cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k8r75
title: Data from: Within the genome, long telomeres are more informative than short telomeres with respect to fitness components in a long-lived seabird

description: Telomeres, DNA-protein structures at chromosome ends, shorten with age,
 and telomere length has been linked to age-related diseases and survival.
 In vitro studies revealed that the shortest telomeres trigger cell
 senescence, but whether the shortest telomeres are also the best biomarker
 of ageing is not known. We measured telomeres in erythrocytes of wild
 common terns Sterna hirundo using terminal restriction fragment analysis.
 This yields a distribution of telomere lengths for each sample, and we
 investigated how different telomere subpopulations (percentiles) varied in
 their relation to age and fitness proxies. Longer telomeres within a
 genome lost more base pairs with age and were better predictors of
 survival than shorter telomeres. Likewise, fitness proxies such as arrival
 date at the breeding grounds and reproductive success were best predicted
 by telomere length at the higher percentiles. Our finding that longer
 telomeres within a genome predict fitness components better than the
 shorter telomeres indicates that they are a more informative ageing
 biomarker. This finding contrasts with the fact that cell senescence is
 triggered by the shortest telomeres. We suggest that this paradox arises,
 because longer telomeres lose more base pairs per unit time and thus
 better reflect the various forms of stress that accelerate telomere
 shortening, and that telomeres primarily function as biomarker because
 their shortening reflects cumulative effects of various stressors rather
 than reflecting telomere-induced cell senescence.
description: BauchBeckerVerhulst_MolEcol_Long-telomeres-better-predict-fitness-proxiesData
DOI: 10.5061/dryad.d51j3
title: Data from: Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species

description: The extent to which genotypic variation at a priori identified candidate
 genes can explain variation in complex phenotypes is a major debate in
 evolutionary biology. Whereas some high-profile genes such as the MHC or
 MC1R clearly do account for variation in ecologically relevant characters,
 many complex phenotypes such as response to parasite infection may well be
 underpinned by a large number of genes, each of small and effectively
 undetectable effect. Here, we characterize a suite of novel candidate
 genes for variation in gastrointestinal nematode (Trichostrongylus tenuis)
 burden among red grouse (Lagopus lagopus scotica) individuals across a
 network of moors in north-east Scotland. We test for associations between
 parasite load and genotypic variation in twelve genes previously
 identified to be differentially expressed in experimentally infected red
 grouse or genetically differentiated among red grouse populations with
 overall different parasite loads. These genes are associated with a broad
 physiological response including immune system processes. Based on
 individual-level generalized linear models, genotypic variants in nine
 genes were significantly associated with parasite load, with effect sizes
 accounting for differences of 514–666 worms per bird. All but one of these
 variants were synonymous or untranslated, suggesting that these may be
 linked to protein-coding variants or affect regulatory processes. In
 contrast, population-level analyses revealed few and inconsistent
 associations with parasite load, and little evidence of signatures of
 natural selection. We discuss the broader significance of these
 contrasting results in the context of the utility of population genomics
 and landscape genomics approaches in detecting adaptive genomic
 signatures.
description: Unphased and phased
 sequence alignmentsContains one unphased
 and one phased FASTA file per locus. The unphased files contain a single
 sequence per individual, where heterozygous sites are coded as ambiguous
 bases and missing sites as "?". The phased files contain two
 reconstructed haplotypes per individual, where missing sites have been
 imputed using PHASE. Note that all files contain polymorphic sites
 only.alignments.zipHaplotype reference panelsContains anonymised known haplotypes for haplotype reconstruction using PHASE.haplotype_reference_panels.zipPhenotypic dataContains the following phenotypic measurements and sampling-related meta data: Age (Y=&lt;1 year, O=&gt;1 year), Sex, comb area (mm^2), body mass (g), population ID (1-21), presence/absence of anthelmintic grit and nematode burden (worms per bird).phenotypes.txt
DOI: 10.5061/dryad.sh487nh
title: Data from: Higher fat stores contribute to persistence of little brown bat populations with white-nose syndrome

description: 1. The persistence of populations declining from novel stressors depends,
 in part, on their ability to respond by trait change via evolution or
 plasticity. White-nose syndrome (WNS) has caused rapid declines in several
 North America bat species by disrupting hibernation behavior, leading to
 body fat depletion and starvation. However, some populations of Myotis
 lucifugus now persist with WNS by unknown mechanisms. 2. We examined
 whether persistence of M. lucifigus with WNS could be explained by
 increased body fat in early winter, which would allow bats to tolerate the
 increased energetic costs associated with WNS. We also investigated if
 bats were escaping infection or resistant to infection as an alternative
 mechanism explaining persistence. 3. We measured body fat in early and
 late winter during initial WNS invasion and eight years later at six sites
 where bats are now persisting. We also measured infection prevalence and
 intensity in persisting populations. 4. Infection prevalence was not
 significantly lower than observed in declining populations. However, at
 two sites, infection loads were lower than observed in declining
 populations. Body fat in early winter was significantly higher in four of
 the six persisting populations than during WNS invasion. 5. Physiological
 models of energy use indicated that these higher fat stores could reduce
 WNS mortality by 58 - 70%. These results suggest that differences in fat
 storage and infection dynamics have reduced the impacts of WNS in many
 populations. Increases in body fat provide a potential mechanism for
 management intervention to help conserve bat populations.
description: fat_dataThese data were collected on Myotis lucifugus (little brown bats) in the northeastern United States and include measurements on life history (sex, age) and body condition (forearm length in millimeters, body mass in grams, and fat amount in grams). Method for measuring fat amount (fat.method) is indicated. The derived value, percent fat, is fat amount divided by body mass.ChengJAE2018_data4dryad.csv
DOI: 10.25607/vjxlve
title: Micro-Computed Tomography (Micro-CT) Morphological Data of Chondrilla nucula and Hexaplex trunculus Subjected to Experimental Climate Change Conditions

description: This dataset includes 3D morphological data for two invertebrate species, Chondrilla nucula and Hexaplex trunculus. These data are part of the MACCIMO project (https://maccimo.hcmr.gr/), which aims to assess the effects of climate change on sessile marine invertebrates. Such organisms are particularly susceptible to climate-related stressors due to their limited motility and inability to escape adverse environmental conditions. Within this framework, 3D analyses were performed using micro-CT scans to evaluate potential morphological changes associated with climate change impacts.
DOI: 10.5061/dryad.sf651
title: Data from: Male body size and condition affects sperm number and production rates in mosquitofish, Gambusia holbrooki

description: Sperm number is an important predictor of paternity when there is sperm
 competition. Sperm number is often measured as maximum sperm reserves, but
 in species where mating is frequent, males will often be replenishing
 their reserves. Thus, variation in how quickly males can produce sperm is
 likely to be important in determining male success in sperm competition.
 Despite this, little is known about how male size, body condition or diet
 affects sperm production rates. We counted sperm number in large and small
 Gambusia holbrooki (eastern mosquitofish) after 3 weeks on either a high
 or low food diet. Sperm number was significantly higher in both larger
 males and in well-fed males. We then stripped ejaculates again either 1,
 2, 3, 4 or 5 days later to investigate subsequent sperm production. The
 rate of sperm replenishment was influenced by an interaction between size
 and diet. Large, well-fed males had consistently high levels of sperm
 available over the 5 days (i.e. rapid replenishment), whereas small poorly
 fed males showed consistently low levels of sperm availability over the 5
 days (i.e. slow replenishment). In contrast, large, poorly fed and small,
 well-fed males increased their sperm numbers over the first 3 days (i.e.
 intermediate replenishment). Our study highlights that when mating is
 frequent and sperm competition is high, size and condition dependence of
 maximal sperm number and of sperm production rate might both contribute to
 variation in male reproductive success.
description: Sperm
 DataSheet 1 contains all the
 data, Sheet 2 contains descriptions of what each column in Sheet 1
 contains
DOI: 10.5061/dryad.31vb0
title: Data from: Proboscis profiler: a tool for detecting acanthocephalan morphotypes

description: Molecular studies conducted over the past 25 years have revealed
 previously unrecognised diversity in the phylum Acanthocephala. Several
 nominal species have been shown to represent complexes of morphologically
 cryptic biological species, a situation potentially confounding the
 analysis of ecological data. A software tool, ‘Proboscis profiler’, was
 developed to detect morphological heterogeneity in collections of
 superficially similar acanthocephalan worms based on the multivariate
 statistical analysis of proboscis hook dimensions. Proboscis profiler
 identifies objective, natural groups in a collection of acanthocephalans
 which may correspond to distinct biological species or populations.
 Initial trials demonstrate that Proboscis profiler can discriminate
 biological acanthocephalan species of the Echinorhynchus gadi Zoega in
 Müller, 1776 complex and differentiate between dorsal and ventral hook
 rows from the proboscis of E. salmonis Müller, 1784. Proboscis profiler is
 free software and can be downloaded from
 http://acanthocephala.sourceforge.net.
description: Hook measurements from
 female Echinorhynchus salmonis (Acanthocephala) from Bothnian Bay, Baltic
 Sea.Hook measurements from
 36 female specimens of Echinorhynchus salmonis Müller, 1784
 (Acanthocephala: Echinorhynchidae) from the Bothnian Bay, Baltic
 Sea.Echinorhynchus_salmonis.csvHook measurements from female Echinorhynchus gadi spp. and Echinorhynchus truttaeHook measurements from female Echinorhynchus gadi spp. from the North Sea and female Echinorhynchus truttae from Scotland.Echinorhynchus_spp.csv
DOI: 10.5061/dryad.0nm3k
title: Data from: Assessing the contributions of reduced immigrant viability and fecundity to reproductive isolation

description: Reduced fitness of immigrants from alternative environments is thought to
 be an important reproductive isolating barrier. Most studies evaluating
 the importance of the relative fitness of immigrants to speciation have
 focused on reduced survival of immigrants (i.e., immigrant inviability).
 However, variation in fecundity appears to have a greater impact on
 variation in fitness than does variation in viability, suggesting that
 reduced fecundity of immigrants could act as an important yet largely
 overlooked reproductive isolating barrier. Using a model and a survey of
 studies of local adaptation, we evaluate the relative strength of reduced
 immigrant viability and fecundity as potential causes of reproductive
 isolation. We found that reduced fecundity as compared to reduced
 viability as a reproductive isolating barrier should increase in
 importance as the relative costs of reproduction increase. Consistent with
 the elevated demands of reproduction reported in the literature, we found
 that reproductive isolation from reduced immigrant fecundity was of
 similar magnitude or greater than that from reduced immigrant viability,
 particularly in the early stages of speciation. These results suggest that
 the important role of differential fecundity in local adaptation extends
 to speciation.
description: Supplementary Material
 TableTable with estimates of
 reproductive isolation for all studies. Complete references in separate
 file.Supplementary_Material_Table.xlsxSupplementary Material ReferencesComplete reference information for studies included in meta-analysis.Supplementary Material_References.docx
DOI: 10.5061/dryad.8n5r3v1
title: Data from: Effects of an early-life paraquat exposure on adult resistance to oxidative stress, plumage colour and sperm performance in a wild bird

description: 1. Early-life stressful conditions can shape individual phenotypes and
 ultimately influence fitness. Oxidative stress is a pervasive threat that
 affects many fitness-related traits and can modulate life-history
 trade-offs. Yet, the extent to which exposure to oxidative stress during
 early life can have long-lasting effects on key fitness-related traits
 remains to be elucidated, particularly in natural populations of
 vertebrates. 2. Using a wild population of great tits Parus major, we
 experimentally dosed 11 day-old birds with paraquat, a pro-oxidant
 molecule, aiming at increasing oxidative stress. One year later, we
 recaptured 39 of them as adult recruiting breeders and quantified effects
 of the paraquat exposure on their resistance to oxidative stress,
 carotenoid-based plumage colouration and male sperm performance. 3.
 Despite the absence of a short-term effect of paraquat on oxidative stress
 measured two days later, the pre-fledging exposure to paraquat induced a
 reduction in individual oxidative damage measured at adulthood.
 Paraquat-dosed individuals also had brighter plumage, but no effect was
 observed on male sperm performance. 4. For the first time in a natural
 population of vertebrates, we experimentally show that an early-life acute
 exposure to a pro-oxidant has long-lasting effects on individual
 resistance to oxidative stress at adulthood. Our results are in line with
 the environmental matching and the hormesis hypotheses but may also
 reflect selective disappearance of individuals with lower resistance to
 oxidative stress.
description: Data from Losdat et al.
 on the long-term effects of paraquatThe file entitled
 "Recruits" contains all the measurements made on the 39 recruits
 during the early-life of the offspring (in 2010) and the measurement of
 colour and oxidative stress taken on the same individuals as adults (in
 2011). The file entitled "Sperm" contains the data on sperm
 performance measured on the individuals in 2011. Each line corresponds to
 the value for a single sperm cell.Recruits_Losdat et al_long-term
 effects of paraquat.zip
DOI: 10.5061/dryad.82jv0
title: Data from: Quality of evidence considered by Health Canada in granting full market authorization to new drugs with a conditional approval: a retrospective cohort study

description: Objectives: This study examines the characteristics of studies that Health
 Canada uses to grant full marketing authorization for products given a
 conditional approval between January 1, 1998 and June 30, 2017. Design:
 Cohort study. Data sources: Journal articles listing drugs that fulfilled
 their conditions and received full marketing authorization, Notice of
 Compliance database, Notice of Compliance with conditions web site,
 Qualifying Notices listing required confirmatory studies,
 clinicaltrials.gov, PubMed, Embase, companies making products being
 analyzed, journal articles resulting from confirmatory studies.
 Interventions: None Primary and secondary outcome measures:
 Characteristics of studies - study design (randomized controlled trials,
 observational), primary outcome used (clinical, surrogate), blinding,
 number of patients in studies, patient median age, number of men and
 women. Results: Eleven companies confirmed 36 publications for 19 products
 (21 indications). Twenty-nine out of the 36 studies were randomized
 controlled trials (RCTs) but only 10 stated if they were blinded. Twenty
 used surrogate outcomes. The median age of patients was 56 (interquartile
 range (IQR) 44, 61). The median number of men per study/trial was 184 (IQR
 58, 514) versus women - 141 (IQR 46, 263). Conclusions: Postmarket studies
 required by Health Canada had more rigorous methodology than those
 required by either the Food and Drug Administration or the European
 Medicines Agency. There were still deficiencies in these studies. The
 absence of blinding in the majority of RCTs may introduce bias in their
 results. The use of surrogate outcomes especially in oncology trials means
 that improvements in survival are not available. The relatively young age
 of patients, even for products for cancer, means that predicting how the
 elderly will respond is often unknown. The almost universal finding that
 men outnumbered number women may make it hard to differentiate responses
 by sex. These results raise potential concerns about the quality of
 evidence that Health Canada accepts.
description: Supplementary file 1
 (PDF format)All data extracted from
 publications based on confirmatory studiesSupplementary file
 1.pdfSupplementary file 1
 (CSV format)All data extracted from
 publications based on confirmatory studiesSupplementary file
 1.csv
DOI: 10.5061/dryad.kf1td
title: Data from: Genetic differentiation and species cohesion in two widespread Central American Begonia species

description: Begonia is one of the ten largest plant genera, with over 1500 species.
 This high species richness may in part be explained by weak species
 cohesion, which has allowed speciation by divergence in allopatry. In this
 study, we investigate species cohesion in the widespread Central American
 Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations
 at microsatellite loci. We then test for post-zygotic reproductive
 barriers using experimental crosses, and assess whether sterility barriers
 are related to intraspecific changes in genome size, indicating major
 genome restructuring between isolated populations. Strong population
 substructure was found for B. heracleifolia (FST=0.364, F′ST=0.506) and B.
 nelumbiifolia (FST=0.277, F′ST=0.439), and Bayesian admixture analysis
 supports the division of most populations into discrete genetic clusters.
 Moderate levels of inferred selfing (B. heracleifolia s=0.40, B.
 nelumbiifolia s=0.62) and dispersal limitation are likely to have
 contributed to significant genetic differentiation (B. heracleifolia
 Jost’s D=0.274; B. nelumbiifolia D=0.294). Interpopulation crosses
 involving a divergent B. heracleifolia population with a genome size ~10%
 larger than the species mean had a ~20% reduction in pollen viability
 compared with other outcrosses, supporting reproductive isolation being
 polymorphic within the species. The population genetic data suggest that
 Begonia populations are only weakly connected by gene flow, allowing
 reproductive barriers to accumulate between the most isolated populations.
 This supports allopatric divergence in situ being the precursor of
 speciation in Begonia, and may also be a common speciation mechanism in
 other tropical herbaceous plant groups.
description: Begonia heracleifolia
 microsatellite dataMicrosatellite genotype
 data for Begonia heracleifolia. Data provided in FSTAT
 formatTwyford_Bherac_microsatdata_FSTAT.datBegonia nelumbiifolia microsatellite dataMicrosatellite genotype data for Begonia nelumbiifolia. Data provided in FSTAT format.Twyford_Bnelum_microsatdata_FSTAT.datBegonia heracleifolia F1 pollen stainability in experimental crossesPollen stainability of experimental Begonia heracleifolia interpopulation crosses. Original seeds were field collected, and F1s generated in the glasshouse.
DOI: 10.5061/dryad.ns624
title: Data from: Evaluating range-expansion models for calculating nonnative species’ expansion rate

description: 1. Species range shifts associated with environmental change or biological
 invasions are increasingly important study areas. However, quantifying
 range expansion rates may be heavily influenced by methodology and/or
 sampling bias. 2. We compared expansion rate estimates of Roesel’s
 bush-cricket (Metrioptera roeselii, Hagenbach 1822), a non-native species
 currently expanding its range in south-central Sweden, from range
 statistic models based on distance measures (mean, median, 95th gamma
 quantile, marginal mean, maximum and conditional maximum) and an
 area-based method (grid occupancy). We used sampling simulations to
 determine the sensitivity of the different methods to incomplete sampling
 across the species’ range. 3. For periods when we had comprehensive survey
 data, range expansion estimates clustered into two groups: (i) those
 calculated from range margin statistics (gamma, marginal mean, maximum and
 conditional maximum: ~3 km/yr), and (ii) those calculated from the central
 tendency (mean and median) and the area-based method of grid occupancy
 (~1.5 km/yr). 4. Range statistic measures differed greatly in their
 sensitivity to sampling effort; the proportion of sampling required to
 achieve an estimate within 10% of the true value ranged from 0.17-0.9.
 Grid occupancy and median were most sensitive to sampling effort, and the
 maximum and gamma quantile the least. 5. If periods with incomplete
 sampling were included in the range expansion calculations, this generally
 lowered the estimates (range 16-72%), with exception of the gamma quantile
 that was slightly higher (6%). 6. Care should be taken when interpreting
 rate expansion estimates from data sampled from only a fraction of the
 full distribution. Methods based on the central tendency will give rates
 approximately half that of methods based on the range margin. The gamma
 quantile method appears to be the most robust to incomplete sampling bias
 and should be considered as the method of choice when sampling the entire
 distribution is not possible.
description: Roeselii_invasion_dataThe .xls file contains the years and relative positions that Roesel's bush-crickets were observed in southern-central Sweden from 1981-2010 during their ongoing invasion of this area. The distance measures are in metres relative to the original observation location (see Preuss et al. 2014, Ecology and Evolution for more details). The observation locations were summarised as the centre of 5x5km landscape squares.