cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qt3j5/1
title: Brown bear genotypes from Slovenia (Northern Dinaric Mountains) - tab delimited txt

description: The dataset contains genotypes of 513 brown bears genotyped on 20 microsatellite loci. They were obtained by genotyping tissue samples of legally killed bears between 2003 and 2008. The genotypes are mostly complete, there are missing data on a single locus in two samples (denoted "NA"). | Columns in the table: | sample - laboratory name of the sample | sex - sex of the animal (recorded by the field crew and rechecked by genotyping the SRY marker) | Genotypes: alleles at each locus are recorded in two columns, e.g. Cxx20_1, Cxx20_2. Missing data are recorded as "NA". | Note: this dataset mostly corresponds to the dataset used in the manuscript: Skrbinšek T, Jelenčič M, Waits L, Kos I, Jerina K, Trontelj P (2012). Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches. Molecular Ecology 21(4): 862-875. Data: doi:10.5061/dryad.22rm1728. This present dataset doesn't have age data for the animals, but includes genotypes of three additional individuals for which we had no age data available.
DOI: 10.5061/dryad.qt652/1
title: Transgene insertion locations and expression

description: For each transgene insertion, we provide the following information (column descriptions): 1) Promoter, Chromosome, Cytogenetic location, Sequence coordinate (Drosophila Genome release 5), Affected gene, Proximal gene (within 10 kb), distal gene (within 10 kb), Whether the transgene is in or near a testis-enriched gene, Whether the transgene is in or near a testis-biased gene, mean beta-galactosidase activity, standard deviation of beta-galactosidase activity, mean relative expression measured by qRT-PCR, standard deviation of relative expression measured by qRT-PCR. Additional notes are provided at the bottom. Format is .xls.
DOI: 10.5061/dryad.r531f/1
title: MasterMSATmegacephalusOrderedLoci_11B

description: Microsatellite data for Microdipodops megacephlaus - 11 loci, 4 populations
DOI: 10.5061/dryad.rn7c5/1
title: Shrub height

description: Positions of non-experimental Ericameria ericoides shrubs used in community analysis.  Shrub position on the stress gradient is given in m.  Canopy height given in cm.
DOI: 10.5061/dryad.ts058.1
title: Data from: Genomic and morphological evidence converge to resolve the enigma of Strepsiptera
DOI: 10.5061/dryad.ts058.2
title: Data from: Genomic and morphological evidence converge to resolve the enigma of Strepsiptera
DOI: 10.5061/dryad.ts058.2/2
title: Niehuis2012_supplementary_data_corrected.tar
DOI: 10.5061/dryad.0dn7s/3
title: Sample locations

description: GPS coordinates for each of the 14 sampled Daphnia magna populations from Storgrundet, a rocky island in the Tvarminne archipelago of Finland.
DOI: 10.5061/dryad.20mf5/1
title: data

description: This dataset aimed to assess the relative importance of evolutionary distance, dispersal mechanism and environmental conditions as drivers of plant-plant interactions in semiarid environments. For doing this, we sampled 11 Stipa tenacissima grassland communities along a climatic gradient spanning from the center to the southeast of Spain. Our study sites have annual precipitation and temperature values ranging from 273 mm to 488 mm and from 13°C to 17°C, respectively. Four environmental variables were collected for each site: irradiance, mean temperature, annual rainfall (collected from available climatic models, Ninyerola et al. 2005-Atlas Climático Digital de la Península Ibérica. Metodología y aplicaciones en bioclimatología y geobotánica. Univ. Autónoma de Barcelona, Bellaterra, Spain), and altitude. At each site we also evaluated particular pairwise interactions for the two dominant nurses in the study area (Q. coccifera shrubs and S. tenacissima tussocks) by using 0.5 m x 0.5 m quadrats (see associated article for further details). With this data, we obtained two indices, the RII (Armas et al. 2004-Ecology 85: 2682–2686) to evaluate the intensity of the interaction, and the Iimp (Seifan et al. 2010-J. Ecol. 98: 356–361) to evaluate the importance of such pairwise interactions. To complement de dataset, phylogenetic distance between the two interacting species and the dispersal mechanism of the beneficiary species were also measured or obtained from available literature. More details from the dataset are given in the “metadata” spreadsheet and in the associated article). Related databases can be found in the dryad data package Data from: Environmental conditions and biotic interactions acting together promote phylogenetic randomness in semi-arid plant communities: new methods help to avoid misleading conclusions. Provisional DOI: doi:10.5061/dryad.d24c7. Gaps in the data are in blank. Field and dispersal mechanism data were collected by S. Soliveres and F.T. Maestre, the phylogenetic distances were calculated by R.Torices. Contact for further information: Dr. Santiago Soliveres (e-mail: santiagosoliverescodina@gmail.com)
DOI: 10.5061/dryad.23g44/18
title: debruynfigS3

description: FIGURE S3.  Dermogenys+Nomorhamphus geographic range evolution.
DOI: 10.5061/dryad.23g44/20
title: debruynfigS5

description: FIGURE S5. Dermogenys+Nomorhamphus species tree based on taxonomy (A) (Collette 2004; Meisner 2001) and a priori paleo-drainage designation (B) (Voris 2000).
DOI: 10.5061/dryad.23g44/21
title: debruynfigS6

description: FIGURE S6. Hemirhamphodon species tree based on taxonomy (A) (Anderson and Collette 1991) and a priori paleo-drainage designation (B) (Voris 2000).
DOI: 10.5061/dryad.37s7b.1
title: Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
DOI: 10.5061/dryad.37s7b.2
title: Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
DOI: 10.5061/dryad.37s7b.2/1.1
title: Catharus_SpTree_AllDataNew_200mil

description: All data, species tree, Figtree file
DOI: 10.5061/dryad.37s7b.2/2.1
title: Catharus_SpTree_New_nuDNA_200mil

description: nuclear data only, species tree, Figtree file
DOI: 10.5061/dryad.37s7b.2/3.1
title: Catharus-SpTree_AllDataNew-Constrained_200mil

description: all data, constrained species tree, Figtree file
DOI: 10.5061/dryad.37s7b.2/4
title: catharusNewick
DOI: 10.5061/dryad.3t19n/1
title: All_holocentrid_ML

description: Alignment of all data for maximum likelihood analysis
DOI: 10.5061/dryad.3t19n/2
title: All_holocentrid_MB2

description: Nexus file for mrBayes analysis with all gene data and partitioning strategy identified.
DOI: 10.5061/dryad.3t19n/3
title: UCLN_ALL_StarBEAST

description: Starbeast input file for gene tree species tree analysis
DOI: 10.5061/dryad.3t19n/4
title: RLC_ALL_StarBEAST

description: Input for gene tree species tree analysis using *beast and the RLC model.
DOI: 10.5061/dryad.609t7/1
title: Tucketal2013_MetaAnalysisData

description: Data set for the publication associated with this Dryad data package, on a meta-analysis on the effects of organic vs conventional farming on biodiversity. This data set contains data collected from the literature, including data necessary for calculating effect sizes, data on taxa and crop type subgroups among effect sizes, and descriptive data giving context of the studies. The data set also includes data collected from Google Earth on the surrounding landscape complexity and heterogeneity for each effect size. The method used to collect these data are described in the associated publication. The data set CSV file was created using Microsoft Excel 2013. See README for more details and metadata.
DOI: 10.5061/dryad.609t7/2
title: PublicationAnalysisScript

description: R code (using R 3.0.1) used for the analysis of the data set for the associated publication. See README for information on how to run the code.
DOI: 10.5061/dryad.653f7/1
title: Genotype and phenotype data of 4 great tit populations
DOI: 10.5061/dryad.6b7c1/1
title: angiosperm-rps11

description: Subset of data obtained under Supplementary Figure 3 from:http://www.nature.com/nature/journal/v424/n6945/suppinfo/nature01743.html
DOI: 10.5061/dryad.6h82b/1
title: flowering phenology data file for 2007

description: Metadata is in file "flPhenology.xy.C1.readMe.txt"
DOI: 10.5061/dryad.6h82b/2
title: flowering phenology data file for 2006

description: Metadata is in file "flPhenology.xy.C1.readMe.txt"
DOI: 10.5061/dryad.6h82b/3
title: flowering phenology data file for 2005

description: Metadata is in file "flPhenology.xy.C1.readMe.txt"
DOI: 10.5061/dryad.6h82b/4
title: Analysis of 2007 dataset- R script

description: Information about this R script is in file "flPhenology.xy.C1.readMe.txt"
DOI: 10.5061/dryad.6r52k/1
title: NowakPlastidData_4Dryad

description: Plastid sequence alignment used for divergence time estimation in the genus Coffea.
DOI: 10.5061/dryad.6r52k/2
title: NowakSAlleles_4Dryad

description: Alignment of Coffea S-RNase allele sequences used for evaluating the extent of trans-specific polymorphism between Madagascan/African Coffea and Mauritian Coffea.
DOI: 10.5061/dryad.6r52k/3
title: Nowak2014_Dryad

description: Results of individual-based simulations conducted to estimate the number of founding individuals responsible for the colonization of Mauritius by Coffea.
DOI: 10.5061/dryad.7287d/1
title: Firman et al. DRYAD
DOI: 10.5061/dryad.8066v/1
title: Genotype data
DOI: 10.5061/dryad.8566p/5
title: Coleman et al. Dwarf galaxias COI haplotype sequences

description: COI haplotype sequences from fin tissue samples collected from 51 dwarf galaxias populations throughout southeast Australia. These haplotype sequences are available from Genbank under accession numbers KC282473 (Hap1)- KC282523 (Hap51).
DOI: 10.5061/dryad.8566p/6
title: Coleman et al. dwarf galaxias CytB haplotype sequences

description: CytB haplotype sequences from fin tissue samples collected from 51 dwarf galaxias populations throughout southeast Australia. These haplotype sequences are available from Genbank under accession numbers KC282539 (Hap1) - KC282620 (Hap82).
DOI: 10.5061/dryad.8j1hb/3
title: ACP.rain.summary_DRYAD

description: The data in this file are summarized rainfall data for each year between 1972-2010. Rainfall data are from the Panama Canal Authority weather station in Gamboa, Panama, and are freely available for download from the Smithsonian Tropical Research Institute. For the purposes of analyses, I defined the rainy season as May 15-November 15.
DOI: 10.5061/dryad.8kq65/22
title: Asimple
DOI: 10.5061/dryad.8kq65/23
title: cytbsimple
DOI: 10.5061/dryad.8kq65/24
title: GAPDsimple
DOI: 10.5061/dryad.8kq65/25
title: ITS1bsimple
DOI: 10.5061/dryad.8kq65/26
title: RAG1simple
DOI: 10.5061/dryad.9v216/1
title: Casupo_13loci_1pop

description: genotypes of 13 microsatellite loci; Venezuelan guppies; field data; genepop file format
DOI: 10.5061/dryad.9v216/2
title: phenotypic_traits

description: Body length, height, total area of orange spots measured on the right side of the body, multilocus heterozygosity (MLH) in 9 loci in Hardy-weinberg equilibrium and in all 13 loci, for each guppy male. Individuals in the same order as in the genepop file with genotypes.
DOI: 10.5061/dryad.cb0f6/1
title: Holman et al Am Nat - Dryad raw data

description: The absolute raw data for the study. Columns show AntID (simply an identifier for that individual), its caste, head size, ovary development measure, and the cuticular chemical data. The latter are the outputs provided by MSD Chemstation and represent the area under the peak in question. These can be transformed to proportions, or to an absolute amount in ng (using the area of the internal standard peak and the correct transformation; see paper for injection volume and concentration).
DOI: 10.5061/dryad.dm08j/1
title: Mesquite file

description: Nexus file with the list of 1018 species native to LVV and their occurrence coded on a standard matrix. Both MP and ML trees included, both Stochastic and MP mappings activated accordingly.
DOI: 10.5061/dryad.f05mk/1
title: Data_Buoroetal2012_JEB

description: Data collected in the field (Scorff river, France). Data file was created using R software. Description of abbreviations can be find in article and code.
DOI: 10.5061/dryad.f05mk/2
title: Models_Buoro et al 2012_JEB

description: Code of the model. Bayesian analysis were conduct using OpenBUGS software.
DOI: 10.5061/dryad.g7046/1
title: Presence-absence dataset of earthworm species in France

description: Presence – absence for each earthworm species at the different localities in France, and information about localities.Contact ---------------------------------For any information please contactJerome Mathieujerome.mathieu@upmc.frSource of the data : Bouché, M.B. (1972) Lombriciens de France: ecologie et systématique. INRA, Paris.
DOI: 10.5061/dryad.g7046/2
title: Traits of earthworms species in France

description: each line is a species, based on Fauna Europaea taxonomy. www.faunaeur.org. This means that we aggregate subspecies into species in some cases. Each column is a trait.species_code : code of the species in sites&species.txtspecies.name : names of the species according to Fauna EuropaeaOther columns describe species characteristicscontact ---------------------------------For any information please contactJerome Mathieujerome.mathieu@upmc.frSource of the data : Bouché, M.B. (1972) Lombriciens de France: ecologie et systématique. INRA, Paris.
DOI: 10.5061/dryad.g9117/1
title: Hynobiidae 12S-ND2 data

description: NEXUS formatted alignment (including a list of excluded characters) of the mitochondrial DNA sequence data used in this study. Museum accession numbers and Genbank accession numbers are provided for each OTU. Qualifier lines are provided with structural information for each gene region.
DOI: 10.5061/dryad.gg3rn/1
title: msat_sequences

description: This file contains the nucleotide sequence information for the described microsatellite markers. Primer sites are indicated in the sequences.
DOI: 10.5061/dryad.h4b48/1
title: HEAA_MER_Data+Scripts

description: This .zip archive contains two directories. The 'Data' directory contains the measured levels of CpG methylation at various places in the humpback whale genome. The 'Scripts' directory contains the R scripts used to analyse this data.
DOI: 10.5061/dryad.hf95d/1
title: Data from RSPB-2013-2843

description: Raw data file from Sánchez-Macouzet et al. 'Better stay together: pair bond duration increases individual fitness independent of age-related variation'
DOI: 10.5061/dryad.j3r20/1
title: Main data set
DOI: 10.5061/dryad.jp13f/1
title: Microsatellite Data for Waselkov and Olsen 2014

description: Microsatellite data for all 38 populations of Amaranthus tuberculatus and all 10 microsatellite loci used in Waselkov and Olsen 2014.  Data is in STRUCTURE format, two lines per individual, with "-9" indicating missing data.
DOI: 10.5061/dryad.k41qk/12
title: 9_LWRh_110722
DOI: 10.5061/dryad.k41qk/13
title: IMa2_AKAM110610_Mito
DOI: 10.5061/dryad.k41qk/8
title: 6_COXlike_110713
DOI: 10.5061/dryad.m7rc3/1
title: TCS input files

description: This is a ZIP file consisting of 33 separate input files for the program TCS version 1.21 (Clement et al. 2000), which creates haplotype networks.  Each file is a separate species.  All specific haplotype details can be found in Table S2 of the online Supporting information for this paper.  Species codes: AA = Ambassis agassizi, AM = Ambassis marianus, AS = Australatya striolata, CA = Caridina indistincta "A", CB = Caridina indistincta "B", CC = Caridina indistincta "C", CH = Cherax dispar "C", CM = Craterocephalus marjoriae, CP = Caridina sp. "D", CS = Craterocephalus stercusmuscarum, GA = Gobiomorphus australis, GP = Glossamia aprion, HC = Hypseleotris compressa, HG = Hypseleotris galii, HK = Hypseleotris klunzingeri, HM = Hypseleotris sp. Midgleys, LU = Leiopotherapon unicolor, MA = Mogurnda adspersa, MD = Melanotaenia duboulayi, MT = Macrobrachium tolmerum, MU = Macrobrachium australiense, NE = Nematalosa erebi, NO = Nannoperca oxleyana, P4 = Paratya australiensis "4", P6 = Paratya australiensis "6", PA = Philypnodon macrostomus, PG = Philypnodon grandiceps, PM = Pseudomugil mellis, PR = Porochilus rendalhi, PS = Pseudomugil signifer, RO = Rhadinocentrus ornatus "SEQ", RS = Retropinna semoni "SEQ", TT = Tandanus tandanus.
DOI: 10.5061/dryad.m7rc3/2
title: Arlequin input files

description: This is a ZIP file consisting of 33 separate Arlequin input files.  Arlequin version 3.5 (Excoffier et al. 2005) was used to calculate overall ΦST for each species separately (populations grouped into river basins).  All specific haplotype details can be found in Table S2 of the online Supporting information for this paper. Species codes: AA = Ambassis agassizi, AM = Ambassis marianus, AS = Australatya striolata, CA = Caridina indistincta "A", CB = Caridina indistincta "B", CC = Caridina indistincta "C", CH = Cherax dispar "C", CM = Craterocephalus marjoriae, CP = Caridina sp. "D", CS = Craterocephalus stercusmuscarum, GA = Gobiomorphus australis, GP = Glossamia aprion, HC = Hypseleotris compressa, HG = Hypseleotris galii, HK = Hypseleotris klunzingeri, HM = Hypseleotris sp. Midgleys, LU = Leiopotherapon unicolor, MA = Mogurnda adspersa, MD = Melanotaenia duboulayi, MT = Macrobrachium tolmerum, MU = Macrobrachium australiense, NE = Nematalosa erebi, NO = Nannoperca oxleyana, P4 = Paratya australiensis "4", P6 = Paratya australiensis "6", PA = Philypnodon macrostomus, PG = Philypnodon grandiceps, PM = Pseudomugil mellis, PR = Porochilus rendalhi, PS = Pseudomugil signifer, RO = Rhadinocentrus ornatus "SEQ", RS = Retropinna semoni "SEQ", TT = Tandanus tandanus.
DOI: 10.5061/dryad.mm54f/1
title: Gene trees and alignments for Musa gene orthogroups

description: These are the orthogroup gene trees and alignments that were used to phylogenetically place the polyploidy events suggested by the Musa acuminata genome.  See the README files for a complete description.
DOI: 10.5061/dryad.mr67p/3
title: LGM_TMM_asc

description: LGM bioclim layers (30 arc sec resolution) of Tanzania, Malawi, and Mozambique
DOI: 10.5061/dryad.mt5sj/1
title: Microsatellite genotype data

description: Microsatellite genotype data
DOI: 10.5061/dryad.nd358/1
title: Chromatic and luminance wing-background and wing-wing contrasts

description: Contains chromatic and luminance wing-background and wing-wing contrasts.
DOI: 10.5061/dryad.q2070/1
title: Impacts of night warming in hot days on aphid

description: Development time, rate and survival of nymph, fecundity and longevity of adult, and life table parameters
DOI: 10.5061/dryad.q5570/1
title: COI and 16s combined aligned

description: Concatenated sequence alignments of COI and 16S, respectively. Used in AMOVA and Phylogenetic analyses.
DOI: 10.5061/dryad.r531f/2
title: MasterMSATpallidusOrderLoci_11B

description: Microdipodops pallidus raw microsatellite data - 10 loci, 2 populations.
DOI: 10.5061/dryad.rd0f6/1
title: Data on latitude and wing length  of calopterygid damselflies (including Tables S1 and S2)

description: "WingLengthAndLatitudinalData.xlsx" is an Exel file consisting of three sheets with data used in the comparative analyses of this paper. The data sheet "Wing Pigment" has wing pigment data from males and females (Table S1). The data sheet "Range Info" has range information for the damselfly species used (Table S2). Finally, the data sheet "Body Size" lists the average total body size of the male species in mm. Total body size is measured from the tip of the head to the tip of the abdomen. Body size data were taken from field guides.
DOI: 10.5061/dryad.rd0f6/10
title: Field body temperature data obtained from IR-photography for male and female Calopteryx splendens and C. virgo

description: Data are field body temperatures and ambient temperatures of 200 individual male and female Calopteryx splendens and C. virgo during the summers of 2009 and 2010 at "Klingavälsåns Naturreservat" (Lunds Kommun, Scania, Sweden). These data are shown in Figure 6C in the article, where the species-specific regression lines are illustrated, and the statistical analyses are shown in Figure S4.
DOI: 10.5061/dryad.rd0f6/11
title: Laboratory experiments on heating rate differences of male and female Calopteryx splendens and C. virgo

description: Data come from a laboratory heating experiment on field-caught male and female Calopteryx splendens and C. virgo during 2009 and 2010, from two field localities: "Klingavälsåns Naturreservat" and "Höje Å, Värpinge", both in southern Sweden. Thorax temperatures were measured using IR-camera prior to heating and after three minutes under a heating lamp. Statistical analyses are provided in Table S5 and the species-specific differences in heating rates are illustrated in Figure S3.
DOI: 10.5061/dryad.rd0f6/12
title: Phenology (date of emergence) for Calopteryx splendens and C. virgo at "Klingavälsåns Naturreservat" in 2002 and 2003

description: Data are individual emergence records (daily counts) of male and female Calopteryx splendens ("CSMale" and "CSFemale", respectively) and C. virgo ("CVMale" and "CVFemale", respectively) at "Klingavälsåns Naturreservat" (Scania, Lunds Kommun, Sweden) during the summers of 2002 and 2003. These data are shown in the article in Figure 6A.
DOI: 10.5061/dryad.rd0f6/2
title: File containing information about the phylogenetic tree used in this paper (in NEXUS-format)

description: "TreeFile" is a nexus format tree file of Calopterygoid damselflies (Odonata: Zygoptera). The tree includes branch labels and lengths, male pigment state, and latitude state. The phylogenetic tree is based on Dumont et al. 2005 Systematic Biology.
DOI: 10.5061/dryad.rd0f6/3
title: Table S3: Additional and complementary BiSSE diversification analyses, excluding different genera

description: Estimated rate parameters from BiSSE diversification analyses when temperate taxa and the ambiguous tropical genera Hetaerina and Mnesarete were excluded (Table 4; Fig. S1). “Temperate taxa excluded” means that those taxa with a ranges above 23° N were excluded from the tree. “All genera, Ambiguous taxa of Mnesarete clear” means no genera were excluded but taxa in the genus Mnesarete with very small (&lt; 5 cells) wing spots were classified as clear-winged. “Temperate taxa, Hetearina and Mnesarete excluded” means these genera and taxa were deleted from the tree. “Temperate taxa excluded”, Hetearina and Mnesarete as clear-winged” means that temperate taxa were excluded and the genera Hetearina and Mnesarete were classified as clear-winged.
DOI: 10.5061/dryad.rd0f6/4
title: Table S4: Analysis of species-specific thermal reaction norms of Calopteryx splendens and C. virgo

description: General Linear Model (GLM), involving three factors (Year, Species, Sex) one continuous covariate (Ambient temperature) and all two-way interactions. Data from Klingavälsåns Naturreservat from the summers of 2009 and 2010 (N = 200). The significant Species * Ambient temperature interaction in the table is illustrated in Fig. 6C (see Results). This interaction show that the two species (C. splendens and C. virgo) differ significantly in the slopes of their thermal reaction norms. Full model: r2 = 0.216; F10,189 = 6.481; P &lt; 0.001.
DOI: 10.5061/dryad.rd78f/1
title: Family means

description: Maternal family means of fitness components and total fitness, which are used to calculate treatment means and estimates of inbreeding depression presented in Table 1 and Figs. 1 and 2. Variable names are explained in the file.
DOI: 10.5061/dryad.rn7c5/2
title: Sand Size

description: Sand particle size and coarse organic matter content in soil samples from 46 paired shrub and shrub-free patches.
DOI: 10.5061/dryad.rn7c5/3
title: Soil Carbon

description: Carbon content in soil samples from a subset of the 46 shrub-free and shrub covered patches.