cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rm2jn70
title: Data from: Effects of demographic stochasticity and life-history strategies on times and probabilities to fixation

description: How life-history strategies influence the evolution of populations is not
 well understood. Most existing models stem from the Wright-Fisher model
 which considers discrete generations and a fixed population size, thus not
 taking into account any potential consequences of overlapping generations
 and demographic stochasticity on allelic frequencies. We introduce an
 individual-based model in which both population size and genotypic
 frequencies at a single bi-allelic locus are emergent properties of the
 model. Demographic parameters can be defined so as to represent a large
 range of r and K life-history strategies in a stable environment, and
 appropriate fixed effective population sizes are calculated so as to
 compare our model to the Wright-Fisher diffusion. Our results indicate
 that models with fixed population size that stem from the Wright-Fisher
 diffusion cannot fully capture the consequences of demographic
 stochasticity on allele fixation in long-lived species with low
 reproductive rates. This discrepancy is accentuated in the presence of
 demo-genetic feedback. Furthermore, we predict that populations with K-
 life-histories should maintain lower genetic diversity than those with r-
 life-histories.
description: DemStochZip file containing main.cpp (main script for simulating diffusion approximations from equations 1a and 1b), an example parameter input file param.txt and the README file.
DOI: 10.5061/dryad.m03h896
title: Data from: Behavioural plasticity under a changing climate; how an experimental local climate affects the nest construction of the zebra finch (Taeniopygia guttata)

description: Successful reproduction in most avian species is dependent on the
 construction of a nest that provides protection and a suitable
 microclimate for the eggs and developing nestlings. Observational studies
 suggest that climatic variation may affect the structure of the nest, but
 to date there have been no attempts to experimentally determine the role
 that local climate plays in the construction of a suitable nest. Using a
 within-individual counter balanced design we investigated how nest
 composition and construction differ in zebra finches breeding in ambient
 conditions of 18°C and 30°C. We found that at 18°C birds built nests that
 were over 20% heavier, and with significantly more thread and less grass
 than those built at 30°C. Our results highlight the degree of plasticity
 in nest building behaviour in relation to local ambient conditions. These
 results suggest that nest building behaviour is one route through which
 birds can respond to a changing climate and modify the microclimate of
 their nest in line with projected changes in ambient conditions.
description: Temp Nest Plasticity
 DataRaw data used for paper
 doi: 10.1111/jav.01717NestTempDryad.csv
DOI: 10.5061/dryad.829
title: Data from: Assessing Progress in Systematics with Continuous Jackknife Function Analysis

description: Systematists expect their hypotheses to be asymptotically precise. As the
 number of phylogenetically informative characters for a set of taxa
 increases, the relationships implied should stabilize on some topology. If
 true, this increasing stability should clearly manifest itself if an index
 of congruence is plotted against the accumulating number of characters.
 Continuous Jackknife Function (CJF) analysis is a new graphical method
 that portrays the extent to which available data converge on a specified
 phylogenetic hypothesis, the reference tree. The method removes characters
 with increasing probability, analyzes the rarefied data matrices
 phylogenetically, and scores the clades shared between each of the
 resulting trees and the reference tree. As more characters are removed,
 the number of shared clades must decrease, but the rate of decrease will
 depend on how decisively the data support the reference tree. Curves for
 stable phylogenies are clearly asymptotic with nearly 100% congruence for
 a substantial part of the curve. Less stable phylogenies lose congruent
 nodes quickly as characters are excluded, resulting in a more linear or
 even a sigmoidal relationship. Curves can be interpreted as predictors of
 whether the addition of new data of the same type is likely to alter the
 hypothesis under test. Continuous Jackknife Function analysis makes
 statistical assumptions about the collection of character data. To the
 extent that CJF curves are sensitive to violations of unbiased character
 collection, they will be misleading as predictors. Convergence of data on
 a reference tree does not guarantee historical accuracy, but it does
 predict that the accumulation of further data under the sampling model
 will not lead to rapid changes in the hypothesis.
description: Miller Data
 SetMiller_ap1.htm
DOI: 10.5061/dryad.9sf96
title: Data from: DISCOMARK: nuclear marker discovery from orthologous sequences using draft genome data

description: High-throughput sequencing has laid the foundation for fast and
 cost-effective development of phylogenetic markers. Here we present the
 program discomark, which streamlines the development of nuclear DNA (nDNA)
 markers from whole-genome (or whole-transcriptome) sequencing data,
 combining local alignment, alignment trimming, reference mapping and
 primer design based on multiple sequence alignments to design primer pairs
 from input orthologous sequences. To demonstrate the suitability of
 discomark, we designed markers for two groups of species, one consisting
 of closely related species and one group of distantly related species. For
 the closely related members of the species complex of Cloeon dipterum s.l.
 (Insecta, Ephemeroptera), the program discovered a total of 78 markers.
 Among these, we selected eight markers for amplification and Sanger
 sequencing. The exon sequence alignments (2526 base pairs) were used to
 reconstruct a well-supported phylogeny and to infer clearly structured
 haplotype networks. For the distantly related species, we designed primers
 for the insect order Ephemeroptera, using available genomic data from four
 sequenced species. We developed primer pairs for 23 markers that are
 designed to amplify across several families. The discomark program will
 enhance the development of new nDNA markers by providing a streamlined,
 automated approach to perform genome-scale scans for phylogenetic markers.
 The program is written in Python, released under a public licence (GNU GPL
 version 2), and together with a manual and example data set available at:
 https://github.com/hdetering/discomark.
description: sequence_alignmentsAligned exon sequence files.phylogenetic treePhylogenetic reconstruction of four representatives of the species complex Cloeon dipterum s.l., including C. peregrinator, based on the exon sequences of the eight newly developed nuclear DNA markers (2,526 base pairs). Bayesian inference was used to reconstruct the tree based on the concatenated supermatrix alignment.concat_8_coding.nex.con.tre
DOI: 10.5061/dryad.fb0f8
title: Data from: Incompressible fluid plays a mechanical role in the development of passive muscle tension

description: Over short time scales, muscle fibres maintain a nearly constant volume of
 intracellular fluid. This fluid is essential to normal biochemical
 function, but its role in determining the mechanical properties of muscle
 has been considered in only a few theoretical analyses. Here we
 investigate the mechanical role of fluid in a fundamental property of
 muscle, its development of passive tension in response to stretch. We test
 a model of muscle structure in which incompressible fluid directly
 influences passive tension by constraining the geometry of intramuscular
 connective tissues. This interaction is demonstrated using a simple
 physical model of muscle morphology comprising a fluid-filled bladder
 wrapped by helical fibres. The behaviour of the model is compared with
 that of isolated bullfrog muscle subjected to an osmotic perturbation of
 intracellular fluid volume. Increasing muscle volume by 40% resulted in
 69% increased passive tension, occurring in a manner consistent with the
 behaviour of the model. These observations support the notion that the
 interaction of connective tissues with the muscle fibres they surround
 influences the mechanical behaviour of whole muscles, and highlight the
 role of fluid as a mechanical component of muscle.
description: Tabulated Force, Length,
 and Pressure Measurements for Stretched Model and MuscleThese tables list the
 force, length, and pressure value for each data point depicted in figures
 1 and 2. Data is provided for isolated semimembranosus muscles and for our
 physical model of muscle.tabulated
 data.csv
DOI: 10.5061/dryad.49v70
title: Data from: Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity

description: One of the persistent problems in biology is understanding how genetic
 variation contributes to phenotypic variation. Associations at many levels
 have been reported, and yet causal inference has remained elusive. We
 propose to rely on the knowledge of causal relationships established by
 molecular biology approaches. The existing molecular knowledge forms a
 firm backbone upon which hypotheses connecting genetic variation,
 transcriptional variation and phenotypic variation can be built. The sex
 determination pathway is a well-established molecular network, with the Yp
 genes as the most downstream target. Our analyses reveal that genetic
 variation in expression for genes known to be upstream in the pathway
 explains variation in downstream targets. Relationships differ between the
 two sexes, and each Yp has a distinct transcriptional pattern. Yp
 expression is significantly negatively correlated with longevity, an
 important life history trait, for both males and females.
description: Longevity_Data_HeredityLongevity data (median time of death) that was correlated with Yp expression in this paper.
DOI: 10.5061/dryad.hk922
title: Data from: Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus

description: Speciation proceeds when gene exchange is prevented between populations.
 Determining the different barriers preventing gene flow can therefore give
 insights into the factors driving and maintaining species boundaries.
 These reproductive barriers may result from intrinsic genetic
 incompatibilities between populations, from extrinsic environmental
 differences between populations, or a combination of both mechanisms. We
 investigated the potential barriers to gene exchange between three
 adjacent ecotypes of an Australian wildflower to determine the strength of
 individual barriers and the degree of overall isolation between
 populations. We found almost complete isolation between the three
 populations mainly due to premating extrinsic barriers. Intrinsic genetic
 barriers were weak and variable amongst populations. There were
 asymmetries in some intrinsic barriers due to the origin of cytoplasm in
 hybrids, which combined with weak selection against hybrids has the
 potential to facilitate gene flow in the system, specifically from Dune
 and Headland ecotypes into the Island ecotype. Overall, these results
 suggest that reproductive isolation between these three populations is
 almost complete despite the absence of geographic barriers, and that the
 main drivers of this isolation are ecologically based, consistent with the
 mechanisms underlying ecological speciation.
description: RIdataData set including the
 strength of Reproductive barriers to gene exchange between 3 populations
 of Senecio lautus. Includes Parental (pure crosses) and F1
 Hybrids
DOI: 10.5061/dryad.7kv8r
title: Data from: Effects of cell-cycle-dependent expression on random fluctuations in protein levels

description: Expression of many genes varies as a cell transitions through different
 cell-cycle stages. How coupling between stochastic expression and cell
 cycle impacts cell-to-cell variability (noise) in the level of protein is
 not well understood. We analyse a model where a stable protein is
 synthesized in random bursts, and the frequency with which bursts occur
 varies within the cell cycle. Formulae quantifying the extent of
 fluctuations in the protein copy number are derived and decomposed into
 components arising from the cell cycle and stochastic processes. The
 latter stochastic component represents contributions from bursty
 expression and errors incurred during partitioning of molecules between
 daughter cells. These formulae reveal an interesting trade-off: cell-cycle
 dependencies that amplify the noise contribution from bursty expression
 also attenuate the contribution from partitioning errors. We investigate
 the existence of optimum strategies for coupling expression to the cell
 cycle that minimize the stochastic component. Intriguingly, results show
 that a zero production rate throughout the cell cycle, with expression
 only occurring just before cell division, minimizes noise from bursty
 expression for a fixed mean protein level. By contrast, the optimal
 strategy in the case of partitioning errors is to make the protein just
 after cell division. We provide examples of regulatory proteins that are
 expressed only towards the end of the cell cycle, and argue that such
 strategies enhance robustness of cell-cycle decisions to the intrinsic
 stochasticity of gene expression.
description: Fig.3Mathematica
 fileFig4_topMatlab fileFig4_bottomMatlab file
DOI: 10.5061/dryad.kq487nj
title: Data from: Implicit violent imagery processing among fans and non-fans of violent music

description: It is suggested that long-term exposure to violent media may decrease
 sensitivity to depictions of violence. However, it is unknown whether
 persistent exposure to music with violent themes affects implicit violent
 imagery processing. Using a binocular rivalry paradigm, we investigated
 whether the presence of violent music influences conscious awareness of
 violent imagery among fans and non-fans of such music. Thirty-two fans and
 48 non-fans participated in the study. Violent and neutral pictures were
 simultaneously presented one to each eye, and participants indicated which
 picture they perceived (i.e. violent percept, neutral percept, or blend of
 two) via key presses, while they heard Western popular music with lyrics
 that expressed happiness or Western extreme-metal music with lyrics that
 expressed violence. We found both fans and non-fans of violent music
 exhibited a general negativity bias for violent imagery over neutral
 imagery regardless of the music genres. For non-fans, this bias was
 stronger while listening to music that expressed violence than while
 listening to music that expressed happiness. For fans of violent music,
 however, the bias was the same while listening to music that expressed
 either violence or happiness. We discussed these results in view of
 current debates on the impact of violent media.
description: Binocular Rivalry
 DatasetDefinitions of
 abbreviations used in the dataset: VM – Violent Music HM – Happy Music VP
 – Violent Percept NP – Neutral Percept PFP – Proportion of First Percept
 MPD – Mean Percept DurationBR_dataset.csv
DOI: 10.5061/dryad.2q2k0q5
title: Data from: A multi-decade experiment shows that fertilization by salmon carcasses enhanced tree growth in the riparian zone

description: As they return to spawn and die in their natal streams, anadromous,
 semelparous fishes such as Pacific salmon import marine‐derived nutrients
 to otherwise nutrient‐poor freshwater and riparian ecosystems. Diverse
 organisms exploit this resource, and previous studies have indicated that
 riparian tree growth may be enhanced by such marine‐derived nutrients.
 However, these studies were largely inferential and did not account for
 all factors affecting tree growth. As an experimental test of the
 contribution of carcasses to tree growth, for 20 yr, we systematically
 deposited all sockeye salmon (Oncorhynchus nerka) carcasses (217,055
 individual salmon) in the riparian zone on one bank of a 2‐km‐long stream
 in southwestern Alaska, reducing carcass accumulation on one bank and
 enhancing it on the other. After accounting for partial consumption and
 movement of carcasses by brown bears (Ursus arctos) and variation in
 salmon abundance and body size, we estimated that 267,620 kg of salmon
 were deposited on the enhanced bank and 45,200 kg on the depleted bank
 over the 20 yr, for a 5.9‐fold difference in total mass. In 2016, we
 sampled needles of 84 white spruce trees (Picea glauca) the dominant
 riparian tree species, for foliar nitrogen (N) content and stable isotope
 ratios (δ15N), and took core samples for annual growth increments. Stable
 isotope analysis indicated that marine‐derived N was incorporated into the
 new growth of the trees on the enhanced bank. Analysis of tree cores
 indicated that in the two decades prior to our enhancement experiment,
 trees on the south‐facing (subsequently the depleted) bank grew faster
 than those on the north‐facing (later enhanced) bank. This difference was
 reduced significantly during the two decades of fertilization, indicating
 an effect of the carcass transfer experiment against the background of
 other factors affecting tree growth.
description: White spruce N and C
 isotope dataSpruce tree location,
 date, historic stream sampling reach, side of stream, distance from bank
 (cm), diameter at breast height (cm), number of stems, distance to a
 heavily used "bear kitchen" (cm), and nitrogen and carbon
 isotope values from August 2016 sampling from Hansen Creek, Alaska,
 USA.Quinn_Hansen_MDN_Isotopes.csv
DOI: 10.5061/dryad.hp730
title: Data from: Colder environments did not select for a faster metabolism during experimental evolution of Drosophila melanogaster

description: The effect of temperature on the evolution of metabolism has been the
 subject of debate for a century; however, no consistent patterns have
 emerged from comparisons of metabolic rate within and among species living
 at different temperatures. We used experimental evolution to determine how
 metabolism evolves in populations of Drosophila melanogaster exposed to
 one of three selective treatments: a constant 16°C, a constant 25°C, or
 temporal fluctuations between 16 and 25°C. We tested August Krogh's
 controversial hypothesis that colder environments select for a faster
 metabolism. Given that colder environments also experience greater
 seasonality, we also tested the hypothesis that temporal variation in
 temperature may be the factor that selects for a faster metabolism. We
 measured the metabolic rate of flies from each selective treatment at 16,
 20.5, and 25°C. Although metabolism was faster at higher temperatures,
 flies from the selective treatments had similar metabolic rates at each
 measurement temperature. Based on variation among genotypes within
 populations, heritable variation in metabolism was likely sufficient for
 adaptation to occur. We conclude that colder or seasonal environments do
 not necessarily select for a faster metabolism. Rather, other factors
 besides temperature likely contribute to patterns of metabolic rate over
 thermal clines in nature.
description: SuppInfo
DOI: 10.5061/dryad.4430n
title: Data from: A hidden Markov model to identify and adjust for selection bias: an example involving mixed migration strategies

description: An important assumption in observational studies is that sampled
 individuals are representative of some larger study population. Yet, this
 assumption is often unrealistic. Notable examples include online
 public-opinion polls, publication biases associated with statistically
 significant results, and in ecology, telemetry studies with significant
 habitat-induced probabilities of missed locations. This problem can be
 overcome by modeling selection probabilities simultaneously with other
 predictor–response relationships or by weighting observations by inverse
 selection probabilities. We illustrate the problem and a solution when
 modeling mixed migration strategies of northern white-tailed deer
 (Odocoileus virginianus). Captures occur on winter yards where deer
 migrate in response to changing environmental conditions. Yet, not all
 deer migrate in all years, and captures during mild years are more likely
 to target deer that migrate every year (i.e., obligate migrators).
 Characterizing deer as conditional or obligate migrators is also
 challenging unless deer are observed for many years and under a variety of
 winter conditions. We developed a hidden Markov model where the
 probability of capture depends on each individual's migration
 strategy (conditional versus obligate migrator), a partially latent
 variable that depends on winter severity in the year of capture. In a
 15-year study, involving 168 white-tailed deer, the estimated probability
 of migrating for conditional migrators increased nonlinearly with an index
 of winter severity. We estimated a higher proportion of obligates in the
 study cohort than in the population, except during a span of 3 years
 surrounding back-to-back severe winters. These results support the
 hypothesis that selection biases occur as a result of capturing deer on
 winter yards, with the magnitude of bias depending on the severity of
 winter weather. Hidden Markov models offer an attractive framework for
 addressing selection biases due to their ability to incorporate latent
 variables and model direct and indirect links between state variables and
 capture probabilities.
description: migdat
DOI: 10.5061/dryad.tc736qr
title: Data from: When males outlive females: sex-specific effects of temperature on lifespan in a cyclic parthenogen

description: Lifespans of males and females frequently differ as a consequence of
 different life history strategies adopted to maximize fitness. It is well
 visible in cyclic parthenogens, such as water fleas of the genus Daphnia,
 where males appear in the population usually only for periods when
 receptive females are available. Moreover, even within one sex, different
 life history strategies and mechanisms regulating lifespan may exist.
 Previous studies suggested that Daphnia males may regulate their lifespan
 by staying in colder waters than females. We hypothesize that such
 behavioural mechanism should be associated with stronger reaction to low
 temperature that is greater lifespan extension in males than in females.
 In this study, we monitored survivorship of Daphnia magna females and
 males of three clonal lines cultured at 16 or 20°C. The results did not
 provide a species-level corroboration of our hypothesis, instead, they
 revealed very strong intraspecific differences in the responses of male
 and female lifespan to temperature change. They further suggest the
 existence of parallel life history strategies, hypotheses whose tests
 would bring new insights into the ecology of males in cyclic parthenogens.
description: When males outlive
 females Archive DataLifespan (LS) data for
 D. magna clones (K), (T) and (B), for males (M) and females (F), recorded
 at temperature (16) and (20) degrees. The death of an individual was
 either observed (fin=1), or an individual lived to the end of the
 experiment (fin=0).When Archive
 Data.txtWhen males outlive
 females Archive CodeAnalysis code for the
 published resultsWhen Archive
 Code.R