cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.88v79
title: Data from: The devil is in the detail: estimating species richness, density, and relative abundance of tropical island herpetofauna

description: Background: One of the basic premises of drawing samples from populations
 is that the samples are representative of the populations. However, error
 in sampling is poorly recognized, and it goes unnoticed especially in
 community ecology. By combining traditional open quadrats used for
 sampling forest floor herpetofauna with intensive bounded quadrats, we
 explore the effect of sampling error on estimates of species richness,
 diversity, and density in the Andaman Islands. Results: Fisher’s α measure
 of species diversity and second order jackknife estimate of species
 richness were not sensitive to number of individuals sampled. Sampling
 error resulted in underestimation of density in both frogs and lizards. It
 influenced relative abundance of individual species resulting in
 underestimation of abundance of small or camouflaged species; and also
 resulted in low precision in lizard species richness estimates.
 Conclusions: Sampling error resulted in underestimation of abundance of
 small, fossorial or camouflaged species. Imperfect detection from less
 intensive sampling method results incorrect estimates of abundance of
 herpetofauna. Fisher’s α for species diversity and second order jackknife
 for species richness were robust measures. These have strong implications
 on inferences made from previous studies as well as sampling strategies
 for future studies. It is essential that these shortfalls are accounted
 for while communities are sampled or when datasets are compared.
description: Key to Andaman lizard
 and frog dataData on the islands that
 were sampled during the studyAndaman frog
 dataData from Andaman
 islands on abundances of frogs from the forest floor. Sampling was done
 using 10 x 10 m quadrats that were open (not fenced) and bounded (that
 were fenced).Andaman lizard
 dataData from Andaman
 islands on abundances of lizards from the forest floor. Sampling was done
 using 10 x 10 m quadrats that were open (not fenced) and bounded (that
 were fenced).
DOI: 10.5061/dryad.68h07
title: Data from: Forest defoliator pests alter carbon and nitrogen cycles

description: Climate change may foster pest epidemics in forests, and thereby the
 fluxes of elements that are indicators of ecosystem functioning. We
 examined compounds of carbon (C) and nitrogen (N) in insect faeces, leaf
 litter, throughfall and analysed the soils of deciduous oak forests
 (Quercus petraea L.) that were heavily infested by the leaf herbivores
 winter moth (Operophtera brumata L.) and mottled umber (Erannis defoliaria
 L.). In infested forests, total net canopy-to-soil fluxes of C and N
 deriving from insect faeces, leaf litter and throughfall were 30- and
 18-fold higher compared with uninfested oak forests, with 4333 kg C ha−1
 and 319 kg N ha−1, respectively, during a pest outbreak over 3 years. In
 infested forests, C and N levels in soil solutions were enhanced and C/N
 ratios in humus layers were reduced indicating an extended canopy-to-soil
 element pathway compared with the non-infested forests. In a microcosm
 incubation experiment, soil treatments with insect faeces showed 16-fold
 higher fluxes of carbon dioxide and 10-fold higher fluxes of dissolved
 organic carbon compared with soil treatments without added insect faeces
 (control). Thus, the deposition of high rates of nitrogen and rapidly
 decomposable carbon compounds in the course of forest pest epidemics
 appears to stimulate soil microbial activity (i.e. heterotrophic
 respiration), and therefore, may represent an important mechanism by which
 climate change can initiate a carbon cycle feedback.
description: Supporting Data
 020916
DOI: 10.15468/dl.a5wqkw
title: Occurrence Download

description: A dataset containing 1190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Actinidia rubricaulis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1190 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001107-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f3s72
title: Data from: The Red Queen lives: epistasis between linked resistance loci

description: A popular theory explaining the maintenance of genetic recombination (sex)
 is the Red Queen Theory. This theory revolves around the idea that
 time-lagged negative frequency-dependent selection by parasites favors
 rare host genotypes generated through recombination. Although the Red
 Queen has been studied for decades, one of its key assumptions has
 remained unsupported. The signature host-parasite specificity underlying
 the Red Queen, where infection depends on a match between host and
 parasite genotypes, relies on epistasis between linked resistance loci for
 which no empirical evidence exists. We performed 13 genetic crosses and
 tested over 7000 Daphnia magna genotypes for resistance to two strains of
 the bacterial pathogen Pasteuria ramosa. Results reveal the presence of
 strong epistasis between three closely linked resistance loci. One locus
 masks the expression of the other two, while these two interact to produce
 a single resistance phenotype. Changing a single allele on one of these
 interacting loci can reverse resistance against the tested parasites. Such
 a genetic mechanism is consistent with host and parasite specificity
 assumed by the Red Queen Theory. These results thus provide evidence for a
 fundamental assumption of this theory and provide a genetic basis for
 understanding the Red Queen dynamics in the Daphnia–Pasteuria system.
description: attachment tests F1 and
 F2excel worksheet
 containing data of three crosses with Daphnia magna that where screened
 for their phenotype with respect to resistance to the bacterial parasite
 Pasteuria ramosa.R code
 recombinationR code used to determine
 the recombination rates between our loci based on our
 observations.
DOI: 10.6084/m9.figshare.31154701
title: The genome of EAAY25

description: Whole-genome sequencing analysis of EAAY25
DOI: 10.6084/m9.figshare.31154701.v1
title: The genome of EAAY25

description: Whole-genome sequencing analysis of EAAY25
DOI: 10.5061/dryad.rd47f
title: Data from: Optimizing countershading camouflage

description: Because the sun and sky are above us, natural illumination is directional
 and the cues from shading reveal shape and depth. However, many animals
 are darker on their backs and, over 100 years ago, it was proposed that
 this phenomenon was camouflage: countering the cues to shape that
 directional illumination creates. However, does this camouflage work in
 practice? We predicted the optimal countershading for different lighting
 conditions and tested this possibility with correspondingly patterned
 model “caterpillars” predated by birds in the wild. Predation rates varied
 with coloration and lighting in exactly the manner predicted. Such
 subtlety in the effects of countershading vindicates conclusions from
 prior evidence demonstrating stronger countershading in animals in more
 brightly lit habitats.
description: Cuthill_et_al_PNAS_dataRaw data file
DOI: 10.5061/dryad.sc3np
title: Data from: Nest predation risk explains variation in avian clutch size

description: Questions about the ecological drivers of, and mechanistic constraints on,
 productivity have driven research on life history evolution for decades.
 Resource availability and offspring mortality are considered among the two
 most important influences on the number of offspring per reproductive
 attempt. We used a factorial experimental design to manipulate food
 abundance and perceived offspring predation risk in a wild avian
 population (red-faced warblers; Cardellina rubrifrons) to identify the
 mechanistic cause of variation in avian clutch size. Additionally, we
 tested whether female quality helped explain the extant variation in
 clutch size. We found no support for the Food Limitation or Female Quality
 Hypotheses, but we did find support for both predictions of the Nest
 Predation Risk Hypothesis. Females that experienced an experimentally
 heightened perception of offspring predation risk responded by laying a
 smaller clutch than females in the control group. Additionally, predation
 rates at artificial nests were highest where red-faced warbler clutch size
 was smallest (at high elevations). Life history theory predicts that an
 individual should invest less in reproduction when high nest predation
 risk reduces the likely benefit from that nesting attempt, and indeed we
 found that birds exhibit phenotypic plasticity in clutch size by laying
 fewer eggs in response to increasing nest predation risk.
description: Artificial Nest
 SurvivalArtificial nest analysis
 dataFemale
 ConditionFemale quality
 dataLaying Period Food
 AbundancePeak laying period food
 abundance dataNest
 ManipulationsExperimental nest
 manipulation data--supplemental food experimental and chipmunk
 introduction experimentNest
 SurvivalRed-faced warbler nest
 success dataNestling
 GrowthNestling growth rate
 dataNestling Period Food
 AbundancePeak nestling period
 food abundance data
DOI: 10.5061/dryad.df119
title: Data from: Indirect food web interactions mediated by rodent cycles: relative roles of lemmings and voles

description: Production cycles in birds are proposed as prime cases of indirect
 interactions in food webs. They are thought to be driven by predators
 switching from rodents to bird nests in the crash phase of rodent
 population cycles. Although rodent cycles are geographically widespread
 and found in different rodent taxa, bird production cycles appear to be
 most profound in the high Arctic where lemmings dominate. We hypothesized
 that this may be due to arctic lemmings inducing stronger predator
 responses than boreal voles. We tested this hypothesis by estimating
 predation rates in dummy bird nests during a rodent cycle in low arctic
 tundra. Here the rodent community consists of a spatially variable mix of
 one lemming (Lemmus lemmus) and two vole species (Myodes rufocanus and
 Microtus oeconomus) with similar abundances. In consistence with our
 hypothesis, lemming peak abundances predicted well crash-phase nest
 predation rates, whereas the vole abundances had no predictive ability.
 Corvids were found to be the most important nest predators. Lemmings
 appear to be accessible to the whole predator community which makes them
 particularly powerful drivers of food web dynamics.
description: Ims et al.
 BiolLetter-DataPredation on artificial
 nests in spring and abundance of three species of small rodents (the
 autumn before) in low-arctic tundra over 3 consecutive
 years.
DOI: 10.5061/dryad.90f03
title: Data from: The mechanical defence advantage of small seeds

description: Seed size and toughness affect seed predators, and size-dependent
 investment in mechanical defence could affect relationships between seed
 size and predation. We tested how seed toughness and mechanical defence
 traits (tissue density and protective tissue content) are related to seed
 size among tropical forest species. Absolute toughness increased with seed
 size. However, smaller seeds had higher specific toughness both within and
 among species, with the smallest seeds requiring over 2000 times more
 energy per gram to break than the largest seeds. Investment in mechanical
 defence traits varied widely but independently of the toughness-mass
 allometry. Instead, a physical scaling relationship confers a toughness
 advantage on small seeds independent of selection on defence traits and
 without a direct cost. This scaling relationship may contribute to seed
 size diversity by decreasing fitness differences among large and small
 seeds. Allometric scaling of toughness reconciles predictions and
 conflicting empirical relationships between seed size and predation.
description: Seed toughness data and
 codeThis zip file contains
 the dataset as a .csv files and an R script for statistical
 analyses.
DOI: 10.5061/dryad.mj5gb
title: Data from: Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae)

description: Hybridisation among taxa with different ploidy levels is often associated
 with hybrid sterility. Clonal reproduction can stabilise these hybrids,
 but pervasive clonality may have a profound impact on the distribution of
 genetic diversity in natural populations. Here we investigate a widespread
 triploid taxon resulting from hybridisation between diploid Mimulus
 guttatus and tetraploid Mimulus luteus, two species that were introduced
 into the United Kingdom (UK) in the nineteenth century. This hybrid,
 Mimulus x robertsii, is largely sterile but capable of prolific vegetative
 propagation and has been recorded in the wild since 1872. We surveyed 40
 Mimulus populations from localities across the UK to examine the current
 incidence of hybrids, and selected seventeen populations for genetic
 analysis using codominant markers. Cluster analyses revealed two main
 groups of genetically distinct individuals, corresponding to either
 diploid (M. guttatus) or polyploid (M. luteus and M. x robertsii) samples.
 Triploid hybrids were found in around 50% of sampled sites, sometimes
 coexisting with one of the parental species (M. guttatus). The other
 parent, M. luteus, was restricted to a single locality. Individual
 populations of M. x robertsii were genetically variable, containing
 multiple, highly heterozygous clones, with the majority of genetic
 variation distributed among- rather than within populations. Our findings
 demonstrate that this largely sterile, clonal taxon can preserve
 non-negligible amounts of genetic variation. The presence of genetically
 variable hybrid populations may provide the material for the continued
 success of asexual taxa in diverse environments.
description: Vallejo-Marin and
 Lye_Genotype data for HDY-12-SP0177_1 Oct 2012Genotype data of 300
 individuals of Mimulus spp. Twelve loci.
DOI: 10.5061/dryad.hq301
title: Data from: Tree species diversity alters plant defence investment in an experimental forest plantation in Southern Mexico

description: The effects of plant species diversity on plant traits conferring
 herbivore resistance (e.g., chemical defences), as well as the mechanisms
 underlying such effects, have received little attention. One potential
 mechanism for diversity effects on plant defences is that increased plant
 growth at high diversity could lead to reduced investment in defences via
 growth-defence trade-offs. We measured tree growth (diameter at breast
 height) and collected leaves for quantification of total phenolics on
 2.5-year old plants of six tropical tree species (N = 597 plants) in a
 young experimental plantation in southern Mexico. Selected plants were
 distributed across 23 plots (21 x 21 m each) classified as monocultures of
 one species (N = 13, 2-3 plots per species) or polycultures (N = 10)
 represented by mixtures of four out of the six species. We found a
 significant negative effect of tree species diversity on total phenolics,
 where polycultures exhibited a 13 percent lower mean concentration than
 monocultures. However, there was marked variation among tree species in
 diversity effects on defences, where some species exhibited strong
 reductions in phenolics in mixtures, whereas others were unresponsive.
 Further, we found no effect of tree species diversity on growth and
 results indicated that the negative effect of diversity on chemical
 defences was not mediated by a growth-defence trade-off. These results
 demonstrate that tree diversity can alter investment in chemical defences
 in long-lived tree species, which has important implications for
 predicting effects on consumers and ecosystem function.
description: Leaf defenses and plant
 growthData on concentration of
 total leaf phenolics and plant growth (diameter at breast height) for six
 species of tropical trees planted at the UADY Tree Diversity Experiment in
 southern Mexico.Dryad
 data.xlsx
DOI: 10.15468/dl.sqvktm
title: Occurrence Download

description: A dataset containing 29877584 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "Geometry POLYGON((16.44571 58.04134,19.30847 58.04134,19.30847 60.24657,16.44571 60.24657,16.44571 58.04134))"
 ]
}

 The dataset includes 29877584 records from 685 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001083-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jp13f
title: Data from: Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus)

description: Premise of the study: The evolution of invasiveness has been extensively
 studied in natural ecosystems; however, far less is known about the
 evolution of agricultural invasiveness, despite the major economic impact
 of weeds on crop productivity. Examining the population structure of
 recently arisen weeds can provide insights into evolutionary avenues to
 invasion of agroecosystems. Weeds that originate from wild plants are the
 most common yet least frequently studied type of agricultural invasive.
 Here we address several questions about the origin of the native North
 American agricultural weed waterhemp (Amaranthus tuberculatus), which
 invaded corn and soy fields in the midwestern United States in the 20th
 century. Methods: We genotyped 38 populations from across the species
 range with 10 microsatellite markers and used these data to assess genetic
 diversity and population structure within and outside the geographical
 region where waterhemp is agriculturally problematic. Key results: We
 found evidence for two ancestral genetic lineages in our data, supporting
 the hypothesis that A. tuberculatus was diverging into two evolutionary
 lineages prior to the 20th century. However, we found no support for the
 hypothesis that agricultural weed populations arose from admixture of
 these two lineages after secondary contact. Our data suggest that eastward
 movement of the western genetic lineage, facilitated by changing
 agricultural practices, is the source of the agricultural invasion of
 waterhemp. Conclusions: This research demonstrates that agricultural
 invasion by native, wild plant species can proceed via different
 evolutionary trajectories from weeds related to domesticated plants, which
 has implications for evolutionary biology and weed control.
description: Microsatellite Data for
 Waselkov and Olsen 2014Microsatellite data for
 all 38 populations of Amaranthus tuberculatus and all 10 microsatellite
 loci used in Waselkov and Olsen 2014. Data is in STRUCTURE format, two
 lines per individual, with "-9" indicating missing
 data.SSR
 Data for Waselkov and Olsen 2014.txt
DOI: 10.5061/dryad.51275
title: Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes and invertebrates

description: Plants are important in urban environments for removing pathogens and
 improving water quality. Seagrass meadows are the most widespread coastal
 ecosystem on the planet. Although these plants are known to be associated
 with natural biocide production, they have not been evaluated for their
 ability to remove microbiological contamination. Using amplicon sequencing
 of the 16S ribosomal RNA gene, we found that when seagrass meadows are
 present, there was a 50% reduction in the relative abundance of potential
 bacterial pathogens capable of causing disease in humans and marine
 organisms. Moreover, field surveys of more than 8000 reef-building corals
 located adjacent to seagrass meadows showed twofold reductions in disease
 levels compared to corals at paired sites without adjacent seagrass
 meadows. These results highlight the importance of seagrass ecosystems to
 the health of humans and other organisms.
description: Datasets: Lamb et al.
 Seagrass ecosystems reduce exposure to pathogens_Datasets
 Includes 3
 datasets for scripts used in Lamb et al. Seagrass ecosystems reduce
 exposure to pathogens_Scripts.R: (1) Enterococcus Assays (Entero.csv), (2)
 Potential pathogens of humans, fishes and marine invertebrates using
 sequencing of 16S rRNA gene (Pathogens.csv) and (3) Prevalence of coral
 diseases (Coral disease.csv). Lamb et al. Seagrass ecosystems
 reduce exposure to pathogens_Datasets.xlsx 
 Scripts: Lamb et al.
 Seagrass ecosystems reduce exposure to pathogens_Scripts
 R scripts used
 in statistical analyses for Figs. 1- 3 and corresponding Supplemental
 Materials. Lamb et al. Seagrass ecosystems
 reduce exposure to pathogens_Scripts.R
DOI: 10.5061/dryad.dt96f84
title: Data from: Early-life telomere length predicts lifespan and lifetime reproductive success in a wild bird

description: Poor conditions during early development can initiate trade-offs that
 favour current survival at the expense of somatic maintenance and
 subsequently, future reproduction. However, the mechanisms that link early
 and late life-history are largely unknown. Recently it has been suggested
 that telomeres, the nucleoprotein structures at the terminal end of
 chromosomes, could link early-life conditions to lifespan and fitness. In
 wild purple-crowned fairy-wrens, we combined measurements of nestling
 telomere length (TL) with detailed life-history data to investigate
 whether early-life TL predicts fitness prospects. Our study differs from
 previous studies in the completeness of our fitness estimates in a highly
 philopatric population. The association between TL and survival was
 age-dependent with early-life TL having a positive effect on lifespan only
 among individuals that survived their first year. Early-life TL was not
 associated with the probability or age of gaining a breeding position.
 Interestingly, early-life TL was positively related to breeding duration,
 contribution to population growth and lifetime reproductive success
 because of their association with lifespan. Thus, early-life TL, which
 reflects growth, accumulated early-life stress and inherited TL, predicted
 fitness in birds that reached adulthood but not noticeably among
 fledglings. These findings suggest that a lack of investment in somatic
 maintenance during development particularly affects late life performance.
 This study demonstrates that factors in early-life are related to fitness
 prospects through lifespan, and suggests that the study of telomeres may
 provide insight into the underlying physiological mechanisms linking
 early- and late-life performance and trade-offs across a lifetime.
description: Eastwood etal_Early life
 TL data_MolEcolFile contains data from
 Eastwood et al. Please see manuscript and read me tab for
 details.Eastwood etal_MolEcol
 data.xlsx