cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kf415
title: Data from: A comparison of single-sample estimators of effective population sizes from genetic marker data

description: In molecular ecology and conservation genetics studies, the important
 parameter of effective population size (Ne) is increasingly estimated from
 a single sample of individuals taken at random from a population and
 genotyped at a number of marker loci. Several estimators are developed,
 based on the information of linkage disequilibrium (LD), heterozygote
 excess (HE), molecular coancestry (MC) and sibship frequency (SF) in
 marker data. The most popular is the LD estimator, because it is more
 accurate than HE and MC estimators and is simpler to calculate than SF
 estimator. However, little is known about the accuracy of LD estimator
 relative to that of SF and about the robustness of all single-sample
 estimators when some simplifying assumptions (e.g. random mating, no
 linkage, no genotyping errors) are violated. This study fills the gaps and
 uses extensive simulations to compare the biases and accuracies of the
 four estimators for different population properties (e.g. bottlenecks,
 nonrandom mating, haplodiploid), marker properties (e.g. linkage,
 polymorphisms) and sample properties (e.g. numbers of individuals and
 markers) and to compare the robustness of the four estimators when marker
 data are imperfect (with allelic dropouts). Extensive simulations show
 that SF estimator is more accurate, has a much wider application scope
 (e.g. suitable to nonrandom mating such as selfing, haplodiploid species,
 dominant markers) and is more robust (e.g. to the presence of linkage and
 genotyping errors of markers) than the other estimators. An empirical data
 set from a Yellowstone grizzly bear population was analysed to demonstrate
 the use of the SF estimator in practice.
description: Simulating and
 estimating NeThis zipped file
 contains the computer programs (source code and executables for Windows),
 parameter setting file, user's guide for simulating and analysing
 genotype data for estimating Ne.Ne.zip
DOI: 10.5061/dryad.23n6p
title: Data from: A generalizable energetics-based model of avian migration to facilitate continental-scale waterbird conservation

description: Conserving migratory birds is made especially difficult because of
 movement among spatially disparate locations across the annual cycle. In
 light of challenges presented by the scale and ecology of migratory birds,
 successful conservation requires integrating objectives, management, and
 monitoring across scales, from local management units to ecoregional and
 flyway administrative boundaries. We present an integrated approach using
 a spatially explicit energetic-based mechanistic bird migration model
 useful to conservation decision-making across disparate scales and
 locations. This model moves a Mallard-like bird (Anas platyrhynchos),
 through spring and fall migration as a function of caloric gains and
 losses across a continental-scale energy landscape. We predicted with this
 model that fall migration, where birds moved from breeding to wintering
 habitat, took a mean of 27.5 d of flight with a mean seasonal survivorship
 of 90.5% (95% CI = 89.2%, 91.9%), whereas spring migration took a mean of
 23.5 d of flight with mean seasonal survivorship of 93.6% (95% CI = 92.5%,
 94.7%). Sensitivity analyses suggested that survival during migration was
 sensitive to flight speed, flight cost, the amount of energy the animal
 could carry, and the spatial pattern of energy availability, but generally
 insensitive to total energy availability per se. Nevertheless, continental
 patterns in the bird-use days occurred principally in relation to wetland
 cover and agricultural habitat in the fall. Bird-use days were highest in
 both spring and fall in the Mississippi Alluvial Valley and along the
 coast and near-shore environments of South Carolina. Spatial sensitivity
 analyses suggested that locations nearer to migratory endpoints were less
 important to survivorship; for instance, removing energy from a 1036 km2
 stopover site at a time from the Atlantic Flyway suggested coastal areas
 between New Jersey and North Carolina, including the Chesapeake Bay and
 the North Carolina piedmont, are essential locations for efficient
 migration and increasing survivorship during spring migration but not
 locations in Ontario and Massachusetts. This sort of spatially explicit
 information may allow decision-makers to prioritize their conservation
 actions toward locations most influential to migratory success. Thus, this
 mechanistic model of avian migration provides a decision-analytic medium
 integrating the potential consequences of local actions to flyway-scale
 phenomena.
description: Lonsdorf et al.
 migration model data and codeLonsdorf et al model
 files.zip
DOI: 10.5061/dryad.b449r
title: Data from: The relationships of the Euparkeriidae and the rise of Archosauria

description: For the first time, a phylogenetic analysis including all putative
 euparkeriid taxa is conducted, using a large data matrix analysed with
 maximum parsimony and Bayesian analysis. Using parsimony, the putative
 euparkeriid Dorosuchus neoetus from Russia is the sister taxon to
 Archosauria + Phytosauria. Euparkeria capensis is placed one node further
 from the crown, and forms a euparkeriid clade with the Chinese taxa
 Halazhaisuchus qiaoensis and ‘Turfanosuchus shageduensis’ and the Polish
 taxon Osmolskina czatkowicensis. Using Bayesian methods, Osmolskina and
 Halazhaisuchus are sister taxa within Euparkeriidae, in turn sister to
 ‘Turfanosuchus shageduensis’ and then Euparkeria capensis. Dorosuchus is
 placed in a polytomy with Euparkeriidae and Archosauria + Phytosauria.
 Although conclusions remain tentative owing to low node support and
 incompleteness, a broad phylogenetic position close to the base of
 Archosauria is confirmed for all putative euparkeriids, and the ancestor
 of Archosauria +Phytosauria is optimized as similar to euparkeriids in its
 morphology. Ecomorphological characters and traits are optimized onto the
 maximum parsimony strict consensus phylogeny presented using squared
 change parsimony. This optimization indicates that the ancestral archosaur
 was probably similar in many respects to euparkeriids, being relatively
 small, terrestrial, carnivorous and showing relatively cursorial limb
 morphology; this Bauplan may have underlain the exceptional radiaton and
 success of crown Archosauria.
description: Supplementary
 InformationSupplementary results,
 discussion, references and figures.Matrix and character
 listsPhylogenetic matrix and
 lists of characters.MatrixPhylogenetic matrix as
 nexus file.
DOI: 10.5061/dryad.1h669
title: Data from: Mitochondrial rate variation among lineages of passerine birds

description: The order Passeriformes comprises the majority of extant avian species.
 Analyses of molecular data have provided important insights into the
 evolution of this diverse order. However, molecular estimates of the
 evolutionary and demographic timescales of passerine species have been
 hindered by a lack of reliable calibrations. This has led to a reliance on
 the application of standard substitution rates to mitochondrial DNA data,
 particularly rates estimated from analyses of the gene encoding cytochrome
 b (CYTB). To investigate patterns of rate variation across passerine
 lineages, we used a Bayesian phylogenetic approach to analyse the
 protein-coding genes of 183 mitochondrial genomes. We found that the most
 commonly used mitochondrial marker, CYTB, has low variation in rates
 across passerine lineages. This lends support to its widespread use as a
 molecular clock in birds. However, we also found that the patterns of
 among-lineage rate variation in CYTB are only weakly related to the
 evolutionary rate of the mitochondrial genome as a whole. Our analyses
 confirmed the presence of mutational saturation at third codon positions
 across the protein-coding genes of the mitochondrial genome, reinforcing
 the view that these sites should be excluded in studies of deep passerine
 relationships. The results of our analyses have provided information that
 will be useful for molecular-clock studies of passerine evolution.
description: PasserineClocks.MitochondrialDNANexus-formatted nucleotide alignments of 12 protein-coding genes from the mitochondrial genomes of 183 passerine species
DOI: 10.5061/dryad.7c63h
title: Data from: Bet-hedging against larval herbivory and seed bank mortality in the evolution of heterocarpy

description: PREMISE OF THE STUDY: Bet-hedging strategies maximize long-term geometric
 fitness at the cost of reduced arithmetic fitness by offsetting different
 mortality risks. Heterocarpic systems accomplish bet-hedging through the
 production of two or more fruit types that vary in dormancy and dispersal
 ability. It is unknown whether heterocarpy also offsets predispersal
 mortality risks. To address this question, we investigated whether
 heterocarpy in Grindelia ciliata (Asteraceae) also offsets mortality risks
 posed by a seed predator Schinia mortua (Noctuidae) to increase plant
 fitness. METHODS: We conducted two manipulative experiments to quantify
 critical life history components of this plant–insect interaction. We
 measured predispersal achene mortality from herbivory, postdispersal
 achene mortality in the seed bank, and seedling emergence. These
 measurements were then used in deterministic models to evaluate
 evolutionary consequences of predispersal seed mortality in G. ciliata.
 KEY RESULTS: Dormant achene types were less vulnerable to herbivory but
 more susceptible to mortality in the seed bank due to delayed seed
 emergence. Nondormant achene types experienced high predispersal mortality
 but low seed bank mortality due to rapid germination. Our
 herbivore-dependent model improved fit between observed and expected
 proportions of dormant and nondormant G. ciliata achenes and showed that
 heterocarpy could evolve in the absence of postgermination mortality.
 CONCLUSIONS: Our study provides empirical support of how predispersal
 herbivory can be equally important to postdispersal seed mortality risks
 in the evolution and maintenance of a heterocarpic reproductive system and
 expands understanding of how bet-hedging theory can be used to understand
 this unique reproductive strategy.
description: Herbivory Dependent
 Bet-Hedging ModelHerbivory Dependent
 Bet-Hedging ModelHerbTwoYear.BetHedgingModelHerbivory Independent Bet-Hedging ModelHerbivory Independent Bet-Hedging ModelNoHerb.two yearAchene PredictorThis file contains data for a sub-model that is used in Density independent and dependent bet-hedging model. These data must be read in (loaded) prior to running bet hedging models.Achene.cor.predictExtreme Herbivory FrequencyThis file holds code that determines extreme herbivory frequency. This file must be loaded prior to running Herbivory dependent modelBG[]Schinia mortua survivalThis file holds survival data of Schinia mortua larvae placed in Grindelia ciliata capitula.Larval survivalGrindelia ciliata Field EmergenceThis file contains all G. ciliata seedling emergence events.ALL.time.depAchene Consumption by S. mortuaThis file contains the number and proportion of consumed and non-consumed G. ciliata achenes for each of the oviposition treatments.Achene.1Achene Consumption with Capitulum Opening and Inoculation DatesAchene Consumption with Capitulum Opening and Inoculation DatesAchene.11
DOI: 10.5061/dryad.4vg33
title: Data from: Genome-wide mapping of targets of maize histone deacetylase hda101 reveals its function and regulatory mechanism during seed development

description: Histone deacetylases (HDACs) control histone acetylation levels by
 removing acetyl group from lysine residues. Maize (Zea mays) HDAC HDA101
 influences several aspects of development, including kernel size; however,
 the molecular mechanism by which HDA101 affects kernel development remains
 unknown. In this study, we find HDA101 regulates the expression of
 transfer cell-specific genes, suggesting their mis-regulation may be
 associated with defects in differentiation of transfer cells and smaller
 kernels of hda101 mutants. To investigate HDA101 function during early
 stages of seed development, we performed genome-wide mapping of HDA101
 binding sites. We observed that HDA101 mainly targets highly and
 intermediately expressed genes. Although loss of HDA101 can induce histone
 hyper-acetylation of its direct targets, this often does not involve
 variation in transcription. A small subset of inactive genes that must be
 negatively regulated during kernel development are also targeted by HDA101
 and its loss leads to hyper-acetylation and increased expression of these
 genes. Finally, we report HDA101 interacts with members of different
 chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like
 co-repressors. Taken together, our results reveal a complex genetic
 network regulated by HDA101 during seed development and provide insights
 into the different mechanisms of HDA101-mediated regulation of
 transcriptionally active and inactive genes.
description: Supplemental
 Dataset
DOI: 10.5061/dryad.d670p
title: Data from: Estimating the effect of competition on trait evolution using maximum likelihood inference

description: Many classical ecological and evolutionary theoretical frameworks posit
 that competition between species is an important selective force. For
 example, in adaptive radiations, resource competition between evolving
 lineages plays a role in driving phenotypic diversification and
 exploration of novel ecological space. Nevertheless, current models of
 trait evolution fit to phylogenies and comparative data sets are not
 designed to incorporate the effect of competition. The most advanced
 models in this direction are diversity-dependent models where evolutionary
 rates depend on lineage diversity. However, these models still treat
 changes in traits in one branch as independent of the value of traits on
 other branches, thus ignoring the effect of species similarity on trait
 evolution. Here, we consider a model where the evolutionary dynamics of
 traits involved in interspecific interactions are influenced by species
 similarity in trait values and where we can specify which lineages are in
 sympatry. We develop a maximum likelihood based approach to fit this model
 to combined phylogenetic and phenotypic data. Using simulations, we
 demonstrate that the approach accurately estimates the simulated parameter
 values across a broad range of parameter space. Additionally, we develop
 tools for specifying the biogeographic context in which trait evolution
 occurs. In order to compare models, we also apply these biogeographic
 methods to specify which lineages interact sympatrically for two
 diversity-dependent models. Finally, we fit these various models to
 morphological data from a classical adaptive radiation (Greater Antillean
 Anolis lizards). We show that models that account for competition and
 geography perform better than other models. The matching competition model
 is an important new tool for studying the influence of interspecific
 interactions, in particular competition, on phenotypic evolution. More
 generally, it constitutes a step toward a better integration of
 interspecific interactions in many ecological and evolutionary processes.
description: Supplementary
 Material
DOI: 10.5061/dryad.mh57b
title: Data from: A synthetic, catalytic and theoretical investigation of an unsymmetrical SCN pincer palladacycle

description: The SCN ligand 2-{3-[(methylsulfanyl)methyl]phenyl}pyridine, 1, has been
 synthesized starting from an initial Suzuki–Miyaura (SM) coupling between
 3-((hydroxymethyl)phenyl)boronic acid and 2-bromopyridine. The C–H
 activation of 1 with in situ formed Pd(MeCN)4(BF4)2 has been studied and
 leads to a mixture of palladacycles, which were characterized by X-ray
 crystallography. The monomeric palladacycle LPdCl 6, where L-H = 1, has
 been synthesized, and tested in SM couplings of aryl bromides, where it
 showed moderate activity. Density functional theory and the atoms in
 molecules (AIM) method have been used to investigate the formation and
 bonding of 6, revealing a difference in the nature of the Pd–S and Pd–N
 bonds. It was found that S-coordination to the metal in the rate
 determining C–H bond activation step leads to better stabilization of the
 Pd(II) centre (by 13–28 kJ mol−1) than with N-coordination. This is
 attributed to the electron donating ability of the donor atoms determined
 by Bader charges. The AIM analysis also revealed that the Pd–N bonds are
 stronger than the Pd–S bonds influencing the stability of key
 intermediates in the palladacycle formation reaction pathway.
description: Royal Society Open
 Science Supplementary info final version
DOI: 10.5061/dryad.7qs68
title: Data from: Dendrogramma is a siphonophore

description: Dendrogramma was the iconic deep-sea animal of 2014, voted among the
 top-ten new species described that year. The two species described are
 mushroom shaped animals, diploblastic, with an apparent gastrovascular
 system that extends from the base of the stalk to bifurcating canals that
 radiate through the flat disc. The authors could not assign the new genus
 to any known animal group with certainty, leading to numerous media
 reports that it belonged to an entirely new phylum. Here we use
 phylogenomic data from newly collected specimens to show that Dendrogramma
 is a cnidarian, specifically a benthic siphonophore in the family
 Rhodaliidae. Although an entire Dendrogramma colony has not been found, we
 hypothesise that the mushroom-like bodies are bracts, possibly used to aid
 buoyancy or as defensive appendages to protect feeding gastrozooids or
 gonads.
description: Read Me
 fileWord document providing
 contents and information on this DRYAD package.Dendro_Dryad_ReadMe_v1.docxDendrogramma partial transcriptomeTrinity assembled Dendrogramma partial transcriptome, zipped fasta format.D6UTout.Trinity.zipPipeline scriptsPhylogenomic pipeline: zipped folder containing eight unix shell scriptsDendro_scripts.zipAncillary filesZipped folder containing ancillary pipeline text files, and excel sample table and newick RAxML tree files.Dendro_files.zipMetazoan phylogenomic data matrixFinal 81 taxa, 251 gene fasta format amino acid alignment.T81_W251_tagdum.zip
DOI: 10.5061/dryad.q8n0v
title: Data from: Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution

description: Chloroplast sequence data are widely used to infer phylogenies of plants
 and algae. With the increasing availability of complete chloroplast genome
 sequences, the opportunity arises to resolve ancient divergences that were
 heretofore problematic. On the flip side, properly analyzing large
 multi-gene data sets can be a major challenge, as these data may be
 riddled with systematic biases and conflicting signals. Our study
 contributes new data from nine complete and four fragmentary chloroplast
 genome sequences across the green algal order Sphaeropleales. Our
 phylogenetic analyses of a 56-gene data set show that analyzing these data
 on a nucleotide level yields a well-supported phylogeny – yet one that is
 quite different from a corresponding amino acid analysis. We offer some
 possible explanations for this conflict through a range of analyses of
 modified data sets. In addition, we characterize the newly sequenced
 genomes in terms of their structure and content, thereby further
 contributing to the knowledge of chloroplast genome evolution.
description: DryadData matrices and
 scripts to repeat all analyses presented in the paper.
DOI: 10.5061/dryad.2361d
title: Data from: Willet be one species or two?: a genomic view of the evolutionary history of Tringa semipalmata

description: The Willet (Tringa semipalmata; Scolopacidae) is composed of 2
 morphologically and vocally distinct subspecies with broadly disjunct
 breeding distributions in North America. Nominate T. s. semipalmata breeds
 in coastal salt and brackish marshes along the Atlantic and Gulf coasts of
 eastern North America and the West Indies, and T. s. inornata breeds in
 wet grasslands and prairies in the northwestern interior of North America.
 To assess divergence and test for hybridization between the 2 subspecies,
 we sampled breeding and wintering populations and collected morphological
 data, mitochondrial DNA sequences from the ND2 locus, and nuclear DNA
 sequences from genomic libraries enriched for ultraconserved elements
 (UCEs). Mitochondrial haplotypes were reciprocally monophyletic between
 the 2 subspecies and indicated divergence approximately 700,000 yr ago.
 The UCE dataset included 4,635 loci containing 19,322 single nucleotide
 polymorphisms (SNPs), and, based on these data, individuals clustered by
 subspecies with no evidence of admixture between them and no substructure
 within subspecies. We identified 42 nuclear loci that contained SNPs fixed
 for alternate alleles between the 2 subspecies. Of the 42 loci with fixed
 differences, a statistically disproportional 17 were Z-linked, indicating
 a role for sexual selection in the divergence of the 2 subspecies.
 Genetic, morphological, ecological, and behavioral differences suggest
 that the 2 Willet subspecies may merit treatment as separate species.
 Further studies are needed to determine the presence of pre- or
 post-mating reproductive isolation.
description: Tringa semipalmata UCE
 alignmentsUCE alignments for all
 Tringa semipalmata individuals included in our study, and separate UCE
 alignments for each subspecies.Oswald_Tringa_semipalmata_UCE_Alignments.zip
DOI: 10.5061/dryad.qh0h1
title: Data from: Prevalence of chronic diseases among older patients in German general practices

description: Aims: To evaluate the prevalence of chronic diseases (CDs) among older
 patients in German general practices (GPs). Methods: A total of 840,319
 patients older than 65 years (359,289 male and 481,030 female) who
 consulted a GP between January and December 2014 were selected. Ten
 different CDs were considered: hypertension, lipid metabolism, diabetes,
 coronary heart disease, cancer, chronic obstructive pulmonary disease,
 heart failure, stroke, chronic kidney disease and osteoporosis. The
 prevalence, defined as the proportion of patients diagnosed with these
 disorders, was estimated. Results: All CDs were very common in older
 subjects. Hypertension was the most common CD, affecting 65.7% of men and
 66.1% of women. Stroke was the least frequent CD, with 6.6% of men and
 5.1% of women displaying this condition. More than one out of two subjects
 had between one and three CDs (men: 57.7% and women: 59.3%). Approximately
 25% of subjects had four or more CDs (men: 26.6% and women: 23.6%).
 Conclusions: Our study showed that the prevalence of CDs is high in the
 German elderly population. Hypertension was the most frequent chronic
 condition and around 25% of patients displayed at least four CDs.
description: Chronic diseases in
 older outpatients in German general practices (2014)File includes 10,000
 patients with following variables: an anonymous patient ID (1-10,000), age
 (years), gender (1 for male, 0 for female), diagnoses (1 for yes, 0 for
 no): hypertension, heart failure, chronic kidney disease, lipid
 metabolism, osteoporosis, COPD, CHD, cancerDA_chronic_diseases_2014.xls