cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprrcd
title: Genes involved in the constitutive production of phenolic compounds in white spruce

description: Conifer forests worldwide are becoming increasingly vulnerable to the
 effects of climate change. Although the production of phenolic compounds
 (PCs) has been shown to be modulated by biotic and abiotic stresses, the
 genetic basis underlying the variation in their constitutive production
 level remains poorly documented in conifers. We used QTL mapping and
 RNA-Seq to explore the complex polygenic network underlying the
 constitutive production of PCs in a white spruce (Picea glauca) full-sib
 family for 2 years. QTL detection was performed for nine PCs and
 differentially expressed genes (DEGs) were identified between individuals
 with high and low PC contents for five PCs exhibiting stable QTLs across
 time. A total of 17 QTLs were detected for eight metabolites, including
 one major QTL explaining up to 91.3% of the neolignan-2 variance. The
 RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid
 biosynthesis, several key transcription factors, and a subset of 137 genes
 showing opposite expression patterns in individuals with high levels of
 the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs
 co-localized with QTLs. Our findings represent a significant step toward
 resolving the genomic architecture of PC production in spruce and
 facilitate the functional characterization of genes and transcriptional
 networks responsible for differences in constitutive production of PCs in
 conifers.
description: Additional methodological details are provided in the following
 publication:   Laoué J, Depardieu C, Gérardi S, Lamothe
 M, Bomal C, Azaiez A, Gros-Louis M-C, Laroche J, Boyle B, Hammerbacher A,
 Isabel N and Bousquet J (2021) Combining QTL<br> Mapping and
 Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds
 Metabolism in the Conifer White Spruce. Front. Plant Sci. 12:675108. doi:
 10.3389/fpls.2021.675108
description: Raw data files provided herein include: 1)
 GCAT_WS-3.3.cluseq.fasta: a gene catalog developped by Rigault et
 al., 2011 which was used as a reference to map reads obtained using
 RNA-Seq in the associated publication. Further details regarding the
 development of the gene catalog are provided in the following publication:
 Rigault P., Boyle B., Lepage P., Cooke JEK, Bousquet J, MacKay JJ. (2011).
 A white spruce gene catalog for conifer genome analyses. Plant Physiology,
 157(1):14-28. doi: 10.1104/pp.111.179663. 2)
 Concentration_metabolites.xlsx: an excel file reporting concentrations
 in phenolic compounds for 164 individuals measured in 2014, and 203
 individuals measured in 2017 (expressed in mg g-1 dry weight). Phenolic
 compounds measured were: astringin, catechin, gallocatechin, isorhapontin,
 neolignan-2
 (4-[1,3-dihydroxy-2-[2-hydroxy-4-(3-hydroxypropyl)phenoxy]propyl]-
 ß-D-xylopyranoside), piceid, procyanidin B1, taxifolin and taxifolin
 glucoside.
DOI: 10.5061/dryad.stqjq2c35
title: Data from: An open spatial capture–recapture model for estimating density, movement, and population dynamics from line-transect surveys

description: The purpose of many wildlife population studies is to estimate density,
 movement, or demographic parameters. Linking these parameters to
 covariates, such as habitat features, provides additional ecological
 insight and can be used to make predictions for management purposes.
 Line-transect surveys, combined with distance sampling methods, are often
 used to estimate density at discrete points in time, whereas
 capture–recapture methods are used to estimate movement and other
 demographic parameters. Recently, open population spatial
 capture–recapture models have been developed, which simultaneously
 estimate density and demographic parameters, but have been made available
 only for data collected from a fixed array of detectors and have not
 incorporated the effects of habitat covariates. We developed a spatial
 capture–recapture model that can be applied to line-transect survey data
 by modeling detection probability in a manner analogous to distance
 sampling. We extend this model to a) estimate demographic parameters using
 an open population framework and b) model variation in density and space
 use as a function of habitat covariates. The model is illustrated using
 simulated data and aerial line-transect survey data for North Atlantic
 right whales in the southeastern United States, which also demonstrates
 the ability to integrate data from multiple survey platforms and
 accommodate differences between strata or demographic groups. When
 individuals detected from line-transect surveys can be uniquely
 identified, our model can be used to simultaneously make inference on
 factors that influence spatial and temporal variation in density,
 movement, and population dynamics.
description: <strong>NARW_2010_OpenSCR_data.Rdata<strong>:
 </strong></strong>Right whale aerial survey,
 photo-identification, and habitat data.
 <strong>Metadata_Gowan_etal_2021_OpenSCR.pdf:
 </strong>Data description for
 ‘NARW_2010_OpenSCR_data.RData’.
 <strong>Gowan_etal_2021_OpenSCR.r:</strong> R code to
 fit the open spatial capture–recapture model to the right
 whale data.
DOI: 10.5061/dryad.hx3ffbgdk
title: Low persistence of genetic rescue across generations in the Arctic fox (Vulpes lagopus)

description: Genetic rescue can facilitate the recovery of small and isolated
 populations suffering from inbreeding depression. Long-term effects are
 however complex and examples spanning over multiple generations under
 natural conditions are scarce. The aim of this study was to test for
 long-term effects of natural genetic rescue in a small population of
 Scandinavian Arctic foxes (Vulpes lagopus). By combining a genetically
 verified pedigree covering almost 20 years with a long-term dataset on
 individual fitness (n=837 individuals), we found no evidence for elevated
 fitness in immigrant F2 and F3 compared to native inbred foxes. Population
 inbreeding levels showed a fluctuating increasing trend and emergence of
 inbreeding within immigrant lineages shortly after immigration. Between
 0-5 and 6-9 years post immigration, the average population size decreased
 by almost 22 % and the average proportion of immigrant ancestry rose from
 14 % to 27 %. Y chromosome analysis revealed that two out of three native
 male lineages were lost from the gene pool, but all founders represented
 at the time of immigration were still contributing to the population at
 the end of the study period through female descendants. The results
 highlight the complexity of genetic rescue and suggest that beneficial
 effects can be brief. Continuous gene flow may be needed for small and
 threatened populations to recover and persist in a longer time
 perspective.
DOI: 10.5061/dryad.x0k6djhj4
title: Endosperm-based incompatibilities in hybrid monkeyflowers

description: The sexual endosperm is an angiosperm innovation central to flowering
 plant reproduction. Genomic interactions between parental alleles control
 its development and help determine seed viability. These interactions are
 characterized by genomic imprinting, where expression from certain genes
 is parent-specific. Unsuccessful imprinting has been linked to failed
 hybridization between plants of different species or ploidies. Here, we
 describe an endosperm-based barrier between Mimulus guttatus, a diploid,
 and M. luteus, an allotetraploid. Hybrid seeds suffer from underdeveloped
 endosperm, reducing viability, when M. guttatus is the seed parent, and
 from arrested endosperm and abortion when M. luteus is the seed parent.
 The two parental species differ in patterns of endosperm DNA methylation,
 expression dynamics, and their sets of imprinted genes; and transgressive
 patterns of methylation and expression emerge in their hybrids. The two
 inherited M. luteus subgenomes, which are genetically distinct but
 epigenetically similar, are expressionally dominant over the M. guttatus
 genome in the hybrid embryo and especially endosperm, where paternal
 imprints, in particular M. luteus', are perturbed. We suggest that
 diverged epigenetic landscapes between parental genomes result in
 epigenetic repatterning in hybrids that drive global shifts in expression
 patterns and can lead to endosperm-based hybridization barriers.
description: All data herein was derived from seeds produced from
 intraspecific or interspecific crosses among lines of <em>Mimulus
 guttatus</em> and <em>M. luteus</em>. All plants were
 stored and all crosses performed at the College of William and Mary in
 either growth chambers or a greenhouse under standardized growth
 conditions. Please refer to the ReadMe files in each directory
 (Cross_section_images, Expression_data, Methylation data, Morphology_data)
 and the 'Methods' section in the associated manuscript for
 further details regarding data collection and processing.
description: For details on file contents, please refer to the ReadMe files
 in each directory (Cross_section_images, Expression_data, Methylation
 data, Morphology_data). Raw sequence data is available on NCBI's
 Sequence Read Archive (SRA# = SUB9317876).
DOI: 10.5061/dryad.9zw3r22dm
title: A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects

description: The amount of genetic variation for fitness within populations tends to
 exceed that expected under mutation-selection-drift balance. Several
 mechanisms have been proposed to actively maintain polymorphism and
 account for this discrepancy, including antagonistic pleiotropy (AP),
 where allelic variants have opposing effects on different components of
 fitness. Here we identify a non-coding indel polymorphism in the fruitless
 gene of Drosophila melanogaster and measure survival and reproductive
 components of fitness in males and females of replicate lines carrying
 each respective allele. Expressing the fruitless region in a hemizygous
 state reveals a pattern of AP, with one allele generating greater
 reproductive fitness and the other conferring greater survival to
 adulthood. Different fitness effects were observed in an alternative
 genetic background, which may reflect dominance reversal and/or epistasis.
 Our findings link sequence-level variation at a single locus with complex
 effects on a range of fitness components, thus helping to explain the
 maintenance of genetic variation for fitness. Transcription factors, such
 as fruitless, may be prime candidates for targets of balancing selection
 since they interact with multiple target loci and their associated
 phenotypic effects.
DOI: 10.5061/dryad.fn2z34tt2
title: Host life-history traits influence the distribution of prophages and the genes they carry

description: Bacterial strains with a short minimal doubling time – “fast-growing”
 hosts – are more likely to contain prophages than their slow-growing
 counterparts. Pathogenic bacterial species are likewise more likely to
 carry prophages. We develop a bioinformatics pipeline to examine the
 distribution of prophages in fast- and slow-growing lysogens, and
 pathogenic and non-pathogenic lysogens, analysing both prophage length and
 gene content for each class. By fitting these results to a mathematical
 model of the evolutionary forces acting on prophages, we predict whether
 the observed differences can be attributed to different rates of lysogeny
 among the host classes, or other evolutionary pressures. We also test for
 significant differences in gene content among prophages, identifying genes
 that are preferentially lost or maintained in each class. We find that
 fast-growing hosts and pathogens have a greater fraction of full-length
 prophages, and our analysis predicts that prophages confer a greater
 benefit, on average, to hosts in these two classes. Rates of lysogeny,
 however, are predicted to be higher in fast-growing hosts but lower in
 pathogens.
DOI: 10.5061/dryad.2280gb5rk
title: Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory

description: In the context of a timberline tree species (Betula ermanii) as “virtual
 island”, we surveyed ectomycorrhizal (EcM) fungal diversity along a 430-m
 vertical gradient on the top of Changbai Mountain, China, sampling fine
 roots and neighboring soils of B. ermanii. Besides elevation, soil
 properties and plant functional traits, endophytic and saprotrophic fungal
 diversity were assessed as candidate predictors to construct integrative
 models. EcM fungal diversity decreased with increasing elevation, and
 exhibited positive diversity to diameter at breast height and negative
 diversity to distance from forest edge relationships in both roots and
 soils. Integrative models further showed that saprotrophic fungal
 diversity was the strongest predictor of EcM fungal diversity, directly
 enhancing EcM fungal diversity in roots and soils. All the metadata were
 stored here for use.
description: Soil properties and plant (root) traits were measured in Lab.
 Geographic variables and tree traits, such as tree height, canopy diameter
 and DBH, were recorded in the field. Spatial vectors (PCNM1 - PCNM
 5) were obtained by the principal coordinates of neighbor matrices (PCNM)
 method.
description: The file includes the basic metadata of the manuscript
 "Saprotrophic fungal diversity predicts ectomycorrhizal fungal
 diversity along the timberline in the framework of island biogeography
 theory". It can be analyzed with the high-throughput sequencing data
 of ITS1 in that paper. Also, please cite it.
DOI: 10.5061/dryad.w3r2280qn
title: Safety of ocrelizumab in patients with relapsing and primary progressive multiple sclerosis

description: Objective: To report safety of ocrelizumab (OCR) up to 7 years in patients
 with relapsing multiple sclerosis (RMS) and primary progressive multiple
 sclerosis (PPMS) enrolled in clinical trials or treated in real-world
 postmarketing settings. Methods: Safety analyses are based on integrated
 clinical and laboratory data for all patients who received OCR in 11
 clinical trials, including the controlled treatment and open-label
 extension (OLE) periods of the phase 2 and 3 trials, plus the phase 3b
 trials VELOCE, CHORDS, CASTING, OBOE, ENSEMBLE, CONSONANCE, and LIBERTO.
 For selected adverse events (AEs), additional postmarketing data were
 used. Incidence rates of serious infections and malignancies were
 contextualized using multiple epidemiologic sources. Results: At data
 cut-off (January 2020), 5,680 patients with multiple sclerosis (MS)
 received OCR (18,218 patient years [PY] of exposure) in clinical trials.
 Rates per 100 PY (95% CI) of AEs (248; 246–251), serious AEs (7.3;
 7.0–7.7), infusion-related reactions (25.9; 25.1–26.6), and infections
 (76.2; 74.9–77.4) were similar to those within the controlled treatment
 period of the phase 3 trials. Rates of the most common serious AEs,
 including serious infections (2.01; 1.81–2.23) and malignancies (0.46;
 0.37–0.57), were consistent with the ranges reported in epidemiologic
 data. Conclusion: Continuous administration of OCR for up to 7 years in
 clinical trials, as well as its broader use for more than 3 years in the
 real-world setting, are associated with a favorable and manageable safety
 profile, without emerging safety concerns in a heterogeneous MS
 population. Classification of Evidence: This analysis provides Class III
 evidence that long-term, continuous treatment with OCR has a consistent
 and favorable safety profile in patients with RMS and PPMS. This study is
 rated Class III because of the use of OLE data and historical controls.
description: Table e-1 - Overview of study designs Table
 e-2 - Patients with AEs leading to treatment discontinuation in the OCR
 all-exposure population<sup>a</sup> Table
 e-3 - Patients with clinically relevant abnormalities in laboratory values
 in the phase 3 studies Table e-4 - NK cell counts
 during the CTP of the phase 3 studies Table e-5
 - Details of confirmed PML cases outside the clinical trials
 setting Table e-6 - Description of serious infections
 associated with IgG levels &lt; LLN Table e-7
 - Details of breast cancer cases reported in the OCR all-exposure
 population Figure e-1 - Change in
 CD4<sup>+</sup> and CD8<sup>+</sup> T cell levels
 in OPERA and ORATORIO Figure e-2 - Change in serum
 IgA and IgM levels in OPERA and ORATORIO
DOI: 10.5061/dryad.5dv41ns5r
title: Data from: Postcrania of Borealestes (Mammaliformes: Docodonta) and the emergence of ecomorphological diversity in early mammals

description: The Middle Jurassic witnessed the early diversification of mammal groups,
 including the stem-mammalian clade, Docodonta. Recent discoveries in China
 indicate docodontans exhibited ecomorphological diversity akin to
 small-bodied mammals living &gt;100 million years later, in the
 Cenozoic. Our understanding of the emergence of this ecological diversity
 is hindered by a lack of Middle Jurassic fossil material from other parts
 of the world. The two partial postcranial skeletons of Borealestes
 described here come from the Kilmaluag Formation, Scotland. These are the
 most complete Mesozoic mammaliaform skeletons currently known from the UK,
 and among the best preserved in Europe. As an early member of Docodonta,
 Borealestes provides key anatomical information for understanding the
 clade’s evolution, and the emergence of mammaliaform ecomorphological
 diversity. Using digital reconstructions from micro-CT and synchrotron
 scans, we describe the postcranial anatomy of Borealestes and provide an
 updated phylogenetic analysis incorporating cranial and postcranial
 characters. We find Borealestes species form a sister group to a clade
 comprising Agilodocodon and Microdocodon. To complement observational
 analyses of the skeleton, we carry out principle components analyses using
 3D landmarks on a comparative dataset of 42 extant mammal taxa. Our
 results indicate Borealestes lacked specialisations for derived locomotor
 behaviour. We detect some similarity in the humerus between Borealestes
 and Ornithorhynchus. Borealestes is morphologically intermediate between
 the robust morphology of fossorial and semi-fossorial/semi-aquatic
 Haldanodon and Docofossor, and the gracile morphology for scansorial
 Agilodocodon and Microdocodon. We suggest ecological diversity in
 Docodonta may arise from an unspecialised basal bauplan, of which
 Borealestes may be representative.
DOI: 10.5061/dryad.n02v6wwwk
title: Do phylogeny and habitat influence admixture among four North American chickadee (family: Paridae) species

description: Hybridization is an important aspect of speciation, yet questions remain
 about the ecological and environmental factors that influence
 hybridization among wild populations. We used microsatellite genotyping
 data and collected land cover and environmental data for four North
 American chickadee species: black-capped Poecile atricapillus, mountain P.
 gambeli, chestnut-backed P. rufescens and boreal P. hudsonicus chickadees.
 Combining these datasets, we sought to examine whether there is evidence
 of admixture between four widely distributed North American chickadee
 species; whether admixture takes place more often between more closely
 related species pairs or between species pairs with more similar
 ecological preferences; and whether certain habitat types have higher
 rates of admixture than others. We detected admixture for five of the six
 species pairs analyzed (chestnut-backed–mountain chickadee pair showed no
 evidence of admixture), and found rates of admixture varied
 geographically, and within taxa pairs. Admixture was higher among less
 closely related species than more closely related species, although
 habitat similarity was not a significant predictor. Finally, rates of
 admixture were higher in urban parkland habitats than deciduous, mixed or
 coniferous forest habitats. Our work indicates admixture occurs frequently
 among North American parids, and habitat and environmental variation may
 play an important role in the frequency and geographic distribution of
 hybridization.
description: We collected blood samples from 1428 chickadees (representing
 four common North American species) from 19 geographic data. Individuals
 were genotyped at five microsatellite loci. We ran species pairs through
 STRUCTURE at each location to identify individuals with mixed ancestry. We
 examined the rate of admixture among species pairs and determined whether
 admixture occurs more frequently between more closely related species
 pairs (i.e. between species within the black-headed clade or brown-headed
 clade) or between species pairs with more similar ecological
 preferences? We also correlate admixture with environment and elevation
 data to identify habitat and environmental characteristics that may
 influence admixture among parids. Habitat and environmental data were
 obtained from the WorldClim dataset for the environmental analyses, and we
 used COI data to examine and characterize the phylogenetic relationship
 among the four chickadee species.
DOI: 10.15468/dl.4wfhn7
title: Occurrence Download

description: A dataset containing 260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "TaxonKey is Philautus leitensis"
 ]
}

 The dataset includes 260 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002849-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0vt4b8gzg
title: Data from: Pellaea zygophylla, a new combination for a distinctive and well-known but neglected fern

description: Pellaea ovata is a widespread species, sexual diploid in Texas
 and northeastern Mexico but an apogamous triploid in northwestern
 Mexico, south to northern Argentina, and on Hispaniola. The type
 belongs to the southern, apogamous triploid form. Although these two forms
 have been discussed repeatedly in the literature, morphological
 distinctions between them have been overlooked and they have not been
 recognized taxonomically. However, they are distinct. Pellaea ovata s.s.
 has puberulent rachides and costae; pinnae usually 2-pinnate with
 a well-defined main axis and pinnules borne singly; fertile
 pinnules ovate, cordate basally and rounded apically. The sexual
 diploid form has rachides and costae glabrous; pinnae
 pseudo-dichotomously branched and pinnules usually paired;
 fertile pinnules narrowly rounded-trapeziform, obliquely truncate to
 cordate basally and truncate apically. Riddell named the sexual
 diploid form Pteris zygophylla, from which I give it the new combination
 Pellaea zygophylla.
description: This dataset is a list of specimens and photographic observations
 consulted in preparation of the manuscript. The original specimen
 and observation data was taken from the following data
 portals: PteridoPortal
 (pteridoportal.org), IBData (ibdata.ib.unam.mx), SEINet (swbiodiversity.org), CCH2 (cch2.org), and iNaturalist (inaturalist.org). In addition to basic accession information to allow these specimens and observations to be unambiguously identified, the dataset includes latitude and longitude coordinates. These coordinates are those provided by the data portal or on the specimen label in most cases. Where coordinates were not provided, I have included coordinates based based on the written locality description for most specimens. These coordinates, and my identifications of specimens, are the only data unique to this dataset at present, the remainder being available through the data portals listed above.
description: The unique portion of the dataset, as described above, is my work
 and in the public domain. The remainder is the work of others, and subject
 to any restrictions placed on it by the people and institutions who have
 made it available through the various online data portals.