cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1968
title: Data from: Genomic-scale capture and sequencing of endogenous DNA from feces

description: Genomic-level analyses of DNA from non-invasive sources would facilitate
 powerful conservation and evolutionary studies in natural populations of
 endangered and otherwise elusive species. However, the typical low
 quantity and poor quality of DNA that is extracted from non-invasive
 samples have generally precluded such work. Here we apply a modified DNA
 capture protocol that, when used in combination with massively-parallel
 sequencing technology, facilitates efficient and highly-accurate
 resequencing of megabases of specified nuclear genomic regions from fecal
 DNA samples. We validated our approach by comparing genetic variants
 identified from corresponding fecal and blood DNA samples of six western
 chimpanzees (Pan troglodytes verus) across more than 1.5 megabases of
 chromosome 21, chromosome X, and the complete mitochondrial genome. Our
 results suggest that it is now feasible to conduct genomic studies in
 natural populations for which constraints on invasive sampling have
 otherwise long been a barrier. The data we collected also provided an
 opportunity to examine western chimpanzee genetic diversity at
 unprecedented scale. Despite high mitochondrial genome diversity (pi =
 0.585%), western chimpanzees have a low ratio (0.42) of X chromosomal (pi
 = 0.034%) to autosomal (chromosome 21 pi = 0.081%) sequence diversity, a
 pattern that may reflect an unusual demographic history of this
 subspecies.
description: DatasetS1Pileup files, sequence files, and genotype information from chimpanzee fecal and blood samples (see ReadMe file)
DOI: 10.5061/dryad.rt01f
title: Data from: The evolutionary origin of somatic cells under the dirty work hypothesis

description: Reproductive division of labor is a hallmark of multicellular organisms.
 However, the evolutionary pressures that give rise to delineated germ and
 somatic cells remain unclear. Here we propose a hypothesis that the
 mutagenic consequences associated with performing metabolic work favor
 such differentiation. We present evidence in support of this hypothesis
 gathered using a computational form of experimental evolution. Our digital
 organisms begin each experiment as undifferentiated multicellular
 individuals, and can evolve computational functions that improve their
 rate of reproduction. When such functions are associated with moderate
 mutagenic effects, we observe the evolution of reproductive division of
 labor within our multicellular organisms. Specifically, a fraction of the
 cells remove themselves from consideration as propagules for multicellular
 offspring, while simultaneously performing a disproportionately large
 amount of mutagenic work, and are thus classified as soma. As a
 consequence, other cells are able to take on the role of germ, remaining
 quiescent and thus protecting their genetic information. We analyze the
 lineages of multicellular organisms that successfully differentiate and
 discover that they display unforeseen evolutionary trajectories: cells
 first exhibit developmental patterns that concentrate metabolic work into
 a subset of germ cells (which we call “pseudo-somatic cells”) and later
 evolve to eliminate the reproductive potential of these cells and thus
 convert them to actual soma. We also demonstrate that the evolution of
 somatic cells enables phenotypic strategies that are otherwise not easily
 accessible to undifferentiated organisms, though expression of these new
 phenotypic traits typically includes negative side effects such as aging.
description: Varying
 FMLvarying-fml.txtCoordination Knockout Experimentsknockouts.txtControl: Multicells cannot evolve pseudo-somatic cellsremoving-pseudosoma.txtIntroduction of Defectorsdefectors.txtRamped FML Environmentramped.txtAging of Multicellsaging.txt
DOI: 10.5061/dryad.m8b96
title: Data from: Impacts of environmental heterogeneity on moss diversity and distribution of Didymodon (Pottiaceae) in Tibet, China

description: Tibet makes up the majority of the Qinghai-Tibet Plateau, often referred
 to as the roof of the world. Its complex landforms, physiognomy, and
 climate create a special heterogeneous environment for mosses. Each moss
 species inhabits its own habitat and ecological niche. This, in
 combination with its sensitivity to environmental change, makes moss
 species distribution a useful indicator of vegetation alteration and
 climate change. This study aimed to characterize the diversity and
 distribution of Didymodon (Pottiaceae) in Tibet, and model the potential
 distribution of its species. A total of 221 sample plots, each with a size
 of 10 × 10 m and located at different altitudes, were investigated across
 all vegetation types. Of these, the 181 plots in which Didymodon species
 were found were used to conduct analyses and modeling. Three noteworthy
 results were obtained. First, a total of 22 species of Didymodon were
 identified. Among these, Didymodon rigidulus var. subulatus had not
 previously been recorded in China, and Didymodon constrictus var.
 constrictus was the dominant species. Second, analysis of the
 relationships between species distributions and environmental factors
 using canonical correspondence analysis revealed that vegetation cover and
 altitude were the main factors affecting the distribution of Didymodon in
 Tibet. Third, based on the environmental factors of bioclimate, topography
 and vegetation, the distribution of Didymodon was predicted throughout
 Tibet at a spatial resolution of 1 km, using the presence-only MaxEnt
 model. Climatic variables were the key factors in the model. We conclude
 that the environment plays a significant role in moss diversity and
 distribution. Based on our research findings, we recommend that future
 studies should focus on the impacts of climate change on the distribution
 and conservation of Didymodon.
description: Data for
 PONE-D-15-15932Didymodon ( including
 species data, sampling plots, and habitat characteristics collected in the
 field work ) and environmental variables (bioclimatic,topographic,and
 vegetation data) which were projected as GIS raster layers in GCS_WGS_1984
 coordinate system, and converted to ASCII format for modeling the
 distribution of Didymodon in Tibet.
DOI: 10.5061/dryad.tn47c
title: Data from: Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

description: The role of hybridization and subsequent introgression has been
 demonstrated in an increasing number of species. Recently, Fontaine et al.
 (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six
 members of the Anopheles gambiae species complex. Their analysis revealed
 a reticulate evolutionary history and pointed to extensive introgression
 on all four autosomal arms. The study further highlighted the complex
 evolutionary signals that the co-occurrence of incomplete lineage sorting
 (ILS) and introgression can give rise to in phylogenomic analyses. While
 tree-based methodologies were used in the study, phylogenetic networks
 provide a more natural model to capture reticulate evolutionary histories.
 In this work, we reanalyse the Anopheles data using a recently devised
 framework that combines the multispecies coalescent with phylogenetic
 networks. This framework allows us to capture ILS and introgression
 simultaneously, and forms the basis for statistical methods for inferring
 reticulate evolutionary histories. The new analysis reveals a phylogenetic
 network with multiple hybridization events, some of which differ from
 those reported in the original study. To elucidate the extent and patterns
 of introgression across the genome, we devise a new method that quantifies
 the use of reticulation branches in the phylogenetic network by each
 genomic region. Applying the method to the mosquito data set reveals the
 evolutionary history of all the chromosomes. This study highlights the
 utility of ‘network thinking’ and the new insights it can uncover, in
 particular in phylogenomic analyses of large data sets with extensive gene
 tree incongruence.
description: MAF.tar
DOI: 10.5061/dryad.vb375
title: Data from: Analysing small insect glands with UV-LDI MS: high-resolution spatial analysis reveals the chemical composition and use of the osmeterium secretion in Themira superba (Sepsidae: Diptera)

description: For many insect species, pheromones are important communication tools, but
 chemical analysis and experimental study can be technically challenging
 because they require the detection and handling of complex chemicals in
 small quantities. One drawback of traditional mass spectrometry methods
 such as gas chromatography mass spectrometry is that whole-body
 extractions from one to several hundred individuals are required, with the
 consequence that intra- and interindividual differences cannot be
 detected. Here, we used the recently introduced UV-LDI MS (ultraviolet
 laser desorption/ionization mass spectrometry) to profile the ‘osmeterium’
 of the sepsid fly Themira superba that is located on the edge of the hind
 tibia of males. Based on analyses of individual legs, we established that
 the gland produced a secretion that consisted of oxygenated hydrocarbons
 and putative isoprenoids. The secretion was first detected 24 h after
 eclosion, and its transfer to the wings of females during mating was
 demonstrated using UV-LDI MS. We then tested whether the secretion had an
 anti-aphrodisiac function, but experimental transfer of the secretion to
 virgin females did not affect mating success or copulation duration.
 Throughout the study, UV-LDI MS proved invaluable, because it allowed
 tracking the natural and experimental transfer of small quantities of
 pheromones to specific body parts of small flies.
description: T superba Male - Raw
 LDIT superba Mated Female -
 Raw LDIT superba Virgin Female
 - Raw LDIOsmeterium Secretion
 Brush ExperimentsScreenshots of UV-LDI
 mass spectrometry data showing the presence (or absence) of osmeterium
 secretion that was manually spread on the female wings with a paint brush.
 Each trial contain data for randomly selected female wings that were
 brushed and the set of male osmeteria that were used to collect the
 secretion.Osmeterium Brush
 Experiments.zipMating Trial Analysis -
 R code"R" code for
 the analysis of data as it was run in R (R Core Team,
 2013)Dryad
 Osmeterium paper mating trial data R
 code.rMating Trial - Raw
 DataRaw data from mate
 trials. The groups have been written in string (brush+, brush- and
 nobrush), but were translated as levels (1, 2 and 3 respectively) in the R
 code file.Dryad Osmeterium paper mating
 trial data.csv
DOI: 10.5061/dryad.h305b15
title: Data from: Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies

description: Consumer genomics enables genetic discovery on an unprecedented scale by
 linking very large databases of personal genomic data with phenotype
 information voluntarily submitted via web-based surveys. These databases
 are having a transformative effect on human genomics research, yielding
 insights on increasingly complex traits, behaviors, and disease by
 including many thousands of individuals in genome-wide association studies
 (GWAS). The promise of consumer genomic data is not limited to human
 research, however. Genomic tools for dogs are readily available, with
 hundreds of causal Mendelian variants already characterized, because
 selection and breeding have led to dramatic phenotypic diversity underlain
 by a simple genetic structure. Here, we report the results of the first
 consumer genomics study ever conducted in a non-human model: a GWAS of
 blue eyes based on more than 3,000 customer dogs with validation panels
 including nearly 3,000 more, the largest canine GWAS to date. We
 discovered a novel association with blue eyes on chromosome 18 (P =
 1.3x10-68) and used both sequence coverage and microarray probe intensity
 data to identify the putative causal variant: a 98.6-kb duplication
 directly upstream of the Homeobox gene ALX4, which plays an important role
 in mammalian eye development. This duplication is largely restricted to
 Siberian Huskies, is strongly associated with the blue-eyed phenotype
 (chi-square P = 5.2x10-290), and is highly, but not completely, penetrant.
 These results underscore the power of consumer-data-driven discovery in
 non-human species, especially dogs, where there is intense owner interest
 in the personal genomic information of their pets, a high level of
 engagement with web-based surveys, and an underlying genetic architecture
 ideal for mapping studies.
description: deane-coe_etal_canine_eye_color_GWASSupplemental data archive for Deane-Coe et al. "Direct-To-Consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication causing blue eyes and heterochromia in Siberian Huskies."
DOI: 10.5061/dryad.pv24v
title: Data from: Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex

description: Instances of parallel ecotypic divergence where adaptation to similar
 conditions repeatedly cause similar phenotypic changes in closely related
 organisms are useful for studying the role of ecological selection in
 speciation. Here we used a combination of traditional and next generation
 genotyping techniques to test for the parallel divergence of plants from
 the Senecio lautus complex, a phenotypically variable groundsel that has
 adapted to disparate environments in the South Pacific. Phylogenetic
 analysis of a broad selection of Senecio species showed that members of
 the S. lautus complex form a distinct lineage that has diversified
 recently in Australasia. An inspection of thousands of polymorphisms in
 the genome of 27 natural populations from the S. lautus complex in
 Australia revealed a signal of strong genetic structure independent of
 habitat and phenotype. Additionally, genetic differentiation between
 populations was correlated with the geographical distance separating them,
 and the genetic diversity of populations strongly depended on geographical
 location. Importantly, coastal forms appeared in several independent
 phylogenetic clades, a pattern that is consistent with the parallel
 evolution of these forms. Analyses of the patterns of genomic
 differentiation between populations further revealed that adjacent
 populations displayed greater genomic heterogeneity than allopatric
 populations and are differentiated according to variation in soil
 composition. These results are consistent with a process of parallel
 ecotypic divergence in face of gene flow.
description: Category_SNPsFETFstConsensus_sequences_RADsConsensus_sequencesFrequencyConsensus_sequences_RADs-2This fasta file contains consensus sequences derived from RADs genotyping of neutral loci in 29 S. lautus populations and the close relative S. madagascariensis. These sequences were used to construct the rooted phylogeny presented in Figure 2B of the manuscript.
DOI: 10.5061/dryad.60p50
title: Data from: Great tits and the city: distribution of genomic diversity and gene-environment associations along an urbanization gradient

description: Urbanization is a growing concern challenging the evolutionary potential
 of wild populations by reducing genetic diversity and imposing new
 selection regimes affecting many key fitness traits. However, genomic
 footprints of urbanization have received little attention so far. Using
 RAD sequencing, we investigated the genome-wide effects of urbanization on
 neutral and adaptive genomic diversity in 140 adult great tits Parus major
 collected in locations with contrasted urbanization levels (from a natural
 forest to highly urbanized areas of a city (Montpellier, France).
 Heterozygosity was slightly lower in the more urbanized sites compared to
 the more rural ones. Low but significant effect of urbanization on genetic
 differentiation was found, at the site-level but not at the nest-level,
 indicative of the geographic scale of urbanization impact and of the
 potential for local adaptation despite gene flow. Gene-environment
 association tests identified numerous SNPs with small association scores
 to urbanization, distributed across the genome, from which a subset of 97
 SNPs explained up to 81% of the variance in urbanization, overall
 suggesting a polygenic response to selection in the urban environment.
 These findings open stimulating perspectives for broader applications of
 high-resolution genomic tools on other cities and larger sample sizes to
 investigate the consistency of the effects of urbanization on the spatial
 distribution of genetic diversity and the polygenic nature of
 gene-urbanization association.
description: perrier-genotypes-parus-majorVCF file containing genotypes of the Parus major individuals. Individual names can be matched with the names found in the individuals.txt file in order to extract site of origin, coordinates, and urbanization scores.perrier-genotypes.vcfperrier-individuals.txt-parus-majorTEXT file containing information (coordinates, site, urbanization scores ) regarding Parus major individual genotyped found in the VCF file.individuals.txt
DOI: 10.5061/dryad.sg0k6
title: Data from: Bats, primates, and the evolutionary origins and diversification of mammalian gammaherpesviruses

description: Gammaherpesviruses (γHVs) are generally considered host specific and to
 have codiverged with their hosts over millions of years. This tenet is
 challenged here by broad-scale phylogenetic analysis of two viral genes
 using the largest sample of mammalian γHVs to date, integrating for the
 first time bat γHV sequences available from public repositories and newly
 generated viral sequences from two vampire bat species (Desmodus rotundus
 and Diphylla ecaudata). Bat and primate viruses frequently represented
 deep branches within the supported phylogenies and clustered among viruses
 from distantly related mammalian taxa. Following evolutionary scenario
 testing, we determined the number of host-switching and cospeciation
 events. Cross-species transmissions have occurred much more frequently
 than previously estimated, and most of the transmissions were attributable
 to bats and primates. We conclude that the evolution of the
 Gammaherpesvirinae subfamily has been driven by both cross-species
 transmissions and subsequent cospeciation within specific viral lineages
 and that the bat and primate orders may have potentially acted as
 superspreaders to other mammalian taxa throughout evolutionary history.
description: Megan results vampire
 bat viromeTITLE: Assigned reads
 from the HTS data DESCRIPTION: MEGAN files corresponding to confirmed
 gammaherpervirus matching reads found within five Desmodus rotundus and
 Diphylla ecaudata vampire bat spleen samples. Viral assignment was
 performed using BLASTX against the GenBank non-redundant protein database
 and mapped with SMALT against a custom-built herpesviral database under a
 stringency of 60%. The γHV-matching reads were further selected by
 reciprocal BLASTX analysis using the following criteria: length of ≥100
 bp, pairwise identity &gt;50%, e-value &lt;10-6, and independent hits to
 two different γHV proteins or at least two different regions of the same
 protein.Vampbat_viromeDRYAD.zip
DOI: 10.5061/dryad.mh77c
title: Data from: Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix

description: Given the drawbacks of implementing multivariate analysis for mapping
 multiple traits in genome-wide association study (GWAS), principal
 component analysis (PCA) has been widely used to generate independent
 ‘super traits’ from the original multivariate phenotypic traits for the
 univariate analysis. However, parameter estimates in this framework may
 not be the same as those from the joint analysis of all traits, leading to
 spurious linkage results. In this paper, we propose to perform the PCA for
 residual covariance matrix instead of the phenotypical covariance matrix,
 based on which multiple traits are transformed to a group of pseudo
 principal components. The PCA for residual covariance matrix allows
 analyzing each pseudo principal component separately. In addition, all
 parameter estimates are equivalent to those obtained from the joint
 multivariate analysis under a linear transformation. However, a fast least
 absolute shrinkage and selection operator (LASSO) for estimating the
 sparse oversaturated genetic model greatly reduces the computational costs
 of this procedure. Extensive simulations show statistical and
 computational efficiencies of the proposed method. We illustrate this
 method in a GWAS for 20 slaughtering traits and meat quality traits in
 beef cattle.
description: 942After quanlity control,
 this experimental population consists of 942 young Simmental bulls born
 between 2008 and 2011, which are originated from Ulgai, Xilingol league,
 Inner Mongolia of China. After weaning, the cattle were moved to Beijing
 Jinweifuren cattle farm and were fattened under the same feeding and
 management environment. Each individual was timely observed for growth and
 development traits until slaughtered from 16 to 18 months old. During the
 period of slaughter, carcass traits and meat quality traits were measured
 according to Institutional Meat Purchase Specifications for fresh beef
 guidelines.
DOI: 10.15468/du7fea
title: Impatiens longcanggouensis (Balsaminaceae): a new species from Sichuan, China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Luo, Qiang, Chen, Hong, Yuan, Ying, Yang, Hong, Liu, Chan, Song, Xinqiang, Ma, Shen (2026): Impatiens longcanggouensis (Balsaminaceae): a new species from Sichuan, China. PhytoKeys 270: 1-12, DOI: 10.3897/phytokeys.270.174879AbstractImpatiens longcanggouensis Q. Luo (Balsaminaceae), a new species from Yingjing County, Sichuan Province, China, is described and illustrated. Its morphology, including pollen and seed characters observed via scanning electron microscopy (SEM), is documented in detail. The new species is morphologically similar to I. recurvicornis, but is readily distinguished by the following combination of characters: leaf margin shallowly arcuate-serrate (vs. serrulate); abaxial leaf surface usually purplish-red (vs. pale green); inflorescence commonly two-flowered (vs. one-flowered); bracts lanceolate, 2–2.5 mm long (vs. ovate, 3–4 mm long); flowers 1.2–1.8 cm long (vs. 3–4 cm long); dorsal petal 6–8 mm in diameter, with two erect, stout rostella along the abaxial mid-vein (vs. dorsal petal ca. 13 mm in diameter with a beaked apex); lower sepal narrowly funnel-form with a spreading mouth (vs. navicular with an oblique mouth); and capsule clavate (vs. linear).