cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1p2s5
title: Data from: In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster Aiton)

description: Wildfire is a major ecological driver of plant evolution. Understanding
 the genetic basis of plant adaptation to wildfire is crucial, because
 impending climate change will involve fire regime changes worldwide. We
 studied the molecular genetic basis of serotiny, a fire-related trait, in
 Mediterranean maritime pine using association genetics. A single
 nucleotide polymorphism (SNP) set was used to identify genotype :
 phenotype associations in situ in an unstructured natural population of
 maritime pine (eastern Iberian Peninsula) under a mixed-effects model
 framework. RR-BLUP was used to build predictive models for serotiny in
 this region. Model prediction power outside the focal region was tested
 using independent range-wide serotiny data. Seventeen SNPs were
 potentially associated with serotiny, explaining approximately 29% of the
 trait phenotypic variation in the eastern Iberian Peninsula. Similar
 prediction power was found for nearby geographical regions from the same
 maternal lineage, but not for other genetic lineages. Association genetics
 for ecologically relevant traits evaluated in situ is an attractive
 approach for forest trees provided that traits are under strong genetic
 control and populations are unstructured, with large phenotypic
 variability. This will help to extend the research focus to ecological
 keystone non-model species in their natural environments, where
 polymorphisms acquired their adaptive value.
description: Ppinaster_serotiny_phenotypesSample names, sample location, UTM coordinates and proportion of serotinous cones of 199 trees phenotyped in the east of the Iberian Peninsula, Spain.Ppinaster_SNPdata_199Ind_251SNPsSample names, UTM coordinates and SNP genotypes for 251 SNPs and 199 Pinus pinaster trees sampled in the east of the Iberian Peninsula, Spain.Ppinaster_11SSRs_199IndSample name, sample location, UTM coordinates and genotypes of 11 nuclear microsatellites for 199 individuals of Pinus pinaster sampled in the east of the Iberian Peninsula.
DOI: 10.5061/dryad.9fq7q
title: Data from: A new species of Allophryne (Anura: Allophrynidae) from the Atlantic Rain Forest biome of eastern Brazil

description: A new species of the genus Allophryne is described and, in contrast to its
 congeners that occur in the Amazon Basin, is based on specimens obtained
 in Uruçuca, State of Bahia, in the Atlantic Rain Forest of eastern Brazil.
 Allophryne relicta sp. nov. is characterized by a medium body size for the
 genus (snout–vent length range 19.9–21.9 mm in males); large head (head
 width about 35% of SVL); large, red-orange eyes, with a large black
 transversal stripe on iris; dorsum covered by few tubercles and many
 scattered black dots; dorsolateral surfaces cream with dark brown,
 elongate, anastomosed spots, and venter clear gray with scattered small
 white tubercles; presence of a line of tubercles on the ventrolateral
 surface of forearm; advertisement call formed by a multi-pulsed note of
 0.509 ± 0.029 s in duration and emitted at intervals of 1.287 ± 0.500 s,
 with notes composed of 28.58 ± 1.84 pulses at a dominant frequency of 3828
 ± 82.28 Hz; call-note emission rate of 34.46 notes/min and pulse emission
 rate of 56.13 ± 1.25 s. The molecular phylogeny supports the placement of
 A. relicta sp. nov. as sister taxon of a clade formed by A. resplendens +
 A. ruthveni.
description: Caramaschi_et_al_2013_Allophryne_relictaThe compressed file contains the TNT file containing the matrix used for phylogenetic analyses and two fasta files containing the alignments, used to produce the matrix. The source data are fragments of the 12S and 16S ribosomal genes.
DOI: 10.5061/dryad.1009
title: Data from: Is morphology really at odds with molecules in estimating fern phylogeny?

description: Using a morphological dataset of 136 vegetative and reproductive
 characters, we infer the tracheophyte phylogeny with an emphasis on early
 divergences of ferns (monilophytes). The dataset comprises morphological,
 anatomical, biochemical, and some DNA structural characters for a taxon
 sample of 35 species, including representatives of all major lineages of
 vascular plants, especially ferns. Phylogenetic relationships among
 vascular plants are reconstructed using maximum parsimony and Bayesian
 inference. Both approaches yield similar relationships and provide
 evidence for three major lineages of extant vascular plants: lycophytes,
 ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade,
 which comprises the fern and seed plant lineages. The fern lineage
 consists of five clades: horsetails, whisk ferns, ophioglossoids,
 marattioids, and leptosporangiate ferns. This lineage is supported by
 characters of the spore wall and has a parsimony bootstrap value of 76%,
 although the Bayesian posterior probability is only 0.53. Each of the five
 fern clades is well supported, but the relationships among them lack
 statistical support. Our independent phylogenetic analyses of
 morphological evidence recover the same deep phylogenetic relationships
 among tracheophytes as found in previous studies utilizing DNA sequence
 data, but differ in some ways within seed plants and within ferns. We
 discuss the extensive independent evolution of the five extant fern clades
 and the evidence for the placement of whisk ferns and horsetails in our
 morphological analyses.
description: Supplementary Appendix
 1Schneideretal Suppl
 appendix1.pdf
DOI: 10.5061/dryad.dp17k
title: Data from: Melanin-based coloration of sneaker male Atlantic salmon is linked to viability and emergence timing of their offspring

description: The ‘good genes’ hypothesis of sexual selection predicts that male
 ornaments are favoured by female mate choice because male ornament reveals
 genetic quality. In species with different male reproductive tactics,
 variation in genetic quality among ‘sneaking’ males has rarely been
 investigated, as usually ‘sneakers’ are thought not to be chosen by
 females. Here we focused on the alternative reproductive tactic in
 Atlantic salmon (Salmo salar Linnaeus, 1758) to test whether the skin
 colour of sneakers may reveal the performance traits of their offspring. A
 fully factorial breeding design was realized between 20 sneakers and two
 females using in vitro fertilization. We quantified the red and dark
 colorations of males and measured the survival of their progeny under
 semi-natural conditions. In addition, the size of offspring and their
 emergence timing from the gravel nest were monitored in the laboratory. We
 found that darker males sired more viable offspring, whereas red
 coloration was negatively correlated with offspring survival.
 Nevertheless, darker and redder male pigmentations were linked to a delay
 in offspring emergence. These results demonstrate that colours can reveal
 individual genetic quality in an alternative male reproductive tactic,
 with male melanin-based coloration being linked to both beneficial and
 detrimental effects for the offspring. Our results imply that sneaker
 ornaments may potentially play a role in both intra- and intersexual
 selection.
description: Data set_Marie-Orleach
 et alMarie-Orleach.et.al_BJLS.2893.R1_DRYAD.xlsx
DOI: 10.5061/dryad.1vp70
title: Data from: Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring

description: Theoretically, the dynamics of clonal and genetic diversities of clonal
 plant populations are strongly influenced by the competition among clones
 and rate of seedling recruitment, but little empirical assessment has been
 made of such dynamics through temporal genetic surveys. We aimed to
 quantify 3 years of evolution in the clonal and genetic composition of
 Zostera marina meadows, comparing parameters describing clonal
 architecture and genetic diversity at nine microsatellite markers.
 Variations in clonal structure revealed a decrease in the evenness of
 ramet distribution among genets. This illustrates the increasing dominance
 of some clonal lineages (multilocus lineages, MLLs) in populations.
 Despite the persistence of these MLLs over time, genetic differentiation
 was much stronger in time than in space, at the local scale. Contrastingly
 with the short-term evolution of clonal architecture, the patterns of
 genetic structure and genetic diversity sensu stricto (that is,
 heterozygosity and allelic richness) were stable in time. These results
 suggest the coexistence of (i) a fine grained (at the scale of a 20 × 30 m
 quadrat) stable core of persistent genets originating from an initial
 seedling recruitment and developing spatial dominance through clonal
 elongation; and (ii) a local (at the scale of the meadow) pool of
 transient genets subjected to annual turnover. This simultaneous
 occurrence of initial and repeated recruitment strategies highlights the
 different spatial scales at which distinct evolutionary drivers and mating
 systems (clonal competition, clonal growth, propagule dispersal and so on)
 operate to shape the dynamics of populations and the evolution of
 polymorphism in space and time.
description: Multilocus genotypes of
 Zostera marina (Brittany, France)This file gives the
 multilocus genotypes of Zostera marina sampling units collected on field.
 Sampling quadrats were designed in meadows, and 30 sampling units were
 collected using random coordinates. The years are available (2009 and
 2012). 9 microsatellite markers were used for
 genotyping.dataDryad.xlsx
DOI: 10.6084/m9.figshare.31151407
title: COLOR DISCRIMINATION UNDER DIM AMBER, RED AND WHITE LIGHTING: THE TRADE-OFF BETWEEN ECOLOGICAL IMPACT AND HUMAN VISUAL PERCEPTION (Dataset)

description: Architectural lighting at night poses emerging challenges for both human well-being and ecological systems. Amber and red lighting have been proposed as mitigation strategies to reduce the environmental impacts of anthropogenic light at night (ALAN). However, the implications of these alternative lighting spectra for human visual perception and tasks performance remain largely unexplored. This study investigated the combined effects of illuminance and spectral composition on human color discrimination under mesopic lighting conditions. Forty-eight participants completed the Farnsworth-Munsell 100-hue test and named 14 color samples under three chromaticities (amber, red, and white) each presented at five illuminance levels (0.1, 1, 5, 10, and 20 lx).
DOI: 10.6084/m9.figshare.31151407.v1
title: COLOR DISCRIMINATION UNDER DIM AMBER, RED AND WHITE LIGHTING: THE TRADE-OFF BETWEEN ECOLOGICAL IMPACT AND HUMAN VISUAL PERCEPTION (Dataset)

description: Architectural lighting at night poses emerging challenges for both human well-being and ecological systems. Amber and red lighting have been proposed as mitigation strategies to reduce the environmental impacts of anthropogenic light at night (ALAN). However, the implications of these alternative lighting spectra for human visual perception and tasks performance remain largely unexplored. This study investigated the combined effects of illuminance and spectral composition on human color discrimination under mesopic lighting conditions. Forty-eight participants completed the Farnsworth-Munsell 100-hue test and named 14 color samples under three chromaticities (amber, red, and white) each presented at five illuminance levels (0.1, 1, 5, 10, and 20 lx).
DOI: 10.5061/dryad.0q08k
title: Data from: Global biogeography of scaly tree ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal

description: Aim: Scaly tree ferns, Cyatheaceae, are a well-supported group of mostly
 tree-forming ferns found throughout the tropics, the subtropics and the
 south-temperate zone. Fossil evidence shows that the lineage originated in
 the Late Jurassic period. We reconstructed large-scale historical
 biogeographical patterns of Cyatheaceae and tested the hypothesis that
 some of the observed distribution patterns are in fact compatible, in time
 and space, with a vicariance scenario related to the break-up of Gondwana.
 Location: Tropics, subtropics and south-temperate areas of the world.
 Methods: The historical biogeography of Cyatheaceae was analysed in a
 maximum likelihood framework using Lagrange. The 78 ingroup taxa are
 representative of the geographical distribution of the entire family. The
 phylogenies that served as a basis for the analyses were obtained by
 Bayesian inference analyses of mainly previously published DNA sequence
 data using MrBayes. Lineage divergence dates were estimated in a Bayesian
 Markov chain Monte Carlo framework using beast. Results: Cyatheaceae
 originated in the Late Jurassic in either South America or Australasia.
 Following a range expansion, the ancestral distribution of the
 marginate-scaled clade included both these areas, whereas Sphaeropteris is
 reconstructed as having its origin only in Australasia. Within the
 marginate-scaled clade, reconstructions of early divergences are hampered
 by the unresolved relationships among the Alsophila, Cyathea and
 Gymnosphaera lineages. Nevertheless, it is clear that the occurrence of
 the Cyathea and Sphaeropteris lineages in South America may be related to
 vicariance, whereas transoceanic dispersal needs to be inferred for the
 range shifts seen in Alsophila and Gymnosphaera. Main conclusions: The
 evolutionary history of Cyatheaceae involves both Gondwanan vicariance
 scenarios as well as long-distance dispersal events. The number of
 transoceanic dispersals reconstructed for the family is rather few when
 compared with other fern lineages. We suggest that a causal relationship
 between reproductive mode (outcrossing) and dispersal limitations is the
 most plausible explanation for the pattern observed.
description: Tables S2-S4. Output
 from Lagrange analysis.Tables include detailed
 results, including all possible reconstructions, from the three separate
 biogeographical analyses using Lagrange.Korall & Pryer Tables
 S2-S4.txtCombined
 datasetThe combined (rbcL,
 rbcL-accD IGS, rbcL-atpB IGS, trnGR, and trnLF) dataset as nexus file.
 Data partitions and excluded characters are listed.Korall and Pryer combined
 dataset
DOI: 10.5061/dryad.th1s6
title: Data from: Cascading effects of predator activity on tick-borne disease risk

description: Predators and competitors of vertebrates can in theory reduce the density
 of infected nymphs (DIN)—an often-used measure of tick-borne disease
 risk—by lowering the density of reservoir-competent hosts and/or the tick
 burden on reservoir-competent hosts. We investigated this possible
 indirect effect of predators by comparing data from 20 forest plots across
 the Netherlands that varied in predator abundance. In each plot, we
 measured the density of questing Ixodes ricinus nymphs (DON), DIN for
 three pathogens, rodent density, the tick burden on rodents and the
 activity of mammalian predators. We analysed whether rodent density and
 tick burden on rodents were correlated with predator activity, and how
 rodent density and tick burden predicted DON and DIN for the three
 pathogens. We found that larval burden on two rodent species decreased
 with activity of two predator species, while DON and DIN for all three
 pathogens increased with larval burden on rodents, as predicted. Path
 analyses supported an indirect negative correlation of activity of both
 predator species with DON and DIN. Our results suggest that predators can
 indeed lower the number of ticks feeding on reservoir-competent hosts,
 which implies that changes in predator abundance may have cascading
 effects on tick-borne disease risk.
description: Cascading effects of
 predator activity on tick-borne disease risk: DatasetAll data used in the
 analyses of the manuscript entitled: Cascading effects of predator
 activity on tick-borne disease riskDataset.xlsx
DOI: 10.15468/dl.2qzefz
title: Occurrence Download

description: A dataset containing 631974 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-126.1847 38.30758,-114.29453 38.30758,-114.29453 48.9993,-126.1847 48.9993,-126.1847 38.30758))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 631974 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000392-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.76p82
title: Data from: Baltic pipefish females need twice as many males as they get

description: Sex role reversal in 2 pipefish species, Syngnathus typhle and Nerophis
 ophidion, is potentially explained by females reproducing twice as fast as
 males. Moreover, in oceanic populations from the Swedish west coast,
 females compete for males with males preferring to mate with larger
 females. However, in a brackish Baltic population of S. typhle, males do
 not prefer larger mates, whereas choosiness remains in the local N.
 ophidion population. We explore whether this absence of male choice in
 brackish S. typhle can be explained by males and females having more
 similar potential reproductive rates here, whereas the sex difference may
 remain in the local N. ophidion population. Contrary to our expectations,
 in both species, females out-reproduced males by a factor of more than 2,
 just as in the oceanic populations. We measured this experimentally as the
 number of males a female potentially could fill with eggs within the time
 span of 1 male pregnancy, in relation to males available in nature. Thus,
 we conclude that sexual selection on females is as strong in brackish as
 in oceanic populations of both species but that targets of selection via
 male choice are shifted to traits other than body size in S. typhle.
 Hence, costs and benefits of choice are probably more important than
 potential reproductive rates to understand mate choice. We suggest that it
 may be misleading to use targets of sexual selection, such as choice for
 large body size, as an indicator of the strength of sexual selection.
description: Pipefish PRR
 dataData from Gotland 2012
 (and some from the Swedish west coast 1987 for comparison), along with the
 statistical tests performed
DOI: 10.5061/dryad.558pm
title: Data from: Association of work-related stress with mental health problems in a special police force unit

description: Objectives. Law and order enforcement tasks may expose special force
 police officers to significant psychosocial risk factors. The aim of this
 work is to investigate the relationship between job stress and the
 presence of mental health symptoms while controlling for
 socio-demographical, occupational and personality variables in special
 force police officers. Method: At different time points, 292 out of 294
 members of the 'VI Reparto Mobile', a special police force
 engaged exclusively in the enforcement of law and order, responded to our
 invitation to complete questionnaires for the assessment of personality
 traits, work-related stress (using the demand-control-support (DCS) and
 the effort-reward-imbalance (ERI) models), and mental health problems such
 as depression, anxiety and burnout. Results: Regression analyses showed
 that lower levels of support and reward and higher levels of effort and
 overcomittment were associated with higher levels of mental health
 symptoms. Psychological screening revealed 21 (7.3%) likely cases of mild
 depression (BDI ≥10). Officers who had experienced a discrepancy between
 work effort and rewards showed a marked increase in the risk of depression
 (OR 7.89 95%CI 2.32-26.82) when compared with their counterparts who did
 not perceive themselves to be in a condition of distress. Conclusions: The
 findings of this study suggest that self-reported work-related stress may
 play a role in the development of mental health problems in police
 officers. The prevalence of mental health symptoms in the cohort
 investigated here was low, but not negligible in the case of depression.
 Since special forces police officers have to perform sensitive tasks for
 which a healthy psychological functioning is needed, the results of this
 study suggest that steps should be taken to prevent distress and improve
 the mental well-being of these workers.
description: dryad2 Genoa police
 stress personality & mental healthData collected in the
 field on police officers of the VI Reparto Mobile of Genoa in 2009. File:
 SPSS 11.5dryad2.xlsx
DOI: 10.5061/dryad.cf3r1
title: Data from: Is HIV short-sighted? Insights from a multistrain nested model

description: An important component of pathogen evolution at the population level is
 evolution within hosts. Unless evolution within hosts is very slow
 compared to the duration of infection, the composition of pathogen
 genotypes within a host is likely to change during the course of an
 infection, thus altering the composition of genotypes available for
 transmission as infection progresses. We develop a nested modeling
 approach that allows us to follow the evolution of pathogens at the
 epidemiological level by explicitly considering within-host evolutionary
 dynamics of multiple competing strains and the timing of transmission. We
 use the framework to investigate the impact of short-sighted within-host
 evolution on the evolution of virulence of human immunodeficiency virus
 (HIV), and find that the topology of the within-host adaptive landscape
 determines how virulence evolves at the epidemiological level. If viral
 reproduction rates increase significantly during the course of infection,
 the viral population will evolve a high level of virulence even though
 this will reduce the transmission potential of the virus. However, if
 reproduction rates increase more modestly, as data suggest, our model
 predicts that HIV virulence will be only marginally higher than the level
 that maximizes the transmission potential of the virus.
description: Is HIV short-sighted? -
 Matlab codesHIV short-sighted - Matlab
 codes.zip