cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.048kf
title: Data from: Loss of genetic diversity and increased embryonic mortality in non-native lizard populations

description: Many populations are small and isolated with limited genetic variation and
 high risk of mating with close relatives. Inbreeding depression is
 suspected to contribute to extinction of wild populations, but the
 historical and demographic factors that contribute to reduced population
 viability are often difficult to tease apart. Replicated introduction
 events in non-native species can offer insights into this problem because
 they allow us to study how genetic variation and inbreeding depression are
 affected by demographic events (e.g. bottlenecks), genetic admixture and
 the extent and duration of isolation. Using detailed knowledge about the
 introduction history of 21 non-native populations of the wall lizard
 Podarcis muralis in England, we show greater loss of genetic diversity
 (estimated from microsatellite loci) in older populations and in
 populations from native regions of high diversity. Loss of genetic
 diversity was accompanied by higher embryonic mortality in non-native
 populations, suggesting that introduced populations are sufficiently
 inbred to jeopardize long-term viability. However, there was no
 statistical correlation between population-level genetic diversity and
 average embryonic mortality. Similarly, at the individual level, there was
 no correlation between female heterozygosity and clutch size, infertility
 or hatching success, or between embryo heterozygosity and mortality. We
 discuss these results in the context of human-mediated introductions and
 how the history of introductions can play a fundamental role in
 influencing individual and population fitness in non-native species.
description: Michaelides_etal_MolEco_MicrosatelliteDataSheet1_Genotypes of 1546 samples from 66 populations. Sheet2_Genotypes of 321 females. Sheet3_Genotypes of 160 offspring. (All individuals were genotyped at 13 microsatellite loci).
DOI: 10.5061/dryad.1h2ft
title: Data from: Adult exposure to ocean acidification is maladaptive for larvae of the Sydney rock oyster Saccostrea glomerata in the presence of multiple stressors

description: Parental effects passed from adults to their offspring have been
 identified as a source of rapid acclimation that may allow marine
 populations to persist as our surface oceans continue to decrease in pH.
 Little is known, however, whether parental effects are beneficial for
 offspring in the presence of multiple stressors. We exposed adults of the
 oyster Saccostrea glomerata to elevated CO2 and examined the impacts of
 elevated CO2 (control = 392; 856 µatm) combined with elevated temperature
 (control = 24; 28°C), reduced salinity (control = 35; 25) and reduced food
 concentration (control = full; half diet) on their larvae. Adult exposure
 to elevated CO2 had a positive impact on larvae reared at elevated CO2 as
 a sole stressor, which were 8% larger and developed faster at elevated CO2
 compared with larvae from adults exposed to ambient CO2. These larvae,
 however, had significantly reduced survival in all multistressor
 treatments. This was particularly evident for larvae reared at elevated
 CO2 combined with elevated temperature or reduced food concentration, with
 no larvae surviving in some treatment combinations. Larvae from
 CO2-exposed adults had a higher standard metabolic rate. Our results
 provide evidence that parental exposure to ocean acidification may be
 maladaptive when larvae experience multiple stressors.
description: Parker_dataData used to create manuscript figures, including: egg size (diameter), total lipid content of eggs, shell length of larvae (day 15), standard metabolic rate of larvae (day 15), percentage of umbonate larvae (day 9), percentage survival of larvae (day 15).
DOI: 10.5061/dryad.1h272
title: Data from: The opsin genes of Amazonian cichlids

description: Vision is a critical sense for organismal survival with visual
 sensitivities strongly shaped by the environment. Some freshwater fishes
 with a Gondwanan origin are distributed in both South American rivers
 including the Amazon, as well as African rivers and lakes. These different
 habitats likely required adaptations to murky and clear environments. In
 this study, we compare the molecular basis of Amazonian and African
 cichlid fishes’ visual systems. We used next generation sequencing of
 genomes and retinal transcriptomes to examine three Amazonian cichlid
 species. Genome assemblies revealed six cone opsin classes (SWS1, SWS2B,
 SWS2A, RH2B, RH2A, LWS) and rod opsin (RH1). However, the functionality of
 these genes varies across species with different pseudogenes found in
 different species. Our results support evidence of an RH2A gene
 duplication event that is shared across both cichlid groups, but which was
 probably followed by gene conversion. Transcriptome analyses show that
 Amazonian species mainly express three opsin classes (SWS2A, RH2A and LWS)
 which likely are a good match to the long wavelength oriented light
 environment of the Amazon basin. Furthermore, analysis of amino acid
 sequences suggest that the short wavelength sensitive genes (SWS2B, SWS2A)
 may be under selective pressures in order to shift their spectral
 properties to a longer wavelength visual palette. Our results agree with
 the ‘sensitivity hypothesis’ where the light environment causes visual
 adaptation. Amazonian cichlid visual systems are likely adapting through
 gene expression, gene loss, and possibly spectral tuning of opsin
 sequences. Such mechanisms may be shared across the Amazonian fish fauna.
description: Amazonian cichlid
 genomes contigsWe are submitting 24
 contigs from three whole genomes assemblies that are unpublished. Three
 Amazonian cichlid species were sampled in the Amazon basin, processed with
 Illumina next generation sequencing, and assembled with Velvet. These
 contigs in particular, contain different opsin genes :SWS1, SWS2B, SWS2A,
 RH2Aa, RH2Ab, RH2B, LWS and RH1. The full genome assemblies will be
 submitted in the near future. We have already annotated a handful of genes
 out of these contigs which are in GenBank (KX382917-57). Reviewers have
 asked us to submit these contigs as part of the raw data for the article.
 Because we have improved on these contig sequences in producing the gene
 annotations, we prefer not to annotate in these contigs as the improved
 sequences are already in GenBank. The gaps (NNNs) are of estimated size
 based on the paired reads spacing of the library that was sequenced by
 Illumina next generation sequencing.24 documents from
 genome_contigs.fasta
DOI: 10.5061/dryad.f0780
title: Data from: Taking movement data to new depths: Inferring prey availability and patch profitability from seabird foraging behavior

description: Detailed information acquired using tracking technology has the potential
 to provide accurate pictures of the types of movements and behaviors
 performed by animals. To date, such data have not been widely exploited to
 provide inferred information about the foraging habitat. We collected data
 using multiple sensors (GPS, time depth recorders, and accelerometers)
 from two species of diving seabirds, razorbills (Alca torda, N = 5, from
 Fair Isle, UK) and common guillemots (Uria aalge, N = 2 from Fair Isle and
 N = 2 from Colonsay, UK). We used a clustering algorithm to identify
 pursuit and catching events and the time spent pursuing and catching
 underwater, which we then used as indicators for inferring prey encounters
 throughout the water column and responses to changes in prey availability
 of the areas visited at two levels: individual dives and groups of dives.
 For each individual dive (N = 661 for guillemots, 6214 for razorbills), we
 modeled the number of pursuit and catching events, in relation to dive
 depth, duration, and type of dive performed (benthic vs. pelagic). For
 groups of dives (N = 58 for guillemots, 156 for razorbills), we modeled
 the total time spent pursuing and catching in relation to time spent
 underwater. Razorbills performed only pelagic dives, most likely
 exploiting prey available at shallow depths as indicated by the vertical
 distribution of pursuit and catching events. In contrast, guillemots were
 more flexible in their behavior, switching between benthic and pelagic
 dives. Capture attempt rates indicated that they were exploiting deep prey
 aggregations. The study highlights how novel analysis of movement data can
 give new insights into how animals exploit food patches, offering a unique
 opportunity to comprehend the behavioral ecology behind different movement
 patterns and understand how animals might respond to changes in prey
 distributions.
description: catchingEventsTotRAZOdataset used to run the dive model for razorbillsboutModel_dfRAZOdataset used to run the bout modelcatchingEventsTotCOGUdataset used to run the dive model for common guillemotsboutModel_dfCOGUdataset used to run the bout model
DOI: 10.5061/dryad.sp2m46f6
title: Data from: Condition dependence of a multicomponent sexual display trait in Drosophila serrata

description: Theory predicts that costly sexual displays should evolve condition
 dependence if the marginal fitness gain from trait exaggeration is greater
 for high- than for low-condition individuals and that the strength of
 condition dependence should increase with the strength of directional
 selection. While there is substantial support for the first prediction,
 evidence for the latter is much weaker. We undertook a quantitative test
 of this prediction for a multivariate sexual display consisting of a suite
 of contact pheromones termed “cuticular hydrocarbons” (CHCs) in Drosophila
 serrata. We performed a dietary manipulation of condition (i.e., the pool
 of metabolic resources available for allocation to fitness-enhancing
 traits) within a half-sibling breeding design, thereby also providing
 insight into the genetic basis of condition dependence. As predicted, the
 linear combination of CHCs under the strongest sexual selection from
 female mate preferences was unusually condition dependent relative to
 other CHC combinations within the population (P = .049). A significant
 positive correlation also existed between the strengths of condition
 dependence and sexual selection among different CHC blends (r = 0.482, P
 &lt; .001). Finally, sires varied in their response to the dietary
 manipulation, demonstrating significant genetic variance in condition
 dependence. Our results are consistent with the evolution of heightened
 condition dependence of sexual displays in response to persistent sexual
 selection.
description: CHC
 dataPlease see
 ReadMe.txtDELCOURT CONDITION
 DEPENDENCE.csv
DOI: 10.6073/pasta/c699680482443efff3ad9f30c2c962a1
title: Streamflow data for Saddle stream, 1999 - ongoing.

description: This is a summary of discharges from the stream draining Niwot Ridge
 Saddle to the south and is based on stage records gauged at a timber
 weir with a 120 degree V-notch plate, located 30 m upstream of Green
 Lakes road. It consists of daily flow volumes.
DOI: 10.5061/dryad.sr148
title: Data from: Playing smart vs. playing safe: the joint expression of phenotypic plasticity and potential bet hedging across and within thermal environments

description: Adaptive phenotypic plasticity evolves when cues reliably predict fitness
 consequences of life-history decisions, whereas bet hedging evolves when
 environments are unpredictable. These modes of response should be jointly
 expressed, because environmental variance is composed of both predictable
 and unpredictable components. However, little attention has been paid to
 the joint expression of plasticity and bet hedging. Here, I examine the
 simultaneous expression of plasticity in germination rate and two
 potential bet-hedging traits – germination fraction and within-season
 diversification in timing of germination – in seeds from multiple seed
 families of five geographically distant populations of Lobelia inflata
 (L.) subjected to a thermal gradient. Populations differ in germination
 plasticity to temperature, in total germination fraction and in the
 expression of potential diversification in the timing of germination. The
 observation of a negative partial correlation between the expression of
 plasticity and germination variance (potential diversification), and a
 positive correlation between plasticity and germination fraction is
 suggestive of a trade-off between modes of response to environmental
 variance. If the observed correlations are indicative of those between
 adaptive plasticity and bet hedging, we expect an optimal balance to exist
 and differ among populations. I discuss the challenges involved in testing
 whether the balance between plasticity and bet hedging depends on the
 relative predictability of environmental variance.
description: Thermogradient
 germination data for Lobelia inflataGermination data
 collected over single 60-day observation period. Columns: Temp=temperature
 °C; Pos=randomized position at a given temperature; Pop=population (see
 paper for details); Geno=genotype ID; GenoTag to provide unique identifier
 for genotypes across populations; Rep=replicate individual within Geno;
 GermT=time to germination (days); Germ=germination within 60 days (0=no,
 1=yes).Simons germination data
 2014.xls
DOI: 10.5061/dryad.38n0n
title: Data from: Reducing early infant mortality in India: results of a prospective cohort of pregnant women utilizing emergency medical services

description: Objectives: To describe the demographic characteristics and clinical
 outcomes of neonates born within 7 days of public ambulance transport to
 hospitals across five states in India. Design: Prospective observational
 study. Setting: Five Indian states using a centralised EMS agency that
 transported 3.1 million pregnant women in 2014. Participants: Over 6 weeks
 in 2014, this study followed a convenience sample of 1,431 neonates born
 to women utilizing a public-private ambulance service for a ‘pregnancy
 related’ problem. Initial calls were deemed ‘pregnancy related’ if
 categorised by EMS dispatchers as ‘pregnancy’, ‘childbirth’, ‘miscarriage’
 or ‘labour pains’. Interfacility transfers, patients absent on ambulance
 arrival, refusal of care, and neonates born to women beyond 7 days of
 using the service were excluded. Main outcome measures: Death at 2, 7 and
 42 days after delivery. Results: Among 1,684 women, 1,411 gave birth to
 1,431 newborns within 7 days of initial ambulance transport. Median
 maternal age at delivery was 23 years (IQR: 21-25). Most mothers were from
 rural/tribal areas (92.5%) and lower social (79.9%) and economic status
 (69.9%). Follow-up rates at 2, 7 and 42 days were 99.8%, 99.3% and 94.1%,
 respectively. Cumulative mortality rates at 2, 7 and 42-days follow-up
 were 41, 53 and 62 per 1000 births, respectively. The perinatal mortality
 rate (PMR) was 53 per 1000. Preterm birth [OR: 2.89, 95% CI: 1.67-5.00],
 twin deliveries (OR: 2.80, 95% CI: 1.10-7.15), and cesarean section (2.21,
 95% CI: 1.15-4.23) were the strongest predictors of mortality.
 Conclusions: The perinatal mortality rate associated with this cohort of
 patients with high-acuity conditions of pregnancy was nearly two times the
 most recent rate for India as a whole (28 per 1000 births). EMS data has
 the potential to provide more robust estimates of PMR, reduce inequities
 in timely access to healthcare, and increase facility-based care through
 service of marginalized populations.
description: Neonatal cohort
 IndiaCohort of neonates born
 to mothers utilizing prehospital ambulance services within 7 days of
 birth
DOI: 10.5061/dryad.896r3
title: Data from: Putting the waste out: a proposed mechanism for transmission of the mycoparasite Escovopsis between leafcutter ant colonies

description: The attine ant system is a remarkable example of symbiosis. An
 antagonistic partner within this system is the fungal parasite Escovopsis,
 a genus specific to the fungal gardens of the Attini. Escovopsis
 parasitizes the Leucoagaricus symbiont that leaf-cutting ants (Acromyrmex,
 Atta) have been farming over the past 8-12 million years. However, it has
 been a puzzle how Escovopsis reaches its host. During a seasonal survey of
 nests of Acromyrmex subterraneus subterraneus in Atlantic rainforest in
 Brazil, Escovopsis was detected in all the sampled fungal garden waste
 tips or middens (n = 111). Middens were built strategically; always below
 the nest entrances. Here, we report the first evidence of a putative
 mechanism for horizontal transmission of Escovopsis between attine
 colonies. It is posited that leaf-cutting ants pick up the spores from
 soil and litter during foraging and vector the mycoparasite between attine
 colonies. Field and laboratory experiments, using Atta laevigata and
 Acromyrmex subterraneus subterraneus, confirm that Escovopsis spores are
 phoretic, and have an in-built dormancy, broken by the presence of their
 Leucoagaricus host. However, in the coevolutionary arms race, Atta ants
 may lose out – despite most species in the genus investing in a more
 advanced waste disposal system – due to the insanitary habits of their
 Acromyrmex neighbours.
description: Dados_middens_SM_2011Data on fungi from leafcutter middens, Viçosa, MG, SE Brazil
DOI: 10.5061/dryad.211gr
title: Data from: Myelin basic protein induces neuron-specific toxicity by directly damaging the neuronal plasma membrane

description: The central nervous system (CNS) insults may cause massive demyelination
 and lead to the release of myelin-associated proteins including its major
 component myelin basic protein (MBP). MBP is reported to induce glial
 activation but its effect on neurons is still little known. Here we found
 that MBP specifically bound to the extracellular surface of the neuronal
 plasma membrane and induced neurotoxicity in vitro. This effect of MBP on
 neurons was basicity-dependent because the binding was blocked by acidic
 lipids and competed by other basic proteins. Further studies revealed that
 MBP induced damage to neuronal membrane integrity and function by
 depolarizing the resting membrane potential, increasing the permeability
 to cations and other molecules, and decreasing the membrane fluidity. At
 last, artificial liposome vesicle assay showed that MBP directly disturbed
 acidic lipid bilayer and resulted in increased membrane permeability.
 These results revealed that MBP induces neurotoxicity through its direct
 interaction with acidic components on the extracellular surface of
 neuronal membrane, which may suggest a possible contribution of MBP to the
 pathogenesis in the CNS disorders with myelin damage.
description: MBP is toxic to primary
 hippocampal neurons in vitroOriginal data of
 statistical graph in Figure 1Jie Zhang et al.
 PlOSONE-Figure1.xlsxToxicity of MBP relies
 on polypeptide basicityOriginal data of
 statistical graph in Figure 4Jie Zhang et al.
 PlOSONE-Figure4.xlsxMBP depolarizes the
 resting membrane potentialOriginal data of
 statistical graph in Figure 5Jie Zhang et al.
 PlOSONE-Figure5.xlsxMBP induces cation
 influxOriginal data of
 statistical graph in Figure 6Jie Zhang et al.
 PlOSONE-Figure6.xlsxMBP interferes with the
 fluidity of the neuronal plasma membraneOriginal data of
 statistical graph in Figure 7Jie Zhang et al.
 PlOSONE-Figure7.xlsxMBP directly disrupts
 the integrity of the lipid bilayer in vitroOriginal data of
 statistical graph in Figure 10Jie Zhang et al.
 PlOSONE-Figure10.xlsxFurther confirmation of
 MBP-induced neurotoxicityOriginal data of
 statistical graph in Figure S1Jie Zhang et al.
 PlOSONE-FigureS1.xlsxNeurotoxicity induced by
 heat-inactivated MBPOriginal data of
 statistical graph in Figure S2Jie Zhang et al.
 PlOSONE-FigureS2.xlsxPRM induces
 neurotoxicityOriginal data of
 statistical graph in Figure S4Jie Zhang et al.
 PlOSONE-FigureS4.xlsxMBP binds to sialic acid
 on neuronal surfaceOriginal data of
 statistical graph in Figure S5Jie Zhang et al.
 PlOSONE-FigureS5.xlsx
DOI: 10.5061/dryad.vf33q
title: Data from: Host ecotype generates evolutionary and epidemiological divergence across a pathogen metapopulation

description: The extent and speed at which pathogens adapt to host resistance varies
 considerably. This presents a challenge for predicting when—and
 where—pathogen evolution may occur. While gene flow and spatially
 heterogeneous environments are recognized to be critical for the
 evolutionary potential of pathogen populations, we lack an understanding
 of how the two jointly shape coevolutionary trajectories between hosts and
 pathogens. The rust pathogen Melampsora lini infects two ecotypes of its
 host plant Linum marginale that occur in close proximity yet in distinct
 populations and habitats. In this study, we found that within-population
 epidemics were different between the two habitats. We then tested for
 pathogen local adaptation at host population and ecotype level in a
 reciprocal inoculation study. Even after controlling for the effect of
 spatial structure on infection outcome, we found strong evidence of
 pathogen adaptation at the host ecotype level. Moreover, sequence analysis
 of two pathogen infectivity loci revealed strong genetic differentiation
 by host ecotype but not by distance. Hence, environmental variation can be
 a key determinant of pathogen population genetic structure and
 coevolutionary dynamics and can generate strong asymmetry in infection
 risks through space.
description: BogHillInfectivity data, Epidemiological data, Genetic data
DOI: 10.15468/dl.2utryn
title: Occurrence Download

description: A dataset containing 415201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Occurrence evidence)",
 "Geometry POLYGON((-104.65895 18.78582,-103.40924 18.78582,-103.40924 20.09053,-104.65895 20.09053,-104.65895 18.78582))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 415201 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000619-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.