cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j1kn5tq6
title: Data from: Robustness of compound Dirichlet priors for Bayesian inference of branch lengths

description: We modified the phylogenetic program MrBayes 3.1.2 to incorporate the
 compound Dirichlet priors for branch lengths proposed recently by Rannala,
 Zhu, and Yang (2012. Tail paradox, partial identifiability and influential
 priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.)
 as a solution to the problem of branch-length overestimation in Bayesian
 phylogenetic inference. The compound Dirichlet prior specifies a fairly
 diffuse prior on the tree length (the sum of branch lengths) and uses a
 Dirichlet distribution to partition the tree length into branch lengths.
 Six problematic data sets originally analyzed by Brown, Hedtke, Lemmon,
 and Lemmon (2010. When trees grow too long: investigating the causes of
 highly inaccurate Bayesian branch-length estimates. Syst. Biol.
 59:145-161) are reanalyzed using the modified version of MrBayes to
 investigate properties of Bayesian branch-length estimation using the new
 priors. While the default exponential priors for branch lengths produced
 extremely long trees, the compound Dirichlet priors produced posterior
 estimates that are much closer to the maximum likelihood estimates.
 Furthermore, the posterior tree lengths were quite robust to changes in
 the parameter values in the compound Dirichlet priors, for example, when
 the prior mean of tree length changed over several orders of magnitude.
 Our results suggest that the compound Dirichlet priors may be useful for
 correcting branch-length overestimation in phylogenetic analyses of
 empirical data sets.
description: USYB-2011-142.SupplOnline supplemental materialUSYB-2011-142.TableS2Online supplemental material, Table S2patch MrBayes3.1.2Apply this patch for the original MrBayes 3.1.2 to get the modified version with compound Dirichlet priorspatchMB3.zip
DOI: 10.5061/dryad.k7c64
title: Data from: Alternative reproductive tactics in female striped mice: heavier females are more likely to breed solitary than communally

description: 1. Alternative reproductive tactics (ARTs) are discrete reproductive
 phenotypes governed by decision rules called strategies. ARTs are fixed
 for life in species with alternative strategies, while tactic expression
 is plastic in species with a single strategy. ARTs have been investigated
 in males of many species, but few studies have tested whether the same
 theoretical framework applies in females. 2. Female striped mice
 (Rhabdomys pumilio) employ three ARTs: communal breeders give birth in a
 nest shared with female kin and a breeding male and show allo-parental
 care; returners give birth away from the shared nest and later return to
 it; and solitary breeders give birth away from the shared nest and do not
 return to the group. 3. Here, studying free-living female striped mice
 over six breeding seasons, we tested whether ARTs arise from alternative
 strategies or a single strategy. 4. We also asked to what extent
 stochastic extrinsic factors explain whether individuals become solitary
 rather than group living. 5. Females switched tactics, consistent with a
 single strategy, so we tested whether this represented a mixed or
 conditional single strategy. Only the latter predicts differences between
 ARTs in traits indicating competitive ability, such as body mass or age,
 before individuals adopt a tactic. We weighed females at conception when
 they were still group living to eliminate potential confounding effects of
 gestation and subsequent social tactic (solitary versus group living) on
 body mass. 6. Females that went on to use a solitary ART were heavier than
 those that became communal breeders and returners, in support of a
 conditional strategy. 7. Solitary breeders also arose through extrinsic
 factors (mortality of all adult female group members). They weighed less
 than females that became solitary while relatives were alive, but did not
 differ in body mass from communal breeders and returners. 8. We conclude
 that ART theory applies to both sexes, with female striped mice following
 a conditional single strategy. Future studies should consider the
 possibility that phenotypes that superficially resemble evolved tactics
 might also arise through non-adaptive extrinsic causes.
description: Alternative reproductive
 tactics in female striped mice - primary field datastripedmouse_rawdata.csvMultiply imputed data set 1impMAT1.csvMultiply imputed data set 2impMAT2.csvMultiply imputed data set 3impMAT3.csvMultiply imputed data set 4impMAT4.csvMultiply imputed data set 5impMAT5.csvMultiply imputed data set 6impMAT6.csvMultiply imputed data set 7impMAT7.csvMultiply imputed data set 8impMAT8.csvMultiply imputed data set 9impMAT9.csvMultiply imputed data set 10impMAT10.csvTransitions between alternative reproductive tactics in female striped micestripedmouse_tactic_transitions.csvComparing solitary breeders and returners with communal breedersreturner_and_solitary.csvStriped mouse breeding synchronybirthsynchrony.csv
DOI: 10.5061/dryad.gf1fp
title: Data from: Parasitic castration promotes coevolutionary cycling but also imposes a cost on sex

description: Antagonistic coevolution between hosts and parasites is thought to drive a
 range of biological phenomena including the maintenance of sexual
 reproduction. Of particular interest are conditions that produce
 persistent fluctuations in the frequencies of genes governing
 host-parasite specificity (coevolutionary cycling), as sex may be more
 beneficial than asexual reproduction in a constantly changing environment.
 While many studies have shown that coevolutionary cycling can lead to the
 maintenance of sex, the effects of ecological feedbacks on the persistence
 of these fluctuations in gene frequencies are not well understood. Here,
 we use a simple deterministic model that incorporates ecological feedbacks
 to explore how parasitic reductions in host fecundity affect the
 maintenance of coevolutionary cycling. We demonstrate that parasitic
 castration is inherently destabilizing and may be necessary for
 coevolutionary cycling to persist indefinitely, but also reduces the
 likelihood that sexually-reproducing individuals will find a fertile
 partner, which may select against sex. These findings suggest that
 castrators can play an important role in shaping host evolution and are
 likely to be good targets for observing fluctuations in gene frequencies
 that govern specificity in host-parasite interactions.
description: Simulation data and
 codePlease see README.txt
 for full description of files.ashby2014.zip
DOI: 10.5061/dryad.f274gs3
title: Data from: Effect of cadmium accumulation on the performance of plants and of herbivores that cope differently with organic defenses

description: Some plants are able to accumulate in their shoots metals at levels that
 are toxic to most other organisms. This ability may serve as a defence
 against herbivores. Therefore, both metal-based and organic defences may
 affect herbivores. However, how metal accumulation affects the interaction
 between herbivores and organic plant defences remains overlooked. To fill
 this gap, we studied the interactions between tomato (Solanum
 lycopersicum), a model plant that accumulates cadmium, and two spidermite
 species, Tetranychus urticae and Tetranychus evansi that, respectively,
 induce and suppress organic plant defences, measurable via the activity of
 trypsin inhibitors. We exposed plants to different concentrations of
 cadmium and measured its effects on mites and plants. In the plant,
 despite clear evidence for cadmium accumulation, we did not detect any
 cadmium effects on traits that reflect the general response of the plant,
 such as biomass, water content, and carbon/nitrogen ratio. Still, we found
 effects of cadmium upon the quantity of soluble sugars and on leaf
 reflectance, where it may indicate structural modifications in the cells.
 These changes in plant traits affected the performance of spider mites
 feeding on those plants. Indeed, the oviposition of both spider mite
 species was higher on plants exposed to low concentrations of cadmium than
 on control plants, but decreased at concentrations above 0.5 mM.
 Therefore, herbivores with contrasting responses to organic defences
 showed a similar hormetic response to metal accumulation by the plants.
 Additionally, we show that the induction and suppression of plant defences
 by these spider-mite species was not affected by the amount of cadmium
 supplied to the plants. Furthermore, the effect of cadmium on the
 performance of spider mites was not altered by infestation with T. urticae
 or T. evansi. Together, our results suggest no interaction between
 cadmium-based and organic plant defences, on our system. This character
 may be useful for plants living in heterogeneous environments, as they may
 use one or the other defence mechanism, depending on their relative
 performance in each environment.
description: Performance of plants
 exposed to cadmium and of infesting spider mitesEach sheet represents a
 measurement. For each entry the trait measured is represented, as well as
 the plant (replicate) from which it was taken and the block. Please note
 that for the traits regarding the performance of spider mites several
 females of each species were tested using leaf discs taken from the same
 plant, having those the same plant ID.alldata.xlsx
DOI: 10.5061/dryad.68738
title: Data from: Biogeographic consequences of nutrient enrichment for plant-herbivore interactions in coastal wetlands

description: A major challenge in ecology is to understand broadscale trends in the
 impact of environmental change. We provide the first integrative analysis
 of the effects of eutrophication on plants, herbivores, and their
 interactions in coastal wetlands across latitudes. We show that
 fertilisation strongly increases herbivory in salt marshes, but not in
 mangroves, and that this effect increases with increasing latitude in salt
 marshes. We further show that stronger nutrient effects on plant nitrogen
 concentration at higher latitudes is the mechanism likely underlying this
 pattern. This biogeographic variation in nutrient effects on
 plant–herbivore interactions has consequences for vegetation, with those
 at higher latitudes being more vulnerable to consumer pressure fuelled by
 eutrophication. Our work provides a novel, mechanistic understanding of
 how eutrophication affects plant–herbivore systems predictably across
 broad latitudinal gradients, and highlights the power of incorporating
 biogeography into understanding large-scale variability in the impacts of
 environmental change.
description: Effect sizes from
 fertilization experimentsEffect sizes from
 fertilization experimentsFertilizationExperiments.xlsEffect sizes from factorial fertilization X herbivore removal experimentsEffect sizes from factorial fertilization X herbivore removal experimentsFactorialExperiments.xls
DOI: 10.5061/dryad.n3h6d
title: Data from: Polymorphisms in a desaturase 2 ortholog associate with cuticular hydrocarbon and male mating success variation in a natural population of Drosophila serrata

description: Elucidating the nature of genetic variation underlying both sexually
 selected traits and the fitness components of sexual selection is
 essential to understanding the broader consequences of sexual selection as
 an evolutionary process. To date, there have been relatively few attempts
 to connect the genetic variance in sexually selected traits with
 segregating DNA sequence polymorphisms. We set out to address this in a
 well-characterized sexual selection system – the cuticular hydrocarbons
 (CHCs) of Drosophila serrata – using an indirect association study design
 that allowed simultaneous estimation of the genetic variance in CHCs,
 sexual fitness and single nucleotide polymorphism (SNP) effects in an
 outbred population. We cloned and sequenced an ortholog of the D.
 melanogaster desaturase 2 gene, previously shown to affect CHC
 biosynthesis in D. melanogaster, and associated 36 SNPs with minor allele
 frequencies &gt; 0.02 with variance in CHCs and sexual fitness. Three
 SNPs had significant multivariate associations with CHC phenotype (q-value
 &lt; 0.05). At these loci, minor alleles had multivariate effects on
 CHCs that were weakly associated with the multivariate direction of sexual
 selection operating on these traits. Two of these SNPs had pleiotropic
 associations with male mating success, suggesting these variants may
 underlie responses to sexual selection due to this locus. There were 15
 significant male mating success associations (q-value &lt; 0.1), and
 interestingly, we detected a nonrandom pattern in the relationship between
 allele frequency and direction of effect on male mating success. The
 minor-frequency allele usually reduced male mating success, suggesting a
 positive association between male mating success and total fitness at this
 locus.
description: RAE CHC, mating success
 and SNP dataFile contains individual
 level CHC mating success data plus denormalised family level SNP data.
 Spreadsheet has explanatory tabs for variable names.Church_et_al_fitness_CHC_SNP_data.xlsCorrected Supplementary Table 1The published Sup Table 1 contained errors. Posted in this file is a corrected version.Church et al. 2015 corrected Supp Table 1.xlsx
DOI: 10.5061/dryad.113v9
title: Data from: Information use shapes the dynamics of range expansions into environmental gradients

description: Globally, the geographical distributions of species are dynamic and
 strongly influenced by dispersal. At the same time, range dynamics feed
 back and may select for increased dispersal at expanding range fronts.
 This interplay between macroecological and evolutionary dynamics happens
 almost universally across environmental gradients and such gradients can
 have a direct impact on the fitness of organisms due to the match or
 mismatch between an individual's environmental optimum and the
 current conditions along the gradient. Importantly, gradients also provide
 individuals with information on environmental changes because dispersing
 individuals may sense whether environmental conditions improve or
 deteriorate. However, the ability of organisms to use this information on
 the environment and to subsequently adjust dispersal decisions
 plastically, that is, deciding to further disperse into the gradient or
 not, has been largely ignored and the macroecological consequences remain
 unclear. We here aim to demonstrate the impact of informed dispersal on
 the eco-evolutionary dynamics of ranges.
description: datahttps://github.com/efronhofer/gradient_invasion
DOI: 10.5061/dryad.hg736
title: Data from: Predictable males and unpredictable females: repeatability of sociability in eastern water dragons

description: There is growing evidence for consistent among-individual variation in
 individual sociability (e.g., tendency to be sociable) in a number of
 species. However, sexes often differ in their social behaviors, as well as
 the selection pressures which they experience. This may translate into
 differences in repeatability of sociability, although this has not yet
 been tested. Here, we investigated whether eastern water dragons
 (Intellegama leseurii) exhibited evidence of consistent among-individual
 variation (i.e., repeatability) in 4 different measurements of
 sociability. Specifically, we measured sociability in 4 ways (degree,
 centrality, proportion of time spent being social, and number of
 preferences), and tested whether there was evidence for sex differences in
 the repeatability of these sociability measurements, or whether observed
 levels of repeatability could be explained by a stable social environment.
 Our findings provide new evidence for sex differences in social
 personality: we found that males were significantly repeatable in 3 of 4
 sociability measurements (degree, centrality, and proportion of time spent
 being social), whereas females were not. Further, we found that these
 differences were not a result of differences in the dynamics of the social
 environment. We discuss our findings in the context of sexual selection,
 as well as sex differences in the evolutionary drivers of social behavior.
description: Raw data_Strickland
 & FrereRaw spatial data used
 for all analysis described in article entitled "Predictable males and
 unpredictable females: repeatability of sociability in eastern water
 dragons".
DOI: 10.5061/dryad.6g35k
title: Data from: Density-dependent habitat selection of spawning Chinook salmon: broad scale evidence and implications

description: 1. An extensive body of theory suggests that density-dependent habitat
 selection drives many fundamental ecological processes. The ideal free
 distribution and the ideal despotic distribution make contrasting
 predictions about the effect of total population size on relative
 abundances among habitats. Empirical assessment of these habitat selection
 models is uncommon because data must be collected over large temporal and
 spatial scales. 2. I ask whether fluctuation in Chinook salmon
 (Oncorhynchus tshawytscha) spawner population size through time leads to
 different relative densities over space. 3. Twenty six years of monitoring
 data on spawning Chinook salmon across the entire coast of Oregon, USA,
 were used to evaluate models that make contrasting statements about the
 interactions of a latent population abundance parameter with physical
 habitat characteristics. 4. There is strong information-theoretic support
 for models that include terms that allow the spatial variation in density
 to change as population size changes through time. Analysis of the best
 model reveals nonlinear isodars, which suggests a “despotic” or
 “preemptive” distribution of individuals across habitats, indicating that
 dominant or early arriving individuals exclude others from breeding sites.
 5. This finding has implications for genetic dynamics, population
 dynamics, and conservation metrics of these highly valued fish. The novel
 application of modeling techniques used here to assess mechanisms of
 habitat selection from observational data can be used in the emerging
 field of eco-evolutionary dynamics.
description: dataX are the counts. L is
 the stream survey length in meters. F is the standardized geomorphic flow
 variable. G is the standardized geomorphic gradient variable. W is the
 standardized geomorphic width variable. NDflow is the mean flow in
 November and/or December.
DOI: 10.5061/dryad.94d37g3
title: Data from: Environmental DNA for the enumeration and management of Pacific salmon

description: Pacific salmon are a keystone resource in Alaska, generating annual
 revenues of well over ~US$500 million/yr. Due to their anadromous life
 history, adult spawners distribute amongst thousands of streams, posing a
 huge management challenge. Currently, spawners are enumerated at just a
 few streams because of reliance on human counters and, rarely, sonar. The
 ability to detect organisms by shed tissue (environmental DNA, eDNA)
 promises a more efficient counting method. However, although eDNA
 correlates generally with local fish abundances, we do not know if eDNA
 can accurately enumerate salmon. Here we show that daily, and near-daily,
 flow-corrected eDNA rate closely tracks daily numbers of returning sockeye
 and coho spawners and outmigrating sockeye smolts. eDNA thus promises
 accurate and efficient enumeration, but to deliver the most robust numbers
 will need higher-resolution stream-flow data, at-least-daily sampling, and
 a focus on species with simple life histories, since shedding rate varies
 amongst jacks, juveniles, and adults.
description: 2014_2015_2016_Auke_qPCR-masterR code and data files to replicate the analyses in Levi, T., Allen, J.M., Bell, D., Joyce, J., Russell, J.R., Tallmon, D.A., Vulstek, S.C., Yang, C.Y., Yu, D.W. 2018. Environmental DNA for the enumeration and management of Pacific salmon. Molecular Ecology Resources. doi:10.1111/1755-0998.12987
DOI: 10.5061/dryad.2m1p0
title: Data from: How a haemosporidian parasite of bats gets around: the genetic structure of a parasite, vector and host compared

description: Parasite population structure is often thought to be largely shaped by
 that of its host. In the case of a parasite with a complex life cycle, two
 host species, each with their own patterns of demography and migration,
 spread the parasite. However, the population structure of the parasite is
 predicted to resemble only that of the most vagile host species. In this
 study we tested this prediction in the context of a vector-transmitted
 parasite. We sampled the haemosporidian parasite Polychromophilus
 melanipherus across its European range, together with its bat fly vector
 Nycteribia schmidlii and its host, the bent-winged bat Miniopterus
 schreibersii. Based on microsatellite analyses, the wingless vector, and
 not the bat host, was identified as the least structured population and
 should therefore be considered the most vagile host. Genetic distance
 matrices were compared for all three species based on a mitochondrial DNA
 fragment. Both host and vector populations followed an
 isolation-by-distance pattern across the Mediterranean, but not the
 parasite. Mantel tests found no correlation between the parasite and
 either the host or vector populations. We therefore found no support for
 our hypothesis; the parasite population structure matched neither vector
 nor host. Instead, we propose a model where the parasite’s gene flow is
 represented by the added effects of host and vector dispersal patterns.
description: Alignment of 704bp
 cytb-fragment of P. melanipheruscytb_Pmelanipherus.fasAlignment of 310 bp. mtDNA control region fragment of M. schreibersiiCR_Mschreibersii.fasAlignment of 480bp. 16SrDNA fragment of N. schmidlii16SrDNA_Nschmidlii.fasMicrosatellite genotype, sex and site of capture of M. schreibersiimicrosats_Mschreibersii.csvMicrosatellite genotype, sex, host and site of capture of N. schmidliimicrosats_Nschmidlii.csv
DOI: 10.15468/dl.wxmz5n
title: Occurrence Download

description: A dataset containing 56774 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lycorma delicatula",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 56774 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000574-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.