cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.96ng4
title: Data from: Precopulatory but not postcopulatory male reproductive traits diverge in response to mating system manipulation in Drosophila melanogaster

description: Competition between males creates potential for pre- and postcopulatory
 sexual selection and conflict. Theory predicts that males facing risk of
 sperm competition should evolve traits to secure their reproductive
 success. If those traits are costly to females, the evolution of such
 traits may also increase conflict between the sexes. Conversely, under the
 absence of sperm competition, one expectation is for selection on male
 competitive traits to relax thereby also relaxing sexual conflict.
 Experimental evolution studies are a powerful tool to test this
 expectation. Studies in multiple insect species have yielded mixed and
 partially conflicting results. In this study, we evaluated male
 competitive traits and male effects on female costs of mating in
 Drosophila melanogaster after replicate lines evolved for more than 50
 generations either under enforced monogamy or sustained polygamy, thus
 manipulating the extent of intrasexual competition between males. We found
 that in a setting where males competed directly with a rival male for
 access to a female and fertilization of her ova polygamous males had
 superior reproductive success compared to monogamous males. When comparing
 reproductive success solely in double mating standard sperm competition
 assays, however, we found no difference in male sperm defense
 competitiveness between the different selection regimes. Instead, we found
 monogamous males to be inferior in precopulatory competition, which
 indicates that in our system, enforced monogamy relaxed selection on
 traits important in precopulatory rather than postcopulatory competition.
 We discuss our findings in the context of findings from previous
 experimental evolution studies in Drosophila ssp. and other invertebrate
 species.
description: rawdata for all
 experimentsThis file includes
 rawdata for all phenotypes described within this study.rawdata_for_dryad.xlsx
DOI: 10.5061/dryad.8004pp3
title: Data from: Using risk of bias domains to identify opportunities for improvement in food- and nutrition-related research: an evaluation of research type and design, year of publication, and source of funding

description: Purpose: This retrospective cross-sectional study aimed to identify
 opportunities for improvement in food and nutrition research by examining
 risk of bias (ROB) domains. Methods: Rating were extracted from critical
 appraisal records for 5675 studies used in systematic reviews conducted by
 three organizations. Variables were as follows: ROB domains defined by the
 Cochrane Collaboration (Selection, Performance, Detection, Attrition, and
 Reporting), publication year, research type (intervention or observation)
 and specific design, funder, and overall quality rating (positive,
 neutral, or negative). Appraisal instrument questions were mapped to ROB
 domains. The kappa statistic was used to determine consistency when
 multiple ROB ratings were available. Binary logistic regression and
 multinomial logistic regression were used to predict overall quality and
 ROB domains. Findings: Studies represented a wide variety of research
 topics (clinical nutrition, food safety, dietary patterns, and dietary
 supplements) among 15 different research designs with a balance of
 intervention (49%) and observation (51%) types, published between 1930 and
 2015 (64% between 2000-2009). Duplicate ratings (10%) were consistent
 (k=0.86-0.94). Selection and Performance domain criteria were least likely
 to be met (57.9% to 60.1%). Selection, Detection, and Performance ROB
 ratings predicted neutral or negative quality compared to positive quality
 (p&lt;0.001). Funder, year, and research design were significant
 predictors of ROB. Some sources of funding predicted increased ROB
 (p&lt;0.001) for Selection (Interventional: industry only and none/not
 reported; Observational: other only and none/not reported) and Reporting
 (Observational: university only and other only). Reduced ROB was predicted
 by combined and other-only funding for intervention research
 (p&lt;0.005). Performance ROB domain ratings started significantly
 improving in 2000; others improved after 1990 (p&lt;0.001). Research
 designs with higher ROB were nonrandomized intervention and time series
 designs compared to RCT and prospective cohort designs respectively
 (p&lt;0.001). Conclusions: Opportunities for improvement in food and
 nutrition research are in the Selection, Performance, and Detection ROB
 domains.
description: Myers Parrott et al
 3-2018 ROBRisk of bias and study
 characteristics of nutrition related research contained in the Academy of
 Nutrition and Dietetics Evidence Analysis Library, the USDA Nutrition
 Evidence Library, and select AHRQ nutrition-related systematic reviews.
 Data in SPSS 24 file and csv with data dictionary in
 Excel.ROB
 in nutrition -related research.zip
DOI: 10.5061/dryad.b3ts34v2
title: Data from: Chromosomal rearrangements do not seem to affect the gene flow in hybrid zones between karyotypic races of the common shrew (Sorex araneus)

description: Chromosomal rearrangements are proposed to promote genetic differentiation
 between chromosomally differentiated taxa and therefore promote
 speciation. Due to their remarkable karyotypic polymorphism, the shrews of
 the Sorex araneus group were used to investigate the impact of chromosomal
 rearrangements on gene flow. Five intraspecific chromosomal hybrid zones
 characterized by different levels of karyotypic complexity were studied
 using 16 microsatellites markers. We observed low levels of genetic
 differentiation even in the hybrid zones with the highest karyotypic
 complexity. No evidence of restricted gene flow between differently
 rearranged chromosomes was observed. Contrary to what was observed at the
 interspecific level, the effect of chromosomal rearrangements on gene flow
 was undetectable within the S. araneus species.
description: Data_Horn et al_ID
 11-0581Genotyping data of the
 five Sorex araneus hybrid zones
DOI: 10.5061/dryad.b96d0
title: Data from: Sexual antagonism in the pistil varies among populations of a hermaphroditic mixed-mating plant

description: Sexual conflicts and their evolutionary outcomes may be influenced by
 population-specific features such as mating system and ecological context;
 however, very few studies have investigated the link between sexual
 conflict and mating system. The self-compatible, mixed-mating
 hermaphrodite Collinsia heterophylla (Plantaginaceae) is thought to
 exhibit a sexual conflict over timing of stigma receptivity. This conflict
 involves 1) delayed stigma receptivity, which intensifies pollen
 competition, and 2) early fertilization forced by pollen, which reduces
 seed set. We investigated the potential for the conflict to occur under
 field conditions and performed greenhouse crosses within eight populations
 to assess its consistency across populations. Flowers were visited, and
 produced seeds after pollination, at all developmental stages, suggesting
 that the conflict can be of significance under natural conditions. In the
 greenhouse, early pollination imposed costs in all populations. Overall,
 the timing of first seed set was most strongly affected by the maternal
 parent, denoting stronger female than male ability to influence onset of
 stigma receptivity. Crosses also revealed a negative relationship between
 donor- and recipient-related onset of receptivity within individuals, a
 novel result hinting at trade-offs in sex-allocation or a history of
 antagonistic selection. Neither timing of stigma receptivity, timing of
 first seed set, nor pollen competitive ability covaried with population
 outcrossing rate. In conclusion, these results indicate that sexually
 antagonistic selection may be present in varying degrees in different
 populations of C. heterophylla, but this variation does not appear to be
 directly related to mating system variation.
description: JEB 12656 Field
 DataCollection of raw data
 from the field experiment conducted for this study.JEB 12656 Glasshouse
 dataRaw data from the
 glasshouse experiments conducted for this study. This contains the
 majority of the data used for this publication. See the sheet titled
 "Readme" if you need any clarifications.JEB 12656
 Microsatellite_genotypesMicrosatellite genotype
 data used to estimate levels of inbreeding for this
 study.
DOI: 10.5061/dryad.49c3jd7
title: Data from: Effect of chemical additives on electrokinetic remediation of Cr-contaminated soil coupled with a permeable reactive barrier

description: Chromium(Cr) contamination in soil, especially Cr(VI) has a serious threat
 to the environment and human health. The electrokinetic remediation (EKR)
 is a promising technology to remediate the Cr(VI). Therefore, EKR coupled
 with a permeable reactive barrier (PRB) was used to treat the Cr(VI)
 contaminated soil in this study. The CTMAB-Z, a modified zeolite (prepared
 by cetyl trimethyl ammonium bromide) alone and a mixture of CTMAB-Z and
 Fe(0) were used as PRB-1 and PRB-2 reactive media, respectively. The
 effect of chemical enhancers/additives i.e. dl-tartaric acid and tween 80
 on EKR of Cr(VI) was also analysed in the contrasting experiments. While,
 the effects of repair time, voltage gradient and dl-tartaric acid
 concentration on Cr(VI) remediation were investigated by utilizing
 multifactor orthogonal experiment which was based on contrasting
 experiments. The contrasting experiment results showed that the highest
 Cr(VI) removal rate(66.27%) and leaching efficiency(71.29%) were observed
 in the experimental group which had dl-tartaric acid and PRB-2.
 Furthermore, the multifactor orthogonal experiment results had depicted
 that the highest Cr(VI) removal rate(80.92%) and leaching
 efficiency(85.25%) were achieved after treating the samples at a voltage
 gradient of 2.5 v/cm for 8 days in presence of 0.15 M concentration of
 dl-tartaric acid. This study demonstrated that Cr(VI) remediation through
 EKR process could be significantly enhanced by the use of PRB and
 additives.
description: Soil
 DataPhysical and chemical
 analysis of soilZeolite
 Data(1)Characterization
 analyses of zeolite before and after modification; (2)Equilibrium
 adsorption experimentContrast Experiments
 DataThe contrast experiments
 dataContrast Experiment
 Data.xlsxMultifactor Experiments
 DataThe multifactor
 experiments dataOptimal combination and
 Cr form DataThe optimal combination
 experiment and Cr form dataOptimal Combination and Cr form
 Data.xlsx
DOI: 10.5061/dryad.38j37
title: Data from: A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

description: Despite the negative economic and ecological impact of weeds, relatively
 little is known about the evolutionary mechanisms that influence their
 persistence in agricultural fields. Here, we use a resurrection approach
 to examine the potential for genotypic and phenotypic evolution in Ipomoea
 purpurea, an agricultural weed that is resistant to glyphosate, the most
 widely used herbicide in current-day agriculture. We found striking
 reductions in allelic diversity between cohorts sampled nine years apart
 (2003 vs. 2012), suggesting that populations of this species sampled from
 agricultural fields have experienced genetic bottleneck events that have
 led to lower neutral genetic diversity. Heterozygosity excess tests
 indicate that these bottlenecks may have occurred prior to 2003. A
 greenhouse assay of individuals sampled from the field as seed found that
 populations of this species, on average, exhibited modest increases in
 herbicide resistance over time. However, populations differed
 significantly between sampling years for resistance: some populations
 maintained high resistance between the sampling years whereas others
 exhibited increased or decreased resistance. Our results show that
 populations of this noxious weed, capable of adapting to strong selection
 imparted by herbicide application, may lose genetic variation as a result
 of this or other environmental factors. We probably uncovered only modest
 increases in resistance on average between sampling cohorts due to a
 strong and previously identified fitness cost of resistance in this
 species, along with the potential that nonresistant migrants germinate
 from the seed bank.
description: SSRResistanceTraits
DOI: 10.5061/dryad.0045q
title: Data from: Natural selection on a measure of parasite resistance varies across ages and environmental conditions in a wild mammal

description: Parasites detrimentally affect host fitness, leading to expectations of
 positive selection on host parasite resistance. However, since immunity is
 costly, host fitness may be maximized at low, but non-zero, parasite
 infection intensities. These hypotheses are rarely tested on natural
 variation in free-living populations. We investigated selection on a
 measure of host parasite resistance in a naturally-regulated Soay sheep
 population using a longitudinal data set, and found negative correlations
 between parasite infection intensity and annual fitness in lambs, male
 yearlings, and adult females. However, having accounted for confounding
 effects of body weight, the effect was only significant in lambs.
 Associations between fitness and parasite resistance were
 environment-dependent, being strong during low-mortality winters, but
 negligible during harsher high-mortality winters. There was no evidence
 for stabilising selection. Our findings reveal processes that may shape
 variation in parasite resistance in natural populations, and illustrate
 the importance of accounting for correlated traits in selection analysis.
description: Hayward et al JEB
 Selection on FECThis data was collected
 in the field over a number of years, and represents raw phenotypic
 observations. Details of treatment of the data prior to analysis are fully
 explained in the corresponding paper.
DOI: 10.5061/dryad.qj153
title: Data from: Description of a new Malagasy treefrog (Boophis) occurring syntopically with its sister species, and a plea for studies on non-allopatric speciation in tropical amphibians

description: Based on concordant differences in male advertisement call, tadpole
 morphology, and absence of haplotype sharing in mitochondrial and nuclear
 DNA markers, we describe a new species of treefrog from Ranomafana
 National Park in the southern central east of Madagascar. In its adult
 stage Boophis narinsi sp. n. is highly similar to its sister species,
 Boophis majori, but appears to differ in having longer hindlimbs. The
 genetic divergences between these two species (2.5-3.3% in a fragment of
 the 16S rRNA gene, depending on fragment length and individual haplotype
 analyzed) are below the threshold typically characterizing distinct
 species of anurans. Together with their relatively small and largely
 overlapping ranges and their sympatric occurrence in Ranomafana National
 Park, this indicates that they potentially could have originated rather
 recently by adaptive speciation under parapatric or sympatric conditions.
 Most studies on amphibian speciation have so far by default assumed
 vicariant speciation. We suggest that alternative speciation scenarios
 should be considered in future works and characterize settings in which
 more reliable assessments of adaptive parapatric or sympatric speciation
 could be carried out.
description: Vences_Boophis_narinsi_description_TableS1Table with voucher specimens and Genbank accession numbersVences_Boophis_narinsi_description_TableS2Distribution of haplotypes among voucher specimens, referring to haplotype networks in publication.
DOI: 10.5061/dryad.fg4bc331
title: Data from: No evidence of inbreeding avoidance despite demonstrated survival costs in a polygynous rodent

description: Individuals are generally predicted to avoid inbreeding because of
 detrimental fitness effects. However, several recent studies have shown
 that limited inbreeding is tolerated by some vertebrate species. Here, we
 examine the costs and benefits of inbreeding in a largely polygynous
 rodent, the yellow-bellied marmot (Marmota flaviventris). We use a
 pedigree constructed from 8 years of genetic data to determine the
 relatedness of all marmots in our study population, and examine offspring
 survival, annual male reproductive success, relatedness between breeding
 pairs, and the effects of group composition on likelihood of male
 reproduction to assess inbreeding in this species. We found decreased
 survival in inbred offspring, but equal net reproductive success among
 males that inbred and those that avoided it. Relatedness between breeding
 pairs was greater than that expected by chance, indicating that marmots do
 not appear to avoid breeding with relatives. Further, male marmots do not
 avoid inbreeding: males mate with equal frequency in groups composed of
 both related and unrelated females and in groups composed of only female
 relatives. Our results demonstrate that inbreeding can be tolerated in a
 polygynous species if the reproductive costs of inbreeding are low and
 individuals that mate indiscriminately do not suffer decreased
 reproductive success.
description: marmat_microsat_data_archive_30oct2011
DOI: 10.5061/dryad.3g141
title: Data from: Hidden diversity within the lizard genus Liolaemus: genetic vs morphological divergence in the L. rothi complex (Squamata:Liolaeminae)

description: Currently, Liolaemus is the second most species-rich reptile genus in the
 world (257 species), and predictions of its real diversity suggest that it
 may be the most diverse genus. Originally, Liolaemus species were
 described as widely distributed and morphologically variable taxa, but
 extensive sampling in previously unexplored geographic areas, coupled with
 molecular and more extensive morphological studies, have discovered an
 unexpectedly high number of previously undetected species. Here, we study
 the level of molecular vs. morphological divergence within the L. rothi
 complex, combining a total of 14 loci (2 mitochondrial and 12 nuclear
 loci) for 97 individuals, as well as morphological data (nine morphometric
 and 15 color pattern variables), that represent all six described species
 of the L. rothi complex, plus two candidate species. We use the
 multi-coalescent species delimitation program iBPP and resolve strong
 differences in molecular divergence; and each species is inferred as an
 independent lineage supported by high posterior probabilities. However,
 morphological differences are not that clear, and our modeling of
 morphological characters suggests differential selection pressures
 implying some level of morphological stasis. We discuss the role of
 natural selection on phenotypic traits, which may be an important factor
 in “hiding” the real diversity of the genus.
description: Fasta
 matrices14 fasta matrices for
 each gene included in analysesfasta-matrices.zipGenBank accession number detailsTable and list with references of each GenBank accession to individuals and genes.GenBank-accessions.zipindividuals-species associationsTable with details of individuals-species associationsImap.txtAppendixAppendix S1, S2 and supplementary Tables.
DOI: 10.5061/dryad.b6k0275
title: Data from: Photoacclimation and induction of light-enhanced calcification in the mesophotic coral Euphyllia paradivisa

description: Corals and their photosymbionts experience inherent changes in light along
 depth gradients, leading them to have evolved several well-investigated
 photoacclimation strategies. As coral calcification is influenced by light
 (a process described as LEC-“light enhanced calcification”), studies have
 sought to determine the link between photosynthesis and calcification, but
 many puzzling aspects still persist. Here we examine the physiology of
 Euphyllia paradivisa, a coral species found at a wide range of depths but
 that is strictly mesophotic in the Red Sea; and also examines the coupling
 between photosynthesis and light-enhanced calcification by investigating
 the response of the coral under several controlled light regimes during a
 long-term experiment. E. paradivisa specimens were collected from 40-50 m
 depth and incubated under three light conditions for a period of one year:
 full-spectrum shallow-water light (~3 m, e.g. shallow-light treatment);
 blue deep-water light (~40 m, e.g. mesophotic-light treatment); or total
 darkness (e.g. dark treatment). Net photosynthesis remained similar in the
 shallow-light treated corals compared to the mesophotic-light treated
 corals, under both low and high light. However, calcification increased
 dramatically with increasing light intensity in the shallow-light treated
 corals suggesting a decoupling between these processes. Photoacclimation
 to shallow-water conditions was indicated by enhanced respiration, a
 higher density of zooxanthellae per polyp, and lower chlorophyll a content
 per cell. The dark-treated corals became completely bleached but did not
 lower their metabolism below that of the mesophotic-light treated corals.
 No Symbiodinium clade shift was found following the year-long light
 treatments. We conclude that E. paradivisa, and its original symbiont
 clade, can adapt to various light conditions by controlling its metabolic
 rate and growth energy investment, and consequently induce LEC.
description: ESM 2 - Photosynthesis
 and calcificationSupporting
 data
DOI: 10.5061/dryad.5fh23
title: Data from: Local adaptation at higher trophic levels: contrasting hyperparasite-pathogen infection dynamics in the field and laboratory

description: Predicting and controlling infectious disease epidemics is a major
 challenge facing the management of agriculture, human and wildlife health.
 Coevolutionarily derived patterns of local adaptation among pathogen
 populations have the potential to generate variation in disease
 epidemiology, however studies of local adaptation in disease systems have
 mostly focused on interactions between competing pathogens or pathogens
 and their hosts. In nature, parasites and pathogens are also subject to
 attack by hyperparasitic natural enemies that can severely impact upon
 their infection dynamics. However, few studies have investigated if this
 interaction varies across combinations of pathogen-hyperparasite strains,
 and if this influences hyperparasite incidence in natural pathogen
 populations. Here, we test if the association between a hyperparasitic
 fungus, Ampelomyces quisqualis, and a single powdery mildew host,
 Podosphaera plantaginis, varies among genotype combinations, and whether
 this drives hyperparasite incidence in nature. Laboratory inoculation
 studies reveal that genotype, genotype x genotype interactions, and local
 adaptation affect hyperparasite infection. However, observations of a
 natural pathogen metapopulation reveal that spatial rather than genetic
 factors predict the risk of hyperparasite presence. Our results highlight
 how sensitive the outcome of biocontrol using hyperparasites is to
 selection of hyperparasite strains.
description: Data 3Population-level data of
 Podosphaera plantaginis used for Figure 1, and Figure
 S1.Metapopulation_Level_dataDeposit.xlsxData 4Data of Ampelomyces and Podosphaera prevalence within fifteen field populations. Used for Figure 4 & Figure 5Within_population_prevalence_DataDeposit.xlsxData 2Laboratory inoculation experiment data used for Figure 3Local_Adaptation_DataDeposit.xlsxData 1Laboratory inoculation experiment data used for Figure 2.GxG_DataDeposit.xlsxMetadataMetadata for all four datasets within this package.MolEcol2016_DataMetadata.rtf