cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sn02v6x15
title: Environmental filtering and convergent evolution determine the ecological specialisation of subterranean spiders

description: 1. Ecological specialisation is an important mechanism enhancing species
 coexistence within a given community. Yet, unravelling the effect of
 multiple selective evolutionary and ecological factors leading the process
 of specialisation remains a key challenge in ecology. Subterranean
 habitats provide highly replicated experimental arenas in which to
 disentangle the relative contribution of evolutionary history (convergent
 evolution vs character displacement) and ecological setting (environmental
 filtering vs competitive exclusion) in driving community assembly. 2. We
 tested alternative hypotheses about the emergence of ecological
 specialisation using the radiation of a lineage of sheet-weaver
 cave-dwelling spiders as model system. We observed that at the local
 scale, a differential specialisation to cave microhabitats generally
 parallels moderate levels of morphological similarity and close
 phylogenetic relatedness among species. Conversely, geographic distance
 contributed little in explaining microhabitat occupation, possibly
 mirroring a limited role of competitive exclusion. Yet, compared to
 non-coexisting species, co-occurring species adapted to different
 microhabitats showed lower morphological niche overlap (i.e. higher
 dissimilarity) and deeper genetic distance. 3. The framework here
 developed suggests that in the subterranean domain, habitat specialisation
 is primarily driven by environmental filtering, secondarily by convergent
 evolution, and only marginally by character displacement or competitive
 exclusion. This pattern results in the establishment of replicated
 communities across geographical space, composed by ecologically equivalent
 species. Such process of community assembly well explains the numerous
 adaptive radiations observed in subterranean habitats, an eco-evolutionary
 pattern well documented in oceanic islands or mountain summit communities.
description: Data and R script associated with this publication:
 Mammola S, Arnedo MA, Fišer C, Cardoso P, Dejanaz AJ, Isaia M.
 (2020) Environmental filtering and convergent evolution determine the
 ecological specialisation of subterranean spiders. Functional
 Ecology.   Files:
 - db_traits.csv (tab-delimited file containing morphological
 measures on the spiders) - db_coord.csv (geographic
 coordinates of the different species) - pruned_tree.phy
 (pruned phylogenetic tree used to calculate patristic distances between
 species) - altitude.tif (Altitudinal raster needed for
 calculating altitudinal range overlap) -
 Analyses_Code.R (R script to generate the analyses)
   Please refer to the main publication for
 further details.
DOI: 10.5061/dryad.59zw3r23v
title: Urinary suPAR: a non-invasive biomarker of infection and tissue inflammation for use in studies of large free-ranging mammals

description: Studies of large free-ranging mammals incorporating physiological
 measurements typically require the collection of urine or faecal samples,
 due to ethical and practical concerns over trapping or darting animals.
 However, there is a dearth of validated biomarkers of immune activation
 and inflammation that can be measured non-invasively. We here evaluate the
 utility of urinary measurements of the soluble form of the urokinase
 plasminogen activator receptor (suPAR), for use as a health marker in
 studies of wild large mammals. We investigate how urinary suPAR
 concentrations change in response to viral infection and surgical trauma
 (inflammation), comparing it to the measurement of a marker of cellular
 immune activation, urinary neopterin, in captive rhesus macaques. We then
 test the field utility of urinary suPAR, assessing the effects of soil and
 faecal contamination, sunlight, storage at different temperatures,
 freeze-thaw cycles, and lyophilization. We find that suPAR concentrations
 rise markedly in response to both infection and surgery-associated
 inflammation, unlike urinary neopterin concentrations, which only rise in
 response to the former. Our field validation demonstrates that urinary
 suPAR is reasonably robust to many of the issues associated with field
 collection, sample processing, and storage, as long as samples can be
 stored in a freezer. Urinary suPAR is thus a promising biomarker
 applicable for monitoring various aspects of health in wild primates and
 potentially also other large mammals.
DOI: 10.5066/p148a2hx
title: Passive seismic depth to bedrock data collected along the Slate River floodplain, CO, USA 2021

description: Using the horizontal-to-vertical spectral-ratio (HVSR) method, we inferred the depth to bedrock at the Slate River Floodplain, CO, USA. The point-scale passive seismic data were collected using Model TEP-3C Tromino seismometers over 20 min or less intervals with the instruments coupled directly to the floodplain ground surface at 42 non-flooded locations during June 2021. The ratio of horizontal-to-vertical Fourier spectra (HVSR), determined using Grilla software (MOHO, S.R.L.), along with the estimated sediment shear-wave velocity, was used to calculate the depth to the bedrock contact. This passive seismic dataset indicates that the deepest bedrock is 16 m below the surface, while the bedrock reaches the surface at the hillslope. This release contains the inferred bedrock depths based on likely shear wave velocities (Vs) intrinsic to the underlying sediment, ranging from 300 m/s to 400 m/s, listed in the processed_data subdirectory in the file 'SLAC_HVSR_June2021.csv.' The range of possible depth to bedrock interpretations is included for demonstration purposes only.
DOI: 10.5061/dryad.bcc2fqz7z
title: Data from: Reporting guidelines for community-based participatory research (CBPR) did not improve the reporting quality of published studies: a systematic review of studies on smoking cessation

description: Although a guideline for reporting the results of community-based
 participatory research (CBPR) was published in 2010, the impact on the
 quality of reporting a CBPR on smoking cessation is unknown. Here we
 provide the raw data of a systematic review that assessed the impact of a
 2010 community-based participatory research reporting guideline. on the
 quality of reporting a CBPR on smoking cessation. Specifically, we
 searched the MEDLINE, Embase, the Cochrane Central Register for Controlled
 Trials (CENTRAL), PsycINFO, and CINAHL databases and included articles
 published up to October 2018 (PROSPERO: CRD42019111668). We assessed
 reporting quality using a 13-item checklist.
DOI: 10.5061/dryad.h44j0zpfx
title: Cuttlefish retrieve whether they smelt or saw a previously encountered item

description: According to the Source Monitoring Framework, the origin of a memory is
 remembered through the retrieval of specific features (e.g. perceptive,
 sensitive, affective signals). In two source discrimination tasks, we
 studied the ability of cuttlefish to remember the modality in which an
 item had been presented several hours ago. In experiment 1, cuttlefish
 were able to retrieve the modality of presentation of a crab (visual vs
 olfactory) sensed before 1h and 3hrs delays. In experiment 2, cuttlefish
 were trained to retrieve the modality of presentation of fish, shrimp, and
 crabs. After training, cuttlefish performed the task with another item
 never encountered before (e.g. mussel). Cuttlefish successfully passed
 transfer tests without and with delay (3hrs). This study is the first to
 show the ability to discriminate between two sensory modalities (i.e. see
 vs smell) in an animal. Taken together, these results suggest that
 cuttlefish can retrieve perceptual features of a previous event, namely
 whether they had seen or smelled an item.
description: The first sheet corresponds to the first experiment and the
 second sheet corresponds to the second experiment. A legend is inserted
 below the test tables for each sheet to make the reading
 clearer. In each table, date, condition, success of the
 trial (Yes/No), success in total, number of trials, and number of trials
 successful out of 10 trials are marked.  Condition 1=
 no stimulation Condition 2=visual stimulation of crab
 (experiment 1), and other items (experiment 2). 
 Condition 3=olfactory stimulation of crab (experiment 1), and
 other items (experiment 2). The order of the condition
 is different than those presented in the article on purpose (because it
 made more sense to present the "no stimulation" after the
 others).  Once cuttlefish reached the learning
 criterion of 8 correct answers out of 10 consecutive trials, it was
 hilighted in blue. The tests are hilighted in red. The results of the
 tests are included in the tables above the legend.  In
 the test tables, conditions, delays, and results are marked.
 "Conditions" is either condition 2 (visual stimulation) or
 condition 3 (olfactory stimulation). Short delay corresponds to 1h, and
 long delay corresponds to 3hrs.
DOI: 10.5061/dryad.59zw3r23w
title: Exploring the role of genetic diversity and relatedness in tree seedling growth and mortality: a multi‐species study in a Bornean rain forest

description: Where conspecific seedlings occur at high densities, density dependent
 processes tend to depress their performance and survival relative to
 co‐occurring heterospecifics. We extend this observation to within‐species
 genetic diversity and relatedness. We posit that seedling growth and
 survival increase where there is higher genetic diversity, and lower
 relatedness, among seedling populations, under the expectation that
 increased genetic dissimilarity among conspecific seedlings affords
 greater resistance to pathogens. We used estimates of individual seedling
 genetic diversity (multilocus heterozygosity (sMLH)) and genetic
 relatedness among conspecific seedlings (pairwise kinship coefficients
 (LRI)), under high and low conspecific seedling density, coupled with
 censuses of seedling growth and mortality over 30 months to
 explore the role of genetic diversity and relatedness on growth and
 mortality of 1,485 seedlings of four dipterocarp species in an undisturbed
 Bornean tropical rain forest. We hypothesized that more genetically
 diverse and less related co‐occurring seedlings would display higher
 survival and growth rates. In three of our four species lower genetic
 diversity increased the probability of mortality over 30 months.
 We observed no effect of genetic diversity on relative growth rates.
 Contrary to our expectations only one species showed a negative effect of
 increased relatedness on mortality. In two of the four species studied,
 seedlings that were more genetically related to neighbouring conspecific
 seedlings in the sample plot were less likely to die, but grew more
 slowly. Synthesis: Our results confirm that genetic diversity and
 relatedness among seedlings shapes survival probabilities differentially
 across species. In contrast we found no differences in mortality and
 growth rates between plots with low and high seedling density. Our results
 suggest that a greater abundance of pollen donors could contribute to
 cohort seedling survival in some species, though not all, and the specific
 mechanisms by which genetic relatedness determines seedling demography
 remain uncertain. These results have conservation and management
 implications in view of changing patterns of gene flow in fragmented,
 exploited, and degraded tropical rain forests, which might differentially
 influence natural regeneration among species.
DOI: 10.5061/dryad.msbcc2ftz
title: Pollution control can help mitigate future climate change impacts on European grayling in the UK

description: Aim We compare the performance of habitat suitability models using climate
 data only or climate data together with water chemistry, land cover and
 predation pressure data to model the distribution of European grayling
 (Thymallus thymallus). From these models, we (1) investigate the
 relationship between habitat suitability and genetic diversity; (2)
 project the distribution of grayling under future climate change and (3)
 model the effects of habitat mitigation on future distributions.
   Location United Kingdom Methods Maxent species distribution
 modelling was implemented using a Simple model (only climate parameters)
 or a Full model (climate, water chemistry, land-use and predation pressure
 parameters).  Areas of high and low habitat suitability were
 designated. Associations between habitat suitability and genetic diversity
 for both neutral and adaptive markers were examined. Distribution under
 minimal and maximal future climate change scenarios was modelled for 2050,
 incorporating projections of future flow scenarios obtained from the
 Centre for Ecology and Hydrology. To examine potential mitigation effects
 within habitats, models were run with manipulation of orthophosphate,
 nitrite and copper concentrations. Results We mapped suitable habitat for
 grayling in the present and the future. The full model achieved
 substantially higher discriminative power than the Simple model. For low
 suitability habitat, higher levels of inbreeding were observed for
 adaptive, but not neutral loci.  Future projections predict a
 significant contraction of highly suitable areas. Under habitat
 mitigation, modelling suggests that recovery of suitable habitat of up to
 10% is possible. Main conclusions Extending the climate-only model
 improves estimates of habitat suitability. Significantly higher inbreeding
 coefficients were found at immune genes, but not neutral markers in low
 suitability habitat indicating a possible impact of environmental stress
 on evolutionary potential. The potential for habitat mitigation to
 alleviate distributional changes under future climate change is
 demonstrated and specific recommendations are made for habitat recovery on
 a regional basis.
description: Species occurence records were accessed from GBIF in 2014
 considering all records since 1990, which had environmental data for the
 rivers in the study area. Records were spatially rarefied at a scale of 30
 km<sup>2</sup> across the latitudinal range and at a scale of
 1 km<sup>2 </sup>for the final subset study area. Furhter, a
 R-script is provided used for the fine tuning of modelling
 parameters.
DOI: 10.5061/dryad.n5tb2rbrx
title: Contrasting patterns of sexually selected traits in Mediterranean and continental populations of European mouflon

description: The expression of sexually selected traits in highly dimorphic ungulates
 may be influenced by environmental quality. Variations in habitat
 conditions can impose different constraints on the allocation of energy
 resources to male life-history traits, and possibly alter the female
 preferences for specific features. Here, we compared the horn growth
 patterns in male European mouflon Ovis aries musimon living in different
 habitats (Mediterranean vs. continental) but sharing a common genetic
 origin. We hypothesized that the expression of sexually selected traits
 such as horn development should be promoted in more favourable habitat
 conditions (i.e., Mediterranean). Using linear mixed models on data
 retrieved from individuals harvested under the same hunting regime, we
 found longer horns and greater individual variance in horn segment length
 in the Mediterranean population than in the continental one. Furthermore,
 Mediterranean rams showed no evidence of compensatory horn growth, as
 opposed to the continental rams. Unexpectedly, horn base circumference was
 greater in the continental habitat than in the Mediterranean one. The
 overall results suggest different patterns of investment in horns in the
 two populations, with seemingly stronger pressure and consequences of
 sexual selection on mouflon rams living in more favourable environments.
 Although the role of hunters’ selectivity cannot be excluded a priori, our
 data suggest that the differences in the expression of sexually selected
 traits in our study populations may be influenced by environmental
 conditions. Because sexual selection can impose substantial fitness costs
 on individuals, further investigations on the trade-offs between
 reproduction and survival would improve our understanding of the dynamics
 of mouflon populations living in different environmental conditions.
DOI: 10.5061/dryad.tmpg4f4vc
title: Modifications of the rainforest frugivore community are associated with reduced seed removal at the community level

description: Tropical rainforests worldwide are under increasing pressure from human
 activities, which are altering key ecosystem processes such as
 plant-animal interactions. However, while the direct impact of
 anthropogenic disturbance on animal communities has been well studied, the
 consequences of such defaunation for mutualistic interactions such as seed
 dispersal remains chiefly understood at the plant species level. We asked
 whether communities of endozoochorous tree species had altered seed
 removal in forests affected by hunting and logging and if this could be
 related to modifications of the frugivore community. At two contrasting
 forest sites in French Guiana, Nouragues (protected) and Montagne de Kaw
 (hunted and partly logged), we focused on four families of
 animal-dispersed trees (Sapotaceae, Myristicaceae, Burseraceae and
 Fabaceae) which represent 88 % of all endozoochorous trees which were
 fruiting at the time and location of the study.  We assessed the
 abundance of the seed dispersers and predators of these four focal
 families by conducting diurnal distance sampling along line transects.
 Densities of several key seed dispersers such as large-bodied primates
 were greatly reduced at Montagne de Kaw, where the specialist frugivore
 Ateles paniscus is probably extinct. In parallel, we estimated seed
 removal rates from fruit and seed counts conducted in one-square-meter
 quadrats placed on the ground beneath fruiting trees. Seed removal rates
 dropped from 77 % at Nouragues to 47 % at Montagne de Kaw, confirming that
 the loss of frugivores associated with human disturbance impacts seed
 removal at the community level. In contrast to Sapotaceae, whose seeds are
 dispersed by mammals only, weaker declines in seed removal for Burseraceae
 and Myristicaceae suggest that some compensation may occur for these bird-
 and mammal-dispersed families, possibly because of the high abundance of
 toucans at the disturbed site. The defaunation process currently occurring
 across many tropical forests could dramatically reduce the diversity of
 entire communities of animal-dispersed trees through seed removal
 limitation.
description: See Methods in Ecological Applications article of the same title
 (Boissier et al. 2020)
description: Three datasets are included: line transect surveys of frugivorous
 and granivorous mammals and birds; fruit consumption of Sapotaceae; seed
 removal of all focal families.
DOI: 10.15468/dl.jubng4
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lissocampus filum",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002144-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d51c59zz7
title: Heaps' law and Heaps functions in tagged texts: Evidences of their linguistic relevance

description: We study the relationship between vocabulary size and text length in a
 corpus of 75 literary works in English, authored by six writers,
 distinguishing between the contributions of three grammatical classes (or
 ``tags,'' namely, nouns, verbs, and others), and analyze the
 progressive appearance of new words of each tag along each individual
 text. We find that, as prescribed by Heaps' law, vocabulary sizes and
 text lengths follow a well-defined power-law relation. Meanwhile, the
 appearance of new words in each text does not obey a power law, and is on
 the whole well described by the average of random shufflings of the text.
 Deviations from this average, however, are statistically significant and
 show systematic trends across the corpus. Specifically, we find that the
 appearance of new words along each text is predominantly retarded with
 respect to the average of random shufflings. Moreover, different tags add
 systematically distinct contributions to this tendency, with verbs and
 others being respectively more and less retarded than the mean trend, and
 nouns following instead the overall mean. These statistical
 systematicities are likely to point to the existence of linguistically
 relevant information stored in the different variants of Heaps' law,
 a feature that is still in need of extensive assessment.
description: The original versions of the corpus files were obtained from the
 public domain (www.gutenberg.org, www.fadedpage.com) and processed to
 eliminate spurious text, not belonging to the original works.
 Computational codes were produced by the authors.
description: This file collection is a complete version of the analyzed
 corpus, and of the codes used to perform the analysis.
 This dataset contains (1) plain-text files with the texts of  75
 literary works in English, used in the analysis of Heaps' law both
 accross the corpus and within each work, as explained in the manuscript
 RSOS-200008 submitted to Royal Society Open Science, and (2) six Python
 codes to perform the Heaps analysis of the texts, plus three auxiliary
 files used by the codes.