cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m5548
title: Data from: Stabilization of golden cages by encapsulation of a single transition metal atom

description: Golden cage doped nanoclusters have attracted great attention in the past
 decade due to their remarkable electronic, optical, and catalytic
 properties. However, the structures of large golden cage doped with Mo and
 Tc are still not well-known because of the challenges in global structural
 searches. Here we report anionic and neutral golden cage doped with a
 transition-metal atom MAu16 (M=Mo and Tc) using Saunders “Kick” stochastic
 automation search method associated with density-functional theory
 calculation (SK-DFT). The geometric structures and electronic properties
 of the doped clusters, MAu16q (M=Mo and Tc; q=0 and −1) are investigated
 by means of DFT theoretical calculations. Our calculations confirm that
 the 4d transition-metal Mo and Tc can be stably encapsulated in the Au16−
 cage, forming in three different configurations, i.e. endohedral cages,
 planar structures and exohedral derivatives. The ground-state structures
 of endohedral cages C2v Mo@Au16– –(a) and C1 Tc@Au16 ––(b) exhibit a
 marked stability, as judged by their high binding energy per atom
 (&gt;2.46 eV), doping energy (0.29 eV) as well as a large HOMO–LUMO
 gap (&gt;0.40 eV). The predicted photoelectron spectra should aid
 future experimental characterization of MAu16– (M= Mo and Tc).
description: Cartesian coordinates
 for stable isomers of MAu16–clustersESM for
 RSOS-171019.doc
DOI: 10.5061/dryad.18pn5
title: Data from: DOG1 expression is predicted by the seed-maturation environment and contributes to geographic variation in germination in Arabidopsis thaliana.

description: Seasonal germination timing of Arabidopsis thaliana strongly influences
 overall life history expression and is the target of intense natural
 selection. This seasonal germination timing depends strongly on the
 interaction between genetics and seasonal environments both before and
 after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that
 has been identified to be associated with natural variation in primary
 dormancy in Arabidopsis thaliana. Here, we report inter-accession
 variation in DOG1 expression and document that DOG1 expression is
 associated with seed-maturation temperature effects on germination; DOG1
 expression increased when seeds were matured at low temperature, and this
 increased expression was associated with increased dormancy of those
 seeds. Variation in DOG1 expression suggests a geographical structure such
 that southern accessions, which are more dormant, tend to initiate DOG1
 expression earlier during seed maturation and achieved higher expression
 levels at the end of silique development than did northern accessions.
 Although elimination of the synthesis of phytohormone ABA results in the
 elimination of maternal temperature effects on dormancy, DOG1 expression
 predicted dormancy better than expression of genes involved in ABA
 metabolism.
description: Data DOG1 Expression and
 Maternal Environment
DOI: 10.5061/dryad.g3p4h
title: Data from: Prior experience and contest outcome: winner effects persist in absence of evident loser effects in a parasitoid wasp

description: The experience of a prior conflict can affect animals' performance
 during a later contest: a victory usually increases while a defeat
 decreases the probability of winning a subsequent conflict. These winner
 and loser effects could result from a reassessment by contestants of their
 perceived fighting abilities. Game-theoretic models based on this
 assumption predict that a loser effect can exist alone or in the presence
 of a winner effect, but a winner effect cannot persist alone, at least
 when contestants are young and without experience of contest. Moreover,
 when both effects coexist, the loser effect is expected to be of a greater
 magnitude and last longer than the winner effect. To date, these
 predictions have been supported by empirical evidence. Here, we show for
 the first time that a winner effect can exist in the absence of any
 evident loser effect, in a parasitoid wasp, Eupelmus vuilleti, when
 fighting for hosts. It consequently raises questions about the possible
 mechanisms involved and challenges the main assumption of previous
 theoretical models. We suggest an alternative explanation for the
 evolution of only winner effects, based on the modification of
 contestants' subjective value of the resource rather than on a
 re-estimation of their fighting abilities.
description: Data of Winner Loser
 effects in Eupelmus vuilletiData concerning the
 following paper, accepted in The American Naturalist (#53493): Prior
 experience and contest outcome: Winner effects persist in absence of
 evident loser effects in a parasitoid wasp. Marlène Goubault & Marie
 Decuignière, Institut de recherche sur la biologie de l’insecte, UMR CNRS
 6035, Université François Rabelais de Tours, 37200 Tours, France.
 marlene.goubault@univ-tours.frData on Dryad WL
 effects.xls
DOI: 10.5061/dryad.86020
title: Data from: Nocturnal migratory songbirds adjust their travelling direction aloft: evidence from a radiotelemetry and radar study

description: In order to fully understand the orientation behaviour of migrating birds,
 it is important to understand when birds set their travel direction.
 Departure directions of migratory passerines leaving stopover sites are
 often assumed to reflect the birds' intended travel directions, but
 this assumption has not been critically tested. We used data from an
 automated radiotelemetry system and a tracking radar at Falsterbo
 peninsula, Sweden, to compare the initial orientation of departing
 songbirds (recorded by radiotelemetry) with the orientation of songbird
 migrants in climbing and level flight (recorded by radar). We found that
 the track directions of birds at high altitudes and in level flight were
 more concentrated than the directions of departing birds and birds in
 climbing flight, which indicates that the birds adjust their travelling
 direction once aloft. This was further supported by a wide scatter of
 vanishing bearings in a subsample of radio-tracked birds that later passed
 an offshore radio receiver station 50 km southeast of Falsterbo. Track
 directions seemed to be more affected by winds in climbing compared with
 level flights, which may be explained by birds not starting to partially
 compensate for wind drift until they have reached cruising altitudes.
description: Track directions and
 vanishing bearingsData collected in the
 field by using radiotelemetry and radar. For information on calculations
 of directions see the manuscript.rådatatabell till
 dryad.xlsx
DOI: 10.5061/dryad.98b31
title: Data from: Patterns in parasitism frequency explained by diet and immunity

description: We sought to explain patterns in parasitism frequency of two specialist
 herbivores (Geometridae) by investigating the influence of plant diet as a
 source of variation in immune response variables important for defense
 against parasitism. Field collected caterpillars (Eois apyraria and Eois
 nympha) were assigned to one of two species in the plant genus Piper
 (Piperaceae): 1) a host species with high diversity of defensive
 chemistry, P. cenocladum C.DC., or 2) a host species with lower investment
 in chemical defense, P. imperiale C.DC. Hemolymph was extracted from fifth
 instar larvae, and immune strength measured unidimensionally using a
 phenoloxidase (PO) enzyme assay. Parasitism data came from 19 years of
 accumulated host plant-caterpillar-parasitoid associations from a
 long-term rearing project at La Selva Biological Station in Costa Rica,
 where the experiment took place. We found that immunity was significantly
 weakened when caterpillars were reared on the host plant with higher
 phytochemical diversity (P. cenocladum). Moreover, host plants inducing a
 weak immune response hosted caterpillars with higher parasitism rates. We
 conclude that patterns in parasitism frequency can be partially explained
 by cascading effects of host plant traits.
description: Eois immune
 dataThe file contains immune
 response data on two species of Eois caterpillars feeding on different
 Piper species.assay_AMS.xlsx
DOI: 10.5061/dryad.63kb3
title: Data from: The dynamics of tent-roosts in the palm Sabal mauritiiformis and their use by bats in a montane dry forest

description: Tent-making bats modify leaves to build refuges. Leaf modification
 involves energetic and defense costs that should be balanced by the
 benefits of tent-roosting. The alteration of the leaf’s vascular system
 reduces the tent’s life expectancy, so to obtain a benefit bats are
 expected to use tents regularly as long as they are functional and not
 modify more leaves than necessary. Over two years we documented the
 dynamics of tent construction and use by Uroderma convexum and other bat
 species in the palm Sabal mauritiiformis in a Colombian transitional dry
 forest. We also assessed tent condition and compared it to nonmodified
 leaves of approximately the same age in focal palms. Probability of tent
 use by U. convexum varied between 57 percent during a reproductive period
 and 4 percent outside of this period. Bats cut the main vein of folioles,
 partially affecting water transport in the leaf. However, there were no
 differences between tents and nonmodified leaves in deterioration scores
 or deterioration rates over one year. During two years, 48 tents were lost
 for different causes, but this loss was balanced by the construction of 51
 new tents. Thus, bats maintained an excess of usable tents. Palm leaves
 are long-lived and seem preadapted to sustain damage and remain viable,
 particularly in species growing in dry environments. We present several
 hypotheses to explain the advantage of maintaining a tent surplus.
description: BatTents_Project
DOI: 10.5061/dryad.3c457
title: Data from: The more the merrier: conspecific density improves performance of gregarious larvae and reduces susceptibility to a pupal parasitoid

description: Aggregation can confer advantages in animal foraging, defense and
 thermoregulation. There is a tight connection between the evolution of
 insect sociality and a highly effective immune system, presumably to
 inhibit rapid disease spread in a crowded environment. This connection is
 less evident for animals that spend only part of their life-cycle in a
 social environment, such as non-eusocial gregarious insects. Our aim was
 to elucidate the effects of group living by the gregarious larvae of the
 Glanville fritillary butterfly with respect to individual performance,
 immunity and susceptibility to a parasitoid. We were also interested in
 the role of family relative to common post-diapause environment in shaping
 life-history traits. Larvae were reared at high or low density and then
 exposed to the pupal parasitoid wasp Pteromalus apum, either in presence
 or absence of a previous immune challenge that was used to measure the
 encapsulation immune response. Surviving adult butterflies were further
 tested for immunity. The wasp offspring from successfully parasitized
 butterfly pupae were counted and their brood sex-ratios assessed. Larvae
 reared at high density grew larger and faster than those at low density.
 Despite high mortality due to parasitism, survival was greater among
 individuals with high pupal immunity in both density treatments. Moreover,
 butterfly pupae reared at high density were able to kill a larger fraction
 of individuals in the parasitoid broods, although this did not increase
 survival of the host. Finally, a larger proportion of variation observed
 in most of the traits was explained by butterfly family than by common
 post-diapause rearing environment, except for adult survival and immunity,
 for which this pattern was reversed. This gregarious butterfly clearly
 benefits from high conspecific density in terms of developmental
 performance and its ability to fight a parasitoid. These positive effects
 may be driven by cooperative interactions during feeding.
description: Larval density
 dataData set life-history
 variables related to butterfly individuals that successfully reached the
 pupal stage. The description of each variable is provided as a comment in
 the Excel file.DENSITY.xlsxLarval survival dataIndividual data of butterfly larvae from the initiation of the experiment describing whether or not they survived until pupation. The description of each variable is provided as a comment in the Excel file.Life.xlsxWasp brood dataA data set including life-history variables about the wasp broods originating from a subset of butterfly pupae that were successfully parasitized by a parasitoid wasp. The description of each variable is provided as a comment in the Excel file.Wasp.xlsxModel selectionR script with model selection based on the three data files.R_script.txt
DOI: 10.5061/dryad.3jf15
title: Data from: Strong selection on male plumage in a hybrid zone between a hybrid bird species and one of its parents

description: Homoploid hybrid speciation (HHS) requires reproductive barriers between
 hybrid and parent species, despite incomplete reproductive isolation (RI)
 between the parents. Novel secondary sexual trait values in hybrids may
 cause prezygotic isolation from both parents, whereas signals inherited by
 the hybrid from one parent species may cause prezygotic isolation with the
 other. Here we investigate whether differences in male plumage function as
 a premating barrier between the hybrid Italian sparrow and one of its
 parent species, the house sparrow, in a narrow Alpine hybrid zone. Italian
 sparrow male plumage is a composite mosaic of the parental traits, with
 its head plumage most similar to its other parent, the Spanish sparrow. We
 use geographical cline analysis to examine selection on three plumage
 traits, 75 nuclear single nucleotide polymorphisms (SNPs) and hybrid
 indices based on these SNPs. Several SNPs showed evidence of restricted
 introgression in the Alps, supporting earlier findings. Crown colour
 exhibited the narrowest plumage cline, representing a 37% (range 4–65%)
 drop in fitness. The cline was too narrow to be due to neutral
 introgression. Only crown colour was significantly bimodal in the hybrid
 zone. Bimodality may be due to RI or a major QTL, although fitness
 estimates suggest that selection contributes to the pattern. We discuss
 the implications with respect to HHS and the species status of the Italian
 sparrow.
description: AlpsSparrowdataAll individual-level SNP and plumage data used in cline-fitting. This includes: genotypes of 75 SNPs; plumage trait values (discriminant axis scores for multivariate traits) for crown colour, cheek colour and eyebrow colour; a molecular hybrid index based on 75 SNPs; a molecular hybrid index based on 4 SNPs. See publication for more details.
DOI: 10.5061/dryad.66j20
title: Data from: Top predators and habitat complexity alter an intraguild predation module in pond communities

description: Predator diversity and habitat complexity frequently influence species
 interactions at lower trophic levels, yet their joint investigation has
 been performed infrequently despite the demonstrated importance of each
 individual factor. We investigated how different top predators and varying
 habitat complexity influence the function of an intraguild predation
 module consisting of two larval salamanders, intraguild predator Ambystoma
 annulatum and intraguild prey A. maculatum. We manipulated predator food
 webs and habitat complexity in outdoor mesocosms. Top predators
 significantly influenced body condition and survival of A. annulatum, but
 habitat complexity had minimal effects on either response. A three-way
 interaction among the covariates top predator identity, habitat complexity
 and A. annulatum survival influenced body condition and survival of A.
 maculatum via a density mediated indirect effect. Different top predator
 combinations had variable effects in different habitat complexity
 treatments on intraguild predator (A. annulatum) survival that
 subsequently influenced intraguild prey (A. maculatum) body condition and
 survival. Future work should consider how different top predators
 influence other food web components, which should vary due to predator
 attributes and the physical environments in which they co-occur.
description: Measurement_dataData on individual body size for both Ringed (A. annulatum) and Spotted (A. maculatum) SalamandersAnderson_Semlitsch_2015_measurement_data.csvSurvival_DataSurvival data for both Ringed (A. annulatum) and Spotted Salamanders (A. maculatum)Anderson_Semlitsch_2015_survival.csvInjuryInjury data summarized by tank from Ringed Salamanders (A. annulatumAnderson_Semlitsch2015_injury.data.csvR script for analysisR code to repeat the analyses and figurestanks1213.dryad.R
DOI: 10.5061/dryad.j6m20
title: Data from: Modeling the dynamics of Plasmodium vivax infection and hypnozoite reactivation in vivo

description: The dynamics of Plasmodium vivax infection is characterized by
 reactivation of hypnozoites at varying time intervals. The relative
 contribution of new P. vivax infection and reactivation of dormant liver
 stage hypnozoites to initiation of blood stage infection is unclear. In
 this study, we investigate the contribution of new inoculations of P.
 vivax sporozoites to primary infection versus reactivation of hypnozoites
 by modeling the dynamics of P. vivax infection in Thailand in patients
 receiving treatment for either blood stage infection alone (chloroquine),
 or the blood and liver stages of infection (chloroquine + primaquine). In
 addition, we also analysed rates of infection in a study in Papua New
 Guinea (PNG) where patients were treated with either artesunate, or
 artesunate + primaquine. Our results show that up to 96% of the P. vivax
 infection is due to hypnozoite reactivation in individuals living in
 endemic areas in Thailand. Similar analysis revealed the around 70% of
 infections in the PNG cohort were due to hypnozoite reactivation. We show
 how the age of the cohort, primaquine drug failure, and seasonality may
 affect estimates of the ratio of primary P. vivax infection to hypnozoite
 reactivation. Modeling of P. vivax primary infection and hypnozoite
 reactivation provides important insights into infection dynamics, and
 suggests that 90–96% of blood stage infections arise from hypnozoite
 reactivation. Major differences in infection kinetics between Thailand and
 PNG suggest the likelihood of drug failure in PNG.
description: Time to Plasmodium vivax
 infectionIndividuals with
 reappearance of pure Plasmodium vivax infection were retreated with either
 chloroquine only (70 individuals ) or chloroquine and primaquine (43
 individuals) and were followed up by microscopy until detection of
 Plasmodium vivax blood stage parasites.DataForPlosNtdPaper9.2.2015MPDAAI2.xlsx
DOI: 10.5061/dryad.8502
title: Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.

description: Reconstructing the chronology of mammalian evolution is a debated issue
 between molecule- and fossil-based inferences. A methodological limitation
 of molecules is the evolutionary rate variation among lineages, precluding
 the application of the global molecular clock. We considered 2422 first
 and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear
 genes for a well-documented set of placentals including an extensive
 sampling of rodents. Using seven independent calibration points and a
 maximum-likelihood framework, we evaluated whether molecular and
 paleontological estimates of mammalian divergence dates may be reconciled
 by the local molecular clocks approach, allowing local constancy of
 substitution rates with variations at larger phylogenetic scales. To
 handle the difficulty of choosing among all possible rate assignments for
 various lineages, local molecular clocks were based on the results of
 branch-length and two-cluster tests. Extensive lineage-specific variation
 of evolutionary rates was detected, even among rodents. Cross-calibrations
 indicated some incompatibilities between divergence dates based on
 different paleontological references. To decrease the impact of a single
 calibration point, estimates derived from independent calibrations
 displaying only slight reciprocal incompatibility were averaged. The
 divergence dates inferred for the split between mice and rats
 (approximately 13-19 Myr) was younger than previously published molecular
 estimates. The most recent common ancestors of rodents, primates and
 rodents, boreoeutherians, and placentals were estimated to be,
 respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks,
 local clocks, and quartet dating analyses suggested a Late Cretaceous
 origin of the crown placental clades followed by a Tertiary radiation of
 some placental orders like rodents.
description: Douzery_JMolEvol_2003Nucleotide alignment concatenation of codon positions 1+2 from 3 nuclear genesDouzery_JMolEvol_2003Reference tree used in molecular dating analyses
DOI: 10.5061/dryad.m74c8nj
title: Data from: Paceless life? a meta-analysis of the pace-of-life syndrome hypothesis

description: The pace-of-life syndrome hypothesis predicts that individual differences
 in behaviour should integrate with morphological, physiological, and
 life-history traits along a slow to fast pace-of-life continuum. For
 example, individuals with a “slow” pace-of-life are expected to exhibit a
 slower growth rate, delayed reproduction, longer lifespans, have stronger
 immune responses, and are expected to avoid risky situations relative to
 “fast” individuals. If supported this hypothesis would help resolve
 ecological and evolutionary questions regarding the origin and maintenance
 of phenotypic variation. Support for the pace-of-life syndrome hypothesis
 has, however, been mixed. Here we conducted a meta-analysis of 42 articles
 and 179 estimates testing the pace-of-life syndrome hypothesis as it
 applies to the integration of behaviours with physiological or
 life-history traits. We found little overall support for the pace-of-life
 syndrome hypothesis with the mean support estimated as r = 0.06. Support
 for the pace-of-life syndrome hypothesis was significantly higher in
 invertebrates (r = 0.23) than vertebrates (r = 0.02) and significantly
 higher when based on phenotypic (r = 0.10) versus genetic correlations (r
 = -0.09). We also found that females exhibited correlations between
 behaviour and life-history and physiology that were opposite the
 predictions of the pace-of-life syndrome hypothesis (r = -0.16) and that
 these correlations significantly differed from those observed in males (r
 = 0.01) or males and females pooled (r = 0.12). It was also the case that
 there was little support for the hypothesis when life-history and
 physiological traits were independently analysed (behaviour ×
 life-history: r = 0.12; behaviour × physiology: r = 0.04). Exploratory
 post-hoc analyses revealed that correlations of behaviour with growth rate
 and hormone levels were more likely to show support for the predictions of
 the pace-of-life syndrome hypothesis. The lack of overall support found in
 our analyses suggests that general assertions regarding phenotypic
 integration due to “pace-of-life” and should be re-evaluated.
description: BEAS-D-17-00146_ArticlesList of 42 articles selected for meta-analysis after screeningBEAS-D-17-00146_PhyloTreePhylogenetic tree built using phyloT for the 30 species used in the meta-analysis (Letunic 2015) Letunic, I. (2015). phyloT : Phylogenetic Tree Generator. [online] Phylot.biobyte.de. Available at: http://phylot.biobyte.de/.BEAS-D-17-00146_DataEffect sizes for meta-analysis of the relationships between behavior x physiology and behavior x life-history correlations based on published data from 42 articles and 30 species and a total of 179 estimate. Each estimate describes the correlation between a behavioral trait (B) and a physiological (P) or life-history trait (LH).BEAS-D-17-00146_AnalysisR code used to complete the meta-analysis