cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qm130
title: Data from: Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

description: Background: The Rhynchosporium species complex consists of hemibiotrophic
 fungal pathogens specialized to different sweet grass species including
 the cereal crops barley and rye. A sexual stage has not been described,
 but several lines of evidence suggest the occurrence of sexual
 reproduction. Therefore, a comparative genomics approach was carried out
 to disclose the evolutionary relationship of the species and to identify
 genes demonstrating the potential for a sexual cycle. Furthermore, due to
 the evolutionary very young age of the five species currently known, this
 genus appears to be well-suited to address the question at the molecular
 level of how pathogenic fungi adapt to their hosts. Results: The genomes
 of the different Rhynchosporium species were sequenced, assembled and
 annotated using ab initio gene predictors trained on several fungal
 genomes as well as on Rhynchosporium expressed sequence tags. Structures
 of the rDNA regions and genome-wide single nucleotide polymorphisms
 provided a hypothesis for intra-genus evolution. Homology screening
 detected core meiotic genes along with most genes crucial for sexual
 recombination in ascomycete fungi. In addition, a large number of cell
 wall-degrading enzymes that is characteristic for hemibiotrophic and
 necrotrophic fungi infecting monocotyledonous hosts were found.
 Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding
 for polyketide synthases and non-ribosomal peptide synthetases. Several of
 these genes are missing from the genome of the closest sequenced relative,
 the poplar pathogen Marssonina brunnea, and are possibly involved in
 adaptation to the grass hosts. Most importantly, six species-specific
 genes coding for protein effectors were identified in R. commune. Their
 deletion yielded mutants that grew more vigorously in planta than the wild
 type. Conclusion: Both cryptic sexuality and secondary metabolites may
 have contributed to host adaptation. Most importantly, however, the
 growth-retarding activity of the species-specific effectors suggests that
 host adaptation of R. commune aims at extending the biotrophic stage at
 the expense of the necrotrophic stage of pathogenesis. Like other
 apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host
 leaves relatively slowly without causing symptoms, reminiscent of the
 development of endophytic fungi. Rhynchosporium may therefore become an
 object for studying the mutualism-parasitism transition.
description: Rhynchosporium
 comparative genomicsThe folder contains
 fasta files alon with mas-, meg- and mts-files (generated with the
 phylogenetic analysis software MEGA 6.06) for the phylogenies shown in
 Figs. 2, 3, 7, 8, 9, 11 and S1.
DOI: 10.5061/dryad.65451
title: Data from: Intra- and intersexual differences in parasite resistance and female fitness tolerance in a polymorphic insect

description: To understand host–parasite interactions, it is necessary to quantify
 variation and covariation in defence traits. We quantified parasite
 resistance and fitness tolerance of a polymorphic damselfly (Ischnura
 elegans), an insect with three discrete female colour morphs but with
 monomorphic males. We quantified sex and morph differences in parasite
 resistance (prevalence and intensity of water mite infections) and
 morph-specific fitness tolerance in the females in natural populations for
 over a decade. There was no evidence for higher parasite susceptibility in
 males as a cost of sexual selection, whereas differences in defence
 mechanisms between female morphs are consistent with correlational
 selection operating on combinations of parasite resistance and tolerance.
 We suggest that tolerance differences between female morphs interact with
 frequency-dependent sexual conflict, which maintains the polymorphism
 locally. Host–parasite interactions can therefore shape intra- and
 intersexual phenotypic divergence and interfere with sexual selection and
 sexual conflict.
description: Water mite parasites on
 Common Bluetail damselfliesThis file contains water
 mite counts on 26677 adult Common Bluetail damselflies (Ischnura elegans).
 Parasite data was collected during the breeding seasons of 2003 to 2016
 and from 16 field populations in southern Sweden. Due to local extinction
 two populations were not sampled in the last 2-3 years and one and three
 new populations, respectively, were added in 2011 and 2012. All
 individuals were classified by sex (0 = female, 1 = male), and adult
 females were classified as one of three heritable colour morphs. Females
 found in copula were brought into the lab for
 oviposition.Parasites.txtFecundity of female damselfliesThis file contains data on fecundity and water mite infections of 3998 females of Ischnura elegans found in copula during field surveys of 16 populations in southern Sweden. These data were collected on every breeding between 2003 and 2016 except for 2010 and 2012. Mated females were classified with respect to colour morph, inspected for water mites and individually housed in the lab until oviposition.Fecundity.txt
DOI: 10.5061/dryad.ht288
title: Data from: Does my posterior look big in this? The effect of photographic distortion on morphometric analyses

description: Most geometric morphometric studies are underpinned by sets of photographs
 of specimens. The camera lens distorts the images it takes, and the extent
 of the distortion will depend on factors such as the make and model of the
 lens and camera and user-controlled variation such as the zoom of the
 lens. Any study that uses populations of geometric data digitized from
 photographs will have shape variation introduced into the data set simply
 by the photographic process. We illustrate the nature and magnitude of
 this error using a 30-specimen data set of Recent New Zealand Mactridae
 (Mollusca: Bivalvia), using only a single camera and camera lens with four
 different photographic setups. We then illustrate the use of
 retrodeformation in Adobe Photoshop and test the magnitude of the
 variation in the data set using multivariate Procrustes analysis of
 variance. The effect of photographic method on the variance in the data
 set is significant, systematic, and predictable and, if not accounted for,
 could lead to misleading results, suggest clustering of specimens in
 ordinations that has no biological basis, or induce artificial
 oversplitting of taxa. Recommendations to minimize and quantify distortion
 include: (1) that studies avoid mixing data sets from different cameras,
 lenses, or photographic setups; (2) that studies avoid placing specimens
 or scale bars near the edges of the photographs; (3) that the same camera
 settings are maintained (as much as practical) for every image in a data
 set; (4) that care is taken when using full-frame cameras; and (5) that a
 reference grid is used to correct for or quantify distortion.
description: Collins and Gazley -
 Mactrid GPA shape and categorical data - main datasetCategorical and
 Procrustes-superimposed coordinate data for the full mactrid dataset.
 Includes eight images each of thirty specimens (four raw photographs taken
 with different camera settings plus the retrodeformed version of each)
 plus ten replicate digitisations for error checking.Collins and Gazley -
 Mactrid GPA shape and categorical data - zoom experimentCategorical and
 Procrustes-superimposed coordinate data for the subsidiary
 'zoom' experiment, used to test for systematic effects of zoom
 level on shape data.
DOI: 10.5061/dryad.sg931
title: Data from: Evolutionary implications of a new transitional blastozoan echinoderm from the mid Cambrian of Czech Republic

description: The primitive blastozoan Felbabkacystis luckae n. gen. n. sp. is described
 from the Drumian Jince Formation, Barrandian area (Czech Republic) based
 on eleven fairly well-preserved specimens. Its unique body plan
 organization is composed of a relatively long stalk-like imbricate
 structure directly connected to the aboral imbricate cup of the test and
 of an adoral vaulted tessellate test supporting the ambulacral and
 brachiolar systems. Its bipartite test, called prototheca, highlights the
 evolution of the body wall among blastozoans. Felbabkacystis n. gen. shows
 the combination of plesiomorphic (imbricate stalk-like appendage) and
 derived features (highly domed peristome, elongate epispires). The new
 genus is interpreted as a transitional form between calyx-bearing and
 theca-bearing blastozoans, and is attributed to the new Family
 Felbabkacystidae. The lithology, the associated fauna and the possession
 of a long stalk suggest that Felbabkacystis was probably a low-level
 suspension feeder in relatively deep settings.
description: Supplementary
 dataAdditional Supporting
 Information may be found in the online version of this article: S1. List
 of taxa and sources of data for the phylogenetic analysis S2. Idealized
 reconstruction of Felbabkacystis n. gen.
DOI: 10.5061/dryad.56p6q
title: Data from: Fire history in a western Fennoscandian boreal forest as influenced by human land use and climate

description: Knowing the historical variation in fire regimes is instrumental in
 managing forests today and in predicting what may happen in the future. By
 cross-dating 745 fire scars in 378 samples of remnant Scots pines, we
 delineated 254 individual forest fires during the past 700 years in a
 74-km2 section of Trillemarka-Rollagsfjell Nature Reserve in south-central
 Norway. Fire sizes, numbers, burn rates, and frequencies were compared
 with historical climate proxies, vegetation maps, and written sources. The
 results revealed patterns consistent with a predominantly climate-driven
 fire regime up to 1625, followed by periods of strong anthropogenic
 influence that increased fire frequency during 1600–1700s and diminished
 fires during 1800–1900s. This was documented by an abrupt increase in
 number of small fires from the early 1600s that markedly shortened fire
 intervals from a median of 73 to 37 yr. This shift in fire frequency
 coincided with a sudden appearance of early-season fires from 1625 and
 onward. Whereas late-season burn rate increased with summer temperature,
 no such relationship was found for early-season fires. These results were
 corroborated by written sources that describe anthropogenic forest fires
 and slash-and-burn cultivation expanding with the increasing population
 from the late 1500s and subsequently diminishing due to increasing timber
 values during 1700–1800s. Whereas human activity strongly influenced the
 fire regime at multidecadal to centennial scales, it was the interannual
 variability in climate that triggered large fire events, especially during
 the pre-1625 period. Prior to 1625, the percentage of years with fire
 tripled from 7% during cold summers (10–12°C) to 21% during warm summers
 (14–16°C). Burn rate increased even more, from 0.01% to 1.3% for the same
 temperature intervals. Ecologically, the post-1625 period is remarkable in
 such a way that human activity, first by greatly increasing fire frequency
 and subsequently almost eradicating fires, possibly influenced the fire
 regime to such an extent that it may be unprecedented for millennia.
description: Data from: Fire history
 in a western Fennoscandian boreal forest as influenced by human land use
 and climateThe forest fire history
 data were collected in a 74-km2 section of Trillemarka-Rollagsfjell Nature
 Reserve in south-central Norway. By cross-dating 745 fire scars in 378
 samples of remnant Scots pines, we delineated 254 individual forest fires
 during the past 700 years. Within the data file, a separate sheet is
 provided for each of the following datasets: 1 Samples, 2 Summer dairy
 farm locations, 3 List of forest fires, 4 Locally calibrated climate
 series, and 5 Raster map pixels.ROLSTAD-etal_Fire-History_Ecol-Monogr.xlsx
DOI: 10.5061/dryad.4g0vt
title: Data from: Linkage into care among newly diagnosed HIV-positive individuals tested through outreach and facility-based HIV testing models in Mbeya, Tanzania: a prospective mixed-method cohort study

description: Objective: Linkage to care is the bridge between HIV testing and HIV
 treatment, care and support. In Tanzania, mobile testing aims to address
 historically low testing rates. Linkage to care was reported at 14% in
 2009 and 28% in 2014. The study compares linkage to care of HIV-positive
 individuals tested at mobile/outreach versus public health facility-based
 services within the first 6 months of HIV diagnosis. Setting: Rural
 communities in four districts of Mbeya Region, Tanzania. Participants: A
 total of 1012 newly diagnosed HIV-positive adults from 16 testing
 facilities were enrolled into a two-armed cohort and followed for 6 months
 between August 2014 and July 2015. 840 (83%) participants completed the
 study. Main outcome: measures We compared the ratios and time variance in
 linkage to care using the Kaplan-Meier estimator and Log rank tests. Cox
 proportional hazards regression models to evaluate factors associated with
 time variance in linkage. Results: At the end of 6 months, 78% of all
 respondents had linked into care, with differences across testing models.
 84% (CI 81% to 87%, n=512) of individuals tested at facility-based site
 were linked to care compared to 69% (CI 65% to 74%, n=281) of individuals
 tested at mobile/outreach. The median time to linkage was 1 day (IQR:
 1–7.5) for facility-based site and 6 days (IQR: 3–11) for mobile/outreach
 sites. Participants tested at facility-based site were 78% more likely to
 link than those tested at mobile/outreach when other variables were
 controlled (AHR=1.78; 95% CI 1.52 to 2.07). HIV status disclosure to
 family/relatives was significantly associated with linkage to care
 (AHR=2.64; 95% CI 2.05 to 3.39). Conclusions: Linkage to care after
 testing HIV positive in rural Tanzania has increased markedly since 2014,
 across testing models. Individuals tested at facility-based sites linked
 in significantly higher proportion and modestly sooner than
 mobile/outreach tested individuals. Mobile/outreach testing models bring
 HIV testing services closer to people. Strategies to improve linkage from
 mobile/outreach models are needed.
description: Quantitative data on
 Linkage to HIV care in Mbeya TanzaniaData collected from
 newly diagnosed HIV individuals with regards to Linkage to HIV care with
 in the first six months of HIV testing either at the facility-based or
 mobile/outreach HIV testing site in the rural settings of Mbeya region in
 Tanzania.The interviews were administered during enrollment (round one),
 then at three months(round two) and last interview at six months( round
 three)since diagnosis.Erica Sanga-Linkage to care
 -Excel LTC DATA- submitted.xls
DOI: 10.5061/dryad.88fh0
title: Data from: Phylogeny of Selaginellaceae: there is value in morphology after all!

description: PREMISE OF THE STUDY: The cosmopolitan lycophyte family Selaginellaceae,
 dating back to the Late Devonian–Early Carboniferous, is notorious for its
 many species with a seemingly undifferentiated gross morphology. This
 morphological stasis has for a long time hampered our understanding of the
 evolutionary history of the single genus Selaginella. Here we present a
 large-scale phylogenetic analysis of Selaginella, and based on the
 resulting phylogeny, we discuss morphological evolution in the group.
 METHODS: We sampled about one-third of the approximately 750 recognized
 Selaginella species. Evolutionary relationships were inferred from both
 chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using
 a Bayesian inference approach. The morphology of the group was studied and
 important features mapped onto the phylogeny. KEY RESULTS: We present an
 overall well-supported phylogeny of Selaginella, and the phylogenetic
 positions of some previously problematic taxa (i.e., S. sinensis and
 allies) are now resolved with strong support. We show that even though the
 evolution of most morphological characters involves reversals and/or
 parallelisms, several characters are phylogenetically informative. Seven
 major clades are identified, which each can be uniquely diagnosed by a
 suite of morphological features. There is value in morphology after all!
 CONCLUSIONS: Our hypothesis of the evolutionary relationships of
 Selaginella is well founded based on DNA sequence data, as well as
 morphology, and is in line with previous findings. It will serve as a firm
 basis for further studies on Selaginella with respect to, e.g., the poorly
 known alpha taxonomy, as well as evolutionary questions such as historical
 biogeographic reconstructions.
description: Selaginella_alignmentAlignment of the combined three-region dataset (rbcL, pgiC, and SQD1). Sequences from "the sanguinolenta group" excluded. Data partitions and excluded characters are listed.Selaginella_BI_con_MrBayesThe Bayesian tree (50% majority consensus) inferred from "Selaginella_alignment.nexus" using MrBayes. Figure 2 in article.
DOI: 10.5061/dryad.sv0q9
title: Data from: Method to assess the temporal persistence of potential biometric features: application to oculomotor, gait, face and brain structure databases

description: We introduce the intraclass correlation coefficient (ICC) to the biometric
 community as an index of the temporal persistence, or stability, of a
 single biometric feature. It requires, as input, a feature on an interval
 or ratio scale, and which is reasonably normally distributed, and it can
 only be calculated if each subject is tested on 2 or more occasions. For a
 biometric system, with multiple features available for selection, the ICC
 can be used to measure the relative stability of each feature. We show,
 for 14 distinct data sets (1 synthetic, 8 eye-movement-related, 2
 gait-related, and 2 face-recognition-related, and one
 brain-structure-related), that selecting the most stable features, based
 on the ICC, resulted in the best biometric performance generally. Analyses
 based on using only the most stable features produced superior
 Rank-1-Identification Rate (Rank-1-IR) performance in 12 of 14 databases
 (p = 0.0065, one-tailed), when compared to other sets of features,
 including the set of all features. For Equal Error Rate (EER), using a
 subset of only high-ICC features also produced superior performance in 12
 of 14 databases (p = 0. 0065, one-tailed). In general, then, for our
 databases, prescreening potential biometric features, and choosing only
 highly reliable features yields better performance than choosing lower ICC
 features or than choosing all features combined. We also determined that,
 as the ICC of a group of features increases, the median of the genuine
 similarity score distribution increases and the spread of this
 distribution decreases. There was no statistically significant similar
 relationships for the impostor distributions. We believe that the ICC will
 find many uses in biometric research. In case of the eye movement-driven
 biometrics, the use of reliable features, as measured by ICC, allowed to
 us achieve the authentication performance with EER = 2.01%, which was not
 possible before.
description: DataForUploadAll initial, raw datasets for all 14 databases
DOI: 10.5061/dryad.ch7kk
title: Data from: Ocean research priorities: similarities and differences among scientists, policymakers, and fishermen in the United States

description: Understanding and solving complex ocean conservation problems requires
 cooperation not just among scientific disciplines but also across sectors.
 A recently published survey that probed research priorities of marine
 scientists, when provided to ocean stakeholders, revealed some agreement
 on priorities but also illuminated key differences. Ocean acidification,
 cumulative impacts, bycatch effects, and restoration effectiveness were in
 the top 10 priorities for scientists and stakeholder groups. Significant
 priority differences were that scientists favored research questions about
 ocean acidification and marine protected areas; policymakers prioritized
 questions about habitat restoration, bycatch, and precaution; and
 fisheries sector resource users called for the inclusion of local
 ecological knowledge in policymaking. These results quantitatively
 demonstrate how different stakeholder groups approach ocean issues and
 highlight the need to incorporate other types of knowledge in the codesign
 of solutions-oriented research, which may facilitate cross-sectoral
 collaboration.
description: respondent_informationDemographic information, detailed best-worst scaling responses, and write-in questions from survey participants.unscaled_ranksRaw scores from Hierarchical Bayesian analysis of survey respondents’ ranking of 25 ocean research questions.ocean_priorities_surveyExample of the ocean priorities survey format
DOI: 10.5061/dryad.4081h
title: Data from: Micromphale sect. Perforantia (Agaricales, Basidiomycetes); expansion and phylogenetic placement

description: DNA sequences show that the traditional genus Micromphale appears to be
 polyphyletic. Nuclear ribosomal LSU and ITS DNA sequences place
 Micromphale sect. Perforantia Singer (typus sect. M. perforans) within
 Gymnopus, comprising a clade sister to a mixture of traditional Gymnopus
 taxa including G. fusipes (typus generis) plus traditional Marasmius sect.
 Androsacei. This study enlarges sect. Perforantia and shows that sect.
 Perforantia is a clade separate from those including Micromphale sect.
 Micromphale and sect. Rhizomorphigena. A new subsection Pinophili is
 proposed to include new species G. pinophilus and G. ponderosae. Eleven
 taxa are accepted at species rank, of which nine are proposed as new,
 mostly morpho-taxa.
description: Gymnopus_LSU_Testset
 Fig85Aligned representative
 ribosomal LSU sequences, 5' end plus representative sequences of
 related taxa used to produce Figure 85.ML tree of
 Gymnopus_LSU_Testset Fig85Nexus file containing
 aligned ribosomal LSU sequences, 5' end plus Maximum Liklihood tree
 files, Figure 85Perforantia_ITSandLSU
 Fig86Aligned ribosomal ITS
 plus LSU sequences for species related to Micromphale (Gymnopus)
 perforans, Figure 86ML tree of
 perforantia_ITSandLSU Fig86Nexus file containing
 aligned ITS + LSU sequences for species related to Micromphale (Gymnopus)
 perforans and maximum likelihood tree files , Figure 86Gymnopus perforans-ITS
 Fig87Aligned Gymnopus
 perforans ribosomal ITS sequences, Figure 87ML tree of Gymnopus
 perforans-ITS Fig87Nexus file of aligned
 Gymnopus perforans ribosomal ITS sequences and Maximum likelihood tree
 files, Figure 87