cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.87tk7
title: Data from: Community composition affects the shape of mate response functions

description: The evolution of mate preferences can be critical for the evolution of
 reproductive isolation and speciation. Heterospecific interference may
 carry substantial fitness costs and result in preferences where females
 are most responsive to the mean conspecific trait with low response to
 traits that differ from this value. However, when male traits are
 unbounded by heterospecifics, there may not be selection against females
 that respond to extreme trait values in the unbounded direction. To test
 how heterospecifics affected the shape of female response functions, I
 presented female Oecanthus tree crickets with synthetic calls representing
 a range of male calls, then measured female phonotaxis to construct
 response functions. The species with the fastest pulse rates in the
 community consistently responded to pulse rates faster than those produced
 by their males, while in the intermediate and slowest pulse rate species
 there was no significant difference between the male trait and the female
 response. This work suggests that species with the most extreme signal in
 the community respond to a greater range of signals, potentially resulting
 in a higher probability of hybridization during secondary contact, and
 revealing interactions between mate recognition and other aspects of
 sexual selection.
description: Female response
 dataThis file contains the
 response data for female Oecanthus crickets from multiple sites in North
 America. The corresponding male data (and original recordings) are
 archived at the Macaulay Library of Natural Sound. For the female data,
 the first columns gives the species and collection locality (collection
 site GPS coordinates are in the associated manuscript). The next column is
 a unique identifier for the individual cricket. The following column gives
 the pulse rate of the stimulus that was played to the insect and the final
 column gives the female response score. The response score is the amount
 of time remaining in a 120 second trial when the cricket made contact with
 the speaker. (For example, if a female responded in 24 seconds, the
 response score would be 120-24=96). By calculating scores in this way,
 females that responded quickly had high response scores, females that
 responded slowly had low response scores, and females that did not respond
 had a response time of zero.Data for
 archiving.xlsx
DOI: 10.5061/dryad.16pg7
title: Data from: Predicting function from sequence in a large multifunctional toxin family

description: Venoms contain active substances with highly specific physiological
 effects and are increasingly being used as sources of novel diagnostic,
 research and treatment tools for human disease. Experimental
 characterisation of individual toxin activities is a severe rate-limiting
 step in the discovery process, and in-silico tools which allow function to
 be predicted from sequence information are essential. Toxins are typically
 members of large multifunctional families of structurally similar proteins
 that can have different biological activities, and minor sequence
 divergence can have significant consequences. Thus, existing predictive
 tools tend to have low accuracy. We investigated a classification model
 based on physico-chemical attributes that can easily be calculated from
 amino-acid sequences, using over 250 (mostly novel) viperid phospholipase
 A2 toxins. We also clustered proteins by sequence profiles, and carried
 out in-vitro tests for four major activities on a selection of isolated
 novel toxins, or crude venoms known to contain them. The majority of
 detected activities were consistent with predictions, in contrast to poor
 performance of a number of tested existing predictive methods. Our results
 provide a framework for comparison of active sites among different
 functional sub-groups of toxins that will allow a more targeted approach
 for identification of potential drug leads in the future.
description: PLA2 AMINO ACID
 seq_all_aligned_finalAlignment of amino-acid
 sequences of phospholipase A2 proteins from viper venom. Identifiers are
 either UniprotKB accession numbers, GenBank accession numbers, or
 author's own labels, the corresponding accession numbers and
 collection details can be found in the supporting material of the
 paper.
DOI: 10.5061/dryad.1mq62
title: Data from: Familiarity affects social network structure and discovery of prey patch locations in foraging stickleback shoals

description: Numerous factors affect the fine-scale social structure of animal groups,
 but it is unclear how important such factors are in determining how
 individuals encounter resources. Familiarity affects shoal choice and
 structure in many social fishes. Here, we show that familiarity between
 shoal members of sticklebacks (Gasterosteus aculeatus) affects both
 fine-scale social organization and the discovery of resources. Social
 network analysis revealed that sticklebacks remained closer to familiar
 than to unfamiliar individuals within the same shoal. Network-based
 diffusion analysis revealed that there was a strong untransmitted social
 effect on patch discovery, with individuals tending to discover a task
 sooner if a familiar individual from their group had previously done so
 than if an unfamiliar fish had done so. However, in contrast to the effect
 of familiarity, the frequency with which individuals had previously
 associated with one another had no effect upon the likelihood of prey
 patch discovery. This may have been due to the influence of fish on one
 another's movements; the effect of familiarity on discovery of an
 empty ‘control’ patch was as strong as for discovery of an actual prey
 patch. Our results demonstrate that factors affecting fine-scale social
 interactions can also influence how individuals encounter and exploit
 resources.
description: Atton et al.
 Familiarity, Networks & Foraging dataThese worksheets contain
 the network structure and patch discovery data used to perform the
 analyses contained in this article.
DOI: 10.5061/dryad.742gv
title: Data from: Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression

description: Accounting for gene-environment (GxE) interactions in complex trait
 association studies can facilitate our understanding of genetic
 heterogeneity under different environmental exposures, improve the ability
 to discover susceptible genes that exhibit little marginal effect, provide
 insight into the biological mechanisms of complex diseases, help to
 identify high-risk subgroups in the population, and uncover hidden
 heritability. However, significant GxE interactions can be difficult to
 find. The sample sizes required for sufficient power to detect association
 are much larger than those needed for genetic main effects, and
 interactions are sensitive to misspecification of the main effects model.
 These issues are exacerbated when working with binary phenotypes and rare
 variants, which bear less information on association. In this work, we
 present a similarity-based regression method for evaluating GxE
 interactions for rare variants with binary traits. The proposed model
 aggregates the genetic and GxE information across markers using genetic
 similarity thus increasing the ability to detect GxE signals. The model
 has a random effects interpretation, which leads to robustness against
 main effect misspecifications when evaluating GxE interactions. We
 construct score tests to examine GxE interactions and a computationally
 efficient EM algorithm to estimate the nuisance variance components. Using
 simulations and data applications, we show that the proposed method is a
 flexible and powerful tool to study the GxE effect in common or rare
 variant studies with binary traits.
description: simulation data and
 code(1) The codes and
 relevant files for simulation studies can also be downloaded at
 http://www4.stat.ncsu.edu/~tzeng/Data/Genetics2014.GxE.binary/ (2) Code
 for simulations: • "simulation_code.sas" is the SAS code to
 perform the simulation, including data generation and analyses •
 "glmm_em_sim.sas" is the SAS macro to calculate the estimates of
 the variance component and covariate coefficients •
 "COSI_geno.zip" is the zipped version of
 "COSI_geno.csv", which contains the 10K haplotypes of 100 rare
 loci generated from COSI. From COSI_geno.csv, we randomly drew two
 haplotypes with replacement to form a subject’s genotype. (3) One
 replication of the simulated data (1500 subjects): •
 "simu.dataset1.Y.E.txt" contains the trait variable and the
 environmental variable • "simu.dataset1.geno.txt" contains the
 simulated genotypessascode_4_Dryad.zip
DOI: 10.5061/dryad.47dq3
title: Data from: Candidate gene analysis suggests untapped genetic complexity in melanin-based pigmentation in birds

description: Studies on melanin-based color variation in a context of natural selection
 have provided a wealth of information on the link between phenotypic and
 genetic variation. Here, we evaluated associations between melanic plumage
 patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops
 borbonicus), a species in which mutations on MC1R do not seem to play any
 role in explaining melanic variation. This species exhibits five plumage
 color variants that can be grouped into three color forms which occupy
 discrete geographic regions in the lowlands of Réunion and a fourth form
 which comprises two color morphs (grey and brown), occurs at high
 elevation, and represents a true color polymorphism. We conducted a
 comprehensive survey of sequence variation in 96 individuals at a series
 of seven candidate genes other than MC1R that have been previously shown
 to influence melanin-based color patterns in vertebrates, including genes
 that have rarely been studied in a wild bird species before: POMC, Agouti,
 TYR, TYRP1, DCT, Corin and SLC24A5. Of these seven genes, two (Corin and
 TYRP1) displayed an interesting shift in allele frequencies between
 lowland and highland forms and a departure from mutation-drift equilibrium
 consistent with balancing selection in the polymorphic highland form only.
 Sequence variation at Agouti, a gene frequently involved in melanin-based
 pigmentation patterning, was not associated with color forms or morphs.
 Thus, we suggest that functionally important changes in loci other than
 those classically studied may beare involved in the color polymorphism
 exhibited by the Réunion grey white-eye and possibly many other non-model
 species.
description: Phased DNA sequences and
 aminoacidsThis file contains all
 the phased sequences used in the study, with heterozygous gaps resolved.
 Fasta containing aminoacids translations are also provided for markers
 used in MK tests.Phased_DNA_sequences_and_amino_acids.zipInformations about individualsThis file contains for each individual included in the study its identifier, its color form/morph, the locality where it was sampled and its sex.Individual_information.xlsx
DOI: 10.5061/dryad.d317663
title: Data from: Australian native mammals recognise and respond to alien predators: a meta-analysis

description: Prey naiveté is a failure to recognise novel predators and thought to
 cause exaggerated impacts of alien predators on native wildlife. Yet there
 is equivocal evidence in the literature for native prey naiveté towards
 aliens. To address this, we conducted a meta-analysis of Australian mammal
 responses to native and alien predators. Australia has the world’s worst
 record of extinction and declines of native mammals, largely due to two
 alien predators introduced some 150 years ago: the feral cat, Felis catus,
 and European red fox, Vulpes vulpes. Analysis of 94 responses to predator
 cues show that Australian mammals consistently recognise alien foxes as a
 predation threat, possibly because of thousands of years experience with
 another canid predator, the dingo, Canis lupus dingo. We also found
 consistent recogntion responses towards feral cats, however in 4 of the 7
 studies available, these responses were of risk-taking behaviour rather
 than antipredator behaviour. Our results suggest that a simple failure to
 recognise alien predators is not behind the ongoing exaggerated impacts of
 alien predators in Australia. Instead, our results highlight an urgent
 need to better understand the appropriateness of antipredator responses in
 prey towards alien predators in order to understand native prey
 vulnerability.
description: Australian mammal
 naiveté meta-analysis dataAustralian mammal
 naiveté meta-analysis dataMeta Analysis Data for
 Dryad.xlsb
DOI: 10.5061/dryad.m38nn11
title: Data from: Incorporating the geometry of dispersal and migration to understand spatial patterns of species distributions

description: Dispersal and migration can be important drivers of species distributions.
 Because the paths followed by individuals of many species are curvilinear,
 spatial statistical models based on rectilinear coordinates systems would
 fail to predict population connectivity or the ecological consequences of
 migration or species invasions. I propose that we view migration/dispersal
 as if organisms were moving along curvilinear geometrical objects called
 smooth manifolds. In that view, the curvilinear pathways become the
 “shortest realised paths” arising from the necessity to minimise mortality
 risks and energy costs. One can then define curvilinear coordinate systems
 on such manifolds. I describe a procedure to incorporate manifolds and
 define appropriate coordinate systems, with focus on trajectories (1D
 manifolds), as parts of mechanistic ecological models. I show how a
 statistical method, known as “manifold learning”, enables one to define
 the manifold and the appropriate coordinate systems needed to calculate
 population connectivity or study the effects of migrations (e.g. in
 aquatic invertebrates, fish, insects and birds). This approach may help in
 the design of networks of protected areas, in studying the consequences of
 invasion, range expansions, or transfer of parasites/diseases. Overall, a
 geometrical view to animal movement gives a novel perspective to the
 understanding of the ecological role of dispersal and migration.
description: Original
 dataPosition data used to
 run Non-linear PCAGimenez-Odata.xlsx
DOI: 10.5061/dryad.r0n89
title: Data from: Validation of the Regicor short physical activity questionnaire for the adult population

description: Objective: To develop and validate a short questionnaire to estimate
 physical activity (PA) practice and sedentary behavior for the adult
 population. Methods: The short questionnaire was developed using data from
 a cross-sectional population-based survey (n=6352) that included the
 Minnesota leisure-time PA questionnaire. Activities that explained a
 significant proportion of the variability of population PA practice were
 identified. Validation of the short questionnaire included a
 cross-sectional component to assess validity with respect to the data
 collected by accelerometers and a longitudinal component to assess
 reliability and sensitivity to detect changes (n=114, aged 35 to 74
 years). Results: Six types of activities that accounted for 87% of
 population variability in PA estimated with the Minnesota questionnaire
 were selected. The short questionnaire estimates energy expenditure in
 total PA and by intensity (light, moderate, vigorous), and includes 2
 questions about sedentary behavior and a question about occupational PA.
 The short questionnaire showed high reliability, with intraclass
 correlation coefficients ranging between 0.79 to 0.95. The Spearman
 correlation coefficients between estimated energy expenditure obtained
 with the questionnaire and the number of steps detected by the
 accelerometer were as follows: 0.36 for total PA, 0.40 for moderate
 intensity, and 0.26 for vigorous intensity. The questionnaire was
 sensitive to detect changes in moderate and vigorous PA (correlation
 coefficients ranging from 0.26 to 0.34). Conclusion: The REGICOR short
 questionnaire is reliable, valid, and sensitive to detect changes in
 moderate and vigorous PA. This questionnaire could be used in daily
 clinical practice and epidemiological studies.
description: Data_FileData file in R formatdata.rda
DOI: 10.5061/dryad.37445
title: Data from: Philip Grime's fourth corner: are there plant species adapted to high disturbance and low productivity?

description: Grime's CSR species life-strategy theory
 (competition-stress-ruderality) provides a conceptual framework to
 classify species into competitive (high productivity, low disturbance),
 stress-tolerant (low productivity, low disturbance) and ruderal (high
 productivity, high disturbance). Importantly, this classification is based
 on the assumption that the niche space of disturbance and productivity is
 filled unevenly: while in productive habitats species can adapt to
 different disturbance regimes, species of low-productivity and disturbed
 habitats do not exist, resulting in a triangular distribution of species
 optima along axes of disturbance and productivity. This assumption has
 often been criticised, but it has not yet been put under a rigorous test.
 Here we use existing data on niche positions of Central European plant
 species to test this hypothesis, namely its prediction that species
 adapted to jointly stressed (low-productive) and disturbed habitats do not
 exist. We use Ellenberg indicator values and newly developed indicator
 values for disturbance as proxies of species positions in the space of
 productivity and disturbance. We found that positions of species optima
 along the gradients of productivity and disturbance severity are not
 independent of each other, with very few species adapted to low-productive
 and severely disturbed habitats. In contrast, there is no relationship
 between productivity and disturbance frequency; a number of species occur
 in low-productive and frequently disturbed habitats. The relationship
 between productivity and disturbance severity can be either due to
 tradeoffs between life history traits responsible for response to
 disturbance and productivity (as originally assumed by Grime) or due to
 historical rarity of severely disturbed habitats in unproductive
 conditions and consequent absence of evolution of species adapted to them.
 Our data are based on one specific flora, shaped by glaciations and early
 introduction of agriculture, but the question of what causes this pattern
 can be resolved by future analyses of floras with different evolutionary
 and ecological histories.
description: dataFile with data on
 individual species. Each line corresponds to one species, with value of
 disturbance frequency indicator value, disturbance severity indicator
 value, and Ellenberg indicator value for nutrients
DOI: 10.5061/dryad.2k24525
title: Data from: Modulation of plant-mediated interactions between herbivores of different feeding guilds: effects of parasitism and belowground interactions

description: Herbivory affects subsequent herbivores, mainly regulated by the
 phytohormones jasmonic (JA) and salicylic acid (SA). Additionally,
 organisms such as soil microbes belowground or parasitoids that develop
 inside their herbivorous hosts aboveground, can change plant responses to
 herbivory. However, it is not yet well known how organisms of trophic
 levels other than herbivores, below- and above-ground, alter the
 interactions between insect species sharing a host plant. Here, we
 investigated whether the parasitoid Aphidius colemani and different soil
 microbial communities (created through plant-soil feedbacks) affect the JA
 and SA signalling pathways in response to the aphid Myzus persicae and the
 thrips Frankliniella occidentalis, as well as subsequent thrips
 performance. Our results show that the expression of the JA-responsive
 gene CaPINII in sweet pepper was more suppressed by aphids than by
 parasitised aphids. However, parasitism did not affect the expression of
 CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced
 thrips performance compared with uninfested plants, but this was not
 observed when aphids were parasitised. Soils where different plant species
 were previously grown, did not affect plant responses or the interaction
 between herbivores. Our study shows that members of the third trophic
 level can modify herbivore interactions by altering plant physiology.
description: raw data on gene
 expression and thrips performance on sweet pepper plantsThis excel data file
 contains one worksheet per figure presented in the manuscript and in the
 supplementary information. Variable names, and levels are explained in the
 last worksheet, named "readme"data Vaello et
 al2018_JdB.xlsx
DOI: 10.5061/dryad.26n2q
title: Data from: Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data

description: The Brownie tag-recovery model is useful for estimating harvest rates but
 assumes all tagged individuals survive to the first hunting season;
 otherwise, mortality between time of tagging and the hunting season will
 cause the Brownie estimator to be negatively biased. Alternatively,
 fitting animals with radio transmitters can be used to accurately estimate
 harvest rate but may be more costly. We developed a joint model to
 estimate harvest and annual survival rates that combines known-fate data
 from animals fitted with transmitters to estimate the probability of
 surviving the period from capture to the first hunting season, and data
 from reward-tagged animals in a Brownie tag-recovery model. We evaluated
 bias and precision of the joint estimator, and how to optimally allocate
 effort between animals fitted with radio transmitters and inexpensive ear
 tags or leg bands. Tagging-to-harvest survival rates from &gt;20
 individuals with radio transmitters combined with 50–100 reward tags
 resulted in an unbiased and precise estimator of harvest rates. In
 addition, the joint model can test whether transmitters affect an
 individual's probability of being harvested. We illustrate
 application of the model using data from wild turkey, Meleagris gallapavo,
 to estimate harvest rates, and data from white-tailed deer, Odocoileus
 virginianus, to evaluate whether the presence of a visible radio
 transmitter is related to the probability of a deer being harvested. The
 joint known-fate tag-recovery model eliminates the requirement to capture
 and mark animals immediately prior to the hunting season to obtain
 accurate and precise estimates of harvest rate. In addition, the joint
 model can assess whether marking animals with radio transmitters affects
 the individual's probability of being harvested, caused by hunter
 selectivity or changes in a marked animal's behavior.
description: White-tailed Deer Case
 StudyVery-high frequency
 (VHF) collar and reward-tag data for a case study on white-tailed deer in
 Pennsylvania from 2009-2011. The data is in the format required by program
 SURVIV, and the additional code to run the integrated Brownie tag-recovery
 and known-fate model is included.DeerDataSubmission.docxTurkey Case StudyVery-high frequency (VHF) collar and reward-tag data for a case study on wild turkey in Pennsylvania from 2010-2012. The data is in the format required by program SURVIV, and the additional code to run the integrated Brownie tag-recovery and known-fate model is included.TurkeyDataSubmission.docx