cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5vh5403
title: Data from: Evidence for allopolyploid speciation in Nymphoides (Menyanthaceae)

description: The floating-leaved aquatic plant genus Nymphoides includes diploid and
 polyploid species that are distributed worldwide. Prior studies found
 widespread incongruence between nuclear and plastid phylogenies, and this
 has prevented the construction of a unified phylogenetic hypothesis for
 the genus. In order to examine whether phylogenetic incongruence resulted
 from ancestral polyploidization events, we obtained DNA sequence data from
 two nuclear loci, phytoene desaturase (PDS) and transmembrane nine (TMN1),
 as well as the plastid trnT-trnF region. Multiple divergent copies of the
 nuclear genes were recovered from several species, and species with the
 most divergent copies were inferred to have originated through
 allopolyploidization. Our data support a scenario in which three groups of
 species descended from allopolyploidization events: a clade of North
 American species (N. aquatica and N. cordata), a clade of neotropical
 species (N. fallax, N. grayana, and N. humboldtiana), and the Australian
 species N. montana. Trees constructed using novel nuclear gene data also
 were incongruent with previously generated nuclear and plastid data,
 however we were able to combine data from four independently evolving
 regions (PDS, TMN1, nuclear internal transcribed spacer, and plastid) to
 generate a single species tree that received strong support at several
 nodes. Sources of incongruence on the species tree involved a relatively
 small subset of species. Overall, the increased data from nuclear loci has
 dramatically improved our understanding of the Nymphoides phylogeny.
description: plastid matK/trnK and
 trnT-trnF alignment This file contains
 aligned DNA sequences for Menyanthaceae species. Sequences from the
 matK/trnK region are followed by sequences from the trnT-trnF region in a
 concatenated alignment. Meny-matKtrnL-cpmatch_16-0712_DNA.nex nuclear phytoene desaturase (PDS) alignment Meny-PDS-trim_16-0601_DNA.nex nuclear transmembrane nine (TMN1) alignment Meny-TMN1-trim_17-0110_DNA.nex plastid matK/trnK and trnT-trnF phylogeny Phylogeny obtained from BEAST analysis of plastid data. Meny-matKtrnL-cpmatch_16-0712_BEAST.tre nuclear phytoene desaturase (PDS) phylogeny Phylogeny obtained from BEAST analysis of PDS data. Meny-PDS-trim_16-0601_BEAST.tre nuclear transmembrane nine (TMN1) phylogeny Phylogeny obtained from BEAST analysis of TMN1 data. Meny-TMN1-trim_17-0110_BEAST.tre Combined data species tree Phylogeny obtained using StarBEAST2 analysis of combined plastid and nuclear data to determine the species tree. Meny-alldata-species_BEAST.tre
DOI: 10.5061/dryad.3768m
title: Data from: Niche opportunities and invasion dynamics in a desert annual community

description: Although many factors influence the ability of exotics to invade
 successfully, most studies focus on only a few variables to explain
 invasion; attempts at theoretical synthesis are largely untested. The
 niche opportunities framework proposes that the demographic success of an
 invader is largely affected by the availability of resources and the
 abundance of its enemies. Here, we use a 31-year study from a desert
 ecosystem to examine the niche opportunities framework via the invasion of
 the annual plant Erodium cicutarium. While the invader remained rare for
 two decades, a decline in granivory combined with an ideal climate window
 created an opportunity for E. cicutarium to escape control and become the
 dominant annual plant in the community. We show that fluctuations in
 consumption and resources can create niche opportunities for invaders and
 highlight the need for additional long-term studies to track the influence
 of changing climate and community dynamics on invasions.
description: R script for glmm
 analysesAnnotated code necessary
 to run the GLMM analyses. Also need the three data files: rodents.csv,
 annuals.csv, precip.csv.Analysis
 code.RAbundance of annual
 plants 1978-2008See manuscript text for
 description of collection methodology.annuals.csvRodent energy requirements 1978-2008See manuscript for a description of rodent data collection methodology and equations used to convert rodent abundances into energy requirements.rodent.csvAnnual winter precipitation 1978-2008Total precipitation from October of the previous year through March of the year noted.precip.csv
DOI: 10.5061/dryad.k5p5cm1
title: Data from: Horn growth variation and hunting selection of the Alpine ibex

description: Selective hunting can affect demographic characteristics and phenotypic
 traits of the targeted species. Hunting systems often involve harvesting
 quotas based on sex, age and/or size categories to avoid selective
 pressure. However, it is difficult to assess whether such regulations
 deter hunters from targeting larger “trophy” animals with longer horns
 that may have evolutionary consequences. Here, we compile 44,088 annually
 resolved and absolutely dated measurements of Alpine ibex (Capra ibex)
 horn growth increments from 8,355 males, harvested between 1978 and 2013,
 in the eastern Swiss Canton of Grisons. We aim to determine whether male
 ibex with longer horns were preferentially targeted, causing animals with
 early rapid horn growth to have shorter lives, and whether such hunting
 selection translated into long‐term trends in horn size over the past four
 decades. Results show that medium‐ to longer‐horned adult males had a
 higher probability of being harvested than shorter‐horned individuals of
 the same age and that regulations do affect the hunters’ behaviour.
 Nevertheless, phenotypic traits such as horn length, as well as body size
 and weight, remained stable over the study period. Although selective
 trophy hunting still occurs, it did not cause a measurable evolutionary
 response in Grisons’ Alpine ibex populations; managed and surveyed since
 1978. Nevertheless, further research is needed to understand whether
 phenotypic trait development is coinfluenced by other, potentially
 compensatory factors that may possibly mask the effects of selective,
 long‐term hunting pressure.
description: HornGrowthIncrementsAnnually resolved and absolutely dated measurements of Alpine ibex (Capra ibex) horn growth increments from 8’355 males, harvested between 1978 and 2013, in the eastern Swiss Canton of Grisons.
DOI: 10.24435/materialscloud:mg-wh
title: Ion sieving in 2D membranes from first principles

description: A first-principles approach for calculating ion separation in solution through 2D membranes is proposed. Ionic energy profiles across the membrane are obtained first, where solvation effects are explicitly simulated by machine-learning molecular dynamics, electrostatic corrections are applied to remove finite-size capacitive effects, and a mean-field treatment of the electrochemical double layer charging is used. Entropic contributions are assessed analytically and through a thermodynamic integration scheme. Ionic separations are then inferred through a microkinetic model of the filtration process, accounting for steady-state charge separation effects across the membrane. The approach is applied to Li+, Na+, K+ sieving through a crown-ether functionalized graphene membrane, with a case study of the mechanisms for a highly selective and efficient extraction of lithium from aqueous solutions.
This record contains the MD trajectories used to generate the energy and free energy profiles of Fig. 4.
DOI: 10.24435/materialscloud:zx-x4
title: Ion sieving in 2D membranes from first principles

description: A first-principles approach for calculating ion separation in solution through 2D membranes is proposed. Ionic energy profiles across the membrane are obtained first, where solvation effects are explicitly simulated by machine-learning molecular dynamics, electrostatic corrections are applied to remove finite-size capacitive effects, and a mean-field treatment of the electrochemical double layer charging is used. Entropic contributions are assessed analytically and through a thermodynamic integration scheme. Ionic separations are then inferred through a microkinetic model of the filtration process, accounting for steady-state charge separation effects across the membrane. The approach is applied to Li+, Na+, K+ sieving through a crown-ether functionalized graphene membrane, with a case study of the mechanisms for a highly selective and efficient extraction of lithium from aqueous solutions.
This record contains the MD trajectories used to generate the energy and free energy profiles of Fig. 4.
DOI: 10.5061/dryad.32q80
title: Data from: Lack of genetic introgression between wild and selectively bred Sydney rock oysters Saccostrea glomerata

description: Sydney rock oysters Saccostrea glomerata are among the most important
 estuarine species on the eastern coast of Australia and also the basis of
 a major aquaculture industry. The industry now largely relies on Sydney
 rock oysters that have been selectively bred for fast growth and disease
 resistance. Selectively bred S. glomerata are currently farmed in
 estuaries that also sustain wild populations of Sydney rock oysters,
 providing the opportunity for interbreeding. This has led to concern that
 gene flow from farmed, selectively bred oysters could alter the genetic
 variability of wild oyster populations. Here, we use next-generation
 genotype-by-sequencing to test for genetic introgression between wild and
 farmed, selectively bred (B2 line) Sydney rock oysters from 2 sites in the
 Georges River, NSW. Strong genetic partitioning was identified between the
 wild and selectively bred populations. There was no evidence of gene flow
 in the form of introgression, even though selectively bred B2 oysters have
 been farmed in the Georges River since the early 1990s. Contrary to our
 expectations, we also found significantly higher levels of genetic
 diversity and heterozygosity in the selectively bred population relative
 to the wild population. The relatively low level of genetic diversity that
 we detected in wild oysters may be particularly relevant to the adaptive
 capacity of this species in the wild.
description: Final filtered SNP data
 for Saccostrea glomerataSNP data for 90 oysters
 at 1200 loci, provided in GenAlEx format (0=Missing data, 1=Reference
 allele, 2=SNP allele) in an Excel file. Population codes match those used
 in the text of the corresponding published manuscript.SNP_data_M12109.xlsx
DOI: 10.5061/dryad.833
title: Data from: Using a null model to recognize significant co-occurrence prior to identifying candidate areas of endemism

description: [No abstract entered]
description: Mast and Nyffeler
 AppendixM&N_Appendix.htm
DOI: 10.5061/dryad.t95q4kg
title: Data from: Prognostic value of serum neurofilaments in patients with clinically isolated syndromes

description: Objectives: To assess the prognostic role of serum neurofilament light
 chains (Nfls) for Clinically Defined Multiple Sclerosis (CDMS) and
 McDonald 2017 MS in patients with Clinically Isolated Syndromes (CIS).
 Methods: we retrospectively analyzed data of patients admitted at our
 neurological department between 2000 to 2015 for a first demyelinating
 event. We evaluated baseline serum Nfls in addition to CSF, MRI, and
 clinical data. Results: Amongst 222 patients who were enrolled (mean
 follow-up 100.6 months), 45 patients (20%) developed CDMS and 141 patients
 (63.5%) developed 2017 MS at two years. Serum Nfls (median 22.0, IQR
 11.6-40.4 pg/ml) were noticeably increased in patients who have suffered a
 recent relapse, with a high number of T2 and Gd enhancing lesions at
 baseline MRI. Serum Nfls were prognostic for both CDMS and McDonald 2017
 MS, with a three-fold and a two-fold respective reduction in CDMS and 2017
 MS risk in those patients with low and extremely low levels of Nfl. The
 results remained unchanged subsequent to adjustment for such established
 MS prognostic factors as oligoclonal bands’ presence, Gd-enhancing lesion,
 and a high T2 lesion load at baseline MRI. Nfls were associated with
 baseline disability but not at follow-up. Conclusions: Serum Nfls have a
 prognostic value for CIS patient conversion to MS. Nfls might play a twin
 role as biomarkers in MS as peak level measurements can act as a
 quantitative marker of serious inflammatory activity, while steady-state
 levels can be a reflection of neurodegenerative and chronic inflammatory
 processes.
description: Supplementary
 dataFigure e.1. Correlation
 between CSF NfL and corresponding serum NfL levels in the whole cohort (A)
 and according to the Presence of Gd-Enhancing Lesions (B) - Figure e.2
 Calibration plots. (A) Survival at 2 years for Clinically Definite MS; (B)
 Survival at 2 years for McDonald 2017 MS.
DOI: 10.15468/dl.v9fkw4
title: Occurrence Download

description: A dataset containing 289084 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-126.49156 39.81548,-114.7683 39.81548,-114.7683 49.40986,-126.49156 49.40986,-126.49156 39.81548))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 289084 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000497-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jg0j5
title: Data from: Developmental and evolutionary history affect survival in stressful environments

description: The world is increasingly impacted by a variety of stressors that have the
 potential to differentially influence life history stages of organisms.
 Organisms have evolved to cope with some stressors, while with others they
 have little capacity. It is thus important to understand the effects of
 both developmental and evolutionary history on survival in stressful
 environments. We present evidence of the effects of both developmental and
 evolutionary history on survival of a freshwater vertebrate, the
 rough-skinned newt (Taricha granulosa) in an osmotically stressful
 environment. We compared the survival of larvae in either NaCl or MgCl2
 that were exposed to salinity either as larvae only or as embryos as well.
 Embryonic exposure to salinity led to greater mortality of newt larvae
 than larval exposure alone, and this reduced survival probability was
 strongly linked to the carry-over effect of stunted embryonic growth in
 salts. Larval survival was also dependent on the type of salt (NaCl or
 MgCl2) the larvae were exposed to, and was lowest in MgCl2, a widely-used
 chemical deicer that, unlike NaCl, amphibian larvae do not have an
 evolutionary history of regulating at high levels. Both developmental and
 evolutionary history are critical factors in determining survival in this
 stressful environment, a pattern that may have widespread implications for
 the survival of animals increasingly impacted by substances with which
 they have little evolutionary history.
description: Raw experimental larval
 survival dataIncludes Animal and
 Female identity, Egg Treatments, Larval Treatments, Egg Survival, Time to
 hatching, Size at Hatching, Developmental Stage at Hatching, and Larval
 Survival.Dryad_Hopkinsetal2014_PLOS.xls
DOI: 10.5061/dryad.fj662
title: Data from: Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation

description: Personality traits are heritable and respond to natural selection, but are
 at the same time influenced by the ontogenetic environment. Epigenetic
 effects, such as DNA methylation, have been proposed as a key mechanism to
 control personality variation. However, to date little is known about the
 contribution of epigenetic effects to natural variation in behaviour.
 Here, we show that great tit (Parus major) lines artificially selected for
 divergent exploratory behaviour for four generations differ in their DNA
 methylation levels at the dopamine receptor D4 (DRD4) gene. This D4
 receptor is statistically associated with personality traits in both
 humans and nonhuman animals, including the great tit. Previous work in
 this songbird failed to detect functional genetic polymorphisms within
 DRD4 that could account for the gene–trait association. However, our
 observation supports the idea that DRD4 is functionally involved in
 exploratory behaviour but that its effects are mediated by DNA
 methylation. While the exact mechanism underlying the transgenerational
 consistency of DRD4 methylation remains to be elucidated, this study shows
 that epigenetic mechanisms are involved in shaping natural variation in
 personality traits. We outline how this first finding provides a basis for
 investigating the epigenetic contribution to personality traits in natural
 systems and its subsequent role for understanding the ecology and
 evolution of behavioural consistency.
description: AssayA-D_All_pyrorunsContain all the individual methylation levels per CpG position for assays A-D. Each tab ($data_$assay_$tissuetype) contains the results from one pyrosequence run and one type of tissue (blood or brain). The columns indicate: SampleID: bird sample Note: EEB score, F is Fast exploring, S is Slow exploring Pos. 1 Meth%: Methylation percentage for CpG position 1 in assayB Pos. 2 Meth%: Methylation percentage for CpG position 2 in assayB Etc. Cell colours indicate quality scores In green: highly reliable methylation scores In yellow: reliable methylation scores In pink: unreliable methylation scores (not used in downstream analyses) SampleID with *_replicate indicates that the DNA sample with this number was used in duplo on this plate for within assay analysis.Analysis_filesThe file All_pyroruns.xlxs contains all the % methylation datapoints per position, per assay, per run, per sample and tissue in one file for analysis in statistical software. The file Replicate_analysis.xlsx contains all % methylation datapoints that were run in duplo within and between assays repeatability analysis.
DOI: 10.5061/dryad.sr02fk0
title: Data from: Non-clonal coloniality: genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx

description: Hydrozoans typically develop colonies through asexual budding of polyps.
 Although colonies of Ectopleura are similar to other hydrozoans in that
 they consist of multiple polyps physically connected through continuous
 epithelia and shared gastrovascular cavity, Ectopleura larynx does not
 asexually bud polyps indeterminately. Instead, after an initial phase of
 limited budding in a young colony, E. larynx achieves its large colony
 size through the aggregation and fusion of sexually (non-clonally)
 produced polyps. The apparent chimerism within a physiologically
 integrated colony presents a potential source of conflict between distinct
 genetic lineages, which may vary in their ability to access the germline.
 In order to determine the extent to which the potential for genetic
 conflict exists, we characterized the types of genetic relationships
 between polyps within colonies, using a RAD-Seq approach. Our results
 indicate that E. larynx colonies are indeed comprised of polyps that are
 clones and sexually reproduced siblings and offspring, consistent with
 their life history. In addition, we found that colonies also contain
 polyps that are genetically unrelated, and that estimates of genome-wide
 relatedness suggests a potential for conflict within a colony. Taken
 together, our data suggests that there are distinct categories of
 relationships in colonies of E. larynx, likely achieved though a range of
 processes including budding, regeneration and fusion of progeny and
 unrelated polyps, with the possibility for a genetic conflict resolution
 mechanism. Together these processes contribute to the re-evolution of the
 ecologically important trait of coloniality in E. larynx.
description: ChangEtAl_StructureFilesStructure-formatted genotype data used for colony-level and population-level analyses, generated using the Populations module of Stacks v.1.44 with parameters as described in Table S3.ChangEtAl_Files_forRelatednessVCF-formatted and Plink-formatted files for each collecting site used for the calculation of within- and between-colony estimates at of genome-wide relatedness. Files were output from the Populations module of Stacks v.1.44, using parameters as described in Table S3.
DOI: 10.5061/dryad.1563
title: Data from: Phylogenetic signal in mitochondrial and nuclear markers in sea anemones (Cnidaria, Actiniaria)

description: The mitochondrial genome of basal animals is generally more slowly
 evolving than that of bilaterians. This difference in rate complicates the
 study of relationships among members of these lineages and the discovery
 of cryptic species or the testing of morphological species concepts within
 them. We explore the properties of mitochondrial and nuclear ribosomal
 genes in the cnidarian order Actiniaria, using both an ordinal-scale and
 familyfamilial-scale sample of taxa. Although the markers do not show
 significant incongruence, they differ in their phylogenetic
 informativeness and the kinds of relationships they resolve. Among the
 markers studied here, the fragments of 12S rDNA and 18S rDNA most
 effectively recover well-supported nodes; those of 16S rDNA and 28S rDNA
 are less effective. The general patterns we observed are similar to those
 in other hexacorallians, although Actiniaria alone show saturation of
 transitions for orderordinal-scale analyses.
description: 12S
 broad12SMay.nex16S broad16SMay.nex18S broad18Smay.nex28S broad28Smay.nexfocused12sfocused16Sfocused18focused 28focused28