cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5x69p8d87
title: Scripts and sample information for: Molecular mechanisms of Eda-mediated adaptation to freshwater in threespine stickleback

description: A main goal of evolutionary biology is to understand the genetic basis of
 adaptive evolution. Although the genes that underlie some adaptive
 phenotypes are now known, the molecular pathways and regulatory mechanisms
 mediating the phenotypic effects of those genes often remain a black box.
 Unveiling this black box is necessary to fully understand the genetic
 basis of adaptive phenotypes, and to understand why particular genes might
 be used during phenotypic evolution. Here, we investigated which genes and
 regulatory mechanisms are mediating the phenotypic effects of the Eda
 haplotype, a locus responsible for the loss of lateral plates and changes
 in the sensory lateral line of freshwater threespine stickleback
 (Gasterosteus aculeatus) populations. Using a combination of RNAseq and a
 cross design that isolated the Eda haplotype on a fixed genomic
 background, we found that the Eda haplotype affects both gene expression
 and alternative splicing of genes related to bone development, neuronal
 development and immunity. These include genes in conserved pathways, like
 the BMP, netrin and bradykinin signalling pathways, known to play a role
 in these biological processes. Furthermore, we found that differentially
 expressed and differentially spliced genes had different levels of
 connectivity and expression, suggesting that these factors might influence
 which regulatory mechanisms are used during phenotypic evolution. Taken
 together, these results provide a better understanding of the mechanisms
 mediating the effects of an important adaptive locus in stickleback and
 suggest that alternative splicing could be an important regulatory
 mechanism mediating adaptive phenotypes.
DOI: 10.5061/dryad.rv15dv4cr
title: Input files for targeted MD and umbrella sampling of cardiac thin filament

description: The cardiac thin filament is comprised of F-actin, tropomyosin, and
 troponin (cTn). cTn is composed of three subunits: troponin C (cTnC),
 troponin I (cTnI), and troponin T (cTnT). To computationally study the
 effect of the thin filament on cTn activation events, we employed targeted
 molecular dynamics followed by umbrella sampling using a model of the thin
 filament to measure the thermodynamics of cTn transition events. Our
 simulations revealed that the thin filament causes an increase in the free
 energy required to open the cTnC hydrophobic patch and causes a more
 favorable interaction between this region and the cTnI switch peptide.
 Mutations to the cTn complex can lead to cardiomyopathy, a collection of
 diseases that present clinically with symptoms of hypertrophy or dilation
 of the cardiac muscle, leading to impairment of the heart’s ability to
 function normally, and ultimately myocardial infarction or heart failure.
 Upon introduction of cardiomyopathic mutations to R145 of cTnI, we
 observed a general decrease in the free energy of opening the cTnC
 hydrophobic patch, which is on par with previous experimental results.
 These mutations also exhibited a decrease in electrostatic interactions
 between cTnI-R145 and actin-E334. After introduction of a small molecule
 to the wild-type cTnI-actin interface to intentionally disrupt
 intersubunit contacts, we successfully observed similar thermodynamic
 consequences and disruptions to the same protein-protein contacts as
 observed with the cardiomyopathic mutations. Computational studies
 utilizing the cTn complex in isolation would have been unable to observe
 these effects, highlighting the importance of using a more physiologically
 relevant thin filament model to investigate the global consequences of
 cardiomyopathic mutations to the cTn complex. 
description: The data being submitted are just starting files to run all
 targeted molecular dynamics and umbrella sampling simulations of the
 cardiac thin filament. Files were created manually by the submitting
 author.
description: .DCD and .PSF files should be opened by a software that can read
 the data (PyMOL, Chimera, Maestro, etc). All other files can be opened in
 a text editor.
DOI: 10.5061/dryad.v9s4mw71r
title: Data for: Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird

description: Animal hosts can adapt to emerging infectious disease through both disease
 resistance, which decreases pathogen numbers, and disease tolerance, which
 limits damage during infection without limiting pathogen replication. Both
 resistance and tolerance mechanisms can drive pathogen transmission
 dynamics. However, it is not well understood how quickly host tolerance
 evolves in response to novel pathogens or what physiological mechanisms
 underlie this defense. Using natural populations of house finches
 (Haemorhous mexicanus) across the temporal invasion gradient of a recently
 emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid
 evolution of tolerance (&lt;25 years). In particular, populations with
 a longer history of MG endemism have less pathology but similar pathogen
 loads compared with populations with a shorter history of MG endemism.
 Further, gene expression data reveal that more targeted immune responses
 early in infection are associated with tolerance. These results suggest an
 important role for tolerance in host adaptation to emerging infectious
 diseases, a phenomenon with broad implications for pathogen spread and
 evolution.
DOI: 10.5061/dryad.8w9ghx3rz
title: Data from: Serum metabolomics predicts treatment response in myasthenia gravis

description: High-dose prednisone is the primary initial therapy for myasthenia gravis
 (MG) but upwards of a third of patients do not respond to treatment. No
 biomarkers can predict clinical responsiveness to corticosteroid
 treatment. We conducted a discovery-based study to identify treatment
 responsive biomarkers in MG using sera obtained at study entry to the
 thymectomy clinical trial (MGTX), an NIH-sponsored randomized, controlled
 study of thymectomy plus prednisone versus prednisone alone. We
 applied ultra-performance liquid chromatography coupled with electro-spray
 quadrupole time of flight mass spectrometry to obtain comparative serum
 metabolomic and lipidomic profiles at study entry to correlate with
 treatment response at 6 months. Treatment response was assessed using
 validated outcome measures of minimal manifestation status (MMS),
 MG-Activities of Daily Living (MG-ADL), Quantitative MG (QMG) score, or a
 strictly defined composite measure of response. Increased levels of
 phospholipids were associated with treatment response as assessed by QMG,
 MMS, and the Responders classification, but all measures showed limited
 overlap in metabolomic profiles, in particular the MG-ADL. A panel
 including histidine, free fatty acid (13:0), γ-cholestenol and guanosine
 was highly predictive of the strictly defined treatment response measure.
 The AUC in Responders' prediction for these markers was 0.90. Pathway
 analysis suggests that xenobiotic metabolism could play a major role in
 treatment resistance. We have defined a metabolomic and lipidomic profile
 that can now undergo validation as treatment predictive markers for MG
 patients undergoing corticosteroid therapy. Distinct metabolomic profiles
 were appreciated for each outcome measure.
description: Serum samples from clinical trial. See manuscript for
 details.
DOI: 10.5061/dryad.2ngf1vhtq
title: Data for: A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria

description: Restorer-of-fertility (Rf) genes have practical applications in hybrid
 seed production as a means to control self-pollination. They encode
 pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria
 where they specifically bind to transcripts that induce cytoplasmic male
 sterility and repress their expression. We have identified a unique
 domain, RfCTD (Restorer-of-fertility C-terminal domain), which
 discriminates Restorer-of-fertility-like (RFL) proteins
 from hundreds of PPR proteins encoded in plant genomes. Using the sequence
 of this domain from hundreds of plant species, we have constructed a
 sequence profile that can quickly and accurately identify RfCTD sequences
 in plant genomes or transcriptomes.  This data set contains PPR
 genes identified in 213 plant genomes (as summarised in accompanying
 table). 
description: The PPR genes were identified in the genome sequences using the
 PPRfinder approach (Cheng <em>et al</em>., 2016, Plant J.
 85:532-47. doi: 10.1111/tpj.13121). Briefly, the genomic sequences were screened for open
 reading frames (ORFs) in six-frame translations with the getorf program of
 the EMBOSS 6.6.0 package (Rice <em>et
 al</em>., 2000, Trends Genet. 16:276-7. doi:
 10.1016/s0168-9525(00)02024-2). Predicted ORFs were screened for
 the presence of P- and PLS-class PPR motifs using hmmsearch from the HMMER
 3.2.1 package (Eddy 2011, PLoS Comput Biol. 7:e1002195. doi:
 10.1371/journal.pcbi.1002195) (http://hmmer.org) and hidden Markov models
 defined by hmmbuild (Cheng et al.,
 2016, Plant J. 85:532-47. doi:
 10.1111/tpj.13121).
 <em>Hmmbuild </em>was used to create the RfCTD
 profile from an alignment of 1,486 non-redundant sequences. The RfCTD
 profile was incorporated into PPRfinder code (Cheng
 <em>et al</em>., 2016, Plant J. 85:532-47. doi:
 10.1111/tpj.13121) and the screen of the genome
 sequences was repeated. Final filtering parameters of hmmsearch score
 &gt;= 50, no overlapping with a PPR motif with a higher score and the
 RfCTD being the last motif in the protein were used to qualify a protein
 as containing RfCTD.
description: The data files are simple fasta files or text files that can be
 opened in any text editor.
DOI: 10.5061/dryad.fj6q5740k
title: Data for: Chronic stress hinders sensory axon regeneration via impairing mitochondrial cristae and OXPHOS

description: Spinal cord injury (SCI) often leads to physical limitations, chronic
 pain, significant life changes, and social isolation, increasing the risk
 of chronic psychological stress such as anxiety and depression. Despite
 the recognition of the negative effects of chronic stress on SCI recovery,
 the mechanisms linking stress and regeneration are not fully understood.
 In this study, we examined the impact of chronic stress on primary sensory
 axon regeneration in a mouse model of preconditioning lesions. Our
 findings showed that chronic stress caused mitochondrial damage and energy
 crisis within primary sensory neurons, hindering the regrowth of their
 central axons. The stress hormone corticosterone was identified as a
 critical factor in this process, impacting satellite glial cells instead
 of neurons by suppressing Kir4.1 expression and leading to increased
 neuronal hyperactivity and elevated ROS levels. These high levels of ROS
 altered the shape of the mitochondrial cristae and disrupted ATP
 production, which is essential for powering axonal regeneration. Our
 results highlight the importance of addressing psychological stress in SCI
 patients to promote sensory-motor rehabilitation.
description: To
 investigate how psychological stress influences axon regeneration, we
 employed a combination of the preconditioning spinal cord injury model and
 the unpredictable chronic mild stress model. Our experimental design
 comprised two mouse models: Pre-SCI and
 Pre-SCI+stress.  In these models, we conducted transcriptomic
 analyses on the lumbar 4-6 ganglions (L4-L6) dorsal root ganglia (DRGs) at
 two distinct post-injury time points, specifically 1-week post-injury (1
 wpi) and 3 weeks post-injury (3 wpi), utilizing
 RNA-sequencing. For the
 Pre-SCI_1w and Pre-SCI+stress_1w groups, DRGs were collected immediately
 after spinal cord injury, which occurred one week after peripheral nerve
 lesions. The only distinction between these two groups was the additional
 1-week stress exposure given to the Pre-SCI+stress_1w group.Similarly, for
 the Pre-SCI_3w and Pre-SCI+stress_3w groups, DRGs were collected two weeks
 post-spinal cord injury, which equates to three weeks after peripheral
 nerve lesions. The Pre-SCI+stress_3w group, however, also underwent a
 3-week stress exposure.
DOI: 10.5061/dryad.9p8cz8wmz
title: Data from: High species diversity of Phintella and Phintella-like spiders (Araneae: Salticidae) in Vietnam revealed by DNA-based species delimitation analyses

description: Salticidae (jumping spiders) usually exhibit pronounced sexual dimorphism
 in adult morphology, particularly body coloration and size and shape of
 the first legs. Consequently, the male and female from the same species
 might be erroneously assigned to different species or even different
 genera, which could generate synonymies in classification if only
 morphological data were used. Phintella is a species-rich genus of
 Salticidae, which currently exhibits 76 named species. However, the
 male–female counterpart is unknown for nearly half of the species. In this
 study, we used a molecular approach to delineate the species boundaries
 for Phintella and Phintella-like specimens collected in Vietnam, using
 morphological information as supporting data. We used three gene fragments
 (mitochondrial COI, 16S-ND1, and nuclear 28S) and biogeographical
 consideration for species delimitation. A total of 22 putative species
 were recognized: 18 species of the genus Phintella, one species of the
 genus Lechia (L. squamata), and three species of the genus Phinteloides.
 Eleven undescribed species were discovered, of which seven have a
 male–female combination, two species have only males, and two species have
 only females. The crown age of Phintella was estimated at the Serravallian
 stage of the Miocene after the increase of species number around 16 MYA.
 The crown ages of most putative species recognized in this study were
 estimated in Pleistocene, and the divergence among sister species likely
 occurred from the mid-Miocene to the Pliocene. Our ancestral range
 reconstruction results showed that the diversification of our ingroup was
 governed by progressive dispersal events, i.e., Phintella and their
 related species in Vietnam diversified while expanding their range on the
 continent. Our results provide fundamental biodiversity data for a
 high-diversity genus in Vietnamese Phintella spiders.
description: # Title of Dataset: --- High species diversity of *Phintella* and
 *Phintella*-like spiders (Araneae: Salticidae) in Vietnam revealed by
 DNA-based species delimitation analyses. ## Description of the Data and
 file structure beast_tree.nex: A final maximum credibility tree, it is
 generated by TreeAnnotator 1.10.4 from beast output. alignments.nex: The
 concatenation of alignments of three genes used in beast: COI, 16S and
 28S. ## Sharing/access Information Links to other publicly accessible
 locations of the data: Genbank accessions: LC105655-LC105663,
 LC105665-LC105672, OP178652-OP178891, OP204510-OP204520 and
 OP204522-OP204618
DOI: 10.5061/dryad.ghx3ffbtf
title: Data from: Single target acuity for moving targets in the common sunfish (Lepomis gibbosus)

description: The common sunfish (Lepomis gibbosus) likely relies on vision for many
 vital behaviors that require the perception of small objects such as
 detection of prey items or body marks of conspecifics. A previous study
 documented the single target acuity (STA) for stationary targets. Under
 many, if not most, circumstances, however, objects of interest are moving
 which is why the current study tested the effect of the ecologically
 relevant parameter motion on sunfish STA. The STA was determined in two
 sunfish for targets moving randomly at a velocity of 3.4 deg/s. The STA
 for moving targets (0.144±0.002 deg) was equal to the STA for stationary
 targets obtained from the same fish individuals under the experimental
 conditions of this/the previous study. Our results contribute to a
 comprehensive understanding of fish vision, extending the large data set
 available on grating acuity.
description: # Single target acuity for moving targets in the common sunfish (*Lepomis
 gibbosus*)
 [https://doi.org/10.5061/dryad.ghx3ffbtf](https://doi.org/10.5061/dryad.ghx3ffbtf) The data set contains excel files with the raw data, session performances and threshold calculations of the two sunfishes. ## Description of the data and file structure File "raw_data" contains all the raw data from Hannah and Lina. The data are collected in pixels (px) and converted to degrees (deg) Included are also the psychometric functions of correct choices as a functions of visual angle to the target. Each data point represents the performance of the sunfish averaged over 36 presentations of the respective target. From the psychometric function, the STA threshold was determined as the 75% threshold by linear interpolation of the last suprathreshold value and the first subthreshold value.  File "session_performances" shows the correct choices in % of fish Hannah and Lina over time in the different stages. File "thresholds" shows how we calucalted the thresholds of fish Hanna and Lina from the linear regressions found in file "raw_data"
DOI: 10.5061/dryad.0p2ngf25m
title: Plant litter chemistry drives long-lasting changes in the catabolic capacities of soil microbial communities

description: Although microbial communities play an important role in explaining plant
 litter decomposition rates, whether and how litter chemistry may alter
 catabolic capacities of soil microbial communities remains poorly studied.
 During a one-year litter decomposition experiment of twelve herbaceous
 species with contrasting litter chemistry, we examined the effect of plant
 litter type (roots vs leaves) and litter chemical traits on the resulting
 capacity of soil microbial communities to degrade a wide range of carbon
 substrates of variable complexity (MicroRespTM method). Litter chemistry
 impacted both the total catabolic activity as well as specific catabolic
 capacities of microbial communities. In early stages of litter
 decomposition total catabolic activity was mainly influenced by the amount
 of C and N in litter leachates, and litter N, P and Mg, then, later, by
 lignin concentrations. Some specific catabolic capacities could also be
 related to litter initial chemistry. Overall, litter trait effects on soil
 microbial communities decreased over time and the relative importance of
 traits shifted during the decomposition process. Our results highlight
 that litter chemistry is a strong driver of catabolic capacities of
 microbial decomposers and, whilst its effect fades with time, it remains
 substantial throughout the litter decomposition process. These
 long-lasting effects of litter chemistry suggest a persistent control on
 microbial catabolic capacities in ecosystems with recurrent litter
 production. Soil microbial catabolic activities were driven by broadly the
 same chemical traits across leaf and root litters. Synthesis. Such
 long-lasting effects of litter chemistry on catabolic capacities of
 microbial communities may represent a substantial indirect driver of the
 decomposition process. Disentangling the relative importance of this
 overlooked effect of litter chemistry on decomposition represents the next
 challenge. We argue that such research line should open ground-breaking
 perspectives for reconsidering our current understanding of the
 mechanistic links between litter traits and decomposition rate.
DOI: 10.5061/dryad.t1g1jwt70
title: Experimental feeding validates nanofluidic array technology for DNA detection of ungulate prey in wolf scats

description: The study of carnivores' diet is a key component to enhance knowledge
 on the ecology of predators and their effect on prey populations. Although
 molecular approaches to detect prey DNA in carnivore scats are improving,
 the validation of their accuracy, a prerequisite for reliable applications
 within ecological frameworks, is still lagging behind the methodological
 advances. Indeed, variation in detection probability among prey species
 can occur, representing a potentially insidious source of bias in
 food-habit studies of carnivores. Calibration of DNA-based methods
 involves the optimization of specificity and sensitivity and, whereas
 priority is usually given to the former to avoid false positives,
 sensitivity is rarely investigated so that false negatives may be largely
 overlooked. We conducted feeding trials with captive wolves (Canis lupus)
 to validate a nanofluidic array technology recently developed for
 detection of multiple prey species in scats. Using 371 scat samples from
 12 wolves fed with a single-prey diet, the sensitivity of our nanofluidic
 array method varied between 0.45 and 0.95 for the six main ungulate prey
 species. The method sensitivity was enhanced by using multiple markers per
 species and by a relatively low threshold for the number of amplifying
 markers required to confirm a detection. Yet, at least two markers should
 be used to avoid false positives. By acknowledging sources of bias in
 sensitivity to reliably interpret results of DNA-based dietary methods,
 our study highlights the relevance of feeding experiments to optimally
 calibrate the relative thresholds to define a positive detection and
 investigate occurrence and extent of biases in sensitivity.
DOI: 10.5061/dryad.s7h44j1bz
title: Genetic diversity and sperm characteristics are not associated in two bluethroat (Luscinia svecica) populations

description: Individual heterozygosity may influence the expression of fitness-related
 traits, via genome-wide or local genetic effects. Earlier studies have
 shown negative relationships between heterozygosity and sperm variation,
 predominantly in captive, highly inbred populations. Little is known about
 the possible influence of variation in heterozygosity on sperm traits in
 wild, outbred populations. We studied two populations of the bluethroat,
 one from the widely distributed northern subspecies (Luscinia. s. svecica)
 and the other from the smaller, more patchily distributed subspecies
 breeding along the French coast of Brittany (L. s. namnetum). The two
 subspecies differed significantly in body size, plumage colour, sperm
 traits and the degree of genetic diversity. However, there was no evidence
 that sperm traits (total length and motility) were influenced by the
 degree of heterozygosity at the individual level. In contrast, we found
 that male body size was positively related to heterozygosity across both
 populations, indicating a possible relationship between overall genetic
 diversity and general vigour or ability to obtain food. We conclude that
 sperm traits are unrelated to levels of heterozygosity in the studied
 outbred and weakly genetically depauperate bluethroat populations.
description: Blood and sperm samples and morphology collected from free-living
 individuals, using mist nets. Samples processed in DNA lab and through
 light microscopy.
description: R v4.2.2.