cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bv188
title: Data from: Within-host competition in genetically diverse malaria infections: parasite virulence and competitive success.

description: Humans and animals often become coinfected with pathogen strains that
 differ in virulence. The ensuing interaction between these strains can, in
 theory, be a major determinant of the direction of selection on virulence
 genes in pathogen populations. Many mathematical analyses of this assume
 that virulent pathogen lineages have a competitive advantage within
 coinfected hosts and thus predict that pathogens will evolve to become
 more virulent where genetically diverse infections are common. Although
 the implications of these studies are relevant to both fundamental biology
 and medical science, direct empirical tests for relationships between
 virulence and competitive ability are lacking. Here we use newly developed
 strain-specific real-time quantitative polymerase chain reaction protocols
 to determine the pairwise competitiveness of genetically divergent
 Plasmodium chabaudi clones that represent a wide range of innate
 virulences in their rodent host. We found that even against their
 background of widely varying genotypic and antigenic properties, virulent
 clones had a competitive advantage in the acute phase of mixed infections.
 The more virulent a clone was relative to its competitor, the less it
 suffered from competition. This result confirms our earlier work with
 parasite lines derived from a single clonal lineage by serial passage and
 supports the virulence-competitive ability assumption of many theoretical
 models. To the extent that our rodent model captures the essence of the
 natural history of malaria parasites, public health interventions which
 reduce the incidence of mixed malaria infections should have beneficial
 consequences by reducing the selection for high virulence.
description: 2006 COMPETITION DATA
 SETSamples were taken from
 mice infected with either one or a pair of Plasmodium chabaudi clones of
 differing virulence. Daily samples were taken on red blood cell density,
 weight and asexual parasite density (by qPCR).
DOI: 10.5061/dryad.7dm1p
title: Data from: A critical evaluation of the volume, relevance and quality of evidence submitted by the tobacco industry to oppose standardised packaging of tobacco products

description: Objectives: To examine the volume, relevance and quality of transnational
 tobacco corporations’ (TTCs) evidence that standardised packaging of
 tobacco products ‘won't work’, following the UK government's
 decision to ‘wait and see’ until further evidence is available. Design
 Content analysis. Setting: We analysed the evidence cited in submissions
 by the UK's four largest TTCs to the UK Department of Health
 consultation on standardised packaging in 2012. Outcome measures: The
 volume, relevance (subject matter) and quality (as measured by
 independence from industry and peer-review) of evidence cited by TTCs was
 compared with evidence from a systematic review of standardised packaging
 . Fisher's exact test was used to assess differences in the quality
 of TTC and systematic review evidence. 100% of the data were second-coded
 to validate the findings: 94.7% intercoder reliability; all differences
 were resolved. Results: 77/143 pieces of TTC-cited evidence were used to
 promote their claim that standardised packaging ‘won't work’. Of
 these, just 17/77 addressed standardised packaging: 14 were industry
 connected and none were published in peer-reviewed journals. Comparison of
 TTC and systematic review evidence on standardised packaging showed that
 the industry evidence was of significantly lower quality in terms of
 tobacco industry connections and peer-review (p&lt;0.0001). The most
 relevant TTC evidence (on standardised packaging or packaging generally,
 n=26) was of significantly lower quality (p&lt;0.0001) than the least
 relevant (on other topics, n=51). Across the dataset, TTC-connected
 evidence was significantly less likely to be published in a peer-reviewed
 journal (p=0.0045). Conclusions: With few exceptions, evidence cited by
 TTCs to promote their claim that standardised packaging ‘won't work’
 lacks either policy relevance or key indicators of quality. Policymakers
 could use these three criteria—subject matter, independence and
 peer-review status—to critically assess evidence submitted to them by
 corporate interests via Better Regulation processes.
description: Hatchard et al. 2014 BMJ
 Open 003757 Dataset finalExcel spreadsheet of
 evidence data - coded for relevance, publication status, independence and
 declaration of conflict of interest.Hatchard et al. 2014 BMJ
 Open 003757 n=37 SRSystematic review data
 coded for subject matter, publication status and independence
 n=37Hatchard et al. 2014 BMJ Open
 003757 nHatchard et al. 2014 BMJ
 Open 003757 n=77 codedTobacco company evidence
 coded for subject matter, publication status and independence
 n=77Hatchard et al. 2014 BMJ Open
 003757 nHatchard et al. 2014 BMJ
 Open 003757 n=77 coiTobacco company evidence
 coded for conflict of interest declared n=77.Hatchard et al. 2014 BMJ Open
 003757 nHatchard et al. 2014 BMJ
 Open 003757 n=143All tobacco company
 research evidence cited in submissions n=143Hatchard et al. 2014 BMJ Open
 003757 n
DOI: 10.5061/dryad.70dj6
title: Data from: Context-dependent sex allocation: constraints on the expression and evolution of maternal effects

description: Despite decades of research, whether vertebrates can and do adaptively
 adjust the sex ratio of their offspring is still highly debated. However,
 this may have resulted from the failure of empirical tests to identify
 large and predictable fitness returns to females from strategic
 adjustment. Here we test the effect of diet quality and maternal condition
 on facultative sex ratio adjustment in the color polymorphic Gouldian
 finch (Erythrura gouldiae), a species that exhibits extreme maternal
 allocation in response to severe and predictable (genetically-determined)
 fitness costs. On high quality diets, females produced a relatively equal
 sex ratio, but over-produced sons in poor dietary conditions. Despite the
 lack of sexual size dimorphism, nutritionally-stressed foster sons were
 healthier, grew faster, and were more likely to survive than daughters.
 Although these findings are in line with predictions from sex allocation
 theory, the extent of adjustment is considerably lower than previously
 reported for this species. Females therefore have strong facultative
 control over sex allocation, but the extent of adjustment is likely
 determined by the relative magnitude of fitness gains and the ability to
 reliably predict sex-specific benefits from environmental (versus genetic)
 variables. These findings may help explain the often inconsistent, weak or
 inconclusive empirical evidence for adaptive sex ratio adjustment in
 vertebrates.
description: Evolution 11-0308 Pryke
 et al complete pdfEvolution 11-0308 Pryke et
 al.pdfEvolution 11-0308 Pryke
 et al. 2011a csvEvolution 11-0308 Pryke et al.
 2011a.csvEvolution 11-0308 Pryke
 et al. 2011b csvEvolution 11-0308 Pryke et al.
 2011b.csv
DOI: 10.5061/dryad.9h225r5
title: Data from: Horizontal partner exchange does not preclude stable mutualism in fungus-growing ants

description: Vertical symbiont transmission tends to stabilize mutualisms by aligning
 the reproductive interests of cooperating species. The attine ants conform
 well to this principle, because all species are nutritionally dependent on
 vertically transmitted and clonally propagated fungal cultivars. Multiple
 mechanisms expressed by both partners constrain cultivar transmission
 between established colonies, but these appear not to preclude horizontal
 transfer during colony founding, consistent with multiple phylogenetic
 analyses indicating at least occasional horizontal transfer. The
 ecological and evolutionary impact of transfers is unknown because,
 although they can be induced in laboratory experiments, they remain
 undocumented in natural colonies. In a large-scale field study, we
 manipulated clusters of newly founded nests and their still portable
 gardens in two sympatric species of Acromyrmex leaf-cutting ants. This
 created mosaics of intact nests, queens without a cultivar, and cultivars
 without a tending queen. We tracked the movements of queens and cultivars
 through direct observation and microsatellite analysis, respectively. This
 showed that horizontal acquisition of incipient gardens is surprisingly
 common, because queens actively searched for replacement cultivars and
 often adopted orphaned gardens. However, these horizontal cultivar
 exchanges are unlikely to destabilize obligate farming mutualisms when
 they are restricted to the founding stage, as colonies eventually commit
 to a single cultivar clone, irreversibly aligning the partners’ fitness
 interests before colonies reproduce.
description: DATAFILE_Howe_2018_Acromyrmex_FungalMicrosatellite_CompleteData_1.0Experimental treatments and results. Contains microsatellite data at 10 loci for samples of the fungal symbionts of Acromyrmex echinatior and Acromyrmex octospinosus, and all information regarding treatments, locations and results for all trials used in Howe et al. 2018.Howe_2018_Acromyrmex_FungalMicrosatellite_CompleteData_1.0.csvRSCRIPT_Howe_2018_Acromyrmex_FungalMicrosatellite_Analysis_1.0.R script that conducts analyses reported in Howe et al., 2018. Also produces all figures, with the exception of those produced in other software.Howe_2018_Acromyrmex_FungalMicrosatellite_Analysis_1.0.R
DOI: 10.5061/dryad.k14tt
title: Data from: δ18O-derived incubation temperatures of oviraptorosaur eggs

description: In order to determine the incubation temperature of eggs laid by non-avian
 dinosaurs, we analysed the oxygen isotope compositions of both eggshell
 carbonate (δ18Oc) and embryo bone phosphate (δ18Op) from seven
 oviraptorosaur eggs with preserved in ovo embryo bones. These eggs come
 from the Upper Cretaceous Nanxiong Formation of Jiangxi Province, China.
 Oviraptorosaur theropods were selected because of their known brooding
 behaviour as evidenced by preserved adult specimens fossilized in brooding
 posture on their clutch. Incubation temperature of these embryos was
 estimated based on the following considerations: eggshell δ18Oc value
 reflects the oxygen isotope composition of egg water fluid; embryo bones
 precipitate from the same egg fluid; and oxygen isotope fractionation
 between phosphate and water is controlled by the egg temperature. A
 time-dependent model predicting the δ18Op evolution of the embryo skeleton
 during incubation as a function of egg temperature was built, and measured
 δ18Oc and δ18Op values used as boundary conditions. According to the model
 outputs, oviraptorosaurs incubated their eggs within a 35–40°C range,
 similar to extant birds and compatible with the known active brooding
 behaviour of these theropod dinosaurs. Provided that both eggshell and
 embryo bones preserved their original oxygen isotope compositions, this
 method could be extended to investigate some reproductive traits of other
 extinct groups of oviparous amniotes.
description: Supplementary
 tablesmodel output of the
 oxygen isotope composition of oviraptorosaur embryo bone
 phosphate
DOI: 10.5061/dryad.8rf3j
title: Data from: A heterogeneous landscape does not guarantee high crop pollination

description: The expansion of pollinator-dependent crops, especially in the developing
 world, together with reports of worldwide pollinator declines, raises
 concern of possible yield gaps. Farmers directly reliant on pollination
 services for food supply often live in regions where our knowledge of
 pollination services is poor. In a manipulative experiment replicated at
 23 sites across an Ethiopian agricultural landscape, we found poor
 pollination services and severe pollen limitation in a common oil crop.
 With supplementary pollination, the yield increased on average by 91%.
 Despite the heterogeneous agricultural matrix, we found a low bee
 abundance, which may explain poor pollination services. The variation in
 pollen limitation was unrelated to surrounding forest cover, local bee
 richness and bee abundance. While practices that commonly increase
 pollinators (restricted pesticide use, flower strips) are an integral part
 of the landscape, these elements are apparently insufficient. Management
 to increase pollination services is therefore in need of urgent
 investigation.
description: Samnegard_Proc_R_Soc_B_2016_Bee_surveySamnegard_Proc_R_Soc_B_2016_Rapeseed_dataSamnegard_Proc_R_Soc_B_2016_Landscape_local_variables
DOI: 10.5061/dryad.h214h8t
title: Data from: The causal relationship between sexual selection and sexual size dimorphism in marine gastropods

description: Sexual size dimorphism is widespread among dioecious species but its
 underlying driving forces are often complex. A review of sexual size
 dimorphism in marine gastropods revealed two common patterns: firstly,
 sexual size dimorphism, with females being larger than males, and secondly
 females being larger than males in mating pairs; both of which suggest
 sexual selection as being causally related with sexual size dimorphism. To
 test this hypothesis, we initially investigated mechanisms driving sexual
 selection on size in three congeneric marine gastropods with different
 degrees of sexual size dimorphism, and, secondly, the correlation between
 male/female sexual selection and sexual size dimorphism across several
 marine gastropod species. Male mate choice via mucus trail following (as
 evidence of sexual selection) was found during the mating process in all
 three congeneric species, despite the fact that not all species showed
 sexual size dimorphism. There was also a significant and strong negative
 correlation between female sexual selection and sexual size dimorphism
 across 16 cases from seven marine gastropod species. These results suggest
 that sexual selection does not drive sexual size dimorphism. There was,
 however, evidence of males utilizing a similar mechanism to choose mates
 (i.e. selecting a female slightly larger than own size) which may be
 widespread among gastropods, and in tandem with present variability in
 sexual size dimorphism among species, provide a plausible explanation of
 the observed mating patterns in marine gastropods.
description: DATA NG et al
 2018Represent a set of
 captured mating pairs from different littorinid species where the size and
 the sex has been recorded. The codification of the data is provided in the
 sme excel sheet than the data.
DOI: 10.5061/dryad.1484
title: Data from: Maternity of emergency queens in the cape honey bee, Apis mellifera capensis

description: During reproductive swarming, some workers of the Cape honey bee, Apis
 mellifera capensis, lay eggs in queen cells, many of which are reared to
 maturity. However, it is unknown if workers are able to lay in queen cells
 immediately after queen loss during an episode of emergency queen rearing.
 In this study we experimentally de-queened colonies and determined the
 maternity of larvae and pupae that were reared as queens. This allowed us
 to determine how soon after queen loss workers contribute to the
 production of new queens. We were further interested to see if workers
 would preferentially raise new queens from queen-laid brood if this was
 introduced later. We performed our manipulations in two different
 settings: an apiary setting where colonies were situated close together
 and a more natural situation in which the colonies were well separated.
 This allowed us to determine how the vicinity of other colonies affects
 the presence of parasites. We found that workers do indeed contribute to
 queen cell production immediately after the loss of their queen, thus
 demonstrating that some workers either have activated ovaries even when
 their colony has a queen or are able to activate their ovaries extremely
 rapidly. Queen-laid brood introduced days after queen loss was ignored,
 showing that workers do not prefer to raise new queens from queen brood
 when given a choice. We also detected non-natal parasitism of queen cells
 in both settings. We therefore conclude that some A. m. capensis genotypes
 specialise in parasitising queen cells.
description: Genotypes of contents of
 queen cellsTable S1
 genotypesFinal.pdf
DOI: 10.5061/dryad.8f97r
title: Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?

description: Classic null models for speciation and extinction give rise to phylogenies
 that differ in distribution from empirical phylogenies. In particular,
 empirical phylogenies are less balanced and have branching times closer to
 the root compared to phylogenies predicted by common null models. This
 difference might be due to null models of the speciation and extinction
 process being too simplistic, or due to the empirical datasets not being
 representative of random phylogenies. A third possibility arises because
 phylogenetic reconstruction methods often infer gene trees rather than
 species trees, producing an incongruity between models that predict
 species tree patterns and empirical analyses that consider gene trees. We
 investigate the extent to which the difference between gene trees and
 species trees under a combined birth–death and multispecies coalescent
 model can explain the difference in empirical trees and birth–death
 species trees. We simulate gene trees embedded in simulated species trees
 and investigate their difference with respect to tree balance and
 branching times. We observe that the gene trees are less balanced and
 typically have branching times closer to the root than the species trees.
 Empirical trees from TreeBase are also less balanced than our simulated
 species trees, and model gene trees can explain an imbalance increase of
 up to 8% compared to species trees. However, we see a much larger
 imbalance increase in empirical trees, about 100%, meaning that additional
 features must also be causing imbalance in empirical trees. This
 simulation study highlights the necessity of revisiting the assumptions
 made in phylogenetic analyses, as these assumptions, such as equating the
 gene tree with the species tree, might lead to a biased conclusion.
description: Supplementary
 FiguresBalance_SI.pdf
DOI: 10.5061/dryad.gv33qc2
title: Data from: The roles of interspecific variability in seed mass and soil resource availability in root system development

description: Aims Because plant roots serve mainly as organs for the uptake of water
 and nutrients, we aimed to test whether the development of seedling roots
 is influenced by the two principal nutrient sources—the substrate and the
 pool stored in the seed itself. Methods Using seven Fabaceae species that
 differ in seed mass, we observed their early root system development under
 four levels of nutrient availability. Transparent-wall rhizoboxes allowed
 us to track root development and to score root system structure (length
 and number of roots), size (depth and width of root system) and shape
 (relative depth and width of root system). Results Seedling root system
 development depended on both the amount of nutrients contained in the
 substrate and on the seed mass of the species. Compared to an average
 seedling, effects of these two nutrient pools were (i) opposite and (ii)
 did not fully overlap. Small-seeded species developed wider root systems
 that branched earlier than large-seeded species. Increased availability of
 nutrients in the substrate led to proliferation of lateral roots, without
 any substantial impacts on the shape of root system or beginning of
 branching. Conclusions The source of the nutrients affected the way they
 were used throughout early root system development, leading to different
 structures and dynamics. This may be one of the mechanistic links
 connecting seed mass and the realized niche of the species.
description: Architecture of seedling
 root systems of seven legumes speciesRoot system
 architectural data about seven legumes species growing in four nutrient
 supply treatment and measured in four time cuts.data.csv
DOI: 10.5061/dryad.d8n64
title: Data from: Rapid prey evolution can alter the structure of predator-prey communities

description: Although microevolution has been shown to play an important role in
 pairwise antagonistic species interactions, its importance in more complex
 communities has received little attention. Here, we used two Pseudomonas
 fluorescens prey bacterial strains (SBW25 and F113) and Tetrahymena
 thermophila protist predator to study how rapid evolution affects the
 structuring of predator–prey communities. Both bacterial strains coexisted
 in the absence of predation, and F113 was competitively excluded in the
 presence of both SBW25 and predator during the 24-day experiment, an
 initially surprising result given that F113 was originally poorer at
 growing, but more resistant to predation. However, this can be explained
 by SBW25 evolving greater antipredatory defence with a lower growth cost
 than F113. These results show that rapid prey evolution can alter the
 structure of predator–prey communities, having different effects depending
 on the initial composition of the evolving community. From a more applied
 perspective, our results suggest that the effectiveness of biocontrol
 bacteria, such as F113, could be weaker in communities characterized by
 intense bacterial competition and protist predation.
description: BpopOD600nmBacterial population density dataTpopCellsmLProtist population densitiesBfrequenciesCFUF113 frequenciesEvolDefenceDefence evolution dataEvolGrowthEvolution of bacterial growthAncDefGrowthAncestral strains' defence and growth
DOI: 10.5061/dryad.32535
title: Data from: Role of stag beetle jaw bending and torsion in grip on rivals

description: In aggressive battles, the extremely large male stag beetle jaws have to
 withstand strongly elevated bite forces. We found several adaptations of
 the male Cyclommatus metallifer jaw morphology for enhanced robustness
 that conspecific females lack. As a result, males improve their grip on
 opponents and they maintain their safety factor (5.2–7.2) at the same
 level as that of females (6.8), despite their strongly elevated bite
 muscle force (3.9 times stronger). Males have a higher second moment of
 area and torsion constant than females, owing to an enhanced
 cross-sectional area and shape. These parameters also increase faster with
 increasing bending moment towards the jaw base in males than in females.
 Male jaws are more bending resistant against the bite reaction force than
 against perpendicular forces (which remain lower in battles). Because of
 the triangular cross section of the male jaw base, it twists more easily
 than it bends. This torsional flexibility creates a safety system against
 overload that, at the same time, secures a firm grip on rivals. We found
 no structural mechanical function of the large teeth halfway along the
 male jaws. Therefore, it appears that the main purpose of these teeth is a
 further improvement of grip on rivals.
description: Slices through male and
 female stag beetle jawsSlices through a male
 and female Cyclommatus metallifer stag beetle jaw. The data have been
 processed using ShapeDesigner software
 (http://www.mechatools.com/en/shapedesigner.html). The file name indicates
 the position of each slice along the jaw.GoyensJ_slices_male_and_female.zip