cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r4m43
title: Data from: Can hook-bending be let off the hook? Bending/unbending of pliant tools by cockatoos

description: The spontaneous crafting of hook-tools from bendable material to lift a
 basket out of a vertical tube in corvids has widely been used as one of
 the prime examples of animal tool innovation. However, it was recently
 suggested that the animals' solution was hardly innovative but
 strongly influenced by predispositions from habitual tool use and nest
 building. We tested Goffin's cockatoo, which is neither a specialized
 tool user nor a nest builder, on a similar task set-up. Three birds
 individually learned to bend hook tools from straight wire to retrieve
 food from vertical tubes and four subjects unbent wire to retrieve food
 from horizontal tubes. Pre-experience with ready-made hooks had some
 effect but was not necessary for success. Our results indicate that the
 ability to represent and manufacture tools according to a current need
 does not require genetically hardwired behavioural routines, but can
 indeed arise innovatively from domain general cognitive processing.
description: Data Laumer et al.,
 2017
DOI: 10.5061/dryad.24251
title: Data from: Correlated evolution of allometry and sexual dimorphism across higher taxa

description: Empirical evidence suggests that Rensch's rule of allometric scaling
 of male and female body size, which states that body size divergence is
 greater across males than females of a clade, is not universal. In fact,
 quantitative genetic theory indicates that the sex under historically
 stronger directional selection will exhibit greater interspecific variance
 in size. Thus, the pattern of covariance between allometry of male and
 female body size and sexual size dimorphism (SSD) across related clades
 allows a test of this causal hypothesis for macroevolutionary trends in
 SSD. We compiled a dataset of published body size estimates from the
 amphibians, a class with predominantly female-biased SSD, to examine
 variation in allometry and SSD among clades. Our results indicate that
 females become the more size-variant sex across species in a family as the
 magnitude of SSD of that family increases. This rejects Rensch's rule
 and implicates selection on females as a driver of both amphibian
 allometry and SSD. Further, when we combine our data into a single
 analysis of allometry for the class, we find a significant non-linear
 allometric relationship between female and male body size. These data
 suggest that allometry changes significantly as a function of size. Our
 results illustrate that the relationship between female and male size
 varies both with the degree of sexual dimorphism and body size of a clade.
description: Amphibian Body
 lengthsAverage body lengths of
 male and female amphibian species (snout-vent length of anurans and
 caudates, total length of caecilians) collated from the published
 literature. When more than one source is listed for a species, the average
 of both sources was used.DeLisle&Rowe_AmphibianData.xlsx
DOI: 10.5061/dryad.mb1d0
title: Data from: Transient dynamics reveal the importance of early life survival to the response of a tropical tree to harvest

description: Exploitation of non-timber forest products can contribute to the
 alleviation of poverty. However, overexploitation can also lead to species
 decline. Studies on the sustainability of harvest often use stationary
 population growth rates to assess harvesting effects. For such frequently
 harvested systems, transient analysis can provide new insights into the
 response of populations to harvest. To test the prediction that the effect
 of harvest differs between transient and asymptotic phases, I used four
 years of demographic data to compare the impact of harvesting bark and
 foliage on the short- and long-term dynamics of African dry zone Mahogany
 Khaya senegalensis in West Africa. The effect of harvest was stronger in
 the short term than in the long term, particularly in the moist region.
 Patterns of transient elasticities also differed from the elasticities of
 long-term growth rates to perturbation of vital rates. Survival at early
 life stages was more important for short-term dynamics than for long-term
 population dynamics. Synthesis and applications. This study illustrates
 that using the asymptotic growth rates to assess the impact of harvest may
 underestimate the short-term effects of harvest. Short-term management
 plans based on the elasticity analysis of long-term growth rates will be
 suboptimal given the relative importance of the survival of
 non-reproductive stages for population dynamics in the near term. Managers
 should use results from elasticity analysis of both long-term and
 short-term population dynamics to develop more realistic management plans.
description: Khaya_MeanMatrices_2004_2007This file includes mean matrices for 12 populations of Khaya senegalensis surveyed in Benin (West Africa) from 2004 to 2007. For each population, I averaged three yearly transition matrices (2004-2005, 2005-2006, 2006-2007). These matrices were built using demographic data was collected from the 12 populations using 1-ha plots for each population (two adjacent subplots of 0.5 ha, separated by the river bed when the population was in a gallery forest.
DOI: 10.5061/dryad.c8n0748
title: Data from: Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription

description: Heterochromatin that is characterized by histone H3 lysine 9 (H3K9)
 methylation assembles on repetitive regions including centromeres.
 Although centromeric heterochromatin is important for faithful segregation
 of chromosomes, its role in maintaining centromere integrity remains
 elusive. Here, we found in fission yeast that heterochromatin suppresses
 gross chromosomal rearrangements (GCRs) at centromeres. Mutations in
 Clr4/Suv39 methyltransferase increased the formation of isochromosomes
 whose breakpoints are present in centromere repeats. H3K9A and H3K9R
 mutations also increased GCRs, suggesting that Clr4 appears to suppress
 GCRs via H3K9 methylation. Both HP1 homologs, Swi6 and Chp2, and an RNAi
 component Chp1 were the chromodomain proteins that are essential for full
 suppression of GCRs. Remarkably, mutations in RNA polymerase II (RNAPII)
 or the transcription factors including Tfs1/TFIIS which facilitates
 restart of backtracked RNAPII specifically bypassed the requirement of
 Clr4 to suppress GCRs. These results demonstrate that heterochromatin
 suppresses GCRs by repressing Tfs1-dependent transcription of centromere
 repeats.
description: Rates of chromosome
 lossRates of spontaneous
 chromosome loss were determined using biologically independent
 cultures.Okita2018_ChL_loss_rate_2.xlsxRates of spontaneous GCRsRates of spontaneous GCRs were determined using biologically independent cultures. A set of GCR rates that appear in one figure in the paper are shown in one sheet.Okita2018_GCR_rate_2.xlsxChromatin Immunoprecipitation (ChIP) dataWe performed ChIP experiments using biologically independent cultures. A set of ChIP data that appear in one figure in the paper are shown in one sheet. The data include the percentage of DNA recovered from ChIP experiments. Each number represents the mean of three measurements in the real time PCR. The value relative to that of adl1 is also shown in one sheet.Okita2018_ChIP_data_2.xlsx
DOI: 10.5061/dryad.gr5t1
title: Data from: Temperature-induced colour change varies seasonally in bearded dragon lizards

description: The benefits of colour change are expected to vary seasonally due to
 changes in reproductive activity, temperature and potentially predation
 risk; yet temporal variation in colour change has seldom been examined. We
 measured colour change in spring and autumn using captive individuals from
 two differently coloured populations of the central bearded dragon lizard,
 Pogona vitticeps. We predicted that colour change should be greater in
 spring than autumn due to added requirements of reproductive and
 territorial activity. To elicit colour change in a standardised way, we
 placed lizards inside temperature controlled chambers and measured colour
 at 15, 25, 35 and 40°C, repeating experiments in spring and autumn.
 Lizards from both populations changed from dark grey to light yellowish or
 orange-brown (increasing luminance and saturation) with increasing
 temperature in both seasons, and both populations changed colour to a
 similar extent. As predicted, the maximum extent of temperature-induced
 colour change (in particular luminance change) was greater in spring than
 autumn. Our results confirm that temperature-induced colour change is
 greater in the peak activity season, likely an adaptation to the greater
 thermal and/or signalling needs of that time of year.
description: Hue, chroma and
 luminance measures and calculationsThis dataset provides
 RGB measurements obtained from linearised and equalised photographs of
 lizards taken remotely during the temperature-dependent experiments. Also
 provides linearisation parameters and describes how these were applied to
 raw values. README included as a tab.HueChromaLuminance_values+parameters.xlsx
DOI: 10.15468/dl.t79a9w
title: Occurrence Download

description: A dataset containing 545 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Leptodeira septentrionalis",
 "Year 1960-2026"
 ]
}

 The dataset includes 545 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000742-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5bv61
title: Data from: Global patterns of insect herbivory in gap and understorey environments, and their implications for woody plant carbon storage

description: Insect herbivory is thought to favour carbon allocation to storage in
 juveniles of shade-tolerant trees. This argument assumes that insect
 herbivory in the understorey is sufficiently intense as to select for
 storage; however, understoreys might be less attractive to insect
 herbivores than canopy gaps, because of low resource availability and—at
 temperate latitudes—low temperatures. Although empirical studies show that
 shade-tolerant species in tropical forests do allocate more photosynthate
 to storage than their light-demanding associates, the same pattern has not
 been consistently observed in temperate forests. Does this reflect a
 latitudinal trend in the relative activity of insect herbivory in gap
 versus understorey environments? To date there has been no global review
 of the effect of light environment on insect herbivory in forests. We
 postulated that if temperature is the primary factor limiting insect
 herbivory, the effect of gaps on rates of insect herbivory should be more
 evident in temperate than in tropical forests; due to low growing season
 temperatures in the oceanic temperate forests of the southern hemisphere,
 the effect of gaps on insect herbivory rates should in turn be stronger
 there than in the more continental temperate climates of the northern
 hemisphere. We examined global patterns of insect herbivory in gaps versus
 understories through meta-analysis of 88 conspecific comparisons of leaf
 damage in contrasting light environments. Overall, insect herbivory in
 gaps was significantly higher than in the understorey; insect herbivory
 was 50% higher in gaps than in understoreys of tropical forests but did
 not differ significantly between gaps and understories in temperate
 forests of either hemisphere. Results are consistent with the idea that
 low resource availability –and not temperature– limits insect herbivore
 activity in forest understoreys, especially in the tropics, and suggest
 the selective influence of insect herbivory on late-successional tree
 species may have been over-estimated.
description: Size effects data for
 DRYADExcel file with original
 data used in the meta-analysis. These data were either digitalized or
 directly extracted from tables or text.Size effects metanalisis data
 for DRYAD.xlsx
DOI: 10.5061/dryad.25sg7
title: Data from: Costly infidelity: low lifetime fitness of extra-pair offspring in a passerine bird

description: Extra-pair copulation (EPC) is widespread in socially monogamous species,
 but its evolutionary benefits remain controversial. Indirect genetic
 benefit hypotheses postulate that females engage in EPC to produce higher
 quality extra-pair offspring (EPO) than within-pair offspring (WPO). In
 contrast, the sexual conflict hypothesis posits that EPC is beneficial to
 males but not to females. Thus, under the sexual conflict hypothesis, EPO
 are predicted to be no fitter than WPO. We tested these two hypotheses
 with a 12 years dataset with complete life-history and pedigree
 information from an isolated island population of house sparrows (Passer
 domesticus). We compared fitness components of EPO and two types of WPO:
 (1) WPO from genetically polyandrous “unfaithful” mothers, and (2) WPO
 from genetically monogamous mothers. We found that all three groups of
 offspring had similar probabilities of hatching and nestling survival.
 Unexpectedly, EPO had the lowest probability of recruiting into the
 breeding population and the lowest lifetime reproductive output. Our
 results indicate that EPO incurred indirect genetic costs, rather than
 benefits, which is contrary to indirect benefit models. Importantly, the
 indirect costs we observed are also underappreciated in current sexual
 conflict models. Our results call for improved theoretical frameworks that
 incorporate indirect costs by extending current sexual conflict models.
description: Data for Costly
 Infedility in EvolutionThis is the data file
 included the data used in the article "Costly infidelity: Low
 lifetime fitness of extra-pair offspring in a passerine bird" in
 EvolutionDataToProvide_Evolution_13-0897.R2.csv
DOI: 10.15468/dl.tyx5jz
title: Occurrence Download

description: A dataset listing the 7 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "Geometry POLYGON((-73.15612 -41.43361,-71.07766 -41.43361,-71.07766 -38.92272,-73.15612 -38.92272,-73.15612 -41.43361))",
 "TaxonKey is Galium"
 ]
}

 The dataset's 7 records were derived from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000731-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b4p43t7
title: Data from: Multi-modal signal evolution in birds: re-examining a standard proxy for sexual selection

description: Sexual selection is proposed to be an important driver of speciation and
 phenotypic diversification in animal systems. However, previous
 phylogenetic tests have produced conflicting results, perhaps because they
 have focused on a single signalling modality (visual ornaments), whereas
 sexual selection may act on alternative signalling modalities (e.g.
 acoustic ornaments). Here we compile phenotypic data from 259 avian sister
 species pairs to assess the relationship between visible plumage
 dichromatism—a standard index of sexual selection in birds—and
 macroevolutionary divergence in the other major avian signalling modality:
 song. We find evidence for a strong negative relationship between the
 degree of plumage dichromatism and divergence in song traits, which
 remains significant even when accounting for other key factors, including
 habitat type, ecological divergence and interspecific interactions. This
 negative relationship is opposite to the pattern expected by a
 straightforward interpretation of the sexual selection-diversification
 hypothesis, whereby higher levels of dichromatism indicating strong sexual
 selection should be related to greater levels of mating signal divergence
 regardless of signalling modality. Our findings imply a ‘trade-off’
 between the elaboration of visual ornaments and the diversification of
 acoustic mating signals, and suggest that the effects of sexual selection
 on diversification can only be determined by considering multiple
 alternative signalling modalities.
description: Dataset from Cooney et
 al "Re-examining a standard proxy for sexual selection: plumage
 dichromatism is negatively correlated with song divergence in passerine
 birds"Dataset_Cooney_etal.xlsxPhylogeny from Cooney et al "Re-examining a standard proxy for sexual selection: plumage dichromatism is negatively correlated with song divergence in passerine birds"Phylogeny_Cooney_etal.tre
DOI: 10.5061/dryad.cs80878
title: Data from: Bacterial communities associated with honeybee food stores are correlated with land use

description: Microbial communities, associated with almost all metazoans, can be
 inherited from the environment. Although the honeybee (Apis mellifera L.)
 gut microbiome is well documented, studies of the gut focus on just a
 small component of the bee microbiome. Other key areas such as the comb,
 propolis, honey, and stored pollen (bee bread) are poorly understood.
 Furthermore, little is known about the relationship between the pollinator
 microbiome and its environment. Here we present a study of the bee bread
 microbiome and its relationship with land use. We estimated bacterial
 community composition using both Illumina MiSeq DNA sequencing and
 denaturing gradient gel electrophoresis (DGGE). Illumina was used to gain
 a deeper understanding of precise species diversity across samples. DGGE
 was used on a larger number of samples where the costs of MiSeq had become
 prohibitive and therefore allowed us to study a greater number of bee
 breads across broader geographical axes. The former demonstrates bee bread
 comprises, on average, 13 distinct bacterial phyla; Bacteroidetes,
 Firmicutes, Alpha‐proteobacteria, Beta‐proteobacteria, and
 Gamma‐proteobacteria were the five most abundant. The most common genera
 were Pseudomonas, Arsenophonus, Lactobacillus, Erwinia, and Acinetobacter.
 DGGE data show bacterial community composition and diversity varied
 spatially and temporally both within and between hives. Land use data were
 obtained from the 2007 Countryside Survey. Certain habitats, such as
 improved grasslands, are associated with low diversity bee breads, meaning
 that these environments may be poor sources of bee‐associated bacteria.
 Decreased bee bread bacterial diversity may result in reduced function
 within hives. Although the dispersal of microbes is ubiquitous, this study
 has demonstrated landscape‐level effects on microbial community
 composition.
description: BB
 bacteriaR scripts and associated
 data files for statistical analysis of bee bread bacterial
 composition.
DOI: 10.5061/dryad.8gt6m3m4
title: Data from: Temperature, size, reproductive allocation, and life-history evolution in a gregarious caterpillar

description: The present study aimed to investigate the relation between growth rate,
 final mass and larval development, and how this relations influence the
 reproductive trade-offs in the context of a gregarious life-style and the
 need to keep an optimal group size. We use as model two sympatric
 populations of the pine processionary moth Thaumetopoea pityocampa,
 occurring in different seasons and thus experiencing different climatic
 conditions. T. pityocampa is a strictly gregarious caterpillar throughout
 the larval period, which occurs during winter in countries all over the
 Mediterranean Basin. However in 1997 a population, in which larval
 development occurs during the summer, was discovered in Portugal, being
 called Summer Population SP, as opposed to the normal Winter Population
 WP, which coexists in the same forest feeding on the same host during the
 winter. Both this populations were monitored during three years, with
 assessment of the length of the larval period and its relation with
 different climatic variables, final mass and adult size, egg size and
 number, colony size, and mortality in different life stages. The SP larval
 period was reduced due to development in the warmer part of the year,
 however reaching the same final mass and adult size as the WP. In spite of
 equal size at maturity, a trade-off between egg size and number was found
 between the two populations: SP produced less but bigger eggs than WP.
 This is the opposite of what is generally found in other Lepidoptera
 species, where development in colder environments leads to larger eggs at
 the expense of fecundity, but corroborates the trend found at a
 macro-geographic scale for T. pityocampa, with females from northern
 latitudes and colder environment, producing more and smaller eggs. Results
 point to the importance of number of eggs in cold environments due to an
 advantage of large colonies when gregarious caterpillars develop in such
 environments, and are discussed according to the major theories regarding
 size in animals.
description: bij_1794_metadataData collected in field and laboratory. See readme file for explanation.
DOI: 10.5061/dryad.3mr46n0
title: Data from: Effects of host species and environmental factors on the prevalence of Batrachochytrium dendrobatidis in northern Europe

description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) poses a major
 threat to amphibian populations. To assist efforts to address such
 threats, we examined differences in Bd host infection prevalence among
 amphibian species and its relations to both local environmental factors in
 breeding habitats and landscape variables measured at three scales (500,
 2000 and 5000 m radii) around breeding sites in southernmost Sweden. We
 sampled 947 anurans of six species in 31 ponds and assessed their
 infection status. We then examined correlations of infection prevalence
 with canopy cover, pond perimeter and pH (treated as local-scale pond
 characteristics), and the number of ponds, area of arable land, area of
 mature forest, number of resident people and presence of sea within the
 three radii (treated as landscape variables). The Bd infection prevalence
 was very low, 0.5-1.0%, in two of the six anuran species (Bufo bufo and
 Rana temporaria), and substantially higher (13-64%) in the other four
 (Bombina bombina, Bufotes variabilis, Epidalea calamita, Rana arvalis). In
 the latter four species Bd infection prevalence was positively associated
 with ponds’ pH (site range: 5.3-8.1), and negatively associated with areas
 of mature forest and/or wetlands in the surroundings. Our results show
 that the infection dynamics of Bd are complex and associated with host
 species, local pond characteristics and several landscape variables at
 larger spatial scales. Knowledge of environmental factors associated with
 Bd infections and differences in species’ susceptibility may help to
 counter further spread of the disease and guide conservation action plans,
 especially for the most threatened species.
description: BDind: Site, amphibian
 species, local and landscape dataBDind.txt