cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jg90h
title: Data from: Extent and variability of interstitial telomeric sequences and their effects on estimates of telomere length

description: Telomeres often shorten with time, although this varies between tissues,
 individuals and species, and their length and/or rate of change may
 reflect fitness and rate of senescence. Measurement of telomeres is
 increasingly important to ecologists, yet the relative merits of different
 methods for estimating telomere length are not clear. In particular the
 extent to which interstitial telomere sequences (ITSs), telomere repeats
 located away from chromosomes ends, confound estimates of telomere length
 is unknown. Here we present a method to estimate the extent of ITS within
 a species and variation among individuals. We estimated the extent of ITS
 by comparing the amount of label hybridized to in-gel telomere restriction
 fragments (TRF) before and after the TRFs were denatured. This protocol
 produced robust and repeatable estimates of the extent of ITS in birds. In
 five species, the amount of ITS was substantial, ranging from 15% to 40%
 of total telomeric sequence DNA. In addition, the amount of ITS can vary
 significantly among individuals within a species. Including ITSs in
 telomere length calculations always underestimated telomere length because
 most ITSs are shorter than most telomeres. The magnitude of that error
 varies with telomere length and is larger for longer telomeres. Estimating
 telomere length using methods that incorporate ITSs, such as Southern blot
 TRF and quantitative PCR analyses reduces an investigator's power to
 detect difference in telomere dynamics between individuals or over time
 within an individual.
description: Interstitial telomeric
 sequence gel dataAll gel data are
 included that were used to calculate telomere lengths and fractional
 content of interstitial telomeric sequences for each species. The file
 contains the date each gel was run, the species and bird identify for each
 lane used on each gel and the optical density data for each lane. Sums of
 optical density and position (kb) determined from size markers were used
 for all calculations as described in the citation. Data from 15 gels are
 included.
DOI: 10.5061/dryad.s5p44
title: Data from: Effects of ultraviolet radiation on photosynthetic performance and N2 fixation in Trichodesmium erythraeum IMS 101

description: Biological effects of ultraviolet radiation (UVR; 280–400 nm) on marine
 primary producers are of general concern, as oceanic carbon fixers that
 contribute to the marine biological CO2 pump are being exposed to
 increasing UV irradiance due to global change and ozone depletion. We
 investigated the effects of UV-B (280–320 nm) and UV-A (320–400 nm) on the
 biogeochemically critical filamentous marine N2-fixing cyanobacterium
 Trichodesmium (strain IMS101) using a solar simulator as well as under
 natural solar radiation. Short exposure to UV-B, UV-A, or integrated total
 UVR significantly reduced the effective quantum yield of photosystem II
 (PSII) and photosynthetic carbon and N2 fixation rates. Cells acclimated
 to low light were more sensitive to UV exposure compared to
 high-light-grown ones, which had more UV-absorbing compounds, most likely
 mycosporine-like amino acids (MAAs). After acclimation under natural
 sunlight, the specific growth rate was lower (by up to 44 %), MAA content
 was higher, and average trichome length was shorter (by up to 22 %) in the
 full spectrum of solar radiation with UVR, than under a photosynthetically
 active radiation (PAR) alone treatment (400–700 nm). These results suggest
 that prior shipboard experiments in UV-opaque containers may have
 substantially overestimated in situ nitrogen fixation rates by
 Trichodesmium, and that natural and anthropogenic elevation of UV
 radiation intensity could significantly inhibit this vital source of new
 nitrogen to the current and future oligotrophic oceans.
description: C fix and N
 fix
DOI: 10.5061/dryad.511ms
title: Data from: The effect of temperature on Drosophila hybrid fitness

description: Mechanisms of reproductive isolation inhibit gene flow between species and
 can be broadly sorted into two categories: prezygotic and postzygotic.
 While comparative studies suggest that prezygotic barriers tend to evolve
 first, postzygotic barriers are crucial for maintaining species boundaries
 and impeding gene flow that might otherwise cause incipient species to
 merge. Most, but not all, postzygotic barriers result from genetic
 incompatibilities between two or more loci from different species, and
 occur due to divergent evolution in allopatry. Hybrid defects result from
 improper allelic interactions between these loci. While some postzygotic
 barriers are environmentally independent, the magnitude of others has been
 shown to vary in penetrance depending on environmental factors. We crossed
 D. melanogaster mutants to two other species, D. simulans and D. santomea,
 and collected fitness data of the hybrids at two different temperatures.
 Our goal was to examine the effect of temperature on recessive
 incompatibility alleles in their genomes. We found that temperature has a
 stronger effect on the penetrance of recessive incompatibility alleles in
 the D. simulans genome than on those in the D. santomea genome. These
 results suggest that the penetrance of hybrid incompatibilities can be
 strongly affected by environmental context, and that the magnitude of such
 gene by environment interactions can be contingent on the genotype of the
 hybrid.
description: The effect of
 temperature on Drosophila hybrid fitness: data filesThis directory includes
 the raw counts for the genetic maps of hybrid inviability in mel/sim and
 mel/san F1 hybrid females at 18ºC. The file also includes all code to
 replicate the analyses in Miller and Matute (2016).dryad.zip
DOI: 10.5061/dryad.qr0rn
title: Data from: Evolution of paternal care in diploid and haplodiploid populations

description: W. D. Hamilton famously suggested that the inflated relatedness of full
 sisters under haplodiploidy explains why all workers in the social
 hymenoptera are female. This suggestion has not stood up to further
 theoretical scrutiny and is not empirically supported. Rather, it appears
 that altruistic sib-rearing in the social hymenoptera is performed
 exclusively by females because this behaviour has its origins in parental
 care, which was performed exclusively by females in the ancestors of this
 insect group. However, haplodiploidy might still explain the sex of
 workers if this mode of inheritance has itself been responsible for the
 rarity of paternal care in this group. Here, we perform a theoretical kin
 selection analysis to investigate the evolution of paternal care in
 diploid and haplodiploid populations. We find that haplodiploidy may
 either inhibit or promote paternal care depending on model assumptions,
 but that under the most plausible scenarios it promotes – rather than
 inhibits – paternal care. Our analysis casts further doubt upon there
 being a causal link between haplodiploidy and eusociality.
description: C++ source code for
 numerical simulationsThe freestanding C++
 program that was used to run numerical simulations and generate figures
 for the manuscript. Must be compiled with a C++11-compatible
 compiler.pater.cpp
DOI: 10.5061/dryad.j331mj8
title: Data from: Mitochondrial complementation: a possible neglected factor behind early eukaryotic sex

description: Sex is ancestral in eukaryotes. Meiotic sex differs from bacterial ways of
 exchanging genetic material by involving the fusion of two cells. We
 examine the hypothesis that fusion evolved in early eukaryotes because it
 was directly beneficial, rather than a passive side-effect of meiotic sex.
 We assume that the uptake of (proto)mitochondria into eukaryotes preceded
 the evolution of cell fusion, and that Muller’s ratchet operating within
 symbiont lineages led to the accumulation of lineage-specific sets of
 mutations in asexual host cells. We examine if cell fusion, and the
 consequent biparental inheritance of symbionts, helps to mitigate the
 effects of this mutational meltdown of mitochondria. In our model, host
 cell fitness improves when two independently-evolved mitochondrial strains
 co-inhabit a single cytoplasm, mirroring mitochondrial complementation
 found in modern eukaryotes. If fusion incurs no cost, we find that an
 allele coding for fusion can invade a population of non-fusers. If fusion
 is costly, there are two thresholds. The first describes a maximal fusing
 rate (probability of fusion per round of cell division) that is able to
 fix. An allele that codes for a rate above this threshold can reach a
 polymorphic equilibrium with non-fusers, as long as the rate is below the
 second threshold, above which the fusion allele is counterselected.
 Whenever it evolves, fusion increases the population-wide level of
 heteroplasmy, which allows mitochondrial complementation and increases
 population fitness. We conclude that beneficial interactions between
 mitochondria are a potential factor that selected for cell fusion in early
 eukaryotes.
description: R scripts +
 dataAll the R scripts used
 to create the model, analyse it, and plot the figures presented in the
 paper and its supplementary material are contained in this .zip folder.
 The data used to plot the figures of the main text is also available.
 Everything also available on
 https://github.com/Redsiana/Escape-from-mitochondriaEscape-from-mitochondria.zip
DOI: 10.5061/dryad.1k894
title: Data from: Predicting invasive species impacts: a community module functional response approach reveals context dependencies

description: 1. Predatory functional responses play integral roles in predator-prey
 dynamics, and their assessment promises greater understanding and
 prediction of the predatory impacts of invasive species. 2. Other
 inter-specific interactions, however, such as parasitism and higher-order
 predation, have the potential to modify predator-prey interactions and
 thus the predictive capability of the comparative functional response
 approach. 3. We used a four-species community module (higher-order
 predator; focal native or invasive predators; parasites of focal
 predators; native prey) to compare the predatory functional responses of
 native Gammarus duebeni celticus and invasive Gammarus pulex amphipods
 towards three invertebrate prey species (Asellus aquaticus, Simulium spp.,
 Baetis rhodani), thus quantifying the context dependencies of parasitism
 and a higher-order fish predator on these functional responses. 4. Our
 functional response experiments demonstrated that the invasive amphipod
 had a higher predatory impact (lower handling time) on two of three prey
 species, which reflects patterns of impact observed in the field. The
 community module also revealed that parasitism had context dependent
 influences, for one prey species, with the potential to further reduce the
 predatory impact of the invasive amphipod or increase the predatory impact
 of the native amphipod in the presence of a higher-order fish predator. 5.
 Partial consumption of prey was similar for both predators and occurred
 increasingly in the order A. aquaticus, Simulium spp., and B. rhodani.
 This was associated with increasing prey densities, but showed no context
 dependencies with parasitism or higher-order fish predator. 6. This study
 supports the applicability of comparative functional responses as a tool
 to predict and assess invasive species impacts incorporating multiple
 context dependencies.
description: Paterson_Functional_ResponsesRaw data used in phenomenological and mechanistic functional response analyses
DOI: 10.5061/dryad.vn541ms8
title: Data from: Sexual selection is ineffectual or inhibits the purging of deleterious mutations in Drosophila melanogaster

description: The effects of sexual selection on population mean fitness are unclear and
 a subject of debate. Recent models propose that, because reproductive
 success may be condition-dependent, much of the genome may be a target of
 sexual selection. Under this scenario, mutations that reduce health, and
 thus non-sexual fitness, may also be deleterious with respect to
 reproductive success, meaning that sexual selection may contribute to the
 purging of deleterious alleles. We tested this hypothesis directly by
 subjecting replicate Drosophila melanogaster populations to two treatments
 that altered the opportunity for sexual selection and then tracked changes
 in the frequency of six separate deleterious alleles with recessive and
 visible phenotypic effects. While natural selection acted to decrease the
 frequency of all six mutations, the addition of sexual selection did not
 aid in the purging of any of them, and for three of them appears to have
 hampered it. Courtship and mating have harmful effects in this species and
 mate choice assays showed that males directed more courtship and mating
 behavior towards wild-type over mutant females, providing a likely
 explanation for sexual selection’s cost. Whether this cost extends to
 other mutations (e.g., those lacking visible phenotypic effects) is an
 important topic for future research.
description: brownsepiaplexusforkedwhiteyellow
DOI: 10.5061/dryad.602hq
title: Data from: Shelter availability mediates decorating in the majoid crab, Camposcia retusa

description: While numerous aquatic and terrestrial species adorn their surface with
 items secured from their surroundings, termed decorating, the physical and
 environmental factors that drive this behaviour are often unclear. One of
 the best-known examples of this phenomenon are the decorator crabs
 (Majoidea), with almost 75% of species known to decorate. Here, we
 examined patterns of decorating in a coral reef-associated majoid,
 Camposcia retusa, to identify what factors determine patterns of, and
 investment in, decorating. Observations of natural decoration patterns
 indicate this species primarily decorate with sponges, fleshy and
 filamentous algae, and detritus. Decorations were primarily distributed on
 the carapace and hind walking legs which may reflect exoskeleton
 morphology. However, decoration cover did not decline with size, as is
 observed in some other majoid species, suggesting the factors driving
 decoration investment remain consistent throughout growth stages. From
 behavioural experiments, we determined that non-uniform decorating is a
 result of active selection, with crabs preferentially decorating their
 hind legs and carapace, with only small items placed on the carapace.
 Decorating in C. retusa appears to function primarily as an anti-predator
 response, with crabs decorating at higher rates when access to shelter is
 limited. This study is the first to quantify the decorating habits of C.
 retusa and suggests that behaviourally-mediated decorating has a primary
 anti-predator function. This study also highlights the value of
 manipulative behavioural experiments as a tool for assessing the
 behavioural mechanisms that drive decorating in animals.
description: Brooker et al. 2017.
 Behav Ecol. DataAll data from Brooker et
 al. 2017. Including 1) wild crab survey data, 2) experiment 1 data (pompom
 size and placement), and 3) experiment 2 data (pompom use with/ without
 shelter).Brooker et al. Behav Ecol.
 Data.xlsx
DOI: 10.5061/dryad.v8m1p
title: Data from: Invasive success and the evolution of enhanced weaponry

description: A key hypothesis that has been proposed to explain plants’ invasive
 success suggests that some invasive species produce allelochemicals that
 are novel against naïve neighbours at the introduced range and therefore
 provide an advantage there (novel weapons hypothesis – NWH). However, a
 seldom-studied hypothesis suggests that invasive populations could not
 only possess novel weapons, but might also evolve their enhanced
 production. Moreover, so far no study has examined both the novelty and
 evolution of allelopathic effects. Here, we examined these two hypotheses
 in a set of experiments with the highly invasive plant Impatiens
 glandulifera. In the first experiment, we examined the evolution of
 allelopathic ability by comparing the inhibitory effects of leaf extracts
 from native versus invasive I. glandulifera on the germination success of
 its dominant neighbour Urtica dioica. In the following experiments, we
 examined the NWH by comparing the germination success of U. dioica seeds
 collected at the native versus invasive range of I. glandulifera, in
 response to either leaf extracts or soil trained with invasive I.
 glandulifera. The results of the first experiment indicate that invasive
 I. glandulifera exert a stronger inhibitory effect on the germination of
 U. dioica compared to their native counterparts, providing support for the
 hypothesis that allelopathic ability can evolve at the invasive range.
 However, the results of the two following experiments reveal no difference
 in the response of U. dioica from the native versus invasive range of I.
 glandulifera, to the allelopathic effects of either the leaf extracts or
 the trained soil. These results therefore do not provide support for the
 NWH, and suggest that increased allelopathy in invasive I. glandulifera
 might have been selected for by other processes. The results of this study
 call for biogeographical experiments that will examine not only the
 novelty but also the evolution of allelopathic effects in invasive plants.
description: Gruntman et al.,
 Data
DOI: 10.5061/dryad.dm88t
title: Data from: Pathogen life-history trade-offs revealed in allopatry

description: Trade-offs in life-history traits is a central tenet in evolutionary
 biology, yet their ubiquity and relevance to realized fitness in natural
 populations remains questioned. Trade-offs in pathogens are of particular
 interest because they may constrain the evolution and epidemiology of
 diseases. Here, we studied life-history traits determining transmission in
 the obligate fungal pathogen, Podosphaera plantaginis, infecting Plantago
 lanceolata. We find that while traits are positively associated on
 sympatric host genotypes, on allopatric host genotypes relationships
 between infectivity and subsequent transmission traits change shape,
 becoming even negative. The epidemiological prediction of this change in
 life-history relationships in allopatry is lower disease prevalence in
 newly established pathogen populations. An analysis of the natural
 pathogen metapopulation confirms that disease prevalence is lower in newly
 established pathogen populations and they are more prone to go extinct
 during winter than older pathogen populations. Hence, life-history
 trade-offs mediated by pathogen local adaptation may influence
 epidemiological dynamics at both population and metapopulation levels.
description: metapopulationInoculations
DOI: 10.4121/0348e487-38c2-477b-935d-e56fdd554595
title: Data accompanying the publication: Investigation of coherent Fourier scatterometry as a calibration tool for determination of steep side wall angle and height of a nanostructure

description: Authors (publication): Anubhav Paul, Jila Rafighdoost, Xiujie Dou, Silvania F. Pereira <br>This dataset contains the MATLAB scripts and supporting data used to reproduce the main simulation, calibration, sensitivity, and validation results in the publication “Investigation of coherent Fourier scatterometry as a calibration tool for determination of steep side wall angle and height of a nanostructure”. It includes simulated normalized far-field cross-sections (ky = 0 plane) for cliff-like nanostructures under TE/TM illumination for multiple side-wall angles and heights, the corresponding calibration-curve data (based on the “visibility” metric), and sensitivity-analysis datasets (e.g., edge roundness and structure position). The dataset also provides experimental/simulated profile comparisons and AFM-derived statistics used for experimental verification.
DOI: 10.4121/0348e487-38c2-477b-935d-e56fdd554595.v1
title: Data accompanying the publication: Investigation of coherent Fourier scatterometry as a calibration tool for determination of steep side wall angle and height of a nanostructure

description: Authors (publication): Anubhav Paul, Jila Rafighdoost, Xiujie Dou, Silvania F. Pereira <br>This dataset contains the MATLAB scripts and supporting data used to reproduce the main simulation, calibration, sensitivity, and validation results in the publication “Investigation of coherent Fourier scatterometry as a calibration tool for determination of steep side wall angle and height of a nanostructure”. It includes simulated normalized far-field cross-sections (ky = 0 plane) for cliff-like nanostructures under TE/TM illumination for multiple side-wall angles and heights, the corresponding calibration-curve data (based on the “visibility” metric), and sensitivity-analysis datasets (e.g., edge roundness and structure position). The dataset also provides experimental/simulated profile comparisons and AFM-derived statistics used for experimental verification.
DOI: 10.5061/dryad.qv4bt
title: Data from: Management of behavioural change in patients presenting with a diagnosis of dementia: a video vignette study with Australian general practitioners

description: Objective: To test the impact of feedback on the proposed management of
 standardised patients presenting with behavioural change with a diagnosis
 of dementia in Australian primary care. Materials and methods: A video
 vignette study was performed with Australian general practitioners (GPs)
 in 2013. Participants viewed six pairs of matched videos depicting people
 presenting changed behaviour in the context of a dementia diagnosis in two
 phases. In both phases GPs indicated their diagnosis and management. After
 phase 1, GPs were offered feedback on management strategies for the
 patients depicted. Analyses focused on identification of change in
 management between the two phases of the study. Factors impacting on the
 intention to coordinate care for such patients were tested in a
 questionnaire based on the Theory of Planned Behaviour. Results:
 Forty-five GPs completed the study. There was significant improvement in
 the proposed management of three of the six scenarios after the
 intervention. Older GPs were more likely to refer appropriately (OR=1.11
 (1.01 to 1.23), p=0.04.). Overall referral to support agencies was more
 likely after the intervention (OR=2.52 (1.53 to 4.14), p&lt;0.001).
 Older GPs were less likely to intend to coordinate care for such patients
 (OR=0.89 (0.81 to 0.98) p=0.02). Participants who felt confident about
 their ability to coordinate care were more likely to do so (OR=3.79 (1.08
 to 13.32) p=0.04). Conclusions: The intervention described in this study
 promoted multidisciplinary management of patients with behavioural
 problems with a diagnosis of dementia. Increasing practitioner confidence
 in their ability to coordinate care may increase the proportion of GPs who
 will respond to patients and carers in this context. Older GPs may benefit
 in particular.
description: BMJ
 OpenBMJ_Open.zip