cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2qt77
title: Data from: Novel distances for Dollo data

description: We investigate distances on binary (presence/absence) data in the context
 of a Dollo process, where a trait can only arise once on a phylogenetic
 tree but may be lost many times. We introduce a novel distance, the
 Additive Dollo Distance (ADD), that applies to data generated under a
 Dollo model, and show that it has some useful theoretical properties
 including an intriguing link to the LogDet/paralinear distance.
 Simulations of Dollo data are used to compare a number of binary distances
 including ADD, LogDet, a restriction-site-based distance, and some simple,
 but to our knowledge previously unstudied, variations on common binary
 distances. The simulations suggest that ADD outperforms other distances on
 Dollo data. Interestingly, we found that the LogDet distance performs
 poorly in the context of a Dollo process, this may have implications for
 its use in connection with conditioned genome reconstruction. We apply the
 ADD to two Diversity Arrays Technology (DArT) datasets, one that broadly
 covers Eucalyptus species and one that focuses on the Eucalyptus series
 Adnataria. We also reanalyse gene family presence/absence data from
 bacterial genomes obtained from the COG database and compare the results
 to previous phylogenies estimated using the conditioned genome
 reconstruction approach. The results for these case studies are largely
 congruent with previous studies, in some cases giving more phylogenetic
 resolution.
description: padd_Dollo_templateAn example input file for use with the perl script for calculating ADD and PADD distances.Online Supplementary MaterialContains instructions on how to use the Perl script for computing ADD and PADD distances. It also contains additional results in the form of 10 supplementary tables and 8 supplementary figures.OnlineSupplementaryMaterial.pdfperl script for calculating ADD and PADDSee the online supplementary material for instructions on use of this script.add_Dollo_dist.plProvenance information for AdnatariaAdnataria case studyThis nexus file contains both the data matrix and the resulting trees for the Adnataria case study.Adnataria_casestudy.nexEucalyptus case studyThis nexus file contains the data matrix and resulting tree for the Eucalyptus case study.Eucalyptus_casestudy.nexGene presence/absence case studyThis nexus file contains the data matrix and resulting tree for the gene presence/absence case study based on the COG database.Cogs_casestudy.nex
DOI: 10.5061/dryad.400b6
title: Data from: Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence

description: Parmelioid lichens are a diverse and ubiquitous group of foliose lichens.
 Generic delimitation in parmelioid lichens has been in a state of flux
 since the late 1960s with the segregation of the large, heterogeneous
 genus Parmelia into numerous smaller genera. Recent molecular phylogenetic
 studies have demonstrated that some of these new genera were monophyletic,
 some were not, and others, previously believed to be unrelated, fell
 within single monophyletic groups, indicating the need for a revision of
 the generic delimitations. This study aims to give an overview of current
 knowledge of the major clades of all parmelioid lichens. For this, we
 assembled a dataset of 762 specimens, including 31 of 33 currently
 accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae).
 We performed maximum likelihood and Bayesian analyses of combined datasets
 including two, three and four loci. Based on these phylogenies and the
 correlation of morphological and chemical characters that characterize
 monophyletic groups, we accept 27 genera within nine main clades. We
 re-circumscribe several genera and reduce Parmelaria to synonymy with
 Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a
 new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y.
 Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic
 rank and 15 new combinations are proposed (in the genera Flavoparmelia,
 Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short
 discussion of the accepted genera is provided and remaining challenges and
 areas requiring additional taxon sampling are identified.
description: Combined_4locusTreeMrBayes consensus tree of four gene combined dataset (ITS, nuLSU, mtSSU, RPB1)combined_min3_max2_ex_2.mb.conCombined 4gene alignment fileThis is combined dataset file of 4 gene in nex format.combined_min3_max2_ex_2.mb
DOI: 10.5061/dryad.94qh5
title: Data from: What is a disease? Perspectives of the public, health professionals, and legislators

description: Objective: To assess the perception of diseases and the willingness to use
 public tax revenue for their treatment among relevant stakeholders.
 Design: A population-based, cross-sectional mailed survey. Setting:
 Finland Participants: 3 000 laypeople, 1 500 doctors, 1 500 nurses
 (randomly identified from the databases of the Finnish Population
 Register, the Finnish Medical Association and the Finnish Nurses
 Association), and all 200 parliament members. Main outcome measures:
 Respondents’ perspectives on a 5-point Likert scale on two claims on 60
 states of being: “[This state of being] is a disease”; and ”[This state of
 being] should be treated with public tax revenue”. Results: Of the 6 200
 individuals approached, 3 280 (53%) responded. Of the 60 states of being,
 ≥80% of respondents considered 12 to be diseases (Likert scale responses
 of “4” and “5”) and five not to be diseases (Likert scale responses of “1”
 and “2”). There was considerable variability in most states, and great
 variability in ten (≥20% of respondents of all groups considered it a
 disease and ≥20% rejected as a disease). Doctors were more inclined to
 consider states of being as diseases than laypeople; nurses and parliament
 members were intermediate (p&lt;0.001), but all groups showed large
 variability. Responses to the two claims were very strongly correlated (r
 = 0.96 [95% CI: 0.94-0.98]; p&lt;0.001). Conclusions: There is large
 disagreement among the public, health professionals, and legislators
 regarding the classification of states of being as diseases and whether
 their management should be publicly funded. Understanding attitudinal
 differences can help to enlighten social discourse on a number of
 contentious public policy issues.
description: FIND Survey Raw
 DataFIND Survey Raw Data,
 for details see Manuscript submitted to BMJ Open
DOI: 10.5061/dryad.37r9p
title: Data from: Genetic variation and risks of introgression in the wild Coffea arabica gene pool in south-western Ethiopian montane rainforests

description: The montane rainforests of SW Ethiopia are the primary centre of diversity
 of Coffea arabica and the origin of all Arabica coffee cultivated
 worldwide. This wild gene pool is potentially threatened by forest
 fragmentation and degradation, and by introgressive hybridization with
 locally improved coffee varieties. We genotyped 703 coffee shrubs from
 unmanaged and managed coffee populations, using 24 microsatellite loci.
 Additionally, we genotyped 90 individuals representing 23 Ethiopian
 cultivars resistant to coffee berry disease (CBD). We determined
 population genetic diversity, genetic structure, and admixture of cultivar
 alleles in the in situ gene pool. We found strong genetic differentiation
 between managed and unmanaged coffee populations, but without significant
 differences in within-population genetic diversity. The widespread
 planting of coffee seedlings including CBD-resistant cultivars most likely
 offsets losses of genetic variation attributable to genetic drift and
 inbreeding. Mixing cultivars with original coffee genotypes, however,
 leaves ample opportunity for hybridization and replacement of the original
 coffee gene pool, which already shows signs of admixture. In situ
 conservation of the wild gene pool of C. arabica must therefore focus on
 limiting coffee production in the remaining wild populations, as
 intensification threatens the genetic integrity of the gene pool by
 exposing wild genotypes to cultivars.
description: Microsatellite genotype
 data of wild Coffea arabicaGenotype data of wild
 Coffea arabica in original Genemapper format and in various derived
 formats (PA, dominant, tetraploid) compatible with R/Polysat,
 R/Introgress, ATetra, Structure and GenAlEx. See readme file for detailed
 description of files.EVA-2012-008-Data.zip
DOI: 10.5061/dryad.c32m0
title: Data from: Loci controlling nitrate reductase activity in maize: ultraviolet-B signaling in aerial tissues increases nitrate reductase activity in leaf and root when responsive alleles are present

description: Environmental factors, such as ultraviolet-B (UV-B) irradiation, have the
 ability to affect pathways such as nitrogen metabolism. As fixed nitrogen
 is the keystone mineral nutrient that controls grain crop yield, any
 alteration in this cycle can be detrimental to plant productivity. Nitrate
 reductase enzyme activity is responsible for the reduction of nitrate to
 nitrite, and nitrate is the major form of nitrogen assimilated in plants.
 In maize (Zea mays L.) production, nitrate assimilation kinetics are
 important for both high- and low-input agricultural systems. Nitrate
 reductase protein activity is controlled by phosphatases and kinases.
 Nitrate reductase activity is responsive to environmental signals such as
 light–dark cycles and UV-B radiation, although the regulatory controls are
 not yet fully understood. We have determined the location of maize genetic
 factors that control nitrate reductase activity and the extent of
 contribution of each of these factors, both locally in the leaf tissue and
 via long-distance signaling loci that affect root nitrate reductase
 activity upon leaf UV irradiation. In the IBM94 recombinant inbred mapping
 population, the loci controlling regulation of nitrate reductase activity
 under UV-B map to different positions than the loci controlling nitrate
 reductase activity in unexposed plants.
description: PPL_1406_sm_AppendixS1Construction of simulations, results of comparison of GLMC and composite interval mapping; details of GLM mixed model for QTL detection, and comparison of QTL detected with in pilot and full experiment and by GLMC and QTLNetwork composite interval mapping.Copy of PPL_1406_sm_TableS1Raw and adjusted trait data for each sample for pilot and full experiment.Copy of PPL_1406_sm_TableS2Expression-QTL genes under leaf nitrate reductase activity QTL. Markers within the nitrate reductase activity QTL region were used to select markers that had significant linkage to expression differences in genes that mapped to the same chromosomal bin. The MZ_IDs for the array oligonucleotides have only been mapped to bin in the B73 Refgen1 sequence, not to the exact genomic location, so some of these eQTL may not be within the nitrate reductase activity QTL region within that bin.Copy of PPL_1406_sm_TableS3Genes located in the same chromosomal region as nitrate reductase activity QTL regions. Flanking genetic markers were localized on the B73 sequence and all genes in the filtered gene set that had genomic locations between those co-ordinates were selected.
DOI: 10.5061/dryad.0n761
title: Data from: Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits

description: Gaussian processes, a class of stochastic processes including Brownian
 motion and the Ornstein–Uhlenbeck process, are widely used to model
 continuous trait evolution in statistical phylogenetics. Under such
 processes, observations at the tips of a phylogenetic tree have a
 multivariate Gaussian distribution, which may lead to suboptimal model
 specification under certain evolutionary conditions, as supposed in models
 of punctuated equilibrium or adaptive radiation. To consider non-normally
 distributed continuous trait evolution, we introduce a method to compute
 posterior probabilities when modeling continuous trait evolution as a Lévy
 process. Through data simulation and model testing, we establish that
 single-rate Brownian motion (BM) and Lévy processes with jumps generate
 distinct patterns in comparative data. We then analyzed body mass and
 endocranial volume measurements for 126 primates. We rejected single-rate
 BM in favor of a Lévy process with jumps for each trait, with the lineage
 leading to most recent common ancestor of great apes showing particularly
 strong evidence against single-rate BM.
description: primates.eastman.isler_pruned.tree.txt126 tip tree resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Branches are measured in units of Ma.primates.eastman.isler_pruned.ecv.data126 row data matrix of endocranial volume (ECV) measurements resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Data has been log-transformed.primates.eastman.isler_pruned.mass.data126 row data matrix of body mass measurements resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Data has been log-transformed.primates.eastman.isler_pruned.massecvratio.data126 row data matrix of ratios of body mass to endocranial volume (ECV) ratios resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Data has been log-transformed.Levy_processes_supplementary_materialsSupplementary materials contains tables of results from simulation study and empirical inference upon primate data. See manuscript for table references. In addition, the supplementary materials contains the signal-to-noise ratio color-coded phylogenies with fully named tips, whereas the manuscript phylogeny only provides family names (Platyrrhini, Catarrhini, and Strepsirrhini).suppmat.pdf
DOI: 10.5061/dryad.jm8vp
title: Data from: Female choosiness leads to the evolution of individually distinctive males

description: Individual recognition is a taxonomically widespread ability that
 underlies a diverse suite of behaviors including the identification of
 individual nest-mates, agonistic opponents, and mating partners. However,
 as yet relatively little is known about the circumstances under which the
 requisite signal diversity can evolve. Here we develop a model describing
 a novel mechanism of individual identity evolution via sexual selection.
 Females choose among a subset of males, but can select the most attractive
 male only when he bears a unique identity signal. This mimics a species in
 which mate assessment and choice are temporally separate, such as when
 females observe males in direct conflict and must subsequently locate the
 winner. When females in our model are choosy at least 10% of the time,
 diversity at individuality signaling loci evolves as a by-product of
 selection on male attractiveness more rapidly than does diversity at
 equivalent loci evolving only under neutral processes. Even at lower
 discrimination rates, drifting signal diversity gives the female choice
 mechanism sufficient traction to drive up average male attractiveness. The
 mechanism we describe here can significantly increase signal diversity at
 even low rates of discrimination by females.
description: STable
 1Basic model - variation
 in female discrimination rateSTable
 2Phenotype variation
 model - females underestimate male quality by up to 20%STable
 3Variable encounter rate
 model - variation in number of individuals females encounter when seeking
 a mateSTable
 4Population size
 variation model
DOI: 10.5061/dryad.q1k76
title: Data from: Domestication and geographic origin of Oryza sativa in China: insights from multilocus analyses of nucleotide variation of O. sativa and O. rufipogon

description: Previous studies have indicated that China is one of the domestication
 centres of Asian cultivated rice (Oryza sativa), and common wild rice (O.
 rufipogon) is the progenitor of O. sativa. However, the number of
 domestication times and the geographic origin of Asian cultivated rice in
 China are still under debate. In this study, 100 accessions of Asian
 cultivated rice and 111 accessions of common wild rice in China were
 selected to examine the relationship between O. sativa and O. rufipogon
 and thereby infer the domestication and evolution of O. sativa in China
 through sequence analyses of six gene regions, trnC-ycf6 in chloroplast
 genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear
 genomes. The results indicated that the two subspecies of O. sativa
 (indica and japonica) were domesticated independently from different
 populations of O. rufipogon with gene flow occurring later from japonica
 to indica; Southern China was the genetic diversity centre of O.
 rufipogon, and the Pearl River basin near the Tropic of Cancer was the
 domestication centre of O. sativa in China.
description: Aligned sequences of all
 lociFinal assembled and
 aligned sequences of trnC-ycf6, cox3, Ehd1, ITS, Hd1 and Waxy. Sequences
 of 8 elites, 92 landraces, 111 accessions of Oryza rufipogon and 1
 accessions of O. barthii were contained for each locus.Aligned sequences of trnC-ycf6,
 cox3, Ehd1, ITS, Hd1 and Waxy.fasta
DOI: 10.5061/dryad.sn5r5
title: Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony

description: Gene transposition puts a new gene copy in a novel genomic environment.
 Moreover, genes moving between the autosomes and the X chromosome
 experience change in several evolutionary parameters. Previous studies of
 gene transposition have not utilized the phylogenetic framework that
 becomes possible with the availability of whole genomes from multiple
 species. Here we used parsimonious reconstruction on the genomic
 distribution of gene families to analyze interchromosomal gene
 transposition in Drosophila. We identified 782 genes that have moved
 chromosomes within the phylogeny of 10 Drosophila species, including 87
 gene families with multiple independent movements on different branches of
 the phylogeny. Using this large catalog of transposed genes, we detected
 accelerated sequence evolution in duplicated genes that transposed when
 compared to the parental copy at the original locus. We also observed a
 more refined picture of the biased movement of genes from the X chromosome
 to the autosomes. The bias of X-to-autosome movement was significantly
 stronger for RNA-based movements than for DNA-based movements, and among
 DNA-based movements there was an excess of genes moving onto the X
 chromosome as well. Genes involved in female-specific functions moved onto
 the X chromosome while genes with male-specific functions moved off the X.
 There was a significant overrepresentation of proteins involving
 chromosomal function among transposed genes, suggesting that genetic
 conflict between sexes and among chromosomes may be a driving force behind
 gene transposition in Drosophila.
description: data, scripts, and
 supporting informationHanHahn2012.tgz
DOI: 10.5061/dryad.q9p4s
title: Data from: Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome

description: The level of within-species polymorphism differs greatly among genes in a
 genome. Many genomic studies have investigated the relationship between
 gene polymorphism and factors such as recombination rate or expression
 pattern. However, the polymorphism of a gene is affected not only by its
 physical properties or functional constraints, but also by natural
 selection on organisms in their environments. Specifically, if
 functionally divergent alleles enable adaptation to different
 environments, locus-specific polymorphism may be maintained by spatially
 heterogeneous natural selection. To test this hypothesis and estimate the
 extent to which environmental selection shapes the pattern of genome-wide
 polymorphism, we define the ‘environmental relevance’ of a gene as the
 proportion of genetic variation explained by environmental factors, after
 controlling for population structure. We found substantial effects of
 environmental relevance on patterns of polymorphism among genes. In
 addition, the correlation between environmental relevance and gene
 polymorphism is positive, consistent with the expectation that balancing
 selection among heterogeneous environments maintains genetic variation at
 ecologically important genes. Comparison of the gene ontology annotations
 shows that genes with high environmental relevance are enriched in unknown
 function categories. These results suggest an important role for
 environmental factors in shaping genome-wide patterns of polymorphism and
 indicate another direction of genomic study.
description: 65_NNon-synonymous
 polymorphism in 65 accessions65_PIAll polymorphism in 65
 accessions65_SSynonymous polymorphism
 in 65 accessions80_NNon-synonymous
 polymorphism in 80 accessions80_PIAll polymorphism in 80
 accessions80_SSynonymous polymorphism
 in 80 accessionsReadMeRead
 me~!!!
DOI: 10.5061/dryad.733d9
title: Data from: Dissecting the contributions of plasticity and local adaptation to the phenology of a butterfly and its host plants

description: Phenology affects the abiotic and biotic conditions that an organism
 encounters and consequently its fitness. For populations of high latitude
 species, spring phenology often occurs earlier in warmer years and
 regions. Here we apply a novel approach to decompose spatiotemporal
 covariation between spring temperature and the phenology of two flowering
 plants, Cardamine pratensis and Alliara petiolata, and a Lepidopteran
 herbivore, Anthocharis cardamines, across the UK, into the contributions
 of plasticity and local adaptation. All three species overlap in the
 time-window over which mean temperatures best predict variation in
 phenology and we find little evidence that the position of time-windows
 varies latitudinally, as expected if they were initiated by day-length.
 The focal species show pronounced temperature-mediated phenological
 plasticity of similar magnitude. While we find no evidence for local
 adaptation in the flowering times of the plants, geographic variation in
 the phenology of the butterfly reveals countergradient local adaptation.
 Geographic variation in the butterfly's phenology appears to be more
 sensitive to variation in temperature than the flowering times of the host
 plants and we find no evidence that coevolution has generated geographic
 variation in adaptive phenological plasticity.
description: butterfly