cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6n9d5
title: Data from: Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

description: Quantifying and assessing changes in biological diversity are central
 aspects of many ecological studies, yet accurate methods of estimating
 biological diversity from sampling data have been elusive. Hill numbers,
 or the effective number of species, are increasingly used to characterize
 the taxonomic, phylogenetic, or functional diversity of an assemblage.
 However, empirical estimates of Hill numbers, including species richness,
 tend to be an increasing function of sampling effort and, thus, tend to
 increase with sample completeness. Integrated curves based on sampling
 theory that smoothly link rarefaction (interpolation) and prediction
 (extrapolation) standardize samples on the basis of sample size or sample
 completeness and facilitate the comparison of biodiversity data. Here we
 extended previous rarefaction and extrapolation models for species
 richness (Hill number qD, where q = 0) to measures of taxon diversity
 incorporating relative abundance (i.e., for any Hill number qD, q &gt;
 0) and present a unified approach for both individual-based (abundance)
 data and sample-based (incidence) data. Using this unified sampling
 framework, we derive both theoretical formulas and analytic estimators for
 seamless rarefaction and extrapolation based on Hill numbers. Detailed
 examples are provided for the first three Hill numbers: q = 0 (species
 richness), q = 1 (the exponential of Shannon's entropy index), and q
 = 2 (the inverse of Simpson's concentration index). We developed a
 bootstrap method for constructing confidence intervals around Hill
 numbers, facilitating the comparison of multiple assemblages of both
 rarefied and extrapolated samples. The proposed estimators are accurate
 for both rarefaction and short-range extrapolation. For long-range
 extrapolation, the performance of the estimators depends on both the value
 of q and on the extrapolation range. We tested our methods on simulated
 data generated from species abundance models and on data from large
 species inventories. We also illustrate the formulas and estimators using
 empirical data sets from biodiversity surveys of temperate forest spiders
 and tropical ants.
description: Data_AntSpecies incidence frequency counts for ant samples from five elevations in northeastern Costa Rica (Longino and Colwell 2011)Data_SpiderSpider species abundance frequency counts in two canopy manipulation treatments (Ellison et al. 2010, Sackett et al. 2011).
DOI: 10.5061/dryad.d0p8h
title: Data from: New insights from bone microanatomy of the Late Triassic Hyperodapedon (Archosauromorpha, Rhynchosauria): implications for archosauromorph growth strategy

description: Bone microanatomy of multiple postcranial skeletal elements of several
 individuals of Hyperodapedon collected from India is reported. This
 reveals that fibrolamellar bone tissue is predominant in the mid- and
 inner cortices, whereas the peripheral region of the cortex is composed of
 either parallel-fibred and/or lamellar bone. The pattern of primary
 osteons mostly ranges between laminar and subplexiform. Such predominance
 of fibrolamellar bone tissue in the cortex suggests an overall fast
 growth, which slowed down considerably later in ontogeny. Four distinct
 ontogenetic stages are identified based on the bone microstructure. During
 the juvenile stage, growth was fast and continuous, but it became
 punctuated during the early and late sub-adult stages. In adult
 individuals, growth was slow and showed periodic interruption but did not
 stop completely, suggesting that Hyperodapedon had an indeterminate growth
 strategy. Interelemental histovariations affecting cortical thickness,
 organization of the vascular network, incidence of growth rings and extent
 of secondary reconstruction are noted. Throughout ontogeny, the femora
 show higher cortical thickness than humeri and tibiae, suggesting
 differential appositional growth rate between the skeletal elements.
 Differences in cortical thickness are noted in the ribs, which suggest
 differential functional constraints based on anatomical site-specific
 occurrences. Although fibrolamellar bone tissue became progressively more
 dominant towards the archosaurs, there are considerable variations in the
 growth patterns of the archosauromorphs. This is exemplified by the bone
 microstructure of Hyperodapedon, which deviates from the generalized
 slow-growth pattern proposed for all basal archosauromorphs, suggesting
 that rapid growth was already present in the archosauromorphs. The
 cortical thickness of various long bones of Hyperodapedon bears similarity
 with that of several extant terrestrial quadrupeds, suggesting that
 Hyperodapedon was essentially a terrestrial quadruped.
description: Mukherjee_Appendix
 S1.R1Appendix S1. Available
 skeletal elements of Hyperodapedon used for bone histology. The alphabets
 ‘a, b’ denote elements from the same individual. Single (*) and double
 (**) asterisks denote measured diameter and width,
 respectively.
DOI: 10.5061/dryad.jd6m0
title: Data from: Prey responses to fine-scale variation in predation risk from combined predators

description: While it is well documented that organisms can express phenotypic
 plasticity in response to single gradients of environmental variation, our
 understanding of how organisms integrate information along multiple
 environmental gradients is limited in many systems. Using the freshwater
 snail Helisoma trivolvis and two common predators (water bugs Belostoma
 flumineum and crayfish Orconectes rusticus), we explored how prey
 integrate information along multiple predation risk gradients (i.e. caged
 predators fed increasing amounts of prey biomass) that induce opposing
 phenotypes. When exposed to single predators fed increasing amounts of
 prey biomass, we detected threshold responses; intermediate amounts of
 consumed biomass induced phenotypic responses, but higher amounts induced
 little additional induction. This suggests that additional increases in
 predator-induced traits with greater predator risk offer minimal increases
 in fitness or that a limit in the response magnitude was reached.
 Additionally, the response thresholds were contingent on the predator and
 focal trait. For shell width, responses were generally detected at a lower
 amount of consumed biomass by water bugs compared to crayfish. Within the
 crayfish treatments, we found that the shell thickness response threshold
 was lower than the shell width response threshold. When we combined
 gradients of consumed biomass from both predators, we found that the
 magnitude of response to one predator was often reduced when the other
 predator was present. Interestingly, these effects were often detected at
 consumed biomass levels that were lower than the threshold concentration
 necessary to elicit a response in the single-predator treatments.
 Moreover, our combined predator treatments revealed that snails shifted
 from discrete responses to more continuous (i.e. graded) responses.
 Together, our results reveal that organisms experiencing multiple
 environmental gradients can integrate this information to make phenotypic
 decisions and demonstrate the novel result that an exposure to multiple
 species of predators can lower the response threshold of prey.
description: Hoverman & Relyea
 Oikos 2015 dataPool means for each of
 the sample dates of the experiment are provided for each experimental
 unit. Metadata is provided in the document.Hoverman & Relyea
 data.xls
DOI: 10.5061/dryad.82fk7
title: Data from: Intralocus tactical conflict: genetic correlations between fighters and sneakers of the dung beetle Onthophagus taurus

description: Males and females differ in their phenotypic optima for many traits, and
 since the majority of genes are expressed in both sexes, some alleles can
 be beneficial to one sex but harmful to the other (intralocus sexual
 conflict; ISC). ISC theory has recently been extended to intrasexual
 dimorphisms, where certain alleles may have opposite effects on the
 fitness of males of different morphs that employ alternative reproductive
 tactics (intralocus tactical conflict; ITC). Here we use a half-sib
 breeding design to investigate the genetic basis for ISC and ITC in the
 dung beetle Onthophagus taurus. We found positive heritabilities and
 intersexual genetic correlations for almost all traits investigated. Next,
 we calculated the intrasexual genetic correlation between males of
 different morphs for horn length, a sexually selected trait, and compared
 it to intrasexual correlations for naturally selected traits in both
 sexes. Intrasexual genetic correlations did not differ significantly
 between the sexes or between naturally and sexually selected traits,
 failing to support the hypothesis that horns present a reduction of
 intrasexual genetic correlations due to ITC. We discuss the implications
 for the idea of developmental reprogramming between male morphs, and
 emphasize the importance of genetic correlations as constraints for the
 evolution of dimorphisms.
description: Data for Buzatto et al
 2015All morphological
 measurements used in the quantitative genetic analyses (paternal
 half-sibling design) described in our manuscript.
DOI: 10.5061/dryad.3qb7t
title: Data from: The release rate of environmental DNA from juvenile and adult fish

description: The environmental DNA (eDNA) technique is expected to become a powerful,
 non-invasive tool for estimating the distribution and biomass of
 organisms. This technique was recently shown to be applicable to aquatic
 vertebrates by collecting extraorganismal DNA floating in the water or
 absorbed onto suspended particles. However, basic information on eDNA
 release rate is lacking, despite it being essential for practical
 applications. In this series of experiments with bluegill sunfish (Lepomis
 macrochirus), we examined the effect of fish developmental stage on eDNA
 release rate. eDNA concentration reached equilibrium 3 days after the
 individual fish were introduced into the separate containers, enabling
 calculation of the eDNA release rate (copies h−1) from individual fish on
 the assumption that the number of eDNA released from the fish per unit
 time equals total degradation in the container (copies h−1). The eDNA
 release rate was 3–4 times higher in the adult (body weight: 30–75 g) than
 in the juvenile group (0.5–2.0 g). Such positive relationship between fish
 size and eDNA release rate support the possibility of biomass rather than
 density estimation using eDNA techniques. However, the eDNA release rate
 per fish body weight (copies h−1 g−1) was slightly higher in the juvenile
 than the adult group, which is likely because of the ontogenetic reduction
 in metabolic activity. Therefore, quantitative eDNA data should be
 carefully interpreted to avoid overestimating biomass when the population
 is dominated by juveniles, because the age structure of the focal
 population is often variable and unseen in the field. eDNA degradation
 rates (copies l−1 h−1), calculated by curve fitting of time-dependent
 changes in eDNA concentrations after fish removal, were 5.1–15.9% per hour
 (half-life: 6.3 h). This suggests that quantitative eDNA data should be
 corrected using a degradation curve attained in the target field.
description: All data underlying the
 findingsData for 3 figures
 (sheets 1-3) and qPCR results for 6 plates (sheets
 7-12)Maruyama_data.xls
DOI: 10.5061/dryad.2pm60
title: Data from: Impact of numerical information on ‘risk knowledge’ regarding human papillomavirus (HPV) vaccination among schoolgirls: a randomised controlled trial

description: Introduction: In Germany the implementation of HPV vaccination for women
 12-17 years of age was accompanied by various campaigns. Evidence based
 information including numerical data was not provided. However, standard
 information leads to overestimation of cancer risk and effects of HPV
 vaccination. Confidence in children’s ability to deal with numerical data
 is low, especially in disadvantaged pupils. The aim of the present study
 was to compare the effects of a standard leaflet with an information
 leaflet supplemented with numerical data on ‘risk knowledge’ regarding HPV
 vaccination among schoolgirls. Methods: Randomised-controlled short-term
 trial. All 108 schoolgirls of seven school classes were asked to
 participate and 105 agreed. Participants were vocational schoolgirls who
 were preparing for grade 10 graduation and who were members of the target
 group for HPV vaccination. The control group was asked to read a standard
 leaflet on HPV vaccination of the German Women's Health Network. The
 intervention group received the same leaflet, but it was supplemented with
 numerical information on cancer risk and assumed effects of the HPV
 vaccination on cancer prevention. As baseline characteristics we surveyed:
 age, vaccination status, attitude towards HPV vaccination and aspects
 regarding migration background. The primary end point was ‘risk
 knowledge’. Questionnaire surveys were performed under experimental
 conditions. Individual randomisation, participants, and intention-to-treat
 data analyses were blinded. The study was approved by the Ministry of
 Education and Culture of Schleswig-Holstein and the ethics committee of
 the Hamburg Chamber of Physicians. Results: We analysed ‘risk knowledge’
 for all 105 randomised participants. Baseline characteristics of the two
 groups were comparable. Numerical risk information recipients were more
 likely to give correct answers compared to standard information
 recipients: Mean value of risk knowledge score (0-5 points): 4.6 ± 1.0 vs.
 2.6 ± 1.2 (mean difference 2.0 (95% CI 1.6-2.4)); (P&lt;0.001). Post
 hoc distractor analysis of single items was performed. Incorrect answers
 of control participants indicated that cervical cancer risk was highly
 overestimated whereas total cancer risk was mostly underestimated, and
 possible impact of HPV vaccination on cancer prevention was overestimated.
 Conclusion: Supplementing health information on HPV vaccination with
 numerical data improves ‘risk knowledge’ among schoolgirls.
description: HPV_Evaluation_englishPASW Statistics_18The coding instructions can be found in the README.doc file.
DOI: 10.5061/dryad.np208d8b
title: Data from: Introgression of domesticated alleles into a wild trout genotype and the impact on seasonal survival in natural lakes

description: We tested the fitness consequences of introgression of fast-growing
 domesticated fish into a wild population. Fry from wild and domesticated
 rainbow trout (Oncorhynchus mykiss) crosses, F1 hybrids, and first- and
 second-generation backcrosses were released into two natural lakes.
 Parentage analysis using microsatellite loci facilitated the
 identification of survivors so fitness was estimated in nature from the
 first-feeding stage. Results indicated that under certain conditions
 domesticated fish survived at least as well as wild fish within the same
 environment. Relative growth and survival of the crosses, however, was
 highly dependent on environment. During the first summer, fastest-growing
 crosses had the highest survival, but this trend was reversed after one
 winter and another summer. Although the F1 hybrids showed evidence of
 outbreeding depression due to disruption of local adaptation, there was
 little evidence of outbreeding depression in the backcrosses, and the
 second-generation backcrosses exhibited a wild-type phenotype. This
 information is relevant for assessing the multigenerational risk of
 escaped or released domesticated fish should they successfully interbreed
 with wild populations and provides information on how to minimize
 detrimental impacts of a conservation breeding and/or management program.
 These data also further understanding of the selection pressures in nature
 that maintain submaximal rates of growth.
description: MicrosatellitesMicrosatellite data used to assign offspring to parents. The ID refers to the individual. All parents are indicated by either an M (for male) or F (for female). All offspring are indicated as Offspring.genotype.csv
DOI: 10.5061/dryad.rt3f3
title: Data from: Male and female helper effects on maternal investment and adult survival in red-winged fairy-wrens

description: Despite its importance for the evolution of cooperative breeding, it has
 proven difficult to determine whether helpers improve their recipients’
 fitness. Helpers affect fitness in multiple ways, both positive and
 negative, but their effects can also be concealed through reduced maternal
 investment. Furthermore, determining the direction of causation is
 difficult, as helper presence may indicate a productive territory, rather
 than high productivity indicating an effect of help. In cooperatively
 breeding red-winged fairy-wrens (Malurus elegans) groups reduce care when
 they have male helpers, but groups with female helpers do not, so
 nestlings receive more food. Thus our predictions vary with helper sex
 rather than helper number, and by studying within-group changes with
 regard to group composition we separate phenotypically plastic responses
 from among-group correlations. Females did not reduce egg size in response
 to an increasing number of female helpers. However, more male or female
 helpers allowed females to lay larger clutches and more female helpers
 reduced re-nesting intervals. There was mixed support for a benefit of
 load lightening: Helpers, but not breeders, gained survival benefits with
 increasing number of male helpers. However, helper survival decreased with
 the number of female helpers, suggesting that increased competition
 counterbalanced these male helper benefits. We also found consistent
 among-group differences, which would have erroneously been interpreted as
 helper effects had we not disentangled the within-group changes with
 regard to group composition. This study highlights the importance of
 assessing carers’ benefits in relation to both group composition and size,
 and of investigating the within-individual plastic response of helper
 effects.
description: Lejeune_et_al_2016_survLejeune_et_al_2016_interval_dataLejeune_et_al_2016_eggs_data
DOI: 10.5061/dryad.v60r7
title: Data from: Stigmergy, collective actions and animal social spacing

description: Collective animal behavior studies have led the way in developing models
 that account for a large number of individuals, but have mostly considered
 situations where alignment and attraction play a key role, such as in
 schooling and flocking. By quantifying how animals react to each
 others' presence, when interaction is via conspecific avoidance
 rather than alignment or attraction, we present a mechanistic insight that
 enables us to link individual behavior and space use patterns. As animals
 respond to both current and past positions of their neighbors, the
 assumption that the relative location of individuals is statistically and
 history-independent is not tenable, underscoring the limitations of
 traditional space use studies. We move beyond that assumption, by
 constructing a framework to analyze spatial segregation of mobile animals
 when neighbor proximity may elicit a retreat, and by linking conspecific
 encounter rate to history-dependent avoidance behavior. Our approach rests
 on the knowledge that animals communicate by modifying the environment in
 which they live, providing a method to analyse social cohesion as
 stigmergy, a form of mediated animal-animal interaction. By considering a
 population of animals that mark the terrain as they move, we predict how
 the spatio-temporal patterns that emerge depend on the degree of stigmergy
 of the interaction processes. We find in particular that non-local
 decision rules may generate a nonmonotonic dependence of the animal
 encounter rate as a function of the tendency to retreat from locations
 recently visited by other conspecifics, which has fundamental implications
 to epidemic disease spread and animal sociality.
description: Simulation code in C for
 stigmergic avoiding animalsThe C code contained
 here simulates the collective movement and interaction of animals in a 2D
 lattice as follows. Each individual moves as a random walker (with
 different type of movement statistics) and deposits a mark over each of
 the lattice location it visits. The deposited mark remains present only
 for a finite amount of time, T, after which it disappears. When another
 individual encounters a foreign mark, it retreats towards the centroid of
 its own active marked area with a probability that decreases as a function
 of the age of the mark. The functional form with which it decays is
 controlled by the response decay exponent. For more details read the
 Material and Methods and Supplementary Information of the
 article.Archive.zip
DOI: 10.5061/dryad.h0h8b
title: Data from: A HRM real-time PCR assay for rapid and specific identification of the emerging pest spotted-wing drosophila (Drosophila suzukii)

description: Spotted wing drosophila (Drosophila suzukii) is an emerging pest that
 began spreading in 2008 and its distribution now includes 13 countries
 across two continents. Countries where it is established have reported
 significant economic losses of fresh produce, such as cherries due to this
 species of fly. At larval stages, it is impossible to identify due to its
 striking similarities with other cosmopolitan and harmless drosophilids.
 Molecular methods allow identification but the current technique of DNA
 barcoding is time consuming. We developed and validated a rapid, highly
 sensitive and specific assay based on real-time PCR and high resolution
 melt (HRM) analysis using EvaGreen DNA intercalating dye chemistry.
 Performance characteristics of this qualitative assay, validation and
 applicability in a New Zealand quarantine framework are discussed.
 Application of this robust and independently validated assay across the
 spectrum of key food production and border protection industries will
 allow us to reduce the further spread of this damaging species worldwide.
description: Sequence alignment for
 real-time PCR assay design for Drosophila suzukiiSequence alignment (in
 FASTA format) of sequences from the study described in Dhami and
 Kumarasimghe 2014 for the development of species-specific real-time PCR
 based assay. Published and downloaded sequences have GenBank accession
 numbers, while unpublished sequences have ID numbers. For more information
 on these sequences please contact the authors. The variable regions (SNPs)
 were manually selected.Drosophila_alignment.txt