cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.891vt38
title: Data from: Coping with the climate: cuticular hydrocarbon acclimation of ants under constant and fluctuating conditions

description: Terrestrial arthropods achieve waterproofing by a layer of cuticular
 hydrocarbons (CHCs). At the same time, CHCs also serve as communication
 signals. To maintain waterproofing under different climate conditions,
 insects adjust the chemical composition of their CHC layer, but this may
 affect the communication via CHC. The detailed acclimatory changes of CHCs
 and how these influence their physical properties are still unknown. Here,
 we studied acclimation in two closely related ant species with distinct
 CHC profiles, Myrmica rubra and Myrmica ruginodis, in response to constant
 or fluctuating temperature and humidity regimes. We measured how
 acclimation affected CHC composition and viscosity, and the ants’ drought
 survival. In both species, CHC composition showed strong, predictable
 responses to temperature regimes. Warm-acclimated individuals had higher
 proportions of linear alkanes, and less methyl-branched or unsaturated
 CHCs. These changes coincided with higher solid content and viscosity of
 CHCs in warm-acclimated ants. Temperature fluctuation caused effects
 similar to constant-cool conditions in M. rubra, but led to entirely
 different profiles in M. ruginodis, suggesting that fluctuating and
 constant conditions pose very different challenges. Acclimation to dry
 conditions led to higher absolute amounts of CHCs, which increased the
 ants’ drought survival, whereas temperature acclimation did not. Hence,
 the temperature-induced CHC changes cannot be explained by the need for
 waterproofing alone. While these changes could be non-adaptive, we propose
 that they serve to maintain a constant CHC viscosity, which may be
 essential for communication and other functions.
description: Data from Coping with
 the climate: Cuticular hydrocarbon acclimation of ants under constant and
 fluctuating conditionsThe Excel file contains
 four sheets: 1) The composition of the cuticular hydrocarbon profile of
 Myrmica rubra, 2) the composition of the cuticular hydrocarbon profile of
 Myrmica ruginodis, 3) data of a drought survival experiment and 4)
 viscosity data measured using microrheology. The compositional data is
 presented as percentages that add up to 100%.Data from Sprenger et al.
 2018.xlsx
DOI: 10.7910/dvn/kmsi22
title: Replication Data for: When Reintegration of Ex-Combatants Turns Deadly: The State’s Role in Preventing Post-Conflict Homicides

description: Replication materials for Sharif & Zuluaga (2026): When Reintegration of Ex-Combatants Turns Deadly: The State’s Role in Preventing Post-Conflict Homicides
DOI: 10.5061/dryad.24jk4
title: Data from: Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya

description: Asian pika species are morphologically ∼similar and have overlapping
 ranges. This leads to uncertainty and species misidentification in the
 field. Phylogenetic analyses of such misidentified samples leads to
 taxonomic ambiguity. The ecology of many pika species remains
 understudied, particularly in the Himalaya, where sympatric species could
 be separated by elevation and/or substrate. We sampled, measured, and
 acquired genetic data from pikas in the Sikkim Himalaya. Our analyses
 revealed a cryptic lineage, Ochotona sikimaria, previously reported as a
 subspecies of O. thibetana. The results support the elevation of this
 lineage to the species level, as it is genetically divergent from O.
 thibetana, as well as sister species, O. cansus (endemic to central China)
 and O. curzoniae (endemic to the Tibetan plateau). The Sikkim lineage
 diverged from its sister species’ about 1.7–0.8 myr ago, coincident with
 uplift events in the Himalaya. Our results add to the recent spate of
 cryptic diversity identified from the eastern Himalaya and highlight the
 need for further study within the Ochotonidae.
description: divergence date table
 Finaldivergecnce date table
 Final.xlsdivergence_CytbND4_xmldivergence_cytb_nd4_4.xmldivergenceTree cytb_nd4divergenceTreecytb_nd4.trecytbFig2a MrbayescytbFig2a_moreOG.nexcytbFig2a RAxMLcytbFig2a_moreOG.phy.reducedSpecies Tree xmlSpTreePartNewBeast.xmlSpecies tree cytb alignmentcytbND4rag1rag2_withThi_cytb.fastaSpecies tree rag1 alignmentcytbND4rag1rag2_withThi_rag1.fastaSpecies tree rag2 alignmentcytbND4rag1rag2_withThi_rag2.fastaSpecies tree ND4 alignmentcytbND4rag1rag2_withThiND4.fasta
DOI: 10.5281/zenodo.18381078
title: Reconfiguration of Mercury's Exosphere during Strong Space Weather Events (Dataset)

description: This repository includes all data presented in the manuscript "Reconfiguration of Mercury's Exosphere during Strong Space Weather Events".
DOI: 10.5281/zenodo.18381079
title: Reconfiguration of Mercury's Exosphere during Strong Space Weather Events (Dataset)

description: This repository includes all data presented in the manuscript "Reconfiguration of Mercury's Exosphere during Strong Space Weather Events".
DOI: 10.5061/dryad.28g37
title: Data from: A general model for estimating macroevolutionary landscapes

description: The evolution of quantitative characters over long timescales is often
 studied using stochastic diffusion models. The current toolbox available
 to students of macroevolution is however limited to two main models:
 Brownian motion and the Ornstein-Uhlenbeck process, plus some of their
 extensions. Here we present a very general model for inferring the
 dynamics of quantitative characters evolving under both random diffusion
 and deterministic forces of any possible shape and strength, which can
 accommodate interesting evolutionary scenarios like directional trends,
 disruptive selection, or macroevolutionary landscapes with multiple peaks.
 This model is based on a general partial differential equation widely used
 in statistical mechanics: the Fokker-Planck equation, also known in
 population genetics as the Kolmogorov forward equation. We thus call the
 model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model
 can be used to describe macroevolutionary landscapes over which
 quantitative traits evolve and, more importantly, we detail how it can be
 fitted to empirical data. Using simulations, we show that the model has
 good behavior both in terms of discrimination from alternative models and
 in terms of parameter inference. We provide R code to fit the model to
 empirical data using either maximum-likelihood or Bayesian estimation, and
 illustrate the use of this code with two empirical examples of body mass
 evolution in mammals. FPK should greatly expand the set of
 macroevolutionary scenarios that can be studied since it opens the way to
 estimating macroevolutionary landscapes of any conceivable shape.
description: Boucher_et_al_Online_AppendicesA PDF file with online appendices.
DOI: 10.5061/dryad.qd450
title: Data from: An updated global dataset for diet preferences in terrestrial mammals: testing the validity of extrapolation

description: 1. Diet is a key trait of an organism’s life history that influences a
 broad spectrum of ecological and evolutionary processes. Kissling et al.
 (2014) compiled a species-specific dataset of diet preferences of mammals
 for 38% of a total of 5364 terrestrial mammalian species assessed for the
 International Union for Conservation of Nature’s Red List, to facilitate
 future studies. The authors imputed dietary data for the remaining 62% by
 using extrapolation from phylogenetic relatives. 2. We collected dietary
 information for 1261 mammalian species for which data were extrapolated by
 Kissling et al. (2014), in order to evaluate the success with which such
 extrapolation can predict true diets. 3. The extrapolation method devised
 by Kissling et al. (2014) performed well for broad dietary categories
 (consumers of plants and animals). However, the method performed
 inconsistently, and sometimes poorly, for finer dietary categories,
 varying in accuracy in both dietary categories and mammalian orders. 4.
 The results of the extrapolation performance serve as a cautionary tale.
 Given the large variation in extrapolation performance, we recommend a
 more conservative approach for inferring mammalian diets, whereby dietary
 extrapolation is implemented only when there is a high degree of
 phylogenetic conservatism for dietary traits. Phylogenetic comparative
 methods can be used to detect and measure phylogenetic signal in diet. If
 data for species are needed, then only the broadest feeding categories
 should be used. This would ensure a greater level of accuracy and provide
 a more robust dataset for further ecological and evolutionary analysis.
description: Combined MammalDIET and
 MammalDIET 2 datasetThe combined mammal
 dietary dataset from Kissling et al. (2014) and the updated collected
 dietary information for 1261 mammalian species.
DOI: 10.5061/dryad.5b1j0
title: Data from: An integrative approach for mapping differentially expressed genes and network components using novel parameters to elucidate key regulatory genes in colorectal cancer

description: For examining the intricate biological processes concerned with colorectal
 cancer (CRC), a systems biology approach integrating several biological
 components and other influencing factors is essential to understand. We
 performed a comprehensive system level analysis for CRC which assisted in
 unravelling crucial network components and many regulatory elements
 through a coordinated view. Using this integrative approach, the
 perceptive of complexity hidden in a biological phenomenon is extensively
 simplified. The microarray analyses facilitated differential expression of
 631 significant genes employed in the progression of disease and supplied
 interesting associated up and down regulated genes like jun, fos and
 mapk1. The transcriptional regulation of these genes was deliberated
 widely by examining transcription factors such as hnf4, nr2f1, znf219 and
 dr1 which directly influence the expression. Further, interactions of
 these genes/proteins were evaluated and crucial network motifs were
 detected to associate with the pathophysiology of CRC. The available
 standard statistical parameters such as z-score, p-value and significance
 profile were explored for the identification of key signatures from CRC
 pathway whereas a few novel parameters representing over-represented
 structures were also designed in the study. The applied approach revealed
 5 key genes i.e. kras, araf, pik3r5, ralgds and akt3 via our novel
 designed parameters illustrating high statistical significance. These
 novel parameters can assist in scrutinizing candidate markers for diseases
 having known biological pathways. Further, investigating and targeting
 these proposed genes for experimental validations, instead being
 spellbound by the complicated pathway will certainly endow valuable
 insight in a well-timed systematic understanding of CRC.
description: CRC Supplementary
 DataThis file contains
 network motifs being used in this study. Two kinds of network motifs were
 included, one is randomly generated and other annotated
 ones.CRCData.zip
DOI: 10.5061/dryad.43sg3
title: Data from: An exotic invader drives the evolution of plant traits that determine mycorrhizal fungal diversity in a native competitor.

description: The symbiosis between land plants and arbuscular mycorrhizal fungi (AMF)
 is one of the most widespread and ancient mutualisms on the planet.
 However, relatively little is known about the evolution of these symbiotic
 plant-fungal interactions in natural communities. In this study, we
 investigated the symbiotic AMF communities of populations of the native
 plant species Pilea pumila (Urticaceae) with varying histories of
 coexistence with an non-mycorrhizal invasive species, Alliaria petiolata
 (Brassicaceae), known to affect mycorrhizal communities. We found that
 native populations of P. pumila with a long history of coexistence with
 the invasive species developed more diverse symbiotic AMF communities.
 This effect was strongest when A. petiolata plants were actively growing
 with the natives, and in soils with the longest history of A. petiolata
 growth. These results suggest that despite the ancient and widespread
 nature of the plant-AMF symbiosis, the plant traits responsible for
 symbiotic preferences can nevertheless evolve rapidly in response to
 environmental changes.
description: AMF occurrence data in
 Pilea pumila rootsfinal PPAM data for
 Dryad2.xlsxAlignment for RaxML
 EPAAligned sequence file
 used for evolutionary placement of short reads. Query sequences (new to
 this study) are listed by their Genbank Accession # (KF38624-KF386347);
 other sequences are references.Lankau and Nodurft alignment
 for RaxML EPA.fasta
DOI: 10.15468/dl.zc9qae
title: Occurrence Download

description: A dataset containing 278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.75436 7.48318,-76.73151 5.53133,-74.40141 5.66775,-74.92682 8.04905,-76.75436 7.48318))",
 "HasGeospatialIssue is false",
 "TaxonKey is Boa constrictor"
 ]
}

 The dataset includes 278 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000501-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.50jc4
title: Data from: Intermittent breeding and constraints on litter size: consequences for effective population size per generation (Ne) and per reproductive cycle (Nb)

description: In iteroparous species, it is easier to estimate Nb = effective number of
 breeders in one reproductive cycle than Ne = effective population size per
 generation. Nb can be used as a proxy for Ne and also can provide crucial
 insights into eco-evolutionary processes that occur during reproduction.
 We used analytical and numerical methods to evaluate effects of
 intermittent breeding and litter/clutch size on inbreeding Nb and Ne.
 Fixed or random litter sizes ≥ 3 have little effect on either
 effective-size parameter; however, in species (e.g., many large mammals)
 in which females can produce only one offspring per cycle, female Nb = ∞
 and overall Nb = 4Nb(male). Intermittent breeding reduces the pool of
 female breeders, which reduces both female and overall Nb; reductions are
 larger in high-fecundity species with high juvenile mortality and increase
 when multiple reproductive cycles are skipped. Simulated data for six
 model species showed that both intermittent breeding and litter-size
 constraints increase Ne, but only slightly. We show how to quantitatively
 account for these effects, which are important to consider when a) using
 Nb to estimate Ne, or b) drawing inferences about male reproductive
 success based on estimates of female Nb.
description: Scripts to repeat the
 studyThese are scripts to
 repeat the published study. Some of the code is LDNe specific and thus is
 not needed to replicate the work.AgeStructureNe.zip
DOI: 10.5061/dryad.532c28n
title: Data from: True homoplasy of retrotransposon insertions in primates

description: How reliable are the presence/absence insertion patterns of the supposedly
 homoplasy-free retrotransposons, that were randomly inserted in the quasi
 infinite genomic space? To systematically examine this question in an
 up-to-date, multi-genome comparison, we screened millions of primate
 transposed Alu SINE elements for incidences of homoplasious precise
 insertions and deletions. In genome-wide analyses, we identified and
 manually verified nine cases of precise parallel Alu insertions of
 apparently identical elements at orthologous positions in two ape lineages
 and twelve incidences of precise deletions of previously established
 SINEs. Correspondingly, eight precise parallel insertions and no exact
 deletions were detected in a comparison of lemuriform primate and human
 insertions spanning the range of primate diversity. With an overall
 frequency of homoplasious Alu insertions of only 0.01% (for
 human-chimpanzee-rhesus macaque) and 0.02-0.04% (for
 human-bushbaby-lemurs) and precise Alu deletions of 0.001-0.002% (for
 human-chimpanzee-rhesus macaque), real homoplasy is not considered to be a
 quantitatively relevant source of evolutionary noise. Thus,
 presence/absence patterns of Alu retrotransposons and, presumably, all
 LINE1-mobilized elements represent indeed the virtually homoplasy-free
 markers they are considered to be. Therefore, ancestral incomplete lineage
 sorting and hybridization remain the only serious sources of conflicting
 presence/absence patterns of retrotransposon insertions, and as such are
 detectable and quantifiable.
description: Supplementary Table
 S1-3Retrotransposon
 presence/absence patternsSupplementary_Table_S1-3.xlsxSupplementary Material File S1-3Alignments of loci with retrotransposon presence/absence patternsSupplementary_Material_File_S1-3.docx
DOI: 10.5061/dryad.451n7
title: Data from: Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits

description: Theory predicts that sex chromsome linkage should reduce intersexual
 genetic correlations thereby allowing the evolution of sexual dimorphism.
 Empirical evidence for sex linkage has come largely from crosses and few
 studies have examined how sexual dimorphism and sex linkage are related
 within outbred populations. Here we use data on an array of different
 traits measured on over 10,000 individuals from two pedigreed populations
 of birds (collared flycatcher and zebra finch) to estimate the amount of
 sex linked genetic variance (h2z). Out of 17 traits examined, eight showed
 a non-zero h2Z estimate but only four were significantly different from
 zero (wing patch size and tarsus length in collared flycatchers, wing
 length and beak colour in zebra finches). We further tested how sexual
 dimorphism and the mode of selection operating on the trait relate to the
 proportion of sex linked genetic variance. Sexually selected traits did
 not show higher h2Z than morphological traits and there was only a weak
 positive relationship between h2Z and sexual dimorphism. However, given
 the relative scarcity of empirical studies it is premature to make
 conclusions about the role sex chromosome linkage in the evolution of
 sexual dimorphism.
description: data_file_dryad_collared_flycatcherZebrafinchdatacontains all datafiles for the zebra finch analysesZlink_DryadData.zipped_file_dryad_collared_flycatcherExplanations_dryadDescription of the different datafiles used for the analyses
DOI: 10.5061/dryad.jb3mj
title: Data from: Not Normal: the uncertainties of scientific measurements

description: Judging the significance and reproducibility of quantitative research
 requires a good understanding of relevant uncertainties, but it is often
 unclear how well these have been evaluated and what they imply. Reported
 scientific uncertainties were studied by analysing 41 000 measurements of
 3200 quantities from medicine, nuclear and particle physics, and
 interlaboratory comparisons ranging from chemistry to toxicology. Outliers
 are common, with 5σ disagreements up to five orders of magnitude more
 frequent than naively expected. Uncertainty-normalized differences between
 multiple measurements of the same quantity are consistent with
 heavy-tailed Student’s t-distributions that are often almost Cauchy, far
 from a Gaussian Normal bell curve. Medical research uncertainties are
 generally as well evaluated as those in physics, but physics uncertainty
 improves more rapidly, making feasible simple significance criteria such
 as the 5σ discovery convention in particle physics. Contributions to
 measurement uncertainty from mistakes and unknown problems are not
 completely unpredictable. Such errors appear to have power-law
 distributions consistent with how designed complex systems fail, and how
 unknown systematic errors are constrained by researchers. This better
 understanding may help improve analysis and meta-analysis of data, and
 help scientists and the public have more realistic expectations of what
 scientific results imply.
description: BaileyDC_Uncertainty_Data_DescriptionAn Excel file with 5 worksheets listing the sources for the datasets analysed in the paper: Medical, Particle, Nuclear, Interlab, Constants.
DOI: 10.5061/dryad.qp0s0
title: Data from: Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation

description: Among the World’s most challenging environments for plant life is the
 Atacama Desert, an arid zone extending over 1300 km and from sea level to
 2000/3000 m along the southwestern Andean foothills. Plants there and in
 the adjacent Mediterranean zone exhibit striking adaptations, and we here
 use a species-rich such group to address the question whether adaptations
 arose in parallel, at different times, or simultaneously. Answering this
 type of question has been a major concern of evolutionary biology over the
 past few years, with a growing consensus that lineages tend to be
 conservative in their vegetative traits and niche requirements. Combined
 nuclear and chloroplast DNA sequences for 112 species of Oxalidales (4900
 aligned nucleotides) yielded a fossil-calibrated phylogeny that includes
 43 of the 54 species of Oxalis occurring in Chile. Distribution models
 (SDMs) for these species that included precipitation, temperature, fog
 and/or vegetation types and the phylogeny were used to reconstruct
 ancestral habitat preferences, relying on likelihood and Bayesian
 techniques. Since uneven collecting can reduce the power of SDMs, we used
 a background sample from 1224 Chilean Oxalis collections to correct models
 for collecting effort. Models with just 10 of 19 bioclim parameters did as
 well as more parameter-rich models. Results reveal that the Oxalis flora
 of Chile consists of seven distant lineages that originated at different
 times prior to the last Andean uplift pulse and some of which had features
 pre-adapting them to seasonally arid or xeric conditions. The
 Mediterranean core zone, south of the Atacama, offered an ecological
 refuge for insufficiently arid-adapted species and harbors a mix of
 ancient and young groups. There is no evidence of rapid adaptive
 radiation.
description: Heibl&Renner_Oxalis_dataHeibl_Renner_Oxalis_data_Dryad+TreeBASE.txtOxalis_Table_S1_Dryad_updateContains GenBank accession numbersOxalis_Table_S1_Dryad.doc