cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.20t9v/34
title: ABC rejection script

description: A script to apply the ABC rejection algorithm to simulated data.
DOI: 10.5061/dryad.20t9v/35
title: ABC generate polymorphism data script

description: A script to generate polymorphism data from reasonable priors using coalescent simulations.
DOI: 10.5061/dryad.20t9v/36
title: Export sets for FUNC script

description: A script to export gene sets for GO analysis with FUNC (Prüfer et al. 2007).
DOI: 10.5061/dryad.20t9v/37
title: ABC simulate BFs script - autosomes

description: A script to simulate Bayenv2 Bayes factors from 10 best demographic simulations (autosomes).
DOI: 10.5061/dryad.3m2n4/1
title: Wild_Lab_Data

description: Sampling and gene expression data for all individuals used in the study of immune variation in the wild, and the accompanying laboratory raised fish. All sampling data used during the analysis are included, including the relative expression values (DeltaDeltaCt) for eight immune genes, and the PC1 scores for each immune grouping type.
DOI: 10.5061/dryad.3m2n4/2
title: Responsiveness_Data

description: Data used in the study of innate immune response potential of laboratory fish from two different Icelandic populations. All data used during analysis is included, along with relative expression values (DeltaDeltaCt) for control and stimulated cells, along with the relative change in expression.
DOI: 10.5061/dryad.483hr/1
title: Etges_etal_2015_MEC_CHCdata

description: Cuticular hydrocarbon amounts for male and female Drosophila mojavensis reared on fermenting agria (Stenocereus gummosus) or organ pipe (S. thurberi) cactus tissues. Samples are based on mature adults grouped by day of egg to adult development time. Two populations were studied, LB, from Las Bocas, Sonora, and PP, from Punta Prieta, Baja California.  Hydrocarbon types and chainlengths are described in Etges and Jackson (2001).
DOI: 10.5061/dryad.65d76/4
title: Hypocotyl

description: Measurements of hypocotyl length collected from a subset of genotypes during the first fluctuating temperature experiment with Arabidopsis thaliana. See README file for details.
DOI: 10.5061/dryad.65d76/5
title: Biomass_Age

description: Data collected during the third fluctuating temperature experiment with Arabidopsis thaliana on biomass accumulation of Col and Col FRI. See README file for details.
DOI: 10.5061/dryad.65d76/6
title: Biomass_Bolt

description: Data collected during the third fluctuating temperature experiment with Arabidopsis thaliana on biomass at the time of bolting for Col and Col FRI. See README file for details.
DOI: 10.5061/dryad.69pg7/1
title: Bioclimatic variables used for ENMs

description: 19 bioclimatic variables for current conditions, Last Glacial Maximum and mid-Holocene (MIROC and CCSM models), extracted from the Wordclim database for the study region (European Alps). Additionally, elevation data and the "surface area" variable are included (see Materials and Methods for more details).
DOI: 10.5061/dryad.6v75k/1
title: borneo dataset

description: Includes liana and tree species, DBH and host used by lianas across 120 sample plots in primary and logged forest
DOI: 10.5061/dryad.7k3h4/1
title: Data for intraspecific and interspecific analysis

description: The zip file includes 1 nexus file for building ML tree, 1 vcf files(snp analysis results) and 1 nexus for SNAPP tree, 1 vcf file and structure file for STRUCTURE analysis
DOI: 10.5061/dryad.7n10n/2
title: Rubens_transcriptome_annotated

description: Output of transcriptome annotation from Blast2Go
DOI: 10.5061/dryad.7n10n/3
title: filter_transcripts

description: python script for filtering initial transcriptome assembly
DOI: 10.5061/dryad.7n10n/5
title: Filtered transcriptome

description: This transcriptome has been filtered to contain only contigs with FPKM value of 0.5 or greater and a minimum contig length of 600 bp. Additionly we retained only isoforms that accounted for 51% or more of the expression of a gene.
DOI: 10.5061/dryad.7n10n/6
title: Unfiltered transcriptome

description: raw trinity output without filtering.
DOI: 10.5061/dryad.7n10n/8
title: Rubens_RSEM_output

description: RSEM output for all pools.
DOI: 10.5061/dryad.8t53k/2
title: Xanthomonas citri - 44 strain PhyML phylogeny SYM model

description: A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 44 strains of Xanthomonas citri. Regions of recombination were removed from the alignment as well as gap-containing columns and +/- 20bp from a gap-containing column. The evolutionary model used was SYM, as chosen with jModeltest 2.1.7.
DOI: 10.5061/dryad.8vj6j/1
title: 20151211_hsc70-4_mrbayes

description: This file is a phylogenetic bayesian analysis with MrBayes for 17 insect species of hsc70-4
DOI: 10.5061/dryad.8vj6j/2
title: 20151211_hsp40_mrbayes

description: This file is a phylogenetic bayesian analysis of hsp40 with MrBayes for 17 species.
DOI: 10.5061/dryad.8vj6j/3
title: 20151211_hsp83_mrbayes

description: This file is a phylogenetic bayesian analysis of hsp83 with MrBayes for 17 species.
DOI: 10.5061/dryad.8vj6j/4
title: 20151211_insect_BIP_hsc70-3_cis-reg_alignment

description: This file is a local alignment of the promoter region of hsc70-3 for 17 insect species used to screen for evolutionary conserved cis-regulatory heat shock elements.
DOI: 10.5061/dryad.93ct6/1
title: METE_SSNT_code

description: Python code to allow replication of "Comparing process-based and constraint-based approaches for modeling macroecological patterns" by Xiao Xiao, James O'Dwyer, and Ethan White.
DOI: 10.5061/dryad.b3f50/1
title: haplotypes_dhfr crt mdr1

description: Plasmodium falciparum resistant markers to Chloroquine and sulphadoxine-pyremethaimne
DOI: 10.5061/dryad.d63sc/1
title: Actino12s OTU Centroid Sequences

description: List of centroid sequences generated in OTU formation after HMMER filtering
DOI: 10.5061/dryad.d63sc/10
title: Supplement Table 6

description: List of species for which we had a reference sequence for each of the four markers used.
DOI: 10.5061/dryad.d63sc/2
title: Actino16s OTU Centroid Sequences

description: List of centroid sequences generated in OTU formation after HMMER filtering
DOI: 10.5061/dryad.d63sc/3
title: Amphibia12s OTU Centroid Sequences

description: List of centroid sequences generated in OTU formation after HMMER filtering
DOI: 10.5061/dryad.d63sc/4
title: Cytb OTU Centroid Sequences

description: List of centroid sequences generated in OTU formation after HMMER filtering
DOI: 10.5061/dryad.d63sc/5
title: Supplement Table 1

description: Electrofishing derived species counts in Juday Creek for each reach from September 2013. Samples are ordered from the most downstream reach (R1) to the most upstream reach (R4).
DOI: 10.5061/dryad.d63sc/6
title: Supplement Table 2

description: Number of reads from each sample (i.e. library) run on the Illumina MiSeq platform for each step of the bioinformatic pipeline.
DOI: 10.5061/dryad.d63sc/7
title: Supplement Table 3

description: Results for all species identified with OTU species assignment. Values of P1 – P7 represent the pathway taken to arrive at species assignment using SAP and USearch (Fig. S1).
DOI: 10.5061/dryad.d63sc/8
title: Supplement Table 4

description: Raw read counts of each species identified, for each sample and all four markers.
DOI: 10.5061/dryad.f862c/81
title: M625E0-Control IgG

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/82
title: M625E0-Control RBC

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/83
title: M625E0-Control RBC+WGA

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/84
title: M625E0-Sepsis RBC C3D

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/85
title: M625E0-Sepsis RBC C4D

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/86
title: M625E0-Sepsis RBC DAF

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/87
title: M625E0-Sepsis RBC IgG

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/88
title: M625E0-Sepsis RBC E0

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.kr076/1
title: Data for Delaplane et al.

description: "block" is independent replication of experiment; "1" was set up in 2012 and "2" in 2013. "col" is unique bee colony within block. "tmt" is experimental colony treatment, ie., insemination dose: 15, 30, or 60 males. "date" is sample date. "time point" mirrors date and was used in the REML analysis to define a uniform correlation across all time points for each colony. "population" is raw colony population of adult bees. "combs" is area of foundation drawn into natural comb (cm2) by bees over two days. "brood" is area of worker brood, all life stages (cm2) on that sampling date. "mites" is number of Varroa mites recovered per 100 adult bees. In all cases, missing data are indicated by a period ".".
DOI: 10.5061/dryad.n0v50/2
title: Figure S2 -  PTR gene tree

description: Maximum clade credibility gene tree from MrBayes analysis of Ptr nuclear data.  Support values are posterior probabilities.
DOI: 10.5061/dryad.n0v50/3
title: Figure S1 - Maximum likelihood bootstrap tree

description: Maximum likelihood analysis of concatenated dataset. Support values are bootstrap scores.
DOI: 10.5061/dryad.n141b/1
title: Howison_et_al_2016_Facultative_Grazing_ArchivedDataset

description: Excel spreadsheet containing 3 datasheets: Redox, Survival and Yield. Data in RAW unprocessed format
DOI: 10.5061/dryad.nt60p/1
title: Hsiao_Statistical_Summary_JN

description: Chart of the assays, measurements, n's, values, statistical tests and p values for the data presented in figures in this paper.
DOI: 10.5061/dryad.p7j2h/1
title: JEB-2016-00019 Braulio & Foellmer

description: This Excel file contains four sheets. The sheets "Ins1" and "Ins1sperm" are almost identical, except that observations with zero sperm transferred were deleted from "Ins1sperm" for ease of analysis. Most variables were centered on the mean, as indicated by the "c" with which the variable names start. Missing observations are retained. Variable names are straight-forward abbreviations of the traits measured.
DOI: 10.5061/dryad.r7pc5/3
title: mapfile_fsoil

description: Mapping file associated with sequencing read files.
DOI: 10.5061/dryad.rn262/1
title: FocalSites_GenGroup_0901_1106

description: Capture records from monthly Trinidadian guppy monitoring of two populations between January 2009 and June 2011. Individual capture histories are coded by stream (CA vs TY), sex (M vs F), and genetic classification (Native-N, Immigrant-I, F1 hybrid - F1, F2 hybrid - F2)
DOI: 10.5061/dryad.rn262/2
title: CA_CMR_genepop_all

description: Microsatellite data in genepop format for Caigual population of Trinidadian guppies
DOI: 10.5061/dryad.rn262/3
title: TY_CMR_genepop_all

description: Microsatellite data in genepop format for Taylor population of Trinidadian guppies
DOI: 10.5061/dryad.t4362/1
title: part0

description: This data package contains all images and point annotations used in the present publication. To access the data download all parts, and then merge using the following command in a linux shell: cat data_package* &gt; merged_data.zip. Then unzip the archive to access the data.
DOI: 10.5061/dryad.t4362/2
title: part1
DOI: 10.5061/dryad.t4362/3
title: part2
DOI: 10.5061/dryad.t4362/4
title: part3
DOI: 10.5061/dryad.t4362/5
title: part4
DOI: 10.5061/dryad.t4362/6
title: part5
DOI: 10.5061/dryad.t4362/7
title: part6
DOI: 10.5061/dryad.t4362/8
title: part7
DOI: 10.5061/dryad.20t9v/38
title: ABC simulate BFs script - X chromosome

description: A script to simulate Bayenv2 Bayes factors from 10 best demographic simulations (X chromosome).
DOI: 10.5061/dryad.20t9v/39
title: ABC simulate FSTs script

description: A script to simulate FST values from a given demographic model.
DOI: 10.5061/dryad.20t9v/40
title: ABC combine ms results script

description: A script to gather ms simulation results into one Matlab file.
DOI: 10.5061/dryad.20t9v/41
title: ABC apply regression script

description: A script to apply a weighted regression in the space of summary statistics as proposed by Beaumont et al. (2002).
DOI: 10.5061/dryad.20t9v/42
title: ABC run ms script

description: A script to run Hudson's ms and return structure with haplotype matrices.
DOI: 10.5061/dryad.20t9v/43
title: ABC summarize data script

description: A script to summarize data provided as a Matlab file.
DOI: 10.5061/dryad.20t9v/44
title: ABC summarize struct. script

description: A script to summarize data in struct. of haplotype matrices.
DOI: 10.5061/dryad.2382q/1
title: Individual-level survival data for Serengeti and Hwange lions

description: The structure of the data in datSH.txt by columns is as follows:  1) "id" = individual identifier: sequence from 1 to 4754;2) "sex" = sex of indvidual: male, female, unknown (m/f/u);3) "dead" = binary indicator of whether death was confirmed at dissapearance: surely dead? (yes/no);4) "cens" = censored observation: individual still alive at end of study? (yes/no);5) "xli" = last seen age of individual i in years;6) "xti" = left-truncation age of individual i (i.e. “first seen”) in years;7) "loc" = location: observation from Serengeti or Hwange (s/h);8) "potEm" = potential emigrant: characteristics of individual at last seen age indicate that the indivdiual may have dispersed (yes/no);9) "im" = immigrant: individual immigrated into the study area (yes/no);10) "unsex" = unsexed: did the indvidual die before sex was determined? (yes/no);11) "outMigr" = out-migrant: expert opinion on whether individual may have dispersed (yes/no), only relevant for Serengeti data.Note that for the binary indicators 1 indicates "yes", 0 indicates "no".Data are based on mark-resighting records of the Hwange and Serengeti lion population, respectively. For details on the data collection protocol, please see the "Materials and methods" section in the associated paper. Further questions can be addressed to Andrew Loveridge (andrew.loveridge@zoo.ox.ac.uk) for the Hwange data and to Craig Packer (packer@umn.edu) for the Serengeti data.
DOI: 10.5061/dryad.2382q/2
title: R code to fit the mortality model

description: R code to fit the Siler mortality model to re-sighting data of male and female lions from two populations (i.e. Hwange National Park and Serengeti National Park, respectively). For running the analysis that is presented in the associated paper, download this file "runsModel.R" and the corresponding functions file "fcts01.R". Furthermore, please download the data file "datSH.txt". Save all files to the same folder. Set your R working directory to that folder using the corresponding line in "runsModel.R". Run the model by running "runsModel.R". When the model is finished, the model output will be automatically stored as an Rdata file to the working directory folder. There will be three output objects, which store the output pertaining to the three model start ages. The three output objects will be a composite name of the nature: outFrom"model start age"_"version".Rdata (e.g. outFrom1_01.Rdata for start age x = 1 and model version 01). Please see the documentation/comments in the code for further details on the starting objects, model fitting process, and the output objects.
DOI: 10.5061/dryad.2382q/3
title: R script containing the functions for running the model

description: This R script contains the functions to set up the starting objects, run the model, and process the model outputs. This R script is sourced by "runsModel.R".
DOI: 10.5061/dryad.3c8s8/1
title: batch_7.2.sumstats.tsv

description: Stacks1.04 populations output provides summary statistics for each locus containing SNPs. To identify sex markers, we split each species into male and female samples: S. chrysomelas males were assigned to Pop 1, S. chrysomelas females were assigned to Pop 2, S. carnatus males were assigned to Pop 3, and S. carnatus females were assigned to Pop 4. See the Stacks manual for headers.
DOI: 10.5061/dryad.3c8s8/2
title: batch_7.catalog.tags.tsv

description: Stacks1.04 denovo_map.pl pipeline was used to construct a catalog of loci from ddRAD-seq reads of S. carnatus and S. chrysomelas samples. .  We specified a minimum depth of coverage (m) of two, a maximum number of mismatches between stacks (alleles) within an individual (M) of two, and a maximum number of mismatches between individuals (n) of one to build the catalog.  M and n allow for assembly of polymorphic loci within individuals and fixed differences among individuals at a locus, respectively. See the Stacks manual for headers.
DOI: 10.5061/dryad.3c8s8/3
title: matches.tsv

description: Samples' stacks are matched to the catalog to create a matches.tsv file for each sample. We counted the matches to the catalog to find the depth of each locus in each individual sample. This file must be unzipped. See the Stacks manual for headers.
DOI: 10.5061/dryad.3c8s8/4
title: Fixed differences

description: This R script was used to identify loci with SNPs that are differently fixed between males and females (ie all males are heterozygous, all females are homozygous). The loci identified are on the sex chromosomes, but given our parameters they have not diverged enough for Stacks to split them into separate loci. We tested the scrip on loci that mapped to select scaffolds where sex-specific markers were found, and then we applied the script to filter the entire sumstats.tsv file.
DOI: 10.5061/dryad.3c8s8/5
title: Filtering for sex-specific loci

description: The R script counts each samples' matches (matches.tsv) to the catalog (Batch_7.catalog.tags.tsv) and tabulates the depth of each locus in each individual. We then filtered for presence in all of one sex and none of the other sex. We identified loci present in all males and no females.
DOI: 10.5061/dryad.44770/1
title: Holocene Iriartea percentages for thirteen lakes in Amazonia

description: The csv file contains the data for 13 lakes in Amazonia. Columns include site name, depth, age, Iriartea percentage, and maize percentage (when available).
DOI: 10.5061/dryad.4tv57/1
title: AA_MVC
DOI: 10.5061/dryad.4tv57/2
title: AA_Standing
DOI: 10.5061/dryad.4tv57/3
title: AA_Wobble
DOI: 10.5061/dryad.4tv57/4
title: AZ_MVC
DOI: 10.5061/dryad.4tv57/5
title: AZ_Seated
DOI: 10.5061/dryad.4tv57/6
title: AZ_Standing
DOI: 10.5061/dryad.4tv57/7
title: AZ_Wobble
DOI: 10.5061/dryad.61vk4/1
title: ExtendedPhenotype

description: Data for manipulations of individual shell nests of Neolamprologus multifasciatus
DOI: 10.5061/dryad.61vk4/2
title: multifasc network data

description: Interaction frequency per five minute observation for each member of five separate communities.
DOI: 10.5061/dryad.6mc10/1
title: Ruggeri_et_al._anchovy_dataset

description: Genotype dataset (corrected for null alleles) for 15 sampling sites and 13 microsatellite loci
DOI: 10.5061/dryad.72551/1
title: Interactions_Asynchrony_Index

description: Table containing the 39 plant-butterfly interactions included in this study. For each year of the study period (1996-2012) we indicate the asynchrony index (number of days) corresponding to the Spring butterfly generations (AI1_spring) and Summer butterfly generations (AI2_summer). Last column represents the butterfly abundance index (number of butterflies of each species recorded each year along the whole sampling season).
DOI: 10.5061/dryad.8t53k/1
title: Xanthomonas citri - 44 strain Mugsy genome alignment

description: A multiple genome alignment of 44 strains of Xanthomonas citri output from the Mugsy genome alignment software
DOI: 10.5061/dryad.8t53k/3
title: Xanthomonas citri - 44 strain concatenated genome alignment (recombination, gaps +/- 20nt removed) FASTA format

description: A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Regions of recombination detected using RDP were removed, as were gap-containing columns and 20 nt surrounding gap-containing columns.
DOI: 10.5061/dryad.8t53k/4
title: Xanthomonas citri - 36 strain PhyML phylogeny GTR model, Reduced A-strain distribution, Contains recombination

description: A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 36 strains of Xanthomonas citri. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination Event 16. The evolutionary model used was GTR.
DOI: 10.5061/dryad.8t53k/5
title: Xanthomonas citri - 36 strain concatenated genome alignment (gaps +/- 20nt removed) FASTA format, Contains recombination

description: A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks.  Gap-containing columns and 20 nt surrounding gap-containing columns were removed. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination event 16.
DOI: 10.5061/dryad.8vj6j/10
title: 20151211_insect_BIP_hsc70-3_tree_alignment

description: This is a nexus file with an amino acid alignment and maximum likelihood(PhyML) phylogenetic reconstruction of hsc70-3 for 17 insect species.
DOI: 10.5061/dryad.8vj6j/11
title: 20151211_insect_hsc70-4_tree_alignment

description: This is a nexus file with an amino acid alignment and maximum likelihood(PhyML) phylogenetic reconstruction of hsc70-4 for 17 insect species.
DOI: 10.5061/dryad.8vj6j/12
title: 20151211_insect_hsp83_tree_alignment

description: This is a nexus file with an amino acid alignment and maximum likelihood(PhyML) phylogenetic reconstruction of hsp83 for 17 insect species.
DOI: 10.5061/dryad.8vj6j/13
title: 20151211_insect_hsc70-5_tree_alignment

description: This is a nexus file with an amino acid alignment and maximum likelihood(PhyML) phylogenetic reconstruction of hsc70-5 for 17 insect species.
DOI: 10.5061/dryad.8vj6j/5
title: 20151211_insect_hsc70-4_cis-reg_alignment

description: This file is a local alignment of the promoter region of hsc70-4 for 17 insect species used to screen for evolutionary conserved cis-regulatory heat shock elements.
DOI: 10.5061/dryad.8vj6j/6
title: 20151211_insect_hsp40_cis-reg_alignment

description: This file is a local alignment of the promoter region of hsc40 for 17 insect species used to screen for evolutionary conserved cis-regulatory heat shock elements.
DOI: 10.5061/dryad.8vj6j/7
title: 20151211_insect_hsc70-5_cis-reg_alignment

description: This file is a local alignment of the promoter region of hsc70-5 for 17 insect species used to screen for evolutionary conserved cis-regulatory heat shock elements.
DOI: 10.5061/dryad.8vj6j/8
title: 20151211_insect_hsp60_cis-reg_alignment

description: This file is a local alignment of the promoter region of hsp60 for 17 insect species used to screen for evolutionary conserved cis-regulatory heat shock elements.
DOI: 10.5061/dryad.8vj6j/9
title: 20151211_insect_hsp83_cis-reg_alignment

description: This file is a local alignment of the promoter region of hsc83 for 17 insect species used to screen for evolutionary conserved cis-regulatory heat shock elements.
DOI: 10.5061/dryad.bd21p/1
title: Combined alignment for phylogenetic analyses

description: Combined Dataset of 16s rRNA and EF Tu aligned reads used for Bayesian and Likelihood Phylogenetic Analyses (Nexus format)
DOI: 10.5061/dryad.bd21p/2
title: 16s only alignment for permutation test

description: Aligned partial 16s rRNA reads used for permutation test (Nexus format)