years of sampling across 5 different woodland
 sites and investigate drivers of infection intensity with a highly
 prevalent gastrointestinal nematode, Heligmosomoides polygyrus. We used a
 Bayesian modelling approach to further quantify if and how each factor
 varied in space and time. Finally, we examined the extent to which a lack
 of spatially or temporally replication (i.e., within single years or
 single sites) would affect which drivers were found to predict H.
 polygyrus infection. Season, host body condition, and sex were the three
 most important determinants of infection intensity; however, the strength
 and even direction of these effects varied in time, but not in space.
 Models fit to single year and site replicates in many cases showed sparse
 and variable detection of effects of factors investigated, highlighting
 the benefits of long-term sampling for separating meaningful ecological
 variation from sampling variation. These results highlight the importance
 of accounting for spatiotemporal variation in determining what drives
 disease dynamics and the need to incorporate replication in both time and
 space when designing sampling regimes. Furthermore, we suggest that
 embracing, rather than simply controlling for, spatiotemporal variation
 can reveal meaningful variation for understanding the factors impacting
 parasitism (e.g. season and host factors) which can improve predictions of
 how wildlife health will respond to change.
DOI: 10.5061/dryad.xgxd254fr
title: sEMG for grasp force estimation

description: This dataset contains sEMG and grasp fore data from 5 volunteers. The data
 collection process is as follows. Five right hand-dominant
 healthy volunteers participated in the experiment were recruited from
 graduate students in the College of Automation, Nanjing University of
 Aeronautics and Astronautics. Of these, there are 4 males and 1 female
 (Aged from 21 to 28, mean 24.2, SD 2.77). Subjects sat in front of a
 computer with their right elbow flexed at approximately 135° and with sEMG
 armbands on their right forearms and grasp force sensor in their right
 hands. Their right arms rested on the table. The sEMG measuring positions
 are Extensor carpi ulnaris, Flexor carpi ulnaris, Flexor digitorum
 superficialis muscle, Flexor carpi radialis, Brachioradialis and Extensor
 digitorum. Subjects will have 10 minutes to familiarize themselves with
 the experiment before experiments. In the experiments, they applied force
 to the grasp force sensor 60 times with roughly four different strength
 levels (25%, 50%, 75% and 100%) according to the prompts of the computer
 software. Prompt of each strength level appears 15 times. They were asked
 to apply force to the grasp force sensor for about one second at each
 action. During this procedure, sEMG and grasp force were recorded
 synchronously. When a subject completed a grasp action and completely
 relaxed his/her arm, he/she could tap the computer's keyboard with
 his/her left hand finger, in which case the computer would randomly output
 a prompt for the next action. In total, we recorded data of 300 actions.
 The experiment mentioned above is approved by the Academic and Ethics
 Committee of Nanjing Tongren Hospital. All participants provided written
 informed consent before the start of the experiments.
description: The dataset contains 300 data files of 5 volunteers. Each
 volunteer's data is placed in a separate folder.
 There are 8 rows of data in each data file. The data in rows 1 to
 6 are sEMG collected from Extensor carpi ulnaris, Flexor carpi ulnaris,
 Flexor digitorum superficialis muscle, Flexor carpi radialis,
 Brachioradialis and Extensor digitorum, respectively. The data in row 7 is
 grasp force data and the data in row 8 is the prompts output by the
 software during the experiments. The units of sEMG data
 and grasp force data are uV and N, respectively.
DOI: 10.5061/dryad.612jm6431
title: Orthosia simulation experiment data

description: Consequences of climate change-driven shifts in the relative timing of
 spring activities of interacting species are insufficiently understood,
 especially for insects. We use a controlled experiment which simulates a
 trophic mismatch scenario in which lepidopteran larvae predominately feed
 on older leaves due to foliage developing faster than larvae growth rates.
 As a case study our experiment uses Orthosia cerasi, which is a widespread
 but declining woodland moth whose UK declines appear to be driven by
 warming temperatures. In the control experiment larvae are fed young oak
 Quercus robur leaves (bud burst stages six and seven), whilst in the
 treatment newly emerged larvae are fed young leaves but then gradually
 transition to feed on older leaves (post bud burst stage seven). We assess
 impacts on duration of the larval stage, pupal size and overwintering
 duration and survival. Larvae in the phenological mismatch treatment had a
 longer larval period, and smaller and lighter pupae. Larval diet did not
 carry over to influence emergence dates as earlier pupation of control
 larvae was balanced by an equivalent increase in the duration of the pupal
 stage. Increased time spent as larvae could increase predation rates from
 avian predators, whilst slowing the seasonal decline in food availability
 for those bird species. Reduced pupal size and weight are indicators of
 lower fecundity in emerging adults. Notably, we find that adults emerging
 from the mismatch treatment exhibited greater rates of abnormal vestigial
 wing development, which is likely to further reduce fitness. Trophic
 mismatches in which caterpillars have reduced availability of young leaves
 may thus contribute to the population declines observed in many woodland
 moth species due to increased mortality at larval stages, and adverse
 effects of early life conditions that reduce the reproductive success of
 emerging adults.
description: NA values in the data set associate with individuals that could
 not be used for that section of analysis see MS for details
DOI: 10.5061/dryad.v41ns1rvd
title: Body size and environment influence both intraspecific and interspecific variation in daily torpor use across hummingbirds

description: 1. Torpor, or a regulated drop in body temperature and metabolic rate,
 allows animals to inhabit energetically costly environments, but among
 torpor-using species, we have a poor understanding of how plasticity in
 torpor use relates to the experienced environment. 2. To better understand
 the ecology of daily torpor, we completed the largest study to date on the
 intraspecific variation of daily torpor use in hummingbirds by exposing
 149 individuals of two hummingbird species to ambient or experimentally
 cooled temperatures in a field setting. 3. The smaller species, a
 latitudinal migrant, used daily torpor frequently under ambient
 conditions. The larger species, an elevational migrant, also used daily
 torpor regularly, but further increased the frequency of daily torpor use
 when experiencing colder temperatures and prior to migration – indicating
 a facultative adaptation. 4. To place our results within a broader
 phylogenetic context, we combined our experimental results with a
 meta-analysis, including 31 species and all major hummingbird clades, and
 found a broad taxonomic pattern in which smaller hummingbirds are more
 likely to use daily torpor than their larger counterparts. Smaller
 hummingbirds may be physiologically constrained, requiring nearly obligate
 daily torpor use, while larger hummingbirds are physiologically more
 flexible and can facultatively respond to changing environmental
 conditions. 5. Our results reveal how physiological traits, such as the
 frequency and depth of daily torpor, can provide a mechanism to understand
 how hummingbird species have established and persisted across broad
 environmental gradients.
DOI: 10.7280/d18698
title: H2 in firn air from Megadunes, Antarctica

description: This dataset contains two items: 1) firn air measurements of H2 from
 Megadunes, Antarctica. 2) atmospheric surface flask air measurements of H2
 from NOAA GML, CSIRO, and AGAGE from 1991-2003 adjusted to a common
 calibration scale.    Firn air was sampled at
 the Megadunes site in central Antarctica  (80.78 °S, 124.49 °E,
 Alt: 2,283 m) Antarctica during January of 2004.  A 3” diameter
 hole was bored to a depth of 70 m using an ice core drill. Drilling was
 paused at 15 unique depths so that firn air could be sampled. The sampling
 method was similar to techniques from previous published firn air studies.
 The hole was sealed above each sampling depth with an inflatable rubber
 packer to prevent contamination from the modern atmosphere. A waste air
 intake was positioned directly below the rubber packer. The waste air
 intake was separated from the sample air intake by a stainless-steel
 baffle with a 2 ¾” diameter. Air was pumped from the waste air intake 3x
 faster than from the sample air intake to ensure that no air that had been
 in contact with the rubber packer was sampled. 34 2 L glass flasks with
 Teflon seals were filled for analysis by the NOAA/GML ESRL Carbon Cycle
 group. Details are given in the following manuscript: J.D.
 Patterson, M. Aydin, A.M. Crotwell, G. Pétron, J.P. Severinghaus,
 P.B. Krummel, R.L. Langenfelds, and E.S. Saltzman H2 in Antarctic firn
 air: atmospheric reconstructions and implications for anthropogenic
 emissions, PNAS, 10.1073/pnas.2103335118, 2021.
description: The firn air samples were analyzed
 for H<sub>2</sub> at NOAA/GML using gas chromatography with a
 mercuric oxide reduction gas analyzer (HgO-RGA). Relative measurement
 uncertainty is estimated at ±2%. The H<sub>2</sub>
 measurements are reported as dry air mole fraction (ppb=nmol
 H<sub>2</sub> mol<sup>-1</sup> air). The
 measurements were corrected for calibration drift, detector non-linearity,
 and gravitational fractionation.
DOI: 10.5061/dryad.kkwh70s40
title: Data from: Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques

description: When natural populations split and migrate to different environments, they
 may experience different selection pressures that can lead to local
 adaptation. To capture the genomic patterns of a local selective sweep, we
 develop XP-nSL, a genomic scan for local adaptation that compares
 haplotype patterns between two populations. We show that XP-nSL has power
 to detect ongoing and recently completed hard and soft sweeps, and we then
 apply this statistic to search for evidence of adaptation to high altitude
 in rhesus macaques. We analyze the whole genomes of 23 wild rhesus
 macaques captured at high altitude (mean altitude &gt; 4000m above sea
 level) to 22 wild rhesus macaques captured at low altitude (mean altitude
 &lt; 500m above sea level) and find evidence of local adaptation in
 the high-altitude population at or near 303 known genes and several
 unannotated regions. We find the strongest signal for adaptation at EGLN1,
 a classic target for convergent evolution in several species living in low
 oxygen environments. Furthermore, many of the 303 genes are involved in
 processes related to hypoxia, regulation of ROS, DNA damage repair,
 synaptic signaling, and metabolism. These results suggest that, beyond
 adapting via a beneficial mutation in one single gene, adaptation to high
 altitude in rhesus macaques is polygenic and spread across numerous
 important biological systems.
description: This data was generated by selscan v1.3.0 and norm v1.3.0, both
 available at https://github.com/szpiech/selscan, using genomic data
 available at http://dx.doi.org/10.5524/100484.
description: README.txt
 Information on data files provided 
 chr*.xpnsl.out.norm.gz
 Normalized XP-nSL scores for each autosome
 
 chr*.xpnsl.out.norm.100kb.windows.gz
 Summary of normalized XP-nSL scores in 100kb non-overlapping
 windows
DOI: 10.5061/dryad.zgmsbcc9r
title: Data from: Climatic effects on niche evolution in a passerine bird clade depend on paleo-climate reconstruction method

description: Climatic niches describe the climatic conditions in which species can
 persist. Shifts in climatic niches have been observed to coincide with
 major climatic change, suggesting that species adapt to new conditions. We
 test the relationship between rates of climatic niche evolution and
 paleo-climatic conditions through time for 71 Old-World flycatcher species
 (Aves: Muscicapidae). We combine niche quantification for all species with
 dated phylogenies to infer past changes in the rates of niche evolution
 rates for temperature and precipitation niches. Paleo-climatic conditions
 were inferred independently using two datasets: a paleo-elevation
 reconstruction and the mammal fossil record. We find changes in climatic
 niches through time, but no or weak support for a relationship between
 niche evolution rates and rates of paleo-climatic change for both
 temperature and precipitation niche and for both reconstruction methods.
 In contrast, the inferred relationship between climatic conditions and
 niche evolution rates depends on paleo-climatic reconstruction method:
 rates of temperature niche evolution are significantly negatively related
 to absolute temperatures inferred using the paleo-elevation model but not
 those reconstructed from the fossil record. We suggest that paleo-climatic
 change might be a weak driver of climatic niche evolution in birds and
 highlight the need for greater integration of different paleo-climate
 reconstructions.
description: A full description of the data sources and processing methods is
 given in the manuscript.  <strong>Climatic
 niches:</strong> Quantification of climatic
 niches (temperature and precipitation) was carried out from range maps as
 described in the publication. Final niche values are available
 here. <b>Paleo-climatic conditions inferred from
 the mammal fossil record: </b> Temperature and
 precipitation values for our study region were inferred from the mammal
 fossil record. Mammal fossil community data was obtained from the NOW
 database (accessible
 online &lt;http://www.helsinki.fi/science/now/&gt;.). Here we
 provide the data that was used in the manuscript and the climatic
 conditions inferred from each fossil locality. 
description: Please see read me file:
 Eyres_Evolution_climatic_niches_README.txt
DOI: 10.15468/dl.jtdehc
title: Occurrence Download

description: A dataset containing 255 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-103.12587 17.72427,-90.78373 17.72427,-90.78373 22.66988,-103.12587 22.66988,-103.12587 17.72427))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Abronia graminea"
 ]
}

 The dataset includes 255 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002797-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.