cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2fp25
title: Data from: Evolution under dietary restriction increases male reproductive performance without survival cost

description: Dietary restriction (DR), a reduction in nutrient intake without
 malnutrition, is the most reproducible way to extend lifespan in a wide
 range of organisms across the tree of life, yet the evolutionary
 underpinnings of the DR effect on lifespan are still widely debated. The
 leading theory suggests that this effect is adaptive and results from
 reallocation of resources from reproduction to somatic maintenance in
 order to survive periods of famine in nature. However, such response would
 cease to be adaptive when DR is chronic and animals are predicted to
 allocate more resources to reproduction. Nevertheless, chronic DR can also
 increase the strength of selection resulting in the evolution of more
 robust genotypes. We evolved Drosophila melanogaster fruitflies on ‘DR’,
 ‘standard’ and ‘high’ adult diets in replicate populations with
 overlapping generations. After ~25 generations of experimental evolution,
 male ‘DR’ flies had higher fitness than males from ‘standard’ and ‘high’
 populations. Strikingly, this increase in reproductive success did not
 come at a cost to survival. Our results suggest that sustained DR selects
 for more robust male genotypes, which are overall better able to convert
 resources into energy, which they allocate mostly to reproduction.
description: Zajitschek et al 2016
 Proc B Data Description of the data
 is provided in the data file.   The updated version
 corrects an error in the 'Male survival' tab of the originally
 uploaded (now deleted) data file (dryad Zajitschek et al 2016
 ProcB Data.xlsx). The original version contained
 data of males and of females in the 'Male survival'
 tab.
DOI: 10.5061/dryad.1844
title: Data from: Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths)

description: Armadillos, anteaters, and sloths (Order Xenarthra) comprise 1 of the 4
 major clades of placental mammals. Isolated in South America from the
 other continental landmasses, xenarthrans diverged over a period of about
 65 Myr, leaving more than 200 extinct genera and only 31 living species.
 The presence of both ancestral and highly derived anatomical features has
 made morphoanatomical analyses of the xenarthran evolutionary history
 difficult, and previous molecular analyses failed to resolve the
 relationships within armadillo subfamilies. We investigated the
 presence/absence patterns of retroposons from ∼7,400 genomic loci,
 identifying 35 phylogenetically informative elements and an additional 39
 informative rare genomic changes (RGCs). DAS-short interspersed elements
 (SINEs), previously described only in the Dasypus novemcinctus genome,
 were found in all living armadillo genera, including the previously
 unsampled Chlamyphorus, but were noticeably absent in sloths. The
 presence/absence patterns of the phylogenetically informative retroposed
 elements and other RGCs were then compared with data from the DNA
 sequences of the more than 12-kb flanking regions of these retroposons.
 Together, these data provide the first fully resolved genus tree of
 xenarthrans. Interestingly, multiple evidence supports the grouping of
 Chaetophractus and Zaedyus as a sister group to Euphractus within
 Euphractinae, an association that was not previously demonstrated. Also,
 flanking sequence analyses favor a close phylogenetic relationship between
 Cabassous and Tolypeutes within Tolypeutinae. Finally, the phylogenetic
 position of the subfamily Chlamyphorinae is resolved by the noncoding
 sequence data set as the sister group of Tolypeutinae. The data provide a
 stable phylogenetic framework for further evolutionary investigations of
 xenarthrans and important information for defining conservation priorities
 to save the diversity of one of the most curious groups of mammals.
description: Moller-Krull2007-MolBiolEvol.tremoller-krull2007-molbiolevolphy.treMoller-Krull2007-MolBiolEvol.nex
DOI: 10.5061/dryad.51d4h
title: Data from: Stacked Bt maize and arthropod predators – exposure to insecticidal Cry proteins and potential hazards

description: Genetically engineered (GE) crops with stacked insecticidal traits expose
 arthropods to multiple Cry proteins from Bacillus thuringiensis (Bt). One
 concern is that the different Cry proteins may interact and lead to
 unexpected adverse effects on non-target species. Bi- and tri-trophic
 experiments with SmartStax maize, herbivorous spider mites (Tetranychus
 urticae) and aphids (Rhopalosiphum padi), and predatory spiders
 (Phylloneta impressa), ladybeetles (Harmonia axyridis), and lacewings
 (Chrysoperla carnea) were conducted. Cry1A.105, Cry1F, Cry3Bb1, and
 Cry34Ab1 moved in a similar pattern through the arthropod food chain. In
 contrast, Cry2Ab2 had highest concentrations in maize leaves, but lowest
 in pollen, and lowest acquisition rates by herbivores and predators. While
 spider mites contained Cry protein concentrations exceeding the values in
 leaves (except Cry2Ab2), aphids contained only traces of any Cry protein.
 Predators contained lower concentrations than their food. Among the
 different predators, ladybeetle larvae showed higher concentrations than
 lacewing larvae and juvenile spiders. Acute effects of SmartStax maize on
 predator survival, development, and weight were not observed. The study
 thus provides evidence that the different Cry proteins do not interact in
 a way that poses a risk to the investigated non-target species under
 controlled laboratory conditions.
description: Data from: Stacked Bt
 maize and arthropod predators: exposure to insecticidal Cry proteins and
 potential hazardsWeight, development, and
 survival data for Phylloneta impressa juvenile spiders, Chrysoperla carnea
 lacewing larvae, and Harmonia axyridis ladybeetle larvae fed with pollen,
 aphids Rhopalosiphum padi, or spider mites Tetranychus urticae from
 SmartStax Bt maize or genetically closest non-Bt hybrid. ELISA Cry protein
 measurements of the previously described predators as well as of food
 items and maize leaves.Raw
 data_resubmission_corrected.xlsx
DOI: 10.5061/dryad.n37q406
title: Data from: Nusinersen in later-onset spinal muscular atrophy: long-term results from the phase 1/2 studies

description: Objective: Report results of intrathecal nusinersen in children with
 later-onset spinal muscular atrophy (SMA). Methods: Analyses included
 children from the phase 1b/2a study (ISIS-396443-CS2; NCT01703988) who
 first received nusinersen during that study and were eligible to continue
 treatment in the extension study (ISIS-396443-CS12; NCT02052791). The
 phase 1b/2a study was a 253-day, ascending dose (3, 6, 9, 12 mg),
 multiple-dose, open-label, multicenter study that enrolled children with
 SMA aged 2 to 15 years. The extension study was a 715-day, single-dose
 level (12 mg) study. Time between studies varied by participant (196–413
 days). Assessments included the Hammersmith Functional Motor
 Scale–Expanded (HFMSE), Upper Limb Module (ULM), Six-Minute Walk Test
 (6MWT), compound muscle action potential (CMAP), and quantitative
 multipoint incremental motor unit number estimation. Safety also was
 assessed. Results: Twenty-eight children were included (SMA Type II, n =
 11; SMA Type III, n = 17). Mean HFMSE scores, ULM scores, and 6MWT
 distances improved by the day 1150 visit (HFMSE: SMA Type II, +10.8
 points; SMA Type III, +1.8 points; ULM: SMA Type II, +4.0 points; 6MWT:
 SMA Type III, +92.0 meters). Mean CMAP values remained relatively stable.
 No children discontinued treatment due to adverse events. Conclusions:
 Nusinersen treatment over ~3 years resulted in motor function improvements
 and disease activity stabilization not observed in natural history
 cohorts. These results document the long-term benefit of nusinersen in
 later-onset SMA, including SMA Type III. Classification of evidence: This
 study provides Class IV evidence that nusinersen improves motor function
 in children with later-onset SMA.
description: Darras et al.
 NEUROLOGY/2018/918938 Supplementary appendixSupplementary appendix
 containing additional methodological details for the manuscript titled
 "Nusinersen in later-onset spinal muscular atrophy: long-term results
 from the phase 1/2 studies"Darras Online Supplementary
 appendix.pdf
DOI: 10.5061/dryad.230ps
title: Data from: Safety of single low-dose primaquine in glucose-6-phosphate dehydrogenase deficient falciparum-infected African males: two open-label, randomized, safety trials

description: Background: Primaquine (PQ) actively clears mature Plasmodium falciparum
 gametocytes but in glucose-6-phosphate dehydrogenase deficient (G6PDd)
 individuals can cause hemolysis. We assessed the safety of low-dose PQ in
 combination with artemether-lumefantrine (AL) or
 dihydroartemisinin-piperaquine (DP) in G6PDd African males with
 asymptomatic P. falciparum malaria. Methods and findings: In Burkina Faso,
 G6PDd adult males were randomized to treatment with AL alone (n = 10) or
 with PQ at 0.25 (n = 20) or 0.40 mg/kg (n = 20) dosage; G6PD-normal males
 received AL plus 0.25 (n = 10) or 0.40 mg/kg (n = 10) PQ. In The Gambia,
 G6PDd adult males and boys received DP alone (n = 10) or with 0.25 mg/kg
 PQ (n = 20); G6PD-normal males received DP plus 0.25 (n = 10) or 0.40
 mg/kg (n = 10) PQ. The primary study endpoint was change in hemoglobin
 concentration during the 28-day follow-up. Cytochrome P-450 isoenzyme 2D6
 (CYP2D6) metabolizer status, gametocyte carriage, haptoglobin, lactate
 dehydrogenase levels and reticulocyte counts were also determined. In
 Burkina Faso, the mean maximum absolute change in hemoglobin was -2.13
 g/dL (95% confidence interval [CI], -2.78, -1.49) in G6PDd individuals
 randomized to 0.25 PQ mg/kg and -2.29 g/dL (95% CI, -2.79, -1.79) in those
 receiving 0.40 PQ mg/kg. In The Gambia, the mean maximum absolute change
 in hemoglobin concentration was -1.83 g/dL (95% CI, -2.19, -1.47) in G6PDd
 individuals receiving 0.25 PQ mg/kg. After adjustment for baseline
 concentrations, hemoglobin reductions in G6PDd individuals in Burkina Faso
 were more pronounced compared to those in G6PD-normal individuals
 receiving the same PQ doses (P = 0.062 and P = 0.022, respectively).
 Hemoglobin levels normalized during follow-up. Abnormal haptoglobin and
 lactate dehydrogenase levels provided additional evidence of mild
 transient hemolysis post-PQ. Conclusions: Single low-dose PQ in
 combination with AL and DP was associated with mild and transient
 reductions in hemoglobin. None of the study participants developed
 moderate or severe anemia; there were no severe adverse events. This
 indicates that single low-dose PQ is safe in G6PDd African males when used
 with artemisinin-based combination therapy.
description: SAFEPRIM Burkina Faso
 Adverse EventsAdverse events SAFEPRIM
 trial Burkina FasoDRYAD_SAFEPRIM Burkina Faso
 Adverse Events.xlsxSAFEPRIM Gambia Adverse
 EventsAdverse events SAFEPRIM
 trial The GambiaDRYAD_SAFEPRIM Gambia Adverse
 Events.xlsxDRYAD SAFEPRIM main
 dataset Burkina FasoLaboratory results from
 clinical trial in Burkina Faso. Data include haemoglobin concentration,
 reticulocyte counts, full haematology and biochemistry.DRYAD SAFEPRIM main
 dataset The GambiaLaboratory results from
 clinical trial in The Gambia. Data include haemoglobin concentration,
 reticulocyte counts, full haematology and biochemistry.
DOI: 10.5061/dryad.tp324
title: Data from: Pivotal effect of early-winter temperatures and snowfall on population growth of alpine Parnassius smintheus butterflies

description: Geographic range shifts in species’ distributions, due to climate change,
 imply altered dynamics at both their northern and southern range limits,
 or at upper and lower elevational limits. There is therefore a need to
 identify specific weather or climate variable(s), and life stages or
 cohorts on which they act, and how these affect population growth.
 Identifying such variables permits prediction of population increase or
 decline under a changing climate, and shifts in a species’ geographic
 range. For relatively well studied groups, such as butterflies, geographic
 range shifts are well documented, but weather variables and mechanisms
 causing those shifts are not well known. The Holarctic butterfly genus
 Parnassius (Papilionidae) inhabits northern and alpine environments
 subject to variable and extreme weather. As such, Parnassius species are
 vulnerable not only to long-term changes in average conditions but
 especially to short-term extreme weather events. We use population growth
 estimates for the alpine butterfly, Parnassius smintheus, from 21
 populations in the Rocky Mountains of Canada, over a 20-year interval,
 combined with techniques of machine learning (randomForests) and
 parametric modeling to identify the important weather variables
 determining population growth. We do this to determine the seasons and
 life-stages of P. smintheus most affected by climate change. Extreme
 minimum and maximum temperatures in November, in combination with November
 snowfall, affect annual population growth most, more so than do mean
 temperatures in November, and more so than weather at any other time of
 year. Populations decline both in years with low extreme minimum
 temperatures in November, and especially in years with high extreme
 maximum temperatures in November, indicating that overwintering eggs are
 particularly vulnerable to early-winter weather. Snowfall ameliorates the
 negative effects of extreme temperatures, particularly for extreme warm
 events. Results provide insight into biological mechanisms by which
 over-wintering eggs might be affected by early winter weather. Short-term
 extreme weather in November, acting on a single pivotal life-stage (egg)
 is a far better predictor of population change of alpine Parnassius
 smintheus butterflies than is the general index of climate, the Pacific
 Decadal Oscillation (PDO).
description: Parnassius smintheus
 populations and weatherSee ReadMe
 fileRoland
 and Matter.xlsx
DOI: 10.5061/dryad.2ng4k
title: Data from: The mutational decay of male-male and hermaphrodite-hermaphrodite competitive fitness in the androdioecious nematode C. elegans

description: Androdioecious Caenorhabditis have a high frequency of self-compatible
 hermaphrodites and a low frequency of males. The effects of mutations on
 male fitness are of interest for two reasons. First, when males are rare,
 selection on male-specific mutations is less efficient than in
 hermaphrodites. Second, males may present a larger mutational target than
 hermaphrodites because of the different ways in which fitness accrues in
 the two sexes. We report the first estimates of male-specific mutational
 effects in an androdioecious organism. The rate of male-specific inviable
 or sterile mutations is ≤ 5 x 10-4/generation, below the rate at which
 males would be lost solely due to those kinds of mutations. The rate of
 mutational decay of male competitive fitness is ~0.17%/generation; that of
 hermaphrodite competitive fitness is ~0.11%/generation. The point estimate
 of ~1.5X faster rate of mutational decay of male fitness is nearly
 identical to the same ratio in Drosophila. Estimates of mutational
 variance (VM) for male mating success and competitive fitness are not
 significantly different from zero, whereas VM for hermaphrodite
 competitive fitness is similar to that of non-competitive fitness. Two
 independent estimates of the average selection coefficient against
 mutations affecting hermaphrodite competitive fitness agree to within
 two-fold, 0.33%-0.5%.
description: competitive fitness
 dataExcel workbook with four
 worksheets. Sheet 1, "malefitness" contains male fitness data;
 sheet two, "malefit_readme" contains descriptions of column
 headings. Sheet 3, "hermfitness" contains hermaphrodite fitness
 data; sheet 4, "hermfit_readme" contains descriptions of column
 headings.Data for
 Heredity_Aug2017.xlsx
DOI: 10.5061/dryad.vv183
title: Data from: Integrative taxonomy improves understanding of native beneficial fauna: revision of the Nearctic Peristenus pallipes complex (Hymenoptera: Braconidae) and implications for release of exotic biocontrol agents

description: The Nearctic Peristenus pallipes complex (Hymenoptera: Braconidae)
 consists of two species groups that are further divided into nine species,
 separated largely using ecological rather than morphological differences.
 The species are re-examined with an integrative approach using
 morphometric multivariate ratios, molecular (COI and CytB), and ecological
 data to test the validity of the nine species. The data support only three
 valid species [P. dayi Goulet, P. mellipes (Cresson) and P. howardi Shaw]
 rather than nine. New synonymies include: P. braunae Goulet under P. dayi
 Goulet 2006 syn.n.; P. carcamoi Goulet, P. otaniae Goulet and P.
 pseudopallipes (Loan) under P. mellipes (Cresson) syn.n., and finally P.
 broadbenti Goulet 2006 and P. gillespiei Goulet 2006 under P. howardi Shaw
 1999 syn.n. In light of these taxonomic revisions, the biology and
 distributions of the Nearctic P. pallipes complex are updated, resulting
 in three morphologically variable, widespread, multivoltine species rather
 than nine largely univoltine species with patchy distributions. The
 integrative taxonomic approach used here allowed for a more accurate
 delineation of native fauna and their potential to be competitively
 displaced by foreign biocontrol agents.
description: Zhang et al Peristenus
 Code 1R code for Fig
 3A-BZhang et al Peristenus
 Code 2R code for Fig 3C-D and
 LDA ratio extractorZhang et al Peristenus
 MasterExcel spreadsheet with
 data for morphometrics analysisZhang et al Peristenus
 MasterText file with data for
 morphometrics analysisZhang et al Peristenus
 ConcatConcatenated CO1 and
 CytB sequences
DOI: 10.5061/dryad.0500c
title: Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes

description: Premise of the study: The use of genome skimming allows systematists to
 quickly generate large data sets, particularly of sequences in high
 abundance (e.g., plastomes); however, researchers may be overlooking data
 in low abundance that could be used for phylogenetic or evo-devo studies.
 Here, we present a bioinformatics approach that explores the low-abundance
 portion of genome-skimming next-generation sequencing libraries in the
 fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed
 Goodeniaceae genome-skimming Illumina libraries were examined for their
 utility in mining low-copy nuclear genes involved in floral symmetry,
 specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were
 generated using multiple assemblers, and BLAST searches were performed for
 CYC1, CYC2, and CYC3 genes. Results: Overall Trinity, SOAPdenovo-Trans,
 and SOAPdenovo implementing lower k-mer values uncovered the most data,
 although no assembler consistently outperformed the others. Using
 SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene
 groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species.
 Alignments of the fragments included the entire coding sequence as well as
 upstream and downstream regions. Discussion: Genome-skimming data sets can
 provide a significant source of low-copy nuclear gene sequence data that
 may be used for multiple downstream applications.
description: CYC1
 AlignmentAlignment of BLAST
 results from all genome skimming datasets for CYC1-like genes. Each line
 represents the accumulative BLAST results from a single
 species.CYC2
 AlignmentAlignment of BLAST
 results from all genome skimming datasets for CYC2-like genes. Each line
 represents the accumulative BLAST results from a single
 species.CYC3A
 AlignmentAlignment of BLAST
 results from all genome skimming datasets for CYC3A-like genes. Each line
 represents the accumulative BLAST results from a single
 species.CYC3B
 AlignmentAlignment of BLAST
 results from all genome skimming datasets for CYC3B-like genes. Each line
 represents the accumulative BLAST results from a single
 species.
DOI: 10.5061/dryad.15dd2j2
title: Data from: Superior stimulation of female fecundity by subordinate males provides a mechanism for telegony

description: When females mate promiscuously, rival males compete to fertilise the ova.
 In theory, a male can increase his success at siring offspring by inducing
 the female to lay more eggs, as well as by producing more competitive
 sperm. Here we report that the evolutionary consequences of fecundity
 stimulation extend beyond rival males, by experimentally uncovering
 effects on offspring. With experiments on the burying beetle Nicrophorus
 vespilloides, we show that smaller subordinate males are better able to
 stimulate female fecundity than larger, dominant males. Furthermore
 dominant males also benefit from the greater fecundity induced by smaller
 males, and so gain from the female’s earlier promiscuity - just as
 predicted by theory. By inducing females to produce more offspring on a
 limited resource, smaller males cause each larva to be smaller, even those
 they do not sire themselves. Fecundity stimulation thus promotes the
 non-genetic inheritance of offspring body size, and provides a mechanism
 for telegony.
description: TelegonyParentage_final_dryad
DOI: 10.5061/dryad.4nt0661
title: Data from: On the relationship between body condition and parasite infection in wildlife: a review and meta‐analysis

description: Body condition metrics are widely used to infer animal health and to
 assess costs of parasite infection. Since parasites harm their hosts,
 ecologists might expect negative relationships between infection and
 condition in wildlife, but this assumption is challenged by studies
 showing positive or null condition–infection relationships. Here, we
 outline common condition metrics used by ecologists in studies of
 parasitism, and consider mechanisms that cause negative, positive, and
 null condition–infection relationships in wildlife systems. We then
 perform a meta‐analysis of 553 condition–infection relationships from 187
 peer‐reviewed studies of animal hosts, analysing observational and
 experimental records separately, and noting whether authors measured
 binary infection status or intensity. Our analysis finds substantial
 heterogeneity in the strength and direction of condition–infection
 relationships, a small, negative average effect size that is stronger in
 experimental studies, and evidence for publication bias towards negative
 relationships. The strongest predictors of variation in study outcomes are
 host thermoregulation and the methods used to evaluate body condition. We
 recommend that studies aiming to assess parasite impacts on body condition
 should consider host–parasite biology, choose condition measures that can
 change during the course of infection, and employ longitudinal surveys or
 manipulate infection status when feasible.
description: Sánchez et al. 2018 EL
 final datasetEffect size information
 (yi, vi); methodological, host, and parasite covariates; and covariates
 for subset analyses to recreate the analyses for Sánchez et al.
 2018.Sánchez et al. 2018 EL
 metadataMetadata for Sánchez et
 al. 2018 CSV.