cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.04qh2/1
title: Zero_Day_Old_Otolith_Data

description: This data was collected in the lab from photos of otoliths taken with Leica Aquire software.  The measurements were calculated with ImageJ software. This file includes data for Standard Length analysis when otolith rings were unreadable.
DOI: 10.5061/dryad.04qh2/2
title: SL_Zero_Day_Old_Otolith_Data

description: This data was collected in the lab from photos of otoliths taken with Leica Aquire software.  The measurements were calculated with ImageJ software.
DOI: 10.5061/dryad.04qh2/3
title: Behavioural_Data

description: This data includes otolith (collected in the lab) and behavioral (collected in the field) data.  Photos of otoliths taken with Leica Aquire software and otolith measurements were calculated with ImageJ software.
DOI: 10.5061/dryad.4mp30/1
title: Summarised family-level data

description: Family-level averages for diversification and climatic niche variables.
DOI: 10.5061/dryad.4mp30/2
title: Summarised genus-level data

description: Genus-level averages for diversification, climatic niche and ecological variables.
DOI: 10.5061/dryad.5b5v4/3
title: von_Ronn_SWALLOW_mig

description: Bayescan files containing the unfiltered SNPs called from the STACKs pipeline used in the outlier analyses - both location and migration groupings are provided.
DOI: 10.5061/dryad.5b5v4/4
title: msats_raw

description: microsatellite genotypes
DOI: 10.5061/dryad.5b5v4/5
title: direct_assort_mate

description: carbon and nitrogen stable isotope values of breeding pairs
DOI: 10.5061/dryad.5b5v4/6
title: cmr_data

description: cmr data used to measure and visualize selection on wing length
DOI: 10.5061/dryad.5b5v4/7
title: sia_data

description: inidvidual carbon and nitrogen stable isotope values
DOI: 10.5061/dryad.5b5v4/8
title: morph_data

description: morphological data
DOI: 10.5061/dryad.5p0n3/1
title: Project33rdBEAST_wfossils copy

description: Bayesian chronogram estimation results
DOI: 10.5061/dryad.5p0n3/2
title: Project33rdGarli copy

description: Maximum likelihood analysis results
DOI: 10.5061/dryad.5p0n3/3
title: Project33rdMrB copy

description: Bayesian analysis results
DOI: 10.5061/dryad.664cp/1
title: Figure2.bayes.concat
DOI: 10.5061/dryad.664cp/2
title: Figure2.ML.concat
DOI: 10.5061/dryad.664cp/3
title: Figure3.UROD
DOI: 10.5061/dryad.664cp/4
title: Figure4.ALAS
DOI: 10.5061/dryad.664cp/5
title: Figure5.ALAD
DOI: 10.5061/dryad.698s5/1
title: RNA in situ hybridization of SAD2-clade desaturases in Ophrys flowers.

description: Additional data for Figure S1: RNA in situ hybridization of SAD2-clade desaturases (SAD1 and SAD2) in Ophrys flowers. (A) Overview illustration showing O. exaltata and O. sphegodes flowers from top and front along with the layout and direction of view of thin sections (starting at the base of the labellum on top toward the apex at the bottom). (B) Two thin sections of O. exaltata labellum, at 3 and 5 mm from the base (top) of the labellum. (C) From top to bottom, O. sphegodes labellum thin sections at 1, 3, 5, 7 and 10 mm from the base (top) of the labellum. The antisense panels show blackish signal in the epidermal layer of O. sphegodes that is clearly stronger than the brownish background signal observed in the sense controls. However, no such difference was observed between sense and antisense signals in O. exaltata epidermis. The difference between O. sphegodes and O. exaltata is consistent with previous gene expression analyses [1, 2] that show SAD2-clade genes to be highly expressed in mature O. sphegodes labellum, whereas expression in O. exaltata labellum was low. The higher level of SAD2 expression as compared to SAD1 expression in O. sphegodes [1, 2] suggests that ISH signal in panel (C) is primarily due to SAD2.References: 1. Xu et al. (2012). PLoS Genet. 8, e1002889.2. Schlüter et al. (2011). Proc. Natl. Acad. Sci. USA 108, 5696-5701.
DOI: 10.5061/dryad.8fb47/10
title: Tapajos-K67 Camera_Part 7 (2011 Jul-Sep)

description: The seventh part of k67 site near-surface camera data, which is used for deriving leaf phenology at k67 site.
DOI: 10.5061/dryad.8fb47/11
title: Tapajos-K67 Camera_Part 8 (2011 Oct-Dec)

description: The eighth part of k67 site near-surface camera data, which is used for deriving leaf phenology at k67 site.
DOI: 10.5061/dryad.8fb47/15
title: Leaf level age-dependent Vcmax at Tapajos-k67 site

description: Ground meaured leaf level age-dependent Vcmax at k67 site via leaf gas exchange measuremnets (by a handheld Licor 6400).
DOI: 10.5061/dryad.8fb47/17
title: Phenocam_K34

description: This is k34 near-surface camera image series, which is used for deriving leaf phenology at k34 site.
DOI: 10.5061/dryad.8fb47/19
title: Litterfall data at Manaus-k34 site

description: Ground based litterfall measurements conducted at k34 site at monthly interval.
DOI: 10.5061/dryad.8fb47/7
title: Tapajos-K67 Camera_Part 4 (2010 Oct-Dec)

description: The fourth part of k67 site near-surface camera data, which is used for deriving leaf phenology at k67 site.
DOI: 10.5061/dryad.8fb47/8
title: Tapajos-K67 Camera_Part 5 (2011 Jan-Mar)

description: The fifth part of k67 site near-surface camera data, which is used for deriving leaf phenology at k67 site.
DOI: 10.5061/dryad.8fb47/9
title: Tapajos-K67 Camera_Part 6 (2011 Apr-Jun)

description: The sixth part of k67 site near-surface camera data, which is used for deriving leaf phenology at k67 site.
DOI: 10.5061/dryad.b7cd6/1
title: Source code for simulations (Pascal/Delphi)

description: ZIP-archive contains 3 files: "emerge.pas" (source code), "parameters.txt" (text file with model parameters to be read by emerge.pas), "results.txt" (text file with results written by emerge.pas). For compiling and further instructions see the first lines in "emerge.pas".
DOI: 10.5061/dryad.g0874/1
title: genotyping_summaries

description: [4 files] Genotyping summaries (numbers of genotyped sites, heterozygosity etc.) for all samples. Summaries are provided for all sites, and also for codon positions 1, 2 and 3.
DOI: 10.5061/dryad.g0874/10
title: Codon Usage

description: Effective number of codons and GC content at the third codon position for each gene.
DOI: 10.5061/dryad.g0874/2
title: structure results

description: [4 files] Results from STRUCTURE analyses, with k = 5,6,7 and 8.
DOI: 10.5061/dryad.g0874/3
title: PCA results

description: Results of Eigenstrat PCA analysis.
DOI: 10.5061/dryad.g0874/6
title: dxy (absolute divergence) for 100kb windows

description: [8 files] Absolute divergence between all pairs of taxa for 100kb windows. Eight types of sites were considered: All sites, intergenic, intronic, codon positions 1, 2, and 3, 4D sites, and 4D sites in low-codon-usage-bias genes.
DOI: 10.5061/dryad.g0874/7
title: Heterozygosity in windows

description: [2 files] heterozygosity (here called "indPi") calculated for non-overlapping 100kb windows. One file corresponds to all samples and the other to two selected Panamanian samples: The inbred reference strain, and two outbred individuals.
DOI: 10.5061/dryad.g0874/9
title: Linkage Disequilibrium

description: [3 files] Linkage disequalibrium data for the Eastern and Western populations. "Background LD" refers to that between unlinked SNPs on different chromosomes. "top100" refers to LD calculated for all SNP pairs on the same scaffold, averaged over the top 100 scaffolds.
DOI: 10.5061/dryad.gd4dc/13
title: per-locus alignments

description: Alignments for 253 loci targeted by capture sequencing. Each file represents one locus, and can consist of alignments for a single or for multiple concatenated reference genome contigs (see manuscript). The files are named by these reference genome contigs. More details about each locus (ID in the original study; type of original study; outlier status) can be found in probes.csv. Each individual in the alignment has two pseudo-haplotypes (H1 and H2). Naming of individuals is in accordance with read files and Figure 1 in the manuscript.
DOI: 10.5061/dryad.gd4dc/14
title: list of capture sequencing probes

description: Table of 120bp probes used for capture sequencing. ref_contig = ID of targeted contig in L. saxatilis reference genome. start, end: start and end of probe sequence in the reference contig. study: study in which the targeted locus was first identified (EXP = gene expression study; RNA = RNAseq study; RAD = RADseq study; LSD = Littorina sequence database; for references please see main text, e.g. Table 1). type: outlier vs. control locus; SP, SW, UK: locus was outlier (1) or non-outlier (0) in earlier work Spain / Sweden / UK, respectively; probe: probe ID; original_locus: ID of targeted locus in the original work.
DOI: 10.5061/dryad.gd4dc/15
title: calculate_dxy

description: Python script using the EggLib library to calculate dxy between ecotypes for multiple loci and locations. Needs one fasta file per locus (containing aligned sequences from both ecotypes from multiple locations) and a text file with the names of the loci of interest.
DOI: 10.5061/dryad.gd4dc/16
title: calculate_pi

description: Python script using the EggLib library to calculate Pi for multiple loci and populations (one population = one ecotype within a location). Needs one fasta file per locus (containing aligned sequences from both ecotypes from multiple locations) and a text file with the names of the loci of interest.
DOI: 10.5061/dryad.gd4dc/17
title: calculate_Fst

description: R script to calculate Fst per locus and location from the output of calculate_pi.py and calculate_dxy.py.
DOI: 10.5061/dryad.gd4dc/18
title: likelihood_analysis

description: R script to calculate probabilities that outliers fall above the 80% quantile of the control Fst distribution in different locations, and to obtain log likelihoods and AICs for different models. Needs "quantile_table.txt" (a table of all loci indicating for each location whether they fall above the 80% quantile or not) as input.
DOI: 10.5061/dryad.gd4dc/19
title: quantile_table

description: Table indicating whether targeted loci showed an Fst estimate above the 80% quantile of the control distribution in the current study. locus = ID of outlier / control locus in original study. contig = location in the current L. saxatilis reference genome. SP / SW / UK = indication whether the locus was an outlier in Spain / Sweden / UK in the original work (0 = non-outlier; 1 = outlier). type = control vs. outlier locus in the original study. S / B / ANG / OCK / T / W = indication whether the locus fell above the 80% quantile of the control Fst distribution in the current work in the six studied locations (TRUE = above, FALSE = below).
DOI: 10.5061/dryad.hk400/1
title: Pollen Sites

description: List of pollen sites included in the analysis with their latitude and longitude.
DOI: 10.5061/dryad.hk400/2
title: Presence/Absence Pollen Data

description: Each .csv file has a presence/absence matrix for the 19 taxa of interest at all sites for every 500 years from 21000BP to 0BP.
DOI: 10.5061/dryad.k6t16/2
title: Müller et al. 2016 Journal of Ecology (2) seeds

description: Data for establishment from seeds collected in the field for Müller et al. 2016. Columns: site (codes for the respective site); plot (codes for the respective plot in site); fungicide (biocide treatment yes/no); disturbance (disturbance treatment yes/no); x (x position within plot); y (y position within plot); species (species name); name (alternative coding for species names); origin (alien /native); Commonness (common/rare); tk25 (number of grid cells occupied in Germany); Family (species family); seedlings (number of seedlings recorded in the field); sowing density (initial number of seeds sown in the field at the respectie position)
DOI: 10.5061/dryad.m27p0/1
title: Iles_Novak_2016_AmNat_ATN_Model_Simulation_Data

description: This is structured data file containing the ATN model simulation results described and analyzed in Iles & Novak 2016.The file contains a cell array for each of the 5790 network simulations performed in Matlab. Each cell array is named ‘ATN_#’, with the ‘#’ corresponding to the network number. Each cell array for each network contains 9 variables, including:    1. the network number: a unique number for each network (1 to 5790)    2. the species richness: the number of species in the simulation; a network level property    3. trophic connectance: the proportion of all possible direct feeding links (L) between species (S) that are realized from the feeding matrix, C = L/S2; a network level property    4. dynamical connectance: a measure of connectance that includes all effects as encapsulated by the non-zero elements of the Community matrix. These include not only consumer-resource effects, but also intraspecific effects, apparent mutualisms and competition between producers; a network level property    5. the feeding matrix: a matrix of 1s and 0s indicating which species feed on which other species defined by the niche model; an interaction level property    6. species trophic levels: a vector of a trophic level values (one for each species) is calculated from the feeding matrix based on methods of Levine 1960; a species level property    7. species body mass: a vector of randomly drawn body masses (one for each species) based on the species trophic level; a species level property)    8. maximum eigenvalue of the Community matrix: a measure of asymptotic stability with which we can exclude unstable networks from the analysis; a network level property    9. Community matrix: a matrix of direct species interaction strengths from which the net effects can be calculated and predictability can be evaluated; the pairwise partial derivatives of the ith species’ growth rate with respect to the biomass of species j (a.k.a. a Jacobian matrix), evaluated at equilibrium biomass densities; an interaction level property
DOI: 10.5061/dryad.nr60n/1
title: Host Resistance Survival by Treatment

description: This data represents the host resistance survival of Gryllus texnesis to the bacterial pathogen Serratia marcescens. All data was collected in the lab on lab-reared populations of Gryllus texensis as described in the methods section of the article. Column headings refer to the following: "RandomID" refers to the random alphanumerical ID assigned to each female subject to ensure a blind experiment. "Treatment" refers to the the one of four treatments each female was assigned to (courtship, copulation, accessory fluids, or intact ejaculate). "Mass" refers to the wet mass of the female on the day of maturity, used as a measure for size. "Pronotum" refers to the width of the pronotum of the female on the day on maturity, used as a measure for size. "DeathHour" refers to the 12-hour block in which the female was found dead.
DOI: 10.5061/dryad.s4h26/1
title: Simulation data on mobile pastoralists in northeastern Nigeria 1

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/2
title: Simulation data on mobile pastoralists in northeastern Nigeria 2

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/3
title: Simulation data on mobile pastoralists in northeastern Nigeria 3

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/4
title: Simulation data on mobile pastoralists in northeastern Nigeria 4

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/5
title: Simulation data on mobile pastoralists in northeastern Nigeria 5

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/6
title: Simulation data on mobile pastoralists in northeastern Nigeria 6

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/7
title: Simulation data on mobile pastoralists in northeastern Nigeria 7

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/8
title: Simulation data on mobile pastoralists in northeastern Nigeria 8

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/9
title: Simulation data on mobile pastoralists in northeastern Nigeria 9

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.3160r/1
title: Tab delimited file of data used in and described in the Patterson et al Challenges paper in Biodiversity Data Journal (2016)

description: Data produced as a result of mapping of GenBank and DRYAD content against Catalogue of Life and subsequent reclassification as described in the 'Challenges' paper.  For full details see publication ('The Challenges Paper'). Tab delimited format.  Fields: Serial Number (as provided by FileMaker software); Input Name (name-string as obtained from source); GN UUID (UUID as created by Global Names as described in the challenges paper); Canonical version (canonical form of name-string as formed by Global Names software); GenBank (indicates if name-string was in the GenBank download); Dryad Original (indicates if the name-string was in the original downloads from DRYAD; DRYAD Preprocessed (indicates if the name-string was in the DRYAD compilation after pre-processing); Scientific Name (indicates if the name-string is a scientific name); Terminal Taxon (indicates if the name-string refers to a species or subordinate taxon); GNXM (classification of matches as formed by Global Names Cross Mapper, details in full publication); GN Matched Name (name-string that Global Names Cross Mapper matched to); GN Matched Canonical Form (canonical form of name-string that Global Names Cross Mapper matched to); Input Rank (rank assigned to name-string by data source); GNXM Matched Rank (rank inferred by Global Names Cross Mapper); GNXM Matched Edit Distance (edit distances as described in associated paper for fuzzy matches found by Global Names Cross Mapper); GNXM Matched Score (confidence measure as described in associated paper for matches found by Global Names Cross Mapper); and Final Annotation (final classification made as a result of the analyses of this paper, and as described in the paper).
DOI: 10.5061/dryad.49rs8/1
title: Chi, sequence alignments

description: Sequences from a total of 22 Iochrominae species were generated from floral bud cDNA prepared from greenhouse or field-collected material. Sequences from six outgroup taxa were retrieved from Genbank or Solgenomics (solgenomics.net).
DOI: 10.5061/dryad.51v22/1
title: Anchored_Phylogenomics

description: Includes all analyses, data, methods, and code for the Anchored Phylogenomics assembly of Storeria.
DOI: 10.5061/dryad.5rn52/1
title: Cross-reactivity test
DOI: 10.5061/dryad.5rn52/2
title: Shortening effect
DOI: 10.5061/dryad.664cp/10
title: FigureS1.3.A
DOI: 10.5061/dryad.664cp/11
title: FigureS1.3.B
DOI: 10.5061/dryad.664cp/13
title: FigureS2.2.FeCH
DOI: 10.5061/dryad.664cp/6
title: Figure6.CPOX_hemF
DOI: 10.5061/dryad.664cp/7
title: Figure7.PPOX
DOI: 10.5061/dryad.664cp/8
title: Figure8.UROS
DOI: 10.5061/dryad.664cp/9
title: FigureS1.1
DOI: 10.5061/dryad.698s5/2
title: RNA in situ hybridization of SAD3 in Ophrys flowers.

description: Additional data for Figure S1: RNA in situ hybridization of SAD3 (the only SAD3-clade member) in Ophrys flowers. The probes were hybridized (A) with four thin sections of O. exaltata at 1, 3, 5 and 7 mm and (B) with two sections of O. sphegodes at 5 and 7 mm from the base of the lip. Antisense signal was detected in the epidermal layer of both species as compared to the sense control, although this is much clearer in panel (A). Previous gene expression analyses showed SAD3 to be ubiquitously expressed in different plant tissues and developmental stages, suggesting it to encode a housekeeping desaturase [1, 2], and these expression data are consistent with ISH despite low signal intensity in panel (B). It should be noted that qualitative absence of clear antisense signal (e.g. in non-epidermal layers) cannot be taken as evidence of absence of SAD3 expression there. References: 1. Xu et al. (2012). PLoS Genet. 8, e1002889.2. Schlüter et al. (2011). Proc. Natl. Acad. Sci. USA 108, 5696-5701.
DOI: 10.5061/dryad.698s5/3
title: RNA in situ hybridization of SAD5-clade desaturases in Ophrys flowers.

description: Additional data for Figure S1: RNA in situ hybridization of SAD5-clade desaturases (SAD5 and SAD6) in Ophrys flowers. Panel (A) shows thin sections of two individuals of O. exaltata and (B) one O. sphegodes individual; for each individual, two sections at 5 and 7 mm from the base (top) of the labellum were analysed. SAD5 antisense probe and sense control are shown for O. sphegodes. The antisense panels show black signal in the epidermal layer of O. exaltata (panel A), but not in O. sphegodes (panel B); O. exaltata antisense signal (panel A) is clearly stronger than the brownish background seen with the sense and antisense probes in O. sphegodes (panel B). This is consistent with the expression pattern reported for SAD5 [1], which is highly expressed in O. exaltata but not in O. sphegodes.References: 1. Xu et al. (2012). PLoS Genet. 8, e1002889.
DOI: 10.5061/dryad.70s5t/1
title: Data for meta-analysis derived from studies comparing timber harvest or tree size to nest site occupancy or productivity in northern goshawks (Accipiter gentilis)

description: These are data derived from published literature for a meta-analysis assessing the degree to which timber harvest and tree size explain productivity and site occupancy in northern goshawks (Accipiter gentilis)We present these data in two alternative formats. (A) An Excel spreadsheet with multiple tabs. This spread sheet includes many comments linked to individual cells explaining the derivation of individual values. (B) A series of .csv files, each corresponding to a different tab in the Excel file. These are the same data as in the Excel sheet, but without the comments linked to individual cells. The Excel tabs / CSV files are as follows:(1) repro_rawThese are the studies that compared productivity (mostly number of fledged young per pair or per nest) to either timber harvest or tree size. We report the individual effects reported in each study and our derivation of the standard effect size ‘r’.(2) repro_per-study_averageFor each study listed in (1), we have calculated an average effect size (both r and Zr), corresponding average sample size (n) and average variance corresponding with Zr (vz). (3) occupancy_rawThese are the studies that compared the occupancy of nest sites or clusters of nest sites to either timber harvest or tree size. We report the individual effects reported in each study and our derivation of the standard effect size ‘r’.(4) occupancy_continent_study_avFor each study listed in (3), we have calculated an average effect size (both r and Zr), corresponding average sample size (n) and average variance corresponding with Zr (vz). (5) occupancy_variable_study_avFor each study listed in (3), we have calculated an average effect size (both r and Zr), corresponding average sample size (n) and average variance corresponding with Zr (vz). There is only one small difference with (4) above. One of the studies examined the correlations between occupancy and both timber harvest history and average tree size. Thus for this study, we calculated two average effects on this sheet, one corresponding to timber harvest and the other corresponding to average tree size. This facilitates comparing effects of tree size to effects of timber harvest.