cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pk0p2ngj2
title: Genome-wide analyses reveal drivers of penguin diversification

description: Penguins are the only extant family of flightless diving birds. They
 currently comprise at least 18 species, distributed from polar to tropical
 environments in the Southern Hemisphere. The history of their
 diversification and adaptation to these diverse environments remains
 controversial. We used 22 new genomes from 18 penguin species to
 reconstruct the order, timing, and location of their diversification, to
 track changes in their thermal niches through time, and to test for
 associated adaptation across the genome. Our results indicate that the
 penguin crown-group originated during the Miocene in New Zealand and
 Australia, not in Antarctica as previously thought, and thatAptenodytesis
 the sister group to all other extant penguin species. We show that lineage
 diversification in penguins was largely driven by changing climatic
 conditions and by the opening of the Drake Passage and associated
 intensification of the Antarctic Circumpolar Current (ACC). Penguin
 species have introgressed throughout much of their evolutionary history,
 following the direction of the ACC, which might have promoted dispersal
 and admixture. Changes in thermal niches were accompanied by adaptations
 in genes that govern thermoregulation and oxygen metabolism. Estimates of
 ancestral effective population sizes (Ne) confirm that penguins are
 sensitive to climate shifts, as represented by three different demographic
 trajectories in deeper time, the most common (in 11 of 18 penguin species)
 being an increasedNebetween 40 and 70 kya, followed by a precipitous
 decline during the Last Glacial Maximum. The latter effect is most likely
 a consequence of the overall decline in marine productivity following the
 last glaciation.
description: Submission of all the information related to the manuscript of
 the penguins phylogenome: - Genomic
 data: Intron, CDS, UCE, and Mitogenome alignment files for
 phylogenetic reconstruction and species tree for all data set and without
 the yellow-eyed penguin genome; and the final dated phylogeny and
 the BEAST files for UCE and Mitogenome. -
 Scripts: <b>Cleaning raw reads</b>:
 scrubReads.pl; <b>Extracting UCE
 markers:</b> extractUces.pl;  <b>Performing MSA for
 introns/cds and cleaning the
 alignment:</b> transExonCapPhyloV3.3.8.pl; <b>Filtering for
 UCE: </b>FilterByTaxNumber.py<b> </b>and<b> </b>FilterUCE.py; <b>RaxML_NG_Astral III: </b>laucher.py<b>, </b>makeDirs.py<b> </b>and process_runner.py; <b>Predicted Niche Occupancy:</b> PNO_Rscript.txt; <b>Introgression:</b> CreateDfoil_input.py; <b>Natural selection:</b> runEte3_sitemodel_contigs.sh
DOI: 10.5061/dryad.zs7h44j4w
title: Data from: Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

description: Establishing hypotheses of relationships is a critical prerequisite for
 any macroevolutionary analysis, but different approaches exist for
 achieving this goal. Amongst palaeontologists using morphological data the
 Bayesian approach is increasingly preferred over parsimony, but this shift
 also alters the way we think about samples of trees. Here we revisit
 stratigraphic congruence as a comparator between Bayesian and parsimony
 samples, but in a new visual context: treespace. Such spaces represent an
 ordination of unique topologies that can also be extended to create a
 “landscape” where altitude represents some comparative measure (here
 congruence with stratigraphy). By co-opting existing visualization tools
 and applying them to a meta-analysis of 128 cladistic data sets we show
 that there is no consistent favouring of either Bayesian or parsimony
 according to stratigraphic congruence metrics, and further that empirical
 treespace visualizations suggest a complex variety of topological
 landscapes. We conclude by arguing that treespaces should become a
 standard exploratory tool in phylogenetic analysis.
description: Meta-analytical data set comprised of a subset of a larger data
 set available at graemetlloyd.com/matr.html.
description: Please see the included README file for more details.
DOI: 10.5061/dryad.tht76hdvt
title: Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence

description: Biocomplexity is an important mechanism for population resilience in
 changing environments. However, we are just beginning to understand how to
 identify biocomplexity so that species management efforts promote
 resilience and stability. Genomic techniques are emerging as an important
 method for identifying biocomplexity. Central Valley (CV) Chinook salmon
 are an example of a species at risk of extinction if better methods for
 identifying and protecting biocomplexity are not employed. To address this
 knowledge gap, we employed restriction site associated DNA sequencing to
 conduct the first genomic study of all major populations of CV Chinook
 salmon. We found greater population structure across the Central Valley
 than previously documented. Additionally, we show evidence for
 differentiation and adaptation within migratory phenotypes despite high
 levels of gene flow. We also determined that genomic data can vastly
 improve our ability to assign individuals to their natal populations, even
 as they mix during migration, a finding that will assist management
 practices. These results demonstrate how genomic study can greatly improve
 our ability to identify and conserve biocomplexity.
description: RAD-sequencing using SbfI restriction enzyme
DOI: 10.5061/dryad.tx95x69t1
title: Risk of hemorrhagic and ischemic stroke in patients with Alzheimer disease: A synthesis of the literature

description: Objective  To assess the risk of hemorrhagic and ischemic stroke
 in patients with Alzheimer disease (AD) compared to non-AD subjects with
 similar risk profiles. Methods  A search was conducted on Embase
 and Medline for reports published up to September 26, 2018. Studies were
 included if they: 1) assessed incidence of stroke in patients diagnosed
 with AD; 2) included patients with no history of stroke; and 3)
 reported outcomes by stroke subtype. The main outcome was relative risk of
 ischemic or hemorrhagic stroke. Further, the rate of stroke occurrence per
 1000 person-years was assessed. A random effects meta-analysis was
 undertaken. The risk of bias in included studies was assessed in terms of
 selection, comparability and outcome. Results  3,605 studies were
 screened in the title and abstract phase after removing duplicates, and 88
 eligible studies were screened for full text. Eight studies met the
 inclusion criteria representing 121,719 subjects (AD=73,044;
 non-AD=48,675). Five studies were included in the relative risk analysis,
 among which four studies applied formal matching criteria of 44,544 AD and
 44,660 non-AD subjects. The included studies were based on nation-wide
 registries from Finland, Sweden, Taiwan (2), UK (2), one clinic-based
 study from the Netherlands and one US population-based cohort. Among AD
 patients, the incidence rate of hemorrhagic stroke was 3.41/1000-person
 years (95% CI 2.70, 4.32) and 2.23 (95% CI 1.72, 2.88) among
 AD-cases and non-AD controls respectively. This is in contrast to
 13.98 (95% CI 9.86, 19.81) and 12.12 (95% CI 7.55, 19.46) for ischemic
 stroke among AD-cases and non-AD controls respectively. Compared to non-AD
 subjects with similar risk profiles, AD patients had a relative risk of
 1.42 (95% CI 1.23, 1.64) for hemorrhagic stroke and 1.15 (95% CI 0.89,
 1.48) for ischemic stroke.   Conclusion 
 Compared to non-AD subjects with similar risk profiles, AD patients are
 likely at higher risk of hemorrhagic, but not ischemic
 stroke.
DOI: 10.15468/dl.5gu33j
title: Occurrence Download

description: A dataset containing 23455 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapercis colias",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 23455 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002106-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9p8cz8wc1
title: Speciation and gene flow in two sympatric small mammals from Madagascar, Microgale fotsifotsy and M. soricoides (Mammalia: Tenrecidae)

description: Madagascar’s shrew tenrecs (Mammalia: Tenrecidae: Microgale, Nesogale)
 form an excellent system for studying speciation. Most species are endemic
 to the island’s eastern moist evergreen forest, a region renowned for high
 levels of biodiversity and a high rate of in situ diversification. We set
 out to understand the speciation dynamics in a clade of recently described
 taxa: Microgale fotsifotsy and M. soricoides, which have nearly identical
 distributions in the moist evergreen forest, and M. nasoloi, which occurs
 in the western dry deciduous forest. A phylogenetic analysis using
 mitochondrial DNA data recovered two distinct clades of M. fotsifotsy: a
 south clade that is sister to M. soricoides, and a north clade that is
 sister to the dry-forest species M. nasoloi. To better understand this
 result, we analyzed cranioskeletal measurements and performed demographic
 analyses using nuclear sequence data from ultraconserved elements. Nuclear
 data found M. fotsifotsy to be monophyletic, but demonstrated that gene
 flow is absent between the north and south clades. The same analyses also
 recovered introgression between M. soricoides and the south clade of M.
 fotsifotsy, which helps to explain the disagreement between the
 mitochondrial and nuclear phylogenies. Morphometric data revealed several
 major differences between M. soricoides and M. fotsifotsy, as well as more
 subtle differences between the two clades of M. fotsifotsy. Our findings
 demonstrate that the use of multiple datasets to understand speciation
 history, and contribute to a growing body of evidence that far-northern
 Madagascar is an important region of microendemism.
DOI: 10.5061/dryad.1jwstqjqx
title: Sex identification PCR-RFLP assay tested in eight species of Sebastes rockfish

description: Files for 'Sex identification PCR-RFLP assay tested in eight species
 of Sebastes rockfish'. Files include a sampling spreadsheet for eight
 species of Sebastes rockfish, and a .fasta file of DNA
 sequences for a male and female from each species for the
 Sch.182255-210250 locus.
DOI: 10.5061/dryad.j0zpc869h
title: Data from: Converting conventional agriculture to poplar bioenergy crops: soil chemistry

description: Woody bioenergy is a viable source of alternative energy; however,
 questions remain on how purpose-grown bioenergy feedstock production
 management impact surface soil chemistry. In order to understand the soil
 processes under poplar (Populus spp.) trees and adjacent agricultural
 sites, surface (0-15 cm) soil samples were collected from four
 northwestern United States locations over a four-year period. Initial and
 final surface soil samples were analyzed for various soil chemical
 parameters, including organic matter, pH, cation exchange capacity and
 nutrient concentrations.  Fields selected to compare poplar and
 agricultural management initially differed in some key soil chemical
 parameters.  Many soil chemical parameters changed over time and
 the magnitude of change often depended on location; however, initial
 differences between management types within any one location did not
 change over time for most soil chemical variables.  Consistent
 in-location differences between management types over time show poplar did
 not alter soil chemical parameters relative to agricultural management
 during the study period. Together all observations indicate that little of
 the overall soil chemistry was impacted by introduction of poplar in the
 traditionally agricultural fields.
description: See methods in linked article.
description: Post transformation data is in "SoilChem.txt".  Data
 column information is listed in "SoilChem Info.txt".  SAS
 scripts for testing ANOVA assumptions, transformations and analysis of the
 data as presented in the linked article are in "file
 SoilChem_archive.sas".
DOI: 10.5061/dryad.pk0p2ngj3
title: Stability maintenance data

description: The relationship between diversity and stability and its maintenance
 mechanisms are important topics in current ecological research. In this
 study of Leymus chinensis grasslands in the Xilin River Basin, Inner
 Mongolia, analyzed the relationship between diversity and stability under
 the joint interactions of complex environmental factors (i.e., climate,
 topography, soil, and human activities) from the perspective of the
 community assembly, and the maintenance mechanisms of diversity and
 stability of the grassland ecosystem. We found that: (i) Functional
 diversity had the highest explanatory power for community stability, and
 the main path relationships among grazing factors, plant functional
 traits, functional diversity, and community stability revealed that niche
 differentiation and the response of species diversity to environmental
 conditions were the key mechanisms for maintaining the relationship
 between community diversity and stability in a grazing-induced degradation
 process. (ii) The differentiation of species diversity was mainly a
 consequence of environmental filtering, whereas the differentiation of
 functional group diversity was mainly caused by differences in
 community-weighted trait means. The differentiation of functional
 diversity mainly depended on the distribution pattern of plant functional
 traits, and higher functional diversity of the community was observed with
 increasing divergence in plant functional traits. (iii) The magnitude of
 community-weighted trait means was mainly determined by climatic factors,
 whereas the environmental filtering on plant functional traits was mainly
 a consequence of the effects of soil factors. An increase in the
 divergence of plant functional traits was correlated with an increase in
 grazing intensity. The convergence of plant functional traits was
 attributed to environmental filtering effects of climatic and topographic
 factors. (ⅳ) Species diversity increased with increasing grazing intensity
 and improvement in soil conditions. The diversity of functional groups
 mainly depended on climatic conditions, and the magnitude of functional
 diversity mainly depended on grazing intensity.
description: Excel spreadsheet contains these tabs: - Table
 S1. Environmental parameters for 69 communities, including four climate,
 three topographic, nine soil, and one grazing intensity
 variables - trait range - stability
 components - trait moments -
 CWM - diversity - degradation
 gradient
DOI: 10.5061/dryad.1g1jwstrf
title: The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees

description: Sexual signaling is an important reproductive barrier known to evolve
 early during the formation of new species, but the genetic mechanisms that
 facilitate the divergence of sexual signals remain elusive. Here we
 isolate a gene linked to the rapid evolution of a signaling trait in a
 pair of nascent neotropical orchid bee lineages, Euglossa dilemma and E.
 viridissima. Male orchid bees acquire chemical compounds from their
 environment to concoct species-specific perfumes to later expose during
 courtship. We found that the two lineages acquire chemically distinct
 perfumes and are reproductively isolated despite low levels of genome-wide
 differentiation. Remarkably, variation in perfume chemistry coincides with
 rapid divergence in few odorant receptor (OR) genes. Using functional
 assays, we demonstrate that the derived variant of Or41 in E. dilemma is
 specific towards its species-specific major perfume compound, whereas the
 ancestral variant in E. viridissima is broadly tuned to multiple odorants.
 Our results show that OR evolution likely played a role in the divergence
 of sexual communication in natural populations.
description: The deposited data represents raw data files used for 1) chemical
 analysis of perfume chemistry and 2) morphometric analysis of mandible
 morphology in a comparative approach of the two sibling orchid bee species
 <em>Euglossa dilemma</em> and <em>E.
 viridissima</em>.<br> <br> 1. All tar.gz files beginning
 with a "PB", "SR", or CLY" (these are unique
 specimen IDs) are gas chromatography - mass spectrometry (GCMS) data files
 of the perfume of the male indicated by the unique specimen id. These are
 raw data files including chromatograms and mass spectrums for each peak
 and can be opened with any standard GCMS analysis software. More
 information about the origin of the individuals can be found in the open
 access publication, specifically Supplementary Table 1 and Supplementary
 Data 1.<br> <br> 2. The mandible files are taken from male
 bees. Individual specimen IDs are indicated for each file.
DOI: 10.5061/dryad.d7wm37pxj
title: Decomposing demographic contributions to the effective population size with moose as a case study

description: Levels of random genetic drift are influenced by demographic factors, such
 as mating system, sex ratio and age structure. The effective population
 size (Ne) is a useful measure for quantifying genetic drift. Evaluating
 relative contributions of different demographic factors to Ne is therefore
 important to identify what makes a population vulnerable to loss of
 genetic variation. Until recently, models for estimating Ne have required
 many simplifying assumptions, making them unsuitable for this task. Here,
 using data from a small, harvested moose population, we demonstrate the
 use of a stochastic demographic framework allowing for fluctuations in
 both population size and age distribution to estimate and decompose the
 total demographic variance and hence the ratio of effective to total
 population size (Ne/N) into components originating from sex, age, survival
 and reproduction. We not only show which components contribute most to
 Ne/N currently, but also which components have the greatest potential for
 changing Ne/N. In this relatively long-lived polygynous system we show
 that Ne/N is most sensitive to the demographic variance of older males,
 and that both reproductive autocorrelations (i.e., a tendency for the same
 individuals to be successful several years in a row) and covariance
 between survival and reproduction contribute to decreasing Ne/N
 (increasing genetic drift). These conditions are common in nature and can
 be caused by common hunting strategies. Thus, the framework presented here
 has great potential to increase our understanding of the demographic
 processes that contribute to genetic drift and viability of populations,
 and to inform management decisions.
description: Since 1992, all new calves that survived the annual hunt during
 autumn have been radio/ GPS collared and measured annually during winter
 (except in 2003 and 2008). In addition, female moose have been observed
 around potential parturition dates and recorded with/without calves. Sex,
 age and tissue samples have been collected<br> from nearly all moose
 harvested on the island.<br> With the collected tissue samples,
 Haanes et al. (2013) constructed a nearly complete genetic pedigree of the
 population based on 22 microsatellite loci. This parent assignment enabled
 the number of offspring to be genetically determined for both sexes. The
 data include individual histories of 207 females and 240 males from 1984
 to 2011, where 111 females and 137 males were alive at the start of their
 first potential mating season (1.5 years old).
description: Three dataset is included, which are used in the analysis: the
 moose pedigree, male moose data, female moose data.
DOI: 10.5061/dryad.12jm63xtb
title: Data and code for: Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells

description: This dataset contains experimental data and custom R code for
 likelihood-based model-fitting associated with the manuscript
 "Stochastic bacterial population dynamics restrict the establishment
 of antibiotic resistance from single cells". In particular, we
 estimate the per-cell establishment probability (i.e. probability that a
 single cell gives rise to a large population) of a resistant strain, in
 the presence of antibiotics at concentrations below its standard minimum
 inhibitory concentration. The experiments are conducted here
 with Pseudomonas aeruginosa, while the model and methods can be
 applied more generally.
description: This dataset contains experimental
 data R code 
 associated with the manuscript: "Stochastic bacterial
 population dynamics restrict the establishment of antibiotic resistance
 from single cells". Please refer to the manuscript and its
 Supplementary Text for detailed methods.
description: Please refer to the files 
 README-seeding.txt for a description of experimental data and R
 code associated with "seeding" experiments and model fitting to
 estimate per-cell establishment probability
 README-other.txt for a description of other experimental
 data
DOI: 10.15468/dl.9dprpv
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vanilla penicillata"
 ]
}

 The dataset includes 15 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002108-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s4mw6m93h
title: Data from: Deleterious mutations show increasing negative effects with age in Drosophila melanogaster

description: Background In order for ageing to evolve in response to a declining
 strength of selection with age, a genetic architecture that allows for
 mutations with age-specific effects on organismal performance is required.
 Our understanding of how selective effects of individual mutations are
 distributed across ages is however poor. Established evolutionary theories
 assume that mutations causing ageing have negative late-life effects,
 coupled to either positive or neutral effects early in life. New theory
 now suggests evolution of ageing may also result from deleterious
 mutations with increasing negative effects with age, a possibility that
 has not yet been empirically explored. Results To directly test how the
 effects of deleterious mutations are distributed across ages, we
 separately measure age-specific effects on fecundity for each of 20
 mutations in Drosophila melanogaster. We find that deleterious mutations
 in general have a negative effect that increases with age, and that the
 rate of increase depends on how deleterious a mutation is early in life.
 Conclusions Our findings suggest that ageing does not exclusively depend
 on genetic variants assumed by the established evolutionary theories of
 ageing. Instead, ageing can result from deleterious mutations with
 negative effects that amplify with age. If increasing negative effect with
 age is a general property of deleterious mutations, the proportion of
 mutations with the capacity to contribute towards ageing may be
 considerably larger than previously believed.