cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.125/15
title: Adelie Penguin Data Set

description: BEAST input files for ancient DNA data sets. Substitution modelswere selected by comparison of Akaike Information Criterion scores,and coalescent priors were chosen using Bayes Factor analysis.
DOI: 10.5061/dryad.125/16
title: Chlorobium Data Set
DOI: 10.5061/dryad.125/17
title: Data Sets and Population Genetic Statistics

description: Summary and neutrality statistics, model abbreviations, and data sources.
DOI: 10.5061/dryad.125/18
title: Boar Data Set
DOI: 10.5061/dryad.125/19
title: Moa Data Set
DOI: 10.5061/dryad.1950/1
title: Ord-TJ-52185R2_data

description: Raw data on background motion occurring in video footage recorded of male Anolis lizards on their territories on Puerto Rico and Jamaica
DOI: 10.5061/dryad.58pq3/1
title: Fierst.Dryad

description: Simulation results
DOI: 10.5061/dryad.7986/1
title: Chinook SNP-Baseline_105loci_10-26-09_HessRevisedONCOR

description: Columbia River Chinook salmon field collectionsGenotypic data are formatted for the software program ONCOR13 microsatellite loci are listed firstFollowed by 92 SNP lociColumns are genotypes at each locus."POP" delineates each collection/population
DOI: 10.5061/dryad.8579/2
title: Machac et al Phylogeny

description: Nexus format of the phylogeny used in our study "Range size heritability in Carnivora is driven by geographic constraints".
DOI: 10.5061/dryad.gc251/1
title: data for dryad_JEB

description: Dataset Key: 1. Is nest-guarding dependent upon nest location? This experiment tested whether the propensity of female lizards to attack egg-eating snakes varied depending upon whether the female was in the nest-site in which she originally laid eggs, or displaced to a novel site located nearby. We tested each female twice: once after displacing the female to a novel nest site located approximately 120 cm from the nest in which she originally laid eggs, and again after the female returned to the original nest. 2. Effects of recent disturbance. We tested for effects of recent disturbance (i.e., moving the female to a novel nest-site) by monitoring the anti-predator responses of an additional 40 egg-guarding females that were disturbed and then immediately tested against an intruding snake. Disturbance consisted of removing a female from her original nest hole, measuring and weighing it, and then returning it to the same hole. Immediately thereafter we encouraged a snake to enter the nest hole. 3. Will females guard conspecific eggs? This set of experiments tested the hypothesis that females can recognize their own eggs, which should result in females failing to defend the eggs of a conspecific. We removed the eggs from nest-guarding females (N = 28, clutch size ranging from 6-8) and immediately either returned the same eggs to the nest (N = 14 females) or replaced them with the same number of eggs from a different female (N = 14 females). We then introduced a snake and recorded the response of each female. 4. Do females defend their shelter-site prior to laying eggs? We re-visited a different set of trials conducted by Huang (2006; Huang, W.-S. 2006. Parental care in the long-tailed skink, Mabuya longicaudata on a tropical Asian island. Animal Behaviour 72:791-795.) on female long-tailed skinks to determine whether reproductive status influences anti-predator behavior towards egg-eating snakes. We divided the 107 females from Huang (2006) according to whether they were gravid (N = 12) or not gravid (N = 95). Female lizards were then tested against an intruding snake and the lizard’s response was recorded.
DOI: 10.5061/dryad.m7n455k0/1
title: Parham et al_Online Appendix  1

description: Example of a justified calibration from hominin primates: (human-chimpanzee node).
DOI: 10.5061/dryad.125/2
title: Bison Data Set
DOI: 10.5061/dryad.125/20
title: Aurochs Data Set

description: BEAST input files for ancient DNA data sets. Substitution modelswere selected by comparison of Akaike Information Criterion scores,and coalescent priors were chosen using Bayes Factor analysis.
DOI: 10.5061/dryad.125/3
title: Cave Bear Data Set
DOI: 10.5061/dryad.125/4
title: Brown Bear Data Set
DOI: 10.5061/dryad.125/5
title: Bowhead Whale Data Set
DOI: 10.5061/dryad.125/6
title: Cave Lion Data Set
DOI: 10.5061/dryad.125/7
title: Cow Data Set
DOI: 10.5061/dryad.125/8
title: Cave Hyaena Data Set
DOI: 10.5061/dryad.125/9
title: Muskox Data Set
DOI: 10.5061/dryad.1783/1
title: Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate

description: AFLP dataset comprising Nacella concinna Antarctic Peninsula populations
DOI: 10.5061/dryad.1868/1
title: CignobilisCmelampygusTOTALATPase6ATPase8COMBINED.nex

description: Mitochondrial ATPase 6 and ATPase 8 DNA sequences utilized in the study in NEXUS format. Also see README file.
DOI: 10.5061/dryad.2003/4
title: Survival and reproduction of lice in incubator across humidity levels

description: This file contains all the data for the incubator survival and reproduction experiments.  It includes adult survival data, number of surviving nymphs per female, and number of eggs laid per female for both C. macrourae3 and C. baculoides at 4 different relative humidity levels (70%, 60%, 50% and 40%).
DOI: 10.5061/dryad.2003/5
title: Change in mass of C. macrourae3 and C. baculoides in incubator

description: This file contains the data for the short-term weight loss trial in an incubator.  It includes average weights for groups C. macourae3 and C. baculoides before and after time spent in a low humidity environment.
DOI: 10.5061/dryad.4pt8h/1
title: Supplementary Materials

description: GMT and R code used in extracting and analyzing data.
DOI: 10.5061/dryad.6mk023c0/2
title: Supplementary Table 1

description: Specimens examined, habitat and measured values of parameters: M = marine species; F = freshwater species; L = land species; SUM = Shizuoka University; SHIN = Shinshu University; BPBM = Bishop Museum; SPMN = Network for Shizuoka Prefecture Museum of Natural History; UMUT = University Museum, University of Tokyo.
DOI: 10.5061/dryad.8042/1
title: Policing_and_worker_fecundity_data

description: Worker policing, queen policing, workers and queens fecundity, survival of worker-laid eggs and queen-laid eggs according to colony size (large colony: 100 workers, small colony: 40 workers) and relatedness among workers in a colony (homogeneous colony: r = 0.75, heterogeneous colony: r = 0.1875).We observed three behavioral patterns: fertile workers were (1) policed by workers, or (2) not policed but self-restrained from reproduction, or (3) non-policed and continued reproduction. We observed colonies where (1) all fertile workers were policed, (2) all fertile workers were not policed and continued reproduction, (3) all fertile workers were not policed but self-restrained from reproduction, and (4) mixture of policing, continued worker reproduction and self-restraint took place.
DOI: 10.5061/dryad.8042/3
title: Colony_size_and_productivity

description: Production of new workers, males and female sexuals by  40 colonies of the ant Temnothorax unifasciatus. The colonies were collected in the field during hibernation time. After three months at artificial summer conditions (day/night: 12h/12h, 25oC/20oC) the colonies began to produce pupae of workers, males and female sexuals. All adults and the eclosing individuals were counted. The data are corrected for different body weight of freshly enclosed  workers (0.107 mg), males (0.16 mg) and female sexuals (0.8 mg).
DOI: 10.5061/dryad.8075/1
title: Locality_data

description: To obtain general information relating to the occurrence of the three pine species and facilitate representative sampling of occurrence points from their whole ranges, we first referenced their distributions described by the Flora of China and the Chinese Virtual Herbarium (CVH) (http://www.cvh.org.cn/englishindex.asp) database. Many of the occurrence records for pine species in the CVH database lack exact geo-coordinates, so we used the information available in the database as a guide, and carried out extensive field surveys to assess the distribution of the three pines in the period 2003 - 2010. In total, we collected 412 geo-referenced occurrence records; 115 for Pinus densata, 149 for P. tabuliformis, and 148 for P. yunnanensis.
DOI: 10.5061/dryad.8078/1
title: Appendix A

description: Evolutionary rates database
DOI: 10.5061/dryad.8098/1
title: Dataset of taxa pair node ages
DOI: 10.5061/dryad.8178/2
title: Species composition

description: A sub sample of bacterial isolates were sequenced at the 16s region (data deposited on NCBI). Here we show the composition of isolates, to the genus level, from each tree we examined and from the surface and interior of leaves.
DOI: 10.5061/dryad.f1468/1
title: 11001 Supplementary Table 1

description: Table of measurements for lower molars (m1 - m3) for all taxa examined in this study. Data compiled from museum collection specimens (abbreviations detailed), from literature sources (detailed) and from specimens collected by the authors (Honda Group in the middle Magdalena Valley, Colombia).
DOI: 10.5061/dryad.m7n455k0/2
title: Parham et al_Online Appendix  2

description: Data for Online Appendix 1 and figure 3.
DOI: 10.5061/dryad.m7n455k0/3
title: Parham et al_Online Appendix 3

description: Examples of justified and unjustified fossil calibrations from ‘non-traditional’ nodes.
DOI: 10.5061/dryad.qt0c2/1
title: 10066 Supplemental Materials

description: Hierarchical categorization of non-infaunal marine Phanerozoic macroinvertebrates according to visual capabilities, and main sources.  1 = blind or very poor vision; 2 = limited vision; 3 = well-developed vision. See main article for details.
DOI: 10.5061/dryad.r4j63pg0/1
title: Sambatti et al data archive

description: This gives an overview of the contents of all remaining data files.
DOI: 10.5061/dryad.1257/2
title: Anolis_krugi_ND2.sqn
DOI: 10.5061/dryad.1261/1
title: Fig. S1
DOI: 10.5061/dryad.1261/2
title: Table S1
DOI: 10.5061/dryad.1261/3
title: Table S2

description: Arlequin input file containing the multilocus genotype of 510 Apis mellifera scutellata drones collected at a single DCA over a period of 3 years. The 12 loci employed for genotyping are shown in the first line. The collection date of each sample is given as Ma, No, Ap, Se and De, referring to March 2004, November 2004, April 2007, September 2007 and December 2007, respectively.
DOI: 10.5061/dryad.1266/1
title: Phylogenic tree of BD080526
DOI: 10.5061/dryad.1271/1
title: data_set_480ind_six_microsat.xls

description: 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci.
DOI: 10.5061/dryad.1272/1
title: Aligned DNA sequences of Arthroleptis xenodactyloides

description: A nexus file containing aligned mitochondrial DNA sequences of Arthroleptis xenodactyloides and related species. Sequences aligned using ClustalX and then trimmed.
DOI: 10.5061/dryad.1276/1
title: C.egesta_alignment_4Dryad.nex

description: Alignment file used for phylogenetic and population genetic analyses on "phylogenetic" dataset described in the article.
DOI: 10.5061/dryad.1280/1
title: Microsatellite genotypes for Pinus pinaster. Spatial genetic structure in Spain
DOI: 10.5061/dryad.6m0f6870/1
title: Mokkonen_etal_empirical_data

description: Data collected from the field experiment and used to generate statistics presented in article. Mf: high-dominance males with low-fecundity sisters, mF: low-dominance males with high-fecundity sisters.
DOI: 10.5061/dryad.6mk023c0/3
title: Supplementary Table 2

description: Lists of repeated measurement of the Raup’s parameter. These lists were obtained from 30-repeated measurement of each specimen.
DOI: 10.5061/dryad.6mk023c0/4
title: Supplementary Table 3

description: Statistics for each the Raup’s parameter of each specimen: Min = minimum; Q1 = lower quartile; Q3 = upper quartile; Max = maximum; SD=standard deviation; CV=coefficient of variation.
DOI: 10.5061/dryad.6mk023c0/5
title: Supplementary Figure 1

description: Three-dimensional contour diagrams depicting the postural stability (1/Λ) and the available space for soft-body (E) values on the Γ-Δ apertural inclination morphospace for various combinations of the translation rate T and umbilical width D (for the whorl translation rate W = 100.2). The positions of actual specimens with parameters close to the values depicted on the diagrams are plotted by symbols representing their respective habitats (land, freshwater, and marine). The criterion for including a specimen on the diagram is that the measured parameters (W, T, and D) fall within a certain range of the plotted values ( , Ts, and Ds), such that W = , T = Ts ± 0.5, and D = Ds ± 0.1.
DOI: 10.5061/dryad.6mk023c0/6
title: Supplementary Figure 2

description: Contour diagrams of 1/Λ (above) and E (below) on the same morphospace shown in Supplementary Figures 1, but with a whorl translation rate of W = 100.6 (see Supplementary Fig. 1 for details.)
DOI: 10.5061/dryad.6mk023c0/7
title: Supplementary Figure 3

description: A, B. Nerita chamaeleon (interim number 700). C, D. Terebra areolata (interim number 2141). E, F. Achatina fulica (interim number L-288). G, H. Acavus haemastoma (interim number L-523). I, J. Aegista vermis (interim number L-93). A, C, E, G, and I. Model parameters are determined from measurements of specimens viewed from lateral (A, C, E, G, and I) and umbilical (B, D, F, H, and J) perspectives. All scale bars, 2 cm.
DOI: 10.5061/dryad.6mk023c0/8
title: Supplementary Figure 4

description: Box and whisker diagrams of each ’of Raup’s parameters. These plots summary sample minimum (Min), lower quartile (Q1), median, upper quartile (Q3), and sample maximum (Max). Black cross (×) indicates the mean of sample.
DOI: 10.5061/dryad.7891/2
title: thousand-constant-rate-trees.tre

description: 1000 phylogenies simulated with the same parameters than the above one (the Newick file was compressed with gzip)
DOI: 10.5061/dryad.7919/1
title: Pseudo-ekmanii-data-set

description: Excel file formated for Genalex
DOI: 10.5061/dryad.8032/1
title: data file DRYAD

description: This file contains the final DNA sequence assembly. DNA sequences: Genbank accession numbers, FJ556592 (Mlh-DDX3Y5); FJ556591 (Mph-DDX3Y5); FJ556593-FJ556597 (mtDNA haplotypes: Mlh1-Mlh17, Mustela lutreola;  Mph25-Mph28, Mustela putorius); FJ589734 (mtDNA haplotype for Mustela sibirica); FJ589735 (mtDNA haplotype for Neovison vison).
DOI: 10.5061/dryad.8075/2
title: Environmental variables

description: To obtain information about the local niches of the three pines, we initially compiled information about 34 environmental variables. The detailed information is listed in this data file.
DOI: 10.5061/dryad.8181/2
title: Phenotype Data

description: This file includes the growth profile data obtained for the parental strains and all segregants. All the yeast segregants are available at the National Culture Yeast Collection (www.ncyc.co.uk/)
DOI: 10.5061/dryad.8343/1
title: habitat character states for Arctostaphylos

description: 1 = chaparral, 2 = forest, 0 = both
DOI: 10.5061/dryad.8913/1
title: Unique MtDNA sequences

description: see README file for key to mtDNA unique sequences; each unique sequence corresponds to one or more field codes, each of which corresponds to an individual frog.
DOI: 10.5061/dryad.8913/15
title: Partial Mantel: Phil sympatry distance

description: Philippine limnonectes sympatry distances for partial mantel test
DOI: 10.5061/dryad.8913/31
title: Locality information

description: Locality information for genetic samples in this study
DOI: 10.5061/dryad.8959/1
title: CDcriscioneME2011lefu507

description: The data file is in the format for CONVERT, a conversion program.  The data include all N=507 individuals used at the start of the analyses and are pre-analysis of identical MLGs or clustering (see publication for details on analysis progression).  There are 7 microsatellite loci and individuals are separated into populations (which are 12 individual hosts, ie infrapopulations).
DOI: 10.5061/dryad.8962/1
title: Irisarri2011_Pipidae_nuclear

description: Nexus file containing the alignment of partial sequences of nine nuclear genes for anurans. The sequences correspond to data retrieved from GenBank and complemented with newly generated sequences of partial nuclear genes. In some cases, chimerical sequences were constructed by merging sequences from different species of the same genera, for which strong evidence exist of being monophyletic.
DOI: 10.5061/dryad.1225/1
title: abundances-S California 1975.xls

description: Proportional abundances of bivalve species in living and death assemblages sampled on the southern California shelf. Living assemblages are represented by unpublished data from the 1975 BLM-funded survey conducted by Alan Hancock Foundation, which we have digitized from rescued print-outs. Death assemblages - data generated by authors of this paper from unprocessed sieve residues of these same samples, archived by the Los Angeles County Museum of Natural History. Mesh size 2 mm. In this study, 2 habitats are represented by sandy muds and muddy sands ranging from 30 to 90 meters of water depth. All stations are outside the impact areas of publicly operated wastewater outfalls.  See the excel file with environmental assignment and samples sizes for each station (sample size can be used to recompute proportional into absolute abundances).
DOI: 10.5061/dryad.1225/2
title: abundances-S California 2003.xls

description: Proportional abundances of bivalve species in living and death assemblages sampled on the southern California shelf. Living assemblages are represented by unpublished data from the 1975 BLM-funded survey conducted by Alan Hancock Foundation, which we have digitized from rescued print-outs. Death assemblages - data generated by authors of this paper from unprocessed sieve residues of these same samples, archived by the Los Angeles County Museum of Natural History. Mesh size 2 mm. In this study, 2 habitats are represented by sandy muds and muddy sands ranging from 30 to 90 meters of water depth. All stations are outside the impact areas of publicly operated wastewater outfalls.  See the excel file with environmental assignment and samples sizes for each station (sample size can be used to recompute proportional into absolute abundances).
DOI: 10.5061/dryad.1225/3
title: Station information.xls

description: Sample sizes of living and death assemblages and sedimentologic, geographic and bathymetric information about the position of individual stations sampled in 1975 and 2003 in the southern California Bight. Stations with muddy sand and sandy mud were analyzed in this study (four habitats in total).
DOI: 10.5061/dryad.1284/1
title: DATA-MEC-09-0209.xls

description: Molecular and Phenotypic data for trees sampled in the field. Plant material: leaves of the current year. Excel file.
DOI: 10.5061/dryad.1285/1
title: Brown trout microsatellite data

description: The file contains microsatellite data (21 loci) from six wild brown trout populations in Western Jutland, Denmark, along with samples from two hatchery strains used for stocking the rivers. The samples from the wild populations consist of contemporary samples (2000-2006) and historical pre-stocking samples (1927-1956), the latter obtained by analyzing DNA from archived scale samples. See Hansen et al. (2009) for further details on the data and study. The file format is MSA [Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167–169].
DOI: 10.5061/dryad.1292/1
title: GenotypeData100304.txt

description: This data is simple tab delimited text and its line break style is UNIX. It contains 9 microsatellite genotypes of 142 maternal trees and 1216 their seeds. In column headings, pop, family, fruit indicates population code, family and fruit ID, respectively. Fruit ID, whose value is 0, indicates that the individual is the maternal tree of seeds that has the same family ID of it. Lia and Lib indicates first and second alleles of the loci, respectively. Li_oc and Lall_oc indicates the outcrossing status of ith locus and over all loci. For example, if the value of L1_oc is 0 or 1, the status of first locus is selfed or outcrossed, respectively. NA indicates no data.
DOI: 10.5061/dryad.1794/1
title: osemales.TXT

description: These data were collected in the Monterey Bay, CA, extracted and sequenced. The file is a nexus file created by MacClade and edited for submission to GenBank.
DOI: 10.5061/dryad.1844/2
title: moller-krull2007-molbiolevolphy.tre
DOI: 10.5061/dryad.1844/3
title: Moller-Krull2007-MolBiolEvol.nex
DOI: 10.5061/dryad.1978/1
title: 7-protein sequence alignment of Synura petersenii

description: The concatenated 7-protein alignment of Synura petersenii (plastid: PSAA, PSBA, PSBC, RBCL; mitochondrion: COB, COX1, COX3) with five closely related Synura and other heterokonts as outgroup taxa that used for the phylogeny analysis.
DOI: 10.5061/dryad.230t0/1
title: Cross Inoculation Data

description: Cross Inoculation Data.csv, Data description: Data used to create Figure 1: Cross inoculation of evolved strains between evolutionary environments. The data gives the area of dispersal of the evolved strains relative to the ancestral strain from which all strains were derived. There are 6 replicate lines, which were averaged to give “Mean Area Relative to Ancestor”. Data was collected in the lab and analysed using ImageJ. Columns correspond to: Strain Replicate: the name allocated to each of the replicate lines, e.g. H1 corresponds to replicate line 1 evolved on hard agar. Agar Type on which Strain was Evolved: Strains were either evolved in hard or liquid agar. Agar Type onto which Strain was Inoculated: Strains were either inoculated onto hard or liquid agar. Area Relative to Ancestor: Area of evolved strain under each treatment group was divided by area of ancestral strain under the same treatment to give a relative measurement of area dispersed. Selection Type: Strains were either under positive or neutral artificial selection for dispersal.
DOI: 10.5061/dryad.5v75d33g/1
title: DurstRoth2011

description: Database of insular rodents. See paper for collection methods and description of variables.
DOI: 10.5061/dryad.7891/3
title: logistic-rates-tree

description: the phylogeny on Fig. 5A
DOI: 10.5061/dryad.7891/6
title: Catarrhini

description: the catarrhine phylogeny
DOI: 10.5061/dryad.8178/1
title: Proportion of bacteria infected by phage inocula Koskella et al local adaptation

description: This sheet shows the proportion of bacterial isolates (20 tested per leaflet) that were susceptible to phages from each of the 32 leaflets. Where tree and leaf codes are the same for bacteria and phage, the combination is sympatric within a leaf. Similarly, when tree number is the same, bacteria and phage are sympatric at the tree level.
DOI: 10.5061/dryad.8913/3
title: BP&P input file 1 for microtympanum and arathooni

description: BP&P input file 1 for microtympanum and arathooni
DOI: 10.5061/dryad.8913/4
title: BP&P input file 2 for microtympanum and arathooni

description: BP&P input file 2 for microtympanum and arathooni
DOI: 10.5061/dryad.8913/5
title: modestus BP&P input file 1

description: modestus BP&P input file 1
DOI: 10.5061/dryad.8913/6
title: modestus BP&P input file 2

description: modestus BP&P input file 2
DOI: 10.5061/dryad.8913/7
title: spT BP&P input file 1

description: spT BP&P input file 1
DOI: 10.5061/dryad.8913/8
title: spT BP&P input file 2

description: spT BP&P input file 2
DOI: 10.5061/dryad.8913/9
title: spV BP&P input file 1

description: spV BP&P input file 1