cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bq4pp7f9
title: Data from: Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus

description: How epistatic interactions between mutations determine the genetic
 architecture of fitness is of central importance in evolution. The study
 of epistasis is particularly interesting for RNA viruses because of their
 genomic compactness, lack of genetic redundancy, and apparent low
 complexity. Moreover, interactions between mutations in viral genomes
 determine traits such as resistance to antiviral drugs, virulence and host
 range. In this study we generated 53 Tobacco etch potyvirus genotypes
 carrying pairs of single-nucleotide substitutions and measured their
 separated and combined deleterious fitness effects. We found that up to
 38% of pairs had significant epistasis for fitness, including both
 positive and negative deviations from the null hypothesis of
 multiplicative effects. Interestingly, the sign of epistasis was
 correlated with viral protein–protein interactions in a model network,
 being predominantly positive between linked pairs of proteins and negative
 between unlinked ones. Furthermore, 55% of significant interactions were
 cases of reciprocal sign epistasis (RSE), indicating that adaptive
 landscapes for RNA viruses maybe highly rugged. Finally, we found that the
 magnitude of epistasis correlated negatively with the average effect of
 mutations. Overall, our results are in good agreement to those previously
 reported for other viruses and further consolidate the view that positive
 epistasis is the norm for small and compact genomes that lack genetic
 robustness.
description: Lalic and Elena Heredity
 raw dataPage 1 contains the raw
 TEV accumulation data generated by qPCR. Page 2 contains the average
 malthusian parameter estimated for each double mutant (with SEM) and the
 corresponding pair of single mutants. Page 3 contains the fitness (W)
 values for each genotype and the computation of epistasis coefficients.
 Page 4 evaluates the inequalities for sign and reciprocal sign
 epistases.
DOI: 10.5061/dryad.5jn04
title: Data from: Worldwide core collections of tea (Camellia sinensis) based on SSR markers

description: Tea (Camellia sinensis (L.) O. Kuntze) is the world’s most popular
 beverage crop. However, to date, no core collection has been selected from
 worldwide germplasm resources on the basis of genotype data. In this
 study, we analyzed 788 tea germplasm accessions using 23 simple sequence
 repeat (SSR) markers. Our population structure analysis divided the
 germplasms into a Japanese group and an exotic group. The latter could be
 divided into var. sinensis and var. assamica. The genetic diversity was
 higher in germplasms from China, Taiwan, India, and Sri Lanka than in
 those from other countries, and low in germplasms from Japan. Using the
 number of SSR alleles as a measure of genetic diversity, we developed a
 core collection consisting of 192 accessions and three subcore collections
 with 96, 48, and 24 accessions. Although the results might be affected by
 marker-selection bias, the core 192 collection adequately covered the
 range of variation of the 788 accessions in floral morphology, and the
 chemical composition of first-flush leaves. These collections will be
 powerful tools for breeding and genetic research in tea.
description: genotypeThis file contains the genotype data of 788 tea accessions used in this study.
DOI: 10.5061/dryad.b32s5
title: Data from: The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae)

description: One of the most powerful drivers of speciation in plants is
 pollinator-mediated disruptive selection, which leads to the divergence of
 floral traits adapted to the morphology and behavior of different
 pollinators. Despite the widespread importance of this speciation
 mechanism, its genetic basis has been explored in only a few groups. Here,
 we characterize the genetic basis of pollinator-mediated divergence of two
 species in genus Ipomopsis, I. guttata and I. tenuifolia, using
 quantitative trait locus (QTL) analyses of floral traits and other
 variable phenotypes. We detected 1-6 QTLs per trait, with each QTL
 generally explaining small to modest amounts of the phenotypic variance of
 a backcross hybrid population. In contrast, flowering time and anthocyanin
 abundance (a metric of colour variation) were controlled by a few QTLs of
 relatively large effect. QTLs were strongly clustered within linkage
 groups, with 26 of 37 QTLs localized to six marker-interval
 "hotspots," all of which harbored pleiotropic QTLs. In contrast
 to other studies that have examined the genetic basis of pollinator
 shifts, our results indicate that, in general, mutations of small to
 modest effect on phenotype were involved. Thus, the evolutionary
 transition between the distinct pollination modes of I. guttata and I.
 tenuifolia likely proceeded incrementally, rather than saltationally.
description: Data for QTL analysis of
 Ipomopsisgenotypes and phenotypes
 of parents and hybridsipomopsisQTLCARTfiles.xls
DOI: 10.15468/ug3644
title: Noideattella and Tolegnaro, Two New Genera of Goblin Spiders from Madagascar, with Comments on the Gamasomorphoid and Silhouettelloid Oonopids (Araneae, Oonopidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Álvarez-Padilla, Fernando, Ubick, Darrell, Griswold, Charles E. (2012): Noideattella and Tolegnaro, Two New Genera of Goblin Spiders from Madagascar, with Comments on the Gamasomorphoid and Silhouettelloid Oonopids (Araneae, Oonopidae). American Museum Novitates 2012 (3745): 1-76, DOI: 10.1206/3745.2, URL: http://www.bioone.org/doi/abs/10.1206/3745.2ABSTRACTTwo new genera of goblin spiders from Madagascar, Noideattella, new genus, and Tolegnaro, new genus, are described with 11 and two species respectively. Noideattella includes N. assumptia, new combination (transferred from Silhouettella), and 10 new species: N. amboa, N. famafa, N. fantara, N. farihy, N. gamela, N. lakana, N. mamba, N. saka, N. tany, and N. tsiba. Tolegnaro includes two new species: T. sagani and T. kepleri. A phylogenetic data matrix of 436 terminals and 341 morphological characters was extracted from the Goblin Spider Planetary Biodiversity Inventory (PBI) descriptive database. The monophyly of Noideattella and Tolegnaro was tested in a phylogenetic analysis of this matrix. In this analysis other oonopid genera recently revised were also recovered as monophyletic and with high support values. A key for all species described here is provided. Noideattella species can be differentiated by having the pars cephalica strongly elevated in lateral view, forming a posterior cone, tibia and metatarsi with spines, and abdomen completely covered by scuta. Tolegnaro species in addition present plumose seta around the pedicel area.KEY WORDS: Phylogenetics, systematics, taxonomy, Arachnida.1 Universidad Nacional Autónoma de México, Facultad de Ciencias, Departamento de Biología Comparada, Lab. Acarología, 3000 Ciudad Universitaria, Col. Copilco Universidad, Del. Coyoacan, México, DF CP 04360.2 California Academy of Sciences, Department of Entomology, 55 Music Concourse Dr., San Francisco, CA 94118.
DOI: 10.5061/dryad.f3h1342
title: Data from: Are forest‐shrubland mosaics of the Cape Floristic Region an example of alternate stable states?

description: The idea of alternate stable states (ASS) has been used to explain the
 juxtaposition of distinct vegetation types within the same climate regime.
 ASS may explain the co‐existence of relatively inflammable closed‐canopy
 Afrotemperate Forest patches (“Forest”) within fire‐prone open‐canopy
 Fynbos in the Cape Floristic Region (CFR) on sandstone‐derived soils. We
 evaluated the hypothesis that although fire and local topography and
 hydrology likely determined the paleogeographic boundaries of Forest,
 present‐day boundaries are additionally imposed by emergent edaphic
 properties and disturbance histories. We studied vegetation and edaphic
 properties of Forest‐Transition‐Fynbos vegetation at two sites within the
 CFR on sandstone‐derived soils and tracked historical change using aerial
 photography. Whereas Forest and Fynbos have changed little in extent or
 density since 1945, Transition vegetation increased into areas formerly
 occupied by Fynbos. Forest soils were ubiquitously more nutrient‐rich than
 Fynbos soils, with Transition soils being intermediate. These edaphic
 differences are not due to geological differences, but instead appear to
 have emerged as a consequence of different nutrient cycling within the
 different ecosystems. Soil nutrients are now so different that a switch
 from Fynbos to Forest is unlikely, in the short term (i.e. decades).
 Floristically and nutritionally, Transitional vegetation is more similar
 to Fynbos than Forest and may be less resilient to changes in exogenous
 drivers (e.g., fire). Our findings are consistent with the idea that
 geologically Forest and Fynbos are largely fire‐derived long‐term ASS,
 with the stability of each state reinforced by marked soil nutrient
 differences. In contrast, the intermediate Transitional vegetation that
 might switch states is unlikely to be stable.
description: Empirical data for
 Cramer et alThe data is in a
 Microsoft Excel spreadsheet with multiple worksheets. The worksheets
 detail the site geographic locations, vegetation cover change (from aerial
 photographs), soil nutrients, soil elemental composition (XRF analysis),
 particle sizes, C and N isotopes, charcoal and vegetation composition for
 each site.Blink_Okloof_Dryad_data.xlsx
DOI: 10.5061/dryad.24275c6
title: Data from: Health IT, hacking, and cybersecurity: national trends in data breaches of protected health information

description: Objective: The rapid adoption of health information technology (IT)
 coupled with growing reports of ransomware, and hacking has made
 cybersecurity a priority in health care. This study leverages federal data
 in order to better understand current cybersecurity threats in the context
 of health IT. Materials and Methods: Retrospective observational study of
 all available reported data breaches in the United States from 2013 to
 2017, downloaded from a publicly available federal regulatory database.
 Results: There were 1512 data breaches affecting 154 415 257 patient
 records from a heterogeneous distribution of covered entities
 (P &lt; .001). There were 128 electronic medical record-related
 breaches of 4 867 920 patient records, while 363 hacking incidents
 affected 130 702 378 records. Discussion and Conclusion: Despite making up
 less than 25% of all breaches, hacking was responsible for nearly 85% of
 all affected patient records. As medicine becomes increasingly
 interconnected and informatics-driven, significant improvements to
 cybersecurity must be made so our health IT infrastructure is
 simultaneously effective, safe, and secure.
description: HHS_BreachDataset_JAMIAOData downloaded from HHS OCR portal: https://ocrportal.hhs.gov/ocr/breach/breach_report.jsf
DOI: 10.5281/zenodo.15922337
title: Green Packaging_180
DOI: 10.5281/zenodo.15922338
title: Green Packaging_180
DOI: 10.5061/dryad.7cm6b
title: Data from: Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae)

description: The present study investigated the genetic diversity, population
 structure, FST outliers, and extent and pattern of linkage disequilibrium
 in five populations of Keteleeria davidiana var. formosana, which is
 listed as a critically endangered species by the Council of Agriculture,
 Taiwan. Twelve amplified fragment length polymorphism primer pairs
 generated a total of 465 markers, of which 83.74% on average were
 polymorphic across populations, with a mean Nei’s genetic diversity of
 0.233 and a low level of genetic differentiation (approximately 6%) based
 on the total dataset. Linkage disequilibrium and HICKORY analyses
 suggested recent population bottlenecks and inbreeding in K. davidiana
 var. formosana. Both STRUCTURE and BAPS observed extensive admixture of
 individual genotypes among populations based on the total dataset in
 various clustering scenarios, which probably resulted from incomplete
 lineage sorting of ancestral variation rather than a high rate of recent
 gene flow. Our results based on outlier analysis revealed generally high
 levels of genetic differentiation and suggest that divergent selection
 arising from environmental variation has been driven by differences in
 temperature, precipitation, and humidity. Identification of ecologically
 associated outliers among environmentally disparate populations further
 support divergent selection and potential local adaptation.
description: K formosana
 AFLPsurv-input-465-5The data file contains
 465 amplified fragment length polymorphism markers generated from 12
 primers pairs for samples of Keteleeria davidiana var.
 formosana.AFLPsurv-input-465-5.txt
DOI: 10.5061/dryad.gh895
title: Data from: Convergent evolution in the explosive Hawaiian Fancy Cased caterpillar radiation

description: Species occurring in unconnected, but similar habitats and under similar
 selection pressures often display strikingly comparable morphology,
 behaviour and life history. On island archipelagos where colonizations and
 extinctions are common, it is often difficult to separate whether similar
 traits are a result of in situ diversification or independent colonization
 without a phylogeny. Here, we use one of Hawaii’s most ecologically
 diverse and explosive endemic species radiations, the Hawaiian fancy case
 caterpillar genus Hyposmocoma, to test whether in situ diversification has
 resulted in convergence. Specifically, we examine whether similar species
 utilizing similar microhabitats independently developed largely congruent
 larval case phenotypes in lineages that are in comparable, but isolated
 environments. Larvae of these moths are found on all Hawaiian Islands and
 are characterized by an extraordinary array of ecomorphs and larval case
 morphology. We focus on the ‘purse cases’, a group that is largely
 specialized for living within rotting wood. Purse cases were considered a
 monophyletic group, because morphological, behavioural and ecological
 traits appeared to be shared among all members. We constructed a phylogeny
 based on nuclear and mitochondrial DNA sequences from 38 Hyposmocoma
 species, including all 14 purse-cased species and 24 of non-purse-cased
 congeners. Divergence time estimation suggests that purse-cased lineages
 evolved independently within dead wood and developed nearly identical case
 morphology twice: once on the distant Northwest Hawaiian Islands between
 15.5 and 9 Ma and once on the younger main Hawaiian Islands around 3.0 Ma.
 Multiple ecomorphs are usually found on each island, and the ancestral
 ecomorph of Hyposmocoma appears to have lived on tree bark. Unlike most
 endemic Hawaiian radiations that follow a clear stepwise progression of
 colonization, purse-cased Hyposmocoma do not follow a pattern of
 colonization from older to younger island. We postulate that the diversity
 of microhabitats and selection from parasitism/predation from endemic
 predators may have shaped case architecture in this extraordinary endemic
 radiation of Hawaiian insects.
description: Phylip sequence data
 fileConcatenated Phylip
 sequence file. Concatenated in the order: CAD, EF-1alpha,
 COI.Hypo_purse_final.phy
DOI: 10.5061/dryad.v6t5m
title: Data from: Ectoparasitism shortens the breeding season in a colonial bird

description: When blood-feeding parasites increase seasonally, their deleterious
 effects may prevent some host species, especially those living in large
 groups where parasites are numerous, from reproducing later in the summer.
 Yet the role of parasites in regulating the length of a host's
 breeding season—and thus the host's opportunity for multiple
 brooding—has not been systematically investigated. The highly colonial
 cliff swallow (Petrochelidon pyrrhonota), a temperate-latitude migratory
 songbird in the western Great Plains, USA, typically has a relatively
 short (eight to nine week) breeding season, with birds rarely nesting late
 in the summer. Colonies at which ectoparasitic swallow bugs (Oeciacus
 vicarius) were experimentally removed by fumigation were over 45 times
 more likely to have birds undertake a second round of nesting than were
 colonies exposed to parasites. Late nesting approximately doubled the
 length of the breeding season, with some birds raising two broods. Over a
 27 year period the percentage of birds engaging in late nesting each year
 increased at a colony site where parasites were removed annually. This
 trend could not be explained by changes in group size, climate or nesting
 phenology during the study. The results suggest that ectoparasitism
 shortens the cliff swallow's breeding season and probably prevents
 many individuals from multiple brooding. When this constraint is removed,
 selection may rapidly favour late nesting.
description: Late nesting presence or
 absence data fileField data collected in
 western Nebraska from 1982 through 2014, showing for each colony whether
 late nesting by cliff swallows occurred and whether the colony site was
 fumigated that year.Late nesting presence or
 absence 5.0.xls
DOI: 10.5061/dryad.cb0b8
title: Data from: Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea

description: Assessing population connectivity is necessary to construct effective
 marine protected areas. This connectivity depends, among other parameters,
 inherently on species dispersal capacities. Isolation by distance (IBD) is
 one of the main modes of differentiation in marine species, above all in
 species presenting low dispersal abilities. This study reports the genetic
 structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu
 Postaire et al., 2016a), a brooding species, from 30 sampling sites in the
 Western Indian Ocean and the Tropical Southwestern Pacific, using 15
 microsatellite loci. At the local scale, genet dispersal relied on asexual
 propagation at short distance, which was not found at larger scales.
 Considering one representative per clone, significant positive FIS values
 (from −0.327*** to 0.411***) were found within almost all sites. Gene flow
 was extremely low at all spatial scales, among sites within islands
 (&lt;10 km distance) and among islands (100 to &gt;11,000 km
 distance), with significant pairwise FST values (from 0.035*** to
 0.645***). A general pattern of IBD was found at the Indo-Pacific scale,
 but also within ecoregions in the Western Indian Ocean province.
 Clustering and network analyses identified each island as a potential
 independent population, while analysis of molecular variance indicated
 that population genetic differentiation was significant at small (within
 island) and intermediate (among islands within province) spatial scales.
 As shown by this species, a brooding life cycle might be corollary of the
 high population differentiation found in some coastal marine species,
 thwarting regular dispersal at distances more than a few kilometers and
 probably leading to high cryptic diversity, each island housing
 independent evolutionary lineages.
description: Database of unique
 Macrorhynchia phoenicea unique MLGs per populationTab delimited text. On
 each line is represented a unique MLG, with haplotypes for 15 loci used in
 all analyses of the publicationBDD_MphoA_Genotypes_DRYAD.txt
DOI: 10.5061/dryad.8496
title: Data from: Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes.

description: Rodentia is the largest order of placental mammals, with approximately
 2,050 species divided into 28 families. It is also one of the most
 controversial with respect to its monophyly, relationships between
 families, and divergence dates. Here, we have analyzed and compared the
 performance of three nuclear genes (von Willebrand Factor,
 interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic
 receptor) for a large taxonomic sampling, covering the whole rodent and
 placental diversity. The phylogenetic results significantly support rodent
 monophyly, the association of Rodentia with Lagomorpha (the Glires clade),
 and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade.
 The resolution of relationships among rodents is also greatly improved.
 The currently recognized families are divided here into seven well-defined
 clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae,
 Myodonta, and Sciuroidea) that can be grouped into three major clades:
 Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade
 (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular
 datings based on these three genes suggest that the rodent radiation took
 place at the transition between Paleocene and Eocene. The divergence
 between rodents and lagomorphs is placed just at the K-T boundary and the
 first splits among placentals in the Late Cretaceous. Our results thus
 tend to reconcile molecular and morphological-paleontological insights.
description: Huchon_MolBiolEvol_2002Nucleotide concatenation of 3 nuclear genes for 42 taxa.Huchon_MolBiolEvol_2002Maximum likelihood tree infered from the concatenation of the 3 nuclear genes.
DOI: 10.5061/dryad.4fp90
title: Data from: Phytoplankton responses to nitrogen enrichment in Pacific Northwest, USA mountain lakes

description: Limited information is available about threshold lake nitrogen
 concentrations necessary to stimulate phytoplankton species and biomass
 responses in remote nitrogen-limited mountain lakes. We conducted in situ
 enrichment bioassays in mountain lakes within Mount Rainier, North
 Cascades, and Olympic National Parks in Washington State, USA to
 characterize phytoplankton species and biomass responses to nitrogen
 enrichment, and associated dissolved inorganic nitrogen (DIN)
 concentration thresholds. Based on biomass and growth measurements,
 phytoplankton were nitrogen-limited or co-limited by nitrogen and
 phosphorus in the nine bioassay lakes. We identified 20 taxa that
 responded to nitrogen enrichment, and estimated response thresholds using
 nitrogen Monod half-saturation constants (K s) for 18 of these taxa. DIN
 thresholds in nitrogen-limited lakes were 13 μg N l−1 for any increase in
 chlorophyll a, and 25 μg N l−1, for an increase beyond typical
 inter-annual chlorophyll a variation. K s values ranged from 0.02 to 77 μg
 N l−1 across most N-responsive taxa, and diatom K s values were higher
 than those previously quantified in U.S. Rocky Mountain lakes.
 Approximately, 75% of sampled mountain lakes in the parks have summer
 dissolved inorganic nitrogen concentrations below biomass response
 thresholds. This finding suggests that phytoplankton in park mountain
 lakes are likely sensitive to future deposition-induced lake nitrogen
 enrichment.
description: experiments_phyto_12_26_15cell densities of phytoplankton taxa in initial lake water and in each experimental replicate. column definitions are provided in ReadMe.txt.park_lakes_db675 dissolved inorganic nitrogen (NO3-N and NH3-N) observations from lakes above 1,200 m sampled between 1988 and 2014 across Mount Rainier, North Cascades, and Olympic National Parks. The database was compiled by Jason Williams. Column definitions and information about data origins and compilation are provided in ReadMe.txtChlachlorophyll a concentrations in initial lake water and in experimental replicates. column definitions are provided in ReadMe.txt