cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7qr02
title: Data from: The effects of sexual selection on life history traits: an experimental study on guppies

description: Sexual selection is often prevented during captive breeding in order to
 maximize effective population size and retain genetic diversity. However,
 enforcing monogamy and thereby preventing sexual selection may affect
 population fitness either negatively by preventing the purging of
 deleterious mutations or positively by reducing sexual conflicts. To
 better understand the effect of sexual selection on the fitness of small
 populations, we compared components of female fitness and the expression
 of male secondary sexual characters in 19 experimental populations of
 guppies (Poecilia reticulata) maintained under polygamous or monogamous
 mating regimes over nine generations. In order to generate treatments that
 solely differed by their level of sexual selection, the middle-class
 neighbourhood breeding design was enforced in the monogamous populations,
 while in the polygamous populations, all females contributed similarly to
 the next generation with one male and one female offspring. This
 experimental design allowed potential sexual conflicts to increase in the
 polygamous populations because selection could not operate on adult-female
 traits. Clutch size and offspring survival showed a weak decline from
 generation to generation but did not differ among treatments. Offspring
 size, however, declined across generations, but more in monogamous than
 polygamous populations. By generation eight, orange- and black-spot areas
 were larger in males from the polygamous treatment, but these differences
 were not statistically significant. Overall, these results suggest that
 neither sexual conflict nor the purging of deleterious mutation had
 important effects on the fitness of our experimental populations. However,
 only few generations of enforced monogamy in a benign environment were
 sufficient to negatively affect offspring size, a trait potentially
 crucial for survival in the wild. Sexual selection may therefore, under
 certain circumstances, be beneficial over enforced monogamy during captive
 breeding.
description: Varaible
 descriptionFile describing the
 variables for the three data sets.Pelabon et al_data
 explanation.docxLife history traits per
 generationData set including
 traits related to the female reproductive output for each population, in
 each treatment at each generation.Pelabon et al_Life history
 traits.txtOffpsring
 SurvivalData on the proportion
 of offpsring per clutch surviving from birth to one year of
 age.Pelabon
 et al_Survival.txtMale
 traitsData on male ornament
 measured on two males per family at the generation 8.Pelabon et al_Male
 traits.txt
DOI: 10.5061/dryad.v0q5035
title: Data from: A spatially explicit hierarchical model to characterize population viability

description: Many of the processes that govern the viability of animal populations vary
 spatially, yet population viability analyses (PVAs) that account
 explicitly for spatial variation are rare. We develop a PVA model that
 incorporates autocorrelation into the analysis of local demographic
 information to produce spatially explicit estimates of demography and
 viability at relatively fine spatial scales across a large spatial extent.
 We use a hierarchical, spatial autoregressive model for capture-recapture
 data from multiple locations to obtain spatially explicit estimates of
 adult survival (Φad), juvenile survival (Φjuv), and juvenile-to-adult
 transition rates (ψ), and a spatial autoregressive model for recruitment
 data from multiple locations to obtain spatially explicit estimates of
 recruitment (R). We combine local estimates of demographic rates in
 stage-structured population models to estimate the rate of population
 change (λ), then use estimates of λ (and its uncertainty) to forecast
 changes in local abundance and produce spatially explicit estimates of
 viability (probability of extirpation, Pex). We apply the model to
 demographic data for the Sonoran desert tortoise (Gopherus morafkai)
 collected across its geographic range in Arizona. There was modest spatial
 variation in λ (0.94–1.03), which reflected spatial variation in Φad
 (0.85–0.95), Φjuv (0.70–0.89), and ψ (0.07–0.13). Recruitment data were
 too sparse for spatially explicit estimates, therefore we used a
 range-wide estimate (R = 0.32 one-year old females per female per year).
 Spatial patterns in demographic rates were complex, but Φad, Φjuv, and λ
 tended to be lower and ψ higher in the northwestern portion of the range.
 Spatial patterns in Pex varied with local abundance. For local abundances
 &gt; 500, Pex was near zero (Pex approached one in the northwestern
 portion of the range and remained low elsewhere. When local abundances
 were Pex &gt; 0.25). This approach to PVA offers the potential to
 reveal spatial patterns in demography and viability that can inform
 conservation and management at multiple spatial scales, provide insight
 into scale-related investigations in population ecology, and improve basic
 ecological knowledge of landscape-level phenomena.
description: Data and R code for
 spatial PVA of Sonoran desert tortoisesThis zip directory
 contains the data and R code required to reproduce the analyses in the
 associated paper.Campbell_et_al_data_and_R_code.zip
DOI: 10.5061/dryad.dt43f
title: Data from: Reliability of single-use PEEP-valves attached to self-inflating bags during manual ventilation of neonates – an in vitro study

description: Introduction International resuscitation guidelines suggest to use
 positive end-expiratory pressure (PEEP) during manual ventilation of
 neonates. Aim of our study was to test the reliability of self-inflating
 bags (SIB) with single-use PEEP valves regarding PEEP delivery and the
 effect of different peak inflation pressures (PIP) and ventilation rates
 (VR) on the delivered PEEP. Methods Ten new single-use PEEP valves from 5
 manufacturers were tested by ventilating an intubated 1kg neonatal manikin
 containing a lung model with a SIB that was actuated by an
 electromechanical plunger device. Standard settings: PIP 20cmH2O, VR
 60/min, flow 8L/min. PEEP settings of 5 and 10cmH2O were studied. A second
 test was conducted with settings of PIP 40cmH2O and VR 40/min. The
 delivered PEEP was measured by a respiratory function monitor (CO2SMO+).
 Results Valves from one manufacturer delivered no relevant PEEP and were
 excluded. The remaining valves showed a continuous decay of the delivered
 pressure during expiration. The median (25th and 75th percentile)
 delivered PEEP with standard settings was 3.4(2.7–3.8)cmH2O when set to
 5cmH2O and 6.1(4.9–7.1)cmH2O when set to 10cmH2O. Increasing the PIP from
 20 to 40 cmH2O led to a median (25th and 75th percentile) decrease in PEEP
 to 2.3(1.8–2.7)cmH2O and 4.3(3.2–4.8)cmH2O; changing VR from 60 to 40/min
 led to a PEEP decrease to 2.8(2.1–3.3)cmH2O and 5.0(3.5–6.2)cmH2O for both
 PEEP settings. Conclusion Single-use PEEP valves do not reliably deliver
 the set PEEP. PIP and VR have an effect on the delivered PEEP. Operators
 should be aware of these limitations when manually ventilating neonates.
description: All data for
 dryadThe table provides the
 data recorded during our in vitro study about the reliability of single
 use peep valves during simulated neonatal ventilation. In contains the
 PIP, PEEP and Vt that could be generated using 10 different peep-valves
 from 5 manufacturers (2 valves each) using different parameter
 settings.Gesamttabelle
 dryad.xls
DOI: 10.7910/dvn/gz6x7u
title: Replication Data for: Observing the Unobservable: Wargaming Cyber Deterrence

description: Replication materials for Redding (2026): Observing the Unobservable: Wargaming Cyber Deterrence
DOI: 10.5061/dryad.26820
title: Data from: Total-evidence dating under the fossilized birth-death process

description: Bayesian total-evidence dating involves the simultaneous analysis of
 morphological data from the fossil record and morphological and sequence
 data from recent organisms, and it accommodates the uncertainty in the
 placement of fossils while dating the phylogenetic tree. Due to the
 flexibility of the Bayesian approach, total-evidence dating can also
 incorporate additional sources of information. Here, we take advantage of
 this and expand the analysis to include information about fossilization
 and sampling processes. Our work is based on the recently described
 fossilized birth-death (FBD) process, which has been used to model
 speciation, extinction and fossilization rates that can vary over time in
 a piecewise manner. So far, sampling of extant and fossil taxa has been
 assumed to be either complete or uniformly at random, an assumption which
 is only valid for a minority of datasets. We therefore extend the FBD
 process to accommodate diversified sampling of extant taxa, which is
 standard practice in studies of higher-level taxa. We verify the
 implementation using simulations and apply it to the early radiation of
 Hymenoptera (wasps, ants and bees). Previous total-evidence dating
 analyses of this dataset were based on a simple uniform tree prior and
 dated the initial radiation of extant Hymenoptera to the late
 Carboniferous (309 Ma). The analyses using the FBD prior under diversified
 sampling, however, date the radiation to the Triassic and Permian (252
 Ma), slightly older than the age of the oldest hymenopteran fossils. By
 exploring a variety of FBD model assumptions, we show that it is mainly
 the accommodation of diversified sampling that causes the push towards
 more recent divergence times. Accounting for diversified sampling thus has
 the potential to close the long-discussed gap between rocks and clocks. We
 conclude that the explicit modeling of fossilization and sampling
 processes can improve divergence time estimates, but only if all important
 model aspects, including sampling biases, are adequately addressed.
description: TE_FBD_SupplementalSupplemental Tables and Figures for manuscript "Total-Evidence Dating under the Fossilized Birth-Death Process".FBD_Suppl.pdf
DOI: 10.5061/dryad.7kp90
title: Data from: Germ banks affect the inference of past demographic events

description: Continuous progress in empirical population genetics based on whole genome
 polymorphism data requires the theoretical analysis of refined models in
 order to interpret the evolutionary history of populations with adequate
 accuracy. Recent studies focus prevalently on the aspects of demography
 and adaptation, whereas age-structure (e.g. in plants via the maintenance
 of seed banks) has attracted less attention. Germ banking, i.e. seed or
 egg dormancy, is a prevalent and important life-history trait in plants
 and invertebrates, which buffers against environmental variability and
 modulates species extinction in fragmented habitats. Within this study, we
 investigate the combined effect of germ banking and time-varying
 population size on the neutral coalescent, and particularly derive the
 allele frequency spectrum under some simplifying assumptions. We then
 perform an ABC analysis using two simple demographic scenarios - a
 population expansion and an instantaneous decline. We demonstrate the
 appreciable influence of seed banks on the estimation of demographic
 parameters depending on the germination rate with biases scaled by the
 square of the germination rate. In the more complex case of a population
 bottleneck, which comprises an instantaneous decline and an expansion
 phase, ignoring information on the germination rate denies reliable
 estimates of the bottleneck parameters via the allelic spectrum. In
 particular, when seeds remain in the bank over several generations, recent
 expansions may remain invisible in the frequency spectrum, whereas ancient
 declines leave signatures much longer than in the absence of seed bank.
description: msdirTBS_SB.tarCompress file containing the c++ code modified from Hudson's mstbs to include coalescent simulations with seed banks. When extracting the content of the tar file, you find 3 pdfs with description of ms and mstbs options (msdoc, msTBSdoc), and one for the seed bank extension (msTBS_SBdoc).seed bank - notebookMathematica notebook to compute the main analytical results in the article (Zivkovic and Tellier).seed bank.nb
DOI: 10.5061/dryad.63t3d
title: Data from: Priority effects are weakened by a short, but not long, history of sympatric evolution

description: Priority effects, or the effects of species arrival history on local
 species abundances, have been documented in a range of taxa. However,
 factors determining the extent to which priority effects affect community
 assembly remain unclear. Using laboratory populations of the bacterium
 Pseudomonas fluorescens, we examined whether shared evolutionary history
 affected the strength of priority effects. We hypothesized that sympatric
 evolution of populations belonging to the same guild would lead to niche
 differentiation, resulting in phenotypic complementarity that weakens
 priority effects. Consistent with this hypothesis, we found that priority
 effects tended to be weaker in sympatrically evolved pairs of immigrating
 populations than in allopatrically evolved pairs. Furthermore, priority
 effects were weaker under higher phenotypic complementarity. However,
 these patterns were observed only in populations with a relatively short
 history of sympatric evolution, and disappeared when populations had
 evolved together for a long time. Together, our results suggest that the
 evolutionary history of organismal traits may dictate the strength of
 priority effects and, consequently, the extent of historical contingency
 in the assembly of ecological communities.
description: ZeeFukami_Week1P. fluorescens abundance data from Week 1.ZeeFukami_Week2P. fluorescens abundance data from Week 2.ZeeFukami_Week7P. fluorescens abundance data from Week 7.ZeeFukami_Week1_MatPhenotype_TotalTrialWeek 1 biofilm mat phenotypesZeeFukami_Week2_MatPhenotypes_formatWeek 2 biofilm mat phenotypesZeeFukami_Week7_MatPhenotypesWeek 7 biofilm mat phenotypes
DOI: 10.5061/dryad.f7g6r
title: Data from: The epigenetic footprint of poleward range-expanding plants in apomictic dandelions

description: Epigenetic modifications, such as DNA methylation variation, can generate
 heritable phenotypic variation independent of the underlying genetic code.
 However, epigenetic variation in natural plant populations is poorly
 documented and little understood. Here, we test whether northward range
 expansion of obligate apomicts of the common dandelion (Taraxacum
 officinale) is associated with DNA methylation variation. We characterized
 and compared patterns of genetic and DNA methylation variation in
 greenhouse-reared offspring of T. officinale that were collected along a
 latitudinal transect of northward range expansion in Europe. Genetic AFLP
 and epigenetic MS-AFLP markers revealed high levels of local diversity and
 modest but significant heritable differentiation between sampling
 locations and between the southern, central and northern regions of the
 transect. Patterns of genetic and epigenetic variation were significantly
 correlated, reflecting the genetic control over epigenetic variation
 and/or the accumulation of lineage-specific spontaneous epimutations,
 which may be selectively neutral. In addition, we identified a small
 component of DNA methylation differentiation along the transect that is
 independent of genetic variation. This epigenetic differentiation might
 reflect environment-specific induction or, in case the DNA methylation
 variation affects relevant traits and fitness, selection of heritable DNA
 methylation variants. Such generated epigenetic variants might contribute
 to the adaptive capacity of individual asexual lineages under changing
 environments. Our results highlight the potential of heritable DNA
 methylation variation to contribute to population differentiation along
 ecological gradients. Further studies are needed using higher resolution
 methods to understand the functional significance of such natural
 occurring epigenetic differentiation.
description: AFLP/MS-AFLP
 dataAFLP profile and
 MspI/HpaII combined MS-AFLP profile and the genetic and geographic
 distances (input files for AMOVA, multivariate dispersion test, Mantel
 tests and PCoAs).EpiRangeShift_VPreite_etal-Data.xlsx
DOI: 10.5061/dryad.67p55
title: Data from: Modularity and rates of evolutionary change in a power-amplified prey capture system

description: The dynamic interplay among structure, function and phylogeny form a
 classic triad of influences on the patterns and processes of biological
 diversification. While these dynamics are widely recognized as important,
 quantitative analyses of their interactions have infrequently been applied
 to biomechanical systems. Here we analyze these factors using a
 fundamental biomechanical mechanism: power amplification. Power-amplified
 systems use springs and latches to generate extremely fast and powerful
 movements. This study focuses specifically on the power amplification
 mechanism in the fast raptorial appendages of mantis shrimp (Crustacea:
 Stomatopoda). Using geometric morphometric and phylogenetic comparative
 analyses, we measured evolutionary modularity and rates of morphological
 evolution of the raptorial appendage’s biomechanical components. We found
 that “smashers” (hammer-shaped raptorial appendages) exhibit lower
 modularity and 10-fold slower rates of morphological change when compared
 to non-smashers (spear-shaped or undifferentiated appendages). The
 morphological and biomechanical integration of this system at a
 macro-evolutionary scale and the presence of variable rates of evolution
 reveal a balance between structural constraints, functional variation, and
 the developmental and genetic roles in evolutionary diversification.
description: dated.phylogenyDated version of the phylogeny from Porter et al. (2010). This is a simple newick file. (Porter, M. L., Y. Zhang, S. Desai, R. L. Caldwell, and T. W. Cronin. 2010. Evolution of anatomical and physiological specialization in the compound eyes of stomatopod crustaceans. Journal of Experimental Biology 213:3473-3486.)engine coordinatesTps file including the coordinates for landmarks configurations of the engine for every specimen digitized in this study. Scale represent centroid size, comments represent species names. This file can be open with any of the tps software (http://life.bio.sunysb.edu/morph/).engine.tpsamplifier coordinatesTps file including the coordinates for landmarks configurations of the amplifier for every specimen digitized in this study. Scale represent centroid size, comments represent species names. This file can be open with any of the tps software (http://life.bio.sunysb.edu/morph/).amplifier.tpstool coordinatesTps file including the coordinates for landmarks configurations of the tool for every specimen digitized in this study. Scale represent centroid size, comments represent species names. This file can be open with any of the tps software (http://life.bio.sunysb.edu/morph/).tool.tps
DOI: 10.5061/dryad.t33v4k14
title: Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

description: Analyses of degraded DNA are typically hampered by contamination,
 especially when employing universal primers such as commonly used in
 environmental DNA studies. In addition to false-positive results, the
 amplification of contaminant DNA may cause false-negative results due to
 competition, or bias, during the PCR. In this study, we test the utility
 of human-specific blocking primers in mammal diversity analyses of ancient
 permafrost samples from Siberia. Using quantitative PCR (qPCR) on human
 and mammoth DNA we first optimised the design and concentration of
 blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient
 permafrost samples amplified with and without the addition of blocking
 primer revealed that DNA sequences from a diversity of mammalian
 representatives of the Beringian megafauna were retrieved only when the
 blocking primer was added to the PCR. Notably, we observe the first
 retrieval of woolly rhinoceros (C. antiquitatis) DNA from ancient
 permafrost cores. In contrast, reactions without blocking primer resulted
 in complete dominance by human DNA sequences. These results demonstrate
 that in ancient environmental analysis, the PCR can be biased towards
 amplification of contaminant sequences to such an extent that retrieval of
 the endogenous DNA is severely restricted. The application of blocking
 primers is a promising tool to avoid this bias and can greatly enhance the
 quantity and the diversity of the endogenous DNA sequences that are
 amplified.
description: Boessenkool_Blocker_seqBoessenkool_Blocker_seq_id
DOI: 10.15468/dl.td35f2
title: Occurrence Download

description: A dataset containing 103312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Basilinna leucotis"
 ]
}

 The dataset includes 103312 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000461-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.40r6p
title: Data from: How feathered are birds? environment predicts both the mass and density of body feathers

description: 1.Studies modelling heat transfer of bird plumage design suggest that
 insulative properties can be attributed to the density and structure of
 the downy layer, while waterproofing is the result of the outer layer,
 comprised of contour feathers. In this study, we test how habitat and
 thermal condition affect feather mass and density of body feathers
 (contour, semiplume and downy feathers) measured on the ventral and dorsal
 sides of the body, using a phylogenetic comparative analysis of 152 bird
 species. 2.Our results demonstrate that feather mass and the density of
 downy feathers are higher in species that inhabit colder environments,
 while total feather density is higher of species breeding under
 intermediate temperatures compared to the ones breeding under more extreme
 conditions. The density of contour feathers, depending on the body region,
 is either quadratically related or negatively correlated to minimum winter
 temperature. 3.The density of contour and downy feathers, measured on both
 sides of the body, is higher in aquatic than in terrestrial birds.
 However, among the former, diving behaviour does not select for further
 increases in body feather mass or density. 4.The results of this study
 provides key insights into how the plumage of birds is adapted to
 different environments and lifestyles and provides a basis for
 understanding the diverse range and the evolution of variation in these
 characteristics.
description: Raw data: Mass and
 density of body feathers. In this table, N is the sample size for each
 parameter. See Material and methods for sources.FEpap_dryad1.docRaw data: Contour feather lengths and the presence of afterfeathers on contour feathers (1, present, 0, absent). N is the sample size for each parameter. See Material and methods for sources.FEpap_dryad2.docFEpap_dryad3