cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.88q04/1
title: MGH_regression

description: Connectome file format file that holds networkX networks for each connectivity type. Each connection in the network represents an ordinary least squares regression with group membership as the variable of interest and age and gender as covariates. For each variable, covariable and a constant term, the beta, pvalue and t-statistic is stored.
DOI: 10.5061/dryad.88q04/2
title: MGHconnectomes

description: tar.gz holding the connectome information of each subject included in the MGH proof-of-concept study. Each subject has a connectome file format (cff) file, and each cff file holds networkX networks for each network type considered.
DOI: 10.5061/dryad.88q04/3
title: MGH_includedSubjects

description: List of subjects included in the MGH analysis. Each subject's URSI identifier, type (patient/control), age, gender, and ses is provided. Additional information about subjects can be obtained from the MIND Clinical Imaging Consortium.
DOI: 10.5061/dryad.8kv2s/1
title: Fig5
DOI: 10.5061/dryad.8kv2s/2
title: Fig6
DOI: 10.5061/dryad.8kv2s/3
title: Fig7
DOI: 10.5061/dryad.8kv2s/4
title: Fig8_and_Fig9
DOI: 10.5061/dryad.8kv2s/5
title: Fig10
DOI: 10.5061/dryad.8kv2s/6
title: Fig11A
DOI: 10.5061/dryad.8kv2s/7
title: Fig11B
DOI: 10.5061/dryad.8kv2s/8
title: Fig12
DOI: 10.5061/dryad.8kv2s/9
title: Fig13
DOI: 10.5061/dryad.97803/1
title: Burt and Clary abandoned ski slopes dataset

description: Species cover data and measured environmental characteristics from large (5m by 20 m) plots on abandoned ski slopes of differing ages since abandonment and differing initial construction methods (graded or cleared) and their paired reference forest plots. Readme information included in first worksheet of the excel file.
DOI: 10.5061/dryad.9bs10/1
title: maternal age file
DOI: 10.5061/dryad.9bs10/2
title: Paternal age file
DOI: 10.5061/dryad.9sk18/4
title: Nestling_Condition_2ndClutch_Males

description: This table contains information on the condition of nestlings (mass, wing, age, etc…) in relation to annual breeding parameters (1 or 2 annual clutch, laying date, clutch size, number of fledglings, …) of males. These data were collected between 1990 and 2014 in western Switzerland.
DOI: 10.5061/dryad.b6d75/1
title: readme

description: Describes the contents of the other files
DOI: 10.5061/dryad.b6d75/2
title: Holman bet hedging - open this one to run the analysis

description: The main R script to run the simulation and produce figures from the simulation results I have archived. It is heavily annotated.
DOI: 10.5061/dryad.b6d75/3
title: Holman bet hedging - functions

description: An R script containing custom functions used in the simulation.
DOI: 10.5061/dryad.b6d75/4
title: Dataset info

description: A .csv file containing information about each of the 49 primary datasets appearing in the study. Contains information necessary for making the Figures in the main R script.
DOI: 10.5061/dryad.b6d75/5
title: Results of simulation - for various Ne values

description: A zip archive, containing many .csv files, containing the results of a full run of the simulation (one for each dataset-parameter space combination). The output is calculated assuming there is no cost of multiple mating (p=0), and Ne has been specified. See readme for further info.
DOI: 10.5061/dryad.b6d75/6
title: Results of simulation - for various p values

description: A zip archive, containing many .csv files, containing the results of a full run of the simulation (one for each dataset-parameter space combination). The output is calculated assuming the cost of multiple mating (p) has been specified, and the critical value of N needs to be calculated. See readme for further info.
DOI: 10.5061/dryad.bv3gm/7
title: Pairwise_relatedness_full_dataset.txt

description: Estimates of pairwise relatedness derived from a full dataset of all clones, using VCFtools.
DOI: 10.5061/dryad.bv3gm/9
title: Pairwise_relatedness_full_MNandILremoved.txt

description: Estimates of pairwise relatedness derived from a reduced dataset of clones, with the Mongolian and Israel clone removed, using VCFtools.
DOI: 10.5061/dryad.c06n3/1
title: README
DOI: 10.5061/dryad.c06n3/2
title: burkDists.csv

description: Comma-delimited data file containing the triplets of distances from each plant to each of the three GPS reference points.
DOI: 10.5061/dryad.c06n3/3
title: trilat.py

description: A simple Python trilateration script to convert the positions of each of the plants in burkDists.csv into GPS coordinates in decimal degrees.
DOI: 10.5061/dryad.c06n3/4
title: mergedUTM.tsv

description: Tab-delimited file containing the positional data used in all downstream analysis in R.
DOI: 10.5061/dryad.c06n3/5
title: scaleAnalysis.R

description: An R script that contains all of the analyses and plotting functions described in the methods of this manuscript. The script depends on a helper script formatData.R.
DOI: 10.5061/dryad.c57h7/1
title: Counts of mapped reads per gene for each of the 12 samples

description: Table showing counts of mapped reads (from htseq-count) per gene for each of the 12 samples. Further output from htseq-count per sample is shown at the bottom of the table, summarizing the total number of mapped reads, reads that were not mapped, and the proportion of total mapped reads. The first table column, "genes" refers to the A. mellifera Official Gene Set 3.2 accession numbers (Elsik et al. 2014). The remaining 12 columns refer to the 12 samples: "wg" = pooled HPG tissue from nurses collected from queenright colonies while feeding worker-destined larvae; "Wg" = pooled HPG tissue from nurses collected from queenless colonies while feeding worker-destined larvae; "Qg" = pooled HPG tissue from nurses collected from queenless colonies while feeding queen-destined larvae; "wh" = pooled head tissue from nurses collected from queenright colonies while feeding worker-destined larvae; "Wh" = pooled head tissue from nurses collected from queenless colonies while feeding worker-destined larvae; "Qh" = pooled head tissue from nurses collected from queenless colonies while feeding queen-destined larvae; "wm" = pooled MG tissue from nurses collected from queenright colonies while feeding worker-destined larvae; "Wm" = pooled MG tissue from nurses collected from queenless colonies while feeding worker-destined larvae; "Qm" = pooled MG tissue from nurses collected from queenless colonies while feeding queen-destined larvae; "wl" = pooled 4th instar worker-destined larvae from queenright colonies; "Wl" = pooled 4th instar worker-destined larvae from queenless colonies; "Ql" = pooled 4th instar queen-destined larvae from queenless colonies
DOI: 10.5061/dryad.c57h7/2
title: raw hive observation data

description: Table of raw observation data of individually-marked bees observed interacting with worker and queen cells in two replicate observation hives. The inferred age of each bee is also shown. "day" = the day of the study following queen removal; "hive" = whether the observation came from replicate hive B or D; "tag color" and "tag #" = the color and number on the tag glued to the mesosoma of the individually-marked bee; "abdomen" = color of paint mark on the abdomen of the individually-marked bees. Together the mesosoma tag and abdomen paint mark were unique and enabled individual identification; "behavior" the observed behavior of the individually-marked bee; "time" the time of the observation; "Observer" = the initials or first name of the observer, see contributors in author list and Acknowledgements;  "age" = the inferred age of the individually-marked bee, based on the date it was added as a newly-emerged bee to the observation hive plus the number of days that had elapsed.
DOI: 10.5061/dryad.f3dn2/50
title: A. coluzzii variant file

description: This file contains variants from all A. coluzzii individuals described in this study (plus a few others). See the README for the list of individual sample ID's from pre- and post-2006 samples that can be used with VCFtools to recreate the figures.
DOI: 10.5061/dryad.g91p3/1
title: Serum cytokine Raw Data for open access

description: The data presented is the raw cytokine levels expressed in pg/ml. Sheet 1 is the data for 12 cytokines for the derivation cohort; Sheet 2 is the data for 3 cytokines for the validation cohort; Sheet 3 has data for 3 cytokines before and after ATT treatment.
DOI: 10.5061/dryad.h2082/10
title: Arlequin

description: Datafiles and results from Arlequin for Mantel tests and AMOVAs.
DOI: 10.5061/dryad.h2082/11
title: Migrate-n

description: Infile, 24 parameter files, and 24 output files from population models tested in Migrate-n.
DOI: 10.5061/dryad.h2082/6
title: *BEAST_region

description: Starbeast xml file and results from analysis of 6 geograhpic regions across the P. streckeri/P. illinoensis species complex using 23 nDNA loci.
DOI: 10.5061/dryad.h2082/7
title: BEAST_DivTime

description: Datafiles and results from divergence time estimation in BEAST using family-level hylid sequences and fossil calibrations.
DOI: 10.5061/dryad.h2082/8
title: IMa2

description: Infiles and results from isolation with migration analyses conducted in IMa2 for divergence time estimation.
DOI: 10.5061/dryad.h2082/9
title: Msats_294ind

description: Microsatellite dataset with 14 loci genotyped for 294 individuals, and results from PCoA analysis of 228 individuals conducted in Genalex.
DOI: 10.5061/dryad.j5r51/31
title: Simulated laminar recordings for input intensity 3.0 sp/ms when synaptic model is conductance based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/32
title: Simulated laminar recordings for input intensity 6.0 sp/ms when synaptic model is conductance based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/33
title: Simulated laminar recordings from reconstructed morphologies for input intensity 0.5 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with reconstructed (rather than artificial) morphologies described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/34
title: Simulated laminar recordings from reconstructed morphologies for input intensity 1.0 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with reconstructed (rather than artificial) morphologies described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/35
title: Simulated laminar recordings from reconstructed morphologies for input intensity 1.5 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with reconstructed (rather than artificial) morphologies described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/36
title: Simulated laminar recordings from reconstructed morphologies for input intensity 2.0 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with reconstructed (rather than artificial) morphologies described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.k15v4/1
title: Decision-making time and homing direction of experimental pigeon flocks.

description: Decision-making time and homing direction of experimental pigeon flocks. Homing direction is difference between the vanishing bearing and the correct direction.
DOI: 10.5061/dryad.m8g90/1
title: Illumina_16SCinara

description: This is an archive containing results of the sequencing of 16S rRNA gene for all samples of the publication (the results have been demultiplexed : each file corresponds to the sequecining of a PCR product).
DOI: 10.5061/dryad.m8g90/2
title: final.aln.count_table

description: this compiles the distribution of sequences across samples (this file can be uploaded to run the R script)
DOI: 10.5061/dryad.m8g90/3
title: final.aln.fasta

description: Final alignment of all unique sequences: output from the Galaxy pipeline, input of  the R script
DOI: 10.5061/dryad.m8g90/4
title: Appendix1_R

description: R script described in the paper to analyse output from Galaxy -produce summary tables (number of sequences per sample before and after applying various thresholds, distribution of sequences across samples , -scripto to conduct diversity analyses described in the paper
DOI: 10.5061/dryad.nd848/1
title: Experimental evolution protective microbe
DOI: 10.5061/dryad.nd848/2
title: Spectrum of protection
DOI: 10.5061/dryad.nd848/4
title: Bacterial cfus
DOI: 10.5061/dryad.nd848/5
title: In vitro suppression of S. aureus
DOI: 10.5061/dryad.nd848/6
title: Superoxide production
DOI: 10.5061/dryad.nh597/2
title: fGC and daily travel distance data

description: Excel file containing data on group ID, fGC concentrations, and daily travel distance.  These data were used to determine whether daily travel distance predicted fGC concentrations.  See manuscript for more information.
DOI: 10.5061/dryad.nh597/3
title: Monthly fGC predictors

description: Excel file containing data on group ID, temporal sequence, group size, cumulative rainfall, average maximum temperature, and fGC concentrations.  These data were used to determine the predictors of fGC concentrations.  See manuscript for more information.
DOI: 10.5061/dryad.nh597/4
title: Monthly ranging pattern predictors

description: Excel file containing data on group ID, temporal sequence, group size, cumulative rainfall, average maximum temperature, evenness of space use, home range size, and average daily travel distance.  These data were used to determine the predictors of monthly ranging patterns.  See manuscript for more information.
DOI: 10.5061/dryad.nh8ph/5
title: Pvirgatum_v1.1_273_with_ChrUn.tar
DOI: 10.5061/dryad.q2t70/1
title: Egg and nest metrics for European starlings

description: Nest data, including laying data. Egg data, including coloration, lysozyme, biliverdin, and carotenoid concentration, and size.
DOI: 10.5061/dryad.rb472/1
title: Elephant weight and height measures

description: Data used to produce weight for age and height for age curves
DOI: 10.5061/dryad.s5pb0/1
title: Turbinaria ornata all field and mesocosm experiments

description: This data sheet is split into 6 different spread sheets. 1) "NvsP Gump" is for the nutrient enrichment mesocosm conducted in flow through tanks at the Gump Station. Ambient water was taken from Gump and treatment were fully crossed with +/- Nitrogen (Ntrt) and +/- Phosphorous (Ptrt) addition. The data includes intital and final heights (ht)  and weights (wt), but the metric of interest in the paper was % Change in wt. Means and standard errors are calculated on the right for each treatment in this sheet. 2) "NvsP Sailing School" is set up the same as "NvsP Gump" except this experiment was conducted starting with ambient water from our second site, Sailing School. 3 and 4) "In situ Gump" and "In situ Sailing School" are data from field experiments at the two respective sites manipulating nutrient enrichments (+/- Nutrients or Ntrt) and access to herbivores (+/- Cage or Ctrt). Again %Change in Wt was the measure of interest  and thalli that were completely lost (% Change Wt = 100%) were dropped from analysis because it cannot be distinguished whether these were lost by herbivory or implementation failure. 5) "Agar Test" contains  initial and final areas for images of the three treatments--Ambient, Control, and +N (Osmocote/fertilizer enriched). "% Change in area" was calculated and used for analysis. Image areas were calculated in ImageJ software. 6) "Toughness Test"--Initial  and final heights (ht) and weights (wt) were measured but "Toughness" was the metric of interested which was the weight required to penetrate the algal thallus by adding incremental amounts of sand to a field penetrometer.
DOI: 10.5061/dryad.td887/1
title: Diapause Reads counts

description: transcript counts from Cufflinks
DOI: 10.5061/dryad.td887/2
title: Normalized read counts for PCA
DOI: 10.5061/dryad.13t18/10
title: Gene tree set 5

description: 16 taxa 60% missing taxa dataset analyzed in NJst.
DOI: 10.5061/dryad.13t18/11
title: Gene tree set 6

description: 29 taxa 20% missing taxa dataset analyzed in NJst.
DOI: 10.5061/dryad.13t18/3
title: Figure S1

description: Histograms depicting variation across ultraconserved elements (UCEs) generated for this study. (A–C) The number of segregating sites, (D–F) length in base pairs, and (G–I) number of taxa are reported for all three sampling strategies (16 taxa each with more than 3000 UCEs, 29 taxa each with more than 2000 UCES, and 44 taxa each with more than 120 UCEs) using 50% missing taxa per locus datasets. Note that datasets allowed for up to 50% missing taxa per locus and contained 2,716, 4,319, and 4,789 UCE loci total (16 taxa, 29 taxa, and 44 taxa, respectively).
DOI: 10.5061/dryad.13t18/4
title: Figures S2-S37

description: Phylogenetic trees from individual analyses performed in this study.
DOI: 10.5061/dryad.13t18/5
title: RAxML_phylip_alignments

description: Zip archive containing the following alignments: Alignment 1: 16 taxa 20% missing taxa dataset analyzed in RAxML. Alignment 2: 16 taxa 30% missing taxa dataset analyzed in RAxML. Alignment 3: 16 taxa 40% missing taxa dataset analyzed in RAxML. Alignment 4: 16 taxa 50% missing taxa dataset analyzed in RAxML. Alignment 5: 16 taxa 60% missing taxa dataset analyzed in RAxML. Alignment 6: 29 taxa 20% missing taxa dataset analyzed in RAxML. Alignment 7: 29 taxa 30% missing taxa dataset analyzed in RAxML. Alignment 8: 29 taxa 40% missing taxa dataset analyzed in RAxML. Alignment 9: 29 taxa 50% missing taxa dataset analyzed in RAxML. Alignment 10: 29 taxa 60% missing taxa dataset analyzed in RAxML. Alignment 11: 44 taxa 20% missing taxa dataset analyzed in RAxML. Alignment 12: 44 taxa 30% missing taxa dataset analyzed in RAxML. Alignment 13: 44 taxa 40% missing taxa dataset analyzed in RAxML. Alignment 14: 44 taxa 50% missing taxa dataset analyzed in RAxML. Alignment 15: 44 taxa 60% missing taxa dataset analyzed in RAxML.
DOI: 10.5061/dryad.13t18/6
title: Gene tree set 1

description: 16 taxa 20% missing taxa dataset analyzed in NJst.
DOI: 10.5061/dryad.13t18/7
title: Gene tree set 2

description: 16 taxa 30% missing taxa dataset analyzed in NJst.
DOI: 10.5061/dryad.13t18/8
title: Gene tree set 3

description: 16 taxa 40% missing taxa dataset analyzed in NJst.
DOI: 10.5061/dryad.13t18/9
title: Gene tree set 4

description: 16 taxa 50% missing taxa dataset analyzed in NJst and ASTRAL.
DOI: 10.5061/dryad.2362q/1
title: Data used in the literature survey
DOI: 10.5061/dryad.2kt43/1
title: Plethodon Data

description: TPS file containing landmark coordinates on the heads of 289 adult Plethodon jordani salamanders. Original data from Adams 2004. Ecology
DOI: 10.5061/dryad.2m6s2/1
title: Gene expression for 6 evolved populations x 2 sexes x 2 mating statuses

description: This text file contains the expression levels of 13995 genes from NimbleGen 12x135k arrays run for 6 experimentally-evolved populations. Males (virgin) and females (virgin and females) from each of the 6 populations were profiled, for 18 total transcriptional profiles.
DOI: 10.5061/dryad.36h28/1
title: Figure3 - Source Data 1

description: Raw data for 3D SBEM High ECS dataset. Viewable in Knossos (www.knossostool.org)
DOI: 10.5061/dryad.36h28/2
title: Figure 3 - Source Data 2

description: Raw data for 3D SBEM Low ECS dataset. Viewable in Knossos (www.knossostool.org)
DOI: 10.5061/dryad.534ng/1
title: TD_AllDates

description: Abiotic and biotic data from all sampling dates. plotid = Plot ID;date = Sample date;rep = Replicate;trt = Water level treatment (0 cm, -10 cm, -20 cm, -30 cm);cover = Cover treatment (HP = Herbaceous plants, LS = Low shrub, WM = Wood-strand mulch, NC = No-cover control, C = No-moss no-cover control);gwc = Gravimetric water content;l = Percent cover of litter;tdiff = Temperature difference between surface and 5 cm depth in the soil (C o);s2aw = distance between the soil and average water level (cm);som = Percent soil organic matter;tmb = Moss biomass 	(g);om = Percent cover of opportunistic mosses;	tm = Percent cover of total moss;om14 = Percent cover of opportunistic mosses in September 2014;tm14 = Percent cover of total moss in September 2014;ll01 = Percent cover litter transformed using a logit;tdiffsq = Temp difference between surface and 5 cm depth in the soil transformed with a square root;tmbsq = Soil organic matter transformed with a square root;oml01 = Percent cover of opportunistic mosses transformed using a logit;tmsq = Percent cover of total moss transformed with a square root;om14l01 = Percent cover of opportunistic mosses in Sept 2014 transformed using a logit;tm14l01 = Percent cover of total moss in Sept 2014 transformed with a square root;
DOI: 10.5061/dryad.534ng/2
title: Trench Sept 2014_NoO

description: Percent cover of vascular and non-vascular species. Absolute and relative for moss species, relativized by total moss cover. plotid = Plot ID;Rep = Replicate;Trt = Water level treatment (0 cm, -10 cm, -20 cm, -30 cm);Cover = Cover treatment (HP = Herbaceous plants, LS = Low shrub, WM = Wood-strand mulch, NC = No-cover control, C = No-moss no-cover control);Litter = Percent cover of litter;WtoS = Soil to average water level;Tdiff = Temperature difference between surface and 5 cm depth in the soil (C o);SOM = Percent soil organic matter;Weeds = Percent cover of unplanted vascular plants;HP = Percent cover of herbaceous plants;LS = Percent cover of low shrubs;TMB = total moss biomass; (g) GWC = Gravimetric water content;
DOI: 10.5061/dryad.606j8/1
title: Spider mite performance on different host plants, before and after tomato adaptation.

description: Performance was quantified as the total population sizes (including eggs and mobile stages) 10 days after the initial inoculation using 35 female mites. The T. urticae London mite strain and the following plant cultivars were used; bean: Phaseolus vulgaris L. cv ‘Prelude’, cucumber: Cucumis sativus L. cv ‘Tanja’, tomato: Solanum lycopersicum L. cv ‘Moneymaker’ and bell pepper: Capsicum annuum L. cv ‘California Wonder’.
DOI: 10.5061/dryad.606j8/2
title: Tomato foliar damage by spider mite feeding

description: Foliar damage was measured using chlorotic spots as described in Kant et al. (2004).
DOI: 10.5061/dryad.606j8/3
title: Differentially expressed genes of T. urticae in the experimental evolutionary set-up

description: Different DEG lists, arising from different transcriptomic comparisons, are shown in different tabs of the excel file. The abbreviations are explained in Table 1 of the main text.
DOI: 10.5061/dryad.606j8/4
title: Differentially expressed genes of tomato in the experimental evolutionary set-up

description: The abbreviations are explained in Table 1 of the main text.
DOI: 10.5061/dryad.606j8/5
title: Annotations of T. urticae genes

description: BLAST2GO- and best-BLAST-hit-annotations are included. T. urticae gene IDs can be accessed at http://bioinformatics.psb.ugent.be/orcae/overview/Tetur
DOI: 10.5061/dryad.606j8/6
title: Annotations of tomato genes

description: ITAG, Blast2GO and EC descriptions for tomato genes are included.
DOI: 10.5061/dryad.688nk/1
title: Data&Scripts

description: All data and R scripts for the analysis of the rate of terminal filament addition and ovary volume.
DOI: 10.5061/dryad.76rb1/1
title: Crypto_COI

description: cytochrome c oxidase subunit 1 data
DOI: 10.5061/dryad.76rb1/2
title: Crypto_ALLTRAV_D5cD6c_phased

description: Toll, putative
DOI: 10.5061/dryad.76rb1/3
title: Crypto_ALLTRAV_E3E4_phased

description: F-Box, putative