cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qj5cr/12
title: Ravinet_et_al_Sec_Cont_Hard_Sweep

description: Computer code for a hard sweep occurring during a period of isolation of a pair of populations under divergent selection; the sweep is followed by gene flow (the model is explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/13
title: Ravinet_et_al_Fig5

description: Computer code used to generate results shown in Fig. 5 in Ravinet et al. (2017). For further details, please see Ravinet et al. (2017), and the separate file "ReadMeFirst".
DOI: 10.5061/dryad.s1d25/1
title: RSPB-2016-1407 Data

description: Data file used in analyses presented in this paper
DOI: 10.5061/dryad.t2v1b/2
title: Simulation codes for PDE and generalised Landau– Levich equation
DOI: 10.5061/dryad.t9t0v/1
title: Louse and host bird body sizes by louse families

description: Louse species (families), louse female total body length (obtained from taxonomic descriptions, see Supplements of our paper), host birds name and body mass (obtained from Dunning, 2008). Families are coded as: M: Menoponidae; R: Ricinidae; P: Philopteridae.
DOI: 10.5061/dryad.t9t0v/2
title: Louse and host bird body sizes by Philopterid guilds

description: Louse species, female total body length, host species, host body mass, and louse guilds. Guilds are coded as: H: 'head lice'; W: wing lice; B: 'body lice'; G: generalists.
DOI: 10.5061/dryad.td356/1
title: Hunter_JEB_2016_Hostgenotype_Totalprogeny

description: These are the data used for the total progeny analysis presented in figure 2.
DOI: 10.5061/dryad.td356/2
title: Hunter_JEB_2016_Hostgenotype_Sex_ratios

description: These are the sex ratio data used for figure 4.  Refer to the manuscript text for descriptions of treatments etc.
DOI: 10.5061/dryad.td356/3
title: Hunter_JEB_2016_Hostgenotype_Develop_time

description: These are the data used for the development time analysis (Fig. 3 a and b).
DOI: 10.5061/dryad.td356/4
title: Hunter_JEB_2016_Hostgenotype_Rickettsiatiter

description: These are the estimates of Rickettsia titer relative to actin titer among the 4 Rickettsia-infected treatments. (Fig. 5)
DOI: 10.5061/dryad.vr954/40
title: Camarasaurus mandible unilateral posterior bite

description: Abaqus input file of a finite-element model of the mandible of Camarasaurus, simulating an unilateral bite at the posterior biting position.
DOI: 10.5061/dryad.2m2r2/1
title: 2009 Genotypes

description: Genotypes for individuals caught in 2009 for CERVUS analysis. In CERVUS format. Age classes & sexes in the Readme.
DOI: 10.5061/dryad.2m2r2/2
title: 2008 Genotypes

description: Genotypes for individuals used in CERVUS analysis caught in 2008. Readme includes the age and sex of individuals used.
DOI: 10.5061/dryad.2m2r2/3
title: Adults

description: Details for each Adult caught over 2008-2009.
DOI: 10.5061/dryad.2th78/1
title: ASD Controls
DOI: 10.5061/dryad.2th78/11
title: Study2_4
DOI: 10.5061/dryad.2th78/12
title: Matlab Scripts
DOI: 10.5061/dryad.2th78/13
title: PROTOCOL FOR PROCESSING RESTING EEG
DOI: 10.5061/dryad.2th78/14
title: TD Controls
DOI: 10.5061/dryad.2th78/8
title: Study2_1
DOI: 10.5061/dryad.2th78/9
title: Study2_2
DOI: 10.5061/dryad.34b84/1
title: Microsatellite genotypes

description: This is a GenAlEx file containing microsatellite genotypes for 229 individuals from 18 Dalechampia scandens populations, genotyped at 30 loci.
DOI: 10.5061/dryad.3h4m5.2/11.2
title: B9_Randomised_TreeRef6_Parts1-28branchlengths_newick

description: File_B9 (newick format).  The ClockstaR [3] treefile containing the trees with the branch  lengths for the 25 randomised morphological partitions, and the original (not randomised) 3 molecular partitions obtained from the MrBayes analysis as per file B2.  Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence.
DOI: 10.5061/dryad.3h4m5.2/12.2
title: B10_Randomised_clockstar_Results

description: File_B10 (pdf).  ClockstaR partition matrices and gap statistics for analysis using randomised morphological partitions, using the guide tree from ref [6].  From the 28 candidate partitions, the analysis preferred very many, or very few, morphological partitions, unlike the corresponding analysis of the original data (File B7, top) which preferred an intermediate number.  Note that the order of partitions in these tables (molecular partitions uppermost) is different to that in Fig. 1, but the same as in Fig. B7.
DOI: 10.5061/dryad.3h4m5.2/13.2
title: B11_ClockstaR_script

description: File_B11 (plain text). ClockstaR R script (and output) for the above analysis.  Note filenames and paths need to be changed as appropriate.
DOI: 10.5061/dryad.3h4m5.2/14.2
title: C1_PartitionFinder

description: File_C1 (zipped, plain text).  Matrix with molecular data for 46 extant taxa (extracted from [6]), in Phylip format (mammals.phy); PartitionFinder [12] command file (cfg) with 71 candidate partitions (by genes and by codons, with noncoding genes treated as single candidate partitions); best scheme with 7 partitions requiring separate substitution models, found by PartitionFinder using the Bayesian Information Criterion with unlinked branch lengths.
DOI: 10.5061/dryad.3h4m5.2/15.2
title: C2_1clock - MrBayes file

description: File_C2 (plain text).  MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using a single relaxed (independent gamma rates) clock for all traits (morphological and molecular).  The sampled ancestor birth-death tree prior [17], and the Markov model of morphological evolution [18,19], were used. Optimal substitution models and substitution-model-partitions were found with PartitionFinder for molecular data (see C1) and with stepping-stone analysis in MrBayes for morphological data as implemented in [10].  Numerous (&gt;20) MCMC runs were initially performed for 5 million generations to investigate tuning, mixing and convergence.  The final analysis was then performed with 4 runs of 20 million generations, with the first 30% of samples discarded as burnin.
DOI: 10.5061/dryad.3h4m5.2/16.2
title: C3_1clock_PostburninTrees&Params_folder

description: File_C3 (zipped, plain text).  The full MCMC tree and parameter output files from the MrBayes analysis in file C1.   Only post-burnin samples are included to reduce file sizes. Run the MrBayes file in C2 (after disabling the MCMC command and setting burnin to 0) to generate consensus trees and statistics from these files.
DOI: 10.5061/dryad.3h4m5.2/17.2
title: C4_1clock_con_fig

description: File_C4 (approximate nexus format).  The majority-rule consensus tree from the MrBayes analysis in files C1-2.  Note: the wrong file was previously uploaded onto Dryad; I thank Joseph Brown for pointing this out.
DOI: 10.5061/dryad.3h4m5.2/18.2
title: C5_1clock_topologyConvergence

description: File_C5 (pdf).  Convergence diagnostics for tree topologies sampled in C2.  (A) AWTY [20] plots demonstrating similar posterior probabilities for all clades across 4 runs, and (B) at different stages in a single run.  The topology convergence statistics from MrBayes and AWTY (standard deviation of split frequencies across runs) were also good ie low, being &lt;0.031 across all comparisons (see top right cells of panel A).  These patterns are consistent with good convergence.  The kink in one of the fitted lines appears to be an artefact of a glitch in AWTY.
DOI: 10.5061/dryad.3h4m5.2/20.2
title: C7_8clocks MrBayes file

description: File_C7 (plain text).  MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using 8 separate relaxed clocks (independent gamma rates; 7 for morphology and 1 for molecular data), as found in analysis B-3.  The sampled ancestor birth-death tree prior [17], and the Markov model of morphological evolution [18,19], were used.  Optimal substitution models and substitution-model-partitions were found with PartitionFinder for molecular data (see C1) and with stepping-stone analysis in MrBayes for morphological data [10].  Numerous (&gt;20) MCMC runs were initially performed for 20 million generations to investigate tuning, mixing and convergence.  The final analysis was then performed with 4 runs and the trees from 10 million post-burnin generations retained	Note: The burnin for each run varies considerably due to variation in time to reach (apparent) stationarity, from 20 million to 50 million.   For computational efficiency, the 4 runs were performed separately and in all cases, the last 10 million steps (after stationarity) were retained. However, the step numbers have been readjusted in file C8 below so they are all identical across runs (ie to a common burnin of 50 million), to facilitate downstream analyses e.g. generating summary statistics in MrBayes.
DOI: 10.5061/dryad.3t6sc/2
title: phase IV clinical studies received by ClinicalTrials.gov between 2004-2014

description: This dataset was downloaded from the Internet at March 18, 2015
DOI: 10.5061/dryad.4462q/1
title: Data regarding the paper "Soil management shapes ecosystem service provision and trade-offs in agricultural landscapes" (Tamburini et al. 2016)

description: The excel file contains data regarding 1) landscape composition, 2) grain yield, 3) disease incidence 4) soil organic matter content, 5) phosphorus saturation, 6) weed species richness and cover, 7) predator abundance, 8) aphid abundance and parasitism rate.
DOI: 10.5061/dryad.4fp47/1
title: SFREC_recruitment

description: Data were collected in a seed addition experiment conducted at the Sierra Foothills Research and Extension Center in central California, USA. Seeds were experimentally added to 1x1 m plots in October of 2012 (90 plots per species x 4 species). Seeds were from four species, including Elymus caput-medusae, Bromus hordeaceus, Centaurea solstitialis, and Carduus pycnocephalus. Variables are as follows: "seeds" = the combination of seeds added and estimated ambient seed rain, "recruits" = the number of stems counted, "soil.moisture" = % volumetric water content estimated using time-domain reflectometry, "biomass" =  total live biomass (g), and block = block number (1-5).
DOI: 10.5061/dryad.5003g/4
title: Primate tree

description: Full phylogenetic tree from primate 10KTree used for analyses.
DOI: 10.5061/dryad.5003g/8
title: R code for analysis

description: This R file contains the examples necessary to reproduce our analyses using the accompanying data set. This code has been written by Jamie Winternitz, who can be contacted at jcwinternitz-at-gmail-dot-com. The file consists of the nine following sections: # 1. Loading and visualizing data # 2. DIC-based model selection for random effects # 3. Heterogeneity estimation # 4. Univariate estimates of moderators and contrasts # 5. Forest plots # 6. Tests for publication bias # 7. Testing if negative MHC effect sizes (indicating similarity) differ from zero # 8. Bivariate models for MHC~Neutral marker correlations # 9. Power analysis for random-effects meta-analysis # 10. Plotting the phylogenetic signal of MHC-associated mate choice
DOI: 10.5061/dryad.5003g/9
title: Human and non-human primate dataset

description: Full dataset used for analyses.
DOI: 10.5061/dryad.5kq4r/1
title: Macquaria_australasica_experimental

description: Contains the data of the quantitative PCR analyses of all the samples from the experimental study.
DOI: 10.5061/dryad.5kq4r/2
title: Macquaria_australasica_experimental_ratios

description: Contains the data of the calculated ratios between nuclear and mitochondrial environmental DNA concentrations for the experimental study.
DOI: 10.5061/dryad.61rq8/1
title: Data associated with Ghanizadeh-Kazeroni et al

description: Excel file containing all data used in the publication. Different experimental responses are presented on separate sheets in the Excel file, and the first sheet (Metadata) provides explanations for each entry.
DOI: 10.5061/dryad.6qf10/1
title: Cuesta_etal_Gloria_Baseline-data_12.11.2016

description: Vegetation baseline data from 13 GLORIA-Andes long-term monitoring sites. The file contains: (1) a matrix of the average cover of each vascular plant species, averaged over the sixteen 1x1 m quadrats in each of the 50 summits, (2) environmental matrix that containes fine and broad-scale habitat variables for each summit, (3) A species richness matrix that contains the total number of species found in the sixteen quadrats established in each summit, and (4) a species richness matrix at the site scale
DOI: 10.5061/dryad.6vd87/1
title: seqAll_mixEUK

description: Demultiplexing file from MiSEQ sequencing (2 x 250 bp) of a Mock community (16 species) amplifiying with the following primers:960F: GGCTTAATTTGACTCAACRCG1419R:  GGGCATCACAGACCTGTTATFor obtaining this file, the paired-end reads were merged togetherusing UPARSE tools (option -fastq_mergepairs with aminimal overlap equal to 150 and no mismatch allowed) (Edgar, 2013).and the merged sequences were then submitted to the following cleaning procedures: (i) no undefined bases (Ns), (ii) a minimum sequence length of 200 bp,and (iii) no sequencing error in theforward and reverse primers.Composition of the mock community:A50 Eukaryota;Rhizaria;Cercozoa;A31 Eukaryota;Alveolata;Perkinsea;A54 Eukaryota;CryptophyceaeA34 Eukaryota;Stramenopiles;Chrysophyceae;A44 Eukaryota;Fungi;PG5-14 Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;ChlorophyceaePG5-26 Eukaryota;Alveolata;Ciliophora;PG5-28 Eukaryota;Fungi;Cryptomycota;BI109 Eukaryota;Fungi;Cryptomycota; (LKM11 clade)B24 Eukaryota;Stramenopiles;Bicosoecida;B64 Eukaryota;Fungi;Chytridiomycota;B79 Eukaryota;Fungi;Dikarya;B26 Eukaryota;Alveolata;PerkinsozoaBA97 Eukaryota;Cryptophyta;B36 Eukaryota;Stramenopiles;Ochrophyta;Chrysophyceae;BA231 Eukaryota;Alveolata;Ciliophora;Alveolate_1;
DOI: 10.5061/dryad.71qt7/2
title: Will82xDT2000-Soybean Rust-Phenotypic Data

description: Field phenotypic data collected in an RIL mapping population derived from a Williams 82 x DT2000 cross.No. of lines: 240 No. of traits studied: 4
DOI: 10.5061/dryad.73s68/1
title: Three_productivities
DOI: 10.5061/dryad.78qq7/1
title: dryad_McClure_et_al_sept2016

description: Data to accompany "QTL analysis of soft scald in two apple populations" published online 14 September 2016 in Horticulture Research, by McClure et al. (doi:10.1038/hortres.2016.43)
DOI: 10.5061/dryad.832t8/1
title: SISCpools_consensus_chr5

description: SNP calls for chromosome 5 from bulked segregant analysis.  F1s were generated from crosses between a self-incompatible and a self-compatible parent of Arabidopsis lyrata, sampled from the Great Lakes region of Eastern North America, which were then crossed amongst themselves to create F2s.   Pools were created from: 1) 10 individuals that were phenotypically self-incompatible; and 2) 10 individuals that were phenotypically self-compatible. Three lanes of separate runs (two 150 bp and one 100 bp paired-end read run) were sequenced on an Illumina GAII instrument for each pool. The Illumina quality-filtered reads were mapped against the A. lyrata reference genome sequence MN47 (Hu et al. 2011) using GenomeMapper (Schneeberger et al. 2009), allowing for up to 10% mismatches/gaps relative to the read length. All alternative alleles relative to the reference base with a minimum frequency within each pool of 10% and a score of at least 25 were called by SHORE, as described (Ossowski et al. 2008). SNP calls (in genes only) were made using SHORE and compared for the two pools against the MN47 reference and for a reference genome constructed from two self-compatible individuals (AL4).  These individuals were created by hybridisation between individuals sampled from the same population used for the self-compatible parent of the pools with the MN47 reference strain.  The genomic sequence thus was determined by subtraction from the MN47 reference.  The data file shows the SNP calls, % of reads with the variant and read coverage for that position.  See readme file for complete details.  


References 

Hu TT, Pattyn P, Bakker EG, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43, 476-481.  doi: 10.1038/ng.807
Ossowski S, Schneeberger K, Clark RM, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. 10.1101/gr.080200.108
Schneeberger K, Hagmann J, Ossowski S, et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biology 10, 1-12. 10.1186/gb-2009-10-9-r98
DOI: 10.5061/dryad.832t8/2
title: SISCpools_consensus_chr7

description: SNP calls for chromosome 5 from bulked segregant analysis.  F1s were generated from crosses between a self-incompatible and a self-compatible parent of Arabidopsis lyrata, sampled from the Great Lakes region of Eastern North America, which were then crossed amongst themselves to create F2s.   Pools were created from: 1) 10 individuals that were phenotypically self-incompatible; and 2) 10 individuals that were phenotypically self-compatible. Three lanes of separate runs (two 150 bp and one 100 bp paired-end read run) were sequenced on an Illumina GAII instrument for each pool. The Illumina quality-filtered reads were mapped against the A. lyrata reference genome sequence MN47 (Hu et al. 2011) using GenomeMapper (Schneeberger et al. 2009), allowing for up to 10% mismatches/gaps relative to the read length. All alternative alleles relative to the reference base with a minimum frequency within each pool of 10% and a score of at least 25 were called by SHORE, as described (Ossowski et al. 2008). SNP calls (in genes only) were made using SHORE and compared for the two pools against the MN47 reference and for a reference genome constructed from two self-compatible individuals (AL4).  These individuals were created by hybridisation between individuals sampled from the same population used for the self-compatible parent of the pools with the MN47 reference strain.  The genomic sequence thus was determined by subtraction from the MN47 reference.  The data file shows the SNP calls, % of reads with the variant and read coverage for that position.  See readme file for complete details.  


References 

Hu TT, Pattyn P, Bakker EG, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43, 476-481.  doi: 10.1038/ng.807
Ossowski S, Schneeberger K, Clark RM, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. 10.1101/gr.080200.108
Schneeberger K, Hagmann J, Ossowski S, et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biology 10, 1-12. 10.1186/gb-2009-10-9-r98
DOI: 10.5061/dryad.832t8/3
title: B70haplotypes

description: Alignment of haplotypes from the gene B70 (Ethylene-responsive protein related; At4g21340). Individual sequences have also been uploaded to Genbank.
DOI: 10.5061/dryad.832t8/4
title: b80haplotypes

description: Alignment of haplotypes found at B80 (U-box domain protein; At4g21350).  Sequences had been uploaded to Genbank for a previous paper (Popset accession 374282218).
DOI: 10.5061/dryad.8md28/1
title: Data for lodgepole pine forests

description: Simulation results and bark beetle susceptibility for lodgepole pine forests
DOI: 10.5061/dryad.8md28/2
title: Data for Douglas-fir forests

description: Simulation results and bark beetle susceptibility for Douglas-fir forests
DOI: 10.5061/dryad.b859k/1
title: clerc_et_al_data

description: .zip file containing two data files. clerc_et_el_adiposedata is the data that was used to compare the fatty acid compositions of the two groups of silver-haired bats. clerc_et_al_BMI_adiposedata is the data that was used to compare the body mass index of individuals that were successfully adipose biopsied and those that were unsuccessfully adipose biopsied
DOI: 10.5061/dryad.c9086/10
title: rareness coefficients

description: ## -- Table rareness -- ##
Information about the rareness coefficient (see text).

accesion: Unique accession identifier.
 r_whole: Rareness coefficient taking the whole collection.
 r_state: Rareness coefficient taking only the state collection.
  r_maiz: Rareness coefficient taking the maize (but not teosinte) collection.
    r_TE: Rareness coefficient taking only teosinte collection.
    r_PL: Rareness coefficient taking only Puebla collection.
    r_TB: Rareness coefficient taking only Tabasco collection.
    r_TL: Rareness coefficient taking only Tlaxcala collection.
    r_GT: Rareness coefficient taking only Guanajuato collection.

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
accesion	varchar(5)	YES	MUL	NULL	
r_whole	double	YES		NULL	
r_state	double	YES		NULL	
r_maiz	double	YES		NULL	
r_TE	double	YES		NULL	
r_PL	double	YES		NULL	
r_TB	double	YES		NULL	
r_TL	double	YES		NULL	
r_GT	double	YES		NULL
DOI: 10.5061/dryad.c9086/2
title: DNA_plates

description: Information about the plate that contains the DNA sample.

DNAplate_id: Numerical identifier (unique per row)
     ESTADO: State (of Mexico) where the accession was originally collected.
  DNA_plate: Plate where the DNA is stored in our facilities.
   DNA_well: Well within plate where the DNA is stored in our facilities. 
   accesion: Unique key for accession.

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
DNAplate_id	int(5)	NO	PRI	NULL	auto_increment
ESTADO	varchar(20)	NO		NULL	
DNA_plate	int(2)	NO		NULL	
DNA_well	varchar(3)	NO		NULL	
accesion	varchar(10)	YES		NULL
DOI: 10.5061/dryad.c9086/3
title: Marker / Allele combinations.

description: ## -- Table MAL -- ##
Information about the Marker / Allele combination
(all reported Marker / Allele combinations are in this table)

     unid: Numerical identifier (unique per row)
 marcador: SSR marker.
id_estado: State identifier.
  lim_inf: Lower limit of the lecture.
  lim_sup: Upper limit of the lecture. 
    alelo: Allele number. 

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
unid	int(5)	NO	PRI	NULL	auto_increment
marcador	varchar(20)	NO	MUL	NULL	
id_estado	varchar(2)	NO		NULL	
lim_inf	float	NO		NULL	
lim_sup	float	NO		NULL	
alelo	int(2)	NO	MUL	NULL
DOI: 10.5061/dryad.c9086/4
title: accessions

description: ## -- Table accession -- ##
Information about each one of the maize accessions reported.

        id: Numerical identifier (unique per row)
    acc_id: Identifier of accession.
acc_id_ori: Original accession identifier (external to our collection).
 localidad: Locality (place) where the accession was collected.
     tipo0: Type 0 (secondary type of maize, can correspond with maize race)
      tipo: Primary type of maize accession as reported by collector.
     tipo2: Type 2 (tertiary type of maize, reported by collector),
    color0: Secondary kernel color (if reported by collector).
     color: Primary kernel color (checked by our curators).
   lat_gra: Latitude of collection; degrees.
   lat_min: Latitude of collection; minutes.
   lat_seg: Latitude of collection; seconds.
   lon_gra: Longitude of collection; degrees.
   lon_min: Longitude of collection; minutes.
   lon_seg: Longitude of collection; seconds.
      asnm: Height above sea level of collection; meters.
     UTM_X: UTM X coordinate of collection.
     UTM_Y: UTM Y coordinate of collection.

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
id	int(3)	NO		NULL	
acc_id	varchar(5)	NO	MUL	NULL	
acc_id_ori	varchar(20)	YES		NULL	
localidad	varchar(100)	YES		NULL	
tipo0	varchar(50)	YES	MUL	NULL	
tipo	varchar(50)	YES		NULL	
tipo2	varchar(50)	YES		NULL	
color0	varchar(50)	YES	MUL	NULL	
color	varchar(50)	YES		NULL	
lat_gra	float	YES		NULL	
lat_min	float	YES		NULL	
lat_seg	float	YES		NULL	
lon_gra	float	YES		NULL	
lon_min	float	YES		NULL	
lon_seg	float	YES		NULL	
asnm	int(4)	YES		NULL	
UTM_X	float	YES		NULL	
UTM_Y	float	YES		NULL