cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q8028q
title: Data from: Fitness costs of phoretic nematodes in the burying beetle, Nicrophorus vespilloides

description: 1. Nicrophorus vespilloides is a social beetle that rears its offspring on
 decomposing carrion. Wild beetles are frequently associated with two types
 of macrobial symbionts, mites and nematodes. 2. Although these organisms
 are believed to be phoretic commensals that harmlessly use beetles as a
 means of transfer between carcasses, the role of these symbionts on N.
 vespilloides fitness is poorly understood. Here we show that nematodes
 have significant negative effects on beetle fitness across a range of worm
 densities and also quantify the density-dependent transmission of worms
 between mating individuals and from parents to offspring. 3. Using
 field-caught beetles, we provide the first report of a new nematode
 symbiont in N. vespilloides, most closely related to Rhabditoides regina,
 and show that worm densities are highly variable across individuals
 isolated from nature but do not differ between males and females. Next, by
 inoculating mating females with increasing densities of nematodes, we show
 that worm infections significantly reduce brood size, larval survival and
 larval mass, and also eliminate the trade-off between brood size and
 larval mass. Finally, we show that nematodes are efficiently transmitted
 between mating individuals and from mothers to larvae, directly and
 indirectly via the carcass, and that worms persist through pupation. 4.
 These results show that the phoretic nematode R. regina can be highly
 parasitic to burying beetles but can nevertheless persist because of
 efficient mechanisms of intersexual and intergenerational transmission. 5.
 Phoretic species are exceptionally common and may cause significant harm
 to their hosts, even though they rely on these larger species for
 transmission to new resources. However, this harm may be inevitable and
 unavoidable if transmission of phoretic symbionts requires nematode
 proliferation. It will be important to determine the generality of our
 results for other phoretic associates of animals.
description: Nematode Data
 Summary
DOI: 10.5061/dryad.k2d8t
title: Data from: Various competitive interactions explain niche separation in crop-dwelling web spiders

description: Competition for resources is a major organizing principle in communities
 of organisms that share similar ecological niches. Niche separation by
 means of exploitation or interference competition was investigated in two
 taxa of crop-inhabiting spiders that overlap in microhabitat use and have
 similar web design. Competition for prey and web sites was tested in
 microcosm experiments with the most common species that build sheet-webs:
 Enoplognatha gemina (Theridiidae) and Alioranus pastoralis (Linyphiidae).
 A field survey over the crop season provided data on spatial and temporal
 dispersion of Enoplognatha spp. (Theridiidae) and linyphiid spiders
 (Linyphiidae) and on availability of prey over the season. In the
 microcosm experiments, both taxa took springtails as prey, but only
 Enoplognatha fed on aphids. Differences in diet, however, could not be
 attributed to either exploitative or interference competition. Spatial
 separation of websites was attained by vertical displacement of webs in
 the vegetation (Enoplognatha) and by avoidance of patches occupied by
 conspecific or heterospecific individuals (linyphiids). In the field,
 densities of linyphiids and Enoplognatha were correlated negatively and
 webs were over-dispersed relative to a random distribution. Both taxa
 colonized the field at the start of the season; linyphiids colonized as
 adults, quickly reproduced, and had a second adult peak; Enoplognatha
 matured in the middle of the season and their numbers remained fairly
 constant over the season. The combined experimental manipulations and
 field data suggest that niche separation occurs at different scales. The
 hypothesis of competition for websites was partially supported, while prey
 preference (or tolerance) and temporal differences in life history stages
 also may explain the negative correlations between densities of the two
 taxa.
description: Collections of spiders
 and prey from wheat fields (Israel)Web building spiders
 (Linyphiidae and Theridiidae) were collected in 1X1m plots. Potential prey
 was collected using sticky traps located horizontally above
 groundData1.xlsPredation of springtails and aphids by spidersResults of microcosm experiment that tested the predation of Collembola and aphids by spiders (Lhinyphiidae and Theridiidae).data2.xlsx
DOI: 10.5061/dryad.m7m4r
title: Data from: Morphological and moisture availability controls of the leaf area-to-sapwood area ratio: analysis of measurements on Australian trees

description: 1. The leaf area-to-sapwood area ratio (LA:SA) is a key plant trait that
 links photosynthesis to transpiration. The pipe model theory states that
 the sapwood cross-sectional area of a stem or branch at any point should
 scale isometrically with the area of leaves distal to that point.
 Optimization theory further suggests that LA:SA should decrease toward
 drier climates. Although acclimation of LA:SA to climate has been reported
 within species, much less is known about the scaling of this trait with
 climate among species. 2. We compiled LA:SA measurements from 184 species
 of Australian evergreen angiosperm trees. The pipe model was broadly
 confirmed, based on measurements on branches and trunks of trees from one
 to 27 years old. Despite considerable scatter in LA:SA among species,
 quantile regression showed strong (0.2 &lt; R1 &lt; 0.65) positive
 relationships between two climatic moisture indices and the lowermost (5%)
 and uppermost (5–15%) quantiles of log LA:SA, suggesting that moisture
 availability constrains the envelope of minimum and maximum values of
 LA:SA typical for any given climate. 3. Interspecific differences in plant
 hydraulic conductivity are probably responsible for the large scatter of
 values in the mid-quantile range and may be an important determinant of
 tree morphology.
description: Supplementary
 information 1_LA_SA Togashi datasetHuber Value dataset for
 183 evergreen angiosperm trees in Australia
DOI: 10.5061/dryad.3fs0q
title: Data from: Gene flow and population structure of a common agricultural wild species (Microtus agrestis) under different land management regimes

description: The impact of landscape structure and land management on dispersal of
 populations of wild species inhabiting the agricultural landscape was
 investigated focusing on the field vole (Microtus agrestis) in three
 different areas in Denmark using molecular genetic markers. The main
 hypotheses were the following: (i) organic farms act as genetic sources
 and diversity reservoirs for species living in agricultural areas and (ii)
 gene flow and genetic structure in the agricultural landscape are
 influenced by the degree of landscape complexity and connectivity. A total
 of 443 individual voles were sampled within 2 consecutive years from two
 agricultural areas and one relatively undisturbed grassland area. As
 genetic markers, 15 polymorphic microsatellite loci (nuclear markers) and
 the central part of the cytochrome-b (mitochondrial sequence) were
 analysed for all samples. The results indicate that management (that is,
 organic or conventional management) was important for genetic population
 structure across the landscape, but that landscape structure was the main
 factor shaping gene flow and genetic diversity. More importantly, the
 presence of organically managed areas did not act as a genetic reservoir
 for conventional areas, instead the most important predictor of effective
 population size was the amount of unmanaged available habitat (core area).
 The relatively undisturbed natural area showed a lower level of genetic
 structuring and genetic diversity compared with the two agricultural
 areas. These findings altogether suggest that political decisions for
 supporting wildlife friendly land management should take into account both
 management and landscape structure factors.
description: Microsatellite
 dataThe data file is in
 GenAlEx format. The first line contains (in order): number of markers
 used, total number of samples, number of populations and number of samples
 per population. Second line: species name and name of each population.
 Third line: columns headers (from 3rd columns onwards: markers names).The
 rest of the file contains the data: 1st column is sample name, 2nd column
 population of belonging, following columns microsatellite data (every
 sample is showed in one line format, therefore two columns are used for
 each marker).DataDryad.xlsx
DOI: 10.5061/dryad.td6tm4f6
title: Data from: The prediction of adaptive evolution: empirical application of the secondary theorem of selection and comparison to the breeder's equation

description: Adaptive evolution occurs when fitness covaries with genetic merit for a
 trait (or traits). The breeder’s equation (BE), in both its univariate and
 multivariate forms, allows us to predict this process by combining
 estimates of selection on phenotype with estimates of genetic
 (co)variation. However, predictions are only valid if all factors causal
 for trait-fitness covariance are measured. While this requirement will
 rarely (if ever) be met in practice, it can be avoided by applying
 Robertson’s secondary theorem of selection (STS). The STS predicts
 evolution by directly estimating the genetic basis of trait-fitness
 covariation with out any explicit model of selection. Here we apply the BE
 and STS to four morphological traits measured in Soay sheep (Ovis aries)
 from St. Kilda. Despite apparently positive selection on heritable size
 traits, sheep are not getting larger. However, while the BE predicts
 increasing size the STS does not, a discrepancy that suggests unmeasured
 factors are upwardly biasing our estimates of selection on phenotype. We
 suggest this is likely to be a general issue, and that wider application
 of the STS could offer at least a partial resolution to the common
 discrepancy between naive expectations and observed trait dynamics in
 natural populations.
description: MorrisseyEtAlEvolution2012DataR data file containing a list. The list is composed of two elements: (1) a data frame containing individual phenotypic measures and covariates, and (2) the pedigree.
DOI: 10.5061/dryad.sc281
title: Data from: Arsenic induces members of the mmu-miR-466-669 cluster which reduces NeuroD1 expression

description: Chronic arsenic exposure can result in adverse development effects
 including decreased intellectual function, reduced birth weight, and
 altered locomotor activity. Previous in vitro studies have shown that
 arsenic inhibits stem cell differentiation. MicroRNAs (miRNAs) are small
 non-coding RNAs that regulate multiple cellular processes including
 embryonic development and cell differentiation. The purpose of this study
 was to examine whether altered miRNA expression was a mechanism by which
 arsenic inhibited cellular differentiation. The pluripotent P19 mouse
 embryonal carcinoma cells were exposed to 0 or 0.5 μM sodium arsenite for
 9 days during cell differentiation, and changes in miRNA expression was
 analyzed using microarrays. We found that the expression of several miRNAs
 important in cellular differentiation, such as miR-9 and miR-199 were
 decreased by 1.9- and 1.6-fold respectively following arsenic exposure,
 while miR-92a, miR-291a, and miR-709 were increased by 3-, 3.7- and
 1.6-fold, respectively. The members of the miR-466-669 cluster and its
 host gene, Scm-Like with four Mbt domains 2 (Sfmbt2), were significantly
 induced by arsenic from 1.5- to 4-fold in a time-dependent manner.
 Multiple miRNA target prediction programs revealed that several neurogenic
 transcription factors appear to be targets of the cluster. When consensus
 anti-miRNAs targeting the miR-466-669 cluster were transfected into P19
 cells, arsenic-exposed cells were able to more effectively differentiate.
 The consensus anti-miRNAs appeared to rescue the inhibitory effects of
 arsenic on cell differentiation due to an increased expression of NeuroD1.
 Taken together, we conclude that arsenic induces the miR-466-669 cluster,
 and that this induction acts to inhibit cellular differentiation in part
 due to a repression of NeuroD1.
description: Expression changes in
 differentiating P19 cells after arsenc exposureP19 cells were
 aggregated into embryoid bodies and then allowed to differentiate for a
 total of 9 days. Cells were continuously exposed to 0 or 0.5uM arsenite
 during this process, along with 1% dimethylsulfoxide (DMSO) to induce
 differentiation. Cells were collected on day 9. Data file is microRNA
 expression using LC Science's murine miRNA microarray (Geo platform
 GPL 21312).Array data for
 Dryad.csv
DOI: 10.5061/dryad.jv75p
title: Data from: The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding

description: Additive diversity partitioning (α, β, and γ) is commonly used to study
 the distribution of species-level diversity across spatial scales. Here,
 we first investigate whether published studies of additive diversity
 partitioning show signs of difficulty attaining species-level resolution
 due to inherent limitations with morphological identifications. Second, we
 present a DNA barcoding approach in order to delineate specimens of stream
 caddisfly larvae (order Trichoptera) and considered the importance of
 taxonomic resolution on classical (additive) measures of beta (β)
 diversity. Caddisfly larvae were sampled using a hierarchical spatial
 design in two regions (sub-Arctic Churchill, Manitoba, Canada; temperate
 Pennsylvania, USA) and then additively partitioned according to Barcode
 Index Numbers (molecular clusters that serve as a proxy for species),
 genus, and family levels; diversity components were expressed as
 proportional species turnover. We screened 114 articles of additive
 diversity partitioning and found that a third reported difficulties with
 achieving species-level identifications, with a clear taxonomic tendency
 towards challenges identifying invertebrate taxa. Regarding our own study,
 caddisfly BINs appeared to show greater sub-regional turnover (e.g.
 proportional additive β) compared to genus or family levels. Diversity
 component studies failing to achieve species resolution due to
 morphological identifications may therefore be underestimating diversity
 turnover at larger spatial scales.
description: Bringloe et
 al.-Trichoptera density data site*taxonThis file contains
 site*taxon density data for Trichoptera sampled in sub-Arctic Churchill
 (Canada) and temperate Pennsylvania. Included is a sheet on environmental
 information from the time of sampling. Note species names may have since
 been revised, but BIN numbers are included so users can check for updates
 in the Barcode of Life Datasystems (BOLD). The BOLD project doi where
 specimen and sequence information is also available is
 dx.doi.org/10.5883/DS-LTLCP.Density data
 site*taxon.xlsxBringloe et al. Master
 Literature Search Additive PartitioningThis excel file includes
 114 articles reviewed for difficulties identifying species when morphology
 is used in diversity component studies. Publication information,
 categorizations and focal taxa information are
 included.Bringloe_et_al._Master_Literature_Search_Additive_Partitioning+1429730347.xlsx
DOI: 10.5061/dryad.q03d6
title: Data from: Condition-dependent trade-off between weapon size and immunity in males of the European earwig

description: Investigating the expression of trade-offs between key life-history
 functions is central to our understanding of how these functions evolved
 and are maintained. However, detecting trade-offs can be challenging due
 to variation in resource availability, which masks trade-offs at the
 population level. Here, we investigated in the European earwig Forficula
 auricularia whether (1) weapon size trades off with three key immune
 parameters – hemocyte concentration, phenoloxidase and prophenoloxidase
 activity - and whether (2) expression and strength of these trade-offs
 depend on male body condition (body size) and/or change after an immune
 challenge. Our results partially confirmed condition dependent trade-offs
 between weapon size and immunity in male earwigs. Specifically, we found
 that after an immune challenge, weapon size trades off with hemocyte
 concentrations in low-condition, but not in good-condition males.
 Contrastingly, weapon size was independent of pre-challenge hemocyte
 concentration. We also found no trade-off between weapon size and
 phenoloxidase activity, independent of body condition and immune
 challenge. Overall, our study reveals that trade-offs with sexual traits
 may weaken or disappear in good-condition individuals. Given the
 importance of weapon size for male reproductive success, our results
 highlight how low-condition individuals may employ alternative
 life-history investment strategies to cope with resource limitation.
description: Dataset with Male size
 & immune measurementsThis is the dataset
 belonging to the paper titled "Condition-dependent trade-off between
 weapon size and immunity in males of the European
 earwig"Data_Forceps_SCIREP.xlsx
DOI: 10.5061/dryad.qb814
title: Data from: Within-host competition and drug resistance in the human malaria parasite Plasmodium falciparum

description: Infections with the malaria parasite Plasmodium falciparum typically
 comprise multiple strains, especially in high-transmission areas where
 infectious mosquito bites occur frequently. However, little is known about
 the dynamics of mixed-strain infections, particularly whether strains
 sharing a host compete or grow independently. Competition between
 drug-sensitive and drug-resistant strains, if it occurs, could be a
 crucial determinant of the spread of resistance. We analyzed 1,341 P.
 falciparum infections in children from Angola, Ghana, and Tanzania and
 found compelling evidence for competition in mixed-strain infections:
 overall parasite density did not increase with additional strains, and
 densities of individual strains (chloroquine-sensitive and
 chloroquine-resistant) were reduced in the presence of competitors. We
 also found that chloroquine-resistant strains exhibited low densities
 compared to chloroquine-sensitive strains (in the absence of chloroquine),
 which may underlie observed declines of chloroquine resistance in many
 countries following retirement of chloroquine as a first-line therapy. Our
 observations support a key role for within-host competition in the
 evolution of drug-resistant malaria. Malaria control and
 resistance-management efforts in high-transmission regions may be
 significantly aided, or hindered, by the effects of competition in
 mixed-strain infections. Consideration of within-host dynamics may spur
 development of novel strategies to minimize resistance while maximizing
 the benefits of control measures.
description: Bushman
 DataThis folder includes all
 data necessary to reproduce the reported findings. Some files overlap in
 content but are formatted to facilitate analysis (R code at
 https://github.com/falciparum/Competition-Analysis.git). Data include
 parasitemia, genotype, age, location, year of sample collection,
 microsatellite genotyping results, MOI frequencies, and certain controls
 used to correct results for mixed-genotype infections.
DOI: 10.5061/dryad.p0p92
title: Data from: Recent speciation and elevated Z-chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals

description: Sex chromosomes potentially have an important role in speciation and often
 have elevated differentiation between closely related species. In birds,
 traits associated with male plumage, female mate preference, and hybrid
 fitness have been linked to the Z-chromosome (females are heterogametic,
 ZW). We tested for elevated Z-differentiation between two recently
 diverged species of Australian ducks, the sexually monochromatic grey teal
 Anas gracilis and the dichromatic chestnut teal A. castanea. Despite
 prominent morphological differences, these two species are genetically
 indistinguishable at both mitochondrial DNA (mean ΦST &lt; 0.0001) and
 17 autosomal loci (mean ΦST = 0.0056). However, we detected elevated
 Z-differentiation (mean ΦST = 0.281) and tentative evidence of an island
 of differentiation on the Z-chromosome. This elevated differentiation was
 explained by a high frequency of derived alleles in chestnut teal that
 were absent in grey teal, which parallels independent evidence for a gain
 in dichromatism from a monochromatic ancestor. Coalescent estimates of
 demographic history and simulations indicated that the elevated
 Z-differentiation was unlikely to be explained by neutral processes, but
 instead supported a role of divergent selection. We discuss evidence for
 models of speciation with gene flow versus adaptive divergence in the
 absence of gene flow and find that both hypotheses are plausible
 explanations of the data. Overall, these teal have the weakest background
 differentiation documented to date for a species showing a large Z-effect,
 and they are an excellent model species for studying speciation genomics
 and the evolution of sexual dichromatism.
description: Specimen data for
 Australian TealSpecimen information for
 23 Chestnut teal (Anas castanea) and 48 grey teal (Anas gracilis),
 including specimen number, DNA number, sex, and collection
 locality.SamplingInformation_AustralianTeal.xlsxPhased FASTA filesFASTA files for phased alleles from 7 Z-chromosome introns and 17 autosomal introns sequenced from chestnut teal and grey teal.AUTE_phased_FASTA_files.zipConcatenated NEXUS filesNEXUS files of concatenated DNA sequences for 7 Z-chromosome loci (69 individuals; 2637 bp) and 17 autosomal loci (71 individuals; 5351 bp). Each individual is represented by a single consensus sequence with polymorphic positions coded by IUPAC ambiguity codes. Missing data are coded as "?".Concatenated_NEXUS_files.zipIMa2 input filesIMa2 input files for 7 Z-chromosome loci and 17 autosomal loci. Sequences are partitioned into two populations "CT" for chestnut teal and "GT" for grey teal. Sequences have been filtered to be consistent with no recombination.IM_input_files.zip