cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v23bt
title: Data from: Tracking changes in life-history traits related to unnecessary virulence in a plant-parasitic nematode

description: Evaluating trade-offs in life-history traits of plant pathogens is
 essential to understand the evolution and epidemiology of diseases. In
 particular, virulence costs when the corresponding host resistance gene is
 lacking play a major role in the adaptive biology of pathogens and
 contribute to the maintenance of their genetic diversity. Here, we
 investigated whether life-history traits directly linked to the
 establishment of plant–nematode interactions, that is, ability to locate
 and move toward the roots of the host plant, and to invade roots and
 develop into mature females, are affected in Meloidogyne incognita lines
 virulent against the tomato Mi-1.2 resistance gene. Virulent and avirulent
 near-isogenic lines only differing in their capacity to reproduce or not
 on resistant tomatoes were compared in single inoculation or pairwise
 competition experiments. Data highlighted (1) a global lack of trade-off
 in traits associated with unnecessary virulence with respect to the
 nematode ability to successfully infest plant roots and (2) variability in
 these traits when the genetic background of the nematode is considered
 irrespective of its (a)virulence status. These data suggest that the
 variation detected here is independent from the adaptation of M. incognita
 to host resistance, but rather reflects some genetic polymorphism in this
 asexual organism.
description: DataSet for
 ECE-2015-06-00341.R1- Distribution of
 Meloidogyne incognita juveniles around tomato root tips at 90, 180, 270
 and 360 min post-inoculation. Ka, Kv, Ma, Mv = Kursk, Morelos avirulent
 and virulent, respectively. - Distribution of Meloidogyne incognita
 females in tomato roots in competition experiments. Ka, Kv, Ma, Mv =
 Kursk, Morelos avirulent and virulent, respectively.dataset_ECE-2015-06-00341-R1.pdf
DOI: 10.5061/dryad.s2b5c
title: Data from: Distributed cognition and social brains: reductions in mushroom body investment accompanied the origins of sociality in wasps (Hymenoptera: Vespidae)

description: The social brain hypothesis assumes the evolution of social behaviour
 changes animals' ecological environments, and predicts evolutionary
 shifts in social structure will be associated with changes in brain
 investment. Most social brain models to date assume social behaviour
 imposes additional cognitive challenges to animals, favouring the
 evolution of increased brain investment. Here, we present a modification
 of social brain models, which we term the distributed cognition
 hypothesis. Distributed cognition models assume group members can rely on
 social communication instead of individual cognition; these models predict
 reduced brain investment in social species. To test this hypothesis, we
 compared brain investment among 29 species of wasps (Vespidae family),
 including solitary species and social species with a wide range of social
 attributes (i.e. differences in colony size, mode of colony founding and
 degree of queen/worker caste differentiation). We compared species means
 of relative size of mushroom body (MB) calyces and the antennal to optic
 lobe ratio, as measures of brain investment in central processing and
 peripheral sensory processing, respectively. In support of distributed
 cognition predictions, and in contrast to patterns seen among vertebrates,
 MB investment decreased from solitary to social species. Among social
 species, differences in colony founding, colony size and caste
 differentiation were not associated with brain investment differences.
 Peripheral lobe investment did not covary with social structure. These
 patterns suggest the strongest changes in brain investment—a reduction in
 central processing brain regions—accompanied the evolutionary origins of
 eusociality in Vespidae.
description: Volumes of brain
 regions- all subjectsVolumes of brain regions
 for all individual subjects, by species and caste.7apr15 DRYAD data
 posting.xlsx
DOI: 10.5061/dryad.h9r0p65
title: Data from: Towards open data blockchain analytics: a Bitcoin perspective

description: Bitcoin is the first implementation of a technology that has become known
 as a 'public permissionless' blockchain. Such systems allow
 public read/write access to an append-only blockchain database without the
 need for any mediating central authority. Instead they guarantee access,
 security and protocol conformity through an elegant combination of
 cryptographic assurances and game theoretic economic incentives. Not until
 the advent of the Bitcoin blockchain has such a trusted, transparent,
 comprehensive and granular data set of digital economic behaviours been
 available for public network analysis. In this article, by translating the
 cumbersome binary data structure of the Bitcoin blockchain into a high
 fidelity graph model, we demonstrate through various analyses the often
 overlooked social and econometric benefits of employing such a novel open
 data architecture. Specifically we show (a) how repeated patterns of
 transaction behaviours can be revealed to link user activity across the
 blockchain; (b) how newly mined bitcoin can be associated to demonstrate
 individual accumulations of wealth; (c) through application of the naïve
 quantity theory of money that Bitcoin's disinflationary properties
 can be revealed and measured; and (d) how the user community can develop
 coordinated defences against repeated denial of service attacks on the
 network. Such public analyses of this open data are exemplary benefits
 unavailable to the closed data models of the 'private
 permissioned' distributed ledger architectures currently dominating
 enterprise-level blockchain development due to existing issues of
 scalability, confidentiality and governance.
description: Fig2: Bitcoin Amounts
 from Source to DestinationPercentage of total
 bitcoins input into each destination block by the block from which they
 are sourced.fig2.csvFig3: Coinbase Extranonce and Spend BlockContains the parsed extranonce of each coinbase transaction, and the block height at which the coinbase was first spent.fig3.csvFig5: Bitcoin Dwell TimeThe dwell time measure for each block, ie the weighted average time since the bitcoins in a block were last spent.fig5.csvFig7: Block Transaction Count by DegreeFor each block, the count of the number of transaction by their in / our degree.fig7.csv
DOI: 10.5061/dryad.vn6n74n
title: Data from: A comprehensive and user-friendly framework for 3D-data visualisation in invertebrates and other organisms

description: Methods for 3D‐imaging of biological samples are experiencing
 unprecedented development, with tools such as X‐ray micro‐computed
 tomography (μCT) becoming more accessible to biologists. These techniques
 are inherently suited to small subjects and can simultaneously image both
 external and internal morphology, thus offering considerable benefits for
 invertebrate research. However, methods for visualising 3D‐data are
 trailing behind the development of tools for generating such data. Our aim
 in this article is to make the processing, visualisation and presentation
 of 3D‐data easier, thereby encouraging more researchers to utilise
 3D‐imaging. Here, we present a comprehensive workflow for manipulating and
 visualising 3D‐data, including basic and advanced options for producing
 images, videos and interactive 3D‐PDFs, from both volume and surface‐mesh
 renderings. We discuss the importance of visualisation for quantitative
 analysis of invertebrate morphology from 3D‐data, and provide example
 figures illustrating the different options for generating 3D‐figures for
 publication. As more biology journals adopt 3D‐PDFs as a standard option,
 research on microscopic invertebrates and other organisms can be presented
 in high‐resolution 3D‐figures, enhancing the way we communicate science.
description: Reconstructed micro-CT
 scan dataMicro-CT scan of a head
 of a female wasp from the genus Ariphron. Additional details in README
 file.170628_Ariphron_ANIC_female_4.471um_head.txm.gzReconstructed micro-CT scan dataMicro-CT scan of the abdomens of both male and female wasps of a species of Catocheilus. Additional details in README file.170721_TLS641_Catocheilus_5.618um_genitalia.txm.gzDetails for two micro-CT data files in packageMicro-CT scan details and specimen collection details.
DOI: 10.5061/dryad.8d7m7
title: Data from: An age-dependent fitness cost of migration? Old trans-Saharan migrating spoonbills breed later than those staying in Europe, and late breeders have lower recruitment

description: 1.Migration is a widespread phenomenon in the animal kingdom. On the basis
 of the considerable variation that exists between and within species, and
 even within populations, we may be able to infer the (age- and
 sex-specific) ecological trade-offs and constraints moulding migration
 systems from assessments of fitness associated with migration and
 wintering in different areas. 2.During three consecutive breeding seasons,
 we compared the reproductive performance (timing of breeding, breeding
 success, chick body condition and post-fledging survival) of Eurasian
 spoonbills Platalea leucorodia that breed at a single breeding site in The
 Netherlands, but migrate different distances (ca. 4,500 km versus 2,000
 km, either or not crossing the Sahara) to and from wintering areas in
 southern Europe and West Africa. Using mark-recapture analysis, we further
 investigated whether survival until adulthood (recruitment probability) of
 chicks hatched between 2006 and 2010 was related to their hatch date and
 body condition. 3.Long-distance migrants bred later, particularly the
 males, and raised chicks of poorer body condition than short-distance
 migrants. Hatch dates strongly advanced with increasing age in
 short-distance migrants, but hardly advanced in long-distance migrants,
 causing the difference in timing of breeding between long- and
 short-distance migrants to be more pronounced among older birds.
 4.Breeding success and chick body condition decreased over the season, and
 chicks that fledged late in the season or in poor condition were less
 likely to survive until adulthood. As a result, long-distance migrants –
 particularly the males and older birds – likely recruit fewer offspring
 into the breeding population than short-distance migrants. This inference
 is important for predicting the population-level consequences of changes
 in winter habitat suitability throughout the wintering range. 5.Assuming
 that the long-distance migrants – being the birds that occupy the
 traditional wintering areas – are not the poorer quality birds, and that
 the observed age-dependent patterns in timing of breeding are driven by
 within-individual effects and not by selective disappearance, our results
 suggest that the strategy of long-distance migration, involving the
 crossing of the Sahara to winter in West Africa, incurred a cost by
 reducing reproductive output, albeit a cost paid only later in life.
description: Full data
 packageContains all data files
 and R-scripts associated with the publication. See readme.txt for more
 details.full_data_package.zip
DOI: 10.5061/dryad.3m1g61k
title: Data from: Distance-decay differs among vertical strata in a tropical rainforest

description: 1. Assemblage similarity decays with geographic distance—a pattern known
 as the distance-decay relationship. While this pattern has been
 investigated for a wide range of organisms, ecosystems, and geographical
 gradients, whether these changes vary more cryptically across different
 forest strata (from ground to canopy) remains elusive. 2. Here, we
 investigated the influence of ground vs arboreal assemblages to the
 general distance-decay relationship observed in forests. We seek to
 explain differences in distance-decay relationships between strata in the
 context of the vertical stratification of assemblage composition,
 richness, and abundance. 3. We surveyed for a climate sensitive model
 organism, amphibians, across vertical rainforest strata in Madagascar. For
 each tree, we defined assemblages of ground-dwelling, understory, or
 canopy species. We calculated horizontal distance-decay in similarity
 across all trees, and across assemblages of species found in different
 forest strata (ground, understory, and canopy). 4. We demonstrate that
 within stratum comparisons exhibit a classic distance-decay relationship
 for canopy and understory communities but no distance-decay relationships
 for ground communities. We suggest that differences in horizontal turnover
 between strata may be due to local scale habitat and resource
 heterogeneity in the canopy, or the influence of arboreal traits on
 species dispersal and distribution. 5. Synthesis: Biodiversity patterns in
 horizontal space were not consistent across vertical space, suggesting
 that canopy fauna may not play by the same set of ‘rules’ as their
 conspecifics living below them on the ground. Our study provides
 compelling evidence that the above-ground amphibian assemblage of tropical
 rainforests is the primary driver of the classical distance-decay
 relationship.
description: Vertical height of
 captured amphibiansSheet 1 contains records
 of each individual amphibian encountered (each row) during a survey. Each
 row contains information regarding which tree that it was caught, the
 species name, and the height where it was captured. The second sheet
 contains information regarding tree and habitat characteristics for each
 survey, including the lat/lon, altitude, date and time of survey, tree
 height, height climbed during survey, and measures of canopy cover, leaf
 layer intersect, small and big stem count/density, DBH of tree, and canopy
 area.Dryad.xlsx
DOI: 10.5061/dryad.15d3s
title: Data from: Clustered or scattered? The impact of habitat quality clustering on establishment and early spread

description: The match between the environmental conditions of an introduction area and
 the preferences of an introduced species is the first prerequisite for
 establishment. Yet, introduction areas are usually landscapes, i.e.
 heterogeneous sets of habitats that are more or less favourable to the
 introduced species. Because individuals are able to disperse after their
 introduction, the quality of the habitat surrounding the introduction site
 is as critical to the persistence of introduced populations as the quality
 of the introduction site itself. Moreover, demographic mechanisms such as
 Allee effects or dispersal mortality can hamper dispersal and affect
 spread across the landscape, in interaction with the spatial distribution
 of favourable habitat patches. In this study, we investigate the impact of
 the spatial distribution of heterogeneous quality habitats on
 establishment and early spread. First, we simulated introductions in
 one-dimensional landscapes for different dispersal rates and either
 dispersal mortality or Allee effects. The landscapes differed by the
 distribution of favourable and less favourable habitats, which were either
 clustered into few large aggregates of the same quality or scattered into
 multiple smaller ones. Second, we tested the predictions of simulations by
 performing experimental introductions of hymenopteran parasitoids
 (Trichogramma chilonis) in "clustered" and "scattered"
 microcosm landscapes. Results highlighted two impacts of the clustering of
 favourable habitat: by decreasing the risks of dispersal from the
 introduction site to unfavourable habitat early during the invasion, it
 increased establishment success. However, by increasing the distance
 between favourable habitat patches, it also hindered the subsequent spread
 of introduced species over larger areas.
description: Simulation
 scriptR script used to
 simulate the invasion data used in the study.simulations.RExperimental dataExperimental data of the invasions of T.chilonis performed for this study.exp_results.txt
DOI: 10.5061/dryad.74940
title: Data from: Reproductive activity triggers accelerated male mortality and decreases lifespan: genetic and gene expression determinants in Drosophila

description: Reproduction and aging evolved to be intimately associated. Experimental
 selection for early-life reproduction drives the evolution of decreased
 longevity in Drosophila whereas experimental selection for increased
 longevity leads to changes in reproduction. Although life history theory
 offers hypotheses to explain these relationships, the genetic architecture
 and molecular mechanisms underlying reproduction–longevity associations
 remain a matter of debate. Here we show that mating triggers accelerated
 mortality in males and identify hundreds of genes that are modulated upon
 mating in the fruit fly Drosophila melanogaster. Interrogation of
 genome-wide gene expression in virgin and recently mated males revealed
 coherent responses, with biological processes that are upregulated
 (testis-specific gene expression) or downregulated (metabolism and
 mitochondria-related functions) upon mating. Furthermore, using a panel of
 genotypes from the Drosophila Synthetic Population Resource (DSPR) as a
 source of naturally occurring genetic perturbation, we uncover abundant
 variation in longevity and reproduction-induced mortality among genotypes.
 Genotypes displayed more than fourfold variation in longevity and
 reproduction-induced mortality that can be traced to variation in specific
 segments of the genome. The data reveal individual variation in
 sensitivity to reproduction and physiological processes that are enhanced
 and suppressed upon mating. These results raise the prospect that
 variation in longevity and age-related traits could be traced to processes
 that coordinate germline and somatic function.
description: longev_aveBranco Schilling average longevity across strains
DOI: 10.5061/dryad.606fq59
title: Data from: Cryptic temporal changes in stock composition explain the decline of a flounder (Platichthys spp.) assemblage

description: Unobserved diversity, such as undetected genetic structure or the presence
 of cryptic species, is of concern for the conservation and management of
 global biodiversity in the face of threatening anthropogenic processes.
 For instance, unobserved diversity can lead to overestimation of maximum
 sustainable yields and therefore to overharvesting of the more vulnerable
 stock components within unrecognized mixed-stock fisheries. We used DNA
 from archival (otolith) samples to reconstruct the temporal (1970–2007)
 genetic makeup of two mixed-stock flounder fisheries in the Åland Sea (AS)
 and the Gulf of Finland (GoF). Both fisheries have hitherto been managed
 as a single stock of European flounders (Platichthys flesus), but were
 recently revealed to target two closely related species: the
 pelagic-spawning P. flesus and the newly described, demersal-spawning P.
 solemdali. While the AS and GoF fisheries were assumed to consist
 exclusively of P. solemdali, P. flesus dominated the GoF flounder
 assemblage (87% of total) in 1983, had disappeared (0%) by 1993, and
 remained in low proportions (10–11%) thereafter. In the AS, P. solemdali
 dominated throughout the sampling period (&gt;70%), and P. flesus
 remained in very low proportions after 1983. The disappearance of P.
 flesus from the GoF coincides in time with a dramatic (~60%) decline in
 commercial landings and worsening environmental conditions in P. flesus’
 northernmost spawning ground, the Eastern Gotland Basin, in the preceding
 4-6 years. These results are compatible with the hypothesis that P. flesus
 in the GoF are a sink population relying on larval subsidies from southern
 spawning grounds and the cause of their disappearance is a cessation of
 larval subsidies. Our results highlight the importance of uncovering
 unobserved genetic diversity and studying spatiotemporal changes in the
 relative contribution of different stock components, and the underlying
 environmental causes, to manage marine resources in the age of rapid
 anthropogenic change.
description: Otolith_dataTab delimited text file containing genotype data of five diagnostic loci for reference Platichthys solemdali and Platichthys flesus samples and for the otolith samples genotyped in this study. These are the raw data used for the Bayesian assignment tests. The file also contains the results of the assignment tests (the posterior probabilities of each sample being P. flesus and P.solemdali). Comment lines start with ###Genetic_data.txtEnvironmental DataEnvironmental and fishery landings data. These include time series of the reproductive volume in the Eastern Gotland Basin (from Ustups et al, 2013), estimated proportion of P. flesus in the Gulf of Finland and the Western Åland Sea (this study) and commercial landings of flounder in the Gulf of Finland (from ICES). Comment lines start with ###Environmental_data.txt
DOI: 10.5061/dryad.024t1
title: Data from: Trade-offs and evolution of thermal adaptation in the Irish potato famine pathogen Phytophthora infestans

description: Temperature is one of the most important environmental parameters with
 crucial impacts on nearly all biological processes. Due to anthropogenic
 activity, average air temperatures are expected to increase by a few
 degrees in coming decades, accompanied by an increased occurrence of
 extreme temperature events. Such global trends are likely to have various
 major impacts on human society through their influence on natural
 ecosystems, food production and biotic interactions, including diseases.
 In this study, we used a combination of statistical genetics, experimental
 evolution and common garden experiments to investigate the evolutionary
 potential for thermal adaptation in the potato late blight pathogen,
 Phytophthora infestans, and infer its likely response to changing
 temperatures. We found a trade-off associated with thermal adaptation to
 heterogeneous environments in P. infestans, with the degree of the
 trade-off peaking approximately at the pathogen's optimum growth
 temperature. A genetic trade-off in thermal adaptation was also evidenced
 by the negative association between a strain's growth rate and its
 thermal range for growth, and warm climates selecting for a low pathogen
 growth rate. We also found a mirror effect of phenotypic plasticity and
 genetic adaptation on growth rate. At below the optimum, phenotypic
 plasticity enhances pathogen's growth rate but nature selects for
 slower growing genotypes when temperature increases. At above the optimum,
 phenotypic plasticity reduces pathogen's growth rate but natural
 selection favours for faster growing genotypes when temperature increases
 further. We conclude from these findings that the growth rate of P.
 infestans will only be marginally affected by global warming.
description: GrowthRateDryadGrowth rate of 140 Phytophthora infestans collected from seven populations over China under five experimental temperaturesTemDryadMonthly mean temperature in the location where the Phytophthora infestans populations were collected