cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fp659276
title: Data from: Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal

description: Identifying natural barriers to movements of hosts associated with
 infectious diseases is essential for developing effective control
 strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for
 humans because its main vector, the raccoon (Procyon lotor), is found near
 residential areas. In Québec, Canada, all cases of RRV found in raccoons
 since 2006 were detected on the eastern side of the Richelieu River,
 suggesting that this river acts as a barrier to gene flow and thus, the
 potential for RRV to spread. The objectives of this study were to
 characterize the genetic structure of raccoon populations and assess the
 effect of the Richelieu River on the population structure in southern
 Québec, Canada. We also evaluated whether RRV spread potential differed
 between sex and at a larger spatial scale. Our analyses revealed a weak
 signal of genetic differentiation among individuals located on each side
 of the Richelieu River. At a larger spatial scale, genetic structuring was
 weak. Our results suggest that rivers might not always efficiently
 restrain raccoon movements and spread of RRV. We suggest that the
 difference in genetic structure found between sexes can be partly
 explained by male movements during the breeding season in winter, when ice
 bridges allow passage over most rivers in Québec.
description: data within RRV
 areaGenetic data for animal
 located within the RRV surveillance area.data sites outside RRV
 areaData for sites on the
 North shore of the St-Lawrence River and on Islands.
DOI: 10.5061/dryad.3n901
title: Data from: Diagnostic performance of alpha-fetoprotein, protein induced by vitamin K absence, osteopontin, Dickkopf-1 and its combinations for hepatocellular carcinoma

description: Background & Aims: Alpha-fetoprotein (AFP) is the most widely used
 serum biomarker for hepatocellular carcinoma (HCC), despite its
 limitations. As complementary biomarkers, protein induced by vitamin K
 absence (PIVKA-II), osteopontin (OPN), and Dickkopf-1 (DKK-1) have been
 proposed. This study aimed to perform a head-to-head comparison of the
 diagnostic performance of AFP, PIVKA-II, OPN and DKK-1 as single or in
 combination to seek the best biomarker or panel, and to investigate the
 clinical factors affecting their performance. Methods: Using 401 stored
 plasma samples obtained from 208 HCC patients and 193 liver cirrhosis
 control patients, plasma AFP, PIVKA-II, OPN and DKK-1 levels were measured
 by ELISA, and receiver operating characteristic curve analyses were
 performed for each biomarker and for every combination of two to four
 markers. Results: Of the four biomarkers, AFP showed the highest area
 under the curve (0.786). The sensitivity and specificity for each single
 biomarker was 62% and 90.2% (AFP&gt;20 ng/mL), 51.0% and 91.2%
 (PIVKA-II&gt;10 ng/mL), 46.2% and 80.3% (OPN&gt;100 ng/mL), and
 50.0% and 80.8% (DKK-1&gt;500 pg/mL), respectively. Among the
 combinations of two biomarkers, AFP&gt;20 ng/mL or DKK-1&gt;500
 pg/mL showed the best diagnostic performance (sensitivity 78.4%,
 specificity 72.5%). Triple or quadruple combination did not improve the
 diagnostic performance further. The patient’s age, etiology and tumor
 invasiveness of HCC affected the performance of each marker. Conclusions:
 AFP was the most useful single biomarker for HCC diagnosis, and the
 combined measurement of AFP and DKK-1 could maximize the diagnostic yield.
 Clinical decision should be based on the consideration of various factors
 affecting the diagnostic performance of each biomarker. Efforts to seek
 novel HCC biomarkers should be continued.
description: HCC_biomarker_160206_data
DOI: 10.5061/dryad.0tc6q
title: Data from: The contemporary genetic pattern of European moose is shaped by postglacial recolonization, bottlenecks, and the geographical barrier of the Baltic Sea

description: To investigate genetic diversity and the population structure of the
 European moose (Alces alces), we analyzed 14 microsatellite loci for 694
 samples collected across 16 localities. The highest genetic diversity was
 detected in Belarus and Russia and the lowest was found in Scandinavia.
 Two major genetic clusters existed, Scandinavian and continental, and some
 further spatial structure was detected. There was high concordance between
 the spatial distribution of microsatellite clusters analyzed in the
 present study and previously recognized mitochondrial DNA clades of moose.
 The split of genetic lineages calculated using approximate Bayesian
 computation (ABC) occurred at the beginning of the Last Glacial Maximum:
 approximately 29 000 and 28 000 years BP. A range-wide bottleneck detected
 by ABC took place 1800–1200 years BP, although a more recent decline in
 moose numbers was also documented in the 18th to early 20th Century.
 Genetic differentiation in European moose increased with geographical
 distance, and the Baltic Sea appeared to be a barrier to gene flow. We
 conclude that isolation in different glacial refugia, postglacial
 colonization, and declines of range and numbers in Holocene shaped the
 present pattern of genetic diversity of European moose. Based on genetic
 divergence and a lack of apparent gene flow, the contemporary Scandinavian
 and continental subpopulations should be treated as separate management
 units.
description: Microsatellite data of
 European moose from 16 localitiesGenAlex input file, data
 of 14 microsatellite lociMoose16pops.xlsx
DOI: 10.5061/dryad.b7m47
title: Data from: Long-term aggregation of larval fish siblings during dispersal along an open coast

description: Pelagic dispersal of most benthic marine organisms is a fundamental driver
 of population distribution and persistence and is thought to lead to
 highly mixed populations. However, the mechanisms driving dispersal
 pathways of larvae along open coastlines are largely unknown. To examine
 the degree to which early stages can remain spatially coherent during
 dispersal, we measured genetic relatedness within a large pulse of newly
 recruited splitnose rockfish (Sebastes diploproa), a live-bearing fish
 whose offspring settle along the US Pacific Northwest coast after spending
 up to a year in the pelagic environment. A total of 11.6% of the recruits
 in a single recruitment pulse were siblings, providing the first evidence
 for persistent aggregation throughout a long dispersal period. Such
 protracted aggregation has profound implications for our understanding of
 larval dispersal, population connectivity, and gene flow within demersal
 marine populations.
description: S.diploproa_recruit_genotypesMicrosatellite (20 loci) genotype data from 491 juvenile Sebastes diploproa recruiting to Oregon in September 2013.S.diploproa_referencePop_genotypesMicrosatellite (20 loci) genotipe data of 94 adult Sebastes diploproa collected off the Oregon Coast in May-July 2015.
DOI: 10.5061/dryad.75c77
title: Data from: Trans-generational parasite protection associated with paternal diet

description: Multiple generations of hosts are often exposed to the same pathogens,
 favoring the evolution of trans-generational defenses. Because females
 have more opportunities to transfer protective molecules to offspring,
 many studies have focused on maternally derived protection. However, males
 of many species can transfer compounds along with sperm, including
 chemicals that could provide protection. Here, we assess maternally and
 paternally derived protection in a monarch butterfly-protozoan parasite
 system where parasite resistance is heavily influenced by secondary plant
 chemicals, known as cardenolides, present in the larval diet of milkweed
 plants. We reared monarch butterflies on medicinal and non-medicinal
 milkweed species, then measured resistance of their offspring to
 infection. We also measured cardenolide content in adult monarchs reared
 on the two species, and in the eggs that they produced. We found that
 offspring were more resistant to infection when their fathers were reared
 on medicinal milkweed, while maternal diet had less of an effect. We also
 found that eggs contained the highest levels of cardenolides when both
 parents were reared on the medicinal species. Moreover, females reared on
 non-medicinal milkweed produced eggs with significantly higher levels of
 cardenolides if they mated with males reared on the medicinal milkweed
 species. However, we found an equivocal relationship between the
 cardenolides present in eggs and parasite resistance in the offspring. Our
 results demonstrate that males reared on medicinal plants can transfer
 protection to their offspring, but the exact mechanism remains unresolved.
 This suggests that paternal protection from parasitism might be important,
 particularly when there are environmental sources of parasite resistance
 and when males transfer spermatophores during mating.
description: Infection Data -
 Experiment 1 & 2Pupal score data
 (measure of infection) for pilot experiment and larger
 repeat.Eggdatacombined.txtEgg Cardenolides - Experiment 1 & 2Chemical analysis of cardenolides in eggs sampled during experiment 1 & 2.CardenolidesEggs_Expt1and2.csvOffspring data - Experiment 2All data collected from offspring in experiment 2.Eggexperiment2.csvCardenolides data - Experiment 3Chemical analysis of cardenolides in plants, adults, and eggs sampled during experiment 3.CardenolideAll_Experiment 3.csv
DOI: 10.5061/dryad.7j2d4
title: Data from: Specialist insect herbivore and light availability do not interact in the evolution of an invasive plant

description: Release from specialist insect herbivores may allow invasive plants to
 evolve traits associated with decreased resistance and increased
 competitive ability. Given that there may be genetic trade-off between
 resistance and tolerance, invasive plants could also become more tolerant
 to herbivores. Although it is widely acknowledged that light availability
 affects tolerance to herbivores, little information is available for
 whether the effect of light availability on tolerance differ between the
 introduced and native populations. We conducted a common garden experiment
 in the introduced range of Alternanthera philoxeroides using ten invasive
 US and ten native Argentinean populations at two levels of light
 availability and in the presence or absence of a specialist stem-boring
 insect Agasicles hygrophila. Plant biomass (total and storage root
 biomass), two allocation traits (root/shoot ratio and branch intensity,
 branches biomass/main stem biomass) and two functional traits (specific
 stem length and specific leaf area), which are potentially associated with
 herbivore resistance and light capture, were measured. Overall, we found
 that A. philoxeroides from introduced ranges had comparable biomass and
 tolerance to specialist herbivores, lower branch intensity, lower specific
 stem length and specific leaf area. Moreover, introduced populations
 displayed higher shade tolerance of storage root biomass and lower plastic
 response to shading in specific stem length. Finally, light availability
 had no significant effect on evolution of tolerance to specialist
 herbivores of A. philoxeroides. Our results suggest that post-introduction
 evolution might have occurred in A. philoxeroides. While light
 availability did not influence the evolution of tolerance to specialist
 herbivores, increased shade tolerance and release from specialist insects
 might have contributed to the successful invasion of A. philoxeroides.
description: raw
 data
DOI: 10.5061/dryad.3p93t
title: Data from: Geographical variation in species' population responses to changes in temperature and precipitation

description: Despite increasing concerns about the vulnerability of species’
 populations to climate change, there has been little overall synthesis of
 how individual population responses to variation in climate differ between
 taxa, with trophic level or geographically. To address this, we extracted
 data from 132 long-term (≥20 years) studies of population responses to
 temperature and precipitation covering 236 animal and plant species across
 terrestrial and freshwater habitats. Temperature tended to have a greater
 overall impact on populations than precipitation, although the effects of
 increased precipitation varied strongly with latitude, being most positive
 at low latitudes. Population responses to increased temperature were
 generally positive, but did not vary significantly with latitude. Studies
 reporting significant climatic trends through time tended to show more
 negative effects of temperature and more positive effects of precipitation
 upon populations than other studies. Our results identify likely
 geographical differences in the effects of climate change on populations
 and communities. Most studies of climate change impacts on biodiversity
 have focussed on temperature and are from middle to high northern
 latitudes; our results suggest their findings may be less applicable to
 low latitudes, where most species occur and where variation in
 precipitation under climate change may be more important in determining
 demographic responses.
description: Full data set used for
 analysisSummarised data
 extracted from reviewed papers which underpins all analysis reported in
 the paper. All column headings should be self-explanatory with reference
 to the final paper.Pearce-Higgins et al Proc Roy
 Soc B data.xlsx
DOI: 10.5061/dryad.6008n
title: Data from: Genetic variation in male-induced harm in Drosophila melanogaster

description: In Drosophila melanogaster, prolonged exposure to males reduces the
 longevity and fecundity of females. This harm arises from the effects of
 male courtship behaviours and the toxic side effects of the accessory
 gland proteins (Acps) in their seminal fluids. Here, we examine the
 relationship between male exposure and its harmful effect on the lifetime
 fitness of his mates, and quantify the genetic basis for this variation.
 We found significant additive genetic variation in the magnitude of harm
 that males impose on females by exposing females to males from a variety
 of hemiclonal backgrounds for either a brief or prolonged period of time
 and measuring their fecundity, a meaningful fitness index. Furthermore, we
 discovered a strong negative correlation between the magnitude of harm and
 the short-term effects of male exposure on female fitness. We discuss the
 evolutionary significance of these results with regards to potential
 life-history trade-offs in females, and its relationship to male body
 size.
description: Raw Fecundity
 DataData file containing the
 measures of individual fecundity (egg count) across all treatments in our
 experiments. This was used in our analysis shown in Figure
 1.Filice_Long_Data_Dryad.csvMean Fecundity and Mass DataMean values of our mass and fecundity data across our 26 hemiclone lines. This was used for our correlation analysis in Figure 2.Fecundity_Mass_data.csvRaw Mass DataRaw data of male hemiclone mass.Hemiclone_male_weights.csvSupplmental R CodesAnnotated R codes used for our data analyses.Filice_Long_Supplmental_R_Codes.R
DOI: 10.6084/m9.figshare.31152310
title: Phenotypic and Genomic Characterization of <i>Trichophyton schoenleinii </i>Isolates from Atypical Favus Cases in China

description: Data of Figure 1. Growth characteristics of <i>Trichophyton schoenleinii </i>isolates from sporadic and endemic regions at different temperatures.Data of Figure 2. Phylogenetic analysis reveals distinct population structure between <i>Trichophyton schoenleinii </i>strains from endemic (Xinjiang) and sporadic regions.Data of Figure 3. Population genetic structure of <i>Trichophyton schoenleinii </i>strains from different geographic regions.<br>Data of Figure 4. Gene family evolution and functional analysis of unique genes in <i>Trichophyton schoenleinii </i>.<br>Data of Figure 5. Phylogenetic position of <i>Trichophyton schoenleinii </i>among dermatophytes based on single-copy orthologous genes.<br>Table 1: Minimum Inhibitory Concentrations of Antifungal Agents against <i>Trichophyton schoenleinii </i><i> </i>(mg/L) .Table 2: Comparison of Genomic Information.Table 3: Gene Ontology (GO) terms enrichment analysis of Ts2918 strain unique genes compared with <i>Trichophyton</i><i> rubrum</i> CBS118892.
DOI: 10.5061/dryad.j6065
title: Data from: The evolution of experience-mediated plasticity in mate preferences

description: Experience of sexual signals can alter mate preferences and influence the
 course of sexual selection. Here, we examine patterns of
 experience-mediated plasticity in mate preferences that can arise in
 response to variation in the composition of mates in the environment. We
 use these patterns to test hypotheses about potential sources of selection
 favouring experience-mediated plasticity. We manipulated signal experience
 of female Enchenopa treehoppers (Hemiptera: Membracidae) in a vibrational
 playback experiment with the following treatments: silence; two types of
 non-preferred signal; preferred signals; and a mixture of preferred and
 non-preferred signals. This experiment revealed plasticity in mate
 preference selectivity, with greatest selectivity in the mixed signal
 treatment, followed by the preferred signal treatment. We found no
 plasticity in peak preference. These results suggest that females have
 been selected to adjust preference selectivity according to the
 variability of potential mates in their social environment, as well as to
 the presence/absence of preferred mates. We discuss how
 experience-mediated plasticity in mate preferences can influence the
 strength of selection on male signals and can result in evolutionary
 dynamics between variation in preferences and signals that either promote
 the maintenance of variation or facilitate rapid trait fixation.
description: Female treehopper
 responses to stimuli varying in frequencyData collected by
 vibrational playback experiment. Each female had the opportunity to
 respond to 19 stimuli varying in frequency (Hz). These are raw data
 responses in excel format for each of these stimuli. Treatment refers to
 the experience females had before becoming sexually receptive (high is
 high frequency, low is low frequency, in relationship to the population
 mean). Replicate refers to the replicate plant that a given female was
 on.dryaddata_plast2.xlsx
DOI: 10.6084/m9.figshare.31152310.v2
title: Phenotypic and Genomic Characterization of <i>Trichophyton schoenleinii </i>Isolates from Atypical Favus Cases in China

description: Data of Figure 1. Growth characteristics of <i>Trichophyton schoenleinii </i>isolates from sporadic and endemic regions at different temperatures.Data of Figure 2. Phylogenetic analysis reveals distinct population structure between <i>Trichophyton schoenleinii </i>strains from endemic (Xinjiang) and sporadic regions.Data of Figure 3. Population genetic structure of <i>Trichophyton schoenleinii </i>strains from different geographic regions.<br>Data of Figure 4. Gene family evolution and functional analysis of unique genes in <i>Trichophyton schoenleinii </i>.<br>Data of Figure 5. Phylogenetic position of <i>Trichophyton schoenleinii </i>among dermatophytes based on single-copy orthologous genes.<br>Table 1: Minimum Inhibitory Concentrations of Antifungal Agents against <i>Trichophyton schoenleinii </i><i> </i>(mg/L) .Table 2: Comparison of Genomic Information.Table 3: Gene Ontology (GO) terms enrichment analysis of Ts2918 strain unique genes compared with <i>Trichophyton</i><i> rubrum</i> CBS118892.
DOI: 10.6084/m9.figshare.31152310.v3
title: Phenotypic and Genomic Characterization of <i>Trichophyton schoenleinii </i>Isolates from Atypical Favus Cases in China

description: Data of Figure 1. Growth characteristics of <i>Trichophyton schoenleinii </i>isolates from sporadic and endemic regions at different temperatures.Data of Figure 2. Phylogenetic analysis reveals distinct population structure between <i>Trichophyton schoenleinii </i>strains from endemic (Xinjiang) and sporadic regions.Data of Figure 3. Population genetic structure of <i>Trichophyton schoenleinii </i>strains from different geographic regions.<br>Data of Figure 4. Gene family evolution and functional analysis of unique genes in <i>Trichophyton schoenleinii </i>.<br>Data of Figure 5. Phylogenetic position of <i>Trichophyton schoenleinii </i>among dermatophytes based on single-copy orthologous genes.<br>Table 1: Minimum Inhibitory Concentrations of Antifungal Agents against <i>Trichophyton schoenleinii </i><i> </i>(mg/L) .Table 2: Comparison of Genomic Information.Table 3: Gene Ontology (GO) terms enrichment analysis of Ts2918 strain unique genes compared with <i>Trichophyton</i><i> rubrum</i> CBS118892.
DOI: 10.5061/dryad.20pj467
title: Data from: Behavioural tactics used by invasive cane toads (Rhinella marina) to exploit apiaries in Australia

description: Behavioural flexibility plays a key role in facilitating the ability of
 invasive species to exploit anthropogenically-created resources. In
 Australia, invasive cane toads (Rhinella marina) often gather around
 commercial beehives (apiaries), whereas native frogs do not. To document
 how toads use this resource, we spool-tracked cane toads in areas
 containing beehives and in adjacent natural habitat without beehives,
 conducted standardized observations of toad feeding behaviour, and ran
 prey-manipulation trials to compare the responses of cane toads versus
 native frogs to honeybees as potential prey. Toads feeding around beehives
 travelled shorter distances per night, and hence used different
 microhabitats, than did toads from nearby control sites without beehives.
 The toads consumed live bees from the hive entrance (rather than dead bees
 from the ground), often climbing on top of one another to gain access to
 the hive entrance. Prey manipulation trials confirm that bee movement is
 the critical stimulus that elicits the toads’ feeding response; and in
 standardized trials, native frogs consumed bees less frequently than did
 toads. In summary, cane toads flexibly modify their movements, foraging
 behaviour and dietary composition to exploit the nutritional opportunities
 created by commercial beehives, whereas native anurans do not.
description: Data for all experiments
 undertaken in "Behavioural tactics used by invasive cane
 toads..."All data described in
 this paper can be found under each tab in the Excel
 file.Data_behavioural tactics of
 cane toads.xlsx