cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.db4r63m
title: Data from: Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata

description: Populations of reef-building corals may harbor genetically distinct
 lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which
 have been shown to affect important colony properties, including growth
 rates and resilience against environmental stress. However, the molecular
 processes underlying these differences are not well understood. In this
 study, we used whole transcriptome sequencing (RNA-seq) to assess gene
 expression differences between 27 samples of the coral Montipora capitata
 predominantly hosting two different Symbiodinium types in clades C and D.
 The samples were further characterized by their origin from two field
 sites on Hawai‘i Island with contrasting environmental conditions,
 including differences in salinity and temperature. We found that
 transcriptome-wide gene expression profiles clearly separated by field
 site first, and symbiont clade second. With 273 differentially expressed
 genes (DEGs, 1.3% of all host transcripts), symbiont clade had a
 measurable effect on host gene expression, but the effect of field site
 proved almost an order of magnitude higher (1957 DEGs, 9.6%). According to
 SNP analysis, we found moderate evidence for host genetic differentiation
 between field sites (FST = 0.046) and among corals harboring alternative
 symbiont clades (FST = 0.036), suggesting that site-related gene
 expression differences are likely due to a combination of local adaptation
 and acclimatization to environmental factors. The correlation between host
 gene expression and symbiont clade may be due to several factors,
 including host genotype or microhabitat selecting for alternative clades,
 host physiology responding to different symbionts, or direct modulation of
 host gene expression by Symbiodinium. However, the magnitude of these
 effects at the level of transcription were unexpectedly small considering
 the contribution of symbiont type to holobiont phenotype.
description: Synonymous SNPs in
 Montipora capitata from Hawaii IslandVCF file containing
 2,524 synonymous SNPs obtained from RNA-seq data of two populations of
 Montipora capitata on Hawaii Island. SNPs were called using Samtools /
 Bowtie2 to map high-quality reads to a reference transcriptome assembly.
 Preliminary SNPs were quality-filtered, and synonymous SNPs extracted by
 comparison to open reading frames using SnpEff.Mcap_synSNPs.vcf
DOI: 10.7927/hzk3-7k35
title: IPCC AR6 Synthesis Report LR Figure 2.4 (b): Market Adoption

description: This panel shows the cumulative global adoption for each technology, in GW of installed capacity for renewable energy and in millions of vehicles for battery-electric vehicles. The vertical dashed line is placed in 2010 to indicate the change over the past decade. The electricity production share reflects different capacity factors; for example, for the same amount of installed capacity, wind produces about twice as much electricity as solar PV. Renewable energy and battery technologies were selected as illustrative examples because they have recently shown rapid changes in costs and adoption, and because consistent data are available. Other mitigation options assessed in the WGIII report are not included as they do not meet these criteria.
DOI: 10.5061/dryad.m930f2m
title: Data from: Statistical structure of locomotion and its modulation by odors

description: Most behaviors such as making tea are not stereotypical but have an
 obvious structure. However, analytical methods to objectively extract
 structure from non-stereotyped behaviors are immature. In this study, we
 analyze the locomotion of fruit flies and show that this non-stereotyped
 behavior is well-described by a Hierarchical Hidden Markov Model (HHMM).
 HHMM shows that a fly's locomotion can be decomposed into a few
 locomotor features, and odors modulate locomotion by altering the time a
 fly spends performing different locomotor features. Importantly, although
 all flies in our dataset use the same set of locomotor features,
 individual flies vary considerably in how often they employ a given
 locomotor feature, and how this usage is modulated by odor. This variation
 is so large that the behavior of individual flies is best understood as
 being grouped into at least 3-5 distinct clusters, rather than variations
 around an average fly.
description: Tao_ozarkar_Beck_Bhandawat_datasetThere are 34 Excel files containing the 2D-coordinates of the fly. The actual arena was 3.2 cm in radius. These data have been normalized such that the data fits in a unit circle with its center at the origin. Therefore, 3.2 cm = 1. The odor-zone was 1.2 cm in diameter. In this dataset, odor-zone is a circle centered at (0,0) with a radius 1.2/3.2 = 0.375.
DOI: 10.5061/dryad.54c5q66
title: Data from: Does the genomic landscape of species divergence in Phaseolus beans coerce parallel signatures of adaptation and domestication?

description: Exploring the genomic architecture of species and populations divergence
 aids understanding how lineages evolve and adapt, and ultimately can show
 the repeatability of evolutionary processes. Yet, the genomic signatures
 associated with divergence are still relatively unexplored, leading to a
 knowledge gap on whether species divergence ultimately differs in its
 genetic architecture from divergence at other spatial scales (i.e.,
 populations, ecotypes). Our goal in this research was to determine whether
 genomic islands of speciation are more prone to harbor within-species
 differentiation due to genomic features, suppressed recombination, smaller
 effective population size or increased drift, across repeated
 hierarchically nested levels of divergence. We used two species of
 Phaseolus beans with strong genepool and population sub-structure produced
 by multiple independent domestications each especially in Andean and
 Mesoamerican / Middle American geographies. We genotyped 22,531
 GBS-derived SNP markers in 209 individuals of wild and cultivated
 Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for
 species-associated divergence. Out of these divergence peaks, 21% were
 recovered in the four within-species between-genepool comparisons and in
 the five within-genepool wild-cultivated comparisons (some of the latter
 did retrieve genuine signatures of the well described multiple
 domestication syndromes). However, genomic regions with overall high
 relative differentiation (measured by FST) coincided with regions of low
 SNP density and regions of elevated delta divergence between-genepools
 (ΔDiv), independent of the scale of divergence. The divergence in
 chromosome Pv10 further coincided with a between-species pericentric
 inversion. These convergences suggest that shared variants are being
 recurrently fixed at replicated regions of the genome, and in a similar
 manner across different hierarchically nested levels of divergence, likely
 as result of genomic features that make certain regions more prone to
 accumulate islands of speciation and within-species divergence. In
 summary, neighboring signatures of speciation, adaptation and
 domestication in Phaseolus beans are influenced by ubiquitous genomic
 constrains, which may continue to fortuitously shape genomic
 differentiation at various others scales of divergence.
description: Sample key file,
 pipeline configuration file and filtered datasetDryad.zip
DOI: 10.5061/dryad.25kg375
title: Data from: Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

description: Estuarine organisms grow in highly heterogeneous habitats and their
 genetic differentiation are driven by selective and neutral processes as
 well as population colonization history. However, the relative importance
 of the processes that underlie genetic structure is still puzzling.
 Scirpus mariqueter is a perennial grass almost limited in the Changjiang
 River estuary and it’s adjacent Qiantang River estuary. Here, using
 amplified fragment length polymorphism (AFLP), a moderate-high level of
 genetic differentiation among populations (range FST: 0.0310-0.3325) was
 showed despite large ongoing dispersal. FLOCK assigned all individuals to
 13 clusters and revealed a complex genetic structure. Some genetic
 clusters were limited in peripheries compared with very mixing
 constitution in centre populations, suggesting local adaptation was more
 likely to occur in peripheral populations. 21 candidate outliers under
 positive selection were detected, and further, the differentiation
 patterns correlated with geographic distance, salinity difference and
 colonization history were analyzed with or without the outliers. Combined
 results of AMOVA and IBD based on different dataset, it was found that the
 effects of geographic distance and population colonization history on
 isolation seemed to be promoted by divergent selection. However,
 none-liner IBE pattern indicates the effects of salinity were overwhelmed
 by spatial distance or other ecological process in certain areas, and also
 suggests that salinity was not the only selective factor driving
 population differentiation. These results together indicate that
 geographic distance, salinity difference and colonization history
 co-contributed in shaping the genetic structure of S. mariqueter, and that
 their relative importance was correlated with spatial scale and
 environment gradient.
description: ece-Sm-AFLP
 data"ece-Sm-AFLP
 data" includes 0-1 matrix of entire loci, outliers and neutral
 dataset in different sheets for all individuals.ece-Sm-Mcheza"ece-Sm-Mcheza" includes the list of potential loci under selection with MCHEZA, DFDIST and BAYESCAN software, respectively.ece-Sm-summary of FLOCKThis data includes the assignment test results from FLOCK analysis
DOI: 10.5061/dryad.n0bf69r
title: Data from: Experimental study of the supercritical CO2 diffusion coefficient in porous media under reservoir conditions

description: Reliable measurement of CO2 diffusion coefficient in consolidated
 oil-saturated porous media is critical for design, performance of carbon
 capture and storage (CCS) and CO2 enhanced oil recovery (EOR) project. In
 this study, a thorough experimental investigation on supercritical CO2
 diffusion in n-decane saturated Berea core (50 and 100 mD) was conducted
 at elevated pressure (10 to 25 MPa) and temperature (333.15 to 373.15 K),
 which simulated the real reservoir condition. Supercritical CO2 diffusion
 coefficients in Berea core were calculated by a model appropriate for
 diffusion in porous media based on Fick’s law. The results show that with
 an increase in pressure, temperature and permeability, the supercritical
 CO2 diffusion coefficient increases correspondingly. The supercritical CO2
 diffusion coefficient first increases slowly at 10 MPa and then grow
 significantly with the increase of pressure. The effect of temperature
 becomes weaker at elevated pressure condition. And the effect of
 permeability keeps steady despite of temperature change in experiments.
 The effect of gas state and porous media on supercritical CO2 diffusion
 coefficient is further discussed by comparing the results in this study
 with previous research. Based on the experimental results, an empirical
 correlation for supercritical CO2 diffusion coefficient in n-decane
 saturated porous media is developed. The experimental results contribute
 to the study of supercritical CO2 diffusion in compact porous media.
description: pressure data summary
 filethis is a summary file
 which include all the experimental data recorded in our
 experiments.
DOI: 10.5061/dryad.n7nm0g4
title: Data from: Physiological and social consequences of gastrointestinal nematode infection in a nonhuman primate

description: Gastrointestinal nematodes are intensely studied models for host-pathogen
 interactions in wildlife, yet consequences of infections are not fully
 understood. Among the potential costs of nematode infection are
 physiological changes caused by immune system activation, reduction or
 reallocation of available energy, as well as potential social consequences
 in terms of decreased social activity or avoidance of infected
 individuals. We used experimental anthelmintic treatment to investigate
 effects of strongyle nematode infection in Barbary macaques (Macaca
 sylvanus), comparing 56 treated to 17 untreated individuals. Deworming
 success was monitored by coproscopy and infection probability estimated
 from patch occupancy models. Increasing strongyle infection probabilities
 were associated with increased fecal glucocorticoid metabolite levels and
 slightly decreased activity, and had no significant effect on energy
 balance quantified as urinary C-peptide levels. The frequency to approach
 into close spatial proximity of a partner was predicted by the partner’s,
 but not focal individual’s infection status, with a tendency towards
 infected individuals being approached less frequently. Although effects
 were weak, they suggest a co-occurrence of sickness and avoidance
 behavior, both possibly shaping social interaction patterns with potential
 consequences for an individual’s social relationships. This study adds to
 the growing body of research on the complex interactions of sociality,
 health and fitness in a group living species.
description: parasite_and_physiological_datasee README fileactivity_datasee README filedyadic_datasee README file
DOI: 10.5061/dryad.61jn743
title: Data from: Phylogenies and diversification rates: variance cannot be ignored

description: A recent pair of articles published in the journal Evolution presented a
 test for assessing the validity of hierarchical macroevolutionary models.
 The premise of the test is to compare numerical point estimates of
 parameters from two levels of analysis; if the estimates differ, the
 hierarchical model is purportedly flawed. The articles in question (Meyer
 and Wiens 2017; Meyer et al. 2018) apply their proposed test to BAMM, a
 scientific software program that uses a Bayesian mixture model to estimate
 rates of evolution from phylogenetic trees. The authors use BAMM to
 estimate rates from large phylogenies (n &gt; 60 tips) and they apply
 the method separately to subclades within those phylogenies (median size:
 n = 3 tips); they find that point estimates of rates differ between these
 levels and conclude that the method is flawed, but they do not test
 whether the observed differences are statistically meaningful. There is no
 consideration of sampling variation and its impact at any level of their
 analysis. Here, I show that numerical differences across groups that they
 report are fully explained by a failure to account for sampling variation
 in their point estimates. Variance in evolutionary rate estimates – from
 BAMM and all other methods – is an inverse function of clade size; this
 variance is extreme for clades with 5 or fewer tips (e.g., 70% of clades
 in the focal study). The articles in question rely on negative results
 that are easily explained by low statistical power to reject their
 preferred null hypothesis, and this low power is a trivial consequence of
 high variance in their point estimates. I describe additional mathematical
 and statistical mistakes that render the proposed testing framework
 invalid on first principles. Evolutionary rates are no different than any
 other population parameters we might wish to estimate, and biologists
 should use the training and tools already at their disposal to avoid
 erroneous results that follow from the neglect of variance.
description: zipped archive of all
 code and dataR code and BAMM analyses
 to replicate analyses described in articlevariance.zip
DOI: 10.5061/dryad.g154580
title: Data from: Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development

description: Zygotic genome activation (ZGA), the onset of transcription after initial
 quiescence, is a major developmental step in many species, which occurs
 after ten cell divisions in zebrafish embryos. How transcription factor
 (TF)-chromatin interactions evolve during early development to support ZGA
 is largely unknown. We establish single molecule tracking in live
 developing zebrafish embryos using reflected light-sheet microscopy to
 visualize two fluorescently labeled TF species, mEos2-TBP and
 mEos2-Sox19b. We further develop a data acquisition and analysis scheme to
 extract quantitative information on binding kinetics and bound fractions
 during fast cell cycles. The chromatin-bound fraction of both TFs
 increases during early development, as expected from a physical model of
 TF-chromatin interactions including a decreasing nuclear volume and
 increasing DNA accessibility. For Sox19b, data suggests the increase is
 mainly due to the shrinking nucleus. Our single molecule approach provides
 quantitative insight into changes of TF-chromatin associations during the
 developmental period embracing ZGA.
description: Tutorial for software
 usageMaple scripts for ITM
 correctionMaple.zipPython scripts for analysis of ITM data and implementation of the modelpython_ITM_analysis.zipData and Python script for residence time fittingpython_residence_time_fitting.zipSPT TBP residence timesSPT_TBP_residence_times.matSPT Sox residence timesSPT_Sox_residence_times.matSPT Sox ITMSPT_Sox_ITM.matSPT TBP ITMSPT_TBP_ITM.matSPT TBP ITM eventsSPT_TBP_ITM_events.matSPT Sox ITM eventsSPT_Sox_ITM_events.matSOX nuclear areasSOX_nuclear_areas.matTBP nuclear areasTBP_nuclear_areas.matSPT TBP ITM events first frameSPT_TBP_ITM_events_ff.matAll data and code combinedRepository_Data_181114.zip
DOI: 10.5061/dryad.54vb7f2
title: Data from: Genetic diversity of Persian Arabian horses and their relationship to other native Iranian horse breeds

description: The principal aims of this study were to explore genetic diversity and
 genome-wide selection signatures in Persian Arabian horses and to
 determine genetic relationship of Persian Arabians with other Iranian
 horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to
 47 mares from the mid to late 19th century, using the equine 670k SNP
 BeadChip. Mean observed and expected heterozygosity were (0.43) and
 (0.45), respectively, average inbreeding measures (FROH and FPED) were
 low, indicating high genetic diversity in Persian Arabian horses. Analysis
 of population genetic structure using STRUCTURE and Principal Component
 Analysis suggested that Persian Arabian horses can be divided into three
 groups, however the groups do not match traditional matrilineal strains.
 In total, 15 genomic regions were identified by at least two of the three
 implemented methods, Tajima’s D, H, and H12, as potentially under
 selection in Persian Arabian horses. Most of these peaks were found on
 chromosome 9, overlapping with QTLs previously associated with horse
 temperament. Biological function analysis of identified candidate genes
 highlighted enrichment of GO term “response to lipopolysaccharide” and
 KEGG pathway “chemokine-mediated signaling pathway”, which are associated
 with immune responses and may have been targets of selection in Persian
 Arabian horses. Independent analyses of SNP data from 30 horses of four
 other Iranian breeds suggested distinct population structure between
 Persian Arabian, and Turkemen and Caspian horse breeds. Overall, the
 results of this study suggest a rich genetic diversity in the Persian
 Arabian horses and a clear genetic differentiation with Turkemen and
 Caspian breeds.
description: Persian horse genotype
 data, plink .bed fileGenotype data for
 Persian horse samples, .bed file for plink file setIR.paper.heredity.bedPersian horse genotype data, plink .bim fileGenotype data for Persian horse samples, .bim for plink file setIR.paper.heredity.bimPersian horse genotype data, plink .fam fileGenotype data for Persian horse samples, .fam file for plink file setIR.paper.heredity.fam
DOI: 10.5061/dryad.v73r8j9
title: Data from: Morphological polymorphism associated with alternative reproductive tactics in a plethodontid salamander

description: Understanding polymorphism is a central problem in evolution and ecology,
 and alternative reproductive tactics (ARTs) provide compelling examples
 for studying the origin and maintenance of behavioral and morphological
 variation. Much attention has been given to examples where
 "parasitic" individuals exploit the reproductive investment of
 "bourgeois" individuals, but some ARTs are instead maintained by
 environmental heterogeneity, with alternative tactics exhibiting
 differential fitness in discontinuous reproductive niches. We use genomic,
 behavioral, karyological, and field observational data to demonstrate one
 such example in plethodontid salamanders. These ARTs
 ("searching" and "guarding" males) are associated with
 different reproductive niches and, unlike most other examples in
 amphibians, demonstrate substantial morphological differences and
 inflexibility within a reproductive season. Evidence suggests the
 existence of these ARTs within three putative species in the two-lined
 salamander (Eurycea bislineata) species complex, with other members of
 this clade fixed for one of the two tactics. We highlight directions for
 future research in this system, including the relationship between these
 ARTs and parental care.
description: R scripts for Pierson et
 al.R
 scripts for fitting logistic regression, conducting t-tests, and
 conducting Fisher's exact tests.Pierson_et_al_R_Scripts.RPierson et al. dataAll field collection and behavioral trial data.Pierson_et_al_Data.xlsxPierson et al. RAxML outputAll RAxML output files.Pierson_et_al_RAxML_output.zipPierson et al. ipyrad input and outputInput files necessary to replicate ipyrad assembly and relevant ipyrad output files.Pierson_et_al_ipyrad_input_output.zip