cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.44tj3
title: Data from: Identification, characterization, and transcription analysis of xylogen-like arabinogalactan proteins in rice (Oryza sativa L.)

description: Background: Xylogen, a chimeric arabinogalactan protein containing a
 non-specific lipid transfer protein domain, can promote xylem cell
 differentiation. No comprehensive study has been carried out on the XYLP
 gene family in rice. As a first step in research on this gene family and
 as a useful strategy in general, a genome-wide analysis of the OsXYLP gene
 family is thus needed. Results: In this study, we identified 21 XYLP genes
 from the rice genome and comprehensively analyzed their protein
 structures, phylogenetic relationships, chromosomal locations, and gene
 duplication status. Our results indicate that gene duplication has played
 major roles in the expansion of the OsXYLP gene family. We used expressed
 sequence tag, microarray, massively parallel signature sequencing, and
 quantitative real-time PCR data to analyze OsXYLP gene expression during
 various developmental stages and under abiotic stress conditions. We found
 that many OsXYLP genes are abundantly expressed in vascular tissues and
 seeds, with some genes regulated under hormonal or abiotic stresses. In
 addition, we identified knockout mutants of OsXYLP7 and OsXYLP16 and
 discovered that the mutant xylp7 has a defect in stem height. Conclusions:
 We analyzed expression profiles of 21 XYLP genes and characterized the
 structures and evolutionary relationships of their proteins. Our results
 demonstrate that the rice XYLP gene family may play roles in plant
 vascular system development and hormone signaling. Among the 21 detected
 OsXYLPs, 19 are newly identified genes encoding arabinogalactan proteins.
 Our results provide comprehensive insights that will assist future
 research on the biological functions of the rice XYLP gene family.
description: Phylogenetic
 relationship of XYLP between rice and Arabidopsis.The unrooted
 phylogenetic tree of 21 OsXYLP and 13 AtXYLP proteins. Four clades of
 XYLPs are show on different color backgrounds. Scale bar represent 0.1
 amino acid substitution per site.Figure
 2.jpgMultiple sequence
 alignments of the nsLTP domain of OsXYLPs and AtXYLPs.Identical (100%),
 conservative (75-99%) and block (50-74%) of similar amino acid residues
 are shaded in black, red and light blue, respectively.Figure
 S1.jpgProtein backbones of
 XYLPs in rice and Arabidopsis.Table
 S1.docProtein structure of
 rice XYLPs.Gray boxes indicate the
 secretory signal sequence predicted by SignalP. The violet boxes indicate
 predicted GPI-anchored signal. Dark red straights indicate
 glycoprotein-like Pro/Ala/Ser/Thr-rich regions (PAST&gt;35%). Light red
 circles with number indicate putative AG glycomodules and its number.
 Yellow and black boxes indicate nsLTP domains; black boxes indicate the
 eight conserved cysteine residues; the numbers in yellow boxes means the
 number of amino acid residues; the green boxes show the hydrophobic
 residues between C5 and C6.Figure 1
 .jpg
DOI: 10.5061/dryad.5kh00
title: Data from: Stepping in the direction of the fall: the next foot placement can be predicted from current upper body state in steady-state walking

description: During human walking, perturbations to the upper body can be partly
 corrected by placing the foot appropriately on the next step. Here, we
 infer aspects of such foot placement dynamics using step-to-step
 variability over hundreds of steps of steady-state walking data. In
 particular, we infer dependence of the ‘next’ foot position on upper body
 state at different phases during the ‘current’ step. We show that a linear
 function of the hip position and velocity state (approximating the body
 center of mass state) during mid-stance explains over 80% of the next
 lateral foot position variance, consistent with (but not proving) lateral
 stabilization using foot placement. This linear function implies that a
 rightward pelvic deviation during a left stance results in a larger step
 width and smaller step length than average on the next foot placement. The
 absolute position on the treadmill does not add significant information
 about the next foot relative to current stance foot over that already
 available in the pelvis position and velocity. Such walking dynamics
 inference with steady-state data may allow diagnostics of stability and
 inform biomimetic exoskeleton or robot design.
description: Human treadmill walking
 position data, 3 markersCompressed file contains
 text files with human walking position data for 3 markers, 10 subjects, 3
 trials. See readme.txt and original article for more
 details.WangSrinivasanBiologyLetters_DryadDataUpload.zip
DOI: 10.5061/dryad.977k6
title: Data from: Synechococcus: 3 billion years of global dominance

description: Cyanobacteria are amongst the most important primary producers on the
 Earth. However, the evolutionary forces driving cyanobacterial species
 diversity remain largely enigmatic due to both their distinction from
 macroorganisms, and an undersampling of sequenced genomes. Thus, we
 present a new genome of a Synechococcus-like cyanobacterium from a novel
 evolutionary lineage. Further, we analyse all existing 16S rRNA sequences
 and genomes of Synechococcus-like cyanobacteria. Chronograms showed
 extremely polyphyletic relationships in Synechococcus, which has not been
 observed in any other cyanobacteria. Moreover, most Synechococcus lineages
 bifurcated after the Great Oxidation Event, including the most abundant
 marine picoplankton lineage. Quantification of horizontal gene transfer
 among 70 cyanobacterial genomes revealed significant differences among
 studied genomes. Horizontal gene transfer levels were not correlated with
 ecology, genome size, or phenotype, but were correlated with the age of
 divergence. All findings were synthetized into a novel model of
 cyanobacterial evolution, characterized by serial convergence of the
 features, i.e. multicellularity and ecology.
description: Multiple sequence
 alignment for phylogenomic analysisProtein Multiple
 sequence alignment recovered from Bio-Hal for phylogenetic analysis in
 Phylip format. There are 70 taxa and more than 46000
 positions.Biohal2.phyPhylogenetic tree based on protein super alignmentPhylogenetic tree based on protein super alignment constructed in RaxML 8.0. Abbrevations of OTUs are explained in ReadMe file.raxmlTreeDryad.treMultiple sequence alignment of 16S rRNAMultiple sequence alignment of 16S rRNA of diverse cyanobacteria with focus on Synechococcus.allsynech19.nex16S rRNA phylogenetic treeA phylogenetic tree constructed using MrBayes 3.2.216SalignDryad.nex
DOI: 10.21223/p3/ekoyz1
title: Dataset for: Heritability for yield components in LBHT potato clones, under warm conditions

description: In anticipation of the effects of global warming on potato cultivation in both tropical and subtropical environments. Since 2004, efforts have turned to the development of a new group in Population B with improved adaptation to warm environments, resistance to late blight and virus, mid-season maturity (90 day growing period under short day length conditions), adaptation to mid elevations, low glycoalkaloids content, along with economically important traits such as high tuber yield, quality for table and industry, denominated LBHT (late blight, heat tolerance). In this context, in order to determine the narrow-sense heritability for yield components in the LBHT population, 32 clones were crossed at the Huancayo station in Peru in 2012 under greenhouse conditions using the North Carolina II mating design, The design was comprised of 4 sets, with 4 female and 4 male progenitors producing 16 full-sib progenies per set, for a total of 64 full-sib families. Tuber families of each progeny were generated in 2013 for evaluation under field conditions. And during 2014 –2015, the progenies were evaluated under field conditions, in three contrasting environments in Peru: San Ramon, La Molina, and Majes, where average temperatures at night were between 15.9 to 22.6ºC, and during the day fluctuated between 22.9 to 27.5ºC. The randomized complete block (RCB) design was used, with 4 sets and 3 replications of 50 genotypes per progeny.
DOI: 10.5061/dryad.pp43m
title: Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation

description: A species’ genetic diversity bears the marks of evolutionary processes
 that have occurred throughout its history. However, robust detection of
 selection in wild populations is difficult and often impeded by lack of
 replicate tests. Here, we investigate selection in pink salmon
 (Oncorhynchus gorbuscha) using genome scans coupled with inference from a
 haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous
 life history which has resulted in temporally isolated (allochronic)
 lineages that remain sympatric through sharing of spawning habitats in
 alternate years. The lineages differ in a range of adaptive traits,
 suggesting different genetic backgrounds. We used genotyping by sequencing
 of haploids to generate a high-density linkage map with 7035 loci and
 screened an existing panel of 8036 loci for signatures of selection. The
 linkage map enabled identification of novel genomic regions displaying
 signatures of parallel selection shared between lineages. Furthermore, 24
 loci demonstrated divergent selection and differences in genetic diversity
 between lineages, suggesting that adaptation in the 2 lineages has arisen
 from different pools of standing genetic variation. Findings have
 implications for understanding asynchronous population abundances as well
 as predicting future ecosystem impacts from lineage-specific responses to
 climate change.
description: Haploid genotypes for
 two pink salmon mapping families X01 and X05This file includes the
 raw haploid genotypes for each of two mapping families (X01 and X05) in
 the respective R/qtl input format. These genotypes represent the raw
 output from STACKS (see associated paper) and thus includes loci that were
 subsequently discarded during the mapping analyses.
DOI: 10.5061/dryad.7cj77
title: Data from: Approximate Bayesian computation reveals the crucial role of oceanic islands for the assembly of continental biodiversity

description: The perceived low levels of genetic diversity, poor interspecific
 competitive and defensive ability, and loss of dispersal capacities of
 insular lineages have driven the view that oceanic islands are
 evolutionary dead ends. Focusing on the Atlantic bryophyte flora
 distributed across the archipelagos of the Azores, Madeira, the Canary
 Islands, Western Europe, and northwestern Africa, we used an integrative
 approach with species distribution modeling and population genetic
 analyses based on approximate Bayesian computation to determine whether
 this view applies to organisms with inherent high dispersal capacities.
 Genetic diversity was found to be higher in island than in continental
 populations, contributing to mounting evidence that, contrary to
 theoretical expectations, island populations are not necessarily
 genetically depauperate. Patterns of genetic variation among island and
 continental populations consistently fitted those simulated under a
 scenario of de novo foundation of continental populations from insular
 ancestors better than those expected if islands would represent a sink or
 a refugium of continental biodiversity. We, suggest that the northeastern
 Atlantic archipelagos have played a key role as a stepping stone for
 transoceanic migrants. Our results challenge the traditional notion that
 oceanic islands are the end of the colonization road and illustrate the
 significant role of oceanic islands as reservoirs of novel biodiversity
 for the assembly of continental floras.
description: SupplementaryInformation_USYB-2014-217_R2Supplementary material includes TABLES S1 to S6 and FIGURES S1 to S3Dataset1_USYB-2014-217_R2DATASET S1. Voucher information (a), including the code sample, geographic coordinates and the geographic origin, and GenBank accession numbers (b) and for each specimen analyzed. A total of 1925 cpDNA and 465 nrDNA sequences were produced for an overall of 649 specimens analyzed. A dash in a given locus column indicates that the sequencing failed; an empty cell indicates that that particular locus was not used for a given species
DOI: 10.5061/dryad.q72q4
title: Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds

description: Although phylogenetic diversity has been suggested to be relevant from a
 conservation point of view, its role is still limited in applied nature
 conservation. Recently, the practice of investing conservation resources
 based on threatened species was identified as a reason for the slow
 integration of phylogenetic diversity in nature conservation planning. One
 of the main arguments is based on the observation that threatened species
 are not evenly distributed over the phylogenetic tree. However this
 argument seems to dismiss the fact that conservation action is a spatially
 explicit process, and even if threatened species are not evenly
 distributed over the phylogenetic tree, the occurrence of threatened
 species could still indicate areas with above average phylogenetic
 diversity and consequently could protect phylogenetic diversity. Here we
 aim to study the selection of important bird areas in Central Asia, which
 were nominated largely based on the presence of threatened bird species.
 We show that although threatened species occurring in Central Asia do not
 capture phylogenetically more distinct species than expected by chance,
 the current spatially explicit conservation approach of selecting
 important bird areas covers above average taxonomic and phylogenetic
 diversity of breeding and wintering birds. We conclude that the spatially
 explicit processes of conservation actions need to be considered in the
 current discussion of whether new prioritization methods are needed to
 complement conservation action based on threatened species.
description: bird-diversity-dataThe file contains four different measures of bird diversity for each grid cell of the study area calculated for breeding and wintering distributions separately: 1) the total number of species (i.e. taxonomic richness), 2) the number of IUCN red list species, 3) phylogenetic richness calculated as the sum of branch lengths between root and tips for the species in a community, 4) phylogenetic distinctiveness calculated as the sum of all branch lengths connecting two species averaged across all species in a community. See also the ReadMe file.
DOI: 10.5061/dryad.7kr08
title: Data from: Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus, Gekkota)

description: The region between the Asian and Australian continental plates (Wallacea)
 demarcates the transition between two differentiated regional biotas.
 Despite this striking pattern, some terrestrial lineages have successfully
 traversed the marine barriers of Wallacea and subsequently diversified in
 newly colonized regions. The hypothesis that these dispersals between
 biogeographic realms are correlated with detectable shifts in evolutionary
 trajectory has however rarely been tested. Here, we analyse the evolution
 of body size in a widespread and exceptionally diverse group of gekkotan
 lizards (Cyrtodactylus), and show that a clade that has dispersed
 eastwards and radiated in the Australopapuan region appears to have
 significantly expanded its body size ‘envelope’ and repeatedly evolved
 gigantism. This pattern suggests that the biotic composition of the
 proto-Papuan Archipelago provided a permissive environment in which new
 colonists were released from evolutionary constraints operating to the
 west of Wallacea.
description: SI1_Cyrt_PLSSummary methods and dataSI2_Cyrt3p_ML_str_cals_mrbMrBayes Input fileSI3_Cyrt3part4cal_ucln_sizeBEAST input fileSI4_CyrtBEASTMCCtreeBEAST tree
DOI: 10.5061/dryad.c47vc
title: Data from: Roses are red, violets are blue - so how much replication should you do? An assessment of variation in the colour of flowers and birds

description: After years of qualitative and subjective study, quantitative colour
 science is now enabling rapid measurement, analysis and comparison of
 colour traits. However, it has not been determined how many replicates one
 needs to accurately quantify a species' colours for studies aimed at
 broad cross-species trait comparison. We address this major methodological
 knowledge gap. We first quantified and assessed the variance in colour
 within and between species. Reflectance spectra of flowers from ten plant
 species and plumage of 20 bird species were measured using a spectrometer,
 and reflectance (i.e. brightness) and tetrahedral colour-space coordinates
 were calculated. analysis of variance (ANOVA) analyses indicate that there
 is far more variation in the colours of birds and flowers between species
 (&gt; 77%) than within species. A Mean Absolute Deviation from the
 Mean test was applied to indicate the sampling replication required for
 each species. Tetrahedral coordinates were sampled precisely with only one
 individual per species. Greater replication was needed to sample
 reflectance with the desired precision, particularly for darker coloured
 species. Our findings will allow researchers to allocate their sampling
 effort in a way that maximises the precision of their colour data
 collection. The fact that only a few replicates per species are necessary
 will greatly facilitate broad cross-species comparisons of colour in the
 future.
description: Dalrymple et al. BJLS.
 dataReflectance spectra and
 colouration summary statistics
DOI: 10.5061/dryad.cc5kn
title: Data from: Mitochondrial genomes of domestic animals need scrutiny

description: More than 1000 complete or near-complete mitochondrial DNA (mtDNA)
 sequences have been deposited in GenBank for eight common domestic animals
 (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close
 wild ancestors or relatives, as well. Nevertheless, few efforts have been
 performed to evaluate the sequence data quality. Herein, we conducted a
 phylogenetic survey of these complete or near-complete mtDNA sequences
 based on mtDNA haplogroup trees for the eight animals. We show that errors
 due to artificial recombination, surplus of mutations, and phantom
 mutations, do exist in 14.5% (194/1342) of mtDNA sequences and all of them
 should be treated with wide caution. We propose some caveats for future
 mtDNA studies of domestic animals.
description: pairwise alignments of
 mtDNAs of domestic animalspairwise_alignment.zip
DOI: 10.5878/mwpw-jv86
title: The Gothenburg SOM Survey 2019
title: SOM-undersökningen i Göteborg 2019
title: Gbg-SOM 2019

description: In the autumn of 2019, the fourth edition of the Gothenburg SOM survey was conducted. A total of 5000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.
description: Hösten 2019 genomfördes för fjärde gången en SOM-undersökning i Göteborgs stad, där totalt 5000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.
DOI: 10.5061/dryad.175cv
title: Data from: High-resolution forest mapping for behavioural studies in the nature reserve ‘Les Nouragues’, French Guiana

description: For animals with spatially complex behaviours at relatively small scales,
 the resolution of a global positioning system (GPS) receiver location is
 often below the resolution needed to correctly map animals’ spatial
 behaviour. Natural conditions such as canopy cover, canyons or clouds can
 further degrade GPS receiver reception. Here we present a detailed,
 high-resolution map of a 4.6 ha Neotropical river island and a 8.3 ha
 mainland plot with the location of every tree &gt;5 cm DBH and all
 structures on the forest floor, which are relevant to our study species,
 the territorial frog Allobates femoralis (Dendrobatidae). The map was
 derived using distance- and compass-based survey techniques, rooted on
 dGPS reference points, and incorporates altitudinal information based on a
 LiDAR survey of the area.
description: Map
 ParareThis ZIP-file contains
 all data shapefiles as well as ArcGIS 9.3 & 10 MXD-files and the
 ArcPAD APM-file that were used to create the maps from this
 publication.
DOI: 10.5878/rsnk-c867
title: The Gothenburg SOM Survey 2019
title: SOM-undersökningen i Göteborg 2019
title: Gbg-SOM 2019

description: In the autumn of 2019, the fourth edition of the Gothenburg SOM survey was conducted. A total of 5000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.
description: Hösten 2019 genomfördes för fjärde gången en SOM-undersökning i Göteborgs stad, där totalt 5000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.