cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sq41r
title: Data from: Response of mountain Picea abies forests to stand-replacing bark beetle outbreaks: neighbourhood effects lead to self-replacement

description: 1. Large, severe disturbances drive many forest ecosystems over the long
 term, but pose management uncertainties when human experience with them is
 limited. Recent continent-scale outbreaks of bark beetles across the
 temperate Northern Hemisphere have raised major concerns as to whether
 coniferous forests will regenerate back towards pre-outbreak condition and
 meet possible reforestation objectives. To date, however, analyses of
 post-outbreak regeneration across broad spatial and temporal scales have
 been rare, and entirely lacking for many regions. 2. Following a series of
 large, severe ( 99% overstorey mortality) outbreaks of spruce bark beetles
 Ips typographus in Central Europe, we capitalized on an extensive forest
 inventory data set (n = 615 plots across 7000 ha) to evaluate regeneration
 dynamics in Norway spruce Picea abies forests across the Bohemian Forest
 Ecosystem (spanning Germany and the Czech Republic). We asked whether
 neighbourhood effects (conspecific advance regeneration of spruce) would
 support prompt regeneration back to spruce forest, or whether the rapid,
 severe canopy mortality would overwhelm this influence and promote pioneer
 and broadleaf species. We tracked 15 years of post-outbreak regeneration
 dynamics (occupancy, density, height, composition) of all tree species and
 evaluated initial variations in successional pathway and structure. 3.
 Median tree regeneration density increased from 400 trees ha−1 at the time
 of outbreak to 2000 trees ha−1 within a decade, and occupancy increased
 from 58% to 76%. The increases were driven by spruce, which primarily
 recruited from advance regeneration, gradually occupying greater height
 classes. Only one broadleaf/pioneer species increased in relative
 proportion, for a brief (&lt;3-year) period before declining again.
 Nevertheless, both pure spruce and spruce–broadleaf stands were common
 and, coupled with wide variations in density and height, contributed to
 diverse early-successional structure. 4. Synthesis and applications.
 Contrary to common expectations, spruce beetle outbreaks in Central Europe
 effectively promoted their host in the long term. Outbreak-affected
 forests are naturally self-replacing even after severe canopy mortality,
 when positive neighbourhood effects of conspecific advance regeneration
 lead to rapid replacement of the dominant species. Thus, natural
 regeneration may be considered among the most effective ways to meet
 possible reforestation objectives in forests destroyed by beetles.
description: forest regeneration
 datasee
 readMe.txtzeppenfeld_et_al_2015_data.zip
DOI: 10.5061/dryad.7h08c
title: Data from: Artificial light at night desynchronises strictly seasonal reproduction in a wild mammal

description: Change in day length is an important cue for reproductive activation in
 seasonally breeding animals to ensure that the timing of greatest maternal
 investment (e.g. lactation in mammals) coincides with favourable
 environmental conditions (e.g. peak productivity). However, artificial
 light at night has the potential to interfere with the perception of such
 natural cues. Following a 5-year study on two populations of wild
 marsupial mammals exposed to different night-time levels of anthropogenic
 light, we show that light pollution in urban environments masks seasonal
 changes in ambient light cues, suppressing melatonin levels and delaying
 births in the tammar wallaby. These results highlight a previously
 unappreciated relationship linking artificial light at night with induced
 changes in mammalian reproductive physiology, and the potential for
 larger-scale impacts at the population level.
description: Robert et al_data
 storeExcel file all data:
 light, melatonin & birth schedules
DOI: 10.5061/dryad.fj472
title: Data from: Post-hatching parental care masks the effects of egg size on offspring fitness: a removal experiment on burying beetles

description: Parents can increase the fitness of their offspring by allocating
 nutrients to eggs and/or providing care for eggs and offspring. Although
 we have a good understanding of the adaptive significance of both egg size
 and parental care, remarkably little is known about the co-evolution of
 these two mechanisms for increasing offspring fitness. Here, we report a
 parental removal experiment on the burying beetle Nicrophorus vespilloides
 in which we test whether post-hatching parental care masks the effect of
 egg size on offspring fitness. As predicted, we found that the parent’s
 presence or absence had a strong main effect on larval body mass, while
 there was no detectable effect of egg size. Furthermore, egg size had a
 strong and positive effect on offspring body mass in the parent’s absence,
 while it had no effect on offspring body mass in the parent’s presence.
 These results support the suggestion that the stronger effect of
 post-hatching parental care on offspring growth masks the weaker effect of
 egg size. We found no correlation between the number and size of eggs.
 However, there was a negative correlation between larval body mass and
 brood size in the parent’s presence, but not in its absence. These
 findings suggest that the trade-off between number and size of offspring
 is shifted from the egg stage towards the end of the parental care period,
 and that post-hatching parental care somehow moderates this trade-off.
description: MonteithAndrewsSmisethJEB2012Data file for relationship between egg size and offspring growth and survival from a laboratory experiment on Nicrophorus vespiloides. The data are based on a parental removal design in which the effect of egg size is compared in the absence or presence of post-hatching parental care.
DOI: 10.5061/dryad.rd01s
title: Data from: Causal link between insulin-like growth factor 1 and growth in nestlings of a wild passerine bird

description: Life history of animals is strongly linked with the variability in
 postnatal growth rates, because the ability to achieve necessary body mass
 early in life is directly connected with the ability to survive and
 reproduce later in life. Surprisingly, little is known about the
 physiological mechanisms connecting food availability with the variability
 of growth in wild animals. We used a hormonal injection treatment in
 free-living nestlings of the pied flycatcher (Ficedula hypoleuca). In
 doing this, we aimed to see how their plasma insulin-like growth factor 1
 (IGF-1) levels and its mediation of growth rate vary in response to
 administration of exogenous IGF-1 during the early period of postnatal
 development. We showed that the levels of IGF-1 as well as growth rate and
 body size, in terms of body mass and tarsus length, were significantly
 higher in IGF-1-injected nestlings, compared with those in the control
 group. These differences became especially pronounced from day 7
 post-hatch onwards during the 13-day nestling period. Additionally, the
 proportional investment into growth was more profoundly downregulated in
 IGF-1-injected nestlings at the end of the nestling period, which achieved
 fledging size earlier, compared with control nestlings. Our results are
 the first to highlight IGF-1 as the causal link between growth conditions
 and variability of growth rate and body size in wild vertebrates.
 Interestingly, the change in IGF-1 levels also showed a plausible,
 distinct adaptive age- and physical maturity-dependent pattern in
 nestlings to match the benefits gained by them when investing in growth,
 with the cost endured during the early days of postnatal development to
 maximize their fitness. Therefore, this mechanism might be among those
 mediating the maintenance of genetic variability in growth rates in
 populations, presumably regardless of the presence of strong directional
 selection acting upon them.
description: data-Lodjak.et.al-2016-FuncEcol-IGF1IGF-1 and growth rate data for pied flycatcher nestlings. IGF-1 injection study.data-Lodjak.et.al-2016-FuncEcol.xlsx
DOI: 10.5061/dryad.2v2m1
title: Data from: Regulatory mechanisms of group distributions in a gregarious arthropod

description: In a patchy environment, how social animals manage conspecific and
 environmental cues in their choice of habitat is a leading issue for
 understanding their spatial distribution and their exploitation of
 resources. Here, we experimentally tested the effects of environmental
 heterogeneities (artificial shelters) and some of their characteristics
 (size and fragmentation) on the aggregation process of a common species of
 terrestrial isopod (Crustacea). One hundred individuals were introduced
 into three different heterogeneous set-ups and in a homogeneous set-up. In
 the four set-ups, the populations split into two aggregates: one large
 (approx. 70 individuals) and one smaller (approx. 20 individuals). These
 aggregates were not randomly distributed in the arena but were formed
 diametrically opposite from one another. The similarity of the results
 among the four set-ups shows that under experimental conditions, the
 environmental heterogeneities have a low impact on the aggregation
 dynamics and spatial patterns of the isopod, merely serving to increase
 the probability of nucleation of the larger aggregation at these points.
 By contrast, the regulation of aggregate sizes and the regular
 distribution of groups are signatures of local amplification processes, in
 agreement with the short-range activator and long-range inhibitor model
 (scale-dependent feedbacks). In other words, we show how small-scale
 interactions may govern large-scale spatial patterns. This experimental
 illustration of spatial self-organization is an important step towards
 comprehension of the complex game of competition among groups in social
 species.
description: Data - Broly et al.
 2015Raw data used for the
 figures
DOI: 10.5061/dryad.24t5j04
title: Data from: From unburnt to salvage logged: quantifying bird responses to different levels of disturbance severity

description: 1. Forests worldwide are increasingly subject to natural and human
 disturbances, including wildfires and logging of varying intensity and
 frequency. Understanding how biodiversity responds to different kinds and
 combinations of natural and human disturbance is critical to enhanced
 forest management. 2. We completed an eight-year study of bird responses
 across a spectrum of disturbance types in Australian Mountain Ash
 (Eucalyptus regnans) forests following wildfires in 2009. 3. We found
 evidence of a gradient in bird species richness over the study duration.
 It was highest in unlogged and unburned (least disturbed) sites,
 decreasing through burnt unlogged forest (subject to high or low intensity
 fire), lower still in logged forest, and lowest in the most disturbed
 sites (subject to salvage logging without island retention). Retention of
 uncut islands within logged areas increased bird species richness above
 that found in areas that had been clearcut. 4. The greatest rate of
 increase per year after disturbance in bird species richness was on sites
 burnt by high severity fire but which were not subject to any form of
 logging. The level of disturbance affected the composition of the bird
 assemblage. Sites that were unlogged and unburned were more likely to
 support species that were larger, more mobile, and nested at greater
 heights above the ground. 5. Synthesis and applications.: All forms of
 logging on burned sites impaired recovery in bird species richness
 relative to sites subject to high severity fire. Alterations in stand
 structure and plant species composition (and hence modification in bird
 habitat suitability) due to logging are the most likely reasons for
 reduced bird species richness and delayed patterns of recovery. This study
 highlights the importance for native bird species of retaining patches of
 unlogged forest not only within otherwise clearcut forest, but also in
 areas that are burned and subject to salvage logging. We therefore suggest
 that the adoption of retention harvesting be expanded to include stands
 disturbed by wildfires.
description: Lindenmayer salvage
 logging birdsData from an 8-year
 study of bird responses across a spectrum of disturbance types in
 Australian Mountain Ash (Eucalyptus regnans) forests following wildfires
 in 2009. We extracted data for 88 plots from three studies within the
 Victorian Tall Eucalypt Forest Plot Network. The plots had varying degrees
 of disturbance in terms of fire and logging. We established three survey
 points in each plot and recorded bird species present at each survey point
 over the period 2009 to 2016 on one or more occasions.
DOI: 10.5061/dryad.78mt2
title: Data from: Plastic responses of some life history traits and cellular components of body size in Aphidius ervi as related to the age of its host Acyrthosiphon pisum

description: Phenotypic plasticity of wing size and shape has been evaluated in
 Aphidius ervi developing in its host, Acyrthosiphon pisum, parasitized at
 seven different ages. The parasitoid wing size was used as an estimator of
 both whole body size and its cellular composition. No size difference was
 observed in A. ervi adults emerged from aphids 1, 2 or 3 days old at
 parasitization. Body size then increased in A. ervi emerged from hosts
 older at parasitization. Body size values as related to host age at
 parasitization were achieved by adjusting developmental time,
 developmental rate or both. Parasitoids of similar size, but developed in
 hosts parasitized at different ages, had different wing cellular
 composition, while the increase of parasitoid body size was related to a
 general increase in both cell area and cell number. These results seem to
 suggest a trade-off between adult size and developmental time, at least
 for parasitoids developed at the two extremes of host ages at
 parasitization, and that A. ervi can reach the same adult size via
 different trajectories, adapting its ontogenetic processes. Wing shape was
 typical for all the different parasitoid classes considered and differed
 strongly between males and females, independent of their size. Parasitoid
 males (haploids) and females (diploids) did not differ in either cell area
 or cell number, suggesting a possible sex-determined dosage compensation
 in somatic tissue endoreplication.
description: data set Trotta et al.,
 2014data experimentally
 collected in lab on Aphidius ervi developed in the host Acyrthosiphon
 pisumdata
 Dryad.xlsx
DOI: 10.5061/dryad.sd1sr
title: Data from: Titi monkey call sequences vary with predator location and type

description: Animal alarm calls can encode information about a predator’s category,
 size, distance or threat level. In non-human primates, alarm calls
 typically refer to broad classes of disturbances, in some instances to
 specific predators. Here, we present the results of a field experiment
 with a New World primate, the black-fronted titi monkey, designed to
 explore the information conveyed by their alarm call system. Adults
 produced sequences consisting of two main alarm call types that conveyed,
 in different parts of the utterance, information about a predator’s type
 and location. In particular, sequence compositions differed depending on
 whether the predator was a mammalian carnivore or a raptor, and whether it
 was detected in a tree or on the ground. This is the first demonstration
 of a sequence-based alarm call system in a non-human animal that has the
 capacity to encode both location and type of predatory threat.
description: Cäsar et al
 2013_BLDescription of data
 collected in the fieldCäsar et al 2013_driad
 BL.xls
DOI: 10.5061/dryad.6v0c1
title: Data from: Maternal investment increases with altitude in a frog on the Tibetan plateau

description: Reproducing females can allocate energy between the production of eggs of
 different size or number, both of which can strongly influence fitness.
 Environmental conditions often drive these reproductive tradeoffs, because
 of direct influences on offspring survival. Many vertebrates show positive
 relationships between female body size and altitude, resulting in the
 production of larger clutches at higher altitudes. We report a different
 tradeoff in the high-altitude endemic frog Rana kukunoris (n=11
 populations, 2000-3500 m): females living at higher altitudes produce
 heavier clutches of larger eggs without a concomitant increase in female
 body size or clutch size. Reproduction at high altitudes thus favours
 current reproduction at a cost to short-term maintenance and growth. The
 harsh environmental conditions at high altitudes can impose strong and
 opposing selection pressure on egg and adult life history stages.
description: data-JEB
DOI: 10.5061/dryad.kq04t
title: Data from: Prevalence of Raynaud's phenomenon and nailfold capillaroscopic abnormalities in Fabry's disease: a cross-sectional study

description: [No description entered]
description: Demographic and clinical
 characteristics of Fabry patients and controlsDataset
 demographics.odsResults of nailfold
 capillaroscopic parametersDataset
 capillaroscopy.ods
DOI: 10.5061/dryad.bf6m4
title: Data from: Speed of adaptation and genomic footprints of host-parasite coevolution under arms race and trench warfare dynamics

description: Coevolution between hosts and their parasites is expected to follow a
 range of possible dynamics, the two extreme cases being called trench
 warfare (or Red Queen) and arms races. Long-term stable polymorphism at
 the host and parasite coevolving loci is characteristic of trench warfare,
 and is expected to promote molecular signatures of balancing selection,
 while the recurrent allele fixation in arms races should generate
 selective sweeps. We compare these two scenarios using a finite size
 haploid gene-for-gene model that includes both mutation and genetic drift.
 We first show that trench warfare do not necessarily display larger
 numbers of coevolutionary cycles per unit of time than arms races. We
 subsequently perform coalescent simulations under these dynamics to
 generate sequences at both host and parasite loci. Genomic footprints of
 recurrent selective sweeps are often found, whereas trench warfare yield
 signatures of balancing selection only in parasite sequences, and only in
 a limited parameter space. Our results suggest that deterministic models
 of coevolution with infinite population sizes do not predict reliably the
 observed genomic signatures, and it may be best to study parasite rather
 than host populations to find genomic signatures of coevolution such as
 selective sweeps or balancing selection.
description: Code R for stochastic
 simulationsstochastic-cstPopSize-GFG-Tellier.rOutcome_Stochastic_unstable_Nplant_5000_N_par_5000Stochastic_unstable_Nplant_5000_N_par_5000.pdfOutcome_Stochastic_stable_Nplant_5000_N_par_5000Stochastic_stable_polycyclic2_Nplant_5000_N_par_5000.pdf
DOI: 10.5061/dryad.8f6nq
title: Data from: The rate and effects of spontaneous mutation on fitness traits in the social amoeba, Dictyostelium discoideum

description: We performed a mutation accumulation (MA) experiment using the social
 amoeba Dictyostelium discoideum to estimate the rate and distribution of
 effects of spontaneous mutations affecting eight putative fitness traits.
 We found that the per generation mutation rate for most fitness components
 is 0.0019 mutations per haploid genome per generation, or larger. This
 rate is an order of magnitude higher than estimates for fitness components
 in the unicellular eukaryote Saccharomyces cerevisiae, even though the
 base-pair substitution rate is two orders of magnitude lower. The high
 rate of fitness-altering mutations observed in this species may be
 partially explained by a large mutational target relative to Saccharomyces
 cerevisiae. Also, fitness-altering mutations may occur primarily at simple
 sequence repeats, which are common throughout the genome, including in
 coding regions, and may represent a target that is particularly likely to
 give fitness effects upon mutation. The majority of mutations had
 deleterious effects on fitness, but there was evidence for a substantial
 fraction, up to 40%, being beneficial for some of the putative fitness
 traits. Competitive ability within the multicellular slug appears to be
 under weak directional selection, perhaps reflecting the fact that slugs
 are sometimes, but not often, comprised of multiple clones in nature.
 Evidence for pleiotropy among fitness components across MA lines was
 absent, suggesting that mutations tend to act on single fitness
 components.
description: Plate growth fitness
 dataHall_et_al_Plate_growth.txtLiquid growth fitness dataHall_et_al_Liquid_growth.txtSlug distance fitness dataHall_et_al_Slug_distance.txtTotal fruiting bodies fitness dataHall_et_al_Total_FB.txtSpores per fruiting body fitness dataHall_et_al_Spores_per_FB.txtTotal spores fitness dataHall_et_al_Total_spores.txtSpore germination fitness dataHall_et_al_Spore_germination.txtCompetitive ability fitness dataHall_et_al_Competitive_ability.txt
DOI: 10.5061/dryad.9022
title: Data from: Contrasting theory with the empirical data of species recognition

description: We tested hypotheses on how animals should respond to heterospecifics
 encountered in the environment. Hypotheses were formulated from models
 parameterized to emphasize four factors that are expected to influence
 species discrimination: mating and territorial interactions; sex
 differences in resource value; environments in which heterospecifics were
 common or rare; and the type of identity cues available for species
 recognition. We also considered the role of phylogeny on contemporary
 responses to heterospecifics. We tested the extent these factors explained
 variation among taxa in species discrimination using a meta-analysis of
 three decades of species recognition research. A surprising outcome was
 the absence of a general predictor of when species discrimination would
 most likely occur. Instead, species discrimination is dictated by the
 benefits and costs of responding to a conspecific or heterospecific that
 are governed by the specific circumstances of a given species. The
 phylogeny of species recognition provided another unexpected finding: the
 evolutionary relationships among species predicted whether courting males
 within species – but not females – would discriminate against
 heterospecifcs. This implies that species recognition has evolved quite
 differently in the sexes. Finally, we identify common pitfalls in
 experimental design that seem to have affected some studies (e.g., poor
 statistical power) and provide recommendations for future research.
description: meta-analysis
 dataComplete dataset used in
 meta-analysis of species recognitionOrd_TJ-10-0799R2_meta_data.txtmeta-analysis sourcesReferences of source data used in meta-analysisOrd_TJ-10-0799R2_meta_sources.txt
DOI: 10.15468/dl.27h4es
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fabiana patagonica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 146 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000915-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.