cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31158364.v1
title: CSA for ratios of intervertebral equine cervical spine.

description: CSA at the intervertebral level of the equine caudal cervical spine is measures by three observers in normal and affected horses.
DOI: 10.5061/dryad.7822f
title: Data from: Why do mixotrophic plants stay green? A comparison between green and achlorophyllous orchid individuals in situ

description: Some forest plants adapt to shade by mixotrophy, i.e., they obtain carbon
 both from photosynthesis and from their root mycorrhizal fungi. Fully
 achlorophyllous species using exclusively fungal carbon (the so-called
 mycoheterotrophic plants) have repeatedly evolved from such mixotrophic
 ancestors. However, adaptations for this evolutionary transition, and the
 reasons why it has happened a limited number of times, remain unknown. We
 investigated this using achlorophyllous variants (i.e., albinos)
 spontaneously occurring in Cephalanthera damasonium, a mixotrophic orchid.
 In two populations, we compared albinos with co-occurring green
 individuals in situ. We investigated vegetative traits, namely, shoot
 phenology, dormancy, CO2 and H2O leaf exchange, mycorrhizal colonization,
 degree of mycoheterotrophy (using 13C abundance as a proxy), and
 susceptibility to pathogens and herbivores. We monitored seed production
 (in natural or experimental crosses) and seed germination. Albinos
 displayed (1) more frequent shoot drying at fruiting, possibly due to
 stomatal dysfunctions, (2) lower basal metabolism, (3) increased
 sensitivity to pathogens and herbivores, (4) higher dormancy and
 maladapted sprouting, and, probably due to the previous differences, (5)
 fewer seeds, with lower germination capacity. Over the growing season,
 green shoots shifted from using fungal carbon to an increasingly efficient
 photosynthesis at time of fruiting, when fungal colonization reached its
 minimum. Conversely, the lack of photosynthesis in fruiting albinos may
 contribute to carbon limitation, and to the above-mentioned trends. With a
 103× fitness reduction, albinos failed a successful transition to
 mycoheterotrophy because some traits inherited from their green ancestors
 are maladaptive. Conversely, mycoheterotrophy requires at least
 degeneration of leaves and stomata, optimization of the temporal pattern
 of fungal colonization and shoot sprouting, and new defenses against
 pathogens and herbivores. Transition to mycoheterotrophy likely requires
 progressive, joint evolution of these traits, while a sudden loss of
 photosynthesis leads to unfit plants. We provide explanations for the
 evolutionary stability of mixotrophic nutrition and for the rarity of
 emergence of carbon sinks in mycorrhizal networks. More broadly, this may
 explain what prevents the emergence of fully heterotrophic taxa in the
 numerous other mixotrophic plant or algal lineages recently described.
description: BD_final_160313The excel file contains all dataset used for the article, including morphological and physiological data on Cephalanthera damasonium green and albino individuals observed in 2006, 2007 and 2008 in Boi and MON sites. For each excel sheet, the corresponding Table or figure presented in the article is mentionned.
DOI: 10.5061/dryad.66hc3
title: Data from: Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity

description: Recent advances in next-generation sequencing (NGS) technologies spur
 progress in determining the microbial diversity in various ecosystems by
 highlighting, for example, the rare biosphere. Currently, high-throughput
 pyrotag sequencing of PCR-amplified SSU rRNA gene regions is mainly used
 to characterize bacterial and archaeal communities, and rarely to
 characterize protist communities. In addition, although taxonomic
 assessment through phylogeny is considered as the most robust approach,
 similarity and probabilistic approaches remain the most commonly used for
 taxonomic affiliation. In a first part of this work, a tree-based method
 was compared with different approaches of taxonomic affiliation (BLAST and
 RDP) of 18S rRNA gene sequences and was shown to be the most accurate for
 near full-length sequences and for 400 bp amplicons, with the exception of
 amplicons covering the V5-V6 region. Secondly, the applicability of this
 method was tested by running a full scale test using an original
 pyrosequencing dataset of 18S rRNA genes of small lacustrine protists
 (0.2–5 µm) from eight freshwater ecosystems. Our results revealed that i)
 fewer than 5% of the operational taxonomic units (OTUs) identified through
 clustering and phylogenetic affiliation had been previously detected in
 lakes, based on comparison to sequence in public databases; ii) the
 sequencing depth provided by the NGS coupled with a phylogenetic approach
 allowed to shed light on clades of freshwater protists rarely or never
 detected with classical molecular ecology approaches; and iii)
 phylogenetic methods are more robust in describing the structuring of
 under-studied or highly divergent populations. More precisely, new
 putative clades belonging to Mamiellophyceae, Foraminifera,
 Dictyochophyceae and Euglenida were detected. Beyond the study of
 protists, these results illustrate that the tree-based approach for NGS
 based diversity characterization allows an in-depth description of
 microbial communities including taxonomic profiling, community structuring
 and the description of clades of any microorganisms (protists, Bacteria
 and Archaea).
description: Cleaned
 sequencespooled_sample_SeqF.fastaAlignments and PhylogeniesPhylogeny_Align.tar.gz
DOI: 10.5061/dryad.6j51n
title: Data from: Evolutionary change during experimental ocean acidification

description: Rising atmospheric carbon dioxide (CO2) conditions are driving
 unprecedented changes in seawater chemistry, resulting in reduced pH and
 carbonate ion concentrations in the Earth’s oceans. This ocean
 acidification has negative but variable impacts on individual performance
 in many marine species. However, little is known about the adaptive
 capacity of species to respond to an acidified ocean, and as a result,
 predictions regarding future ecosystem responses remain incomplete. Here
 we demonstrate that ocean acidification generates striking patterns of
 genome-wide selection in purple sea urchins (Strongylocentrotus
 purpuratus) cultured under different CO2 levels. We examined genetic
 change at 19,493 loci in larvae from seven adult populations cultured
 under realistic future CO2 levels. Although larval development and
 morphology showed little response to elevated CO2, we found substantial
 allelic change in 40 functional classes of proteins involving hundreds of
 loci. Pronounced genetic changes, including excess amino acid
 replacements, were detected in all populations and occurred in genes for
 biomineralization, lipid metabolism and ion homeostasis, gene classes that
 build skeletons and interact in pH regulation. Such genetic change
 represents a neglected and important impact of ocean acidification that
 may influence populations that show few outward signs of response to
 acidification. Our results demonstrate the capacity for rapid evolution in
 the face of ocean acidification and show that standing genetic variation
 could be a reservoir of resilience to climate change in this coastal
 upwelling ecosystem. However, effective response to strong natural
 selection demands large population sizes and may be limited in species
 impacted by other environmental stressors.
description: Pespeni_LarvalSelection_AlleleFrequencyDataThis data file is a text tab delimited file with a single row for every SNP identified in this study (19,516). There are allele frequency data for each of 4 treatment x day conditions, for each of 7 populations. This data file also contains annotation and read depth information. See README file for more details.
DOI: 10.5061/dryad.kn543
title: Data from: Daily foraging patterns in free-living birds: exploring the predation-starvation trade-off

description: Daily patterns in the foraging behaviour of birds are assumed to balance
 the counteracting risks of predation and starvation. Predation risks are a
 function of the influence of weight on flight performance and foraging
 behaviours that may expose individuals to predators. Although recent
 research sheds light on daily patterns in weight gain, little data exist
 on daily foraging routines in free-living birds. In order to test the
 predictions of various hypotheses about daily patterns of foraging, we
 quantified the activity of four species of passerines in winter using
 radio frequency identification receivers built into supplemental feeding
 stations. From records of 472,368 feeder visits by tagged birds, we found
 that birds generally started to feed before sunrise and continued to
 forage at a steady to increasing rate throughout the day. Foraging in most
 species terminated well before sunset, suggesting their desired level of
 energy reserves was being reached before the end of the day. These results
 support the risk-spreading theorem over a long-standing hypothesis
 predicting bimodality in foraging behaviour purportedly driven by a
 tradeoff between the risks of starvation and predation. Given the
 increased energetic demands experienced by birds during colder weather,
 our results suggest that birds’ perceptions of risk are biased towards
 starvation avoidance in winter.
description: rfid_analysis_fileThese data were collected in Ithaca, NY using a network of RFID-enabled supplemental feeding stations. Passive integrated transponders were attached to individual birds. See README file for more details.
DOI: 10.5281/zenodo.18194700
title: ST36 acupoint alleviates cardiac fibrosis through A2AR-dependent regulation of microcirculation

description: Supplementary Table 1 included raw data corresponding to Figure 2 and 3, organized into four sheets.  Sheet A: Percentage of cardiac fibrosis in Sham, ISO, ISO+ST36, ISO+PC6, and ISO+SA groups. Sheet B: Heart weight to body weight ratio (HW/BW).  Sheet C: Echocardiographic parameters.  Sheet D: Electrocardiogram (ECG) parameters across groups.

 

Supplementary Table 2 contained raw data corresponding to Figure 4, with two sheets. Sheet A: Parameters from laser speckle contrast imaging in Sham, ISO, and ISO+ST36 groups. Sheet B: Hemodynamic variables.

 

Supplementary Table 3 contained raw data corresponding to Figure 5, with four sheets.

Sheet A: A2A receptor protein levels detected by immunohistochemistry in Sham, ISO, and ISO+ST36 groups. Sheet B: Gene expression of A2AR and A1R by qPCR. Sheet C: Serum cytokine levels measured by ELISA. Sheet D: Ventricular cytokine levels measured by ELISA.

 

Supplementary Table 4 included raw data for Figure 6 and 7, organized into four sheets. Sheet A: Percentage of cardiac fibrosis in ISO, ISO+ST36, ISO+caffeine, and ISO+caffeine+ST36 groups.  Sheet B: HW/BW.  Sheet C: Echocardiographic parameters.  Sheet D: ECG parameters.

 

Supplementary Table 5 contained raw data related to Figure 8, with two sheets. Sheet A: Laser speckle contrast imaging parameters in ISO, ISO+ST36, ISO+caffeine, and ISO+caffeine+ST36 groups. Sheet B: Hemodynamic variables.

 

Supplementary Table 6 included raw data supporting Figure 9, with four sheets. Sheet A: A2A protein levels by IHC in ISO, ISO+ST36, and ISO+caffeine+ST36 groups. Sheet B: PCR-based expression of A2AR and A1R. Sheet C: Serum cytokine levels by ELISA. Sheet D: Ventricular cytokine levels by ELISA.
DOI: 10.5281/zenodo.18194701
title: ST36 acupoint alleviates cardiac fibrosis through A2AR-dependent regulation of microcirculation

description: Supplementary Table 1 included raw data corresponding to Figure 2 and 3, organized into four sheets.  Sheet A: Percentage of cardiac fibrosis in Sham, ISO, ISO+ST36, ISO+PC6, and ISO+SA groups. Sheet B: Heart weight to body weight ratio (HW/BW).  Sheet C: Echocardiographic parameters.  Sheet D: Electrocardiogram (ECG) parameters across groups.

 

Supplementary Table 2 contained raw data corresponding to Figure 4, with two sheets. Sheet A: Parameters from laser speckle contrast imaging in Sham, ISO, and ISO+ST36 groups. Sheet B: Hemodynamic variables.

 

Supplementary Table 3 contained raw data corresponding to Figure 5, with four sheets.

Sheet A: A2A receptor protein levels detected by immunohistochemistry in Sham, ISO, and ISO+ST36 groups. Sheet B: Gene expression of A2AR and A1R by qPCR. Sheet C: Serum cytokine levels measured by ELISA. Sheet D: Ventricular cytokine levels measured by ELISA.

 

Supplementary Table 4 included raw data for Figure 6 and 7, organized into four sheets. Sheet A: Percentage of cardiac fibrosis in ISO, ISO+ST36, ISO+caffeine, and ISO+caffeine+ST36 groups.  Sheet B: HW/BW.  Sheet C: Echocardiographic parameters.  Sheet D: ECG parameters.

 

Supplementary Table 5 contained raw data related to Figure 8, with two sheets. Sheet A: Laser speckle contrast imaging parameters in ISO, ISO+ST36, ISO+caffeine, and ISO+caffeine+ST36 groups. Sheet B: Hemodynamic variables.

 

Supplementary Table 6 included raw data supporting Figure 9, with four sheets. Sheet A: A2A protein levels by IHC in ISO, ISO+ST36, and ISO+caffeine+ST36 groups. Sheet B: PCR-based expression of A2AR and A1R. Sheet C: Serum cytokine levels by ELISA. Sheet D: Ventricular cytokine levels by ELISA.
DOI: 10.5061/dryad.93s3n
title: Data from: Lights out: the evolution of bacterial bioluminescence in Loliginidae

description: Representatives of several metazoan clades engage in symbiotic
 interactions with bioluminescent bacteria, but the evolution and
 maintenance of these interactions remain poorly understood. Uroteuthis is
 a genus of loliginid squid (Cephalopoda: Loliginidae) characterized by
 paired ventral photophores (light organs) housing bioluminescent bacteria.
 While previous phylogenetic studies have suggested that Uroteuthis is
 closely related to Loliolus, a genus of non-bioluminescent species, this
 relationship remains unresolved. To illuminate Uroteuthis and Loliolus
 phylogeny and its implications for the evolution of bioluminescence in
 Loliginidae, we generated sequences from two mitochondrial genes from
 Uroteuthis specimens sampled from several sites in the Indian and western
 Pacific Oceans. We combined these data with data from GenBank, analyzed
 the concatenated data set using maximum likelihood and Bayesian methods,
 and reconstructed the evolution of bacterial bioluminescence on the
 resulting phylogenies. Our analyses support the hypothesis that Uroteuthis
 is paraphyletic with respect to Loliolus. Furthermore, our reconstructions
 suggest that the symbiosis between loliginid squid and bioluminescent
 bacteria evolved once in the ancestor of Loliolini (the clade comprising
 Uroteuthis and Loliolus), but was subsequently lost in the ancestor of
 Loliolus. These findings could have profound implications for our
 understanding of the evolution of symbiotic bioluminescence in squid.
description: Loliolini cox1 + rrnL
 NEXUS file (Mesquite format)Concatenated cytochrome
 c oxidase subunit I (cox1) + large mitochondrial ribosomal RNA subunit
 (rrnL) data set comprising GenBank sequences and sequences collected for
 this study. Mesquite-format NEXUS file, used for phylogeny estimation in
 Garli, RAxML and MrBayes; includes best-known likelihood tree found using
 partitioned ML analysis in Garli.LolioliniCOI16S.nexLoliolini cox1 + rrnL NEXUS file (simplified)Simplified NEXUS file of concatenated cox1/rrnL data for various loliginid squid, including gene boundaries and inferred codon positions for cox1.LolioliniCOI16S.simple.nexLoliolini cox1 + rrnL NEXUS file (reduced for *BEAST analysis)Reduced concatenated cytochrome c oxidase subunit I (cox1) + large mitochondrial ribosomal RNA subunit (rrnL) data file used for *BEAST species-tree analysisLoliolini.speciestree.nexMapping file for *BEAST analyses of Loliolini cox1 + rrnL data set (tab-delimited text)Species-OTU mapping file used in conjunction with the reduced concatenated cox1 + rrnL data file for *BEAST species-tree analysisLoliolini.mapping.txt
DOI: 10.5061/dryad.tp02t
title: Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula

description: Sequence data for &gt;20 000 annotated genes from 56 accessions of
 Medicago truncatula were used to identify potential targets of positive
 selection, the determinants of evolutionary rate variation and the
 relative importance of positive and purifying selection in shaping
 nucleotide diversity. Based upon patterns of intraspecific diversity and
 interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are
 subject to strong purifying selection and 1% of the sampled genes harbour
 a signature of positive selection. Combining polymorphism with expression
 data, we estimated the distribution of fitness effects and found that the
 proportion of deleterious mutations is significantly greater for expressed
 genes than for genes with undetected transcripts (nonexpressed) in a
 previous RNA-seq experiment and greater for broadly expressed genes than
 those expressed in only a single tissue. Expression level is the strongest
 correlate of evolutionary rates at nonsynonymous sites, and despite
 multiple genomic features being significantly correlated with evolutionary
 rates, they explain less than 20% of the variation in nonsynonymous rates
 (dN) and &lt;15% of the variation in either synonymous rates (dS) or
 dN:dS. Among putative targets of selection were genes involved in defence
 against pathogens and herbivores, genes with roles in mediating the
 relationship with rhizobial symbionts and one-third of annotated
 histone-lysine methyltransferases. Adaptive evolution of the
 methyltransferases suggests that positive selection in gene expression may
 have occurred through evolution of enzymes involved in epigenetic
 modification.
description: Coding sequences for
 20,968 putative genes in 56 Medicago truncatula
 accessionsNucleotide data from
 20,968 putative coding sequences (CDS) obtained by sequencing the full
 genomes of 56 Medicago truncatula accessions drawn from a core collection
 sampled from across the species range. The archive contains a separate
 FASTA file for each CDS.Mt56cds.tar.gzSummary statistics fileSummary statistics file for all 20,968 putative coding sequences. The file also includes expression data for six tissue types, namely nodule, blade, flower, root, pod, and bud.MKTest_expression.txt.gz
DOI: 10.5061/dryad.q0158
title: Data from: Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation.

description: Organisms can protect themselves against future environmental change. An
 example is cross-protection, where physiological adaptation against a
 present environmental stressor can protect an organism against a future
 stressor. Another is anticipation, where an organism uses information
 about its present environment to trigger gene expression and other
 physiological changes adaptive in future environments.
 "Predictive" abilities like this exist in organisms that have
 been exposed to periodic changes in environments. It is unknown how
 readily they can evolve. To answer this question, we carried out
 laboratory evolution experiments in the yeast Saccharomyces cerevisiae.
 Specifically, we exposed three replicate populations of yeast to
 environments that varied cyclically between two stressors, salt stress and
 oxidative stress, every 10 generations, for a total of 300 generations. We
 evolved six replicate control populations in only one of these stressors
 for the same amount of time. We analyzed fitness changes and genome-scale
 expression changes in all these evolved populations. Our populations
 evolved asymmetric cross protection, where oxidative stress protects
 against salt stress but not vice versa. Gene expression data also suggest
 the evolution of anticipation and basal gene expression changes that occur
 uniquely in cyclic environments. Our study shows that highly complex
 physiological states that are adaptive in future environments can evolve
 on very short evolutionary time scales.
description: Microarray
 dataCEL files containing
 data collected for yeast experimentsMicroarray_data_submission.zip
DOI: 10.5061/dryad.f0b50
title: Data from: Missing data estimation in morphometrics: how much is too much?

description: Fossil-based estimates of diversity and evolutionary dynamics mainly rely
 on the study of morphological variation. Unfortunately, organism remains
 are often altered by post-mortem taphonomic processes such as weathering
 or distortion. Such a loss of information often prevents quantitative
 multivariate description and statistically controlled comparisons of
 extinct species based on morphometric data. A common way to deal with
 missing data involves imputation methods that directly fill the missing
 cases with model estimates. Over the last several years, several
 empirically determined thresholds for the maximum acceptable proportion of
 missing values have been proposed in the literature, whereas other studies
 showed that this limit actually depends on several properties of the study
 dataset and of the selected imputation method, and is by no way
 generalizable. We evaluate the relative performances of seven multiple
 imputation techniques through a simulation-based analysis under three
 distinct patterns of missing data distribution. Overall, Fully Conditional
 Specification and Expectation-Maximization algorithms provide the best
 compromises between imputation accuracy and coverage probability. Multiple
 imputation (MI) techniques appear remarkably robust to the violation of
 basic assumptions such as the occurrence of taxonomically or anatomically
 biased patterns of missing data distribution, making differences in
 simulation results between the three patterns of missing data distribution
 much smaller than differences between the individual MI techniques. Based
 on these results, rather than proposing a new (set of) threshold value(s),
 we develop an approach combining the use of multiple imputations with
 procrustean superimposition of principal component analysis results, in
 order to directly visualize the effect of individual missing data
 imputation on an ordinated space. We provide an R function for users to
 implement the proposed procedure.
description: Supplementary Material
 S1Supplementary Figures
 S1Supplementary Material
 S2Supplementary Material
 S2. Tutorial to compute multiple imputations and R functions to compute
 averaged imputation and 95% confidence ellipses in ordinated principal
 axes
DOI: 10.5061/dryad.8d8h7
title: Data from: Tracking individuals shows spatial fidelity is a key regulator of ant social organization

description: Ants live in organized societies with a marked division of labor among
 workers, but little is known about how this is generated. We use a
 tracking system to continuously monitor individually-tagged workers in six
 colonies of the ant Camponotus fellah over 41 days. Network analyses of
 over 9 million interactions revealed three distinct groups that differ in
 behavioral repertoires. Each group represents a functional behavioral unit
 with workers moving from one group to the next as they age. The rate of
 interactions was much higher within- than between groups. The precise
 information on spatial and temporal distribution of all individuals
 permitted calculation of the expected rates of within- and between-group
 interactions. These values suggest that the network of interaction within
 colonies is primarily mediated by age-induced changes in the spatial
 location of workers.
description: tracking_dataThis zip files contains data from tracking experiments in the ant Camponotus fellah. There are 268 files (described in the READMD.txt) containing data on the social networks, behavior, spatial structure, expected and observed interaction frequencies, and information spread from all ants in six colonies of Camponotus fellah.