cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r2t49
title: Data from: Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

description: Although the role of lateral gene transfer is well recognized in the
 evolution of bacteria, it is generally assumed that it has had less
 influence among eukaryotes. To explore this hypothesis, we compare the
 dynamics of genome evolution in two groups of organisms: cyanobacteria and
 fungi. Ancestral genomes are inferred in both clades using two types of
 methods: first, Count, a gene tree unaware method that models gene
 duplications, gains and losses to explain the observed numbers of genes
 present in a genome; second, ALE, a more recent gene tree-aware method
 that reconciles gene trees with a species tree using a model of gene
 duplication, loss and transfer. We compare their merits and their ability
 to quantify the role of transfers, and assess the impact of taxonomic
 sampling on their inferences. We present what we believe is compelling
 evidence that gene transfer plays a significant role in the evolution of
 fungi.
description: Tree A
 concatenateFasta files, alignments
 and Gblock output for the concatenate used to create the Tree
 A.TreeAConcatenate.zipCountSessionsCount sessions for FungiTree A, FungiTree B and CyanobacteriaALEFungi.tarALE files for fungi familiesALEcyano.tarALE files for cyanobacteriaSpecies TreeSpecies Tree for Cyano, Fungi Tree A and Fungi Tree B, with branch lengths estimated using PhyML LG08 + Gammaspeciestrees.zip
DOI: 10.5061/dryad.615p248
title: Data from: Quantifying how constraints limit the diversity of viable routes to adaptation

description: Convergent adaptation can occur at the genome scale when independently
 evolving lineages use the same genes to respond to similar selection
 pressures. These patterns provide insights into the factors that
 facilitate or constrain the diversity of genetic responses that contribute
 to adaptive evolution. A first step in studying such factors is to
 quantify the observed amount of repeatability relative to expectations
 under a null hypothesis. Here, we formulate a novel metric to quantify the
 constraints driving the observed amount of repeated adaptation in pairwise
 contrasts based on the hypergeometric distribution, and then generalize
 this for simultaneous analysis of multiple lineages. This metric is
 explicitly based on the probability of observing a given amount of
 repeatability by chance under an arbitrary null hypothesis, and is readily
 compared among different species and types of trait. We also formulate a
 metric to quantify the effective proportion of genes in the genome that
 have the potential to contribute to adaptation. As an example of how these
 metrics can be used to draw inferences, we assess the amount of
 repeatability observed in existing datasets on adaptation to antibiotics
 in yeast and climate in conifers. This approach provides a method to test
 a wide range of hypotheses about how different kinds of factors can
 facilitate or constrain the diversity of genetic responses observed during
 adaptive evolution.
description: Data and
 scriptsThis file includes the
 data and scripts necessary to generate all results in the
 manuscript.convergence_archive_dryad.zip
DOI: 10.5061/dryad.hf46s
title: Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

description: Selective breeding of dogs has resulted in repeated artificial selection
 on breed-specific morphological phenotypes. A number of quantitative trait
 loci associated with these phenotypes have been identified in genetic
 mapping studies. We analyzed the population genomic signatures observed
 around the causal mutations for 12 of these loci in 25 dog breeds, for
 which we genotyped 25 individuals in each breed. By measuring the
 population frequencies of the causal mutations in each breed, we
 identified those breeds in which specific mutations most likely
 experienced positive selection. These instances were then used as positive
 controls for assessing the performance of popular statistics to detect
 selection from population genomic data. We found that artificial selection
 during dog domestication has left characteristic signatures in the
 haplotype and nucleotide polymorphism patterns around selected loci that
 can be detected in the genotype data from a single population sample.
 However, the sensitivity and accuracy at which such signatures were
 detected varied widely between loci, the particular statistic used, and
 the choice of analysis parameters. We observed examples of both hard and
 soft selective sweeps and detected strong selective events that removed
 genetic diversity almost entirely over regions &gt;10 Mbp. Our study
 demonstrates the power and limitations of selection scans in populations
 with high levels of linkage disequilibrium due to severe founder effects
 and recent population bottlenecks.
description: Raw Genotyping
 DataData from: Shannon et
 al. (2015) Genetic structure in village dogs reveals a Central Asian
 domestication origin. Dryad Digital Repository.
 http://dx.doi.org/10.5061/dryad.v9t5hImputed Data
 (.tfam)chr_1_to_38.imputed.tfamImputed Data (.tped)chr_1_to_38.imputed.tpedHapFLK ResultsHapFLK genome-wide results, chromosomes 1 to 38chr_1_to_38.hapflkiHS ResultsNormalized iHS results for chromosomes 1, 3, 4, 5, 10, 11, 15, 27, and 32iHS_results.zipnSL ResultsNormalized nSL results for chromosomes 1, 3, 4, 5, 10, 11, 15, 27, and 32nSL_results.zipH ResultsH results for chromosomes 1, 3, 4, 5, 10, 11, 15, 27, and 32H_results.zippi, Tajima's D, and H12 Resultspi, Tajima's D, and H12 results for chromosomes 1, 3, 4, 5, 10, 11, 15, 27, and 32, for window sizes of 25, 51, 101, and 201Window_Scans_results.zipCLR ResultsCLR results for chromosomes 1, 3, 4, 5, 10, 11, 15, 27, and 32CLR_results.zipSamples Identifier FileList of all samples used, with their sample codes and breedsamples.txt
DOI: 10.5061/dryad.t51fm80
title: Data from: Forest loss in protected areas and intact forest landscapes: a global analysis

description: In spite of the high importance of forests, global forest loss has
 remained alarmingly high during the last decades. Forest loss at a global
 scale has been unveiled with increasingly finer spatial resolution, but
 the forest extent and loss in protected areas (PAs) and in large intact
 forest landscapes (IFLs) have not so far been systematically assessed.
 Moreover, the impact of protection on preserving the IFLs is not well
 understood. In this study we conducted a consistent assessment of the
 global forest loss in PAs and IFLs over the period 2000–2012. We used
 recently published global remote sensing based spatial forest cover change
 data, being a uniform and consistent dataset over space and time, together
 with global datasets on PAs’ and IFLs’ locations. Our analyses revealed
 that on a global scale 3% of the protected forest, 2.5% of the intact
 forest, and 1.5% of the protected intact forest were lost during the study
 period. These forest loss rates are relatively high compared to global
 total forest loss of 5% for the same time period. The variation in forest
 losses and in protection effect was large among geographical regions and
 countries. In some regions the loss in protected forests exceeded 5% (e.g.
 in Australia and Oceania, and North America) and the relative forest loss
 was higher inside protected areas than outside those areas (e.g. in
 Mongolia and parts of Africa, Central Asia, and Europe). At the same time,
 protection was found to prevent forest loss in several countries (e.g. in
 South America and Southeast Asia). Globally, high area-weighted forest
 loss rates of protected and intact forests were associated with high gross
 domestic product and in the case of protected forests also with high
 proportions of agricultural land. Our findings reinforce the need for
 improved understanding of the reasons for the high forest losses in PAs
 and IFLs and strategies to prevent further losses.
description: Global forest
 dataGlobal forest extent
 (year 2000) and loss (total of years 2000-2012) data at 30 arc-second
 resolution from the research article ‘Forest Loss in Protected Areas and
 Intact Forest Landscapes: A Global Analysis’, which includes a full
 description of the data creation process. The here provided data are
 derived from data published in the study ‘High-Resolution Global Maps of
 21st-Century Forest Cover’.
DOI: 10.5061/dryad.mn686
title: Data from: Examining the business case and models for sustainable multifunctional edible landscaping enterprises in the Phoenix Metro Area

description: This study assesses whether multifunctional edible landscaping business
 models provide a sufficient business case at enterprise and city scales to
 justify widespread implementation. First, semi-structured interviews were
 conducted with four landscaping entrepreneurs, and the information
 obtained from the interviews was utilized to carry out a business model
 comparison with the Business Model Canvas framework. The comparison showed
 that the landscaping enterprises using multifunctional edible landscaping
 methods possessed a greater range of value propositions and revenue
 streams, enhancing their competitive advantage. Second, a GIS landscape
 analysis of seven Phoenix metro area cities was carried out to identify
 landscapes that were suited for becoming multifunctional edible
 landscapes. The GIS analysis identified single family residential,
 residential recreational open space, municipal parks, and municipal
 schools as being suitable landscapes, and that the area of these
 landscapes in the seven cities exceeded 180,000 acres. Third, scenarios
 were created using interview and GIS data to estimate potential value
 creation and return on investment of implementing multifunctional edible
 landscaping in the cities of interest. The scenarios found that the
 potential value creation of edible landscaping ranged between $3.9 and $66
 billion, and that positive return on investment (ROI) could be achieved in
 11 out of 12 scenarios within one to five years. Finally, the paper
 concludes by discussing potential long-term implications of implementing
 multifunctional edible urban landscaping, as well as possible future
 directions for multifunctional landscaping business model development and
 research.
description: GIS and Scenario
 dataContains GIS shape and
 mxd files used for 7 Arizona Maricopa County cities (Phoenix, Scottsdale,
 Tempe, Mesa, Glendale, Chandler, and Gilbert) landscape distribution maps
 and landscape area calculations. Also contains a powerpoint file with
 value creation and ROI scenario figures with accompanying calculation
 spreadsheet data embedded.
DOI: 10.5061/dryad.308g1h54
title: Data from: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the
 salamanders, a clade of amphibians that includes 613 species. Salamander
 genome sizes range from ∼14 Gb to ∼120 Gb. Because genome size is
 correlated with nucleus and cell sizes, as well as other traits,
 morphological evolution in salamanders has been profoundly affected by
 genomic gigantism. However, the molecular mechanisms driving genomic
 expansion in this clade remain largely unknown. Here, we present the first
 comparative analysis of transposable element (TE) content in salamanders.
 Using high-throughput sequencing, we generated genomic shotgun data for
 six species from the Plethodontidae, the largest family of salamanders. We
 then developed a pipeline to mine TE sequences from shotgun data in taxa
 with limited genomic resources, such as salamanders. Our summaries of
 overall TE abundance and diversity for each species demonstrate that TEs
 make up a substantial portion of salamander genomes, and that all of the
 major known types of TEs are represented in salamanders. The most abundant
 TE superfamilies found in the genomes of our six focal species are
 similar, despite substantial variation in genome size. However, our
 results demonstrate a major difference between salamanders and other
 vertebrates: salamander genomes contain much larger amounts of LTR
 retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase
 in genome size that occurred in salamanders was likely accompanied by a
 shift in TE landscape. These results suggest that increased proliferation
 of LTR retrotransposons was a major molecular mechanism contributing to
 genomic expansion in salamanders.
description: Plethodontid salamanders
 shotgun readsThe uploaded zip file
 contains the 454 shotgun reads (in fasta format) for six species of
 plethodontid salamanders: Aneides flavipunctatus, Batrachoseps
 nigriventris, Bolitoglossa occidentalis, Bolitoglossa rostrata,
 Desmognathus ochrophaeus, and Eurycea tynerensis.
DOI: 10.5061/dryad.4sr5b16
title: Data from: Arena size modulates functional responses via behavioral mechanisms

description: Laboratory-based functional response experiments, in which foraging rates
 are measured across a range of resource densities, are central for
 determining trophic interaction strength. Historically these experiments
 often are performed in arbitrarily sized arenas, with larger sized
 organisms generally used in larger arenas. However, arena size influences
 foraging rates and therefore also estimates of the functional response
 parameters, particularly space clearance rate (attack rate). We
 hypothesized that non-random movement within arenas by predators and prey
 may explain this effect. To test this hypothesis, we video-recorded
 Schizocosa ocreata wolf spiders (predators) and flightless Drosophila
 melanogaster prey in circular arenas of three different sizes to reveal
 thigmotactic behavior. We then estimated foraging rates and space
 clearance rates from feeding trials performed at a single, low prey
 density in three differently-size arenas in either annular (ring-shaped)
 or circular arenas. Annular arenas mitigated the effects of predator and
 prey aggregation and thus controlled the experienced prey density near
 arena edges. Unlike the circular arenas, annular arenas produced similar
 foraging rates and space clearance rate estimates across arena sizes,
 confirming that it is the increased density of prey along edges that
 generates the previously observed arena size effect. Our results provide a
 key insight into how animal behavior and experimental design must be
 considered for the accurate interpretation of foraging rates, both when
 considering standalone functional responses and when making comparisons
 across experiments.
description: Spider
 ForagingResults from foraging
 trials in two types of arenas (circular and annular).SpiderForaging.xlsxSpider TrackingMovement data of spiders in circular arenas of three sizes, divided into three sheets (tabs). Trial number is given in column A. Spider's location is given in columns B and C. Conversion from pixels to millimeters is given in column D. Location of arena center is given in pixels in columns E and F. Radius of the arena is given in pixels in column G.SpiderTracking.xlsxFlyTrackingFly movement in circular arenas, presented in matlab data files obtained via ctrax. Data files are labeled with a letter to indicate arena size (S, M, or L) and a number to indicate trial number. X and Y are fly positions in pixels. Note that associated arena centers, radii, and correct pixel to milllimeter conversions are given in Fly Tracking Arena Data.Fly Tracking Arena DataArena data associated with the Fly Tracking data. Arena size is given in column A. Replicate number is given in column B. Arena center in pixels is given in columns C and D. Arena radius is given in pixels in column E. Conversion from pixels to millimeters is given in column F.FlyTrackingArenaData.xlsx
DOI: 10.5061/dryad.s57d6
title: Data from: Distribution and functionality of copy number variation across European cattle populations

description: Copy number variation (CNV), which is characterized by large-scale losses
 or gains of DNA fragments, contributes significantly to genetic and
 phenotypic variation. Assessing CNV across different European cattle
 populations might reveal genetic changes responsible for phenotypic
 differences, which have accumulated throughout the domestication history
 of cattle as consequences of evolutionary forces that act upon them. To
 explore pattern of CNVs across European cattle, we genotyped 149
 individuals, that represent different European regions, using the Illumina
 Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were
 identified in 149 samples using a Hidden Markov Model (HMM) as employed in
 PennCNV. Animals originating from several breeds of British Isles, and
 Balkan and Italian regions, on average, displayed higher abundance of CNV
 counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs)
 were identified by aggregating CNVs overlapping in at least two animals.
 The hierarchical clustering of CNVRs indicated low differentiation and
 sharing of high-frequency CNVRs between European cattle populations.
 Various CNVRs identified in the present study overlapped with olfactory
 receptor genes and genes related to immune system. In addition, we also
 detected a CNV overlapping the Kit gene in English longhorn cattle which
 has previously been associated with color-sidedness. To conclude, we
 provide a comprehensive overview of CNV distribution in genome of European
 cattle. Our results indicate an important role of purifying selection and
 genomic drift in shaping CNV diversity that exists between different
 European cattle populations.
description: cow_lrr_filesThe “cow_lrr_files.zip” contains total signal intensity (LRR) and B allele frequency signal (BAF) data of 100 cattle samples (100 sample text files). The zip folder also includes “snp_list.txt” file which contains the information about SNP id, chromosome id and Base-pair position. Please note that the markers’ order in “snp_list.txt” file align with the order of these markers in a sample text file. For example, the first row of a sample text file displays LRR and BAF value of the first marker in “snp_list.txt” file.
DOI: 10.5061/dryad.km140
title: Data from: Distinct roles of visual, parietal, and frontal motor cortices in memory-guided sensorimotor decisions

description: Mapping specific sensory features to future motor actions is a crucial
 capability of mammalian nervous systems. We investigated the role of
 visual (V1), posterior parietal (PPC), and frontal motor (fMC) cortices
 for sensorimotor mapping in mice during performance of a memory-guided
 visual discrimination task. Large-scale calcium imaging revealed that V1,
 PPC, and fMC neurons exhibited heterogeneous responses spanning all task
 epochs (stimulus, delay, response). Population analyses demonstrated
 unique encoding of stimulus identity and behavioral choice information
 across regions, with V1 encoding stimulus, fMC encoding choice even early
 in the trial, and PPC multiplexing the two variables. Optogenetic
 inhibition during behavior revealed that all regions were necessary during
 the stimulus epoch, but only fMC was required during the delay and
 response epochs. Stimulus identity can thus be rapidly transformed into
 behavioral choice, requiring V1, PPC, and fMC during the transformation
 period, but only fMC for maintaining the choice in memory prior to
 execution.
description: Calcium imaging data
 from V1, PPC, and fMC during visual delayed response
 taskGoard_DFF_data.zip
DOI: 10.5061/dryad.dq91858
title: Data from: Genetic analysis of sugarcane mosaic virus resistance in the Wisconsin Diversity Panel of maize

description: Sugarcane mosaic virus (SCMV) and Maize dwarf mosaic virus can cause yield
 loss in maize (Zea mays L.). Previous studies identified two key genomic
 regions controlling host resistance: Scmv1 on chromosome 6 and Scmv2 on
 chromosome 3. In this study a diverse set of 578 inbreds adapted to a
 northern US Corn Belt environment, was inoculated at the three-leaf stage
 with SCMV and rated for presence of virus symptoms at 7, 10, 14, 21, 28,
 and 35 d after inoculation. Scmv1 was present in all resistant inbreds. A
 single-nucleotide polymorphism associated with SCMV resistance was found 5
 Mb downstream of the putative location of Scmv1, and resistance at this
 downstream locus was correlated with a group of inbreds containing the
 presence allele of a 2.7-Mb presence–absence variation (PAV) in the region
 encompassing Scmv1. The Scmv2 region was associated with resistance 35 d
 after inoculation only among the inbreds containing the presence allele,
 including Scmv1. Several other loci unlinked to Scmv1 and Scmv2 were
 associated with resistance in this panel, providing evidence for
 multigenic modification of the efficacy of Scmv1 and Scmv2. Sixty-nine
 inbreds representing haplotype variation in the region surrounding Scmv1
 on chromosome 6 were inoculated with SCMV at the three- and six-leaf
 stage. Symptom development was reduced when inoculation was delayed to the
 six-leaf stage, but 24 inbreds became fully symptomatic after 35 d
 regardless of the growth stage at inoculation. Inbreds with the presence
 allele of the PAV encompassing Scmv1 were more resistant to SCMV when
 inoculation was delayed to the six-leaf stage than those that had the
 absence allele. Inbreds with the absence allele were susceptible
 regardless of growth stage at inoculation.
description: WIDIVv2_596g_436576SNPs_imputed_hapmapImputed SNP RNA-seq data for 596 individuals from the Wisconsing Diversity Panel in hapmap format
DOI: 10.5061/dryad.3344d
title: Data from: Archaeogenomic evidence reveals prehistoric matrilineal dynasty

description: For societies with writing systems, hereditary leadership is documented as
 one of the hallmarks of early political complexity and governance. In
 contrast, it is unknown whether hereditary succession played a role in the
 early formation of prehistoric complex societies that lacked writing. Here
 we use an archaeogenomic approach to identify an elite matriline that
 persisted between 800 and 1130 CE in Chaco Canyon, the centre of an
 expansive prehistoric complex society in the Southwestern United States.
 We show that nine individuals buried in an elite crypt at Pueblo Bonito,
 the largest structure in the canyon, have identical mitochondrial genomes.
 Analyses of nuclear genome data from six samples with the highest DNA
 preservation demonstrate mother–daughter and grandmother–grandson
 relationships, evidence for a multigenerational matrilineal descent group.
 Together, these results demonstrate the persistence of an elite matriline
 in Chaco for ∼330 years.
description: Kennett_et_al_NCOMMS_PuebloBonito_Room33.tarComplete ancient mitogenomes from Room 33 in Pueblo Bonito, New Mexico, USA. MYcroarray MYbaits system references used in probe design: 140429. Supplemental data 2 aligned using MAFFT.Kennett_et_al_2016_NCOMMS_Dryad_3344d_Kennett_et_al_2016_supplementary_bam_files.xlsx