cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9031
title: Data from: Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula

description: BACKGROUND: Flowering date in annual plants, and perception of symbiotic
 nitrogen-fixing rhizobium in legumes, are strongly selected traits. We
 asked if natural selection can be detected at key genes of the flowering
 and rhizobia recognition pathways in the model legume Medicago truncatula.
 RESULTS: We examined nucleotide variation among 57 accessions from natural
 populations in 53 gene fragments: 11 genes involved in flowering, 5 genes
 involved in nitrogen-fixing bacteria recognition, and 37 genes used as
 control loci. We detected 1757 polymorphic sites yielding an average
 nucleotide diversity of 0.003 per site. We found that accessions were
 structured in two groups consistent with geographical origins and that
 nucleotide diversity was not consistent with a neutral, constant-sized
 population but rather suggests recent expansion yielding more rare alleles
 than expected. Using coalescent simulations, we detected strong departure
 from selective neutrality in flowering genes within each group and showed
 that genetic differentiation between groups at several nodulation and
 flowering genes has probably been driven by recent selection. CONCLUSION:
 We quantify the intensity of purifying selection in M. truncatula and show
 that putative footprints of natural selection can be detected at different
 time scales in both flowering and symbiotic pathways.
description: alignmentsZip contains all nucleotide sequences in the form of alignments for each gene fragment studied. The alignments contain annotation about the intron/exon boundaries and are provided in nexus (.nex) format.
DOI: 10.5061/dryad.g0q01
title: Data from: Aquatic polymers can drive pathogen transmission in coastal ecosystems

description: Gelatinous polymers including extracellular polymeric substances (EPSs)
 are fundamental to biophysical processes in aquatic habitats, including
 mediating aggregation processes and functioning as the matrix of biofilms.
 Yet insight into the impact of these sticky molecules on the environmental
 transmission of pathogens in the ocean is limited. We used the zoonotic
 parasite Toxoplasma gondii as a model to evaluate polymer-mediated
 mechanisms that promote transmission of terrestrially derived pathogens to
 marine fauna and humans. We show that transparent exopolymer particles, a
 particulate form of EPS, enhance T. gondii association with marine
 aggregates, material consumed by organisms otherwise unable to access
 micrometre-sized particles. Adhesion to EPS biofilms on macroalgae also
 captures T. gondii from the water, enabling uptake of pathogens by
 invertebrates that feed on kelp surfaces. We demonstrate the acquisition,
 concentration and retention of T. gondii by kelp-grazing snails, which can
 transmit T. gondii to threatened California sea otters. Results highlight
 novel mechanisms whereby aquatic polymers facilitate incorporation of
 pathogens into food webs via association with particle aggregates and
 biofilms. Identifying the critical role of invisible polymers in
 transmission of pathogens in the ocean represents a fundamental advance in
 understanding and mitigating the health impacts of coastal habitat
 pollution with contaminated runoff.
description: Microcsopy data for
 aggregation experimentsData was collected by
 laboratory experiments, spiking T. gondii and surrogate microspheres into
 seawater samples. coloumn headings include Jar (treatment) number,
 replicate number, membrane replicate number (three per replicate), and raw
 counts of each particle type (DG surrogate, GB surrogate, and T. gondii
 oocysts)TEP
 Toxo Snow Data for Dryad Proceedings B ALL EXPERIMENTS MF RAW
 DATA.xlsxImage J aggregate
 dimensions - aggregation experimentsData contains long and
 short axes as well as volume derived from right cylinder and ellipsoid
 equations for the macroaggregates in jars used for aggregation
 experiments. Columns include treatment type, replciate number, number of
 aggregates, and corresonding long axis, short axis, and volume of each
 aggregate. Data was obtained using the software Image
 J.TEP Toxo
 Snow Data for Dryad Proceedings B ALL EXPERIMENTS AGG PIC RAW
 DATA.xlsx
DOI: 10.15482/usda.adc/27180105
title: Data from: Enhanced survival of mass reared Mediterranean fruit flies via regular diurnal temperature oscillations

description: Effectively mass rearing insects is critical for research, for environmentally friendly technologies like Sterile Insect Technique (SIT), producing biological control agents, and enabling novel methods such as those based on genetics or symbionts. While constant temperature conditions are typically used in mass rearing, based on the idea that there is an optimum value that produces the most fit insects, homeostatic conditions do not reflect the real world, potentially impacting insect performance in the field. We investigated the performance of mass-reared adult Mediterranean fruit flies (Medflies) under constant (Const24: 24 °C) and oscillating (Osc2: 24 ± 2 °C, Osc5: 24 ± 5 °C) temperature regimes. Male and female survivorship, flight ability, and female fecundity were assessed across the temperature regimes. Additionally, we compared adult medfly performance under environmental chamber and outdoor conditions to determine if temperature and humidity as simulated in the chambers resulted in similar performance outcomes for the insects as being outdoors. Male medflies under the Osc 5 treatment had higher survival probability at 55 days post-emergence compared to the constant temperature regime, while females showed no significant differences in survivorship among temperature regimes. Flight ability and fecundity were not significantly affected by temperature regimes, though the Osc 5 group showed the highest fecundity. Comparisons between environmental chamber and outdoor conditions revealed minimal differences in performance metrics. Our findings suggest that the performance of mass reared male adult medflies under temperature variance in the field can be improved by oscillating temperature regimes in mass-rearing facilities.
DOI: 10.15482/usda.adc/27180105.v1
title: Data from: Enhanced survival of mass reared Mediterranean fruit flies via regular diurnal temperature oscillations

description: Effectively mass rearing insects is critical for research, for environmentally friendly technologies like Sterile Insect Technique (SIT), producing biological control agents, and enabling novel methods such as those based on genetics or symbionts. While constant temperature conditions are typically used in mass rearing, based on the idea that there is an optimum value that produces the most fit insects, homeostatic conditions do not reflect the real world, potentially impacting insect performance in the field. We investigated the performance of mass-reared adult Mediterranean fruit flies (Medflies) under constant (Const24: 24 °C) and oscillating (Osc2: 24 ± 2 °C, Osc5: 24 ± 5 °C) temperature regimes. Male and female survivorship, flight ability, and female fecundity were assessed across the temperature regimes. Additionally, we compared adult medfly performance under environmental chamber and outdoor conditions to determine if temperature and humidity as simulated in the chambers resulted in similar performance outcomes for the insects as being outdoors. Male medflies under the Osc 5 treatment had higher survival probability at 55 days post-emergence compared to the constant temperature regime, while females showed no significant differences in survivorship among temperature regimes. Flight ability and fecundity were not significantly affected by temperature regimes, though the Osc 5 group showed the highest fecundity. Comparisons between environmental chamber and outdoor conditions revealed minimal differences in performance metrics. Our findings suggest that the performance of mass reared male adult medflies under temperature variance in the field can be improved by oscillating temperature regimes in mass-rearing facilities.
DOI: 10.5061/dryad.qh4fd46
title: Data from: Quantifying the links between land use and population growth rate in a declining farmland bird

description: Land use is likely to be a key driver of population dynamics of species
 inhabiting anthropogenic landscapes, such as farmlands. Understanding the
 relationships between land use and variation in population growth rates is
 therefore critical for the management of many farmland species. Using 24
 years of data of a declining farmland bird in an integrated population
 model, we examined how spatiotemporal variation in land use (defined as
 habitats with “Short” and “Tall” ground vegetation during the breeding
 season) and habitat‐specific demographic parameters relates to variation
 in population growth taking into account individual movements between
 habitats. We also evaluated contributions to population growth using
 transient life table response experiments which gives information on
 contribution of past variation of parameters and real‐time elasticities
 which suggests future scenarios to change growth rates. LTRE analyses
 revealed a clear contribution of Short habitats to the annual variation in
 population growth rate that was mostly due to fledgling recruitment,
 whereas there was no evidence for a contribution of Tall habitats. Only
 18% of the variation in population growth was explained by the modeled
 local demography, the remaining variation being explained by apparent
 immigration (i.e., the residual variation). We discuss potential
 biological and methodological reasons for high contributions of apparent
 immigration in open populations. In line with LTRE analysis, real‐time
 elasticity analysis revealed that demographic parameters linked to Short
 habitats had a stronger potential to influence population growth rate than
 those of Tall habitats. Most particularly, an increase of the proportion
 of Short sites occupied by Old breeders could have a distinct positive
 impact on population growth. High‐quality Short habitats such as grazed
 pastures have been declining in southern Sweden. Converting low‐quality to
 high‐quality habitats could therefore change the present negative
 population trend of this, and other species with similar habitat
 requirements.
description: data used for the
 IPMContains the data used
 in the IPM and its descriptiondataIPM.xlsxRdataContains all data in a format ready to use in order to run the IPM in jags (script of the IPM available in the Appendix section).data_IPMhabitat.RData
DOI: 10.5061/dryad.jv920
title: Data from: Honeybee nutrition is linked to landscape composition

description: Declines in insect pollinators in Europe have been linked to changes in
 land use. Pollinator nutrition is dependent on floral resources (i.e.,
 nectar and pollen), which are linked to landscape composition. Here, we
 present a stratified analysis of the nutritional composition of beebread
 in managed honeybee hives with a view to examining potential sources of
 variation in its nutritional composition. Specifically, we tested the
 hypothesis that beebread composition correlates with local land use and
 therefore available floral resources. The results demonstrated that the
 starch, lipid, and moisture contents of beebread are all highly conserved
 across hives, whereas levels of protein and nonreducing sugar increased as
 the year progressed, reducing sugars, however, decreased during the first
 half of the year and then increased toward the end. Local land use around
 hives was quantified using data from the Countryside Survey 2007 Land
 Cover Map. Bee-bread protein content was negatively correlated with
 increasing levels of arable and horticultural farmland surrounding hives
 and positively correlated with the cover of natural grasslands and
 broadleaf woodlands. Reducing sugar content was also positively correlated
 with the amount of broad-leaved woodland in a 3 Km² radius from the hives.
 Previous studies on a range of invertebrates, including honeybees,
 indicate that dietary protein intake may have a major impact on correlates
 of fitness, including longevity and immune function. The finding that
 beebread protein content correlates with land use suggests that landscape
 composition may impact on insect pollinator well-being and provides a link
 between landscape and the nutritional ecology of socially foraging insects
 in a way not previously considered.
description: Bee bread nutritional
 and CS2007 dataData on the nutritional
 composition of bee bread, from each of the hive locations and associated
 Countryside Survey land cover data for each of the
 hives.bee
 bread2012.txt
DOI: 10.5061/dryad.5fs6j
title: Data from: A new specimen of large-bodied basal enantiornithine Bohaiornis from the early Cretaceous of China and the inference of feeding ecology in Mesozoic birds

description: A new specimen of Bohaiornis guoi from the Jiufotang Formation, comprising
 a nearly complete skeleton, sheds light on enantiornithine morphological
 variation and ecological specialization. The new specimen was collected
 from near Lamadong Village in Liaoning Province, which is the same area
 where the sub-adult holotype specimen was reported. It provides new
 information on the cranial and pectoral girdle anatomy of the species,
 e.g., broad nasal, strikingly robust acromion, medially curved
 acrocoracoid process. In contrast to the holotype, the newly referred
 specimen has small rounded stones in the thoracic region that in other
 extinct taxa has been interpreted as direct evidence of diet. Direct
 evidence of diet is so far unknown in other Enantiornithes. Specifically
 the lack of “stomach stones” or gastroliths in enantiornithines despite
 their excellent fossil record has been proposed to be related to their
 insectivorous diet as well as to their arboreal ecology. We hypothesize
 that cranial morphology as well as the number and shape of the preserved
 stones in Bohaiornis may be most consistent with a raptorial ecology
 previously unknown for Enantiornithes and considered rare for Avialae.
 While rostrum shape has a strong relationship to feeding ecology in living
 birds, in basal avialan birds most diversity is in dental morphology,
 number, and distribution of the teeth.
description: Appendix
 IIAppendix
 1.docxAppendix
 1
DOI: 10.5061/dryad.cv2d5
title: Data from: Multigenerational exposure to silver ions and silver nanoparticles reveals heightened sensitivity and epigenetic memory in Caenorhabditis elegans

description: The effects from multigenerational exposures to engineered nanoparticles
 (ENPs) in their pristine and transformed states are currently unknown
 despite such exposures being an increasingly common scenario in natural
 environments. Here, we examine how exposure over 10 generations affects
 the sensitivity of the nematode Caenorhabditis elegans to pristine and
 sulfidized Ag ENPs and AgNO3. We also include populations that were
 initially exposed over six generations but kept unexposed for subsequent
 four generations to allow recovery from exposure. Toxicity of the
 different silver forms decreased in the order AgNO3, Ag ENPs and Ag2S
 ENPs. Continuous exposure to Ag ENPs and AgNO3 caused pronounced
 sensitization (approx. 10-fold) in the F2 generation, which was sustained
 until F10. This sensitization was less pronounced for Ag2S ENP exposures,
 indicating different toxicity mechanisms. Subtle changes in size and
 lifespan were also measured. In the recovery populations, the sensitivity
 to Ag ENPs and AgNO3 resulting from the initial multigenerational exposure
 persisted. Their response sensitivity for all endpoints was most closely
 related to the last ancestral exposed generation (F5), rather than
 unexposed controls. The mechanisms of transgenerational transfer of
 sensitivity are probably organized through the epigenome, and we encourage
 others to investigate such effects as a priority for mechanistic
 toxicology.
description: Liefspan, size and
 reproduction data for all generations and silver formsThe file contains the
 raw data of the multigenerational experiment on the effect of silver ions
 and nanoparticles on C. elegans described in the publication. It includes
 data for each silver form and each generation on the lifespan in days,
 body size as volumetric length and reproduction in number of offspring
 produced by individual.Tox raw
 data_all.xlsx
DOI: 10.5061/dryad.3td28
title: Data from: Assessing reproductive isolation using a contact zone between parapatric lake-stream stickleback ecotypes

description: Ecological speciation occurs when populations evolve reproductive
 isolation as a result of divergent natural selection. This isolation can
 be influenced by many potential reproductive barriers, including selection
 against hybrids, selection against migrants, and assortative mating. How
 and when these barriers act and interact in nature is understood for
 relatively few empirical systems. We used a mark-recapture experiment in a
 contact zone between lake and stream three-spined sticklebacks
 (Gasterosteus aculeatus, Linnaeus) to evaluate the occurrence of hybrids
 (allowing inferences about reproductive isolation), the inter-annual
 survival of hybrids (allowing inferences about selection against hybrids),
 and the shift in lake-like versus stream-like characteristics (allowing
 inferences about selection against migrants). Genetic and morphological
 data suggest the occurrence of hybrids and no selection against hybrids in
 general, a result contradictory to a number of other studies of
 sticklebacks. However, we did find selection against more lake-like
 individuals, suggesting a barrier to gene flow from the lake into the
 stream. Combined with previous work on this system, our results suggest
 that multiple (most weakly and often asymmetric) barriers must be
 combining to yield substantial restrictions on gene flow. This work
 provides evidence of a reproductive barrier in lake-stream sticklebacks
 and highlights the value of assessing multiple reproductive barriers in
 natural contexts.
description: Allele
 scoresAllele scores for all
 fish included in studyallele_scores.txtIndividual fish dataMetadata for each fish including individual id, year caught, and habitatindividual_fish_data.csvLandmark dataLandmark data for all fish included in geometric morphometric analysislandmark_data.csv
DOI: 10.5061/dryad.8481
title: Data from: A geographic test of species selection using planktonic foraminifera during the Cretaceous/Paleogene mass extinction

description: Species selection has received a great deal of theoretical attention but
 it has rarely been empirically tested. It is important to determine the
 level of selection that operated during a particular extinction event
 because it can help distinguish between traits that were actually
 responsible for extinction and those that were merely correlated with it.
 Here, we present a test that can help distinguish between organismal and
 species-level selection, which we demonstrate using the high-resolution
 fossil record of planktonic foraminifera species recorded in deep-sea
 sediment cores. Our test examines the fate of survivors and victims during
 the Cretaceous/Paleogene (K/Pg) mass extinction within single geographic
 regions, where all individuals experience the same selection pressures.
 Selection at the organismal level implies that individual members of
 surviving species are more fit than those of victimized species, and
 therefore should be more likely to survive in affected areas; conversely,
 selection at the species level implies individuals will suffer equally
 within an affected area. We find that survivors of the mass extinction
 suffered very high extirpation rates in cores where the overall extinction
 rate was high, indicating that individual members of the surviving species
 were generally no more fit than individual members of extinct species.
 Rather, these species were able to survive because they possessed
 advantageous species-level traits, such as larger geographic ranges and
 greater abundances than victimized species. This geographic pattern of
 extirpation suggests that selection operated at the species, rather than
 organismal, level during the K/Pg mass extinction of planktonic
 foraminifera.
description: Appendix
 S1Species trait
 data.AppendixS1.txtAppendix S2Core data.AppendixS2.txt
DOI: 10.5061/dryad.33380
title: Data from: Human circulating antibody-producing B cell as a predictive measure of mucosal immunity to poliovirus

description: Background: The "gold standard" for assessing mucosal immunity
 after vaccination with poliovirus vaccines consists in measuring virus
 excretion in stool after challenge with oral poliovirus vaccine (OPV).
 This testing is time and resource intensive, and development of
 alternative methods is a priority for accelerating polio eradication. We
 therefore evaluated circulating antibody-secreting cells (ASCs) as a
 potential means to evaluate mucosal immunity to poliovirus vaccine.
 Methods: 199 subjects, aged 10 years, and previously immunized repeatedly
 with OPV, were selected. Subjects were assigned to receive either a
 booster dose of inactivated poliovirus vaccine (IPV), bivalent OPV (bOPV),
 or no vaccine. Using a micro-modified whole blood-based ELISPOT assay
 designed for field setting, circulating poliovirus type-specific IgA- and
 IgG-ASCs, including gut homing ?4?7+ ASCs, were enumerated on days 0 and 7
 after booster immunization. In addition, serum samples collected on days
 0, 28 and 56 were tested for neutralizing antibody titers against
 poliovirus types 1, 2, and 3. Stool specimens were collected on day 28
 (day of bOPV challenge), and on days 31, 35 and 42 and processed for
 poliovirus isolation. Results: An IPV dose elicited blood IgA- and IgG-ASC
 responses in 84.8 to 94.9% of subjects, respectively. In comparison, a
 bOPV dose evoked corresponding blood ASC responses in 20.0 to 48.6% of
 subjects. A significant association was found between IgA- and IgG-ASC
 responses and serum neutralizing antibody titers for poliovirus type 1, 2,
 3 (p&lt;0.001). In the IPV group, ?4?7+ ASCs accounted for a
 substantial proportion of IgA-ASCs and the proportion of subjects with a
 positive ?4?7+ IgA-ASC response to poliovirus types 1, 2 and 3 was 62.7%,
 89.8% and 45.8%, respectively. A significant association was observed
 between virus excretion and ?4?7+ IgA- and/or IgG-ASC responses to
 poliovirus type 3 among immunized children; however, only a weak
 association was found for type 1 poliovirus. Discussion: Our results
 suggest that virus-specific blood ASCs, especially for type 3 poliovirus,
 can serve as surrogate of mucosal immunity after vaccination. Further
 studies are needed to evaluate the duration of such memory responses and
 to assess the programmatic utility of this whole blood-based mucosal ASC
 testing for the polio eradication program.
description: ELISPOT data for PloS
 One 24_10_15ELISPOT data_Polio Study
 Moradabad_Plos One