cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zkh1893c0
title: Data from: Ruderals naturalize, competitors invade: varying roles of plant adaptive strategies along the invasion continuum

description: 1. It is increasingly recognized that the factors facilitating plant
 invasions depend on the stage along the
 introduction-naturalization-invasion continuum. Adaptative strategies,
 i.e., combinations of functional traits that represent overall fitness in
 the face of one or more selection pressures, have shown promise in
 explaining plant invasions. However, whether adaptive strategy patterns
 change with the stages of plant invasion is not yet known.  2.
 Using the Pladias Database of the Czech Flora and Vegetation, we explored
 how Grime’s adaptive strategies (competitors, stress-tolerators, ruderals;
 CSR) and introduction pathways (deliberate vs. accidental) relate to plant
 invasion along the introduction-naturalization-invasion continuum. 3.
 Phylogenetically corrected ANOVAs showed that naturalized species
 (referring to non-invasive naturalized species in this study) were mostly
 R-selected, whereas invasive species tended to be C-selected. The results
 of phylogenetic regression analysis further confirmed that across the
 deliberately and accidentally introduced species, R- and C-selection were
 positively related to naturalization and invasion success, respectively.
 We also found that deliberate introduction was negatively related to
 naturalization success and grid-cell occupancy of naturalized species,
 likely due to the different CSR strategies possessed by deliberately and
 accidentally introduced aliens. 4. Our study provides empirical evidence
 that different adaptive strategies are associated with species that have
 reached different invasion stages and confirms the usefulness of the CSR
 strategy framework for understanding plant invasion. It has implications
 for predicting and preventing potential high-impact invaders. For example,
 our results show that naturalized C-selected species have a higher
 probability of becoming invasive than naturalized R-selected species.
 Therefore, management actions are essential to prevent further
 introductions and spread of competitors.
DOI: 10.5061/dryad.gb5mkkwrg
title: Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats

description: In the largest DNA-based study of domestic cat to date, 11,036 individuals
 (10,419 pedigreed cats from 91 breeds and breed types and 617
 non-pedigreed cats) were genotyped via commercial panel testing,
 elucidating the distribution and frequency of known genetic variants
 associated with blood type, disease and physical traits across cat breeds.
 Blood group determining variants, which are relevant clinically and in cat
 breeding, were genotyped to assess the across breed distribution of blood
 types A, B and AB. Extensive panel testing identified 13
 disease-associated variants in 48 breeds or breed types for which the
 variant had not previously been observed, strengthening the argument for
 panel testing across populations. The study also indicates that multiple
 breed clubs have effectively used DNA testing to reduce disease-associated
 genetic variants within certain pedigreed cat populations.
 Appearance-associated genetic variation in all cats is also discussed.
 Additionally, we combined genotypic data with phenotype information and
 clinical documentation, actively conducted owner and veterinarian
 interviews, and recruited cats for clinical examination to investigate the
 causality of a number of tested variants across different breed
 backgrounds. Lastly, genome-wide informative SNP heterozygosity levels
 were calculated to obtain a comparable measure of the genetic diversity in
 different cat breeds. This study represents the first comprehensive
 exploration of informative Mendelian variants in felines by screening over
 10,000 domestic cats. The results qualitatively contribute to the
 understanding of feline variant heritage and genetic diversity and
 demonstrate the clinical utility and importance of such information in
 supporting breeding programs and the research community. The work also
 highlights the crucial commitment of pedigreed cat breeders and registries
 in supporting the establishment of large genomic databases that when
 combined with phenotype information can advance scientific understanding
 and provide insights that can be applied to improve the health and welfare
 of cats.
DOI: 10.5061/dryad.02v6wwq53
title: Effects of an alternative host on the prevalence and infection intensity of a bumble bee parasite

description: Several bee parasites are transmitted through flowers, and some of them
 can infect multiple host species. Given the shared use of flowers by bee
 species, parasites can potentially encounter multiple host species, which
 could affect the evolution of parasite virulence. We used the
 trypanosomatid parasite Crithidia bombi and its host, the common eastern
 bumble bee (Bombus impatiens), to explore the effect of infecting an
 alternative host, the alfalfa leaf-cutter bee (Megachile rotundata), on
 parasite infectivity and ability to replicate. We conducted a serial
 passage experiment on primary and alternative hosts, assessing infectivity
 and intensity of infection during five passes. Parasite cells from each
 pass through the alternative host were also used to infect a group of
 primary hosts. We found that serial passes through the alternative host
 increased infectivity, but there was no effect on intensity of infection.
 Interestingly, both the probability and intensity of infection on the
 primary host increased after serial passage through the alternative host.
 This increase in intensity of infection could be due to maladaptation
 after selection of new C. bombi strains has occurred in the alternative
 host. This study suggests that host switching has the potential to affect
 the adaptation of bee parasites to their hosts.
description: These data are from a laboratory serial passage experiment in
 which Crithidia bombi were passed through the alternative host (AA
 treatment) or back to the primary host (AB treatment). We compared
 prevalence and intensity of infection between these two treatments and
 relative to a Bombus impatiens (primary host) control. Trials included up
 to 5 passes. 
description: ReadMe file is included.
DOI: 10.15468/dl.kxxsjb
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cyclobalanopsis championii"
 ]
}

 The dataset includes 402 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003050-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0zpc86706
title: Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

description: Background: Mathematical models predict that community-wide access to HIV
 testing-and-treatment can rapidly and substantially reduce new HIV
 infections. Yet several large universal test-and-treat HIV prevention
 trials in high-prevalence epidemics demonstrated variable reduction in
 population-level incidence. Methods: To elucidate patterns of HIV spread
 in universal test-and-treat trials we quantified the contribution of
 geographic-location, gender, age and randomized-HIV-intervention to HIV
 transmissions in the 30-community Ya Tsie trial in Botswana (estimated
 trial population: 175,664). Results: Deep-sequence phylogenetic analysis
 revealed that most inferred HIV transmissions within the trial occurred
 within the same or between neighboring communities, and between
 similarly-aged partners. Transmissions into intervention communities from
 control communities were more common than the reverse post-baseline (30%
 [12.2 – 56.7] versus 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3]
 versus 5% [0.9 – 22.9]) compatible with a benefit from
 treatment-as-prevention. Conclusion: Our findings suggest that population
 mobility patterns are fundamental to HIV transmission dynamics and to the
 impact of HIV control strategies. Funding: This study was supported by the
 National Institute of General Medical Sciences (U54GM088558); the Fogarty
 International Center (FIC) of the U.S. National Institutes of Health (D43
 TW009610); and the President’s Emergency Plan for AIDS Relief through the
 Centers for Disease Control and Prevention (CDC) (Cooperative agreements
 U01 GH000447 and U2G GH001911).
DOI: 10.48656/mh4n-g234
title: French Corpus of Causal Connectives, Discourse Relations, and Subjectivity FreCaDiS
DOI: 10.48656/z9f1-5x09
title: French Corpus of Causal Connectives, Discourse Relations, and Subjectivity FreCaDiS
DOI: 10.5061/dryad.6djh9w133
title: Darwin’s Hawkmoth (Xanthopan praedicta) responds to bat ultrasound at sonar-jamming rates: Acoustic data set

description: This paper reveals that Xanthopan praedicta (Lepidoptera: Sphingidae) is
 part of the bat-moth coevolutionary dynamic. I played recordings of bat
 echolocation to live X. praedicta and found that males respond with such
 dense ultrasound they can likely jam bat sonar. Female X. praedicta and
 two other sphingid species do not produce ultrasonic responses.
DOI: 10.5061/dryad.sbcc2fr84
title: Evaluating refugia in recent human evolution in Africa: Supplementary information

description: Homo sapiens have adapted to an incredible diversity of habitats around
 the globe. This capacity to adapt to different landscapes is clearly
 expressed within Africa, with Late Pleistocene Homo sapiens populations
 occupying savannahs, woodlands, coastlines and mountainous terrain. As the
 only area of the world where Homo sapiens have clearly persisted through
 multiple glacial-interglacial cycles, Africa is the only continent where
 classic refugia models can be formulated and tested to examine and
 describe changing patterns of past distributions and human
 phylogeographies. The potential role of refugia has frequently been
 acknowledged in the Late Pleistocene palaeoanthropological literature, yet
 explicit identification of potential refugia has been limited by the
 patchy nature of palaeoenvironmental and archaeological records, and the
 low temporal resolution of climate or ecological models. Here, we apply
 potential climatic thresholds on human habitation, rooted in ethnographic
 studies, in combination with high resolution model datasets for
 precipitation and biome distributions to identify persistent refugia
 spanning the Late Pleistocene (130-10 thousand years ago). We present two
 alternate models suggesting that between 27-66% of Africa may have
 provided refugia to Late Pleistocene human populations, and examine
 variability in precipitation, biome, and ecotone distributions within
 these refugial zones.
description: Analytical Code: All data used are available from open access
 online portals (e.g. OSF) or directly from R packages listed in the
 code. Table 1: All data are summarised from the
 referenced literature. The upper and lower age estimates derive from the
 confidence interval of chronometric dating, with the mid-age used for
 analysis calculated as a simple average of the two. For individual dates,
 the mid-age matches the central age estimate. Where an archaeological
 assemblage is constrained by two or more dates, the upper-most and
 lower-most confidence interval are used, integrating assessment from
 original reports.
description: The analytical code produces the component datasets and
 illustrations for Figure 1-3, including the datasets used solely for
 visualisation in Figure 6. Table SI1 presents
 co-ordinate data used to produce Figure 4, and chronological data used to
 produce Figure 5.
DOI: 10.5061/dryad.hmgqnk9jt
title: Growth and photosynthetic responses of encroaching tree seedlings to CO2 and stress interactions

description: 1. Woody encroachment in southern African savanna has been partly
 attributed to rising atmospheric CO2 fertilising the growth of C3 trees
 but less so that of competing C4 grasses. However, growth conditions
 (resource availability, competition, rooting space, and herbivory) must be
 suitable for the effects of elevated CO2 (eCO2) to be realised. 2. This
 research investigated the interactions between the positive effect of eCO2
 on tree seedling growth and limitations imposed by drought, disturbance,
 and competition with C4 grasses. Seedlings of the prolific encroacher C3
 tree Vachellia karroo were grown at ambient (400 ppm) or eCO2 (800 ppm) in
 Open-Top Chambers and exposed to a variety of stresses and disturbances
 typical of savanna systems. Photosynthetic, growth and allocation
 responses to eCO2 and other treatments were determined. 3. Unsurprisingly,
 we show strong growth and water-saving responses of V. karroo seedlings to
 eCO2 when in the absence of competition and herbivory. However, the
 addition of either competition or simulated herbivory in the first season
 of growth moderated this, while neither drought nor shading diminished the
 eCO2 effect relative to similarly treated plants grown at ambient [CO2].
 4. Synthesis. We demonstrate that eCO2-induced C3 stimulation in
 encroaching savanna species such as V. karroo will be inconsistent across
 time and space. This research does not detract from the suggestion that
 increasing atmospheric CO2 is implicated in woody encroachment, but rather
 that eCO2 benefits to C3 tree seedlings are only realised when growth
 conditions are suitable. Inconsistencies in eCO2 response will translate
 into spatial and temporal variation in seedling responses to eCO2 and
 CO2-driven woody encroachment, explaining some of the variability observed
 in woody encroachment across geographic regions and disturbance gradients.
description: Data for all experiments are combined into one dataset. This
 means that it will appear that there are missing values but this is just
 because of joining different datasets, so look for data of the interaction
 desired. Please feel free to contact me if you would like data that was
 not included in this manuscipt but is likely to have been
 collected.
DOI: 10.5061/dryad.08kprr54d
title: CamoEvo: an open access toolbox for artificial camouflage evolution experiments

description: Camouflage research has long shaped our understanding of evolution by
 natural selection, and elucidating the mechanisms by which camouflage
 operates remains a key question in visual ecology. However, the vast
 diversity of colour patterns found in animals and their backgrounds,
 combined with the scope for complex interactions with receiver vision
 presents a fundamental challenge for investigating optimal camouflage
 strategies. Genetic algorithms have provided a potential method for
 accounting for these interactions, but with limited accessibility. Here,
 we present CamoEvo, an open-access toolbox for investigating camouflage
 pattern optimisation by using tailored genetic algorithms, animal and egg
 maculation theory and artificial predation experiments. This system allows
 for camouflage evolution within the span of just 10-30 generations (~1-2
 min per generation), producing patterns that are both significantly harder
 to detect and that are optimised to their background. CamoEvo was built in
 ImageJ to allow for integration with an array of existing open access
 camouflage analysis tools. We provide guides for editing and adjusting the
 predation experiment and genetic algorithm as well as an example
 experiment. The speed and flexibility of this toolbox makes it adaptable
 for a wide range of computer based phenotype optimisation experiments.
description: <strong>Background Treatment
 Photos.</strong> Background photos were
 photographed using an ASUS A002 smartphone calibrated with imageJ using a
 5% reflectance standard. The scrubland backgrounds were photographed in
 Fordingbridge, Hampshire, England [50.93200,-1.78300], while the leaf
 litter and spring vegetation photos were collected from Headley, Surrey,
 England [51.26549,-0.26992]. Uncalibrated copies of the photos are
 available on request (ghancockzoology@gmail.com). <strong>Prey Phenotypes and Capture Data.</strong> All prey patterns were generated by the CamoEvo toolbox under selection from 9 volunteers (age 20-30) recruited at the University of Exeter. Each volunteer was randomly assigned treatment and given an hour to complete the experiment on their own computer. The capture time and image measurements were then submitted back to the experimenters. The images were then remeasured to provide measures for GabRat A and GabRat B, in addition to measures for the whole background. Survival status and presentation order was also added manually using Excel as all the data rows are in order.
description: Running the statistical analyses simply requires the R code and
 the Population Data. If the user wishes to regenerate the stimuli used,
 they will need a copy of CamoEvo available here.
DOI: 10.5061/dryad.ngf1vhhw3
title: Data from: Scale-dependence of landscape heterogeneity effects on plant invasions

description: Invasive alien species are amongst the most concerning threats to native
 biodiversity worldwide, and the level of landscape heterogeneity is
 considered to affect spatial patterns of their occurrence and spread.
 However, as previous studies on these associations report contrasting
 results, the role of landscape heterogeneity on its susceptibility to
 invasions remains poorly understood. Landscape heterogeneity is usually
 described by two measures: configuration and composition. Both measures
 may differently affect invasive species and these impacts may be
 additionally scale-dependent. Nevertheless, their relative contribution to
 invasion patterns is poorly known. We investigated the effect of two
 landscape heterogeneity components: configuration (edge density) and
 composition (number and evenness of land-cover types) measured at
 different spatial scales (from within 0.25 km to 5 km of the studied
 localities) on the local abundance of one of the most invasive alien plant
 species in Europe, the North American goldenrods (Solidago canadensis and
 S. gigantea). Using publicly available geospatial environmental data and a
 novel method based on remote analysis of Google Street View images, we
 collected and analyzed large dataset on goldenrod occurrence along 1347
 roadside transects in agricultural landscapes of Poland. Both the
 compositional and configurational heterogeneity were positively associated
 with the local abundance of goldenrods, however the effect size of these
 relationships was dependent on spatial scale. While
 abundance-heterogeneity associations were most pronounced at the largest
 spatial scale for compositional heterogeneity, the pattern was the
 opposite for configurational heterogeneity. Landscape heterogeneity is a
 clear correlate of plant invasion potential, with occurrences of invasive
 plants generally higher in more heterogeneous landscapes. However,
 scale-dependence of this association means that researchers and
 practitioners may miss the association if only concentrating on a single
 spatial scale. While increasing heterogeneity of rural landscapes is
 widely introduced as a way to promote farmland biodiversity, we show that
 it may also support invasive plants and thus conflict with original goals
 of biodiversity-oriented strategies. Therefore, we suggest implementing
 regular management and eradication schemes in most heterogeneous
 landscapes. Finally, we demonstrate how remote analysis of plant invasions
 using existing imagery can advance our understanding of invasion biology.
DOI: 10.5061/dryad.66t1g1k3r
title: Data from: Fertiliser application modulates the impact of interannual climate fluctuations and plant-to-plant interactions on the dynamics of annual species in a Mediterranean grassland

description: Background: Climate and land-use changes, which include the application of
 various types of organic and inorganic fertilisers, have
 been reducing the species diversity of Mediterranean
 grasslands and threatening their conservation.
 Annual plants are one of the most diverse functional groups of
 species in these grasslands, despite suffering
 competitive pressure from perennial herbaceous and woody species, and they
 are essential for ecosystem functioning and stability. 
 Aims: To
 quantify how fertilisation modulates the impact of plant-to-plant interactions and climate fluctuations on the dynamics of annuals in Mediterranean grasslands. We hypothesised that the application of sewage sludge would increase competition between functional groups, reducing the abundance of annuals in the long-term, but would buffer the negative impacts of drought on the year-to-year fluctuation of the diversity of annuals. Methods: In a semi-natural species-rich Mediterranean grassland in northern Spain, we analysed the changes in the taxonomical and functional composition and diversity of annuals over 14 years in response to variations in the abundance of perennial herbaceous and woody species, climate fluctuations, and fertilisation with sewage sludge. We quantified separately the patterns of year-to-year fluctuations and long-term trends.  Results: The frequency and diversity of annuals decreased with a higher abundance of perennial herbaceous species, drought in June, and cold winters. The addition of sewage sludge decreased the abundance of annuals in the long-term, seemed to promote competition between annuals and other functional groups at an interannual scale, and mitigated the negative effects of drought and cold. Conclusions: Fertilisation influences differently the temporal response of annuals to climate fluctuations and plant-to-plant interactions.
DOI: 10.5061/dryad.6t1g1jx19
title: Data for: Termite nest evolution fostered social parasitism by termitophilous rove beetles

description: Colonies of social insects contain large amounts of resources often
 exploited by specialized social parasites. While some termite species host
 numerous parasitic arthropod species, called termitophiles, others host
 none. The reason for this large variability remains unknown. Here we
 report that the evolution of termitophily in rove beetles is linked to
 termite nesting strategies. We compared one-piece nesters, whose entire
 colony life is completed within a single wood piece, to foraging species,
 which exploit multiple physically separated food sources. Our
 epidemiological model predicts that characteristics related to foraging
 (e.g., extended colony longevity and frequent interactions with other
 colonies) increase the probability of parasitism by termitophiles. We
 tested our prediction using literature data. We found that foraging
 species are more likely to host termitophilous rove beetles than one-piece
 nesters: 99.6% of known termitophilous species were associated with
 foraging termites, while 0.4% were associated with one-piece nesters.
 Notably, the few one-piece nesting species hosting termitophiles were
 those having foraging potential and access to soil. Our phylogenetic
 analyses confirmed that termitophily primarily evolved with foraging
 termites. These results highlight that the evolution of complex termite
 societies fostered social parasitism, explaining why some species have
 more social parasites than others.
description: All data were collected through a literature survey. Please see
 the method section of the paper in detail.