cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72ps3
title: Data from: Parasites structuring ecological communities: the mistletoe footprint in Mediterranean pine forests

description: 1. The capacity of parasitic plants in structuring natural communities is
 increasingly recognized. These plants can affect the structure,
 composition and productivity of plant communities by modifying the
 competitive balance between hosts and non-host species and by altering the
 quantity and quality of resources entering the soil. Despite the progress
 made in this field, there is still a lack of integrative studies showing
 the structuring capacity of parasitic plants in forest ecosystems, where
 their effect may be less detectable due to the long lifespan of the
 system. 2. In this study we evaluate the long-term impact of Viscum album
 subsp. austriacum on the woody-plant community of a Mediterranean
 pineland. This mistletoe remains several years on the same host, exerting
 long-lasting, spatially concentrated effects on community and ecosystem
 characteristics. Mistletoe concentrates zoochorous seeds and induces
 changes in the soil fertility and light availability beneath the canopy of
 parasitized trees, which have the potential to facilitate zoochorous-plant
 colonization, recruitment, and growth at the same time as it weakens the
 host. Here, we analyse whether mistletoe-driven changes could result in a
 nucleus of zoochorous woody plants nourished by the abundant organic
 detritus accumulated under the host. We also analyse whether mistletoe
 effects can expand after host death. 3. We selected unparasitized,
 parasitized, and dead parasitized Pinus nigra trees, in which we studied
 the joint effect of mistletoe-mediated changes in soil nutrient and light
 availability, with the seed rain, seed predation, seedling establishment,
 plant recruitment, and plant growth. Light- and soil-nutrient resources
 were greater under parasitized trees, and intensified after host death.
 The seed rain was maximum under parasitized trees, where seedling
 recruitment proved more likely. Sapling density, richness, and growth
 increased with the development of parasitism. 4. Our findings show that
 Viscum album exerts a strong and lasting impact on the structure and
 dynamics of Mediterranean pinelands, with parasitized trees acting as
 centres for the establishment and growth of colonizing fleshy-fruited
 woody species, which, over the long term, promote vegetation shifts by
 limiting dominant pine trees and facilitating less represented
 fleshy-fruited shrubs.
description: Data_parasites
 structuring ecological communitiesData collected in the
 field. All details are described within the paperFE_Mellado&Zamora_2017.xls
DOI: 10.5061/dryad.t77nc
title: Data from: Dynamic social behaviour in a bacterium: Pseudomonas aeruginosa partially compensates for siderophore loss to cheats

description: Cooperation underlies diverse phenomena including the origins of
 multicellular life, human behaviour in economic markets and the mechanisms
 by which pathogenic bacteria cause disease. Experiments with
 microorganisms have advanced our understanding of how, when and why
 cooperation evolves, but the extent to which microbial cooperation can
 recapitulate aspects of animal behaviour is debated. For instance,
 understanding the evolution of behavioural response rules (how should one
 individual respond to another’s decision to cooperate or defect?) is a key
 part of social evolution theory, but the possible existence of such rules
 in social microbes has not been explored. In one specific context
 (biparental care in animals), cooperation is maintained if individuals
 respond to a partner’s defection by increasing their own investment into
 cooperation, but not so much that this fully compensates for the
 defector’s lack of investment. This is termed ‘partial compensation.’
 Here, I show that partial compensation for the presence of non-cooperating
 ‘cheats’ is also observed in a microbial social behaviour: the cooperative
 production of iron-scavenging siderophores by the bacterium Pseudomonas
 aeruginosa. A period of evolution in the presence of cheats maintains this
 response, whereas evolution in the absence of cheats leads to a loss of
 compensatory behaviour. These results demonstrate i) the remarkable
 flexibility of bacterial social behaviour; ii) the potential generality of
 partial compensation as a social response rule; and iii) the need for
 mathematical models to explore the evolution of response rules in
 multi-player social interactions.
description: Partial compensation for
 siderophore cheating in Pseudomonas aeruginosaSpreadsheet (.xls)
 containing raw lab data used to draw figures, Minitab & R output for
 key analyses and an extra figure to illustrate that a comparable effect to
 the one reported is shown in a different wild-type P. aeruginosa
 strain.ForDryad.xls
DOI: 10.5061/dryad.6gv70
title: Data from: Is active management the key to the conservation of saproxylic biodiversity? Pollarding promotes the formation of tree hollows

description: Trees with hollows are key features sustaining biodiversity in wooded
 landscapes. They host rich assemblages of often highly specialised
 organisms. Hollow trees, however, have become rare and localised in
 Europe. Many of the associated biota is thus declining or endangered. The
 challenge of its conservation, therefore, is to safeguard the presence of
 hollow trees in sufficient numbers. Populations of numerous species
 associated with tree hollows and dead wood are often found in habitats
 that were formed by formerly common traditional silvicultural practices
 such as coppicing, pollarding or pasture. Although it has been
 occasionally mentioned that such practices increase the formation of
 hollows and the availability of often sun-exposed dead wood, their effect
 has never been quantified. Our study examined the hollow incidence in
 pollard and non-pollard (unmanaged) willows and the effect of pollarding
 on incremental growth rate by tree ring analysis. The probability of
 hollow occurrence was substantially higher in pollard than in non-pollard
 trees. Young pollards, especially, form hollows much more often than
 non-pollards; for instance, in trees of 50 cm DBH, the probability of
 hollow ocurrence was ~0.75 in pollards, but only ~0.3 in non-pollards. No
 difference in growth rate was found. Pollarding thus leads to the rapid
 formation of tree hollows, a habitat usually associated with old trees. It
 is therefore potentially a very important tool in the restoration of
 saproxylic habitats and conservation of hollow-dependent fauna. If applied
 along e.g. roads and watercourses, pollarding could also be used to
 increase landscape connectivity for saproxylic organisms. In reserves
 where pollarding was formerly practiced, its restoration would be
 necessary to prevent loss of saproxylic biodiversity. Our results point to
 the importance of active management measures for maintaining availability,
 and spatial and temporal continuity of deadwood microhabitats.
description: Sebek_et_al_PollardingComparison of hollow formation between pollard and unmanaged trees. The worksheet "Hollow incidence" gives information on presence/absence (1/0)of hollows (cavities) in trees. The worksheet "Incremental growth" contains measurements of tree rings from 8 pollard and 10 unmanaged trees. See the article for more information on study design.
DOI: 10.5061/dryad.17483
title: Data from: Blood mercury levels of zebra finches are heritable: implications for the evolution of mercury resistance

description: Mercury is a ubiquitous metal contaminant that negatively impacts
 reproduction of wildlife and has many other sub-lethal effects. Songbirds
 are sensitive bioindicators of mercury toxicity and may suffer population
 declines as a result of mercury pollution. Current predictions of mercury
 accumulation and biomagnification often overlook possible genetic
 variation in mercury uptake and elimination within species and the
 potential for evolution in affected populations. We conducted a study of
 dietary mercury exposure in a model songbird species, maintaining a
 breeding population of zebra finches (Taeniopygia guttata) on standardized
 diets ranging from 0.0–2.4 μg/g methylmercury. We applied a quantitative
 genetics approach to examine patterns of variation and heritability of
 mercury accumulation within dietary treatments using a method of mixed
 effects modeling known as the 'animal model'. Significant
 variation in blood mercury accumulation existed within each treatment for
 birds exposed at the same dietary level; moreover, this variation was
 highly repeatable for individuals. We observed substantial genetic
 variation in blood mercury accumulation for birds exposed at intermediate
 dietary concentrations. Taken together, this is evidence that genetic
 variation for factors affecting blood mercury accumulation could be acted
 on by selection. If similar heritability for mercury accumulation exists
 in wild populations, selection could result in genetic differentiation for
 populations in contaminated locations, with possible consequences for
 mercury biomagnification in food webs.
description: Buck et al 2016
 heritability of mercury in zebra finchesThere are two tabs to
 this Excel file. One contains the concentration of total mercury (parts
 per million) in the blood of zebra finches. The other tab contains the
 pedigree information that was used in the ASReml analyses reported in the
 associated paper.Buck et al 2016
 ZEFI_HgHeritability.xlsx
DOI: 10.5061/dryad.g8n63
title: Data from: Multiple sexual signals and behavioral reproductive isolation in a diverging population

description: Sexual trait divergence has been shown to play a role in the evolution of
 reproductive isolation. While variation in multiple sexual signals is
 common among closely related species, little is known about the role of
 these different axes of phenotype variation with respect to the evolution
 of behavioral reproductive isolation. Here we study a unique population of
 barn swallows (Hirundo rustica transitiva) which can only be distinguished
 phenotypically from its neighboring populations based on two features of
 male plumage: exaggerated expression of both long tail streamers and dark
 ventral coloration. Using phenotype manipulation experiments, we conducted
 a paternity study to examine whether both traits are sexually selected.
 Our results show that an exaggerated form of the local male phenotype
 (with both tail elongation and color darkening) is favored by local
 females whereas males whose phenotypes were manipulated to look like males
 of neighboring subspecies suffered paternity losses from their social
 mates. These results confirm the multiple signaling role of the unique
 tail and color combination in our diverging population and suggest a novel
 possibility according to which multiple sexual signals may also be used to
 discriminate among males from nearby populations when pre-zygotic
 reproductive isolation is adaptive.
description: Transitiva
 manipulationSubspecies tail
 lengthSubspecies
 coloration
DOI: 10.5061/dryad.md40s
title: Data from: Evolution of resource use along a gradient of stress leads to increased facilitation

description: The stress-gradient hypothesis (SGH) posits that the relative importance
 of facilitative interactions versus negative interactions increases as
 levels of abiotic stress increase. Originally formulated in empirical
 studies of plant populations, in recent years the SGH has been found to
 describe how interactions change in response to stress in a wide range of
 species including algae, mussels and moths. However, there has been little
 theory attempting to predict patterns from first principles in relation to
 different types of interactions. Here, we use mathematical models of
 microbial populations to investigate whether patterns consistent with the
 SGH arise when species interact through resource use and allelopathy.
 Evolution alters the degree to which competition for resource use versus
 facilitation (cross-feeding) occurs. Our results are consistent with the
 SGH; species interactions evolve to be more facilitative as average stress
 intensifies. This occurs because at greater stress the species evolve to
 become specialists on either of the two resources thereby decreasing
 overlap in resource use and increasing facilitation through cross-feeding.
 In addition, the production of toxic allelopathic compounds decreases as
 stress intensifies due to density-dependent effects. Our results suggest
 that the SGH could arise through fundamental interactions that are common
 to many organisms and therefore that the SGH could be a more widespread
 phenomenon than previously recognised.
description: no allelopathy model
 dataSpecies abundance and
 resource use data from model runs with various levels of
 gamma.allelopathy model
 dataSpecies abundance,
 resource use and antimicrobial production data from model runs with
 various levels of gamma.script for both models
 with annotationR script for
 models.
DOI: 10.5061/dryad.f624r
title: Data from: The importance of spinner dolphin (Stenella longirostris) resting habitat: implications for management

description: Linking key ecological characteristics with animal behaviour is essential
 for identifying and protecting important habitats that support life
 functions. Spinner dolphins display a predictable diurnal behavioural
 pattern where they forage offshore at night and return to sheltered bays
 during daytime to rest. These bays, which are also subject to considerable
 use by humans, have long been recognized as key habitats for this species
 although the extent to which dolphins rely on specific characteristics of
 these habitats for rest has not been quantified. An integration of
 boat-based and land-based group focal follow sampling regimes and three
 gradient boosting generalized additive models were developed to identify
 habitat features that contribute to the occurrence of resting spinner
 dolphins in coastal waters off Hawai'i Island. Two ‘in-bay’ models
 used data collected within bays, and a third ‘coastal’ model (near-shore,
 outside of bays) used data collected both inside and outside of bays. The
 coastal model identified that spinner dolphins were unlikely to rest
 outside sheltered bays. In-bay models showed that dolphins rested
 throughout daylight hours within bays with a peak resting period between
 10.00 h to 14.00 h. The models also identified bottom-substrate-type as an
 important predictor of rest. Pseudo R2 values of 0·61 and 0·70 for the
 in-bay models and 0·66 for the coastal model showed that these models
 provided a good fit to the behavioural data for the occurrence of resting
 spinner dolphins. Synthesis and application. To date, studies evaluating
 spinner dolphin resting habitat have focussed on areas inside bays only.
 Here, we combined data collected inside and outside bays, and illustrate
 that should resting spinner dolphins be displaced from resting bays, they
 are unlikely to engage in resting behaviour elsewhere. Results provide
 further information on the importance of bays as important habitat for
 resting spinner dolphins. To mitigate the disturbance from human
 interactions during important rest periods, we recommend that management
 keep the spinner dolphin resting areas free from human activities. Our
 quantitative approach where models explicitly link behaviour with habitat
 characteristics is applicable to identify important habitats for
 protection of other taxa.
description: The importance of
 spinner dolphin (Stenella longirostris) resting habitat: Implications for
 managementThe combined boat-based
 and land-based group focal follow data to determine the resting behaviour
 of spinner dolphins across a range of available habitats, inside four bays
 and along open coastline adjacent to the bays.JAEData.txt
DOI: 10.5061/dryad.585fd
title: Data from: Effect of cellulases and xylanases on refining process and kraft pulp properties

description: Samples of bleached kraft pine cellulosic pulp, either treated with an
 enzyme preparation (a Thermomyces lanuginosus xylanase, an Aspergillus sp.
 cellulase, and a multienzyme preparation NS-22086 containing both these
 activities) or untreated, were refined in a laboratory PFI mill. The
 treatment with cellulases contained in the last two preparations
 significantly improved the pulp’s susceptibility to refining (the target
 freeness value of 30°SR was achieved in a significantly shorter time),
 increased water retention value (WRV) and fines contents while the
 weighted average fiber length was significantly reduced. These changes of
 pulp parameters caused deterioration of paper strength properties. The
 treatment with the xylanase, which partially hydrolyzed xylan, small
 amounts of which are associated with cellulose fibers, only slightly
 loosened the structure of fibers. These subtle changes positively affected
 the susceptibility of the pulp to refining (refining energy was
 significantly reduced) and improved the static strength properties of
 paper. Thus, the treatment of kraft pulps with xylanases may lead to
 substantial savings of refining energy without negative effects on paper
 characteristics.
description: 1 - Control - without
 enzymeProperties of pulp and
 paper for samles not treated with enzyme2 -
 CellulaseProperties of pulp and
 paper treated by Aspergillus sp. cellulase3 -
 NS-22086Properties of pulp and
 paper treated with NS-220864 -
 XylanaseProperties of pulp and
 paper treated by T. lanuginosus xylanase
DOI: 10.15468/dl.vpgb9v
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Hypsiglena jani",
 "Year 1960-2026"
 ]
}

 The dataset includes 121 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000736-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.48r68
title: Data from: Coral reef degradation is not correlated with local human population density

description: The global decline of reef-building corals is understood to be due to a
 combination of local and global stressors. However, many reef scientists
 assume that local factors predominate and that isolated reefs, far from
 human activities, are generally healthier and more resilient. Here we show
 that coral reef degradation is not correlated with human population
 density. This suggests that local factors such as fishing and pollution
 are having minimal effects or that their impacts are masked by global
 drivers such as ocean warming. Our results also suggest that the effects
 of local and global stressors are antagonistic, rather than synergistic as
 widely assumed. These findings indicate that local management alone cannot
 restore coral populations or increase the resilience of reefs to
 large-scale impacts. They also highlight the truly global reach of
 anthropogenic warming and the immediate need for drastic and sustained
 cuts in carbon emissions.
description: World+humanData used in the analysis of: Bruno, J. F. and Valdivia, A. Coral reef degradation is not correlated with local human population density. Sci. Rep. 6, 29778; doi: 10.1038/srep29778 (2016). File includes site meta-data, coral and macroalgal cover, coordinates (lat, long), and the density of humans (number of human residents within 25, 50 and 100 km of each site).
DOI: 10.5061/dryad.57sg5
title: Data from: The evolutionary conservation of the A Disintegrin-like and Metalloproteinase domain with Thrombospondin-1 motif metzincins across vertebrate species and their expression in teleost zebrafish

description: Background: The A Disintegrin-like and Metalloproteinase domain with
 Thrombospondin-1 motifs (ADAMTS) enzymes comprise 19 mammalian
 zinc-dependent metalloproteinases (metzincins) with homologues in a wide
 range of invertebrates. ADAMTS enzymes have a broad range of functions in
 development and diseases due to their extracellular matrix remodelling
 activity. Here, we report a detailed characterisation of their
 evolutionary conservation across vertebrates. Results: Using
 bioinformatics complemented with de novo sequencing, gene sequences for
 ADAMTS enzymes were obtained from a variety of organisms. Detailed
 evolutionary analyses revealed a high level of conservation across
 vertebrates with evidence of ADAMTS gene expansion during two rounds of
 whole genome duplication (WGD) in vertebrates, while tandem duplication
 events and gene loss were also apparent. However, the additional round of
 teleost-specific WGD did not have a significant effect on ADAMTS gene
 family members suggesting their conserved roles have remained constant in
 teleost fish. Quantitative reverse-transcriptase polymerase chain reaction
 analysis revealed dynamic expression of adamts genes throughout zebrafish
 embryonic development reflecting the key conserved roles they play in
 vertebrate embryogenesis. Notably, several adamts mRNAs were maternally
 expressed with a dramatic increase in mRNA levels coinciding with zygotic
 expression and organogenesis. Broad adamts mRNA expression was also
 demonstrated in several adult organs indicating potential roles in adult
 homeostasis. Conclusions: Our data highlight the evolution of the ADAMTS
 gene family through duplication processes across metazoans supplemented by
 a burst of amplification through vertebrate WGD events. It also strongly
 posits the zebrafish as a potential model species to further elucidate the
 function of ADAMTS enzymes during vertebrate development.
description: ComplData__Brunet_etal_BMC_6624500221359074.tarSequence alignment data for ADAMTS proteins across species.
DOI: 10.5061/dryad.t7qm4
title: Data from: Degree of specialization is related to body size in herbivorous insects: a phylogenetic confirmation

description: Numerous studies have suggested a general relationship between the degree
 of host specialization and body size in herbivorous animals. In insects,
 smaller species are usually shown to be more specialized than
 larger-bodied ones. Various hypotheses have attempted to explain this
 pattern but rigorous proof of the body size-diet breadth relationship has
 been lacking, primarily because the scarceness of reliable phylogenetic
 information has precluded formal comparative analyses. Explicitly using
 phylogenetic information for a group of herbivores (geometrid moths) and
 their host plant range, we perform a comparative analysis to study the
 body size-diet breadth relationship. Considering several alternative
 measures of body size and diet breadth, our results convincingly
 demonstrate without previous methodological issues – a first for any taxon
 – a positive association between these traits, which has implications for
 evaluating various central aspects of the evolutionary ecology of
 herbivorous insects. We additionally demonstrate how the methods used in
 this study can be applied in assessing hypotheses to explain the body
 size-diet breadth relationship. By analyzing the relationship in
 tree-feeders alone and finding that the positive relationship remains, the
 result suggests that the body size-diet breadth relationship is not solely
 driven by the type of host plant that species feed on.
description: FemaleBodyMassIndividual raw data for female body mass of species used in analyses28SD1Previously unpublished 28SD1 sequences28SD2Previously unpublished 28SD2 sequencesCOIPreviously unpublished COI sequencesEf1aPreviously unpublished EF1a sequencesGAPDHPreviously unpublished GAPDH sequencesIDHPreviously unpublished IDH sequencesRpS5Previously unpublished RpS5 sequencesWGLPreviously unpublished WGL sequences