cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.538044t
title: Data from: Long term effects of superoxide and DNA repair on lizard telomeres

description: Telomeres are the non-coding protein-nucleotide ‘caps’ at chromosome ends
 that contribute to chromosomal stability by protecting the coding parts of
 the linear DNA from shortening at cell division, and from erosion by
 reactive molecules. Recently, there has been some controversy between
 molecular and cell biologists, on the one hand, and evolutionary
 ecologists on the other, regarding whether reactive molecules erode
 telomeres during oxidative stress. Many studies of biochemistry and
 medicine have verified these relationships in cell culture, but other
 researchers have failed to find such effects in free-living vertebrates.
 Here we use a novel approach to measure free radicals (superoxide),
 mitochondrial ‘content’ (a combined measure of mitochondrial number and
 size in cells), telomere length and DNA damage at two primary time points
 during the mating season of an annual lizard species (Ctenophorus pictus).
 Superoxide levels early in the mating season vary widely and elevated
 levels predict shorter telomeres both at that time as well as several
 months later. These effects are likely driven by mitochondrial content,
 which significantly impacts late season superoxide (cells with more
 mitochondria have more superoxide), but superoxide effects on telomeres
 are counteracted by DNA repair as revealed by 8-hydroxy-2’-deoxyguanosine
 assays. We conclude that reactive oxygen species and DNA repair are
 fundamental for both short- and long-term regulation of lizard telomere
 length with pronounced effects of early-season cellular stress detectable
 on telomere length near lizard death.
description: Olsson et al.Long Term
 effects of SuperoxideTelomere and reactive
 oxygen species data
DOI: 10.5061/dryad.1j833
title: Data from: Genetic relatedness influences plant biomass accumulation in eelgrass (Zostera marina)

description: In multispecies assemblages, phylogenetic relatedness often predicts total
 community biomass. In assemblages dominated by a single species,
 increasing the number of genotypes increases total production, but the
 role of genetic relatedness is unknown. We used data from three published
 experiments and a field survey of eelgrass (Zostera marina), a
 habitat-forming marine angiosperm, to examine the strength and direction
 of the relationship between genetic relatedness and plant biomass. The
 genetic relatedness of an assemblage strongly predicted its biomass, more
 so than the number of genotypes. However, contrary to the pattern observed
 in multispecies assemblages, maximum biomass occurred in assemblages of
 more closely related individuals. The mechanisms underlying this pattern
 remain unclear; however, our data support a role for both trait
 differentiation and cooperation among kin. Many habitat-forming species
 interact intensely with conspecifics of varying relatedness; thus, genetic
 relatedness could influence the functioning of ecosystems dominated by
 such species.
description: Plot level data used in
 all analyses of the relationship between Zostera relatedness and plant
 biomassAll data were field
 collected and represent biomass and trait data collected from our previous
 work cited in this paper.Data_for_AmNat.xls
DOI: 10.5061/dryad.8809
title: Data from: Differential maternal testosterone allocation among siblings benefits both mother and offspring in the Zebra Finch Taeniopygia guttata

description: Parents are selected to preferentially invest in the offspring with
 highest reproductive value. One mechanism to achieve this is the
 modification of competitive asymmetries between siblings by maternal
 hormones. In many organisms, offspring value varies according to birth
 position in the brood, which determines survival chances and competitive
 advantage over access to resources. In birds, variation in yolk androgen
 allocation over the laying sequence is thought to modulate dominance of
 senior chicks over junior brood mates. We tested this hypothesis in zebra
 finches, which show a natural decreasing pattern of within-clutch
 testosterone allocation. We abolished these within-clutch differences by
 experimentally elevating yolk testosterone levels in eggs 2-6 up to the
 level of the egg 1, and assessed fitness measures for junior (eggs 2-6)
 and senior (egg 1) offspring, and their mothers. T-injected eggs hatched
 later than control eggs. Junior but not senior chicks in T broods attained
 poorer phenotypic quality compared with control broods, which was not
 compensated by positive effects on seniors. Mothers were generally
 unaffected by clutch treatment. Thus, naturally decreasing within-clutch
 yolk testosterone allocation appears to benefit all family members, and
 does not generally enhance brood reduction by favoring senior chicks, in
 contrast to widely held assumption.
description: Boncoraglio et al
 database Dryad fileOriginal data collected
 in the lab. File created with Excel 2003. No abbreviations used for column
 headings.
DOI: 10.15468/dl.r763jb
title: Occurrence Download

description: A dataset containing 540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizocodon ilicifolius",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 540 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001149-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.03jd7
title: Data from: Genetic differentiation in the stingless bee, Scaptotrigona xanthotricha Moure, 1950 (Apidae, Meliponini): a species with wide geographic distribution in the Atlantic rainforest

description: Stingless bees are important pollinators that are severely threatened by
 anthropic interference, resulting in a strong population decline.
 Scaptotrigona xanthotricha has a wide distribution in the Atlantic
 Rainforest, ranging from the northeastern state of Bahia to Santa Catarina
 in southern Brazil. To understand the genetic structure of S.
 xanthotricha, 12 species-specific microsatellite loci were analyzed in 42
 colonies sampled throughout the species range. The results indicated 5
 distinct clusters throughout the sampled area with high rates of genetic
 diversity, and the greatest diversity was found in southern Bahia. Greater
 differentiation was observed between samples from the extremes of the
 distribution, with an F ST value of 0.189 between cluster 1 and 5. The
 genetic differentiation analysis for all loci had an F ST value of 0.113,
 a result that is consistent with the analysis of molecular variance, which
 revealed 7.72% of the variation occurring between groups. The Mantel
 correlation between a genetic differentiation matrix and a geographic
 distance matrix (r = 0.184, P = 0.043) indicated a tendency toward
 increased differentiation with increased distance. This study revealed the
 profile of differentiation and distribution of genetic diversity in this
 species and indicates parameters that should be considered in future
 taxonomic revisions and activities for its management and conservation.
description: Scaptotrigona
 Genotypes
DOI: 10.5061/dryad.km646
title: Data from: Adult mortality probability and nest predation rates explain parental effort in warming eggs with consequences for embryonic development time

description: Parental behavior and effort vary extensively among species. Life history
 theory suggests that age-specific mortality could cause this interspecific
 variation, but past tests have focused on fecundity as the measure of
 parental effort. Fecundity can cause costs of reproduction that confuse
 whether mortality is the cause or consequence of parental effort. We focus
 on a trait, parental time and effort in warming embryos, which varies
 widely among species of diverse taxa and is not tied to fecundity. We
 conducted studies on songbirds of four continents and show that time spent
 warming eggs varies widely among species and latitudes, and is not
 correlated with clutch size. Adult and offspring (nest) mortality
 explained most of the interspecific variation in time and effort that
 parents spend warming eggs measured by average egg temperatures. Parental
 effort in warming eggs is important because embryonic temperature can
 influence embryonic development period and, hence, exposure time to
 predation risk. We show through correlative evidence and experimental
 swapping of embryos between species that parentally induced egg
 temperatures cause interspecific variation in embryonic development
 period. The strong association of age-specific mortality with parental
 effort in warming eggs and the subsequent effects on embryonic development
 time are unique results that can advance understanding of broad geographic
 patterns of life history variation.
description: Life_history_dataLife history data for songbirds on four continentsSwap_dataData for the egg swaps in South Africa
DOI: 10.5061/dryad.68b3g
title: Data from: Epigenetic mutations can both help and hinder adaptive evolution

description: Epigenetic variation is being integrated into our understanding of
 adaptation, yet we lack models on how epigenetic mutations affect
 evolution that includes de novo genetic change. We model the effects of
 epigenetic mutations on the dynamics and endpoints of adaptive walks-a
 process where a series of beneficial mutations move a population towards a
 fitness optimum. We use an individual-based model of an asexual
 population, where mutational effects are drawn from Fisher's
 geometric model. We find cases where epigenetic mutations speed adaptation
 or result in populations with higher fitness. However, we also find cases
 where they slow adaptation or result in populations with lower fitness.
 The effect of epigenetic mutations on adaptive walks depends crucially on
 their stability and fitness effects relative to genetic mutations, with
 small-effect epigenetic mutations generally speeding adaptation, and
 epigenetic mutations with the same fitness effects as genetic mutations
 slowing adaptation. Our work reveals a complex relationship between
 epigenetic mutations and natural selection and highlights the need for
 empirical data.
description: R code for simulations
 and analysisThis file contains R
 code for running the simulations described in the manuscript and some
 functions that were written to analyse the data.short_individual.r
DOI: 10.5061/dryad.b8ch0
title: Data from: Analyzing movement behavior and dynamic space-use strategies among habitats using multi-event capture-recapture modeling

description: 1.The environment of most species is heterogeneous at different spatial
 and temporal scales; this heterogeneity can have a direct effect on
 various components of fitness. As a consequence, individual space-use and
 movement strategies are central issues in ecology and conservation and
 receive considerable attention from researchers. 2.In the last 30 years,
 this issue has led to the development of capture–recapture models that
 allow movement between sites to be quantified, while handling imperfect
 detection. For studies involving numerous recapture sites in which the
 emphasis is on dispersal or migration rather than movement between
 particular sites, Lagrange et al. recently proposed a parsimonious CR
 multi-event model that contrasts individuals that move and individuals
 that stay in place, irrespective of the sites involved. 3.In this study,
 we developed a generalized version of this model to allow survival
 probability and movement probability to differ for different types of
 habitat to which the individual sites may be assigned. We investigated the
 potential of this new parameterization by studying the movements of an
 amphibian, the yellow-bellied toad (Bombina variegata), in a set of
 breeding and resting/foraging ponds. 4.Our capture-recapture multi-event
 model provides a highly flexible tool allowing users to model movements
 within and between several habitats. This approach can be potentially used
 to study movement behavior and space-use strategies of a wide range of
 taxa.
description: Capture-recapture
 dataDATA.txt
DOI: 10.5061/dryad.t6m6091
title: Data from: Behavioral thermoregulation in Locusta migratoria manilensis (Orthoptera: Acrididae) in response to the entomopathogenic fungus, Beauveria bassiana

description: Insects such as locusts and grasshoppers can reduce the effectiveness of
 pathogens and parasites by adopting different defense strategies. We
 investigated the behavioral thermopreference of Locusta migratoria
 manilensis (Meyen) (Orthoptera: Acrididae) induced by the fungus Beauveria
 bassiana, and the impact this behavior had on the fungal mycosis under
 laboratory conditions. By basking in higher temperature locations,
 infected nymphs elevated their thoracic temperature to 30-32.6 °C, which
 is higher than the optimum temperature (25°C) for B. bassiana conidial
 germination and hyphal development. A minimum thermoregulation period of 3
 h/day increased survival of infected locusts by 43.34%. The therapeutic
 effect decreased when thermoregulation was delayed after initial
 infection. The fungus grew and overcame the locusts as soon as the
 thermoregulation was interrupted, indicating that thermoregulation helped
 the insects to cope with infection but did not completely rid them of the
 fungus. A significant enhancement in the number of haemocytes was observed
 in infected thermoregulating locusts, reaching levels that were even
 higher than those observed in the controls. In contrast, haemocyte
 concentration was severely reduced in infected insects that did not
 thermoregulate. In infected non-thermoregulating locusts, the reduction in
 haemocyte number was accompanied by an increase in fungal blastospore
 concentration that was obvious in the haemolymph by day four. In contrast,
 no circulating blastospores were found in the haemolymph of infected
 thermoregulating locusts three days post-inoculation. We also examined the
 phagocytic activity of infected insects in vivo by using fluorescein
 isothiocyanate (FITC)-labelled silica beads. The proportion of beads that
 was engulfed by haemocytes in infected, thermoregulating insects was
 similar to that in the controls throughout the experiment, whereas the
 rate of phagocytosis in infected, non-thermoregulating insects
 progressively decreased after infection. These findings demonstrated that
 behavioural thermoregulation can adversely affect B. bassiana mycosis in
 infected L. migratoria manilensis, thereby limiting the development of
 lethal entomopathogenic fungi in locusts. This is apparently accomplished
 through an increase in the levels of haemocytes, leading to greater
 phagocytic activity under certain environmental conditions.
description: The data of 9 figures in
 PONE-D-18-18118Behavioral thermoregulation in
 Locusta migratoria manilensis (Orthoptera Acrididae) in response to the
 entomopathogenic fungus, Beauveria
 bassiana.xlsx
DOI: 10.5061/dryad.7pm1470
title: Data from: Age-dependent effects of predation risk on night-time hypothermia in two wintering passerine species

description: Small animals that winter at northern latitudes need to maximize energy
 intake and minimize energy loss. Many passerine birds use night-time
 hypothermia to conserve energy. A potential cost of night-time hypothermia
 with much theoretical (but little empirical) support is increased risk of
 night-time predation, due to reduced vigilance and lower escape speed in
 hypothermic birds. This idea has never been tested in the wild. We,
 therefore, increased perceived predation risk in great tits (Parus major)
 and blue tits (Cyanistes caeruleus) roosting in nest-boxes during cold
 winter nights to measure any resultant effect on their use of night-time
 hypothermia. Roosting birds of both species that experienced their first
 winter were less prone to use hypothermia as an energy-saving strategy at
 low ambient temperatures when exposed to increased perceived predation
 risk either via handling (great tits) or via predator scent manipulation
 (blue tits). However, we did not record such effects in birds that were in
 their second winter or beyond. Our results suggest that effects of
 increased predation risk are age- and temperature specific. This could be
 caused by age-related differences in experience and subsequent risk
 assessment, or by dominance-related variation in habitat quality between
 young and old birds. Predation risk could, through its effect on use and
 depth of night-time hypothermia, be important for total energy management
 and winter survival for resident birds at northern latitudes.
description: Body temperature data on
 great- and blue titsField data on body
 temperature in great- and blue tits together with all parameters used in
 the analyses. Sheet 1: great tit data, Sheet 2: blue tit data, Sheet 3:
 metadata, description of column headingsAndreassonetal2018.xlsx
DOI: 10.5061/dryad.3q7bh
title: Data from: Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?

description: Australian spiny mountain crayfish (Euastacus, Parastacidae) and their
 ecotosymbiotic temnocephalan flatworms (Temnocephalida, Platyhelminthes)
 may have co-occurred and interacted through deep time, during a period of
 major environmental change. Therefore, reconstructing the history of their
 association is of evolutionary, ecological, and conservation significance.
 Here, time-calibrated Bayesian phylogenies of Euastacus species and their
 temnocephalans (Temnohaswellia and Temnosewellia) indicate
 near-synchronous diversifications from the Cretaceous. Statistically
 significant cophylogeny correlations between associated clades suggest
 linked evolutionary histories. However, there is a stronger signal of
 codivergence and greater host specificity in Temnosewellia, which
 co-occurs with Euastacus across its range. Phylogeography and analyses of
 evolutionary distinctiveness (ED) suggest that regional differences in the
 impact of climate warming and drying had major effects both on crayfish
 and associated temnocephalans. In particular, Euastacus and Temnosewellia
 show strong latitudinal gradients in ED and, conversely, in geographical
 range size, with the most distinctive, northern lineages facing the
 greatest risk of extinction. Therefore, environmental change has, in some
 cases, strengthened ecological and evolutionary associations, leaving
 host-specific temnocephalans vulnerable to coextinction with endangered
 hosts. Consequently, the extinction of all Euastacus species currently
 endangered (75%) predicts coextinction of approximately 60% of the studied
 temnocephalans, with greatest loss of the most evolutionarily distinctive
 lineages.
description: xml_filesInput DNA sequence and methodology files for phylogenetic analysis in the program BEAST, in xml file format, for Euastacus, Temnosewellia and Temnohaswellia
DOI: 10.5061/dryad.hn66t
title: Data from: Effects of exposure to pile driving sounds on the lake sturgeon, Nile tilapia, and hogchoker

description: Pile driving and other impulsive sound sources have the potential to
 injure or kill fishes. One mechanism that produces injuries is the rapid
 motion of the walls of the swim bladder as it repeatedly contacts nearby
 tissues. To further understand the involvement of the swim bladder in
 tissue damage a specially-designed wave tube was used to expose three
 species to pile driving sounds. Species included lake sturgeon (Acipenser
 fulvecens) with an open (physoclistous) swim bladder, Nile tilapia
 (Oreochromis niloticus) with a closed (physostomous) swim bladder, and the
 hogchoker (Trinectes maculates) a flatfish without a swim bladder. There
 were no visible injuries in any of the exposed hogchokers, while a variety
 of injuries were observed in the lake sturgeon and Nile tilapia. At the
 loudest cumulative and single strike sound exposure levels, the Nile
 tilapia had the highest total injuries and the most severe injuries per
 fish. As exposure levels decreased, the number and severity of injuries
 were more similar between the two species. These results suggest that the
 presence and type of swim bladder correlated with injury at higher sound
 levels, while the extent of injury at lower sound exposure levels was
 similar for both kinds of swim bladders.
description: Data
 Sheet
DOI: 10.5061/dryad.66d5f
title: Data from: Trophic cascades in the bryosphere: The impact of global change factors on top-down control of cyanobacterial N2-fixation

description: Trophic cascades in which predatory organisms regulate organisms at lower
 trophic levels are important drivers of species dynamics, but effects of
 trophic cascades on ecosystem fluxes and processes, and the conditions
 under which top-down control is important, remain unresolved. We
 manipulated the structure of food webs in boreal mosses to show that
 moss-inhabiting microfauna exerted top-down control of N2-fixation by
 moss-associated cyanobacteria. However, organisms of higher trophic levels
 alleviated this top-down control, likely through feeding on bacterivorous
 microfauna. These effects of food web structure on cyanobacterial N2
 fixation were dependent on global change factors and strongly suppressed
 under N fertilization. Our findings illustrate how food web interactions
 and trophic cascades can regulate boreal ecosystem N cycling. In boreal
 ecosystems, carbon uptake is generally strongly N-limited, and shifting
 trophic control of N cycling under global change is therefore likely to
 impact significantly on ecosystem functioning.
description: Nitrogen fixation rates,
 moss biomass gain, and moss nitrogen gainCyanobacterial N
 fixation rates, moss biomass gain, and moss N gain in response to moss
 food-web structure, precipitation regime, and N
 addition.Data file for
 Dryad.xlsx
DOI: 10.5061/dryad.hq6c7
title: Data from: The within-host dynamics of infection in trans-generationally primed flour beetles

description: Many taxa exhibit plastic immune responses initiated after primary
 microbial exposure that provide increased protection against
 disease-induced mortality and the fitness costs of infection. In several
 arthropod species, this protection can even be passed from parents to
 offspring through a phenomenon called trans-generational immune priming.
 Here, we first demonstrate that trans-generational priming is a repeatable
 phenomenon in flour beetles (Tribolium castaneum) primed and infected with
 Bacillus thuringiensis (Bt). We then quantify the within-host dynamics of
 microbes and host physiological responses in infected offspring from
 primed and unprimed mothers by monitoring bacterial density and using
 mRNA-seq to profile host gene expression, respectively, over the acute
 infection period. We find that priming increases inducible resistance
 against Bt around a critical temporal juncture where host septicaemic
 trajectories, and consequently survival, may be determined in unprimed
 individuals. Our results identify a highly differentially expressed
 biomarker of priming, containing an EIF4-e domain, in uninfected
 individuals, as well as several other candidate genes. Moreover, the
 induction and decay dynamics of gene expression over time suggest a
 metabolic shift in primed individuals. The identified bacterial and gene
 expression dynamics are likely to influence patterns of bacterial fitness
 and disease transmission in natural populations.
description: qPCR_data_MolEcol_Feb2017The Bt density and TC009881 expression data as determined by qPCR