cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72551
title: Data from: Phenological asynchrony in plant–butterfly interactions associated with climate: a community-wide perspective

description: Although much information has been accumulated on the effects of climate
 change on particular species worldwide, research aimed at assessing how
 such change influences biotic interactions from a community-wide
 perspective is still in its infancy. We contribute to filling in this gap
 by analyzing a 17-year (1996–2012) dataset that includes records of
 flower-visitation interactions between 12 butterfly species and 17 plant
 species in a coastal wetland area in northeastern Iberian Peninsula. We
 assessed the extent to which temporal asynchronies between plants and
 adult butterflies are influenced by different climatic variables that
 affect both plant and insect phenologies. Temperature and degree of
 aridity at various monthly summaries were used as predictors of the
 plant–butterfly phenological asynchrony. We identified the seasonal window
 with the greatest effect on asynchronies for two butterfly generations
 (spring and summer), and assessed whether the magnitude of asynchrony is
 associated with the level of butterfly specialization. We used generalized
 linear mixed models considering a total of 39 plant-butterfly
 interactions. Average asynchrony was higher in the spring generation and
 dry conditions during winter lead to decreased temporal overlap with
 flowers in this butterfly generation, whereas dry conditions in the spring
 lead to decreased temporal overlap in the summer butterfly generation. The
 magnitude of the effect was consistently small at the community level (all
 interactions pooled). Moreover, no clear climatic trend over the study
 time frame was detected. Finally, specialized and generalized butterflies
 in their resource use as adults were similarly vulnerable to asynchronies,
 in contrast to previous predictions of greater mutualistic disruptions in
 species with narrower niches. We conclude that a least in the
 Mediterranean region, phenological asynchronies might be more affected by
 aridity level than by temperature itself, and thus the former can be a key
 climatic trait to make better predictions in this region.
description: Interactions_Asynchrony_IndexTable containing the 39 plant-butterfly interactions included in this study. For each year of the study period (1996-2012) we indicate the asynchrony index (number of days) corresponding to the Spring butterfly generations (AI1_spring) and Summer butterfly generations (AI2_summer). Last column represents the butterfly abundance index (number of butterflies of each species recorded each year along the whole sampling season).AsynchronyIndex_Donoso_etal_2015.xlsx
DOI: 10.5061/dryad.h7234
title: Data from: Gynaecological cancer follow-up: national survey of current practice in the UK

description: Objective: To establish a baseline of national practice for follow-up
 after treatment for gynaecological cancer. Design: Questionnaire survey.
 Setting: Gynaecological cancer centres and units. Geographical location:
 UK Participants: Members of the British Gynaecological Cancer Society and
 the National Forum of Gynaecological Oncology Nurses. Interventions: A
 questionnaire survey. Outcome measures: To determine schedules of
 follow-up, who provides it and what routine testing is used for patients
 who have had previous gynaecological cancer. Results: A total of 117
 responses were obtained; 115 (98%) reported hospital scheduled regular
 follow-up appointments. Two involved General Practitioners. Follow-up was
 augmented or replaced by telephone follow-up in 29 (25%) and patient
 initiated appointments in 38 responses (32%). A total of 80 (68%) cancer
 specialists also offered combined follow-up clinics with other
 specialties. Clinical examinations for hospital based follow-up were
 mainly performed by doctors (67% for scheduled regular appointments and
 63% for patient initiated appointments) while telephone follow-up care was
 provided in the majority by nurses (76%). Most respondents provided
 routine tests (76/117 (65%)), from which 66/76 (87%) reported carrying out
 surveillance tests for ovarian cancer, 35/76 (46%) for cervical cancer,
 8/76 (11%) for vulval cancer and 7/76 (9%) for endometrial cancer. Usually
 patients were discharged after five years (82/117 (70%)), whereas three
 (3%) were discharged after four years, nine (8%) after three and one (1%)
 after two years. Conclusions: Practice varied but most used a standard
 hospital based protocol of appointments for five years and routine tests
 were performed usually for women with ovarian cancer. A minority utilised
 nurse-led or telephone follow-up. General Practitioners were rarely
 involved in routine care. A randomised study comparing various models of
 follow-up could be considered.
description: Gynaecological Cancer
 Survey datasetThis file contains the
 dataset for the manuscript “Gynaecological cancer follow-up: National
 survey of current practice in the UK”. The data was collected using the
 Bristol Online Survey (BOS). All methods are described in the associated
 manuscript. The column headings correspond to each of the questions in the
 survey which are described in a separate worksheet in the excel
 spreadsheet.GCS_dataset.xlsb
DOI: 10.5061/dryad.9r35r
title: Data from: Exploring the potential health impact and cost-effectiveness of AIDS vaccine within a comprehensive HIV/AIDS response in low- and middle-income countries

description: Background: The Investment Framework Enhanced (IFE) proposed in 2013 by
 the Joint United Nations Programme on HIV/AIDS (UNAIDS) explored how
 maximizing existing interventions and adding emerging prevention options,
 including a vaccine, could further reduce new HIV infections and
 AIDS-related deaths in low- and middle-income countries (LMICs). This
 article describes additional modeling which looks more closely at the
 potential health impact and cost-effectiveness of AIDS vaccination in
 LMICs as part of UNAIDS IFE. Methods: An epidemiological model was used to
 explore the potential impact of AIDS vaccination in LMICs in combination
 with other interventions through 2070. Assumptions were based on
 perspectives from research, vaccination and public health experts, as well
 as observations from other HIV/AIDS interventions and vaccination
 programs. Sensitivity analyses varied vaccine efficacy, duration of
 protection, coverage, and cost. Results: If UNAIDS IFE goals were fully
 achieved, new annual HIV infections in LMICs would decline from 2.0
 million in 2014 to 550,000 in 2070. A 70% efficacious vaccine introduced
 in 2027 with three doses, strong uptake and five years of protection would
 reduce annual new infections by 44% over the first decade, by 65% the
 first 25 years and by 78% to 122,000 in 2070. Vaccine impact would be much
 greater if the assumptions in UNAIDS IFE were not fully achieved. An AIDS
 vaccine would be cost-effective within a wide range of scenarios.
 Interpretation: Even a modestly effective vaccine could contribute
 strongly to a sustainable response to HIV/AIDS and be cost-effective, even
 with optimistic assumptions about other interventions. Higher efficacy
 would provide even greater impact and cost-effectiveness, and would
 support broader access. Vaccine efficacy and cost per regimen are critical
 in achieving cost-effectiveness, with cost per regimen being particularly
 critical in low-income countries and at lower efficacy levels.
description: Dataset - Harmon et al
 2015Excel Results file for
 Harmon et al 2015.
DOI: 10.5061/dryad.fg5j52t5
title: Data from: Abiotic heterogeneity drives parasite local adaptation in coevolving bacteria and phages

description: Spatial abiotic heterogenity can result in divergent selection, hence
 might increase the magnitude of host-parasite local adaptation (the mean
 difference in fitness of sympatric versus allopatric host-parasite
 combinations). We explicitly tested this hypothesis by measuring local
 adapation in experimentally coevolved populations of bacteria and viruses
 evolved in the same or different nutrient media. Consistent with previous
 work, we found that mean levels of evolved phage infectivity and bacteria
 resistance varied with nutrient concentration, with maximal levels at
 nutrient concentrations that supported the greatest densities of bacteria.
 Despite this variation in evolved mean infectivity and resistance between
 treatments, we found that parasite local adaptation was greatly increased
 when measured between populations evolved in different, compared to the
 same, media. This pattern is likely to have resulted from different media
 imposing divergent selection on bacterial hosts, and phages in turn
 adapting to their local hosts. These results demonstrate that the abiotic
 environment can play a strong and predictable role in driving patterns of
 local adaptation.
description: lopezpascuaetalJEB2012dataResistance of specific bacteria-phage combinations
DOI: 10.5061/dryad.bq8j8
title: Data from: Experimental parasite community ecology: intraspecific variation in a large tapeworm affects community assembly

description: Non-random species associations occur in naturally-sampled parasite
 communities. The processes resulting in predictable community structure
 (e.g. particular host behaviours, cross-immunity, interspecific
 competition) could be affected by traits that vary within a parasite
 species, like growth or antigenicity. We experimentally infected
 three-spined sticklebacks with a large tapeworm (Schistocephalus solidus)
 that impacts the energy needs, foraging behaviour, and immune reactions of
 its host. The tapeworms came from two populations, characterized by high
 or low growth in sticklebacks. Our goal was to evaluate how this parasite,
 and variation in its growth, affects the acquisition of other parasites.
 Fish infected with S. solidus were placed into cages in a lake to expose
 them to the natural parasite community. We also performed a lab experiment
 in which infected fish were exposed to a fixed dose of a common trematode
 parasite. In the field experiment, infection with S. solidus affected the
 abundance of four parasite species, relative to controls. For two of the
 four species, changes occurred only in fish harbouring the high-growth S.
 solidus; one species increased in abundance and the other decreased. These
 changes did not appear to be directly linked to S. solidus growth though.
 The parasite exhibiting elevated abundance was the same trematode used in
 the lab infection. In that experiment, we found a similar infection
 pattern, suggesting that S. solidus affects the physiological
 susceptibility of fish to this trematode. Associations between S. solidus
 and other parasites occur and vary in direction. However, some of these
 associations were contingent on the S. solidus population, suggesting that
 intraspecific variability can affect the assembly of parasite communities.
description: Lab experiment
 dataLab_exp.csvField experiment dataField_exp.csv
DOI: 10.5061/dryad.52n61
title: Data from: High food abundance permits the evolution of placentotrophy: evidence from a placental lizard, Pseudemoia entrecasteauxii

description: Mechanisms of reproductive allocation are major determinants of fitness
 because embryos cannot complete development without receiving sufficient
 nutrition from their parents. The nourishment of offspring via placentae
 (placentotrophy) has evolved repeatedly in vertebrates, including multiple
 times in squamate reptiles (lizards and snakes). Placentotrophy has been
 suggested to evolve only if food is sufficiently abundant throughout
 gestation to allow successful embryogenesis. If scarcity of food prevents
 successful embryogenesis, females should recoup nutrients allocated to
 embryos via abortion, reabsorption, and/or cannibalism. We tested these
 hypotheses in the placentotrophic Southern Grass Skink, Pseudemoia
 entrecasteauxii. We fed females one of four diets (high constant, high
 variable, low constant, and low variable) during gestation, and tested the
 effects of both food amount and schedule of feeding on developmental
 success, cannibalism rate, placental nutrient transport, offspring size,
 and maternal growth and body condition. Low food availability reduced
 developmental success, placental nutrient transport, offspring size, and
 maternal growth and body condition. Cannibalism of offspring also
 increased when food was scarce. Schedule of feeding did not affect
 offspring or mothers. We suggest that high food abundance and ability to
 abort and cannibalize poor-quality offspring are permissive factors
 necessary for placentotrophy to be a viable strategy of reproductive
 allocation.
description: Van Dyke et al
 data
DOI: 10.5061/dryad.nf781
title: Data from: The lek mating system of the worm pipefish (Nerophis lumbriciformis): a molecular maternity analysis and test of the phenotype-linked fertility hypothesis

description: The origin and maintenance of mating preferences continues to be an
 important and controversial topic in sexual selection research. Leks and
 lek-like mating systems, where individuals gather in particular spots for
 the sole purpose of mate choice, are particularly puzzling, because the
 strong directional selection imposed by mate choice should erode genetic
 variation among competing individuals and negate any benefit for the
 choosing sex. Here, we take advantage of the lek-like mating system of the
 worm pipefish (Nerophis lumbriciformis) to test the phenotype-linked
 fertility hypothesis for the maintenance of mating preferences. We use
 microsatellite markers to perform a parentage analysis, along with a
 mark-recapture study, to confirm that the worm pipefish has an unusual
 mating system that strongly resembles a female lek, where females display
 and males visit the lek to choose mates. Our results show that the most
 highly ornamented females occupy positions near the centre of the breeding
 area, and males mating with these females receive fuller broods with
 larger eggs compared to males mating with less ornamented females. We also
 conduct a laboratory experiment to show that female ornaments are
 condition dependent and honestly signal reproductive potential. Overall,
 these results are consistent with the predictions of a sex-independent
 version of the phenotype-linked fertility hypothesis, as male preference
 for female ornaments correlates with fertility benefits.
description: Dryad_Nerophis_lumbriciformisMicrosatellite data from the Viana (Portugal) Nerophis lumbriciformis population. On the first page, the unique adult genotypes are presented (used for the construction of Table 1, using GENALEX and CERVUS). The second page contains the genotypes of embryos and potential parents, including recaptures (used in PARFEX for the parentage analysis).
DOI: 10.5061/dryad.61cg073t
title: Data from: Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny

description: A principal objective for phylogenetic experimental design is to predict
 the power of a dataset to resolve nodes in a phylogenetic tree. However,
 proactively assessing the potential for phylogenetic noise compared to
 signal in a candidate dataset has been a formidable challenge.
 Understanding the impact of collection of additional sequence data to
 resolve recalcitrant internodes at diverse historical times will
 facilitate increasingly accurate and cost-effective phylogenetic research.
 Here, we derive theory based on the fundamental unit of the phylogenetic
 tree, the quartet, that applies estimates of the state space and the rates
 of evolution of characters in a dataset to predict phylogenetic signal and
 phylogenetic noise and therefore to predict the power to resolve
 internodes. We develop and implement a Monte Carlo approach to estimating
 power to resolve as well as deriving a nearly equivalent, faster
 deterministic calculation. These approaches are applied to describe the
 distribution of potential signal, polytomy, or noise for two example
 datasets, one recent (CO1 and 28S sequences from Diplazontinae parasitoid
 wasps) and one deep (eight nuclear genes and a phylogenomic sequence for
 diverse microbial eukaryotes including Stramenopiles, Alveolata, and
 Rhizaria). The predicted power of resolution for the loci analyzed is
 consistent with the historic use of the genes in phylogenetics.
description: Table S1: Deep microbial
 eukaryote sequences.Table
 S1.pdfTable S2: Monte Carlo
 results for the ((SA)R) node.Table
 S2.pdfTable S3: Monte Carlo
 results for the Alveolate node.Table
 S3.pdfTable S6: Monte Carlo
 results for the ((SR)A) node.Table
 S6.pdfTable S4: Deterministic
 approximation results for the ((SA)R) node.Table
 S4.pdfTable S5: Deterministic
 approximation results for the Alveolate node.Table
 S5.pdfTable S7: Deterministic
 approximation results for the ((SR)A) node.Table
 S7.pdf
DOI: 10.5061/dryad.jk832
title: Data from: Why we are not dead 100 times over

description: The possibility of pervasive weak selection at tens or hundreds of
 millions of sites across the genome, suggested by recent studies of silent
 site DNA sequence variation and divergence, raises the problem of the
 survival of the population in the face of the large genetic load that may
 result. Two alternative resolutions of this problem are presented for
 populations where recombination is sufficiently frequent that different
 sites under selection evolve independently. One invokes weak stabilizing
 selection, of the magnitude compatible with abundant silent site
 variability. This can be shown to produce only a modest genetic load, due
 to the effectiveness of even weak stabilizing selection in keeping the
 trait mean close to the optimum. The other invokes soft selection, whereby
 individuals compete for a limiting resource whose abundance determines the
 absolute fitness of the population. Weak purifying selection at a large
 number of sites produces only a small variance in fitness among
 individuals within the population, due to the fact that most sites are
 fixed rather than polymorphic. Even when it produces a large genetic load,
 it is compatible with the observations when selection is soft. It may be
 very difficult to distinguish between these two possibilities.
description: stabselbin3Fortran 77 computer program used to generate results shown in Table 1 of papersimresultsFile of output from computer program Stabselbin3, on which results shown in Table 1 are based.
DOI: 10.5061/dryad.632dn89
title: Data from: How to map forest structure from aircraft, one tree at a time

description: Forest structure is strongly related to forest ecology and it is a key
 parameter to understand ecosystem processes and services. Airborne laser
 scanning (ALS) is becoming an important tool in environmental mapping. It
 is increasingly common to collect ALS data at high enough point density to
 recognize individual tree crowns (ITCs) allowing analyses to move beyond
 classical stand level approaches. In this paper an effective and simple
 method to map ITCs, and their stem diameter and above ground biomass is
 presented. ALS data were used to delineate ITCs and to extract ITCs’
 height and crown diameter; then using newly developed allometries the
 ITCs’ DBH and AGB were predicted. Gini coefficient of DBHs was also
 predicted and mapped aggregating ITCs predictions. Two datasets from
 spruce dominated temperate forests were considered: one was used to
 develop the allometric models, while the second was used to validate the
 methodology. The proposed approach provides accurate predictions of
 individual DBH and AGB (R2 = 0.85 and 0.78, respectively) and of tree size
 distributions. The proposed method had a higher generalization ability
 compared to a standard area based method, in particular for the prediction
 of the Gini coefficient of DBHs. The delineation method used detected more
 than 50% of the trees with DBH &gt;10 cm. The detection rate was
 particularly low for trees with DBH below 10 cm, but they represent a
 small amount of the total biomass. The Gini coefficient of the DBH
 distribution was predicted at plot level with R2 = 0.46. The approach
 described in this work, easy applicable in different forested areas, is an
 important development of the traditional area based remote sensing tools
 and can be applied for more detailed analysis of forest ecology and
 dynamics.
description: Paneveggio
 datasetThese are the data of
 the Paneveggio dataset. These are the data of the field measured trees. It
 is a table with five columns: 1) "PlotID": ID of the field plot;
 2) "Height_m": field measured tree height in meters; 3)
 "CD_m": field measured crown diameter in meters; 4)
 "DBH_cm": field measured DBH in centimeters; and 5)
 "AGB_kg": field estimated AGB in kilograms.paneveggio_field_data.csvPellizzano datasetThese are the data of the Pellizzano dataset. These are the data of the detected ITCs. It is a table with six columns: 1) "PlotID": ID of the field plot; 2) "Height_m": ALS-derived height of the detected ITC in meters; 3) "CD_m": ALS-derived crown diameter of the detected ITC in meters; 4) "H_F_m": field measured tree height in meters of the tree associated to that ITC; 5) "DBH_F_cm": field measured tree DBH in centimeters of the tree associated to that ITC; and 6) "AGB_F_kg": field estimated tree AGB in kilograms of the tree associated to that ITC.pellizzano_itc_data.csv
DOI: 10.5061/dryad.tj590
title: Data from: Fatal attraction? Intraguild facilitation and suppression among predators

description: Competition and suppression are recognized as dominant forces that
 structure predator communities. Facilitation via carrion provisioning,
 however, is a ubiquitous interaction among predators that could offset the
 strength of suppression. Understanding the relative importance of these
 positive and negative interactions is necessary to anticipate
 community-wide responses to apex predator declines and recoveries
 worldwide. Using state-sponsored wolf (Canis lupus) control in Alaska as a
 quasi-experiment, we conducted snow track surveys of apex, meso-, and
 small predators to test for evidence of carnivore cascades (e.g.,
 mesopredator release). We analyzed survey data using an integrative
 occupancy and structural equation modeling framework to quantify the
 strengths of hypothesized interaction pathways, and we evaluated
 fine-scale spatiotemporal responses of non-apex predators to wolf activity
 clusters identified from radio-collar data. Contrary to the carnivore
 cascade hypothesis, both meso- and small predator occupancy patterns
 indicated guild-wide, negative responses of non-apex predators to wolf
 abundance variations at the landscape scale. At the local scale, however,
 we observed a near guild-wide, positive response of non-apex predators to
 localized wolf activity. Local-scale association with apex predators due
 to scavenging could lead to landscape patterns of mesopredator
 suppression, suggesting a key link between occupancy patterns and the
 structure of predator communities at different spatial scales.
description: SEMdatawlfclusterdata