cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2f6m7
title: Data from: Patients with primary biliary cholangitis and fatigue present with depressive symptoms and selected cognitive deficits, but with normal attention performance and brain structure

description: Background: In primary biliary cholangitis (PBC) fatigue is a major
 clinical challenge of unknown etiology. By demonstrating that fatigue in
 PBC is associated with an impaired cognitive performance, previous studies
 have pointed out the possibility of brain abnormalities underlying fatigue
 in PBC. Whether structural brain changes are present in PBC patients with
 fatigue, however, is unclear. To evaluate the role of structural brain
 abnormalities in PBC patients severely affected from fatigue we,
 therefore, performed a case-control cerebral magnetic resonance imaging
 (cMRI) study and correlated changes of white and grey brain matter with
 the cognitive and attention performance. Methods: 20 female patients with
 PBC and 20 female age-matched controls were examined in this study. The
 assessment of fatigue, psychological symptoms, cognitive and attention
 performance included clinical questionnaires, established cognition tests
 and a computerized test battery of attention performance. T1-weighted cMRI
 and diffusion tensor imaging (DTI) scans were acquired with a 3 Tesla
 scanner. Structural brain alterations were investigated with voxel-based
 morphometry (VBM) and DTI analyses. Results were correlated to the
 cognitive and attention performance. Results: Compared to healthy
 controls, PBC patients had significantly higher levels of fatigue and
 associated psychological symptoms. Except for an impairment of verbal
 fluency, no cognitive or attention deficits were found in the PBC cohort.
 The VBM and DTI analyses revealed neither major structural brain
 abnormalities in the PBC cohort nor correlations with the cognitive and
 attention performance. Conclusions: Despite the high burden of fatigue and
 selected cognitive deficits, the attention performance of PBC patients
 appears to be comparable to healthy people. As structural brain
 alterations do not seem to be present in PBC patients with fatigue,
 fatigue in PBC must be regarded as purely functional. Future studies
 should evaluate, whether functional brain changes underlie fatigue in PBC.
description: Neurophysiological and
 MRI data 1The files contain
 neurophysiological and MRI (T2 weighted MRI, Diffusion Tensor Imaging)
 data from 20 patients with primary biliary cholangitis and 20
 controls.Neurophysiological and
 MRI data 2The files contain
 neurophysiological and MRI (T2 weighted MRI, Diffusion Tensor Imaging)
 data from 20 patients with primary biliary cholangitis and 20
 controls.Neurophysiological and
 MRI data 3The files contain
 neurophysiological and MRI (T2 weighted MRI, Diffusion Tensor Imaging)
 data from 20 patients with primary biliary cholangitis and 20
 controls.Neurophysiological and
 MRI data 4The files contain
 neurophysiological and MRI (T2 weighted MRI, Diffusion Tensor Imaging)
 data from 20 patients with primary biliary cholangitis and 20
 controls.
DOI: 10.21227/kx3c-1043
title: "Survey Dataset on Students\u2019 Social Media Usage, Addiction Severity, Sleep, Mental Well-Being, and Academic Impact"

description: "nn"
DOI: 10.5061/dryad.q2610
title: Data from: Intercolony movement of pre-breeding seabirds over oceanic scales: implications of cryptic age-classes for conservation and metapopulation dynamics

description: Aim: Demographic linkage between subpopulations plays a critical role in
 population processes. Metapopulation dynamics, however, remains one of the
 most poorly understood aspects of population biology. This is especially
 true for small, pelagic seabirds because their discrete subpopulations are
 located on offshore islands, separated by vast areas of open ocean, making
 monitoring logistically challenging. Seabird populations often contain
 large numbers of immature pre-breeders that may be important for
 subpopulation connectivity and demography, but are poorly studied. Here we
 provide evidence for intercolony movement of pre-breeding Leach's
 storm-petrels Oceanodroma leucorhoa among three colonies spanning the
 North Atlantic Ocean. We discuss their influence on metapopulation
 dynamics and the extinction risk of a subpopulation under threat from
 extreme predation. Location: North Atlantic Ocean Islands (Scotland,
 Canada & Iceland). Methods: We use a novel application of Bayesian
 stable isotope mixing models to infer recent movement of pre-breeding
 birds between three major breeding populations in the North Atlantic.
 Carbon and nitrogen stable isotope values from breeding birds (central
 place foragers) sampled at each colony were used as model sources and
 pre-breeding birds as model mixtures. Results: Of 134 pre-breeding
 Leach's storm-petrels sampled at three colonies across the North
 Atlantic, five had isotope mixing model estimates dissimilar (&lt;
 25%) to their colony of capture and were instead isotopically similar to
 another breeding region. Nineteen further pre-breeders had highly mixed
 signatures (&lt; 50% for the colony of capture), indicating possible
 recent movement between colonies. Main conclusions: Our findings provide
 evidence for interpopulation connectivity of pre-breeding Leach's
 storm-petrels among colonies spanning the North Atlantic. These results
 highlight the significance of cryptic young age-classes in metapopulation
 dynamics and the demographic processes. Moreover, they provide us with a
 better understanding of how one subpopulation remains extant, despite
 experiencing extreme predation rates.
description: Bicknell et al -
 Inter-colony movement of pre-breeding seabirds - Supplementary
 DataRaw stable isotope
 values of Leach's storm-petrel blood samples and calanus copepod CPR
 samples. Mixing model parameters for the original and sensitivity models
 with results of models comparison.Random sampling process and
 calculations.
DOI: 10.5061/dryad.nc0gc
title: Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies

description: Background: The brood of ants and other social insects is highly
 susceptible to pathogens, particularly those that penetrate the soft
 larval and pupal cuticle. We here test whether the presence of a pupal
 cocoon, which occurs in some ant species but not in others, affects the
 sanitary brood care and fungal infection patterns after exposure to the
 entomopathogenic fungus Metarhizium brunneum. We use a) a comparative
 approach analysing four species with either naked or cocooned pupae and b)
 a within-species analysis of a single ant species, in which both pupal
 types co-exist in the same colony. Results: We found that the presence of
 a cocoon did not compromise fungal pathogen detection by the ants and that
 species with cocooned pupae increased brood grooming after pathogen
 exposure. All tested ant species further removed brood from their nests,
 which was predominantly expressed towards larvae and naked pupae treated
 with the live fungal pathogen. In contrast, cocooned pupae exposed to live
 fungus were not removed at higher rates than cocooned pupae exposed to
 dead fungus or a sham control. Consistent with this, exposure to the live
 fungus caused high numbers of infections and fungal outgrowth in larvae
 and naked pupae, but not in cocooned pupae. Moreover, the ants
 consistently removed the brood prior to fungal outgrowth, ensuring a clean
 brood chamber. Conclusion: Our study suggests that the pupal cocoon has a
 protective effect against fungal infection, causing an adaptive change in
 sanitary behaviours by the ants. It further demonstrates that brood
 removal - originally described for honeybees as “hygienic behaviour” – is
 a widespread sanitary behaviour in ants, which likely has important
 implications on disease dynamics in social insect colonies.
description: TRAGUST_Correlation-Removal-FungalOutgrowth_dataTRAGUST_Daily-Brood-intake_dataTRAGUST_Daily-Brood-removal_dataTRAGUST_GroomingFrequency_dataTRAGUST_NrBrood_Presentation_Intake_Removal_FungalOutgrowth_data
DOI: 10.15468/dl.gmxudk
title: Occurrence Download

description: A dataset containing 7464 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rostellularia adscendens",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 7464 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000459-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gx4e8b
title: Occurrence Download

description: A dataset containing 2788 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Holbrookia elegans"
 ]
}

 The dataset includes 2788 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000458-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2018h
title: Data from: Rapid evolution of cheating mitochondrial genomes in small yeast populations

description: Outcrossed sex exposes genes to competition with their homologues,
 allowing alleles that transmit more often than their competitors to spread
 despite organismal fitness costs. Mitochondrial populations in species
 with biparental inheritance are thought to be especially susceptible to
 such cheaters because they lack strict transmission rules like meiosis or
 maternal inheritance. Yet the interaction between mutation and natural
 selection in the evolution of cheating mitochondrial genomes has not been
 tested experimentally. Using yeast experimental populations, we show that
 although cheaters were rare in a large sample of spontaneous
 respiratory-deficient mitochondrial mutations (petites), cheaters evolve
 under experimentally enforced outcrossing even when mutation supply and
 selection are restricted by repeatedly bottlenecking populations.
description: Counts of petite and
 grande colonies for spontaneous and evolved petites.Three spreadsheets are
 included: "spontaneous" gives the counts of petite and grande
 colonies for spontaneous petite mutants; "spont.posteriors"
 gives the MCMC estimates for the spontaneous mutants; "evolved"
 gives the counts of petite and grande colonies for the three ancestors (X,
 Y, and Z) selected at each of five effective population sizes (1, 3, 10,
 32, 100). The mip1-deleted control is also included on the
 "evolved" and "spontaneous"
 spreadsheets.Jasmin_Zeyl_Evolution_petites_data.xlsx
DOI: 10.5061/dryad.8k0d8
title: Data from: Genetic architecture of sensory exploitation: QTL mapping of female and male receiver traits in an acoustic moth

description: The evolution of extravagant sexual traits by sensory exploitation occurs
 if males incidentally evolve features that stimulate females owing to a
 pre-existing environmental response that arose in the context of natural
 selection. The sensory exploitation process is thus expected to leave a
 specific genetic imprint, a pleiotropic control of the original
 environmental response and the novel sexual response in females. However,
 females may be subsequently selected to improve their discrimination of
 environmental and sexual stimuli. Accordingly, responses may have diverged
 and the original genetic architecture may have been modified. These
 possibilities may be considered by studying the genetic architecture of
 responses to male signals and to the environmental stimuli that were
 purportedly ‘exploited’ by those signals. However, no previous study has
 addressed the genetic control of sensory exploitation. We investigated
 this question in an acoustic pyralid moth, Achroia grisella, in which a
 male ultrasonic song attracts females and perception of ultrasound likely
 arose in the context of detecting predatory bats. We examined the genetic
 architecture of female response to bat echolocation signals and to male
 song via a cartographic study of quantitative trait loci (QTL) influencing
 these receiver traits. We found several QTL for both traits, but none of
 them were colocalized on the same chromosomes. These results indicate that
 – to the extent to which male A. grisella song originated by the process
 of sensory exploitation – some modification of the female responses
 occurred since the origin of the male signal.
description: Achroia_phenotypes_femalesPhenotypes measured in Achroia grisella females. Data used for the QTL analysis.Achroia_phenotypes_malesPhenotypes measured in Achroia grisella males. Data used for the QTL analysis.Achroia_genotypes_femalesGenotypes of Achroia grisella females. 0 / 1 = absence / presence of AFLP markers. Data used for the QTL analysis.Achroia_genotypes_malesGenotypes of Achroia grisella males. 0 / 1 = absence / presence of AFLP markers. Data used for the QTL analysis.
DOI: 10.5061/dryad.kt71r
title: Data from: Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation

description: Understanding the effects of landscape heterogeneity on spatial genetic
 variation is a primary goal of landscape genetics. Ecological and
 geographic variables can contribute to genetic structure through
 geographic isolation, in which geographic barriers and distances restrict
 gene flow, and ecological isolation, in which gene flow among populations
 inhabiting different environments is limited by selection against
 dispersers moving between them. Although methods have been developed to
 study geographic isolation in detail, ecological isolation has received
 much less attention, partly because disentangling the effects of these
 mechanisms is inherently difficult. Here, I describe a novel approach for
 quantifying the effects of geographic and ecological isolation using
 multiple matrix regression with randomization. I explored the parameter
 space over which this method is effective using a series of
 individual-based simulations and found that it accurately describes the
 effects of geographic and ecological isolation over a wide range of
 conditions. I also applied this method to a set of real-world datasets to
 show that ecological isolation is an often overlooked but important
 contributor to patterns of spatial genetic variation and to demonstrate
 how this analysis can provide new insights into how landscapes contribute
 to the evolution of genetic variation in nature.
description: MMRR function R
 scriptR script for
 'MMRR' function that performs Multiple Matrix Regression with
 Randomization analysis.MMRR.RBcanorus_GeneticDistanceMatrixBufo canorus genetic distance matrix. Pairwise FST values for B. canorus populations, part of an example dataset for MMRR analysis.Bcanorus_GeographicDistanceMatrixBufo canorus geographic distance matrix. Pairwise geographic distances for B. canorus populations (standardized), part of an example dataset for MMRR analysis.Bcanorus_EnvironmentalDistanceMatrixBufo canorus environmental distance matrix. Pairwise environmental distances for B. canorus populations (standardized), part of an example dataset for MMRR analysis.
DOI: 10.5061/dryad.77077
title: Data from: Integrative testing of how environments from the past to the present shape genetic structure across landscapes

description: Tests of the genetic structure of empirical populations typically focus on
 the correlative relationships between population connectivity and
 geographic and/or environmental factors in landscape genetics. However,
 such tests may overlook or misidentify the impact of such factors on
 genetic structure, especially when connectivity patterns differ between
 past and present populations because of shifting environmental conditions
 over time. Here we account for the underlying demographic component of
 population connectivity associated with a temporarily dynamic landscape in
 tests of the factors structuring population genetic variation in an
 Australian lizard, Lerista lineopunctulata, from 24 nuclear loci.
 Correlative tests didn't support significant effect from factors
 associated with a static contemporary landscape. However, spatially
 explicit demographic modeling of genetic differentiation shows that
 changes in environmental conditions (as estimated from paleoclimatic data)
 and corresponding distributional shifts from the past to present landscape
 significantly structures genetic variation. Results from model-based
 inference (i.e., from an integrative modeling approach that generates
 spatially explicit expectations that are tested with Approximate Bayesian
 Computation) contrasts with those from correlative analyses, highlighting
 the importance of expanding the landscape genetic perspective to tests the
 links between pattern and process, revealing how factors shape patterns of
 genetic variation within species.
description: current_vegasc file that describes suitability of each deme based on ecological niche modeling of current climate condition using MaxEnt. Original suitability score (0-1) was classified into 20 bins (0-20) with equal intervals, which inform differences in carrying capacities of each deme.current_class.asc21k_vegasc file that describes suitability of each deme based on ecological niche modeling of the climate condition in Last Glacial Maximum (LGM) using MaxEnt. Original suitability score (0-1) was classified into 20 bins (0-20) with equal intervals, which inform differences in carrying capacities of each deme.21k_class.ascABCsimulationEstimates of demographic/genetic parameters under three scenarios: ibd, cENM, dENM (see manuscript for description). 5000 closest simulations were retained in each scenario after 1 million runs. Logarithmic values of carrying capacities, migration rate, ancestral population size, and mutation rates were estimated from 6 PLSs (see the manuscript for description of PLS) converted from original 34 summary statistics.Focal_node_IBRRegions (focal node locations) defined for isolation by resistance analyses in circuitscape. Regions were defined according to the population definition in Figure 1. Each region consists of the minimum number of demes that contains sampling locations.ll_contemp.asc
DOI: 10.5061/dryad.4n9b4
title: Data from: Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.

description: It is becoming increasingly evident that adoption of different
 reproductive strategies, such as sexual selfing and asexuality, greatly
 impacts genome evolution. In this study, we test theoretical predictions
 on genomic maladaptation of selfing lineages using empirical data from the
 model fungus Neurospora. We sequenced the genomes of four species
 representing distinct transitions to selfing within the history of the
 genus, as well as the transcriptome of one of these, and compared with
 available data from three outcrossing species. Our results provide
 evidence for a relaxation of purifying selection in protein-coding genes
 and for a reduced efficiency of transposable element silencing by Repeat
 Induced Point mutation. A reduction in adaptive evolution was also
 identified in the form of reduced codon usage bias in highly expressed
 genes of selfing Neurospora, but this result may be confounded by
 mutational bias. Potentially counteracting these negative effects, the
 nucleotide substitution rate and the spread of transposons is reduced in
 selfing species. We suggest that differences in substitution rate relate
 to the absence of the asexual pathway producing conidia in selfing
 Neurospora. Our results support the dead-end theory and show that
 Neurospora genomes bear signatures of both sexual and asexual reproductive
 mode.
description: 2789_alignments.tar2789 multiple sequence alignment of protein-coding genes from 7 Neurospora species
DOI: 10.5061/dryad.1127
title: Data from: The genetics of phenotypic plasticity in plant defense: trichome production in Mimulus guttatus

description: Insect herbivory is a major driving force of plant evolution. Phenotypic
 plasticity and developmental variation provide a means for plants to cope
 with variable herbivory. We characterized the genetics of developmental
 variation and phenotypic plasticity in trichome density, a putative
 defensive trait of Mimulus guttatus (yellow monkeyflower). Our results are
 evaluated in relation to the optimal defense theory, which provides
 testable predictions for plastic and developmental patterns in defense
 traits. We found that both developmental stage and simulated insect damage
 affected trichome production, but in different ways. Plants were more
 likely to produce at least some trichomes on later leaves than on earlier
 leaves, regardless of damage. Damage did not affect the average
 probability of producing trichomes, but it did increase the density of
 hairs on trichome‐positive plants. We mapped trichome quantitative trait
 loci (QTL) by selectively genotyping a large panel of recombinant inbred
 lines derived from two highly divergent populations. Several highly
 pleiotropic QTL influenced multiple aspects of the trichome phenotype
 (constitutive, developmental, and/or plastic responses). Only one of the
 QTL influenced trichome induction following damage. In a result that is
 consistent with a central prediction of optimal defense theory, the high
 allele at this location was from the ancestral population with low
 constitutive trichome production.
description: RIL.Trait values and
 sample size data.docMean phenotypes and
 sample sizes for each RIL included in the QTL study.
DOI: 10.5061/dryad.9sk7h
title: Data from: Sexual imprinting: What strategies should we expect to see in nature?

description: Sexual imprinting occurs when juveniles learn mate preferences by
 observing the phenotypes of other members of their populations, and it is
 ubiquitous in nature. Imprinting strategies, that is which individuals and
 phenotypes are observed and how strong preferences become, vary among
 species. Imprinting can affect trait evolution and the probability of
 speciation, and different imprinting strategies are expected to have
 different effects. However, little is known about how and why different
 imprinting strategies evolve, or which strategies we should expect to see
 in nature. We used a mathematical model to study how the evolution of
 sexual imprinting depends on 1) imprinting costs and 2) the sex-specific
 fitness effects of the phenotype on which individuals imprint. We found
 that even small fixed costs prevent the evolution of sexual imprinting,
 but small relative costs do not. When imprinting does evolve, we
 identified the conditions under which females should evolve to imprint on
 their fathers, their mothers, or on other members of their populations.
 Our results provide testable hypotheses for empirical work and help to
 explain the conditions under which sexual imprinting might evolve to
 promote speciation.
description: Chaffee et al
 codesThis zip file contains
 the MATLAB code for the models used to generate the results in Chaffee et
 al. (2013, Evolution). The folder includes a readme file describing the
 individual .m files.