cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sp95
title: Data from: Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees

description: Within-host competition is predicted to drive the evolution of virulence
 in parasites, but the precise outcomes of such interactions are often
 unpredictable due to many factors including the biology of the host and
 the parasite, stochastic events and co-evolutionary interactions. Here, we
 use a serial passage experiment (SPE) with three strains of a
 heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis
 mellifera) to assess how evolving under increasing competitive pressure
 affects parasite virulence and fitness evolution. The results show an
 increase in virulence after successive generations of selection and
 consequently faster production of spores. This faster sporulation,
 however, did not translate into more spores being produced during this
 longer window of sporulation; rather, it appeared to induce a loss of
 fitness in terms of total spore production. There was no evidence to
 suggest that a greater diversity of competing strains was a driver of this
 increased virulence and subsequent fitness cost, but rather that
 strain-specific competitive interactions influenced the evolutionary
 outcomes of mixed infections. It is possible that the parasite may have
 evolved to avoid competition with multiple strains because of its
 heterothallic mode of reproduction, which highlights the importance of
 understanding parasite biology when predicting disease dynamics.
description: Evisonetal_2015_JEBSurvival data and spore counts
DOI: 10.5061/dryad.33st2
title: Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis

description: One of the most devastating emerging pathogens of wildlife is the chytrid
 fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of
 amphibian species around the world. Genomic data from pure Bd cultures has
 advanced our understanding of Bd phylogenetics, genomic architecture, and
 mechanisms of virulence. However pure cultures are laborious to obtain and
 whole genome sequencing is comparatively expensive, so relatively few
 isolates have been genetically characterized. Thus we still know little
 about the genetic diversity of Bd in natural systems. The most common
 non-invasive method of sampling Bd from natural populations is to swab
 amphibian skin. Hundreds of thousands of swabs have been collected from
 amphibians around the world, but Bd DNA collected via swabs is often low
 in quality and/or quantity. In this study, we developed a custom Bd
 genotyping assay using the Fluidigm Access Array platform to amplify 192
 carefully-selected regions of the Bd genome. We obtained robust sequence
 data for pure Bd cultures and field-collected skin swabs. This new assay
 has the power to accurately discriminate among the major Bd clades,
 recovering the basic tree topology previously revealed using whole genome
 data. Additionally, we established a critical value for initial Bd load
 for swab samples (150 Bd genomic equivalents) above which our assay
 performs well. By leveraging advances in microfluidic multiplex PCR
 technology and the globally distributed resource of amphibian swab
 samples, non-invasive skin swabs can now be used to address critical
 spatial and temporal questions about Bd and its effects on declining
 amphibian populations.
description: Bd Fluidigm consensus
 sequences by ampliconZip file of cleaned and
 aligned consensus sequences by amplicomBd_fluidigm_aligned_cleaned_consensus_byamplicon.zipBd Fluidigm Primer TableTable of 192 primer pairs used with relevant information such as amplicon size, chromosome, and marker referenceBd_Fluidigm_Primer_Table.docx
DOI: 10.5061/dryad.s420s
title: Data from: Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

description: Background and Aims. Bee orchids (Ophrys) have become the most popular
 model system for studying reproduction via insect-mediated
 pseudo-copulation and for exploring the consequent, putatively adaptive,
 evolutionary radiations. However, despite intensive past research, both
 the phylogenetic structure and species diversity within the genus remain
 highly contentious. Here, we integrate next-generation sequencing and
 morphological cladistics techniques to clarify the phylogeny of the genus.
 Methods. At least two accessions of each of the ten species groups
 previously circumscribed from large-scale cloned nuclear ribosomal
 internal transcibed spacer (nrITS) sequencing were subjected to
 restriction site-associated sequencing (RAD-seq). The resulting matrix of
 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to
 construct an unrooted network and a rooted maximum likelihood phylogeny. A
 parallel morphological cladistic matrix of 43 characters generated both
 polymorphic and non-polymorphic sets of parsimony trees before being
 mapped across the RAD-seq topology. Key Results. RAD-seq data strongly
 support the monophyly of nine out of ten groups previously circumscribed
 using nrITS and resolve three major clades; in contrast, supposed
 microspecies are barely distinguishable. Strong incongruence separated the
 RAD-seq trees from both the morphological trees and traditional
 classifications; mapping of the morphological characters across the
 RAD-seq topology rendered them far more homoplastic. Conclusions. The
 comparatively high level of morphological homoplasy reflects extensive
 convergence, whereas the derived placement of the fusca group is
 attributed to paedomorphic simplification. The phenotype of the most
 recent common ancestor of the extant lineages is inferred, but it
 post-dates the majority of the character state changes that typify the
 genus. RAD-seq may represent the high-water mark of the contribution of
 molecular phylogenetics to understanding evolution within Ophrys; further
 progress will require large-scale population-level studies that integrate
 phenotypic and genotypic data in a cogent conceptual framework.
description: Ophrys_34ind_4159charPhylip datafile of SNPs filtered from RADseq data.Ophrys_32ind_4060charPhylip file of SNPs derived from RADseq data for ingroup only.
DOI: 10.5061/dryad.g90hd
title: Data from: Short term variation in sperm competition causes sperm mediated epigenetic effects on early offspring performance in the zebrafish

description: The inheritance of non-genetic factors is increasingly seen to play a
 major role in ecology and evolution. While the causes and consequences of
 epigenetic effects transmitted from the mother to the offspring have
 received ample attention, much less is known about how variation in the
 condition of the father affects the offspring. Here, we manipulated the
 intensity of sperm competition experienced by male zebrafish Danio rerio
 to investigate the potential for sperm-mediated epigenetic effects over a
 relatively short period of time. We found that the rapid responses of
 males to varying intensity of sperm competition not only affected sperm
 traits as shown previously, but also the performance of the resulting
 offspring. We observed that males exposed to high intensity of sperm
 competition produced faster swimming and more motile sperm, and sired
 offspring that hatched over a narrower time frame but exhibited a lower
 survival rate than males exposed to low intensity of sperm competition.
 Our results provide striking evidence for short-term paternal effects and
 the possible fitness consequences of such sperm-mediated non-genetic
 factors not only for the resulting offspring but also for the female.
description: EjaculateTraitsEjaculate traits for each Male. Longevity: time of motility from activation until no longer motile (in seconds), 2 replicates per male. Density: sperm counts of visible field (2 per Male). Volume: Ejaculate volume (microliter) A: before setup of experiment, B: at IVF, C: 2 weeks after end of experiment.SpermMotilityNumber of total sperm and motile sperm recorded, 10 seconds post activation.SpermVelocitySperm swimming speed parameters recorded (VCL, VAP, VSL) at 4 time points (10 / 20/30/40 seconds post activation).LarvalSurvivalSurvival at 4 points (from 3h post fertilisation to 1 week of age). Reported are numbers of offspring alive / dead for each clutch.HatchingNumbers of offspring hatched / unhatched within any given clutch, measured in 2 hr time intervalsfrom 48 hours post fertilisation until 80 hours post fertilisation (or less, if all offspring had hatched prior to this point in time). File also contains information in MaleID, FemaleID, Treatment and experimental Block.
DOI: 10.5061/dryad.s4t435r
title: Data from: Taking advantage of hybrid bioinspired intelligent algorithm with decoupled extended Kalman filter for optimizing growing and pruning radial basis function network

description: The Growing and Pruning Radial Basis Function (GAP-RBF) network is a
 promising sequential learning algorithm for prediction analysis, but the
 parameter selection of such a network is usually a non-convex problem and
 makes it difficult to handle. In this paper, a hybrid bio-inspired
 intelligent algorithm is proposed to optimize GAP-RBF. In specific, the
 excellent local convergence of PSO and the extensive search ability of GA
 are both considered to optimize the weights and bias term of GAP-RBF.
 Meanwhile, a competitive mechanism is proposed to make the hybrid
 algorithm choose the appropriate individuals for effective search and
 further improve its optimiation ability. Moreover, a Decoupled EKF (DEKF)
 method is introduced in this study to reduce the size of error covariance
 matrix and decrease the computational complexity for performing real-time
 predictions. In the experiments, three classic forecasting issues
 including abalone age, Boston house price and auto MPG are adopted for
 extensive test, and the experimental results show that our method performs
 better than PSO and GA these two single bio-inspired optimization
 algorithms. What is more, our method via DEKF achieves the better results
 in comparison with the state-of-art sequential learning algorithms, such
 as GAP-RBF, MRAN, RANEKF and RAN.
description: Abalone
 datasetAbalone dataset includes
 4177 samples, and each sample is composed of seven continuous input
 attributes, one nominal attribute and one integer
 output.Abalone
 data.txtBoston house price
 datasetBoston house price
 dataset includes 506 samples, and each sample comprises of 12 continuous
 input attributes, one binary-valued attribute and one continuous
 outputAuto MPG
 datasetAuto MPG dataset
 includes 398 samples, and each sample is composed of seven inputs (four
 continuous ones and three multivalued discrete ones) and one continuous
 output (the fuel consumption).
DOI: 10.5061/dryad.3h771
title: Data from: Extrapair paternity rates vary with latitude and elevation in Emberizid sparrows

description: Mating systems can vary among species and populations and thus influence
 evolutionary trajectories, ecological traits, and population demography.
 The siring of offspring by an extrapair male, or extrapair paternity
 (EPP), is a widespread and varied phenomenon in all vertebrate classes.
 However, we do not understand all of the factors associated with variation
 in EPP rates. The breeding synchrony hypothesis suggests that EPP rates
 should increase with latitude and elevation, whereas the paternal care
 hypothesis predicts that EPP rates should decrease with elevation. To
 address these hypotheses, we investigated how population EPP rates vary
 over elevation and latitude in emberizid sparrows. In comparative analyses
 including the effects of phylogeny, the relationship between EPP rates and
 elevation depended on latitude. EPP rates were greater in higher-latitude
 populations. But within higher-latitude populations, EPP rates decreased
 with increasing elevation. These findings provide support for both the
 breeding synchrony and paternal care hypotheses, suggesting that in
 lower-latitude, higher-elevation populations, the need for male parental
 care does not outweigh the benefits of seeking extrapair fertilizations in
 populations with relatively synchronous breeding. In contrast, at
 higher-latitude, higher-elevation sites, the need for male parental care
 is greater and might drive lower rates of extrapair mating despite highly
 synchronous breeding.
description: collated EPP
 dataTable containing all of
 the extra-pair paternity (EPP) data compiled from the primary literature
 and through personal communication. We used these data in all of our
 analyses.mcmc
 tracesThese pdfs show the MCMC
 estimates for both fixed and random effects in our main analyses (with
 relative number of broods containing extra-pair young as the response
 variable, and relative number of extra-pair young as the response
 variable), described in the main text of the paper as well as in our
 supplementary online material. The full R call that we used for these
 analyses is available in online appendix A.
DOI: 10.5061/dryad.55kd0
title: Data from: The role of prezygotic isolation mechanisms in the divergence of two parasite species

description: Background: The formation of reproductive barriers in diverging lineages
 is a prerequisite to complete speciation according to the biological
 species concept. In parasites with complex life cycles, speciation may be
 driven by adaptation to different intermediate hosts, yet diverging
 lineages can still share the same definitive host where reproduction takes
 place. In these cases, prezygotic isolation mechanisms should evolve very
 early and be particularly strong, preventing costly unfavourable matings.
 In this study, we investigated the importance of prezygotic barriers to
 reproduction in two cestode species that diverged 20–25mya and show an
 extraordinary degree of specificity to different intermediate hosts. Both
 species share the same definitive hosts and hybridize in the laboratory.
 Yet, natural hybrids have so far not been detected. Methods: We used a
 combination of different experiments to investigate the role of prezygotic
 barriers to reproduction in the speciation of these parasites. First, we
 investigated whether hybridization is possible under natural conditions by
 exposing lab-reared herring gulls (Larus argentatus, the definitive hosts)
 to both parasites of either sympatric or allopatric combinations. In a
 second experiment, we tested whether the parasites prefer conspecifics
 over parasites from a different species in dichotomous mate choice trials.
 Results: Our results show that the two species hybridize under natural
 conditions with parasites originating either from sympatric or allopatric
 populations producing hybrid offspring. Surprisingly, the mate choice
 experiment indicated that both parasite species prefer mates of the
 different species to conspecifics. Conclusions: Neither fundamental
 constraints against hybridization in a natural host nor assortative mate
 choice sufficiently explain the persistent segregation of the two tapeworm
 species in nature. Hence, postzygotic ecological selection against hybrids
 is presumably the more important driving force limiting gene flow between
 the two parasite sister species.
description: Mate choice in
 SchistocephalusThis data was obtained
 from two experiments testing for prezygotic isolation between
 Schistocephalus solidus and S. pungitii.Henrich&Kalbe_MateChoiceSchistocephalus.xlsx
DOI: 10.5061/dryad.qv0sk
title: Data from: Intertemporal similarity: discounting as a last resort

description: Standard models of intertemporal choice assume that individuals discount
 future payoffs by integrating reward amounts and time delays to generate a
 discounted value. Alternative models propose that, rather than integrate
 across them, individuals compare within attributes (amounts and delays) to
 determine if differences in one attribute outweigh differences in another
 attribute. For instance, the similarity model 1) compares the two reward
 amounts to determine whether they are similar, 2) compares the similarity
 of the two time delays, and then 3) makes a decision based on these
 similarity judgments. Here, I tested discounting models against
 attribute-based models that use similarity judgments to make choices. I
 collected intertemporal choices and similarity judgments for the reward
 amounts and time delays from participants in three experiments. All
 experiments tested the ability of discounting and similarity models to
 predict intertemporal choices. Model generalization analyses showed that
 the best predicting models started with similarity judgments and then, if
 similarity failed to make a prediction, resorted to discounting models.
 Similarity judgments also matched intertemporal choice data demonstrating
 both the magnitude and sign effects, thereby accounting for behavioral
 data that contradict many discounting models. These results highlight the
 possibility that attribute-based models such as the similarity models
 provide alternatives to discounting that may offer insights into the
 process of making intertemporal choices.
description: Data for Intertemporal
 Similarity: Discounting as a Last ResortThese data were
 collected in three experiments in which human participants were asked to
 make binary intertemporal choices, staircase intertemporal choices, and
 similarity judgments for reward amounts and time delays. Experiment 1 used
 real rewards and delays and was conducted in Berlin, Germany. Experiments
 2 and 3 used hypothetical rewards and delays and were conducted in
 Lincoln, Nebraska.stevens_2015_data.zip
DOI: 10.5061/dryad.6kc60
title: Data from: The evolutionary economics of embryonic-sac fluids in squamate reptiles

description: The parchment-shelled eggs of squamate reptiles take up substantial water
 from the nest environment, enabling the conversion of yolk into neonatal
 tissue and buffering the embryo against the possibility of subsequent dry
 weather. During development, increasing amounts of water are stored in the
 embryonic sacs (i.e., membranes around the embryo: amnion, allantois, and
 chorion). The evolution of viviparity (prolonged uterine retention of
 developing embryos) means that embryonic-sac fluid storage now imposes a
 cost (increased maternal burdening), confers less benefit (because the
 mother buffers fetal water balance), and introduces a potential conflict
 among uterine siblings (for access to finite water supplies). Our data on
 nine species of squamate reptiles and published information on three
 species show that the embryonic-sac fluids comprise around 33% of neonatal
 mass in viviparous species versus 94% in full-term eggs of oviparous
 squamates. Data on parturition in 149 vipers (Vipera aspis, a viviparous
 species) show that larger offspring store more fluids in their fetal sacs
 and that an increase in litter size is associated with a decrease in
 fluid-sac mass per offspring. Overall, the evolutionary transition from
 oviparity to viviparity may have substantially altered selective forces on
 offspring packaging and created competition among offspring for access to
 water reserves during embryonic development.
description: ESF REPTILES BONNET
 XRaw
 data used for the main analyses. Note that additional details (e.g.
 parturition date, total body size) and explanations about each variable
 (e.g. measurements, exclusion of several data) can be provided. Contact X
 Bonnet in this case.
DOI: 10.5061/dryad.v03d73s
title: Data from: Assessment of polytraumatized patients according to the Berlin Definition: Does the addition of physiological data really improve interobserver reliability?

description: Background Several new definitions for categorizing the severely injured
 as the Berlin Definition have been developed. Here, severely injured
 patients are selected by additive physiological parameters and by the
 general Abbreviated Injury Scale (AIS)-based assessment. However, all
 definitions should conform to an AIS severity coding applied by an expert.
 We examined the dependence of individual coding on defining injury
 severity in general and in identifying polytrauma according to several
 definitions. A precise definition of polytrauma is important for quality
 management. Methods We investigated the interobserver reliability (IR)
 between several polytrauma definitions for identifying polytrauma using
 several cut-off levels (ISS ≥16, ≥18, ≥20, ≥25 points, and the Berlin
 Definition). One hundred and eighty-seven patients were included for
 analyzing IR of the polytrauma definitions. IR for polytrauma definitions
 was assessed by Cohen’s kappa. Results IR for identifying polytrauma
 according to the relevant definitions showed moderate agreement
 (&lt;0.60) in the ISS cutoff categories (ISS ≥16, ≥18, and ≥20
 points), while ISS ≥25 points just reached substantial agreement (0.62)
 and the Berlin Definition demonstrated a correlation of 0.77 which is
 nearly perfect agreement (&gt;0.80). Conclusion Compared with the
 ISS-based definitions of polytrauma, the Berlin Definition proved less
 dependent on the individual rater. This underlines the need to redefine
 the selection of severely injured patients. Using the Berlin Definition
 for identifying polytrauma could improve the comparability of patient data
 across studies, in trauma center benchmarking, and in quality assurance.
description: Original data
 Interobserver reliability in polytrauma definitionThe final dataset and
 accompanying code of interobserver reliability in polytrauma
 definitionData Pothmann Intraobserver
 Polytrauma.xlsx
DOI: 10.5061/dryad.gv047
title: Data from: A single origin of extreme matrotrophy in African mabuyine skinks

description: Most mammals and approximately 20% of squamates (lizards and snakes) are
 viviparous, whereas all crocodilians, birds and turtles are oviparous.
 Viviparity evolved greater than 100 times in squamates, including multiple
 times in Mabuyinae (Reptilia: Scincidae), making this group ideal for
 studying the evolution of nutritional patterns associated with viviparity.
 Previous studies suggest that extreme matrotrophy, the support of
 virtually all of embryonic development by maternal nutrients, evolved as
 many as three times in Mabuyinae: in Neotropical Mabuyinae (63 species),
 Eumecia (2 species; Africa) and Trachylepis ivensii (Africa). However, no
 explicit phylogenetic hypotheses exist for understanding the evolution of
 extreme matrotrophy. Using multilocus DNA data, we inferred a species tree
 for Mabuyinae that implies that T. ivensii (here assigned to the
 resurrected genus Lubuya) is sister to Eumecia, suggesting that extreme
 matrotrophy evolved only once in African mabuyine skinks.
description: sBEAST_11genes_2mtrates*BEAST v1.8.2 input file used for phylogenetic inference of Mabuyinae, using mitochondrial and nuclear DNA sequence data. Mitochondrial loci include ND2 and 16S, and nuclear loci include regions of BDNF, BRCA1, BRCA2, CMOS, EXPH5, KIF24, MC1R, MXRA5, and RAG1 protein coding genes. Includes DNA sequence data for 14 mabuyine and 2 outgroup taxa.