cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.758g8
title: Data from: Microbiome symbionts and diet diversity incur costs on the immune system of insect larvae

description: Communities of symbiotic microorganisms that colonize the gastrointestinal
 tract play an important role in food digestion and protection against
 opportunistic microbes. Diet diversity increases the number of symbionts
 in the intestines, a benefit that is considered to impose no cost for the
 host organism. However, less is known about the possible immunological
 investments that hosts have to make in order to control the infections
 caused by symbiont populations that increase due to diet diversity. By
 using taxonomical composition analysis of the 16S rRNA V3 region, we show
 that Enterococci are the dominating group of bacteria in the midgut of the
 larvae of the greater wax moth (Galleria mellonella). We found that the
 number of colony-forming units (CFU) of Enterococci and expressions of
 certain immunity-related antimicrobial peptide (AMP) genes such as
 Gallerimycin, Gloverin, 6-tox, Cecropin-D and Galiomicin increased in
 response to a more diverse diet, which in turn decreased the encapsulation
 response of the larvae. Treatment with antibiotics significantly lowered
 the expression of all AMP genes. Diet and antibiotic treatment interaction
 did not affect the expression of Gloverin and Galiomicin AMP genes, but
 significantly influenced the expression of Gallerimycin, 6-tox and
 Cecropin-D. Taken together, our results suggest that diet diversity
 influences microbiome diversity and AMP gene expression, ultimately
 affecting an organism's capacity to mount an immune response.
 Elevated basal levels of immunity-related genes (Gloverin and Galiomicin)
 might act as a prophylactic against opportunistic infections and as a
 mechanism that controls the gut symbionts. This would indicate that a
 diverse diet imposes higher immunity costs on organisms.
description: Microbiome
 JEXBIO/2017/169227 data fileJEXBIO:2017:169227.xlsx
DOI: 10.5061/dryad.5r2q8t8
title: Data from: Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts

description: While changes in the abundance of keystone predators can have cascading
 effects resulting in regime shifts, the role of mesopredators in these
 processes remains underexplored. We conducted annual surveys of rocky reef
 communities that varied in the recovery of a keystone predator (sea otters
 Enhydra lutris) and the mass mortality of a mesopredator (sunflower sea
 star Pycnopodia helianthoides) due to an infectious wasting disease. By
 fitting a population model to empirical data, we show that sea otters had
 the greatest impact on the mortality of large sea urchins, but that
 Pycnopodia decline corresponded to a 311% increase in medium urchins and a
 30% decline in kelp densities. Our results reveal predator complementarity
 in size-selective prey consumption strengthens top-down control on
 urchins, affecting the resilience of alternative reef states by
 reinforcing kelp forests and eroding urchin barrens. We reveal previously
 underappreciated species interactions within a 'classic' trophic
 cascade and regime shift, highlighting the critical role of middle-level
 predators in mediating rocky reef state transitions.
description: READMEThis file explains all
 of the variables in each of the datasets required to conduct the analyses
 used in the article: “Sudden collapse of a mesopredator reveals its
 complementary role in mediating rocky reef regime shifts." These data
 files were generated from subtidal SCUBA surveys collected over four years
 (2013-2016) at 11 rocky reef sites on the central coast of British
 Columbia led by Jenn M. Burt, Kyle W. Demes, and Anne K.
 Salomon.Burt_CC-DiveSurveys2013-2016_QuadCountsThis data file has information for counts of red urchins (within size categories) and all adult kelp species (Laminariales, stipes &gt;15cm) within 1x1m quadrats (n=18), across 11 survey sites conducted annually over 4 years (2013-2016) on the central coast of BC, Canada.Burt_CC-DiveSurveys2013-2016_Site_Sum_statsThis data file has information summarized for each annual subtidal survey site (n=11) across all survey years (n=4) for sea otter occupation, Pycnopodia biomass, density and biomass of red sea urchins (sm, med, lg), kelp density. Surveys conducted on the central coast of BC (2013-2016).Burt_CC-DiveSurveys2013-2016_UrchSizeThis data file is used for running the simulation code to estimate urchin growth transition probabilities (details in electronic supplementary material, Appendix M1). This data file is a continuous list containing every single entry for every recorded and measured (to the nearest cm) red urchin (n=3451) across all quadrats (n=18 per site, each 1x1m) from all sites (n=11) in all years (n=4, 2013-2016).Burt_et_al_analysis_codeThis is an R markdown file that contains all the code to run all of the analyses in the Burt et al. paper "Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts."
DOI: 10.5061/dryad.s1q0h
title: Data from: Sexual selection in a hermaphroditic plant through female reproductive success

description: Sexual selection is well accepted as a mechanism of shaping traits in
 animals. However, whether and how floral traits are sexually selected in
 hermaphroditic plants remains less clear. Here, we use Passiflora
 incarnata to address how floral traits that affect pollination success are
 selected via female function. We manipulated the ecological context by
 limiting pollination and adding resources to expand the phenotypic
 distribution and alter the intensity of sexual selection. Total sexual
 selection favoured lower style deflexion because of its impact on pollen
 receipt and subsequent seed number. However, total selection on style
 deflexion was not significant, indicating additional selection on style
 deflexion through routes other than mating. Limited pollination and
 enhanced resources were expected to alter the distribution of pollen
 deposition and seed production and therefore intensify the Bateman
 gradient – the relationship between pollen receipt and seed production.
 Indeed, the Bateman gradient was strongest when pollination was limited,
 suggesting potential for sexual selection to influence floral trait
 evolution under these conditions. Overall, we found floral traits may be
 shaped by sexual selection through female reproductive success in this
 hermaphroditic plant. These results support manipulations to enhance the
 variance in mating as a mechanism to understand patterns of sexual
 selection.
description: Sexual selection in a
 hermaphroditic plant through female reproductive successSS data for
 Dryad.xlsx
DOI: 10.5061/dryad.tg658
title: Data from: Fledgling adoption in European Blackbirds: an unrecognised phenomenon in a well-known species

description: Adoption behaviour is well-known in birds, but the majority of adoption
 studies concern the nestling phase of birds’ lives, whereas fledgling
 adoption is a much less well-known phenomenon, especially in passerines.
 During 17 years of observations, we collected data on the fate of 238
 broods of European Blackbirds Turdus merula. In 171 cases fledglings were
 fed only by their own parents, in 24 cases the fledglings were given to
 adoption, while in 43 cases at least one fledgling was cared for by foster
 parents. Our analyses suggest that fledgling adoption in Blackbirds
 occurred under conditions that are consistent with the predictions of two
 hypotheses that explain the adoption phenomenon in birds. First, adoptions
 involved young fledglings of roughly the same age as the foster parents’
 offspring and in the context of a short distance between the biological
 parents and foster parents’ nests: this gave rise to errors in foster
 parents recognizing their own young – in line with the Reproductive Error
 Hypothesis. Second, adoptions also occurred in instances where the
 distance between nests and the age difference between the adopted and the
 foster parents’ own fledglings was twice as great compared to the
 conditions suggesting erroneous adoption. The longer distance between
 nests and the bigger age difference are in line with the Intergeneration
 Conflict Hypothesis.
description: Blackbird adoption raw
 datadata.xls
DOI: 10.5061/dryad.1998
title: Data from: Genetic divergence in morphology-performance mapping between Misty Lake and inlet stickleback

description: Different environments should select for different aspects of organismal
 performance, which should lead to correlated divergence in morphological
 traits that influence performance. The result should be genetic divergence
 in aspects of performance, morphology, and associations (“maps”) between
 morphology and performance. Testing this hypothesis requires quantifying
 performance and morphology in multiple populations after controlling for
 environmental differences, but this is rarely done. We used a
 common-garden experiment to examine morphology and several aspects of
 swimming performance within and between the lake and inlet populations of
 threespine stickleback (Gasterosteus aculeatus) from the Misty system,
 Vancouver Island, Canada. Controlling for body size, lake stickleback had
 shallower bodies, larger caudal fins, and smaller pelvic girdles. With or
 without morphological covariates, lake stickleback showed greater
 performance in both sustained and burst swimming. In contrast, inlet
 stickleback had greater maneuverability than lake stickleback in some
 analyses. Morphology-performance relationships were decoupled when
 considering variation within versus between populations. Moreover,
 morphology-performance mapping differed between the two populations. Based
 on these observations we advance an hypothesis for why populations
 adapting to different environments should show adaptive genetic divergence
 in morphology-performance mapping.
description: Morphology and sustained
 swimming dataThese are the data used
 for the morphological analyses reported in Table 1 and for the UCRIT
 analyses reported in Table 2. They are data collected for lab reared
 stickleback. The file is microsoft excel (.xlsx).morphology and sustained
 swimming data DRYAD.xlsburst swimming
 dataThese are the data used
 for the path models and for the DNET* and WBAR analyses reported in Table
 2. They are data collected for lab reared stickleback. The file is
 microsoft excel (.xlsx).
DOI: 10.5061/dryad.d25s3
title: Data from: Sand lizard (Lacerta agilis) phenology in a warming world

description: Background: Present-day climate change has altered the phenology (the
 timing of periodic life cycle events) of many plant and animal populations
 worldwide. Some of these changes have been adaptive, leading to an
 increase in population fitness, whereas others have been associated with
 fitness decline. Representing short-term responses to an altered weather
 regime, hitherto observed changes are largely explained by phenotypic
 plasticity. However, to track climatically induced shifts in optimal
 phenotype as climate change proceeds, evolutionary capacity in key
 limiting climate- and fitness-related traits is likely to be crucial. In
 order to produce realistic predictions about the effects of climate change
 on species and populations, a main target for conservation biologists is
 thus to assess the potential of natural populations to respond by these
 two mechanisms. In this study we use a large 15-year dataset on an
 ectotherm model, the Swedish sand lizard (Lacerta agilis), to investigate
 how higher spring temperature is likely to affect oviposition timing in a
 high latitude population, a trait strongly linked to offspring fitness and
 survival. Results: With an interest in both the short- and potential
 long-term effect of rising temperatures, we applied a random regression
 model, which yields estimates of population-level plasticity and
 among-individual variation in the average, as well as the plastic,
 response to temperature. Population plasticity represents capacity for
 short-term adjustments whereas variation among individuals in a
 fitness-related trait indicates an opportunity for natural selection and
 hence for evolutionary adaptation. The analysis revealed both
 population-level plasticity and individual-level variation in average
 laying date. In contrast, we found no evidence for variation among females
 in their plastic responses to spring temperature, which could demonstrate
 a similarity in responses amongst females, but may also be due to a lack
 of statistical power to detect such an effect. Conclusion: Our findings
 indicate that climate warming may have positive fitness effects in this
 lizard population through an advancement of oviposition date. This
 prediction is consistent over shorter and potentially also longer time
 scales as the analysis revealed both population-level plasticity and
 individual-level variation in average laying date. However, the genetic
 basis for this variation would have to be examined in order to predict an
 evolutionary response.
description: Sand lizard (Lacerta
 agilis) phenology in a warming worldDryad.xls
DOI: 10.5061/dryad.8cs4f
title: Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

description: The description of genetic population structure over a species’ geographic
 range can provide insights into its evolutionary history and also support
 effective management efforts. Assessments for globally distributed species
 are rare, however, requiring significant international coordination and
 collaboration. The global distribution of demographically discrete
 populations for the humpback whale Megaptera novaeangliae is not fully
 known, hampering the definition of appropriate management units. Here, we
 present the first circumglobal assessment of mitochondrial genetic
 population structure across the species’ range in the Southern Hemisphere
 and Arabian Sea. We combine new and existing data from the mitochondrial
 (mt)DNA control region that resulted in a 311 bp consensus sequence of the
 mtDNA control region for 3009 individuals sampled across 14 breeding
 stocks and subpopulations currently recognized by the International
 Whaling Commission. We assess genetic diversity and test for genetic
 differentiation and also estimate the magnitude and directionality of
 historic matrilineal gene flow between putative populations. Our results
 indicate that maternally directed site fidelity drives significant genetic
 population structure between breeding stocks within ocean basins. However,
 patterns of connectivity differ across the circumpolar range, possibly as
 a result of differences in the extent of longitudinal movements on feeding
 areas. The number of population comparisons observed to be significantly
 differentiated were found to diminish at the subpopulation scale when
 nucleotide differences were examined, indicating that more complex
 processes underlie genetic structure at this scale. It is crucial that
 these complexities and uncertainties are afforded greater consideration in
 management and regulatory efforts.
description: Rosenbaum_et_al_HaplotypeFrequencyTableHaplotype Frequency Table
DOI: 10.5061/dryad.4bd210n
title: Data from: How symbiosis and ecological context influence the variable expression of transgenerational wing induction upon fungal infection of aphids

description: Aphids, like most animals, mount a diverse set of defenses against
 pathogens. For aphids, two of the best studied defenses are
 symbiont-conferred protection and transgenerational wing induction. Aphids
 can harbor bacterial symbionts that provide protection against pathogens,
 parasitoids and predators, as well as against other environmental
 stressors. In response to signals of danger, aphids also protect not
 themselves but their offspring by producing more winged than unwinged
 offspring as a way to ensure that their progeny may be able to escape
 deteriorating conditions. Such transgenerational wing induction has been
 studied most commonly as a response to overcrowding of host plants and
 presence of predators, but recent evidence suggests that pea aphids
 (Acyrthosiphon pisum) may also begin to produce a greater proportion of
 winged offspring when infected with fungal pathogens. Here, we explore
 this phenomenon further by asking how protective symbionts, pathogen
 dosage and environmental conditions influence this response. Overall,
 while we find some evidence that protective symbionts can modulate
 transgenerational wing induction in response to fungal pathogens, we
 observe that transgenerational wing induction in response to fungal
 infection is highly variable. That variability cannot be explained
 entirely by symbiont association, by pathogen load or by environmental
 stress, leaving the possibility that a complex interplay of genotypic and
 environmental factors may together influence this trait.
description: Aphid-Fungus_Experiment_Data
DOI: 10.5061/dryad.40655hr
title: Data from: Carcharodontosaurian remains (Dinosauria, Theropoda) from the Upper Jurassic of Portugal

description: A new specimen of a theropod dinosaur found in the Upper Jurassic
 (Freixial Formation, late Tithonian) of the Lusitanian Basin is described.
 It corresponds to a single individual and includes a sequence of
 articulated caudal vertebrae, an almost complete right pes, and other
 fragments of the appendicular skeleton. The specimen includes the most
 complete pes of a theropod dinosaur currently known in the Lusitanian
 Basin and represents one of the youngest skeletal records of theropod
 dinosaurs currently known in the Portuguese Upper Jurassic. A systematic
 analysis of this specimen is performed and it shows a combination of
 characters that allows us to interpret it as belonging to an allosauroid
 taxon. Within this clade the material from Cambelas shares a few features
 with some carcharodontosaurids, including the presence of a lateral lamina
 extending along the anterior end of the centrum in the caudal vertebra and
 of a low vertical crest on the lateral surface of the femoral lesser
 trochanter. The set of remains described here shares some unusual features
 with another specimen previously described in the Portuguese fossil
 record, which also presents some synapomorphies of Carcharodontosauria.
 However, no autapomorphy or exclusive character combination can be
 recognized in the specimen here described in order to describe it as a new
 form. The presence of this specimen suggests a greater diversity in the
 allosauroid theropod fauna from the Late Jurassic of the Lusitanian Basin
 than currently known and probably expands the temporal record of
 Carcharodontosauria up to upper Tithonian of south-western Europe.
description: Malafaiaetal_Supplementary Data 1List of osteological elements collected in the Cambelas fossil siteMalafaiaetal_SupplementayData1.pdfMalafaiaetal_Supplementary Data 2Measurements of the caudal vertebrae of SHN.019.Malafaiaetal_Supplementary Data 3Measurements of the appendicular elements of SHN.019.
DOI: 10.5061/dryad.4q3d3
title: Data from: Duration of cord clamping and neonatal outcomes in very preterm infants

description: Background: Delayed cord clamping (DCC, ≥30s) increases blood volume in
 newborns and is associated with fewer blood transfusions and short-term
 neonatal complications. The optimal timing of cord clamping for very
 preterm infants should maximize placental transfusion without interfering
 with stabilization and resuscitation. Aim: We compared the effect of
 different durations of DCC, 30-45s vs. 60-75s, on delivery room (DR) and
 neonatal outcomes in preterm infants &lt;32 weeks gestational age
 (GA). Methods: This is a single-center prospective observational study.
 Data were collected prospectively from eligible infants from two groups:
 30-45s DCC group (January 2008 to February 2011, n = 187) and 60-75s DCC
 group (March 2011 to April 2014, n = 166). Results: The 60-75s DCC group
 compared to the 30-45s DCC group had higher hematocrits at &lt;2 hours
 (49.2% vs. 47.4%, p = 0.02). In infants &lt;28 weeks GA, the 12–36
 hours hematocrit was higher in the 60-75s DCC group compared to the 30-45s
 DCC group (47.9% vs. 42.1%, p = 0.002). The 60-75s DCC group had
 reductions in DR intubation (11% vs. 22%, p = 0.004), hypothermia on
 admission (1% vs. 5%, p = 0.01), surfactant therapy (13% vs. 28%, p =
 0.001), intubation in the first 24 hours (20% vs. 34%, p = 0.004), any
 intubation (27% vs. 40%, p = 0.007), and any red blood cell transfusion
 (20% vs. 33%, p = 0.008) during the hospitalization compared to the 30-45s
 DCC group. These reductions remained significant after adjusting for GA,
 gender and &gt;48 hours of antenatal steroid exposure. There was no
 difference between the two groups in neonatal death, intraventricular
 hemorrhage, chronic lung disease, late onset sepsis, necrotizing
 enterocolitis and severe retinopathy of prematurity. Conclusion: In this
 study cohort increasing DCC duration from 30-45s to 60-75s is associated
 with decreased hypothermia on admission, neonatal respiratory
 interventions and red blood cell transfusions without increase in neonatal
 mortality and morbidities.
description: Song_DCC_PlosOne_datadryad9.16.15
DOI: 10.15468/dl.59gd6h
title: Occurrence Download

description: A dataset containing 2379 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lycium barbarum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2379 records from 238 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000948-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c0ss8
title: Data from: Poison and alarm: the Asian hornet Vespa velutina uses sting venom volatiles as alarm pheromone

description: In colonial organisms, alarm pheromones can provide a key fitness
 advantage by enhancing colony defense and warning of danger. Learning
 which species use alarm pheromone and the key compounds involved therefore
 enhances our understanding of how this important signal has evolved.
 However, our knowledge of alarm pheromones is more limited in the social
 wasps and hornets as compared to the social bees and ants. Vespa velutina
 is an economically important and widespread hornet predator that attacks
 humans and honey bees. This species is native to Asia and has now invaded
 Europe. Despite growing interest in V. velutina, it was unknown if it
 possessed an alarm pheromone. We show that these hornets use sting venom
 as an alarm pheromone. Sting venom volatiles were strongly attractive to
 hornet workers and triggered attacks. Two major venom fractions,
 consisting of monoketones and diketones, also elicited attack. We used
 GC-EAD and identified 13 known and three unknown aliphatic ketones and
 alcohols in venom that elicited conspicuous hornet antennal activity. Two
 of the unknown compounds may be an undecen-2-one and an
 undecene-2,10-dinone. Three major compounds (heptan-2-one nonan-2-one, and
 undecan-2-one) triggered attacks, but only nonan-2-one did so at
 biologically relevant levels (10 hornet equivalents). Nonan-2-one thus
 deserves particular attention. However, the key alarm releasers for V.
 velutina remain to be identified. Such identification will help to
 illuminate the evolution and function of alarm compounds in hornets.
description: V.velutina alarm
 pheromone data