cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0n624
title: Data from: Breeding phenological response to spring weather conditions in common Finnish birds: resident species respond stronger than migratory species

description: National bird-nest record schemes provide a valuable data source to study
 large-scale changes in basic breeding biology and effects of climate
 change on birds. Using nest-record scheme data from 26 common Finnish
 breeding bird species from whole Finland, we estimated the laydate of the
 first egg for 129 063 nesting attempts. We then investigated the
 relationship of mean spring temperature and spring precipitation sum to
 changes in the onset of laying over the period 1961–2012. In addition, we
 examine differences in response to these climatic variables for species
 grouped for different life history strategies; migration, diet and
 habitat. Finally, we test whether body size is related to the strength of
 phenological response. We show that 26 common Finnish breeding bird
 species have advanced their laying dates over time and to an increase in
 the mean spring temperature over the study period. When species are
 grouped according life history strategies, we find that breeding
 phenological change is negatively associated with changes in the mean
 spring temperature where residents respond strongest to changes in mean
 spring temperature, but also short- and long-distance migrants advance
 laydates with increasing spring temperatures. Breeding phenological change
 is also associated with spring precipitation, where resident species delay
 and short-distance migrants advance the onset of breeding. In addition we
 find that omnivorous species respond stronger than insectivorous species
 to changes in spring temperature. In contrast to results from an earlier
 study, we do not find evidence that small-sized species respond stronger
 to spring temperature than large-sized species. As climate warming is
 predicted to continue in the future, long-term citizen science schemes,
 such as the Finnish nest-card scheme, prove to be a valuable
 cost-effective way to monitor the environment and allow investigation into
 how species are responding to changes in their environment.
description: Mean laydate per species
 per year (1961-2012)Laydates for 26 common
 breeding bird species in Finland were estimated based on nest-card data.
 The data here contains mean laydates (and standard deviation) per bird
 species per year for the period 1961-2012, including the number of
 nestcards on which each mean laydate was based on.mean laydate per year per
 species.txt
DOI: 10.5061/dryad.bt0ns
title: Data from: The distribution of fitness effects in an uncertain world

description: The distribution of fitness effects (DFE) among new mutations plays a
 critical role in adaptive evolution and the maintenance of genetic
 variation. While fitness landscape models predict several key features of
 the DFE, most theory to date focuses on predictable environmental
 conditions, while ignoring stochastic environmental fluctuations that
 feature prominently in the ecology of many organisms. Here, we derive an
 extension of Fisher's geometric model that incorporates two common
 effects of environmental variation: (1) non-adaptive
 genotype-by-environment interactions (GxE), in which the phenotype of a
 given genotype varies across environmental contexts; and (2) random
 fluctuation of the fitness optimum, which generates fluctuating selection.
 We show that both factors cause a mismatch between the DFE within single
 generations and the distribution of geometric mean fitness effects
 (averaged over multiple generations) that governs long-term evolutionary
 change. Such mismatches permit strong evolutionary constraints – despite
 an abundance of beneficial fitness variation within single environmental
 contexts – and to conflicting DFE estimates from direct versus indirect
 inference methods. Finally, our results suggest an intriguing parallel
 between the genetics and ecology of evolutionary constraints, with
 environmental fluctuations and pleiotropy placing qualitatively similar
 limits on the availability of adaptive genetic variation.
description: DFE sim n = 5
 dimensionsDFE sim n
 DFE sim n = 10
 dimensionsDFE sim n
 DFE sim n = 25
 dimensionsDFE sim n
DOI: 10.5061/dryad.8qm34
title: Data from: A longitudinal study of age-related changes in Haemoproteus infection in a passerine bird

description: Blood parasites such as malaria and related haemosporidians commonly
 infect vertebrate species including birds. Understanding age-specific
 patterns of parasite infections is crucial for quantifying the fitness
 consequences of parasitism for hosts and for understanding parasite
 transmission dynamics. We analyzed longitudinal and cross-sectional
 infection data in house martins Delichon urbica, a migratory bird
 suffering from intense haemosporidian infection. We separated within- from
 among-individual effects of age on prevalence. Our results showed that the
 probability of blood parasite infection increased as individual house
 martins aged. We also showed that the prevalence of infection decreased
 with age at last reproduction when controlling for age, showing a
 selective disappearance of infected birds from the population (i.e.
 selection). The estimated effect of age on prevalence was underestimated
 two- to three-fold if not accounting for such selection. This study
 highlights the importance of taking among-individual heterogeneity in the
 capacity to fight a disease into account because such heterogeneity can
 mask age-related patterns of infection. These findings emphasize the
 relevance of considering within- and among-individual patterns of
 infection in order to understand parasite-induced mortality and the
 potential for parasite transmission.
description: AVION DATOS
 SENESCENCIA_revisadosAn excel file containing
 data from longitudinal study in house martins across 13 years of
 study
DOI: 10.5061/dryad.87035
title: Data from: Selective disappearance of individuals with high levels of glycated haemoglobin in a free-living bird

description: Although disruption of glucose homeostasis is a hallmark of ageing in
 humans and laboratory model organisms, we have little information on the
 importance of this process in free-living animals. Poor control of blood
 glucose levels leads to irreversible protein glycation. Hence, levels of
 protein glycation are hypothesized to increase with age and to be
 associated with a decline in survival. We tested these predictions by
 measuring blood glycated haemoglobin in 274 adult collared flycatchers of
 known age and estimating individual probability of recapture in the
 following 2 years. Results show a strong decrease in glycated haemoglobin
 from age 1 to 5 years and an increase thereafter. Individuals with high
 levels of glycated haemoglobin had a lower probability of recapture, even
 after controlling for effects of age and dispersal. Altogether, our
 findings suggest that poor control of glucose homoeostasis is associated
 with lower survival in this free-living bird population, and that the
 selective disappearance of individuals with the highest glycation levels
 could account for the counterintuitive age-related decline in glycated
 haemoglobin in the early age categories.
description: Full
 datasetThe dataset includes all
 the variables used in the main text and in supplementary
 analyses.Dataset for
 publication.xls
DOI: 10.5061/dryad.t9t0v
title: Data from: Size matters for lice on birds: coevolutionary allometry of host and parasite body size

description: Body size is one of the most fundamental characteristics of all organisms.
 It influences physiology, morphology, behavior, and even interspecific
 interactions such as those between parasites and their hosts. Host body
 size influences the magnitude and variability of parasite size according
 to Harrison's Rule (HR: positive relationship between host and
 parasite body sizes) and Poulin’s Increasing Variance Hypothesis (PIVH:
 positive relationship between host body size and the variability of
 parasite body size). We analyzed parasite-host body size allometry for 581
 species of avian lice (~15% of known diversity) and their hosts. We
 applied phylogenetic generalized least squares methods to account for
 phylogenetic non-independence controlling for host and parasite
 phylogenies separately and variance heterogeneity. We tested HR and PIVH
 for the major families of avian lice (Ricinidae, Menoponidae,
 Philopteridae), and for distinct ecological guilds within Philopteridae.
 Our data indicate that most families and guilds of avian lice follow both
 HR and PIVH; however, Ricinids did not follow PIVH and the "body
 lice" guild of Philopterid lice did not follow HR or PIVH. We discuss
 mathematical and ecological factors that may be responsible for these
 patterns, and we discuss the potential pervasiveness of these
 relationships among all parasites on Earth.
description: Louse and host bird body
 sizes by louse familiesLouse species
 (families), louse female total body length (obtained from taxonomic
 descriptions, see Supplements of our paper), host birds name and body mass
 (obtained from Dunning, 2008). Families are coded as: M: Menoponidae; R:
 Ricinidae; P: Philopteridae.Families_data_all.csvLouse and host bird body sizes by Philopterid guildsLouse species, female total body length, host species, host body mass, and louse guilds. Guilds are coded as: H: 'head lice'; W: wing lice; B: 'body lice'; G: generalists.Philopteridae_louse_data.csv
DOI: 10.5061/dryad.v25vk
title: Data from: Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

description: Horizontal gene transfer mediated by broad-host-range plasmids is an
 important mechanism of antibiotic resistance spread. While not all
 bacteria maintain plasmids equally well, plasmid persistence can improve
 over time, yet no general evolutionary mechanisms have emerged. Our goal
 was to identify these mechanisms, and to assess if adaptation to one
 plasmid affects the permissiveness to others. We experimentally evolved
 Pseudomonas sp. H2 containing multi-drug resistance plasmid RP4,
 determined plasmid persistence and cost using a joint
 experimental-modeling approach, resequenced evolved clones, and
 reconstructed key mutations. Plasmid persistence improved in fewer than
 600 generations because the fitness cost turned into a benefit. Improved
 retention of naive plasmids indicated that the host evolved towards
 increased plasmid permissiveness. Key chromosomal mutations affected two
 accessory helicases and the RNA polymerase β-subunit. Our and other
 findings suggest that poor plasmid persistence can be caused by a high
 cost involving helicase-plasmid interactions that can be rapidly
 ameliorated.
description: ResultsSection2.1This plasmid persistence dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 100 generation period for populations consisting of ancestral host (Hanc) and plasmid (Panc), evolved host (Hev) and plasmid (Pev), permutations HancPev and HevPanc, as well as control evolved hosts containing the ancestral plasmid (Hev*Panc).ResultsSection2.2This competition assay dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 48 generation period for mixed populations consisting of plasmid-containing (ancestral host and plasmid or evolved host and plasmid) and their respective plasmid-free segregants (ancestral host or evolved host only, respectively).ResultsSection2.3This plasmid persistence dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 100 generation period for populations consisting of ancestral or evolved hosts containing one of three alternative plasmids, pB10, Rsa and IncQ.ResultsSection2.4This plasmid persistence dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 100 generation period for populations consisting of ancestral or evolved hosts with reconstructed mutant or ancestral helicase alleles.
DOI: 10.5061/dryad.4jh42
title: Data from: A systematic review of methods for studying consumer health YouTube videos, with implications for systematic reviews

description: Background. YouTube is an increasingly important medium for consumer
 health information – with content provided by healthcare professionals,
 government and non-government organizations, industry, and consumers
 themselves. It is a rapidly developing area of study for healthcare
 researchers. We examine the methods used in reviews of YouTube consumer
 health videos to identify trends and best practices. Methods and
 Materials. Published reviews of consumer-oriented health-related YouTube
 videos were identified through PubMed. Data extracted from these studies
 included type of journal, topic, characteristics of the search, methods of
 review including number of reviewers and method to achieve consensus
 between reviewers, inclusion and exclusion criteria, characteristics of
 the videos reported, ethical oversight, and follow-up. Results.
 Thirty-three studies were identified. Most were recent and published in
 specialty journals. Typically, these included more than 100 videos, and
 were examined by multiple reviewers. Most studies described
 characteristics of the videos, number of views, and sometime
 characteristics of the viewers. Accuracy of portrayal of the health issue
 under consideration was a common focus. Conclusion. Optimal transparency
 and reproducibility of studies of YouTube health-related videos can be
 achieved by following guidance designed for systematic review reporting,
 with attention to several elements specific to the video medium.
 Particularly when seeking to replicate consumer viewing behavior,
 investigators should consider the method used to select search terms, and
 use a snowballing rather than a sequential screening approach.
 Discontinuation protocols for online screening of relevance ranked search
 results is an area identified for further development.
description: characteristics of
 published youtube video reviewsData extracted from
 published manuscripts, Excel spreadsheet with two tabs, one for the
 orginal sample and another for newer manuscripts. The row titled PMID
 indicates the PubMed ID number,and identifies that article that the data
 is taken from.DE on review methods
 V2.xls
DOI: 10.5061/dryad.74854
title: Data from: The body-size dependence of trophic cascades

description: Trophic cascades are indirect positive effects of predators on resources
 via control of intermediate consumers. Larger-bodied predators appear to
 induce stronger trophic cascades (a greater rebound of resource density
 toward carrying capacity), but how this happens is unknown because we lack
 a clear depiction of how the strength of trophic cascades is determined.
 Using consumer resource models, we first show that the strength of a
 trophic cascade has an upper limit set by the interaction strength between
 the basal trophic group and its consumer and that this limit is approached
 as the interaction strength between the consumer and its predator
 increases. We then express the strength of a trophic cascade explicitly in
 terms of predator body size and use two independent parameter sets to
 calculate how the strength of a trophic cascade depends on predator size.
 Both parameter sets predict a positive effect of predator size on the
 strength of a trophic cascade, driven mostly by the body size dependence
 of the interaction strength between the first two trophic levels. Our
 results support previous empirical findings and suggest that the loss of
 larger predators will have greater consequences on trophic control and
 biomass structure in food webs than the loss of smaller predators.
description: Data DeLong et al Am Nat
 Figure 3Data for Figure 3 in the
 manuscript. Functional response values are handling time (h, days), area
 of capture (a, mL per pred per day), e (predators per prey). These data
 are compiled from the literature, with sources given in the file. The
 algae growth rate data are from Tang 1995 (see text for full reference)
 and for algae density from DeLong and Vasseur 2012 J. Animal Ecology.
 Mortality rate data are also compiled from the literature, with sources
 indicated in the file as well as method of calculation.
DOI: 10.5061/dryad.k70h6
title: Data from: Speciation of two desert poplar species triggered by Pleistocene climatic oscillations

description: Despite the evidence that the Pleistocene climatic fluctuations have
 seriously affected the distribution of intraspecific diversity, less is
 known on its impact on interspecific divergence. In this study, we aimed
 to test the hypothesis that the divergence of two desert poplar species
 Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the
 Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two
 species to estimate the divergence time between them and to test whether
 gene flow occurred after species separation. Divergence time between the
 two species was estimated to be 0.66–1.37 million years ago (Ma), a time
 at which glaciation was at its maximum in China and deserts developed
 widely in central Asia. Isolation-with-Migration model also indicated that
 the two species had diverged in the presence of gene flow. We also
 detected evidence of selection at GO in P. euphratica and to a lesser
 extent at PhyB2. Together, these results underscore the importance of
 Pleistocene climate oscillations in triggering plant speciation as a
 result of habitats divergence.
description: sample code of populus
 pruinosa and populus euphraticaincluding all detailed
 locations of populations mentioned in this manuscriptPopulus euphratica
 sequenceincluding all Populus
 euphratica sequence analyzed in this manuscriptPopulus pruinosa
 sequenceincluding all Populus
 pruinosa sequence analyzed in this manuscript
DOI: 10.5061/dryad.k272c
title: Data from: Trust thy neighbour in times of trouble: background risk alters how tadpoles release and respond to disturbance cues

description: In aquatic environments, uninjured prey escaping a predator release
 chemical disturbance cues into the water. However, it is unknown whether
 these cues are a simple physiological by-product of increased activity or
 whether they represent a social signal that is under some control by the
 sender. Here, we exposed wood frog tadpoles (Lithobates sylvaticus) to
 either a high or low background risk environment and tested their
 responses to disturbance cues (or control cues) produced by tadpoles from
 high-risk or low-risk backgrounds. We found an interaction between risk
 level associated with the cue donor and cue recipient. While disturbance
 cues from low-risk donors did not elicit an antipredator response in
 low-risk receivers, they did in high-risk receivers. In addition,
 disturbance cues from high-risk donors elicited a marked antipredator
 response in both low- and high-risk receivers. The response of high-risk
 receivers to disturbance cues from high-risk donors was commensurate to
 other treatments, indicating an all-or-nothing response. Our study
 provides evidence of differential production and perception of social cues
 and provides insights into their function and evolution in aquatic
 vertebrates. Given the widespread nature of disturbance cues in aquatic
 prey, there may exist a social signalling system that remains virtually
 unexplored by ecologists.
description: Experiment Raw
 DataExcel spreadsheet of raw
 data from the experiment. See second sheet ('metadata') for
 definitions of each data column.Bairos-Novak_et_al_rawdata.xlsxR Script for Data AnalysisAn R script file with comments to obtain the test statistics and values observed in the manuscript.Bairos-Novak_et_al_Rscript.R
DOI: 10.5061/dryad.q3r30
title: Data from: Deconstructing the landscape of fear in stable multi-species societies

description: Animal distributions are influenced by variation in predation risk in
 space, which has been described as the “landscape of fear.” Many studies
 suggest animals also reduce predation risk by eavesdropping on
 heterospecific alarm calls, allowing them to occupy otherwise risky
 habitats. One unexplored area of study is understanding how different
 species’ alarms vary in quality, and how this variation is distributed in
 the landscape. We tested this phenomenon in a unique system of avian mixed
 species flocks in Amazonian rainforests: flock mates (eavesdropping
 species) strongly associate with alarm-calling antshrikes (genus
 Thamnomanes), which act as sentinel species. Up to 70 species join these
 flocks, presumably following antshrike behavioral cues. Since flocks in
 this region of the Amazon are exclusively led by a single antshrike
 species, this provides a unique natural system to compare differences in
 sentinel quality between flocks. We simulated predation threat by flying
 three species of live trained raptors (predators) towards flocks to
 compare sentinel probability to (1) produce alarm calls, and (2) encode
 information about magnitude and type of threat within such alarm calls.
 Our field experiments show significant differences in the probability of
 different sentinel species to produce alarm calls and distinguish
 predators. This variation may have important fitness consequences and
 shape the “landscape of fear” for eavesdropping species.
description: R Code for all
 AnalysesRcodeforAnalyses.RData for Alarm Calls by Flock TypeALARM1.csvCommunity Composition DataSpecies composition data by flock type. Each of two flock types represents a different habitatBraySentinel.csvCanopy Cover and Canopy HeightCanopy Cover and Height Data for forest habitat sampled within each flock for both flock typesRaptor Vegetation Analysis.csv
DOI: 10.5061/dryad.9kk0748
title: Data from: Evaluation of the novel avocado/soybean unsaponifiable Arthrocen to alter joint pain and inflammation in a rat model of osteoarthritis

description: Background: Avocado/soybean unsaponifiables such as Arthrocen have been
 reported to reduce cartilage catabolism and chondrocytic synthesis of
 inflammatory mediators associated with osteoarthritis (OA). While there is
 some clinical evidence that avocado/soybean unsaponifiables can reduce OA
 pain, no preclinical studies have corroborated this observation. The
 present study determined whether addition of an avocado/soybean
 unsaponifiable (Arthrocen) to the drinking water of OA rats reduced direct
 and referred joint pain. Methods: OA was induced in male Wistar rats by
 intra-articular injection of sodium monoiodoacetate (MIA: 0.3mg) and
 animals were allowed to recover for 14 days. Arthrocen was added to the
 drinking water which was available to animals ad libitum. On day 30, joint
 pain was assessed by dynamic incapacitance while referred pain was
 determined by von Frey hair algesiometry. Results: The joint damage
 induced by MIA injection was severe and was consistent with end-stage OA.
 Arthrocen consumption (approximately 35 mg/day) attenuated the joint
 oedema associated with MIA injection. Hindlimb weight bearing also
 significantly improved in Arthrocen-treated rats (P&lt;0.05); however,
 von Frey hair mechanosensitivity was unaffected by this treatment.
 Conclusions: These data indicate that Arthrocen has the potential to
 reduce joint inflammation and pain associated with end-stage OA.
description: Arthrocen & OA
 (PlosOne)Raw data of pain as
 assessed by weight bearing and vonFrey hair algesiometry. Inflammation
 assess by joint oedema.