cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gr5n3
title: Data from: The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region

description: Developmental responses to nutritional variation represent one of the
 ecologically most important classes of adaptive plasticity. However,
 knowledge of genome-wide patterns of nutrition-responsive gene expression
 is limited. Here, we studied genome-wide transcriptional responses to
 nutritional variation and their dependency on trait and sex in the beetle
 Onthophagus taurus. We find that averaged across the transcriptome,
 nutrition contributes less to overall variation in gene expression than do
 sex or body region, but that for a modest subset of genes nutrition is by
 far the most important determinant of expression variation. Furthermore,
 our results reject the hypothesis that a common machinery may underlie
 nutrition-sensitive development across body regions. Instead, we find that
 magnitude (measured by number of differentially expressed contigs),
 composition (measured by functional enrichment) and evolutionary
 consequences (measured by patterns of sequence variation) are heavily
 dependent on exactly which body region is considered and the degree of
 sexual dimorphism observed on a morphological level. More generally, our
 findings illustrate that studies into the developmental mechanisms and
 evolutionary consequences of nutrition-biased gene expression must take
 into account the dynamics and complexities imposed by other sources of
 variation in gene expression such as sexual dimorphism and trait type.
description: SNP data summary for
 DRYADAll gene expression data
 are deposited at NCBI GEO accession number GSE58496. This data file
 includes counts of SNPs for each contig used in the analysis of patterns
 of genetic variation.
DOI: 10.5061/dryad.d20g3
title: Data from: The value of trophic interactions for ecosystem function: dung beetle communities influence seed burial and seedling recruitment in tropical forests

description: Anthropogenic activities are causing species extinctions, raising concerns
 about the consequences of changing biological communities for ecosystem
 functioning. To address this, we investigated how dung beetle communities
 influence seed burial and seedling recruitment in the Brazilian Amazon.
 First, we conducted a burial and retrieval experiment using seed mimics.
 We found that dung beetle biomass had a stronger positive effect on the
 burial of large than small beads, suggesting that anthropogenic reductions
 in large-bodied beetles will have the greatest effect on the secondary
 dispersal of large-seeded plant species. Second, we established mesocosm
 experiments in which dung beetle communities buried Myrciaria dubia seeds
 to examine plant emergence and survival. Contrary to expectations, we
 found that beetle diversity and biomass negatively influenced seedling
 emergence, but positively affected the survival of seedlings that emerged.
 Finally, we conducted germination trials to establish the optimum burial
 depth of experimental seeds, revealing a negative relationship between
 burial depth and seedling emergence success. Our results provide novel
 evidence that seed burial by dung beetles may be detrimental for the
 emergence of some seed species. However, we also detected positive impacts
 of beetle activity on seedling recruitment, which are probably because of
 their influence on soil properties. Overall, this study provides new
 evidence that anthropogenic impacts on dung beetle communities could
 influence the structure of tropical forests; in particular, their capacity
 to regenerate and continue to provide valuable functions and services.
description: Location of seed mimics
 in the soilThe depths of seed
 mimics recovered from soil beneath mesocosms during 2012
 experimentsBead burial in 2012
 mesocosms.xlsxBeetle species with
 traits in 2012 mesocosmsDung beetle species
 recovered from mesocosms during 2012 experiments with continuous and
 categorical trait informationBeetles species with
 traits in 2014 mesocosmsSpecies list with
 continuous and categorical trait information of dung beetles recovered
 from 2014 mesocosm experimentsSeedling emergence and
 survival within germination plotsThe emergence and
 survival of seeds planted at various depths, either with or without
 dungSeedling emergence and
 survival within mesocosmsThe emergence and
 survival success of seeds buried by dung beetles
DOI: 10.5061/dryad.6rj63
title: Data from: Relative costs of offspring sex and offspring survival in a polygynous mammal

description: Costs of reproduction are expected to be ubiquitous in wild animal
 populations and understanding the drivers of variation in these costs is
 an important aspect of life-history evolution theory. We use a 43 year
 dataset from a wild population of red deer to examine the relative
 importance of two factors that influence the costs of reproduction to
 mothers, and to test whether these costs vary with changing ecological
 conditions. Like previous studies, our analyses indicate fitness costs of
 lactation: mothers whose calves survived the summer subsequently showed
 lower survival and fecundity than those whose calves died soon after
 birth, accounting for 5% and 14% of the variation in mothers'
 survival and fecundity, respectively. The production of a male calf
 depressed maternal survival and fecundity more than production of a
 female, but accounted for less than 1% of the variation in either fitness
 component. There was no evidence for any change in the effect of calf
 survival or sex with increasing population density.
description: GENERAL STATEMENT,
 PLEASE READ THIS BEFORE USING THE DATAFecundity
 dataFecundityData.txtSurvival dataSurvivalData.txt
DOI: 10.5061/dryad.2h1c4
title: Data from: Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

description: Determining the genetic bases of adaptations and their roles in speciation
 are prominent issues in evolutionary biology. Cichlid fish species flocks
 are a prime example of recent rapid radiations often associated with
 adaptive phenotypic divergence from a common ancestor within a short
 period of time. In several radiations of freshwater fishes divergence in
 eco-morphological traits including body shape, color, lips and jaws, are
 thought to underlie their ecological differentiation, specialization and –
 ultimately – speciation. The Midas cichlid species complex (Amphilophus
 spp.) of Nicaragua provides one of the few known examples of sympatric
 speciation where species have rapidly evolved different but parallel
 morphologies in young crater lakes. This study identified significant QTL
 for body shape, using SNPs generated via ddRAD sequencing and geometric
 morphometric analyses of a cross between two ecologically and
 morphologically divergent, sympatric cichlid species endemic to crater
 Lake Apoyo: an elongated limnetic species (A. zaliosus) and a high-bodied
 benthic species (A. astorquii). A total of 453 genome-wide informative
 SNPs were identified in 240 F2 hybrids. These markers were used to
 construct a genetic map in which 25 linkage groups were resolved.
 Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two
 most highly supported QTL-linked genomic regions, genes that might
 contribute to divergence in body shape along the benthic-limnetic axis in
 Midas cichlid sympatric adaptive radiations were identified. These results
 suggest that few genomic regions of large effect contribute to early-stage
 divergence in Midas cichlids.
description: Raw_CoordinatesRaw x,y coordinates for the landmarks and semilandmarks of the individuals used for QTL mapping. Phenotype missing for specimen 628.GenotypesGenotype information in "loc" format (JoinMap) of the 220 F2 individuals used in the QTL mapping.Sample_InfoDescription of the dataset. For each individual (F2 progeny or Parent), the barcode used and the Illumina RAD library are provided.
DOI: 10.5061/dryad.d1c8046
title: Data from: Tick-borne disease risk in a forest food web

description: Changes to the community ecology of hosts for zoonotic pathogens,
 particularly rodents, are likely to influence the emergence and prevalence
 of zoonotic diseases worldwide. However, the complex interactions between
 abiotic factors, pathogens, vectors, hosts, and both food resources and
 predators of hosts are difficult to disentangle. Here we (1) use 19 years
 of data from six large field plots in southeastern New York to compare the
 effects of hypothesized drivers of interannual variation in Lyme disease
 risk, including the abundance of acorns, rodents, and deer, as well as a
 series of climate variables; and (2) employ landscape epidemiology to
 explore how variation in predator community structure and forest cover
 influences spatial variation in the infection prevalence of ticks for the
 Lyme disease bacterium, Borrelia burgdorferi, and two other important
 tick-borne pathogens, Anaplasma phagocytophilum and Babesia microti.
 Acorn-driven increases in the abundance of mice were correlated with a
 lagged increase in the abundance of questing nymph-stage Ixodes scapularis
 ticks infected with Lyme disease bacteria. Abundance of white-tailed deer
 two years prior also correlated with increased density of infected nymphal
 ticks, although the effect was weak. Density of rodents in the current
 year was a strong negative predictor of nymph density, apparently because
 high current abundance of these hosts can remove nymphs from the
 host-seeking population. Warm, dry spring or winter weather was associated
 with reduced density of infected nymphs. At the landscape scale, the
 presence of functionally diverse predator communities or of bobcats, the
 only obligate carnivore, was associated with reduced infection prevalence
 of I. scapularis nymphs with all three zoonotic pathogens. In the case of
 Lyme disease, infection prevalence increased where coyotes were present
 but smaller predators were displaced or otherwise absent. For all
 pathogens, infection prevalence was lowest when forest cover within a 1km
 radius was high. Taken together, our results suggest that a food web
 perspective including bottom-up and top-down forcing is needed to
 understand drivers of tick-borne disease risk, a result that may also
 apply to other rodent-borne zoonoses. Prevention of exposure based on
 ecological indicators of heightened risk should help protect public
 health.
description: Lyme_Study_Dataset_READMELyme_Study_Dataset.csv
DOI: 10.5061/dryad.3f4jr01
title: Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species

description: Targeted capture coupled with high throughput sequencing can be used to
 gain information about nuclear sequence variation at hundreds to thousands
 of loci. Divergent reference capture makes use of molecular data of one
 species to enrich target loci in other (related) species. This is
 particularly valuable for non-model organisms, for which often no a priori
 knowledge exists regarding these loci. Here, we have used targeted capture
 to obtain data for 809 nuclear coding DNA sequences (CDS) in a non-model
 organism, the Eurasian lynx Lynx lynx, using baits designed with the help
 of the published genome of a related model organism (the domestic cat
 Felis catus). Using this approach, we were able to survey intraspecific
 variation at hundreds of nuclear loci in L. lynx across the species’
 European range. A large set of bi-allelic candidate SNPs was then
 evaluated using a high throughput SNP-genotyping platform (Fluidigm),
 which we then reduced to a final 96 SNP-panel based on assay performance
 and reliability; validation was carried out with 100 additional Eurasian
 lynx samples not included in the SNP discovery phase. The 96 SNP-panel
 developed from CDS performed very successfully in the identification of
 individuals and in population genetic structure inference (including the
 assignment of individuals to their source population). In keeping with
 recent studies, our results show that genic SNPs can be valuable for
 genetic monitoring of wildlife species.
description: CDS-baits and SNP
 dataThis ZIP folder contains
 bait sequences (FASTA), the 96 SNP-panel, SNP genotypes (Illumina and
 Fluidigm), and an R script. Details can be found in the READ ME
 file.DRYAD.zip
DOI: 10.5061/dryad.1g2n6d2
title: Data from: The impact of within-host ecology on the fitness of a drug-resistant parasite

description: Background and objectives: The rate of evolution of drug resistance
 depends on the fitness of resistant pathogens. The fitness of resistant
 pathogens is reduced by competition with sensitive pathogens in untreated
 hosts and so enhanced by competitive release in drug-treated hosts. We set
 out to estimate the magnitude of those effects on a variety of fitness
 measures, hypothesizing that competitive suppression and competitive
 release would have larger impacts when resistance was rarer to begin with.
 Methodology: We infected mice with varying densities of drug-resistant
 Plasmodium chabaudi malaria parasites in a fixed density of drug-sensitive
 parasites and followed infection dynamics using strain-specific
 quantitative PCR. Results: Competition with susceptible parasites reduced
 the absolute fitness of resistant parasites by 50-100%. Drug treatment
 increased the absolute fitness from 2- to &gt;10 000-fold. The
 ecological context and choice of fitness measure was responsible for the
 wide variation in those estimates. Initial population growth rates poorly
 predicted parasite abundance and transmission probabilities. Conclusions
 and implications: (i) The sensitivity of estimates of pathogen fitness to
 ecological context and choice of fitness measure make it difficult to
 derive field-relevant estimates of the fitness costs and benefits of
 resistance from experimental settings. (ii) Competitive suppression can be
 a key force preventing resistance from emerging when it is rare, as it is
 when it first arises. (iii) Drug treatment profoundly affects the fitness
 of resistance. Resistance evolution could be slowed by developing drug use
 policies that consider in-host competition.
description: Raw data Huijben et al
 2018 EMPHRodent malaria data on
 asexual parasite densities, gametocyte densities, weight and red blood
 cell densities throughout course of infection (day 3-49). Data used in
 Huijben, S., Chan, B.H.K., Nelson, W.A. & Read, A.F. (2018). The
 impact of within-host ecology on the fitness of a drug-resistant parasite.
 Evolution, Medicine, and Public Health 2018(1): 127–137 and Huijben, S.,
 Chan, B.H.K., & Read, A.F. (2015). The relevance of undetectably rare
 resistant malaria parasites in treatment failure: experimental evidence
 from Plasmodium chabaudi. American Journal of Hygiene and Tropical
 Medicine 92: 1214-1221.
DOI: 10.5061/dryad.rn228
title: Data from: Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America

description: We investigate population genetic structuring in Margaritifera falcata, a
 freshwater mussel native to western North America, across the majority of
 its geographical range. We find shallow rangewide genetic structure,
 strong population-level structuring and very low population diversity in
 this species, using both mitochondrial sequence and nuclear microsatellite
 data. We contrast these patterns with previous findings in another
 freshwater mussel species group (Anodonta californiensis/A. nuttalliana)
 occupying the same continental region and many of the same watersheds. We
 conclude that differences are likely caused by contrasting life history
 attributes between genera, particularly host fish requirements and
 hermaphroditism. Further, we demonstrate the occurrence of a ‘hotspot’ for
 genetic diversity in both groups of mussels, occurring in the vicinity of
 the lower Columbia River drainage. We suggest that stream hierarchy may be
 responsible for this pattern and may produce similar patterns in other
 widespread freshwater species.
description: MargPops48_UTMsThis is a list of the spatial coordinates for the populations and subpopulations referenced in the paper.GAEPopReg20Nov12This is a file of raw microsatellite genotypes by population for Margaritifera falcata in the western United States. The data are in GenAlEx format.Margaritifera falcata COI-F mitochondrial haplotypesThis is a spreadsheet delineating mitochondrial haplotypes and associated GenBank accessiong numbers for a set of Margaritifera falcata samples from the western United States.MargHaplos19Oct12_Dryad.xlsx
DOI: 10.5061/dryad.m2n6f
title: Data from: Secondary metabolites in floral nectar reduce parasite infections in bumblebees

description: The synthesis of secondary metabolites is a hallmark of plant defence
 against herbivores. These compounds may be detrimental to consumers, but
 can also protect herbivores against parasites. Floral nectar commonly
 contains secondary metabolites, but little is known about the impacts of
 nectar chemistry on pollinators, including bees. We hypothesized that
 nectar secondary metabolites could reduce bee parasite infection. We
 inoculated individual bumblebees with Crithidia bombi, an intestinal
 parasite, and tested effects of eight naturally occurring nectar chemicals
 on parasite population growth. Secondary metabolites strongly reduced
 parasite load, with significant effects of alkaloids, terpenoids and
 iridoid glycosides ranging from 61 to 81%. Using microcolonies, we also
 investigated costs and benefits of consuming anabasine, the compound with
 the strongest effect on parasites, in infected and uninfected bees.
 Anabasine increased time to egg laying, and Crithidia reduced bee
 survival. However, anabasine consumption did not mitigate the negative
 effects of Crithidia, and Crithidia infection did not alter anabasine
 consumption. Our novel results highlight that although secondary
 metabolites may not rescue survival in infected bees, they may play a
 vital role in mediating Crithidia transmission within and between colonies
 by reducing Crithidia infection intensities.
description: Richardson_et_al_2015This MS Excel table includes four datasets described in our publication. There are two experiments, abbreviated as "exp1" and "exp2". The former has just one tab in the table; the latter has three tabs, each attributed according to what data they present. All column headings are defined in an additional metadata tab, and no other user guidance should be necessary.
DOI: 10.5061/dryad.mb32q
title: Data from: Longitudinal study of performance on the Ruff Figural Fluency Test in persons aged 35 years or older

description: The Ruff Figural Fluency Test (RFFT) is a cognitive test to measure
 executive function. Longitudinal studies have shown that repeated testing
 improves performance on the RFFT. Such a practice effect may hinder the
 interpretation of test results in a clinical setting. Therefore, we
 investigated the longitudinal performance on the RFFT in persons aged
 35–82 years. Performance on the RFFT was measured three times over an
 average follow-up period of six years in 2,515 participants of the
 Prevention of REnal and Vascular ENd-stage Disease (PREVEND) study in
 Groningen, the Netherlands: 53% men; mean age (SD), 53 (10) years. The
 effect of consecutive measurements on performance on the RFFT was
 investigated with linear multilevel regression models that also included
 age, gender, educational level and the interaction term consecutive
 measurement number x age as independent variables. It was found that the
 mean (SD) number of unique designs on the RFFT increased from 73 (26) at
 the first measurement to 79 (27) at the second measurement and to 83 (26)
 at the third measurement (p&lt;0.001). However, the increase per
 consecutive measurement number was negatively associated with age and
 decreased with 0.23 per one-year increment of age (p&lt;0.001). The
 increase per consecutive measurement number was not dependent on
 educational level. Similar results were found for the median (IQR) number
 of perseverative errors which showed a small but statistically significant
 increase with repeating testing: 7 (3–13) at the first measurement, 7
 (4–14) at the second measurement and 8 (4–15) at the third measurement
 (ptrend = 0.002). In conclusion, the performance on the RFFT improved by
 repeating the test over an average follow-up period of three to six years.
 This practice effect was the largest in young adults and not dependent on
 educational level.
description: RFFT longitudinal data
 Groningen the NetherlandsIBM SPSS Statistics
 version 22 file including the individual data on longitudinal performance
 on the Ruff Figural Fluency Test (RFFT) of 2,515 participants of the
 Prevention of Renal and Vascular ENd-stage Disease (PREVEND) study, city
 of Groningen, the Netherlands. Performance on the RFFT was measured three
 times over an average follow-up period of six years.RFFT longitudinal data
 Groningen the NetherlandsCSV file including the
 individual data on longitudinal performance on the Ruff Figural Fluency
 Test (RFFT) of 2,515 participants of the Prevention of Renal and Vascular
 ENd-stage Disease (PREVEND) study, city of Groningen, the Netherlands.
 Performance on the RFFT was measured three times over an average follow-up
 period of six years.
DOI: 10.5061/dryad.d71c1
title: Data from: Investigating processes of neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae)

description: Andean uplift and the collision of North and South America are thought to
 have major implications for the diversification of the Neotropical biota.
 However, few studies have investigated how these geological events may
 have influenced diversification. We present a multilocus phylogeny of 102
 Protieae taxa (73% of published species), sampled pantropically, to test
 hypotheses about the relative importance of dispersal, vicariance, habitat
 specialization, and biotic factors in the diversification of this
 ecologically dominant tribe of Neotropical trees. Bayesian
 fossil-calibrated analyses date the Protieae stem at 55 Mya. Biogeographic
 analyses reconstruct an initial late Oligocene/early Miocene radiation in
 Amazonia for Neotropical Protieae, with several subsequent late Miocene
 dispersal events to Central America, the Caribbean, Brazil's Atlantic
 Forest, and the Chocó. Regional phylogenetic structure results indicate
 frequent dispersal among regions throughout the Miocene and many instances
 of more recent regional in situ speciation. Habitat specialization to
 white sand or flooded soils was common, especially in Amazonia. There was
 one significant increase in diversification rate coincident with
 colonization of the Neotropics, followed by a gradual decrease consistent
 with models of diversity-dependent cladogenesis. Dispersal, biotic
 interactions, and habitat specialization are thus hypothesized to be the
 most important processes underlying the diversification of the Protieae.
description: Alignment and
 TreeAlignment of DNA
 sequences and tree. Nexus format.S15484.nex