cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8b490
title: Data from: Ecological selection as the cause and sexual differentiation as the consequence of species divergence?

description: Key conceptual issues about speciation go unanswered without consideration
 of non-mutually exclusive factors. With tests based on speciation theory,
 we exploit the island distribution and habitat differences exhibited by
 the Caribbean cricket Amphiacusta sanctaecrucis, and with an analysis of
 divergent ecological selection, sexually selected differentiation, and
 geographic isolation, address how these different factors interact. After
 testing for divergent selection by comparing neutral genetic and
 morphological divergence in one ecological (mandible shape) and one sexual
 (male genitalia shape) trait, we examine whether ecological or sexual
 selection is the primary mechanism driving population divergence. We find
 that while all three factors—isolation, ecological, and sexual
 selection—contribute to divergence, and that their interaction determines
 the stage of completeness achieved during the speciation process, as
 measured by patterns of genetic differentiation. Moreover, despite the
 striking diversity in genitalic shapes across the genus Amphiacusta which
 suggests that sexual selection drives speciation, the significant
 differences in genitalia shape between forest habitats revealed here
 implies that ecological divergence may be the primary axis of divergence.
 Our work highlights critical unstudied aspects in speciation –
 differentiating the cause from the consequence of divergence—and suggests
 avenues for further disentangling the roles of natural and sexual
 selection in driving divergence in Amphiacusta.
description: Amphiacusta
 sanctaecrucis morphological and microsatellite dataOneal&KnowlesDryad.zip
DOI: 10.5061/dryad.3f863
title: Data from: Moving in groups: how density and unpredictable motion affect predation risk

description: One of the most widely applicable benefits of aggregation is a per capita
 reduction in predation risk. Many factors can contribute to this but, for
 moving groups, an increased difficulty in tracking and targeting one
 individual amongst many has received particular attention. This “confusion
 effect” has been proposed to result from a bottleneck in information
 processing, a hypothesis supported by both modelling and experiment. If
 the competition for limited attention is localised to the particular part
 of the visual field where the target is located, prey density is likely to
 be the key factor rather than group numbers per se. Furthermore,
 unpredictability of prey movement may enhance confusion, but both factors
 have received insufficient attention from empiricists: undoubtedly because
 of the difficulty of experimental manipulation in natural systems. We used
 a computer-based target tracking task with human subjects to manipulate
 effects of number and density independently, in factorial combination with
 motion path predictability. Density, rather than number, drove the
 confusion effect in our experiment and acted synergistically with the
 unpredictability of the direction of motion. The experimental paradigm we
 present offers the potential for isolating other factors affecting
 predation success on group-living prey, and forging links with the
 psychological literature on object tracking and visual search.
description: ConfusionDataRaw data from visual search experiment described in Scott-Samuel et al. (2015) doi 10.1007/s00265-015-1885-1SubjectAgeAndGenderParticipant age and gender information, relating to raw data in ConfusionData.txt
DOI: 10.5061/dryad.5r2f8
title: Data from: Tigers in the Terai: strong evidence for meta-population dynamics contributing to tiger recovery and conservation in the Terai Arc Landscape

description: The source populations of tigers are mostly confined to protected areas,
 which are now becoming isolated. A landscape scale conservation strategy
 should strive to facilitate dispersal and survival of dispersing tigers by
 managing habitat corridors that enable tigers to traverse the matrix with
 minimal conflict. We present evidence for tiger dispersal along
 transboundary protected areas complexes in the Terai Arc Landscape, a
 priority tiger landscape in Nepal and India, by comparing camera trap
 data, and through population models applied to the long term camera trap
 data sets. The former showed that 11 individual tigers used the corridors
 that connected the transboundary protected areas. The estimated population
 growth rates using the minimum observed population size in two protected
 areas in Nepal, Bardia National Park and Suklaphanta National Park showed
 that the increases were higher than expected from growth rates due to in
 situ reproduction alone. These lines of evidence suggests that tigers are
 recolonizing Nepal’s protected areas from India, after a period of
 population decline, and that the tiger populations in the transboundary
 protected areas complexes may be maintained as meta-population. Our
 results demonstrate the importance of adopting a landscape-scale approach
 to tiger conservation, especially to improve population recovery and long
 term population persistence.
description: Tiger Demography in
 Shuklaphanta and Babai ValleyDemographic Population
 Size of Tigers in Shuklaphanta National Park and Babai Valley in Bardia
 National Park. This also include the details on common tiger between Nepal
 and India transboundary protected areaData.xlsxGIS file of MCP from Suklaphanta and BabaiFile contains year wise the locations where tiger were captured and these information were used to develop MCPData Shared.rar
DOI: 10.5061/dryad.q6784
title: Data from: Competing metabolic strategies in a multilevel selection model

description: The evolutionary mechanisms of energy efficiency have been addressed. One
 important question is to understand how the optimized usage of energy can
 be selected in an evolutionary process, especially when the immediate
 advantage of gathering efficient individuals in an energetic context is
 not clear. We propose a model of two competing metabolic strategies
 differing in their resource usage, an efficient strain which converts
 resource into energy at high efficiency but displays a low rate of
 resource consumption, and an inefficient strain which consumes resource at
 a high rate but at low yield. We explore the dynamics in both well-mixed
 and structured populations. The selection for optimized energy usage is
 measured by the likelihood that an efficient strain can invade a
 population of inefficient strains. It is found that the parameter space at
 which the efficient strain can thrive in structured populations is always
 broader than observed in well-mixed populations.
description: READMEA README file with
 information about the code.structured population
 scriptBASH example script for
 running the structured populations code.structured_scriptnon structured populations scriptBASH example script for running the non structured populations code.unstructured_scriptstructured population codeC++ code for calculation of the quantities related to structured populations.structured_population.cppMakefileMakefile with the instructions to compile the code.non structured population codeC++ code for calculation of the quantities related to non structured populations.unstructured_population.cppgroups_elements.hppC++ file containing necessary functions for the main coderandom.hppC++ file containing necessary functions for the main codeprint_file.hppC++ file containing necessary functions for the main codephysical_values.hppC++ file containing necessary functions for the main code
DOI: 10.5061/dryad.67p6d
title: Data from: Kin recognition affects plant communication and defence

description: The ability of many animals to recognize kin has allowed them to evolve
 diverse cooperative behaviours; such ability is less well studied for
 plants. Many plants, including Artemisia tridentata, have been found to
 respond to volatile cues emitted by experimentally wounded neighbours to
 increase levels of resistance to herbivory. We report that this
 communication was more effective among A. tridentata plants that were more
 closely related based on microsatellite markers. Plants in the field that
 received cues from experimentally clipped close relatives experienced less
 leaf herbivory over the growing season than those that received cues from
 clipped neighbours that were more distantly related. These results
 indicate that plants can respond differently to cues from kin, making it
 less likely that emitters will aid strangers and making it more likely
 that receivers will respond to cues from relatives. More effective defence
 adds to a growing list of favourable consequences of kin recognition for
 plants.
description: Figure
 2Receiver and Donor refer
 to plant identification numbers in the field. "r" is the
 estimate of relatedness between receiver and donor using Queller and
 Goodnight's method. Damage is the percentage of leaves on the
 receiver plant damaged over the growing season. "x" and
 "y" refer to spatial coordinates scaled so that the means are
 zero. Spblock refers to the spatial block that each plant grew
 in.Figure
 3Plant refers to the
 plant identification number used in the field. "DamClRel" is the
 proportion of leaves that were damaged on the assay branch that received
 volatiles from a close relative. "RelatedClRel" is the estimate
 of relatedness "r" between the donor and receiver (assay).
 "DamDisRel" is the proportion of leaves that were damaged on the
 assay branch that received volatiles from a distant relative.
 "RelatedDisRel" is the estimate of relatedness "r"
 between the donor and receiver (assay).Karban et al 2013
 Fig3B.xlsx
DOI: 10.5061/dryad.78cc8
title: Data from: Metabolic adaptations in a range-expanding arthropod

description: Despite an increasing number of studies documenting life-history evolution
 during range expansions or shifts, we lack a mechanistic understanding of
 the underlying physiological processes. In this explorative study, we used
 a metabolomics approach to study physiological changes associated with the
 recent range expansion of the two-spotted spider mite (Tetranychus
 urticae). Mite populations were sampled along a latitudinal gradient from
 range core to edge and reared under benign common garden conditions for
 two generations. Using gas chromatography–mass spectrometry, we obtained
 metabolic population profiles, which showed a gradual differentiation
 along the latitudinal gradient, indicating (epi)genetic changes in the
 metabolome in association with range expansion. These changes seemed not
 related with shifts in the mites’ energetic metabolism, but rather with
 differential use of amino acids. Particularly, more dispersive northern
 populations showed lowered concentrations of several essential and
 nonessential amino acids, suggesting a potential downregulation of
 metabolic pathways associated with protein synthesis.
description: metabolomics of a range
 expanding arthropod_results of GC-MS analysisThis file contains the
 outcomes of the GC-MS analysis described in Van Petegem et al.
 2016_Metabolomics of a range expanding arthropod. The analysis was
 performed for two-spotted spider mites collected in nine localities along
 this species' latitudinal expansion gradient. For each of the 43
 metabolites that were detected in the mite samples (5 samples per
 locality), nmol/sample is given.
DOI: 10.5061/dryad.gp2tc
title: Data from: Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe

description: Background: Invasive species can be a major threat to native biodiversity
 and the number of invasive plant species is increasing across the globe.
 Population genetic studies of invasive species can provide key insights
 into their invasion history and ensuing evolution, but also for their
 control. Here we genetically characterise populations of Impatiens
 glandulifera, an invasive plant in Europe that can have a major impact on
 native plant communities. We compared populations from the species’ native
 range in Kashmir, India, to those in its invaded range, along a
 latitudinal gradient in Europe. For comparison, the results from 39 other
 studies of genetic diversity in invasive species were collated. Results:
 Our results suggest that I. glandulifera was established in the wild in
 Europe at least twice, from an area outside of our Kashmir study area. Our
 results further revealed that the genetic diversity in invasive
 populations of I. glandulifera is unusually low compared to native
 populations, in particular when compared to other invasive species.
 Genetic drift rather than mutation seems to have played a role in
 differentiating populations in Europe. We find evidence of limitations to
 local gene flow after introduction to Europe, but somewhat less
 restrictions in the native range. I. glandulifera populations with
 significant inbreeding were only found in the species’ native range and
 invasive species in general showed no increase in inbreeding upon leaving
 their native ranges. In Europe we detect cases of migration between
 distantly located populations. Human activities therefore seem to, at
 least partially, have facilitated not only introductions, but also further
 spread of I. glandulifera across Europe. Conclusions: Although multiple
 introductions will facilitate the retention of genetic diversity in
 invasive ranges, widespread invasive species can remain genetically
 relatively invariant also after multiple introductions. Phenotypic
 plasticity may therefore be an important component of the successful
 spread of Impatiens glandulifera across Europe.
description: ImpatiensGlanduliferaGenotype data from nine microsatellite loci. Data from 378 individuals from 13 populations located in five European countries and Kashmir, India. Alleles are given as length of the amplified fragments. Missing data is denoted with -9.
DOI: 10.5061/dryad.t2f61
title: Data from: Quality expectations and tolerance limits of trial master files (TMF) - Developing a risk-based approach for quality assessments of TMFs

description: This article addresses the question of when a trial master file (TMF) can
 be considered sufficiently accurate and complete: What attributes does the
 TMF need to have so that a clinical trial can be adequately reconstructed
 from documented data and procedures? Clinical trial sponsors face
 significant challenges in assembling the TMF, especially when dealing with
 large, international, multicenter studies; despite all newly introduced
 archiving techniques it is becoming more and more difficult to ensure that
 the TMF is complete. This is directly reflected in the number of
 inspection findings reported and published by the EMA in 2014. Based on
 quality risk management principles in clinical trials the authors defined
 the quality expectations for the different document types in a TMF and
 furthermore defined tolerance limits for missing documents. This
 publication provides guidance on what type of documents and processes are
 most important, and in consequence, indicates on which documents and
 processes trial team staff should focus in order to achieve a high-quality
 TMF. The members of this working group belong to the CQAG Group (Clinical
 Quality Assurance Germany) and are QA (quality assurance) experts
 (auditors or compliance functions) with long-term experience in the
 practical handling of TMFs.
description: Risk_analysis_TMF_publication_20150803Risk_analysis_TMF_publication.odt
DOI: 10.5061/dryad.3td2f
title: Data from: Public sharing of research datasets: a pilot study of associations

description: The public sharing of primary research datasets potentially benefits the
 research community but is not yet common practice. In this pilot study, we
 analyzed whether data sharing frequency was associated with funder and
 publisher requirements, journal impact factor, or investigator experience
 and impact. Across 397 recent biomedical microarray studies, we found
 investigators were more likely to publicly share their raw dataset when
 their study was published in a high-impact journal and when the first or
 last authors had high levels of career experience and impact. We estimate
 the USA's National Institutes of Health (NIH) data sharing policy
 applied to 19% of the studies in our cohort; being subject to the NIH data
 sharing plan requirement was not found to correlate with increased data
 sharing behavior in multivariate logistic regression analysis. Studies
 published in journals that required a database submission accession number
 as a condition of publication were more likely to share their data, but
 this trend was not statistically significant. These early results will
 inform our ongoing larger analysis, and hopefully contribute to the
 development of more effective data sharing initiatives. **Earlier version
 presented at ASIS&T and ISSI Pre-Conference: Symposium on
 Informetrics and Scientometrics 2009**
description: Microarray study
 attributes and data sharing status397 rows, one row for
 each study that created gene expression microarray data as identified by
 Ochsner et al. (doi:10.1038/nmeth1208-991). Attributes of each study are
 included in 23 columns. Dependent variable is called
 is_data_shared.Piwowar_Metrics2009_rawdata.csvStatistical analysis R scriptStatistical R script for analysis and graphics as presented in the paper.Piwowar_Metrics2009_statistics.R
DOI: 10.5061/dryad.4s4h4
title: Data from: Individual variation in male reproductive behaviour is linked to temporal heterogeneity in predation risk

description: Variation in predation risk is a major driver of ecological and
 evolutionary change, and, in turn, of geographical variation in behaviour.
 While predation risk is rarely constant in natural populations, the extent
 to which variation in predation risk shapes individual behaviour in wild
 populations remains unclear. Here, we investigated individual differences
 in reproductive behavior in 16 Trinidadian guppy populations and related
 it to the observed variation in predator biomass each population
 experienced. Our results show that high heterogeneity in predator biomass
 is linked to individual behavioural diversification. Increased
 within-population heterogeneity in predator biomass is also associated
 with behavioural polymorphism. Some individuals adjust the frequency of
 consensual mating behaviour in response to differences in sex ratio
 context, while others display constantly at elevated frequencies. This
 pattern is analogous to a “live fast, die young” pace-of-life syndrome.
 Notably, both high and low mean differences in predator biomass led to a
 homogenization of individual frequency of consensual mating displays.
 Overall, our results demonstrate that individual behavioural variation is
 associated with heterogeneity in predator biomass, but not necessarily
 with changes in mean values of predator biomass. We suggest that
 heterogeneity in predator biomass is an informative predictor of adaptive
 responses to changes in biotic conditions.
description: Miguel_Barbosa_dataRaw data on individual sexual behaviour and CV and mean population predator biomass
DOI: 10.5061/dryad.c959s
title: Data from: Genetic admixing of two evergreen oaks, Quercus acuta and Q. sessilifolia (subgenus Cyclobalanopsis), is the result of interspecific introgressive hybridization

description: In forests worldwide, Quercus is a major genus; however, the boundaries
 between the constituent species are relatively weak, and hybridization is
 reported frequently. In this study, we examined Quercus acuta and Quercus
 sessilifolia (subgenus Cyclobalanopsis), which have a putative hybrid—Q. x
 takaoyamensis. We investigated leaf morphological traits and
 microsatellites of Q. acuta and Q. sessilifolia in the area where the two
 species are both found. Although the leaf traits overlapped, the two
 species could be distinguished morphologically as demonstrated by
 principal component analysis based on a range of these traits. They were
 also genetically differentiated, with F ST = 0.104. However, they shared
 most of the alleles at all eight loci examined, and considerable genetic
 admixing was detected. Admixture analysis demonstrated that Q. acuta and
 Q. sessilifolia, respectively, contained 11 and 24 % of individuals with a
 probability of less than 0.9 of being correctly assigned to their species.
 Model-based testing showed that this admixing was created by not only
 shared ancestral polymorphism but also by hybridization. Effective
 population size and migration rate were estimated using the coalescent
 approach. We estimated 8.843 and 71.98 effective numbers of migrants per
 generation to Q. acuta and Q. sessilifolia, respectively. Theoretically,
 one to ten migrants per generation are required to prevent complete
 genetic differentiation. Based on the results of this study, it appears
 that genetic admixing, with sharing of most alleles, is probably common in
 the two species and is maintained by interspecific introgressive
 hybridization.
description: data140303This is a simple comma separated values (.csv) file. See details in readme file.
DOI: 10.5061/dryad.477dp5c
title: Data from: Sex differences in the drivers of reproductive skew in a cooperative breeder

description: Many cooperatively breeding societies are characterized by high
 reproductive skew, such that some socially dominant individuals breed,
 while socially subordinate individuals provide help. Inbreeding avoidance
 serves as a source of reproductive skew in many high-skew societies, but
 few empirical studies have examined sources of skew operating alongside
 inbreeding avoidance, or compared individual attempts to reproduce
 (reproductive competition) with individual reproductive success. Here we
 use long-term genetic and observational data to examine factors affecting
 reproductive skew in the high-skew cooperatively breeding southern pied
 babbler (Turdoides bicolor). When subordinates can breed, skew remains
 high, suggesting factors additional to inbreeding avoidance drive skew.
 Subordinate females are more likely to compete to breed when older or when
 ecological constraints on dispersal are high, but heavy subordinate
 females are more likely to successfully breed. Subordinate males are more
 likely to compete when they are older, during high ecological constraints,
 or when they are related to the dominant male, but only the presence of
 within-group unrelated subordinate females predicts subordinate male
 breeding success. Reproductive skew is not driven by reproductive effort,
 but by forces such as intrinsic physical limitations and intra-sexual
 conflict (for females), or female mate choice, male mate-guarding and
 potentially reproductive restraint (for males). Ecological conditions or
 ‘outside options’ affect the occurrence of reproductive conflict,
 supporting predictions of recent synthetic skew models. Inbreeding
 avoidance together with competition for access to reproduction may
 generate high skew in animal societies, and disparate processes may be
 operating to maintain male vs. female reproductive skew in the same
 species.
description: comp
 femalesFactors associated with
 competition among femalescomp
 malesFactors associated with
 competition among malesreprod success
 femalesFactors associated with
 breeding success among femalesreprod success
 malesFactors associated with
 breeding success among males