cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3b4d8
title: Data from: Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster.

description: When ectotherms are exposed to low temperatures, they enter a cold-induced
 coma (chill coma) that prevents resource acquisition, mating, oviposition,
 and escape from predation. There is substantial variation in time taken to
 recover from chill coma both within and among species, and this variation
 is correlated with habitat temperatures such that insects from cold
 environments recover more quickly. This suggests an adaptive response, but
 the mechanisms underlying variation in recovery times are unknown, making
 it difficult to decisively test adaptive hypotheses. We use replicated
 lines of Drosophila melanogaster selected in the laboratory for fast
 (hardy) or slow (susceptible) chill-coma recovery times to investigate
 modifications to metabolic profiles associated with cold adaptation. We
 measured metabolite concentrations of flies before, during, and after cold
 exposure using NMR spectroscopy to test the hypotheses that hardy flies
 maintain metabolic homeostasis better during cold exposure and recovery,
 and that their metabolic networks are more robust to cold-induced
 perturbations. The metabolites of cold-hardy flies were less cold
 responsive and their metabolic networks during cold exposure were more
 robust, supporting our hypotheses. Metabolites involved in membrane lipid
 synthesis, tryptophan metabolism, oxidative stress, energy balance, and
 proline metabolism were altered by selection on cold tolerance. We discuss
 the potential significance of these alterations.
description: Chill coma recovery time
 for cold-hardy and susceptible fliesChill coma recovery
 times assayed on the day metabolomics samples were collected for the
 experiments.CCR
 times.xlsx
DOI: 10.5061/dryad.h373j
title: Data from: Recognizing false positives: synthetic oligonucleotide controls for environmental DNA surveillance

description: Environmental DNA (eDNA) is increasingly used for surveillance and
 detection of species of interest in aquatic and soil samples. A
 significant risk associated with eDNA methods is potential false positive
 results due to laboratory contamination. To minimize and quantify this
 risk, we designed and validated a set of synthetic oligonucleotides for
 use as species-specific positive PCR controls for several high-profile
 aquatic invasive species. The controls consist of species-specific
 sequences for the species of interest, with the addition of a synthetic
 insert containing recognition sites for several restriction enzymes.
 Following PCR, the presence of the synthetic insert can be detected using
 gel electrophoresis, restriction enzyme digests, or DNA sequencing. For
 quantitative PCR (qPCR), false positives in environmental samples can also
 be detected using a fluorescent probe designed to detect the synthetic
 insert. The generation of synthetic controls is a cost-effective,
 reproducible method that increases the power and reliability of eDNA
 testing by eliminating misinterpretation of false positive results from
 laboratory contamination.
description: Asian carp qPCR
 detection sensitivityEach worksheet shows the
 qPCR threshold cycle (mean and standard deviation based on six replicates)
 for detection of biological and synthetic targets for a species of Asian
 carp [bighead carp (Hypophthalmichthys nobilis), silver carp (H.
 molitrix), and grass carp (Ctenopharyngodon idella)] based on biological
 reference samples and synthetic positive controls.Asian_carp_synthetic_control_sensitivity_qPCR_results.xlsx
DOI: 10.5061/dryad.2bj8g
title: Data from: Unravelling anisogamy: egg size and ejaculate size mediate selection on morphology in free-swimming sperm

description: Gamete dimorphism (anisogamy) defines the sexes in most multicellular
 organisms. Theoretical explanations for its maintenance usually emphasize
 the size-related selection pressures of sperm competition and zygote
 survival, assuming that fertilization of all eggs precludes selection for
 phenotypes that enhance fertility. In external fertilizers, however,
 fertilization is often incomplete due to sperm limitation, and the risk of
 polyspermy weakens the advantage of high sperm numbers that is predicted
 to limit sperm size, allowing alternative selection pressures to target
 free-swimming sperm. We asked whether egg size and ejaculate size mediate
 selection on the free-swimming sperm of Galeolaria caespitosa, a marine
 tubeworm with external fertilization, by comparing relationships between
 sperm morphology and male fertility across manipulations of egg size and
 sperm density. Our results suggest that selection pressures exerted by
 these factors may aid the maintenance of anisogamy in external fertilizers
 by limiting the adaptive value of larger sperm in the absence of
 competition. In doing so, our study offers a more complete explanation for
 the stability of anisogamy across the range of sperm environments typical
 of this mating system and identifies new potential for the sexes to
 coevolve via mutual selection pressures exerted by gametes at
 fertilization.
description: fertsuccessdryad.csv
DOI: 10.5061/dryad.55062
title: Data from: Multi-functional crest display in hoopoes Upupa epops

description: Animals can engage in visual displays, which may target conspecifics,
 heterospecifics or both. Here we studied the function of the flamboyant
 crest-raising display of hoopoes (Upupa epops) in experiments performed
 with males in captivity. Males were exposed to sounds of a conspecific
 (male hoopoe song), a potential predator (human voice), and two controls
 (the song of a blackbird, Turdus merula, and background noise). These
 stimuli were presented to males in the presence and absence of females.
 Males raised the crest with a significantly higher probability when
 confronted with stimuli indicating potential threats (rival mate or
 predator) than with controls. The crest display was frequent when
 confronted with both kinds of threats independently of the presence of a
 female, suggesting that it was directed to the predator and the rival
 male. The probability of raising the crest was not related to body
 condition, and there was a marginally but not significant negative
 relationship between probability of raising the crest and the number of
 black spots on the crest feathers, which may suggest that crest display
 could be informing about male quality. Therefore, male hoopoes display the
 crest in a heterospecific context in response to detection of potential
 threats, which could be a deceptive or pursuit-deterrent signal. The
 results also support a role of the crest in sexual selection, suggesting
 that crest display in male hoopoes may serve multiple functions.
description: experiment results
 hoopoe crest displayResults of experiments
 in which different sounds were played to male hoopoes in the presence and
 absence of females. Results show the crest display behaviour as a response
 to different stimuli.Data
 Dryad.xlsx
DOI: 10.34810/data2815
title: Replication Data for: "CheShImP: Democratising Magnetic Resonance Spectroscopic Imaging Data Processing"

description: MRI images (proton and chemical shift) data extracted from a Bruker 3T BioSpec system using ParaVision 360 V3.4 and processed CSI and EPSI spectroscopic images corresponding to the validation of an automated platform to process MRI chemical shift images (CheShImP). We assessed the platform on unfertilised chicken eggs, a male mice and microfluidic platforms. We evaluated both proton (1H) and carbon (13C) spectroscopy, as well as enzymatic reactions. Hence, this data provides examples to process using CheShImP (developed in MATLAB), an easy-to-use, open-source platform as well as how to handle the output data from the platform using common Python code. To access the software presented in this work and explanation documentation on how to use it, access the GitHub repository https://github.com/DavidGomezCabeza/CheShImP.
DOI: 10.5061/dryad.8t581
title: Data from: Winter food limits timing of pre-alternate molt in a short-distance migratory bird

description: 1. Molt is critical for fitness for many organisms for several reasons: it
 allows growth and maintains the function of the integument for protection,
 thermoregulation and communication. 2. Feather molt in birds is costly and
 therefore typically does not overlap with migration or reproduction. In
 spring, the rapid succession of pre-alternate molt, migration (if a
 migrant), and breeding suggests that timing of molt could constrain the
 initiation of breeding. A tradeoff between time spent molting and breeding
 might also limit molt quality. 3. The proximate basis for the timing of
 pre-alternate molt initiation is not well known, though it typically
 occurs during a resource poor time of year. Food limitation combined with
 fitness consequences of molting earlier suggests that plasticity in timing
 of pre-alternate molt in response to food abundance should be
 advantageous. 4. We experimentally tested, for the first time, if food
 abundance influences the timing of molt in the wild. We conducted a
 controlled food supplementation experiment on free-living swamp sparrows
 (Melospiza georgiana) preceding and during the time of natural
 pre-alternate molt (January–March 2009, 2010). 5. Supplemented birds began
 molting the body, face, and crown earlier than control birds (11, 14, and
 8 days earlier, respectively) indicating that food abundance limits the
 initiation of molt. Along with interannual variation, these results
 indicate that photoperiod is not the sole cue for initiation of molt. 6.
 Both control and supplemented birds molted in sequence, starting with the
 body, followed by the crown 9 days later, and the face 11 days after the
 body. The presence of a sequence further suggests energetic limitation of
 molt or possibly a strategy to molt specific regions first to ensure
 completion or at an optimal time. 7. This study provides novel
 experimental evidence that food abundance can: i) limit pre-alternate molt
 timing and ii) limit molt timing in the wild. Food limitation of molt
 timing could allow earlier breeding or production of higher quality
 feathers, and thus cascade through other life history stages and affect
 reproductive success. These results indicate that food availability is a
 cue for molt initiation, possibly acting secondarily to photostimulation.
description: Swamp sparrow
 prealternate molt timing dataMolt initiation date,
 sex, age, and treatment for all swamp sparrows (Melospiza georgiana) used
 in the study.
DOI: 10.5061/dryad.9fg8m
title: Data from: Polyspermy in birds: sperm numbers and embryo survival

description: Polyspermy is a major puzzle in reproductive biology. In some taxa,
 multiple sperm enter the ovum as part of the normal fertilisation process,
 while in others, penetration of the ovum by more than one sperm is lethal.
 In birds, several sperm typically enter the germinal disc, yet only one
 fuses with the female pronucleus. It is unclear whether supernumerary
 sperm play an essential role in the avian fertilisation process and, if
 they do, how females regulate the progression of sperm through the oviduct
 to ensure an appropriate number reach the ovum. Here we show that when
 very few sperm penetrate the avian ovum, embryos are unlikely to survive
 beyond the earliest stages of development. We also show that when the
 number of inseminated sperm is limited, a greater proportion than expected
 progresses to the site of fertilisation, indicating that females
 compensate for low sperm numbers in the oviduct. Our results confirm an
 essential role for supernumerary sperm in the processes of fertilisation
 and early embryogenesis, providing an exciting expansion of our
 understanding of sperm function in birds.
description: Domestic fowl embryo
 survival dataEmbryo survival data for
 domestic fowl inseminated with either high or low sperm numbers dose.
 Includes fertile eggs only.dom fowl embryo surv_fertilised
 eggs only.csvDomestic fowl
 fertilisation success dataFertilisation success
 data for domestic fowl inseminated with either high or low sperm numbers.
 Includes only eggs penetrated by at least one sperm.dom fowl fertilisation
 success.csvDomestic fowl sperm
 numbers dataData on the number of
 sperm reaching the ovum after inseminations with either high or low sperm
 numbers in domestic fowl.dom fowl sperm
 numbers.csvZebra finch embryo
 survival dataEmbryo survival data for
 zebra finches after either natural (high) or artificial (low)
 inseminations. Includes fertile eggs only.zf embryo surv_fertilised eggs
 only.csvZebra finch
 fertilisation success dataFertilisation success
 data for zebra finches after natural (high) and artificial (low)
 inseminations. Includes only eggs penetrated by at least one
 sperm.zf
 fertilisation success.csvZebra finch sperm
 numbers dataData on the number of
 sperm reaching the ovum after natural (high) and artificial (low)
 inseminations in the zebra finch. Data include only eggs that were reached
 by at least one sperm.zf sperm
 numbers.csv
DOI: 10.5061/dryad.p0mf1
title: Data from: Evidence for an optimal level of connectivity for establishment and colonization

description: Dispersal is usually associated with the spread of invasive species, but
 it also has two opposing effects, one decreasing and the other increasing
 the probability of establishment. Indeed, dispersal both slows population
 growth at the site of introduction and increases the likelihood of
 surrounding habitat being colonised. The connectivity of the introduction
 site is likely to affect dispersal, and, thus, establishment, according to
 the dispersal behaviour of individuals. Using individual-based models and
 microcosm experiments on minute wasps, we demonstrated the existence of a
 hump-shaped relationship between connectivity and establishment in
 situations in which individual dispersal resembled a diffusion process.
 These results suggest that there is an optimal level of connectivity for
 the establishment of introduced populations locally at the site of
 introduction, and regionally over the whole landscape.
description: Simulation
 scriptR script used to
 simulate the invasion data used in the study.Simulaion_script.RExperimental dataExperimental data of the invasions of T.chilonis performed for this study.Experimental_data (3).txt
DOI: 10.5061/dryad.8j28r94
title: Data from: Persistently rare species experience stronger negative frequency dependence than common species: a statistical attractor that is hard to avoid

description: Aim: Why are so many species rare, yet persistent? Possibly, rare species
 experience strong negative frequency dependence (NFD, i.e. strong
 intraspecific competition relative to interspecific competition), which
 both makes them rare and buffers them against extinction. A second, not
 mutually exclusive, possibility is that rare species that experience weak
 NFD go extinct quickly due to demographic and environmental stochasticity.
 Both possibilities predict that persistent rare species will experience
 stronger NFD than common ones. Yenni et al. (2017) confirmed this
 prediction in a range of mostly-terrestrial communities. Here we test that
 prediction in lake zooplankton, and explore its theoretical basis.
 Location: 53 temperate lakes Time period: 1970-2011 Major taxa studied:
 Cladocerans, copepods Methods: We used long-term time series data to
 estimate the covariance between strength of NFD and mean frequency
 (relative abundance) for crustacean zooplankton. We used a randomization
 test to ask whether the covariance between NFD and mean frequency is
 stronger than expected, given sampling error. We also calculated the
 covariance between NFD and mean frequency in simulated communities from
 three different ecological models. Results: Rare species experience
 significantly stronger NFD than common species in over half of the
 communities. The distribution of associations between NFD and rarity is
 skewed towards weak associations, which always occur in communities with
 high evenness. All three theoretical models reproduce these empirical
 results, even though they are based on different mechanisms (demographic
 or environmental stochasticity, and mathematical constraints on possible
 NFD-frequency relationships). Main conclusions: Rare species typically
 experience stronger NFD than common ones because there are many different
 ecological scenarios in which they will do so, and only a few scenarios in
 which they won't. Like several other macroecological patterns, the
 tendency for rare species to experience stronger NFD than common ones is a
 "statistical attractor" that is hard to avoid.
description: R code for theoretical
 modelsR code to simulate the
 three stochastic ecological models described in the associated paper.
 Contact Jeremy Fox (jefox@ucalgary.ca) with questions.models of rarity and NFD - for
 GEB.Rempirical results
 summaryComma-delimited text
 file summarizing the empirical results. Each row gives data for one site.
 Variables are Lake.ID (unique identifier for each site), cov.NFD.freq
 (covariance between log-transformed strength of negative frequency
 dependence and log-transformed mean frequency), richness (the number of
 species included in the analysis), and gini (the Gini coefficient, a
 measure of the evenness of species' frequencies). Contact Jeremy Fox
 with questions (jefox@ucalgary.ca).zoop results
 summary.csv
DOI: 10.5061/dryad.7tc36
title: Data from: Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer

description: There is increasing evidence showing that microbes can influence
 plant-insect interactions. In addition, various studies have shown that
 aboveground pathogens can alter the interactions between plants and
 insects. However, little is known about the role of soil-borne pathogens
 in plant-insect interactions. It is also not known how environmental
 conditions, that steer the performance of soil-borne pathogens, might
 influence these microbe-plant-insect interactions. Here, we studied
 effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion
 avenae) using wheat (Triticum aestivum) as a host. In a greenhouse
 experiment, we tested how different levels of soil organic matter (SOM)
 and fertilizer addition influence the interactions between plants and
 aphids. To examine the influence of the existing soil microbiome on the
 pathogen effects, we used both unsterilized field soil and sterilized
 field soil. In unsterilized soil with low SOM content, R. solani addition
 had a negative effect on aphid biomass, whereas it enhanced aphid biomass
 in soil with high SOM content. In sterilized soil, however, aphid biomass
 was enhanced by R. solani addition and by high SOM content. Plant biomass
 was enhanced by fertilizer addition, but only when SOM content was low, or
 in the absence of R. solani. We conclude that belowground pathogens
 influence aphid performance and that the effect of soil pathogens on
 aphids can be more positive in the absence of a soil microbiome. This
 implies that experiments studying the effect of pathogens under sterile
 conditions might not represent realistic interactions. Moreover,
 pathogen-plant-aphid interactions can be more positive for aphids under
 high SOM conditions. We recommend that soil conditions should be taken
 into account in the study of microbe-plant-insect interactions.
description: Dataset
DOI: 10.5061/dryad.7751k
title: Data from: Local adaptation within a hybrid species

description: Ecological divergence among populations may be strongly influenced by
 their genetic background. For instance, genetic admixture through
 introgressive hybridization or hybrid speciation is likely to affect the
 genetic variation and evolvability of phenotypic traits. We studied
 geographic variation in two beak dimensions and three other phenotypic
 traits of the Italian sparrow (Passer italiae), a young hybrid species
 formed through interbreeding between house sparrows (P. domesticus) and
 Spanish sparrows (P. hispaniolensis). We found that beak morphology was
 strongly influenced by precipitation regimes and that it appeared to be
 the target of divergent selection within Italian sparrows. Interestingly,
 however, the degree of parental genetic contribution in the hybrid species
 had no effect on phenotypic beak variation. Moreover, beak height
 divergence may mediate genetic differentiation between populations,
 consistent with isolation-by-adaptation within this hybrid species. The
 study illustrates how hybrid species may be relatively unconstrained by
 their admixed genetic background, allowing them to adapt rapidly to
 environmental variation.
description: DRYAD
 HEREDITYMorphological, Genetic
 and climatic estimates for the study populations
DOI: 10.5061/dryad.bt6p645
title: Data from: Variations in the glucosinolates of the individual edible parts of three stem mustards (Brassica juncea)

description: The composition and content of glucosinolates were investigated in the
 edible parts (petioles, peel, and flesh) of tuber mustard, bamboo shoots
 mustard, and baby mustard by high performance liquid chromatography to
 reveal the association between the different cooking methods and their
 glucosinolate profiles. Eight glucosinolates were identified from tuber
 mustard and baby mustard, including three aliphatic glucosinolates, four
 indole glucosinolates, and one aromatic glucosinolate. Only six of the
 eight glucosinolates were detected in bamboo shoots mustard. The results
 show that the distribution and content of glucosinolates varied widely
 among the different tissues and species. The highest contents of
 glucosinolates in tuber mustard, bamboo shoots mustard, and baby mustard
 were found in flesh, petioles, and peel, respectively. The content of
 total glucosinolates ranged from 5.21 μmol/g dry weight in bamboo shoots
 mustard flesh to 25.64 μmol/g dry weight in baby mustard peel. Aliphatic
 glucosinolates were predominant in the three stem mustards, followed by
 indole and aromatic glucosinolates. Sinigrin was the predominant
 glucosinolate in the three stem mustards. Sinigrin content in tuber
 mustard was slightly higher than that in baby mustard and much higher than
 that in bamboo shoots mustard, suggesting that the pungent-tasting stem
 mustards contained more sinigrin. In addition, a principal components
 analysis showed that bamboo shoots mustard was distinguishable from the
 other two stem mustards. A variance analysis indicated that the
 glucosinolates were primarily influenced by a species × tissue
 interaction. The correlations among glucosinolates were also analyzed.
description: RSOS-182054--Raw
 Data