cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9dt70kb5
title: Data from: The contribution of a pollinating seed predator to selection on Silene latifolia females

description: Interactions, antagonistic or mutualistic, can exert selection on plant
 traits. We explored the role of Hadena bicruris, a pollinating seed
 predator, as a selective agent on its host, the dioecious plant Silene
 latifolia. We exposed females from artificial-selection lines (many, small
 flowers (SF) vs. few, large flowers (LF)) to this moth. Infestation did
 not differ significantly between lines, but the odds of attacked fruits
 aborting were higher in SF females. We partitioned selection between that
 caused by moth attack and that resulting from all other factors. In both
 lines, selection via moth attack for fewer, smaller flowers contrasted
 with selection via other factors for more flowers. In LF females,
 selection via the two components was strongest and selection via moth
 attack also favoured increased fruit abortion. This suggests that the
 moths act as more of a selective force on flower size and number via their
 predating than their pollinating role.
description: flowers_BurkhardtetalThe file contains data on individual flowers of 64 female Silene latifolia plants arising from selection lines that were grown in a common garden in the presence of the pollinating seed predator of the plant. The data file was created using Excel 2011. Detailed information on the data is provided in the ReadMe file.plants_BurkhardtetalThis file contains summary data for 64 female Silene latifolia plants arising from selection lines (the same plants as in flowers_Burkhardtetal file) grown in a common garden in the presence of the pollinating seed predator. The file was created using Excel 2011. Detailed information on the data is provided in the ReadMe file.sizes_BurkhardtetalThis data file contains the measurements of flower size taken on female plants of Silene latifolia. These plants were arising from selection lines and grown in the greenhouse. The file was created using Excel 2011. Detailed information on the data is provided in the ReadMe file.
DOI: 10.5061/dryad.mn03c
title: Data from: Evidence for the introduction of the Asian red alga Neosiphonia japonica and its introgression with Neosiphonia harveyi (Ceramiales, Rhodophyta) in the Northwest Atlantic

description: There is currently conflict in the literature on the taxonomic status of
 the reportedly cosmopolitan species Neosiphonia harveyi, a common red alga
 along the coast of Atlantic Canada and New England, USA. Neosiphonia
 harveyi sensu lato was assessed using three molecular markers: COI-5P, ITS
 and rbcL. All three markers clearly delimited three genetic species groups
 within N. harveyi sensu lato in this region, which we identified as N.
 harveyi, N. japonica and Polysiphonia akkeshiensis (here resurrected from
 synonymy with N. japonica). Although Neosiphonia harveyi is considered by
 some authors to be introduced to the Atlantic from the western Pacific, it
 was only confirmed from the North Atlantic suggesting it is native to this
 area. In contrast, Neosiphonia japonica was collected from only two sites
 in Rhode Island, USA, as well as from its reported native range in Asia
 (South Korea), which when combined with data in GenBank indicates that
 this species was introduced to the Northwest Atlantic. The GenBank data
 further indicate that N. japonica was also introduced to North Carolina,
 Spain, Australia and New Zealand. Despite the fact that all three markers
 clearly delimited N. harveyi and N. japonica as distinct genetic species
 groups, the ITS sequences for some N. harveyi individuals displayed mixed
 patterns and additivity indicating introgression of nuclear DNA from N.
 japonica into N. harveyi in the Northwest Atlantic. Introgression of DNA
 from an introduced species to a native species (i.e. “genetic pollution”)
 is one of the possible consequences of species introductions, and we
 believe this is the first documented evidence for this phenomenon in red
 algae.
description: ITS sequence
 alignmentAn alignment of ITS
 sequences that were used to create a neighbor-joining tree for Figure
 1COI-5P sequence
 alignmentAn alignment of COI-5P
 sequences that were used to create a neighbor-joining tree for Figure
 1rbcL sequence
 alignmentAn alignment of rbcL
 sequences that were used to create a neighbor-joining tree for Figure
 3Figure 3 rbcL
 treeA
 neighbor-joining tree generated from rbcL sequence dataFigure 1 COI-5P
 treeA
 neighbor-joining tree generated from COI-5P sequence
 dataFigure 1 ITS
 treeA
 neighbor-joining tree generated from ITS sequence data
DOI: 10.5061/dryad.d88dg
title: Data from: Mosaic patterns of diversification dynamics following the colonization of Melanesian islands

description: The fate of newly settled dispersers on freshly colonized oceanic islands
 is a central theme of island biogeography. The emergence of increasingly
 sophisticated methods of macroevolutionary pattern inference paves the way
 for a deeper understanding of the mechanisms governing these
 diversification patterns on lineages following their colonization of
 oceanic islands. Here we infer a comprehensive molecular phylogeny for
 Melanesian Exocelina diving beetles. Recent methods in historical
 biogeography and diversification rate inference were then used to
 investigate the evolution of these insects in space and time. An
 Australian origin in the mid-Miocene was followed by independent
 colonization events towards New Guinea and New Caledonia in the late
 Miocene. One colonization of New Guinea led to a large radiation of
 &gt;150 species and 3 independent colonizations of New Caledonia gave
 rise to about 40 species. The comparably late colonizations of Vanuatu,
 Hawaii and China left only one or two species in each region. The
 contrasting diversification trajectories of these insects on Melanesian
 islands are likely accounted for by island size, age and availability of
 ecological opportunities during the colonization stage.
description: Matrix Exocelina
 Melanesia PaperData matrix in Nexus and
 Geneious format
DOI: 10.5061/dryad.db1h7
title: Data from: Characteristics of NPS use in patients admitted to acute psychiatric services in Southeast Scotland: a retrospective cross-sectional analysis following public health interventions

description: Objectives: Assess the impact of selective prohibition and seizure of NPS
 supply on NPS use prevalence within psychiatric admissions and evaluate
 demographic characteristics of current NPS users. Design: A 6-month
 retrospective cross-sectional analysis of discharge letters between 1st
 October 2015 – 31st March 2016. Setting: General Psychiatry inpatients and
 Intensive Home Treatment Team community patients at a psychiatric hospital
 in a Scottish city. Participants: All participants were between the ages
 18-65. After application of exclusion criteria, 473 discharge letters of
 General Psychiatry patients were deemed suitable for analysis and 264
 Intensive Home Treatment Team (IHTT) patient discharge letters were
 analysed. Interventions: A nationwide Temporary Class Drug Order (TCDO)
 was placed on 10th April 2015 reclassifying methylphenidate-related
 compounds as Class B substances. On 15th October 2015, local Forfeiture
 Orders were granted to Trading Standards permitting the seizure of NPS
 supplies. Primary and secondary outcome measures: The primary outcome
 measure was to determine the prevalence of NPS use in two cohorts.
 Secondly, demographic features of patients and details regarding their
 psychiatric presentation were analysed. Results: The prevalence of NPS use
 in General Psychiatry and IHTT patients was 6.6% and 3.4%, respectively.
 Inpatients using NPS compared to non-users were more likely to be male
 (OR: 2.92, 95% CI: 1.28-6.66, p=0.009), have a forensic history (OR: 5.03,
 CI: 2.39-10.59, p&lt;0.001) and be detained under an Emergency
 Detention Certificate (OR: 3.50, CI: 1.56-7.82, p=0.004). NPS users were
 also more likely to be diagnosed under ICD-10 F10-19 (OR: 9.97, CI:
 4.62-21.49, p&lt;0.001). Conclusions: Compared to previous work,
 psychiatric inpatient NPS use has fallen. NPS continue to be used by a
 demographic previously described resulting in presentations consistent
 with a drug-induced psychosis and at times requiring detention under the
 Mental Health Act. Further research is required to evaluate the
 effectiveness of the recent prohibition of all NPS.
description: General Psychiatry
 dataGeneral Psychiatry
 README.docxIHTT
 dataIHTT
 README.docx
DOI: 10.5061/dryad.rk0pq
title: Data from: Intraspecific support for the polygyny-vs.-polyandry hypothesis in the bulldog ant Myrmecia brevinoda

description: The number of queens per colony and the number of matings per queen are
 the most important determinants of the genetic structure of ant colonies,
 and understanding their interrelationship is essential to the study of
 social evolution. The polygyny-versus-polyandry hypothesis argues that
 polygyny and polyandry should be negatively associated since both can
 result in increased intracolonial genetic variability and have costs.
 However, evidence for this long-debated hypothesis has been lacking at the
 intraspecific level. Here, we investigated the colony genetic structure in
 the Australian bulldog ant Myrmecia brevinoda. The numbers of queens per
 colony varied from 1 to 6. Nestmate queens within polygynous colonies were
 on average related (rqq = 0.171±0.019), but the overall relatedness
 between queens and their mates was indistinguishable from zero (rqm =
 0.037±0.030). Queens were inferred to mate with 1 to 10 males. A lack of
 genetic isolation by distance among nests indicated the prevalence of
 independent colony foundation. In accordance with the
 polygyny-versus-polyandry hypothesis, the number of queens per colony was
 significantly negatively associated with the estimated number of matings
 (Spearman rank correlation R = -0.490, P = 0.028). This study thus
 provides rare intraspecific evidence for the polygyny-versus-polyandry
 hypothesis. We suggest that high costs of multiple matings and the strong
 effect of multiple mating on intracolonial genetic diversity may be
 essential to the negative association between polygyny and polyandry, and
 that any attempt to empirically test this hypothesis should place emphasis
 upon these two key underlying aspects.
description: Sample locations and
 microsatellite dataGeographic locations and
 microsatellite data for the 20 sampled colonies (23 nests) in this
 paper.Mbrev_RawData.xls
DOI: 10.5061/dryad.0pm3v
title: Data from: A tight balance between natural selection and gene flow in a southern African arid-zone endemic bird

description: Gene flow is traditionally thought to be antagonistic to population
 differentiation and local adaptation. However, recent studies have
 demonstrated that local adaptation can proceed provided that selection is
 greater than the homogenising effects of gene flow. We extend these
 initial studies by combining ecology (climate), phenotype (body size),
 physiological genetics (oxidative phosphorylation genes) and neutral loci
 (nuclear microsatellites and introns) to test whether selection can
 counter-balance gene flow and hence promote local adaptation in a bird
 whose distribution spans an aridity gradient. Our results show that the
 Karoo scrub-robin’s climatic niche is spatially structured, providing the
 potential for local adaptation to develop. We found remarkably discordant
 patterns of divergence among mtDNA, morphology and neutral loci. For the
 mitochondrial genes, two amino acid replacements, strong population
 structure and reduced gene flow were associated with the environmental
 gradient separating western coastal sites from the interior of southern
 Africa. In contrast, morphology and the neutral loci exhibited variation
 independent of environmental variables, and revealed extensive levels of
 gene flow across the aridity gradient, 50 times larger than the estimates
 for mitochondrial genes. Together, our results suggest that selective
 pressures on physiology, mediated by the mitochondrial genome, may well be
 a common mechanism for facilitating local adaptation to new climatic
 conditions.
description: MicrosatellitesGenotypic data for eleven microsatellites; missing data coded as zero.PointLocalitySite name and GPS coordinate (latitude, longitude) in decimal degreesMorphologyMorphological data: body mass (g) and tarsus-length (mm)
DOI: 10.5061/dryad.28v87
title: Data from: Experimental defaunation of terrestrial mammalian herbivores alters tropical rain forest understory diversity

description: It has been suggested that tropical defaunation may unleash community-wide
 cascading effects, leading to reductions in plant diversity. However,
 experimental evidence establishing cause–effect relationships thereof is
 poor. Through a 5 year exclosure experiment, we tested the hypothesis that
 mammalian defaunation affects tree seedling/sapling community dynamics
 leading to reductions in understorey plant diversity. We established plot
 triplets (n = 25) representing three defaunation contexts:
 terrestrial-mammal exclosure (TE), medium/large mammal exclosure (PE) and
 open access controls (C). Seedlings/saplings 30–100 cm tall were marked
 and identified within each of these plots and re-censused three times to
 record survival and recruitment. In the periods 2010–2011 and 2011–2013,
 survival was greater in PE than in C plots and recruitment was higher in
 TE plots than in C plots. Overall, seedling density increased by 61% in TE
 plots and 23% in PE plots, whereas it decreased by 5% in C plots. Common
 species highly consumed by mammals (e.g. Brosimum alicastrum and
 Ampelocera hottlei) increased in their abundance in TE plots. Rarefaction
 curves showed that species diversity decreased in TE plots from 2008 to
 2013, whereas it remained similar for C plots. Given the prevalence of
 tropical defaunation, we posit this is an anthropogenic effect threatening
 the maintenance of tropical forest diversity.
description: Data base Dynamics
 seedling/sapling communityThis database contains
 data from survival and recruitment of seedling/sapling community,
 collected from 2008 to 2013 in southern Mexico.Data base
 Proceedings2.xls
DOI: 10.5061/dryad.h838q
title: Data from: Long-term acclimation to elevated pCO2 alters carbon metabolism and reduces growth in the Antarctic diatom Nitzschia lecointei

description: Increasing atmospheric CO2 levels are driving changes in the seawater
 carbonate system, resulting in higher pCO2 and reduced pH (ocean
 acidification). Many studies on marine organisms have focused on
 short-term physiological responses to increased pCO2, and few on
 slow-growing polar organisms with a relative low adaptation potential. In
 order to recognize the consequences of climate change in biological
 systems, acclimation and adaptation to new environments are crucial to
 address. In this study, physiological responses to long-term acclimation
 (194 days, approx. 60 asexual generations) of three pCO2 levels (280, 390
 and 960 µatm) were investigated in the psychrophilic sea ice diatom
 Nitzschia lecointei. After 147 days, a small reduction in growth was
 detected at 960 µatm pCO2. Previous short-term experiments have failed to
 detect altered growth in N. lecointei at high pCO2, which illustrates the
 importance of experimental duration in studies of climate change. In
 addition, carbon metabolism was significantly affected by the long-term
 treatments, resulting in higher cellular release of dissolved organic
 carbon (DOC). In turn, the release of labile organic carbon stimulated
 bacterial productivity in this system. We conclude that long-term
 acclimation to ocean acidification is important for N. lecointei and that
 carbon overconsumption and DOC exudation may increase in a high-CO2 world.
description: Longterm
 dataData from laboratory
 experiment on the sea ice diatom Nitzschia lecointei. Data columns in all
 data files are explained in more detail in the separate Readme
 file.Longterm.csvCumulative generations cleanClean version of longterm data, i.e. without NAcumgen.csvSpecific BCP cleanClean version of longterm data, i.e. without NASpec_BCP.csvSpecific PP DOC cleanClean version of longterm data, i.e. without NASpec_PP_DOC.csvSpecific PP POC cleanClean version of longterm data, i.e. without NASpec_PP_POC.csvSpecific PP TOT cleanClean version of longterm data, i.e. without NASpec_PP_TOT.csvR ScriptsR Scripts (written in R 3.1.1)Scripts.txt
DOI: 10.5061/dryad.9v2g5
title: Data from: Influence of geography and environment on patterns of genetic differentiation in a widespread submerged macrophyte, Eurasian watermilfoil (Myriophyllum spicatum L., Haloragaceae)

description: The effects of geographic and environmental variables on the pattern of
 genetic differentiation have been thoroughly studied, whereas empirical
 studies on aquatic plants are rare. We examined the spatial genetic
 differentiation of 58 Myriophyllum spicatum populations distributed
 throughout China with 12 microsatellite loci, and we analyzed its
 association with geographic distance, geographic barriers, and
 environmental dissimilarity using causal modeling and multiple matrix
 regression with randomization (MMRR) analysis. Two genetic clusters were
 identified, and their geographic distribution suggested mountain ranges as
 a barrier to gene flow. The causal modeling revealed that both climate and
 geographic barriers significantly influenced genetic divergence among M.
 spicatum populations and that climate had the highest regression
 coefficient according to the MMRR analysis. This study showed that
 geography and environment together played roles in shaping the genetic
 structure of M. spicatum and that the influence of environment was
 greater. Our findings emphasized the potential importance of the
 environment in producing population genetic differentiation in aquatic
 plants at a large geographic scale.
description: Genotype
 dataMicrosatellite genotype
 of 869 Myriophyllum spicatum inviduals from 58
 populations.Genotype.txtBioclim dataBioclim variables (Bio1-Bio19) for the 43 sites used in landscape genetic analysis.Bioclim.txt
DOI: 10.5061/dryad.b78fb
title: Data from: Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

description: Due to the reduction of population density and/or the environmental
 changes it induces, selective logging could affect the demography,
 reproductive biology and evolutionary potential of forest trees. This is
 particularly relevant in tropical forests where natural population
 densities can be low and isolated trees may be subject to outcross pollen
 limitation and/or produce low quality selfed seeds that exhibit inbreeding
 depression. Comparing reproductive biology processes and genetic diversity
 of populations at different densities can provide indirect evidence of the
 potential impacts of logging. Here, we analysed patterns of genetic
 diversity, mating system and gene flow in three Central African
 populations of the self-compatible legume timber species Erythrophleum
 suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha).
 The comparison of inbreeding levels among cohorts suggests that selfing is
 detrimental as inbred individuals are eliminated between seedling and
 adult stages. Levels of genetic diversity, selfing rates (about 16%) and
 patterns of spatial genetic structure (Sp about 0.006) were similar in all
 three populations. However, the extent of gene dispersal differed markedly
 among populations: the average distance of pollen dispersal increased with
 decreasing density (from 200 m in the high-density population to 1000 m in
 the low-density one). Overall, our results suggest that the reproductive
 biology and genetic diversity of the species are not be affected by
 current logging practices. However, further investigations need to be
 conducted in low-density populations to evaluate (i) if pollen limitation
 may reduce seed production and (ii) the regeneration potential of the
 species.
description: Genotypes (9
 microsatellites) and coordinates of individuals (adults, seedlings, seeds)
 used in the studyColumn A: Individual ID;
 Colum B: Country of origin; Colum C: cohort of the individual (adult,
 seedling, seed); Columns D and E: coordinates of the individuals (degree
 decimals); Colmums F to W: genotypes of the individuals at the 9 nuclear
 SSR (23, 4, 3, 18, 14, 6, 17, 7 and 1).Duminil_DRYAD.xlsx
DOI: 10.5061/dryad.09qc0
title: Data from: Aggressive chemotherapy and the selection of drug resistant pathogens

description: Drug resistant pathogens are one of the key public health challenges of
 the 21st century. There is a widespread belief that resistance is best
 managed by using drugs to rapidly eliminate target pathogens from patients
 so as to minimize the probability that pathogens acquire resistance de
 novo. Yet strong drug pressure imposes intense selection in favor of
 resistance through alleviation of competition with wild-type populations.
 Aggressive chemotherapy thus generates opposing evolutionary forces which
 together determine the rate of drug resistance emergence. Identifying
 treatment regimens which best retard resistance evolution while maximizing
 health gains and minimizing disease transmission requires empirical
 analysis of resistance evolution in vivo in conjunction with measures of
 clinical outcomes and infectiousness. Using rodent malaria in laboratory
 mice, we found that less aggressive chemotherapeutic regimens
 substantially reduced the probability of onward transmission of resistance
 (by &gt;150-fold), without compromising health outcomes. Our
 experiments suggest that there may be cases where resistance evolution can
 be managed more effectively with treatment regimens other than those which
 reduce pathogen burdens as fast as possible.
description: Datasets Huijben et al
 2013 PLoS PathDatasets of Experiment 1
 and Experiment 2 in Huijben et al 2013 PLoS Pathogens 9: e1003578. Given
 are mouse body weight, red blood cell density, asexual parasite density of
 resistant genotype, asexual parasite density of susceptible genotype,
 gametocyte density of resistant genotype, gametocyte density of
 susceptible genotype from days 3-49 post-infection (daily up to day 21,
 three times a week for remaining time). Measurement units are given in
 excel file.