cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63th8
title: Data from: Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications

description: Although whole-genome sequencing is becoming more accessible and feasible
 for nonmodel organisms, microsatellites have remained the markers of
 choice for various population and conservation genetic studies. However,
 the criteria for choosing microsatellites are still controversial due to
 ascertainment bias that may be introduced into the genetic inference. An
 empirical study of red deer (Cervus elaphus) populations, in which
 cross-specific and species-specific microsatellites developed through
 pyrosequencing of enriched libraries, was performed for this study. Two
 different strategies were used to select the species-specific panels:
 randomly vs. highly polymorphic markers. The results suggest that reliable
 and accurate estimations of genetic diversity can be obtained using random
 microsatellites distributed throughout the genome. In addition, the
 results reinforce previous evidence that selecting the most polymorphic
 markers leads to an ascertainment bias in estimates of genetic diversity,
 when compared with randomly selected microsatellites. Analyses of
 population differentiation and clustering seem less influenced by the
 approach of microsatellite selection, whereas assigning individuals to
 populations might be affected by a random selection of a small number of
 microsatellites. Individual multilocus heterozygosity measures produced
 various discordant results, which in turn had impacts on the
 heterozygosity-fitness correlation test. Finally, we argue that picking
 the appropriate microsatellite set should primarily take into account the
 ecological and evolutionary questions studied. Selecting the most
 polymorphic markers will generally overestimate genetic diversity
 parameters, leading to misinterpretations of the real genetic diversity,
 which is particularly important in managed and threatened populations.
description: Microsatellite
 panelsThis zip file comprise
 the microsatellite panels in genepop format used in this study:
 Species-Specific panel of 10 Random Sampling loci (SS-10RS) - 25 pools of
 10 species-specific markers were sampled randomly; Species-Specific Most
 Polymorphic panel of 10 loci (SS-10MP) - the ten most polymorphic
 species-specific markers were selected; Species-Specific panel of 35 loci
 (SS-35) - the whole set of 35 autosomal loci.R input files used to
 perform the mixed linear modelsThis file comprise the
 individual database (i.e multilocus heterozygosity parameters and fitness
 related traits) and an example of R input file analysis used in this study
 for assessing the heterozygosity fitness correlation.R input files to performed the
 mixed linear models.zipCharacteristics of
 microsatellites isolated and tested in this studyThis zip file comprise
 the processed 454-sequences (fas.file) and the references codes and
 characteristics of microsatellites isolated and tested in this study
 (excel.file).
DOI: 10.5061/dryad.7p52d
title: Data from: Cis- and trans-acting genetic factors contribute to heterogeneity in the rate of crossing over between the Drosophila simulans clade species

description: In the genus Drosophila, variation in recombination rates has been found
 within and between species. Genetic variation for both cis- and
 trans-acting factors has been shown to affect recombination rates within
 species, but little is known about the genetic factors that affect
 differences between species. Here we estimate rates of crossing over for
 seven segments that tile across the euchromatic length of the X chromosome
 in the genetic backgrounds of three closely related Drosophila species. We
 first generated a set of Drosophila mauritiana lines each having two
 semi-dominant visible markers on the X chromosome and then introgressed
 these doubly marked segments into the genetic backgrounds of its sibling
 species, D. simulans and D. sechellia. Using these 21 lines (7 segments, 3
 genetic backgrounds) we tested whether recombination rates within the
 doubly marked intervals differed depending on genetic background. We find
 significant heterogeneity among intervals and among species backgrounds.
 Our results suggest that a combination of both cis- and trans-acting
 factors have evolved among the three D. simulans clade species and
 interact to affect recombination rate.
description: Cattani et al
 JEB2012Data and descriptive
 analysis
DOI: 10.5061/dryad.qh100
title: Data from: Making it last: storage time and temperature have differential impacts on metabolite profiles of airway samples from cystic fibrosis patients

description: Metabolites of human or microbial origin have the potential to be
 important biomarkers of disease state in cystic fibrosis (CF). Clinical
 sample collection and storage conditions may impact metabolite abundances
 with clinical relevance. We measured the change in metabolite composition
 based on untargeted gas chromatography mass spectrometry (GC-MS) when CF
 sputum samples were stored at either 4°C, -20°C, or -80°C with one or two
 freeze-thaw cycles. Daily time points were taken for one week and then
 weekly for 4 weeks (4°C) and 8 weeks (-20°C). The metabolites in samples
 stored at -20°C maintained similar abundances compared to -80°C over the
 course of eight weeks (average change in Bray-Curtis distance: 0.06±0.04),
 and were also stable after one or two freeze-thaw cycles. However,
 metabolite profiles of samples stored at 4°C shifted after one day and
 continued to change over the course of four weeks (average change in
 Bray-Curtis distance: 0.31±0.12). Several amino acids and other metabolite
 abundances increased with time when stored at 4°C, but remained constant
 at -20°C. Storage temperature was a significant factor driving the
 metabolite composition (PERMANOVA R2 = 0.32 to 0.49, p= &lt;0.001). CF
 sputum samples stored at -20°C at the time of sampling maintain a
 relatively stable untargeted GC-MS profile. Samples should be frozen on
 the day of collection, as more than one day at 4°C impacts the global
 composition of the metabolites in the sample.
description: Gas Chromatography Mass
 Spec dataUntargetted GC-MS data
 obtained form UC Davis West Coast Metabolomics Center
 (http://metabolomics.ucdavis.edu/). Values given are intensities of each
 measured metabolite for each sputum sample.Raw_data_dataDryad_upload.xlsx
DOI: 10.5061/dryad.vv804
title: Data from: Tackling intraspecific genetic structure in distribution models better reflects species geographical range

description: Genetic diversity provides insight into heterogeneous demographic and
 adaptive history across organisms’ distribution ranges. For this reason,
 decomposing single species into genetic units may represent a powerful
 tool to better understand biogeographical patterns as well as improve
 predictions of the effects of GCC (global climate change) on biodiversity
 loss. Using 279 georeferenced Iberian accessions, we used classes of three
 intraspecific genetic units of the annual plant Arabidopsis thaliana
 obtained from the genetic analyses of nuclear SNPs (single nucleotide
 polymorphisms), chloroplast SNPs, and the vernalization requirement for
 flowering. We used SDM (species distribution models), including climate,
 vegetation, and soil data, at the whole-species and genetic-unit levels.
 We compared model outputs for present environmental conditions and with a
 particularly severe GCC scenario. SDM accuracy was high for genetic units
 with smaller distribution ranges. Kernel density plots identified the
 environmental variables underpinning potential distribution ranges of
 genetic units. Combinations of environmental variables accounted for
 potential distribution ranges of genetic units, which shrank dramatically
 with GCC at almost all levels. Only two genetic clusters increased their
 potential distribution ranges with GCC. The application of SDM to
 intraspecific genetic units provides a detailed picture on the
 biogeographical patterns of distinct genetic groups based on different
 genetic criteria. Our approach also allowed us to pinpoint the genetic
 changes, in terms of genetic background and physiological requirements for
 flowering, that Iberian A. thaliana may experience with a GCC scenario
 applying SDM to intraspecific genetic units.
description: Arabidopsis_data_279accessions_20jan16
DOI: 10.5061/dryad.3hj96
title: Data from: Tang-Nai-Kang alleviates pre-diabetes and metabolic disorders by inducing a gene expression switch toward fatty acid oxidation in SHR.Cg-Leprcp ⁄NDmcr rats

description: Increased energy intake and reduced physical activity can lead to obesity,
 diabetes and metabolic syndrome. Transcriptional modulation of metabolic
 networks has become a focus of current drug discovery research into the
 prevention and treatment of metabolic disorders associated with energy
 surplus and obesity. Tang-Nai-Kang (TNK), a mixture of five herbal plant
 extracts, has been shown to improve abnormal glucose metabolism in
 patients with pre-diabetes. Here, we report the metabolic phenotype of
 SHR.Cg-Leprcp/NDmcr (SHR/cp) rats treated with TNK. Pre-diabetic SHR/cp
 rats were randomly divided into control, TNK low-dose (1.67 g/kg) and TNK
 high-dose (3.24 g/kg) groups. After high-dose treatment for 2 weeks, the
 serum triglycerides and free fatty acids in SHR/cp rats were markedly
 reduced compared to controls. After 3 weeks of administration, the high
 dose of TNK significantly reduced the body weight and fat mass of SHR/cp
 rats without affecting food consumption. Serum fasting glucose and insulin
 levels in the TNK-treated groups decreased after 6 weeks of treatment.
 Furthermore, TNK-treated rats exhibited obvious improvements in glucose
 intolerance and insulin resistance. The improved glucose metabolism may be
 caused by the substantial reduction in serum lipids and body weight
 observed in SHR/cp rats starting at 3 weeks of TNK treatment. The mRNA
 expression of NAD+-dependent deacetylase sirtuin 1 (SIRT1) and genes
 related to fatty acid oxidation was markedly up-regulated in the muscle,
 liver and adipose tissue after TNK treatment. Furthermore, TNK promoted
 the deacetylation of two well-established SIRT1 targets, PPARγ coactivator
 1α (PGC1α) and forkhead transcription factor 1 (FOXO1), and induced the
 phosphorylation of AMP-activated protein kinase (AMPK) and acetyl-CoA
 carboxylase (ACC) in different tissues. These observations suggested that
 TNK may be an alternative treatment for pre-diabetes and metabolic
 syndrome by inducing a gene expression switch toward fat oxidation through
 the activation of SIRT1 and AMPK signaling.
description: in vivo experiment
 datain vivo
 data.xlsxqPCR raw
 dataqPCR.xlsxWestern Blot raw dataWB.xlsxActin Ct valuesactin qPCR data.xlsx
DOI: 10.5061/dryad.sn711
title: Data from: Senescence rates and late adulthood reproductive success are strongly influenced by personality in a long lived seabird

description: Studies are increasingly demonstrating that individuals differ in their
 rate of ageing, and this is postulated to emerge from a trade-off between
 current and future reproduction. Recent theory predicts a correlation
 between individual personality and life-history strategy, and from this
 comes the prediction that personality may predict the intensity of
 senescence. Here we show that boldness correlates with reproductive
 success and foraging behaviour in wandering albatrosses, with strong
 sex-specific differences. Shy males show a strong decline in reproductive
 performance with age, and bold females have lower reproductive success in
 later adulthood. In both sexes, bolder birds have longer foraging trips
 and gain more mass per trip as they get older. However, the benefit of
 this behaviour appears to differ between the sexes, such that it is only
 matched by high reproductive success in males. Together our results
 suggest that personality linked foraging adaptations with age are strongly
 sex-specific in their fitness benefits and that the impact of boldness on
 senescence is linked to ecological parameters.
description: Dryad Submission Patrick
 and Weimerskirch, PRSBThree data sheets 1.
 Reproductive success data 2. Foraging trip duration data 3. Mass change
 data
DOI: 10.5061/dryad.vm752
title: Data from: Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

description: Coexistence of two or more populations by frequency-dependent selection is
 common in nature, and it often arises even in well-mixed experiments with
 microbes. If ecology is to be incorporated into models of population
 genetics, then it is important to represent accurately the functional form
 of frequency-dependent interactions. However, measuring this functional
 form is problematic for traditional fitness assays, which assume a
 constant fitness difference between competitors over the course of an
 assay. Here, we present a theoretical framework for measuring the
 functional form of frequency-dependent fitness by accounting for changes
 in abundance and relative fitness during a competition assay. Using two
 examples of ecological coexistence that arose in a long-term evolution
 experiment with Escherichia coli, we illustrate accurate quantification of
 the functional form of frequency-dependent relative fitness. Using a
 Monod-type model of growth dynamics, we show that two ecotypes in a
 typical cross-feeding interaction—such as when one bacterial population
 uses a byproduct generated by another—yields relative fitness that is
 linear with relative frequency.
description: nuoM competition
 dataColony count data from
 6-day competitions between admixtures of nuoM+ and nuoM-
 clones.nuoM_competition_data.csvS and L competition dataColony count data from 6-day and 12-day competitions between S and L clones.S_L_competition_data.csvFit competition data to linear frequency dependenceMathematica notebook that fits competition data to a linear paramaterization of frequency-dependent fitness.Fit competition data to FD_linear.nbFit competition data to quadratic frequency dependenceMathematica notebook that fits competition data to a quadratic paramaterization of frequency-dependent fitness.Fit competition data to FD_quadratic.nbCross-feeding Monod model and fit to linear frequency dependenceMonod model of a cross-feeding interaction, including dynamics of daily resource use and growth. Fits post-growth cycle relative frequencies to a linear parameterization of frequency dependent fitness.Monod model and fit to linear FD_crossfeeding.nbBlack Queen Monod model and fit to linear frequency dependenceMonod model of a black queen interaction, including dynamics of daily resource use, toxin reduction, and growth. Fits post-growth cycle relative frequencies to a linear parameterization of frequency dependent fitness.Monod model and fit to linear FD_black queen.nb
DOI: 10.5061/dryad.fp94d
title: Data from: Patient characteristics associated with tuberculosis treatment default: a cohort study in a high-incidence area of Lima, Peru

description: Background: Although tuberculosis (TB) is usually curable with
 antibiotics, poor adherence to medication can lead to increased
 transmission, drug resistance, and death. Prior research has shown several
 factors to be associated with poor adherence, but this problem remains a
 substantial barrier to global TB control. We studied patients in a
 high-incidence district of Lima, Peru to identify factors associated with
 premature termination of treatment (treatment default). Methods: We
 conducted a prospective cohort study of adult smear-positive TB patients
 enrolled between January 2010 and December 2011 with no history of TB
 disease. Descriptive statistics and multivariable logistic regression
 analyses were performed to determine risk factors associated with
 treatment default. Results: Of the 1233 patients studied, 127 (10%)
 defaulted from treatment. Patients who defaulted were more likely to have
 used illegal drugs (OR = 4.78, 95% CI: 3.05-7.49), have
 multidrug-resistant TB (OR = 3.04, 95% CI: 1.58-5.85), not have been
 tested for HIV (OR = 2.30, 95% CI: 1.50-3.54), drink alcohol at least
 weekly (OR = 2.22, 95% CI: 1.40-3.52), be underweight (OR = 2.08, 95% CI:
 1.21-3.56), or not have completed secondary education (OR = 1.55, 95% CI:
 1.03-2.33). Conclusions: Our study identified several factors associated
 with defaulting from treatment, suggesting a complex set of causes that
 might lead to default. Addressing these factors individually would be
 difficult, but they might help to identify certain high-risk patients for
 supplemental intervention prior to treatment interruption. Treatment
 adherence remains a barrier to successful TB care and reducing the
 frequency of default is important for both the patients’ health and the
 health of the community.
description: Lima TB Treatment
 Default DataThe attached information
 is the minimum necessary to reproduce our results.
DOI: 10.5061/dryad.h3b41
title: Data from: Can't live with them, can't live without them? Balancing mating and competition in two-sex populations

description: Two-sex populations are usually studied through frequency-dependent models
 that describe how sex ratio affects mating, recruitment, and population
 growth. However, in two-sex populations, mating and recruitment should
 also be affected by density and by its interactions with sex ratio.
 Density may have positive effects on mating (Allee effects) but negative
 effects on other demographic processes. In this study, we quantified how
 positive and negative inter-sexual interactions balance in two-sex
 populations. Using a dioecious grass (Poa arachnifera), we established
 experimental field populations that varied in density and sex ratio. We
 then quantified mating success (seed fertilization) and non-mating
 demographic performance, and integrated these responses to project
 population-level recruitment. Female mating success was positively
 density-dependent, especially at female-biased sex ratios. Other
 demographic processes were negatively density dependent and, in some
 cases, frequency dependent. Integrating these results showed that
 mate-finding Allee effects dominated other types of density-dependence,
 giving rise to recruitment that increased with density and peaked at
 intermediate sex ratios. Our results reveal, for the first time, the
 balance of positive and negative inter-sexual interactions in
 sex-structured populations. Models that account for both density- and sex
 ratio- dependence, particularly in mating, may be necessary for
 understanding and predicting two-sex population dynamics.
description: Data and analysis R
 scriptsData, metadata, and
 analysis R scripts associated to the article "Can't live with
 them, can't live without them? Balancing mating and competition in
 two-sex populations".MatingVsCompetition_CodeData.rar
DOI: 10.5061/dryad.j1g5dh23
title: Data from: Lepidostroma vilgalysii, a new basidiolichen from the New World

description: The lichenized basidiomycete Lepidostroma vilgalysii is described from
 Mexico based on morphological analyses. The species is only the second
 representative of the family Lepidostromataceae documented from the New
 World, and is one of the few described lichens with an inverted
 morphology, with the algae in a layer at the base of the thallus.
 Molecular sequence data from the nuclear ribosomal LSU locus are used to
 confirm the placement of the holotype in Lepidostroma and to evaluate the
 molecular distinctiveness of the species from all other described species
 in the family and genus.
description: Lepidostroma_RAxML_analysesInput and output files for backbone-constrained topological and bootstrap searches performed with RAxML.sequence_renamerA Perl script written primarily to take fasta files downloaded from GenBank and transform the complex sequence identifiers to a standardized format as follows: Genus_species_GenBankAccNum_GenInfoIdLepidostroma_LSUFull nuclear ribosomal LSU alignment for the data matrix that was analyzed phylogenetically, including exclusion sets, the backbone constraint tree, and the best RAxML tree resulting from the ML analyses.
DOI: 10.5061/dryad.167d5
title: Data from: Sex-specific graphs: Relating group-specific topology to demographic and landscape data

description: Sex-specific genetic structure is a commonly observed pattern among
 vertebrate species. Facing differential selective pressures, individuals
 may adopt sex-specific life history traits that ultimately shape genetic
 variation among populations. Although differential dispersal dynamics are
 commonly detected in the literature, few studies have used genetic
 structure to investigate sex-specific functional connectivity. The recent
 use of graph theoretic approaches in landscape genetics has demonstrated
 network capacities to describe complex system behaviours where network
 topology represents genetic interaction among subunits. Here, we partition
 the overall genetic structure into sex-specific graphs, revealing
 different male and female dispersal dynamics of a fisher (Pekania [Martes]
 pennanti) metapopulation in southern Ontario. Our analyses based on
 network topologies supported the hypothesis of male-biased dispersal.
 Furthermore, we demonstrated that the effect of the landscape, identified
 at the population level, could be partitioned among sex-specific strata.
 We found that female connectivity was negatively correlated with snow
 depth, whereas connectivity among males was not. Our findings underscore
 the potential of conducting sex-specific analysis by identifying landscape
 elements or configuration that differentially promotes or impedes
 functional connectivity between sexes, revealing processes that may
 otherwise remain cryptic. We propose that the sex-specific graph approach
 would be applicable to other vagile species where differential
 sex-specific processes are expected to occur.
description: Microsatellite genotypes
 of fisher (Pekania [Martes] pennanti, Erxleben, 1777) of the Great Lakes
 region, Ontario, CanadaThis fisher genetic
 database contains 722 individuals from 34 townships. Each individual is
 scored at 16 microsatellite loci. Township (or Site ID), sex, sample ID,
 coordinates and alleles in two column format are provided. See also: Carr
 D, Bowman J, Kyle CJ et al. (2007) Rapid homogenization of multiple
 sources: genetic structure of a recolonizing population of fishers. The
 Journal of Wildlife Management, 71, 1853–1861.FisherGenotypes.csv