cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.db428
title: Data from: Quantifying demographic uncertainty: Bayesian methods for integral projection models (IPMs)

description: Integral projection models (IPMs) are a powerful and popular approach to
 modeling population dynamics. Generalized linear models form the
 statistical backbone of an IPM. These models are typically fit using a
 frequentist approach. We suggest that hierarchical Bayesian statistical
 approaches offer important advantages over frequentist methods for
 building and interpreting IPMs, especially given the hierarchical nature
 of most demographic studies. Using a stochastic IPM for a desert cactus
 based on a 10-year study as a worked example, we highlight the application
 of a Bayesian approach for translating uncertainty in the vital rates
 (e.g., growth, survival, fertility) to uncertainty in population-level
 quantities derived from them (e.g., population growth rate). The best-fit
 demographic model, which would have been difficult to fit under a
 frequentist framework, allowed for spatial and temporal variation in vital
 rates and correlated responses to temporal variation across vital rates.
 The corresponding posterior probability distribution for the stochastic
 population growth rate (λS) indicated that, if current vital rates
 continue, the study population will decline with nearly 100% probability.
 Interestingly, less-supported candidate models that did not include
 spatial variance and vital rate correlations gave similar estimates of λS.
 This occurred because the best-fitting model did a much better job of
 fitting vital rates to which the population growth rate was weakly
 sensitive. The cactus case study highlights several advantages of Bayesian
 approaches to IPM modeling, including that they: (1) provide a natural fit
 to demographic data, which are often collected in a hierarchical fashion
 (e.g., with random variance corresponding to temporal and spatial
 heterogeneity); (2) seamlessly combine multiple data sets or experiments;
 (3) readily incorporate covariance between vital rates; and, (4) easily
 integrate prior information, which may be particularly important for
 species of conservation concern where data availability may be limited.
 However, constructing a Bayesian IPM will often require the custom
 development of a statistical model tailored to the peculiarities of the
 sampling design and species considered; there may be circumstances under
 which simpler methods are adequate. Overall, Bayesian approaches provide a
 statistically sound way to get more information out of hard-won data, the
 goal of most demographic research endeavors.
description: Quantifying demographic
 uncertainty: Bayesian methods for Integral Projection Models (IPMs)
 ParametersComma delimited file
 (csv) containing parameter estimates used to construct the posterior
 distributions for calculating the stochastic population growth rate and
 the sensitivities of the associated vital rates. The first row of the file
 contains the names of the parameters.ElderdMiller_cholla.all.params.post.csv
DOI: 10.5061/dryad.32s2t
title: Data from: Climate drives adaptive genetic responses associated with survival in big sagebrush (Artemisia tridentata)

description: A genecological approach was used to explore genetic variation for
 survival in Artemisia tridentata (big sagebrush). Artemisia tridentata is
 a widespread and foundational shrub species in western North America. This
 species has become extremely fragmented, to the detriment of dependent
 wildlife, and efforts to restore it are now a land management priority.
 Common garden experiments were established at three sites with seedlings
 from 55 source-populations. Populations included each of the three
 predominant subspecies, and cytotype variations. Survival was monitored
 for five-years to assess differences in survival between gardens and
 populations. We found evidence of adaptive genetic variation for survival.
 Survival within gardens differed by source-population and a substantial
 proportion of this variation was explained by seed climate-of-origin.
 Plants from areas with the coldest winters had the highest levels of
 survival, while populations from warmer and drier sites had the lowest
 levels of survival. Survival was lowest, 36%, in the garden that was prone
 to the lowest minimum temperatures. These results suggest the importance
 of climatic driven genetic differences and their effect on survival.
 Understanding how genetic variation is arrayed across the landscape and
 its association with climate can greatly enhance the success of
 restoration and conservation.
description: Temperature data for
 gardensData for climate from
 three common garden sites, Ephraim, Majors Flat, and
 Orchards.daily_temps.csvThree garden survivalData for survival of Artemisia tridentata (Big Sagebrush) from three common garden sites.3gardsurv_2015.csvPopulation climate dataClimate data from 55 source populations.prov_clim_contemp.csv
DOI: 10.5061/dryad.rn931
title: Data from: Seasonal influenza vaccination delivery through community pharmacists in England: evaluation of the London pilot

description: Objective: To evaluate the effectiveness and cost of the pan-London
 pharmacy initiative, a programme that allows administration of seasonal
 influenza vaccination to eligible patients at pharmacies. Design: We
 analysed 2013–15 data on vaccination uptake in pharmacies via the Sonar
 reporting system, and the total vaccination uptake via 2011–15 ImmForm GP
 reporting system data. We conducted an online survey of London pharmacists
 who participate in the programme to assess time use data, vaccine choice,
 investment costs, and opinions about the programme. We conducted an online
 survey of London GPs to assess vaccine choice of vaccine and opinions
 about the pharmacy vaccine delivery programme. Setting: All London
 boroughs. Participants: London-based GPs, and pharmacies that currently
 offer seasonal flu vaccination. Interventions: Not applicable. Main
 outcome measures: Comparison of annual vaccine uptake in London across
 risk groups from years before pharmacy vaccination introduction to after
 pharmacy vaccination introduction. Completeness of vaccine uptake
 reporting data. Cost to the NHS of flu vaccine delivery at pharmacies with
 that at GPs. Cost to pharmacists of flu delivery. Opinions of pharmacists
 and GPs regarding the flu vaccine pharmacy initiative. Results: No
 significant change in the uptake of seasonal vaccination in any of the
 risk groups as a result of the pharmacy initiative. While on average a
 pharmacy-administered flu vaccine dose costs the NHS up to £2.35 less than
 a dose administered at a GP, a comparison of the two recording systems
 suggests there is substantial loss of data. Conclusions: Flu vaccine
 delivery through pharmacies shows potential for improving convenience for
 vaccine recipients. However, there is no evidence that vaccination uptake
 increases and the use of two separate recording systems leads to time
 consuming data entry and missing vaccine record data.
description: GP_Pharmacy_Survey_Data_LondonLondon General Practitioner and London Pharmacist responses to survey (questions given as Appendices in manuscript)Combined_SurveyData_uploadDryad.xls
DOI: 10.5061/dryad.d364t
title: Data from: The effects of Medieval dams on genetic divergence and demographic history in brown trout populations

description: Background: Habitat fragmentation has accelerated within the last century,
 but may have been ongoing over longer time scales. We analyzed the timing
 and genetic consequences of fragmentation in two isolated lake-dwelling
 brown trout populations. They are from the same river system (the Gudenå
 River, Denmark) and have been isolated from downstream anadromous trout by
 dams established ca. 600-800 years ago. For reference, we included ten
 other anadromous populations and two hatchery strains. Based on analysis
 of 44 microsatellite loci we investigated if the lake populations have
 been naturally genetically differentiated from anadromous trout for
 thousands of years, or have diverged recently due to the establishment of
 dams. Results: Divergence time estimates were based on 1) Approximate
 Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow
 model. Both methods suggested divergence times ca. 600-800 years bp,
 providing strong evidence for establishment of dams in the Medieval as the
 factor causing divergence. Bayesian cluster analysis showed influence of
 stocked trout in several reference populations, but not in the focal lake
 and anadromous populations. Estimates of effective population size using a
 linkage disequilibrium method ranged from 244 to &gt; 1,000 in all but
 one anadromous population, but were lower (153 and 252) in the lake
 populations. Conclusions: We show that genetic divergence of lake-dwelling
 trout in two Danish lakes reflects establishment of water mills and
 impassable dams ca. 600-800 years ago rather than a natural genetic
 population structure. Although effective population sizes of the two lake
 populations are not critically low they may ultimately limit response to
 selection and thereby future adaptation. Our results demonstrate that
 populations may have been affected by anthropogenic disturbance over
 longer time scales than normally assumed.
description: Hansen_et_al_2014_Salmo_truttaGenotype data for 44 microsatellite loci. The abbreviations correspond to those used in the publication. The data file is in Microsat Analyzer (MSA) Format (Dieringer, Daniel & Schlötterer, Christian (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3 (1), 167-169).
DOI: 10.5061/dryad.6qd19
title: Data from: Effects of vulture exclusion on carrion consumption by facultative scavengers

description: Vultures provide an essential ecosystem service through removal of
 carrion, but globally, many populations are collapsing and several species
 are threatened with extinction. Widespread declines in vulture populations
 could increase the availability of carrion to other organisms, but the
 ways facultative scavengers might respond to this increase have not been
 thoroughly explored. We aimed to determine whether facultative scavengers
 increase carrion consumption in the absence of vulture competition and
 whether they are capable of functionally replacing vultures in the removal
 of carrion biomass from the landscape. We experimentally excluded 65
 rabbit carcasses from vultures during daylight hours and placed an
 additional 65 carcasses that were accessible to vultures in forested
 habitat in South Carolina, USA during summer (June–August). We used
 motion-activated cameras to compare carrion use by facultative scavenging
 species between the experimental and control carcasses. Scavenging by
 facultative scavengers did not increase in the absence of competition with
 vultures. We found no difference in scavenger presence between control
 carcasses and those from which vultures were excluded. Eighty percent of
 carcasses from which vultures were excluded were not scavenged by
 vertebrates, compared to 5% of carcasses that were accessible to vultures.
 At the end of the 7-day trials, there was a 10.1-fold increase in the
 number of experimental carcasses that were not fully scavenged compared to
 controls. Facultative scavengers did not functionally replace vultures
 during summer in our study. This finding may have been influenced by the
 time of the year in which the study took place, the duration of the
 trials, and the spacing of carcass sites. Our results suggest that under
 the warm and humid conditions of our study, facultative scavengers would
 not compensate for loss of vultures. Carcasses would persist longer in the
 environment and consumption of carrion would likely shift from vertebrates
 to decomposers. Such changes could have substantial implications for
 disease transmission, nutrient cycling, and ecosystem functioning.
description: Camera
 DataImage analysis data from
 wildlife cameras
DOI: 10.5061/dryad.34702
title: Data from: DNA barcoding and minibarcoding as a powerful tool for feather mite studies

description: Feather mites (Astigmata: Analgoidea and Pterolichoidea) are among the
 most abundant and commonly occurring bird ectosymbionts. Basic questions
 on the ecology and evolution of feather mites remain unanswered because
 feather mite species identification is often only possible for adult
 males, and it is laborious even for specialized taxonomists, thus
 precluding large-scale identifications. Here, we tested DNA barcoding as a
 useful molecular tool to identify feather mites from passerine birds.
 Three hundred and sixty-one specimens of 72 species of feather mites from
 68 species of European passerine birds from Russia and Spain were
 barcoded. The accuracy of barcoding and minibarcoding was tested.
 Moreover, threshold choice (a controversial issue in barcoding studies)
 was also explored in a new way, by calculating through simulations the
 effect of sampling effort (in species number and species composition) on
 threshold calculations. We found one 200-bp minibarcode region that showed
 the same accuracy as the full-length barcode (602 bp) and was surrounded
 by conserved regions potentially useful for group-specific degenerate
 primers. Species identification accuracy was perfect (100%) but decreased
 when singletons or species of the Proctophyllodes pinnatus group were
 included. In fact, barcoding confirmed previous taxonomic issues within
 the P. pinnatus group. Following an integrative taxonomy approach, we
 compared our barcode study with previous taxonomic knowledge on feather
 mites, discovering three new putative cryptic species and validating three
 previous morphologically different (but still undescribed) new species.
description: host_distribution
DOI: 10.5061/dryad.7p2r4
title: Data from: Plant-derived differences in the composition of aphid honeydew and their effects on colonies of aphid-tending ants

description: In plant–ant–hemipteran interactions, ants visit plants to consume the
 honeydew produced by phloem-feeding hemipterans. If genetically based
 differences in plant phloem chemistry change the chemical composition of
 hemipteran honeydew, then the plant's genetic constitution could have
 indirect effects on ants via the hemipterans. If such effects change ant
 behavior, they could feed back to affect the plant itself. We compared the
 chemical composition of honeydews produced by Aphis nerii aphid clones on
 two milkweed congeners, Asclepias curassavica and Asclepias incarnata, and
 we measured the responses of experimental Linepithema humile ant colonies
 to these honeydews. The compositions of secondary metabolites, sugars, and
 amino acids differed significantly in the honeydews from the two plant
 species. Ant colonies feeding on honeydew derived from A. incarnata
 recruited in higher numbers to artificial diet, maintained higher queen
 and worker dry weight, and sustained marginally more workers than ants
 feeding on honeydew derived from A. curassavica. Ants feeding on honeydew
 from A. incarnata were also more exploratory in behavioral assays than
 ants feeding from A. curassavica. Despite performing better when feeding
 on the A. incarnata honeydew, ant workers marginally preferred honeydew
 from A. curassavica to honeydew from A. incarnata when given a choice. Our
 results demonstrate that plant congeners can exert strong indirect effects
 on ant colonies by means of plant-species-specific differences in aphid
 honeydew chemistry. Moreover, these effects changed ant behavior and thus
 could feed back to affect plant performance in the field.
description: Chemical and
 experimental data for Pringle et al. 2014 Ecol EvolThe zipped file contains
 5 excel workbooks and a ReadMe file. The excel workbooks contain chemical
 data on sugars/carbohydrates, amino acids, and cardenolides, as well as
 experimental data from the forced-diet and choice experiments described in
 the manuscript.Pringle.etal.EcolEvol.zip
DOI: 10.5061/dryad.bj00s
title: Data from: Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny

description: The endosymbiotic bacterium Wolbachia enhances its spread via vertical
 transmission by generating reproductive effects in its hosts, most notably
 cytoplasmic incompatibility (CI). Additionally, frequent interspecific
 horizontal transfer is evident from a lack of phylogenetic congruence
 between Wolbachia and its hosts. The mechanisms of this lateral transfer
 are largely unclear. To identify potential pathways of Wolbachia
 movements, we performed multilocus sequence typing of Wolbachia strains
 from bees (Anthophila). Using a host phylogeny and ecological data, we
 tested various models of horizontal endosymbiont transmission. In general,
 Wolbachia strains seem to be randomly distributed among bee hosts.
 Kleptoparasite-host associations among bees as well as other ecological
 links could not be supported as sole basis for the spread of Wolbachia.
 However, cophylogenetic analyses and divergence time estimations suggest
 that Wolbachia may persist within a host lineage over considerable
 timescales and that strictly vertical transmission and subsequent random
 loss of infections across lineages may have had a greater impact on
 Wolbachia strain distribution than previously estimated. Although general
 conclusions about Wolbachia movements among arthropod hosts cannot be
 made, we present a framework by which precise assumptions about shared
 evolutionary histories of Wolbachia and a host taxon can be modelled and
 tested.
description: Wolbachia MLST
 alignmentsA combined file
 containing MLST alignments of large and small Wolbachia dataset, both in
 ClonalFrame input file format. Also, a Nexus file of 100 best trees of
 Wolbachia strains from bee hosts, as inferred with MrBayes. These trees
 were used asinput in BayesTraits analysesWolbachia_files.zipBee phylogeny dataA combined file including an alignment of LW-rhodopsin of bees and an xml file which was used as input file for BEAST analysesBee_files.zip
DOI: 10.5061/dryad.5k7f1
title: Data from: Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral

description: Within populations of brooding sessile corals, sperm dispersal constitutes
 the mechanism by which gametes interact and mating occurs, and forms the
 first link in the network of processes that determine species-wide
 connectivity patterns. However, almost nothing is known about sperm
 dispersal for any internally fertilizing coral. In this study, we
 conducted a parentage analysis on coral larvae collected from an area of
 mapped colonies, in order to measure the distance sperm disperses for the
 first time in a reef-building coral and estimated the mating system
 characteristics of a recently identified putative cryptic species within
 the Seriatopora hystrix complex (ShA; Warner et al. 2015). We defined
 consensus criteria among several replicated methods (COLONY 2.0, Cervus
 3.0, MLTR v3.2) to maximize accuracy in paternity assignments. Thirteen
 progeny arrays indicated that this putative species produces exclusively
 sexually-derived, primarily outcrossed larvae (mean tm=0.999) in multiple
 paternity broods (mean rp=0.119). Self-fertilization was directly detected
 at low frequency for all broods combined (2.8%), but comprised 23% of
 matings in one brood. Although over 82% of mating occurred between
 colonies within 10 m of each other (mean sperm dispersal = 5.5 m ±4.37
 SD), we found no evidence of inbreeding in the established population.
 Restricted dispersal of sperm compared to slightly greater larval
 dispersal appears to limit inbreeding among close relatives in this
 cryptic species. Our findings establish a good basis for further work on
 sperm dispersal in brooding corals and provide the first information about
 the mating system of a newly identified and abundant cryptic species.
description: Summary table of all
 data ExcelExcel spreadsheet with
 labeled columns of data, including: sample name, life stage (mother,
 established colony, larva), origin in study site (main/ outside quadrat,
 maternal colony), colony size, spatial coordinates, genotypes (2 columns
 per locus)WarnerData_SeriatoporaParentage
 Analysis.xlsSummary table of all
 data CSVCSV table with labeled
 columns of data, including: sample name, life stage (mother, established
 colony, larva), origin in study site (main/ outside quadrat, maternal
 colony), colony size, spatial coordinates, genotypes (2 columns per
 locus)WarnerData_SeriatoporaParentage
 Analysis.csv
DOI: 10.5061/dryad.418b0
title: Data from: Structure and composition of altered riparian forests in an agricultural Amazonian landscape

description: Deforestation and fragmentation influence the microclimate, vegetation
 structure, and composition of remaining patches of tropical forest. In the
 southern Amazon, at the frontier of cropland expansion, forests are
 converted and fragmented in a pattern that leaves standing riparian
 forests whose dimensions are mandated by the Brazilian National Forest
 Code. These altered riparian forests share many characteristics of
 well-studied upland forest fragments, but differ because they remain
 connected to larger areas of forest downstream, and because they may
 experience wetter soil conditions because reduction of forest cover in the
 surrounding watershed raises groundwater levels and increases stream
 runoff. We compared forest regeneration, structure, composition, and
 diversity in four areas of intact riparian forest and four areas each of
 narrow, medium, and wide altered riparian forests that have been
 surrounded by agriculture since the early 1980s. We found that seedling
 abundance was reduced by as much as 64% and sapling abundance was reduced
 by as much as 67% in altered compared to intact riparian forests. The most
 pronounced differences between altered and intact forest occurred near
 forest edges and within the narrowest sections of altered riparian
 forests. Woody plant species composition differed and diversity was
 reduced in altered forests compared to intact riparian forests. However,
 despite being fragmented for several decades, large woody plant biomass
 and carbon storage, the number of live or dead large woody plants,
 mortality rates, and the size distribution of woody plants did not differ
 significantly between altered and intact riparian forests. Thus, even in
 these relatively narrow forests with high edge : area ratios, we saw no
 evidence of the increases in mortality and declines in biomass that have
 been found in other tropical forest fragment studies. However, because of
 the changes in both species community and reduced regeneration, it is
 unclear how long this relative lack of change will be sustained.
 Additionally, Brazil recently passed a law in their National Forest Code
 allowing narrower riparian buffers than those studied here in restored
 areas, which could affect their long-term sustainability.
description: Nagy_et_al_combined_dataThis file contains the following data in separate sheets: Importance Value Index, Leaf Area Index, large woody plants, microclimate, species composition, environmental data for analysis of species composition, large woody plant distribution, vegetation cover, and water table. Each of the above sheets in excel has an accompanying metadata sheet offering further explanation of the data.