cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5488t
title: Data from: Facultative use of thelytokous parthenogenesis for queen production in the polyandrous ant Cataglyphis cursor

description: The evolutionary paradox of sex remains one of the major debates in
 evolutionary biology. The study of species capable of both sexual and
 asexual reproduction can elucidate factors important in the evolution of
 sex. One such species is the ant Cataglyphis cursor, where the queen
 maximises the transmission of her genes by producing new queens (gynes)
 asexually while simultaneously maintaining a genetically diverse workforce
 via the sexual production of workers. We show that the queen can also
 produce gynes sexually, and may do so to offset the costs of asexual
 reproduction. We genotyped 235 gynes from 18 colonies, and found that half
 were sexually produced. A few colonies contained both sexually and
 asexually produced gynes. While workers in this species can also use
 thelytoky, we found no evidence of worker production of gynes based on
 genotypes of 471 workers from the six colonies producing sexual gynes.
 Gynes are thus mainly, and potentially exclusively, produced by the queen.
 Simulations of gynes inbreeding level following one to ten generations of
 automictic thelytoky suggest that the queen switches between or combines
 thelytoky and sex, which may reduce the costs of inbreeding. This is
 supported by the relatively small size of inbred gynes in one colony,
 though we found no relationship between the level of inbreeding and immune
 parameters. Such facultative use of sex and thelytoky by individual queens
 contrasts with other known forms of parthenogenesis in ants, which are
 typically characterised by distinct lineages specialising in one strategy
 or the other.
description: Doums et al Jeb 2013
 dryad dataMicrosatellite data of
 individual ants collected in the field in two populations St Cyprien and
 Argeles (South of France). For each individual, the population of origin,
 the colony number, the caste (queen, gyne (for the young queen), worker)
 as well as the individual identity are given. The individuals surligned in
 red were removed from the analysis because they were either triploid or
 foreigner. For the queen and gyne, we also provided values of leg size
 (length of the tibia in mm) phenoloxidase activity (Vmax of the Po for the
 active form and PPO for the precursor), the mating status (1 = filled
 spermatheca, 0 = empty spermatheca) and the wing status (1 = presence of
 wing, 0 = no wing).
DOI: 10.5061/dryad.ph81m
title: Data from: Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

description: Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules
 encoded on retroelements called retrons and produced by the action of
 retron reverse transcriptases. Retrons are widespread in bacteria but the
 natural function of msDNA has remained elusive despite 30 years of study.
 The major roadblock to elucidation of the function of these unique
 molecules has been the lack of any identifiable phenotypes for mutants
 unable to make msDNA. We report that msDNA of the zoonotic pathogen
 Salmonella Typhimurium is necessary for colonization of the intestine.
 Similarly, we observed a defect in intestinal persistence in an
 enteropathogenic E. coli mutant lacking its retron reverse transcriptase.
 Under anaerobic conditions in the absence of msDNA, proteins of central
 anaerobic metabolism needed for Salmonella colonization of the intestine
 are dysregulated. We show that the msDNA-deficient mutant can utilize
 nitrate, but not other alternate electron acceptors in anaerobic
 conditions. Consistent with the availability of nitrate in the inflamed
 gut, a neutrophilic inflammatory response partially rescued the ability of
 a mutant lacking msDNA to colonize the intestine. These findings together
 indicate that the mechanistic basis of msDNA function during Salmonella
 colonization of the intestine is proper production of proteins needed for
 anaerobic metabolism. We further conclude that a natural function of msDNA
 is to regulate protein abundance, the first attributable function for any
 msDNA. Our data provide novel insight into the function of this mysterious
 molecule that likely represents a new class of regulatory molecules.
description: Fig 1CD 7A S4 Raw data
 mouse elfenbein et alRaw data from figure 1C,
 1D, 7A, and S4.Figure 5 raw data
 elfenbein etalRaw data for Figure
 5Figure 6 raw data
 elfenbein etalRaw data for Figure
 6Figure S1 raw data hela
 elfenbein et alRaw data for figure
 S1Figure S3 Raw data
 motility elfenbein et alRaw data for Figure
 S3
DOI: 10.5061/dryad.697hm
title: Data from: Phylogeographic heterogeneity of the brown macroalga Sargassum horneri (Fucaceae) in the northwestern Pacific in relation to late Pleistocene glaciation and tectonic configurations

description: Pleistocene glacial oscillations and associated tectonic processes are
 believed to have influenced the historical abundances and gradients of
 organisms in the Asia Northwest Pacific (ANP) Ocean. However, accumulating
 evidence indicates that factors shaping tempo-spatial population dynamics
 and distribution patterns of marine taxa vary with biogeographical
 latitude, pelagic behavior and oceanographic regimes. To detect what kinds
 of historical and contemporary factors affected genetic connectivity,
 phylogeographic profiles of littoral macroalga Sargassum horneri in the
 ANP were analyzed based on mitochondrial (Cox3) and chloroplast (rbcL)
 data sets. Five distinct clades were recovered. A strong signature of
 biogeographical structure was revealed (ФCT = 0.487, P &lt; 0.0001)
 derived from remarkable differentiation in clade distribution, as clade I
 is highly harboured along Chinese marginal seas (Yellow-Bohai Sea, East
 China Sea and South China Sea), whereas clades II-V are discontinuously
 scattered around the main Islands of Japan. Furthermore, two secondary
 contact regions were identified along the south Japan-Pacific coastline.
 This significant differentiation between the two basins may reflect
 historical glacial isolation in the northwestern Pacific, which is
 congruent with the estimates of clade divergence and demographic expansion
 during the late Quaternary low sea levels. Analysis of molecular variance
 and the population-pair statistic FST also revealed significant genetic
 structural differences between Chinese marginal seas and the Japanese
 basin. This exceptional phylogeographic architecture in S. horneri,
 initially shaped by historical geographic isolation during the late
 Pleistocene ice age and physical biogeographic barriers, can be
 complicated by oceanographic regimes (ocean surface currents) and
 relocating behavior such as oceanic drifting.
description: Cox3
 sequencesThe original sequencing
 results of mitochondrial Cox3 gene for 30 populations of Sargassum
 horneri.rbcL
 sequencesThe original sequencing
 results of chloroplast rbcL gene of eight population from Chinese
 coastline, together with five rbcL gene sequences from
 Japan.Haplotype and locality
 (Cox3)MtDNA Cox3 haplotypes
 and distribution information of Sargassum horneri examined in this
 study.Haplotype and locality
 (rbcL)CpDNA rbcL haplotypes
 and distribution information of Sargassum horneri examined in this
 study.
DOI: 10.5061/dryad.6kd25
title: Data from: Bounds to parapatric speciation: A dobzhansky-muller incompatibility model involving autosomes, X chromosomes and mitochondria

description: We investigate the conditions for the origin and maintenance of
 postzygotic isolation barriers, so called (Bateson-)Dobzhansky-Muller
 incompatibilities or DMIs, among populations that are connected by gene
 flow. Specifically, we compare the relative stability of pairwise DMIs
 among autosomes, X chromosomes, and mitochondrial genes. In an analytical
 approach based on a continent-island framework, we determine how the
 maximum permissible migration rates depend on the genomic architecture of
 the DMI, on sex bias in migration rates, and on sex-dependence of allelic
 and epistatic effects, such as dosage compensation. Our results show that
 X-linkage of DMIs can enlarge the migration bounds relative to autosomal
 DMIs or autosome-mitochondrial DMIs, in particular in the presence of
 dosage compensation. The effect is further strengthened with male-biased
 migration. This mechanism might contribute to a higher density of DMIs on
 the X chromosome (large X-effect) that has been observed in several
 species clades. Furthermore, our results agree with empirical findings of
 higher introgression rates of autosomal compared to X-linked loci.
description: Code & Simulations
 for Fig. A.1-A.3 in SIIn the Mathematica
 Notebook we provide the programming code for numerical calculations,
 simulations and the simulation data used for Figures A.1, A.2 and A.3 of
 Section A of the Supporting Information. Please find detailed commentary
 on the codes in the Mathematica Notebook.Simulation_Code_Data_Archive_Hoellinger_Hermisson_2017.nb
DOI: 10.5061/dryad.j92fs
title: Data from: The evolutionary history of Darwin's finches: speciation, gene flow, and introgression in a fragmented landscape

description: Many classic examples of adaptive radiations take place within fragmented
 systems such as islands or mountains, but the roles of mosaic landscapes
 and variable gene flow in facilitating species diversification is poorly
 understood. Here we combine phylogenetic and landscape genetic approaches
 to understand diversification in Darwin's finches, a model adaptive
 radiation. We combined sequence data from 14 nuclear introns,
 mitochondrial markers, and microsatellite variation from 51 populations of
 all 15 recognized species. Phylogenetic species-trees recovered seven
 major finch clades: ground, tree, vegetarian, Cocos Island, grey and green
 warbler finches, and a distinct clade of sharp-beaked ground finches
 (Geospiza cf. difficilis) basal to all ground and tree finches. The ground
 and tree finch clades lack species-level phylogenetic structure.
 Interisland gene flow and interspecies introgression vary geographically
 in predictable ways. First, several species exhibit concordant patterns of
 population divergence across the channel separating the Galápagos platform
 islands from the separate volcanic province of northern islands. Second,
 peripheral islands have more admixed populations while central islands
 maintain more distinct species boundaries. This landscape perspective
 highlights a likely role for isolation of peripheral populations in
 initial divergence, and demonstrates that peripheral populations may
 maintain genetic diversity through outbreeding during the initial stages
 of speciation.
description: ALL_finches_speciesStructure File of all Galapagos finches used in microsatellite analyses. Island of origin is noted by a numerical key. 1) Daphne 2) Santa Cruz 3) Santiago 4) Genovesa 5) Rabida 6) Albany 7) Espanola 8) Wolf (Wenman) 9) Pinzon 10) Darwin (Culpepper) 11) Marchena 12) Champion 13) Gardner 14) Floreana 15) Santa Fe 16) San Cristobal 17) Pinta 18) Fernandina 19) IsabelaALL_finches_pop.txt
DOI: 10.5061/dryad.fp4h2
title: Data from: Comparison of diets for largemouth and smallmouth bass in Eastern Lake Ontario using DNA barcoding and stable isotope analysis

description: Largemouth (LMB: Micropterus salmoides) and Smallmouth Bass (SMB:
 Micropterus dolomieu) are important species in the recreational fisheries
 of the Laurentian Great Lakes. The invasion of the Round Goby (Neogobius
 melanostomus) into these lakes has changed several facets of black bass
 biology, but there is still much to learn about the relationship between
 these species. Previous dietary analyses have shown Round Goby to be
 important prey for bass, but have been limited by low visual
 identification rates of dissected stomach items. Within the present study,
 DNA barcoding and stable isotope analysis improve prey identification and
 provide a more quantitative dietary analysis of adult black bass in Lake
 Ontario, comparing the importance of Round Goby as prey between these two
 species. Eighty-four LMB (406mm fork length ±4mm SEM) and two hundred
 sixty-four SMB (422mm ±2mm) obtained as tournament mortalities had prey
 identified using DNA-based methods. Round Goby was the most prevalent prey
 species for both predators. The diet of LMB was three times more diverse
 than that of SMB, which almost entirely consists of Round Goby. Our
 results provide further support that recent increases in the size of Lake
 Ontario bass are a result of Round Goby consumption, and that the effects
 of this dietary shift on body condition are greater for SMB. Techniques
 developed in this study include: reverse-oriented dual priming
 oligonucleotides used as blocking primers for predator DNA, and an
 automated design approach of restriction fragment length polymorphism
 tests for identifying prey DNA barcodes.
description: Sequence
 DataChromatogram quality
 scores, partial COI barcode sequences and probability of placement for all
 prey identified with DNA barcoding.Morphological
 DataMorphological
 information regarding the Largemouth Bass and Smallmouth Bass used in this
 study, as well as the visual identification data of prey dissected from
 their stomachs. Sample collection sites included in the README
 file.
DOI: 10.5061/dryad.h75rk
title: Data from: Cold-seeking behaviour mitigates reproductive losses from fungal infection in Drosophila

description: 1. Animals must tailor their life history strategies to suit the
 prevailing conditions and respond to hazards in the environment. Animals
 with lethal infections are faced with a difficult choice: to allocate more
 resources to reproduction and suffer higher mortality or to reduce
 reproduction with the expectation of enhanced immunity and late-age
 reproduction. But, how they do this is largely unknown. 2. Here, we have
 investigated the temperature preference of the fruit fly, Drosophila
 melanogaster, during infection with the fungal pathogen, Metarhizium
 robertsii, and the consequences of temperature preference on life history
 traits. We have used multiple measurements to assess the fitness
 consequences of temperature including age-specific changes in mortality
 rate and reproduction, providing more sensitive measures of accounting for
 variation in fitness with age. 3. We report that D. melanogaster optimizes
 its life history by exploiting thermal variation. Fungus-infected fruit
 flies seek out cooler temperatures, which immediately reduces their
 fecundity but, ultimately, increases their lifetime reproductive success.
 Colder temperatures reduced fungal growth rates both in vivo and in vitro,
 indicating that cooler temperatures increased resistance to the infection.
 4. By comparing life history responses in infected and control animals, we
 found that cold seeking in infected animals facilitates a trade off
 between early- and late-age reproduction, but does not otherwise provide
 life history benefits that are specific to infected animals. These results
 indicate that cold-seeking is a mechanism for reducing the reproductive
 costs of infection. In contrast, uninfected control flies prefer warmer
 temperatures that optimise reproductive success via a rapid propagation
 strategy. 5. These findings help explain how life history trade-offs are
 mediated and how animals cope with infection, which will be increasingly
 important given the recent emergence of fungal pathogens and global
 climate change.
description: Hunt_et_al_2015_Dryad_data_sheetsRaw data collected from laboratory experiments used for the following analyses: sheet 1. Age-specific fecundity, sheet 2. In vivo fungal growth, sheet 3. Tolerance (Mortality vs. CFUs), sheet 4. Intrinsic rate of increase, sheet 5. Lifetime reproductive success, sheet 6. Survival (individual vials), sheet7. Mortality (population cages), sheet 8. Temperature preference. Key: NT - no treatment, HT - heat-killed fungal treatment, MR - Live fungal treatment.Hunt_et_el_2015_Dryad_data_sheets.xlsx
DOI: 10.5061/dryad.96bc0
title: Data from: Sex-related online behaviors, perceived peer norms and adolescents’ experience with sexual behavior: testing an integrative model

description: Research on the role of sex-related Internet use in adolescents’ sexual
 development has often isolated the Internet and online behaviors from
 other, offline influencing factors in adolescents’ lives, such as
 processes in the peer domain. The aim of this study was to test an
 integrative model explaining how receptive (i.e., use of sexually explicit
 Internet material [SEIM]) and interactive (i.e., use of social networking
 sites [SNS]) sex-related online behaviors interrelate with perceived peer
 norms in predicting adolescents’ experience with sexual behavior.
 Structural equation modeling on longitudinal data from 1,132 Dutch
 adolescents (Mage T1 = 13.95; range 11-17; 52.7% boys) demonstrated
 concurrent, direct, and indirect effects between sex-related online
 behaviors, perceived peer norms, and experience with sexual behavior. SEIM
 use (among boys) and SNS use (among boys and girls) predicted increases in
 adolescents’ perceptions of peer approval of sexual behavior and/or in
 their estimates of the numbers of sexually active peers. These
 perceptions, in turn, predicted increases in adolescents’ level of
 experience with sexual behavior at the end of the study. Boys’ SNS use
 also directly predicted increased levels of experience with sexual
 behavior. These findings highlight the need for multisystemic research and
 intervention development to promote adolescents’ sexual health.
description: Data from: Sex-related
 Online Behaviors, Perceived Peer Norms and Adolescents’ Experience with
 Sexual Behavior: Testing an Integrative ModelSPSS file containing
 data from: Sex-related Online Behaviors, Perceived Peer Norms and
 Adolescents’ Experience with Sexual Behavior: Testing an Integrative
 ModelPLOS
 ONE data.savData from: Sex-related
 Online Behaviors, Perceived Peer Norms and Adolescents’ Experience with
 Sexual Behavior: Testing an Integrative ModelCVS file containing data
 from: Sex-related Online Behaviors, Perceived Peer Norms and Adolescents’
 Experience with Sexual Behavior: Testing an Integrative
 ModelPLOS
 ONE data.csv
DOI: 10.5061/dryad.3hq923hn
title: Data from: Maintaining genetic diversity and population panmixia through dispersal and not gene flow in a holocyclic heteroecious aphid species

description: Heteroecious holocyclic aphids exhibit both sexual and asexual
 reproduction and alternate among primary and secondary hosts. Most of
 these aphids can feed on several related hosts, and invasions to new
 habitats may limit the number of suitable hosts. For example, the aphid
 specialist Aphis glycines survives only on the primary host buckthorn
 (Rhamnus spp.) and the secondary host soybean (Glycine max) in North
 America where it is invasive. Owing to this specialization and sparse
 primary host distribution, host colonization events could be localized and
 involve founder effects, impacting genetic diversity, population structure
 and adaptation. We characterized changes in the genetic diversity and
 structure across time among A. glycines populations. Populations were
 sampled from secondary hosts twice in the same geographical location: once
 after secondary colonization (early season), and again immediately before
 primary host colonization (late season). We tested for evidence of founder
 effects and genetic isolation in early season populations, and whether or
 not late-season dispersal restored genetic diversity and reduced
 fragmentation. A total of 24 single-nucleotide polymorphisms and 6
 microsatellites were used for population genetic statistics. We found
 significantly lower levels of genotypic diversity and more genetic
 isolation among early season collections, indicating secondary host
 colonization occurred locally and involved founder effects. Pairwise FST
 decreased from 0.046 to 0.017 in early and late collections, respectively,
 and while genetic relatedness significantly decreased with geographical
 distance in early season collections, no spatial structure was observed in
 late-season collections. Thus, late-season dispersal counteracts the
 secondary host colonization through homogenization and increases genetic
 diversity before primary host colonization.
description: glycines_dryadPopulation genetic data for Aphis glycines using 26 loci (20 SNPs and 6 microsatellites) in GenePop format
DOI: 10.5061/dryad.8qd33
title: Data from: Drug repurposing: a systematic approach to evaluate candidate oral neuroprotective interventions for secondary progressive multiple sclerosis

description: Objective: To develop and implement an evidence based framework to select,
 from drugs already licenced, candidate oral neuroprotective drugs to be
 tested in secondary progressive multiple sclerosis. Design: Systematic
 review of clinical studies of oral putative neuroprotective therapies in
 MS and four other neurodegenerative diseases with shared pathological
 features, followed by systematic review and meta-analyses of the in vivo
 experimental data for those interventions. We presented summary data to an
 international multi-disciplinary committee, which assessed each drug in
 turn using pre-specified criteria including consideration of mechanism of
 action. Results: We identified a short list of fifty-two candidate
 interventions. After review of all clinical and pre-clinical evidence we
 identified ibudilast, riluzole, amiloride, pirfenidone, fluoxetine,
 oxcarbazepine, and the polyunsaturated fatty-acid class (Linoleic Acid,
 Lipoic acid; Omega-3 fatty acid, Max EPA oil) as lead candidates for
 clinical evaluation. Conclusions: We demonstrate a standardised and
 systematic approach to candidate identification for drug rescue and
 repurposing trials that can be applied widely to neurodegenerative
 disorders.
description: MS PLoS
 datasetExcel file extract from
 MS Access database describing clinical studies indentified in the review,
 and our assessment of their risk of bias