cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j38b7
title: Data from: Data sharing through an NIH central database repository: a cross-sectional survey of BioLINCC users

description: Objective To characterise experiences using clinical research data shared
 through the National Institutes of Health (NIH)'s Biologic Specimen
 and Data Repository Information Coordinating Center (BioLINCC) clinical
 research data repository, along with data recipients’ perceptions of the
 value, importance and challenges with using BioLINCC data. Design and
 setting Cross-sectional web-based survey. Participants All investigators
 who requested and received access to clinical research data from BioLINCC
 between 2007 and 2014. Main outcome measures Reasons for BioLINCC data
 request, research project plans, interactions with original study
 investigators, BioLINCC experience and other project details. Results
 There were 536 investigators who requested and received access to clinical
 research data from BioLINCC between 2007 and 2014. Of 441 potential
 respondents, 195 completed the survey (response rate=44%); 89% (n=174)
 requested data for an independent study, 17% (n=33) for pilot/preliminary
 analysis. Commonly cited reasons for requesting data through BioLINCC were
 feasibility of collecting data of similar size and scope (n=122) and
 insufficient financial resources for primary data collection (n=76). For
 95% of respondents (n=186), a primary research objective was to complete
 new research, as opposed to replicate prior analyses. Prior to requesting
 data from BioLINCC, 18% (n=36) of respondents had contacted the original
 study investigators to obtain data, whereas 24% (n=47) had done so to
 request collaboration. Nearly all (n=176; 90%) respondents found the data
 to be suitable for their proposed project; among those who found the data
 unsuitable (n=19; 10%), cited reasons were data too complicated to use
 (n=5) and data poorly organised (n=5). Half (n=98) of respondents had
 completed their proposed projects, of which 67% (n=66) have been
 published. Conclusions Investigators were primarily using clinical
 research data from BioLINCC for independent research, making use of data
 that would otherwise have not been feasible to collect.
description: Dryad BioLINCC Survey
 Data 16-09-01This is the deidentified
 data from the 2015 cross-sectional survey of investigators who requested
 and received access to clinical research data from BioLINCC between 2007
 and 2014.READ ME Dryad BioLINCC Survey
 16-09-01.txtData Dictionary BioLINCC
 Survey 16-09-01This file lists and
 describes the variables from the 2015 cross-sectional BioLINCC
 survey.
DOI: 10.5061/dryad.b4h75
title: Data from: Mortality and lamb body mass growth in free-ranging domestic sheep – environmental impacts including lethal and non-lethal impacts of predators

description: The management and recovery of large predator populations in areas where
 human persecution has driven them to ecological extinction requires a
 solid understanding of the effects of both predation and food limitation
 on prey populations. We used 11 yr of data on reported losses among 17.3
 million free-ranging sheep Ovis aries in the Norwegian farming industry to
 elucidate the relative roles of climate, vegetation characteristics, sheep
 densities, lamb body mass and densities of predators and alternative prey
 on the number of lambs and ewes lost on summer pastures. We first examined
 whether predator densities predicted autumn lamb body mass through
 possible impacts of predators on body growth (non-lethal effects) but
 found no evidence for such effects in our study system. This might be due
 to weak anti-predator behavioral responses in domesticated sheep. However,
 autumn lamb body mass was predicted by both sheep density and winter and
 spring weather conditions, probably through food availability. Losses of
 both lambs and ewes were positively and strongly related to the density of
 Eurasian lynx Lynx lynx, wolverine Gulo gulo and brown bear Ursus arctos.
 In addition, food availability and spring weather conditions were
 associated to losses of lambs, while precipitation in May predicted losses
 of ewes. There was little evidence for interaction effects of predator
 species on losses, suggesting that most of the effects of the predators
 were additive to each other. Given the strong effect of predator densities
 on sheep losses, we conclude that changing livestock husbandry practices
 towards a system that actively protects sheep and/or active management of
 predator densities may be necessary to reduce sheep losses where predators
 are recolonizing.
description: Data at the county
 levelThe origin of the
 different variables is given in the article. The column headings refer to
 the variable names used in the article. The predator density is given per
 1000 km2 and the roe deer density as the number of animal shot per 10
 km2.Dryad_County_Level.csvData at the municipality levelThe origin of the different variables is given in the article. The column headings refer to the variable names used in the article. See legends in tables 2, 3 and 4 for details on the units used.Dryad_Municipality_Level.csv
DOI: 10.5061/dryad.6m8c0
title: Data from: Helper effects in the azure-winged magpie Cyanopica cyana in relation to highly-clumped nesting pattern and high frequency of conspecific nest-raiding

description: In avian cooperative breeding systems, many benefits obtained by social
 pairs from the presence of helpers have been uncovered. However, until
 now, the factors that determine the type of assistance helpers provide and
 the responses of social pairs have not been well illustrated. We examined
 the contribution of helpers to cooperative groups and the relevant
 responses of dominant pairs in the azure-winged magpie Cyanapica cyana
 which breeds on the Tibetan Plateau. We used the capture–mark–recapture
 method to identify helpers. Results showed that helpers were mostly the
 yearling sons of dominant pairs. They mainly contributed to the
 cooperative group in three ways, courtship-feeding the incubation female,
 provisioning the brood, and defending the nest. For responses of dominant
 pairs, we unexpectedly found that clutch size was not influenced by the
 presence of helpers at the nest. However, cooperative groups had higher
 brood feeding rates than biparental nests and their feeding pattern also
 differed to that of the latter. Consequently, nestlings in cooperative
 groups had larger fledging body mass than that in biparental nests. By
 examining reasons for nest failure, we revealed that conspecific
 nest-raiding contributed to more nest failure than any other natural
 predators. Because of the contribution of helpers in defending against
 both predators and conspecific nest-raiders, cooperative groups had higher
 survival rate than biparental nests. Thus, our findings suggest that in a
 highly-clumped nesting pattern, factors concerning the risk of nest
 predation, rather than that influencing food supply, play an important
 role in determining helper effects and responses of aided dominant pairs.
description: helper effect data
 deposited into the achieving system
DOI: 10.5061/dryad.2hf40
title: Data from: Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity

description: The increasing availability of DNA sequence data enables exciting new
 opportunities for fungal ecology. However, it amplifies the challenge of
 how to objectively classify the diversity of fungal sequences into
 meaningful units, often in the absence of morphological characters. Here,
 we test the utility of modern multilocus Bayesian coalescent-based methods
 for delimiting cryptic fungal diversity in the orchid mycorrhiza
 morphospecies Serendipita vermifera. We obtained 147 fungal isolates from
 Caladenia, a speciose clade of Australian orchids known to associate with
 Serendipita fungi. DNA sequence data for 7 nuclear and mtDNA loci were
 used to erect competing species hypotheses by clustering isolates based
 on: (a) ITS sequence divergence, (b) Bayesian admixture analysis, and (c)
 mtDNA variation. We implemented two coalescent-based Bayesian methods to
 determine which species hypothesis best fitted our data. Both methods
 found strong support for eight species of Serendipita among our isolates,
 supporting species boundaries reflected in ITS divergence. Patterns of
 host plant association showed evidence for both generalist and specialist
 associations within the host genus Caladenia. Our findings demonstrate the
 utility of Bayesian species delimitation methods and suggest that wider
 application of these techniques will readily uncover new species in other
 cryptic fungal lineages.
description: FUNECO_605_SerendipitaATP6Sequence data: locus ATP6FUNECO_605_SerendipitaC11488Sequence data: locus C11488FUNECO_605_SerendipitaC11804Sequence data: locus C11804FUNECO_605_SerendipitaC16699Sequence data: locus C16699FUNECO_605_SerendipitaC28586Sequence data: locus C28586FUNECO_605_SerendipitaITS1-4Sequence data: locus ITSFUNECO_605_SerendipitaLSUSequence data: locus LSUFUNECO_605_StarbeastXMLStarbeast XML files for four species delimitation hypotheses: T=2, T=3, T=7, and T=8
DOI: 10.5061/dryad.t34m9
title: Data from: Experimental food supplementation reveals habitat-dependent male reproductive investment in a migratory bird

description: Environmental factors can shape reproductive investment strategies and
 influence the variance in male mating success. Environmental effects on
 extrapair paternity have traditionally been ascribed to aspects of the
 social environment, such as breeding density and synchrony. However,
 social factors are often confounded with habitat quality and are
 challenging to disentangle. We used both natural variation in habitat
 quality and a food supplementation experiment to separate the effects of
 food availability—one key aspect of habitat quality—on extrapair paternity
 (EPP) and reproductive success in the black-throated blue warbler,
 Setophaga caerulescens. High natural food availability was associated with
 higher within-pair paternity (WPP) and fledging two broods late in the
 breeding season, but lower EPP. Food-supplemented males had higher WPP
 leading to higher reproductive success relative to controls, and when in
 low-quality habitat, food-supplemented males were more likely to fledge
 two broods but less likely to gain EPP. Our results demonstrate that food
 availability affects trade-offs in reproductive activities. When food
 constraints are reduced, males invest in WPP at the expense of EPP. These
 findings imply that environmental change could alter how individuals
 allocate their resources and affect the selective environment that drives
 variation in male mating success.
description: WPP Model Table
 1Dataset supporting the
 results examining the effects of natural variation in food availability on
 within-pair paternity (Table 1 Model 1).Model1Table1Data.csvEPP Model Table 1Dataset supporting the results examining the effects of natural variation in food availability on extrapair paternity (Table 1 Model 2).Model2Table1Data.csvDouble brooding Model Table 1Dataset supporting the results examining the effects of natural variation in food availability on double brooding (Table 1 Model 3).Model3Table1Data.csvTable 2Dataset supporting the results examining the effects of food supplementation on within-pair paternity, extrapair paternity, double brooding and total reproductive success (Table 2 Models 1-4).Model1to4Table2Data.csvPoisson ModelDataset supporting the results investigating the relative contribution of within-pair paternity, extrapair paternity and double brooding on total reproductive success (Figure 2).ResultsSecDTableS3Data.csv
DOI: 10.5061/dryad.129vg
title: Data from: Seedling resistance, tolerance and escape from herbivores: insights from co-dominant canopy tree species in a resource-poor African rain forest

description: Although plants can reduce the impacts of herbivory in multiple ways,
 these defensive traits are often studied in isolation and an understanding
 of the resulting strategies is incomplete. In the study reported here,
 empirical evidence was simultaneously evaluated for the three main sets of
 traits available to plants: (1) resistance through constitutive leaf
 traits, (2) tolerance to defoliation, and (3) escape in space, for three
 caesalpiniaceous tree species Microberlinia bisulcata, Tetraberlinia
 bifoliolata and T. korupensis, which co-dominate groves within the lowland
 primary rain forest of Korup National Park (Cameroon). Mesh cages were
 placed around individual wild seedlings to exclude insect herbivores at 41
 paired canopy-gap and understorey locations. After following growth and
 survival for c. 2 yr, caged and control treatments were removed, leaves
 harvested to determine nutrient and phenolic concentrations, leaf mass per
 area estimated, and seedling performance in gaps followed for a further c.
 2 yr to quantify tolerance to the leaf harvesting. The more nutrient-rich
 leaves of the weakly shade-tolerant M. bisulcata were damaged much more in
 gaps than the two strongly shade-tolerant Tetraberlinia species, which had
 higher leaf mass per area and concentrations of total phenols. Conversely,
 the faster-growing M. bisulcata was better able to tolerate defoliation in
 terms of height growth (re-flushing capacity), but not at maintaining
 overall leaf numbers, than the other two species. Across gaps,
 insect-mediated Janzen-Connell effects were most pronounced for M.
 bisulcata, less so for T. korupensis, and not detectable for T.
 bifoliolata. The three species differed distinctly in their secondary
 metabolic profiles. Taken together, the results suggested a conceptual
 framework linking the three sets of traits, one in which the three
 co-dominant species adopt different strategies towards herbivore pressure
 depending on their different responses to light availability. This study
 is one of the first in a natural forest ecosystem to examine resistance
 to, tolerance of, and escape from herbivory among a group of co-occurring
 tropical tree species.
description: Tree seedlings'
 growth, mortality, leaf damage and light availablityMain
 dataframe.1.growth,mortality,damage,light.xlsNutrient concentrations in leaves of tree seedlingsMain dataframe.2.leaf macronutrients.xlsTotal phenols in leaves of tree seedlingsMain dataframe.3.polyphenols.xlsLMA of tree seedlingsMain dataframe.4.leaf mass per area.xls
DOI: 10.5061/dryad.315
title: Data from: A quantitative survey of local adaptation and fitness trade-offs

description: The long history of reciprocal transplant studies testing the hypothesis
 of local adaptation has shown that populations are often adapted to their
 local environments. Yet many studies have not demonstrated local
 adaptation, suggesting that sometimes native populations are no better
 adapted than are genotypes from foreign environments. Local adaptation may
 also lead to trade-offs, in which adaptation to one environment comes at a
 cost of adaptation to another environment. I conducted a survey of
 published studies of local adaptation to quantify its frequency and
 magnitude and the costs associated with local adaptation. I also
 quantified the relationship between local adaptation and environmental
 differences and the relationship between local adaptation and phenotypic
 divergence. The overall frequency of local adaptation was 0.71, and the
 magnitude of the native population advantage in relative fitness was 45%.
 Divergence between home site environments was positively associated with
 the magnitude of local adaptation, but phenotypic divergence was not. I
 found a small negative correlation between a population's relative
 fitness in its native environment and its fitness in a foreign
 environment, indicating weak trade-offs associated with local adaptation.
 These results suggest that populations are often locally adapted but
 stochastic processes such as genetic drift may limit the efficacy of
 divergent selection.
description: LA
 DataLA_data_Hereford.xls
DOI: 10.5061/dryad.k6491
title: Data from: Phenotypic and genetic integration of personality and growth under competition in the sheepshead swordtail, Xiphophorus birchmanni

description: Competition for resources including food, physical space, and potential
 mates is a fundamental ecological process shaping variation in individual
 phenotype and fitness. The evolution of competitive ability, in particular
 social dominance, depends on genetic (co)variation among traits causal
 (e.g., behavior) or consequent (e.g., growth) to competitive outcomes. If
 dominance is heritable, it will generate both direct and indirect genetic
 effects (IGE) on resource-dependent traits. The latter are expected to
 impose evolutionary constraint because winners necessarily gain resources
 at the expense of losers. We varied competition in a population of
 sheepshead swordtails, Xiphophorus birchmanni, to investigate effects on
 behavior, size, growth, and survival. We then applied quantitative genetic
 analyses to determine (i) whether competition leads to phenotypic and/or
 genetic integration of behavior with life history and (ii) the potential
 for IGE to constrain life history evolution. Size, growth, and survival
 were reduced at high competition. Male dominance was repeatable and
 dominant individuals show higher growth and survival. Additive genetic
 contributions to phenotypic covariance were significant, with the G matrix
 largely recapitulating phenotypic relationships. Social dominance has a
 low but significant heritability and is strongly genetically correlated
 with size and growth. Assuming causal dependence of growth on dominance,
 hidden IGE will therefore reduce evolutionary potential.
description: Data from Boulton et al.
 Evolution paperBoulton et al archived data
 set.txt
DOI: 10.5061/dryad.g00v5
title: Data from: Sex without sex chromosomes: genetic architecture of multiple loci independently segregating to determine sex ratios in the copepod Tigriopus californicus

description: Sex determining systems are remarkably diverse and may evolve rapidly.
 Polygenic sex determination systems are predicted to be transient and
 evolutionarily unstable yet examples have been reported across a range of
 taxa. Here we provide the first direct evidence of polygenic sex
 determination in Tigriopus californicus, a harpacticoid copepod with no
 heteromorphic sex chromosomes. Using genetically distinct inbred lines
 selected for male- and female-biased clutches, we generated a genetic map
 with 39 SNPs across 12 chromosomes. Quantitative trait locus mapping of
 sex ratio phenotype (the proportion of male offspring produced by an F2
 female) in four F2 families revealed six independently segregating
 quantitative trait loci on five separate chromosomes, explaining 19% of
 the variation in sex ratios. The sex ratio phenotype varied among loci
 across chromosomes in both direction and magnitude, with the strongest
 phenotypic effects on chromosome 10 moderated to some degree by loci on
 four other chromosomes. For a given locus, sex ratio phenotype varied in
 magnitude for individuals derived from different dam lines. These data,
 together with the environmental factors known to contribute to sex
 determination, characterize the underlying complexity and potential
 lability of sex determination, and confirm the polygenic architecture of
 sex determination in T. californicus.
description: Tigriopus sex ratio
 phenotype and genotype dataData from intercross
 design F2 females. Initially started with 2 lines (male-biased and
 female-biased selection lines) in each of 2 populations (San Diego,
 California, USA (SD) and Agiuliar, Bamfield, BC, Canada (AG)). Each row
 represents an individual F2 female and gives her phenotype (number of
 brood, number of males, females in brood) and her genotype at 46 SNP loci.
 See ReadMe.txt for more information.genopheno.csvQTL raw dataqtl_all_raw.csv
DOI: 10.5061/dryad.rm3n1
title: Data from: Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)

description: Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species
 endemic to the island of Taiwan. A warming climate and competition from
 subtropical tree species has limited the range of Taiwan spruce to the
 higher altitudes of the island. Using seeds sampled from an area in the
 central mountain range of Taiwan, 15 nuclear loci were sequenced in order
 to measure genetic variation and to assess the long-term genetic stability
 of the species. Genetic diversity is low and comparable to other spruce
 species with limited ranges such as Picea breweriana, Picea chihuahuana,
 and Picea schrenkiana. Importantly, analysis using approximate Bayesian
 computation (ABC) provides evidence for a drastic decline in the effective
 population size approximately 0.3–0.5 million years ago (mya). We used
 simulations to show that this is unlikely to be a false-positive result
 due to the limited sample used here. To investigate the phylogenetic
 origin of Taiwan spruce, additional sequencing was performed in the
 Chinese spruce Picea wilsonii and combined with previously published data
 for three other mainland China species, Picea purpurea, Picea
 likiangensis, and P. schrenkiana. Analysis of population structure
 revealed that P. morrisonicola clusters most closely with P. wilsonii, and
 coalescent analyses using the program MIMAR dated the split to 4–8 mya,
 coincidental to the formation of Taiwan. Considering the population
 decrease that occurred after the split, however, led to a much more recent
 origin.
description: 4CL
 sequencesSequences for the locus
 4CL.4cl.all.fastaEBS sequencesSequences for the locus EBS.ebs.all.fastaM002 sequencesSequences for the locus M002.m002.all.fastaPCH sequencesSequences for the locus PCH.pch.all.fastaSB16 sequencesSequences for the locus SB16.SB16.all.fastaSB29 sequencesSequences for the locus SB29.sb29.all.fastaSB62 sequencesSequences for the locus SB62.sb62.all.fastaSE1390 sequencesSequences for the locus SE1390.SE1390.all.fasta