cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8682/1
title: DryadData

description: These data appear in the supplemental online material for this article.  Details of field studies and column descriptions may be found in the publication.
DOI: 10.5061/dryad.8682/2
title: BaboonComputationWorksheet

description: Excel workbook showing the computational details for estimating the hazard rates for female and male baboons in this study. Male deaths were estimated based on age-structure beginning at their dispersal age. These ratios were further adjusted to reflect the rate at which the female population was growing.
DOI: 10.5061/dryad.8979/1
title: PIII_PII

description: Sequence alignment (.fas) of translated PIII and PII SVMPs used for tests of adaptive molecular evolution in the manuscript
DOI: 10.5061/dryad.8979/2
title: PII_PI

description: Sequence alignment (.fas) of translated PII and PI SVMPs used for tests of adaptive molecular evolution in the manuscript
DOI: 10.5061/dryad.8982/1
title: Taiwan_Indonesia_AFLP data_for_publication

description: AFLP binary data
DOI: 10.5061/dryad.8984/2
title: highly_supported_positions_only
DOI: 10.5061/dryad.8994/1
title: Dryad files

description: "collapse_trails.m" is MatLab code used to test the resistance and resilience of simulated incipient species pairs to disturbance.  "select6t_sc.m", "mateD6kt_sc.m", and "checkspec.m" are functions called by "collapse_trials.m".  Files beginning in "rs" are the simulated incipient species pairs used in the published study.  Alternatively, new simulated incipient species can be generated by modifying "collapse_trials.m".
DOI: 10.5061/dryad.9116/1
title: Bretman et al MEC-11-0191 data

description: Excel file contains spatial distance and relatedness for pairs of crickets, maximum adult distance moved, distance between offspring first sighting and mother's mean position and full genotypes at 13 microsatellite loci for all individuals.
DOI: 10.5061/dryad.j5g76/1
title: Microsatellite raw data (seven markers) of di- and tetraploid Arabidopsis arenosa and A. lyrata ssp. petraea from Eastern Austria and the Western Carpathians

description: Data are deposited as BAPS input file. Individuals are listed in the first column. Their unique identification numbers comprise a population number first and an individual number second. In rare cases a third number is found between these two, which further characterizes the population and refers to our internal unique identifier system. POP stands for "population". Taxonomic assignment of the populations is as follows: diploid Arabidopsis arenosa (126-915141), tetraploid A. arenosa (03-81), diploid A. lyrata ssp. petraea (115-74), tetraploid A. lyrata ssp. petraea (01-140). In columns two-eight the microsatellite markers are listed (ATTS0392, SLL2, ICE13, ICE7, NGA162, ICE14, AthZFPG). Each allele of each marker was annotated with a two digit code number.
DOI: 10.5061/dryad.1365/1
title: AFLP data matrix of Eichhornia crassipes

description: AFLP data matrix of 49 water hyacinth (Eichhornia crassipes) populations from its native and introduced ranges. If you have any problem with the data, please contact zhang@ips.unibe.ch.
DOI: 10.5061/dryad.1369/1
title: Sequenced fragments of the Hsp82 gene for Anopheles baimaii mosquitoes
DOI: 10.5061/dryad.1369/2
title: Sequenced fragments of the Hsp82 gene for Anopheles dirus mosquitoes
DOI: 10.5061/dryad.1369/3
title: Sequenced fragments of the Hsp82 gene for Anopheles scanloni mosquitoes
DOI: 10.5061/dryad.1369/4
title: Sequenced fragments of the Est6 gene for Anopheles baimaii mosquitoes
DOI: 10.5061/dryad.1369/5
title: Sequenced fragments of the Est6 gene for Anopheles dirus mosquitoes
DOI: 10.5061/dryad.1369/6
title: Sequenced fragments of the Est6 gene for Anopheles scanloni mosquitoes
DOI: 10.5061/dryad.1701/1
title: bodyparametersofpairedbirdsusedinthisstudy.xls

description: body parameters of paired birds used in this study. We collected them in the field.
DOI: 10.5061/dryad.7998/10
title: STRUCTURE .spj file for eastern Caribbean A. aspera populations
DOI: 10.5061/dryad.7998/7
title: STRUCTURE Data File for all A. aspera populations

description: This is the project file for the STRUCTURE analyses covering all A. aspera populations. The .spj file containing the run parameters are contained in a separate file.
DOI: 10.5061/dryad.7998/8
title: STRUCTURE Data File for eastern Caribbean A. aspera populations

description: This is the project file for the STRUCTURE analyses covering the eastern Caribbean A. aspera populations. The .spj file containing the run parameters are contained in a separate file.
DOI: 10.5061/dryad.7998/9
title: STRUCTURE Data File for western Caribbean A. aspera populations

description: This is the project file for the STRUCTURE analyses covering the western Caribbean A. aspera populations. The .spj file containing the run parameters are contained in a separate file.
DOI: 10.5061/dryad.8048/4
title: R code to analayze effective population sizes

description: R code used to analyze effective population sizes; Figure 2
DOI: 10.5061/dryad.8048/5
title: R code to determine our best estimate of the dominance coefficient in each environment

description: R code to produce figures 3, S4, S5 -- what is the best estimate of dominance?  Note, competition and effective population size R code must be run first in the same session.
DOI: 10.5061/dryad.8987/1
title: TotalPonyfishMolEcol65_Simple

description: Nexus file of genetic data
DOI: 10.5061/dryad.1369/7
title: Sequenced fragments of the NinaE gene for Anopheles baimaii mosquitoes
DOI: 10.5061/dryad.1369/8
title: Sequenced fragments of the NinaE gene for Anopheles dirus mosquitoes
DOI: 10.5061/dryad.1369/9
title: Sequenced fragments of the NinaE gene for Anopheles scanloni mosquitoes
DOI: 10.5061/dryad.1381/1
title: Measurements of snout-vent length and head width of African frogs

description: Tab-delimited file containing measurements of snout-vent length and head width for sub-Saharan frog genera Arthroleptis and Phrynobatrachus.
DOI: 10.5061/dryad.1385/1
title: Microsatellite data
DOI: 10.5061/dryad.1385/2
title: Microsatellite Primers

description: This file lists the primers used to amplify the microsatellite loci. Loci identifier numbers correspond to row 3 of the file "Microsatellite data".
DOI: 10.5061/dryad.1390/1
title: Sendai_COI+ND5.nex

description: Partial mitochondrial COI + ND5 sequences of moths collected in Sendai, Japan.
DOI: 10.5061/dryad.1390/2
title: Sendai_Tpi.nex

description: Partial Tpi sequences of moths collected in Sendai, Japan.
DOI: 10.5061/dryad.1390/3
title: Sendai_Period.nex

description: Partial Period sequences of moths collected in Sendai, Japan.
DOI: 10.5061/dryad.1995/1
title: Hoffman dryad submission 16_09_10

description: AFLP datafiles for Margarella antarctica and Nacella concina
DOI: 10.5061/dryad.7855/1
title: payne_occurrence_size

description: tab delimited text file containing list of occurrences and specimen sizes for each sample
DOI: 10.5061/dryad.7855/2
title: payne_abundance

description: tab delimited text file containing list of specimen counts by genus for each sample
DOI: 10.5061/dryad.7891/1
title: constant-rate-tree

description: the phylogeny on Fig. 4A
DOI: 10.5061/dryad.8073/1
title: Silver_fox_dataset_DRYAD

description: mtDNA sequences for 3 breeding lines of russian silver foxes
DOI: 10.5061/dryad.8570/1
title: sequin

description: This Zip file includes ND4 and cyt-b sequences created using sequin. The text file shows the Genbank Nos. of each sequence.
DOI: 10.5061/dryad.8635/1
title: Genotype dataset of ground tit for Dryad

description: The dataset includes genotype information of all the ground tit individuals used in this paper.
DOI: 10.5061/dryad.8989/1
title: Husby et al Supplementary Material

description: Supplementary Table A1-A4 from Husby et al (in press).
DOI: 10.5061/dryad.9031/1
title: alignments

description: Zip contains all nucleotide sequences in the form of alignments for each gene fragment studied. The alignments contain annotation about the intron/exon boundaries and are provided in nexus (.nex) format.
DOI: 10.5061/dryad.1172/1
title: Tanganyika-SADs of metacommunities.Rdata

description: Five vectors with simulated abundances of individual ostracod species for the Lake Tanganyika in neutral metacommunities differing in the migration rates (m = 0.005, m = 0.05, m = 0.145, m = 0.25, m = 0.5). Format: .Rdata files for R-language
DOI: 10.5061/dryad.1172/3
title: Copano-SADs of metacommunities.Rdata

description: Five vectors with simulated abundances of individual ostracod species for the Lake Tanganyika in neutral metacommunities differing in the migration rates (m = 0.005, m = 0.05, m = 0.145, m = 0.25, m = 0.5). Format: .Rdata files for R-language
DOI: 10.5061/dryad.1390/4
title: Sendai_Ldh.nex

description: Partial Ldh sequences of moths collected in Sendai, Japan.
DOI: 10.5061/dryad.1390/5
title: Niimi_COI+ND5.nex

description: Partial mitochondrial COI + ND5 sequences of moths collected in Niimi, Okayama, Japan.
DOI: 10.5061/dryad.1390/6
title: Niimi_Tpi.nex

description: Partial Tpi sequences of moths collected in Niimi, Okayama, Japan.
DOI: 10.5061/dryad.1390/7
title: Niimi_Period.nex

description: Partial Period sequences of moths collected in Niimi, Okayama, Japan.
DOI: 10.5061/dryad.1390/8
title: Niimi_Ldh.nex

description: Partial Ldh sequences of moths collected in Niimi, Okayama, Japan.
DOI: 10.5061/dryad.1400/1
title: Pgillii.cytb.nex

description: Aligned cyt b data for all individuals with the taxa labels in nexus file format.
DOI: 10.5061/dryad.1400/2
title: Pgillii.S7.nex

description: Aligned S7 data for all individuals with the taxa labels in nexus file format.
DOI: 10.5061/dryad.1400/3
title: redundanttaxa.xls

description: This spreadsheet contains three worksheets.  The first is labeled 'Localities' and gives the province, locality number, locality name, Field ID, and Drainage for each locality.  the first three columns are available in the publication and associated online supplementary material.  The Field ID corresponds to the taxa labels used in the nexus files.  The first two numbers are the year they were collected and the last numbers are the collection number.  Thus, a taxa label that reads 'PG0701.04' would be the species Poecilia gillii collected in 2007 in the first collection locality and the fourth fish from that locality.  The second and third worksheet provide the taxa labels with their associated haplotype as found in the publication for each of the respective loci.
DOI: 10.5061/dryad.1405/1
title: Warramaba sp. COI sequences

description: COI sequences in MEGA format, grouped according to species/lineage
DOI: 10.5061/dryad.7891/5
title: agamids

description: the agamid phylogeny
DOI: 10.5061/dryad.7944/3
title: Appendix1_CultureList

description: Specimen list, including GenBank and University of Alberta Microfungus Collection and Herbarium accession numbers.
DOI: 10.5061/dryad.7944/4
title: Appendix2_SingleLocusNetworks

description: Single locus parsimony networks for G. clavigera, L. longiclavatum, and O. montium.
DOI: 10.5061/dryad.7996/1
title: Kingsolver&Diamond.Selection_dataset_2010Nov

description: Standardized selection coefficients, derived from Kingsolver et al (2001, American Naturalist) and Siepielski et al (2009, Ecology Letters)
DOI: 10.5061/dryad.8259/2
title: Appendix S3

description: Phylogenetic hypothesis used in the study.
DOI: 10.5061/dryad.8623/3
title: underdom.tar

description: Data simulated with underdominance. Each file in the compressed directory is for a different set of model parameters and each file contains ten replicates. Genotypes are given as 0 (homozygote), 1 (heterozygote), or 2 (homozygote).
DOI: 10.5061/dryad.8797/2
title: Nucgenotypesaelleni_griveaudi_islands

description: Individual genotypes for all 10 microsatellite loci, in Arlequin format
DOI: 10.5061/dryad.8797/3
title: Dloop_aell_grivesamplingsites

description: Description of haplotype sequences and haplotype composition of each sampled population
DOI: 10.5061/dryad.8797/4
title: Dloop_aell_grivesamplingsites

description: break-down of haplotype composition of each population, in arlequin format
DOI: 10.5061/dryad.8797/5
title: D-loop_haplogroups

description: Individual haplotypes and their haplogroup assignation
DOI: 10.5061/dryad.9011/1
title: Results_Cloning_DHPLC_GenbankAcc

description: This table includes results from cloning and direct sequencing after DHPLC collection, along with the Genbank accession numbers of the retrieved sequences. Reference is made to Figure 3 in the paper.
DOI: 10.5061/dryad.q757q/4
title: Lithobates (Rana) pipiens microsatellite data
DOI: 10.5061/dryad.1172/2
title: Copano Bay cores data.txt

description: Absolute abundances of mollusks in two sediment cores sampled by sieving in the Copano Bay. Core 1 - C1 is represented by nine layers. Core 2 - C2 is represented by 14 layers. Core 1 was simulated in Tomasovych and Kidwell 2010. Format: tab-delimited txt.file. The source citation for these data and details about sampling are in: Powell, E. N., and R. J. Stanton, Jr. 1995. The application of guild and tier structure and energy flow in paleoecologic analysis: an example using parautochthonous death assemblages from a variable salinity bay. Historical Biology 10:281-327.Powell, E. N., and R. J. Stanton, Jr. 1996. The application of size-frequency distribution and energy flow in paleoecologic analysis: an example using parautochthonous death assemblages from a variable salinity bay. Palaeogeography Palaeoclimatology Palaeoecology 124:195-231.
DOI: 10.5061/dryad.1409/1
title: Dryad data file.xls

description: Datafile containing AFLP, microsatellite and mtDNA datafiles.
DOI: 10.5061/dryad.1416/1
title: DataPlottedInFig1.xlsx

description: Raw data for Figure 1 in original article
DOI: 10.5061/dryad.1416/2
title: RawDataFile.txt
DOI: 10.5061/dryad.1421/1
title: Symonds & Tattersall data 1.xls

description: Morphological and Geographical data used in the analyses
DOI: 10.5061/dryad.1421/2
title: Symonds & Tattersall data 2.doc
DOI: 10.5061/dryad.1435/1
title: R workspace with all Carex pachystachya data

description: R workspace with Carex pachystachya genetic and chromosome data, and geographic coordinates. Load into R using the "load" command. Two objects are contained in the workspace: (1) a table named "coordAndChrom3" that contains Whitkus's voucher numbers, diploid chromosome counts, and decimal latitude and longitude for each population; and (2) "whitkusFinal", a list of two matrices, the first a matrix of allele frequencies indexed by locus (rows) and population (columns), the second a matrix of sample sized indexed in the same manner.
DOI: 10.5061/dryad.1435/2
title: Zip file to conduct Carex scoparia analyses in R

description: A zip file with an R workspace and a source file that executes all analyses conducted in R to generate Table 2. To execute, unzip the files into your working directory, load the file called "scopariaWorkspace.Rdata" into R, then source the file called "27may08analyses.R". Please note that the mantel tests are set to run for 200 permutations in this file, to make life easy when you are running... these mantel tests were actually run for 20,000 permutations for the final paper. Please email me if you have trouble running this.
DOI: 10.5061/dryad.1435/3
title: NEXUS file for Carex scoparia and outgroups

description: A nexus file for Carex scoparia and outgroups. Original binned data are in a separate file.
DOI: 10.5061/dryad.1451/1
title: tableS3.csv

description: Data table for 287 species included in this study. Asterisk indicates missing data. Dry weight is given in mg; egg volume is given in mm3. Parental care by the ovipositing female is coded as "No care" (abandonment after oviposition), "Guarding" (post-oviposition guarding of eggs or young) or "Provisioning" (pre- or post-oviposition supplying of food).
DOI: 10.5061/dryad.1637/1
title: Source code for partitioning live-dead variation in taphonomic analyses

description: Source code (R language) for partitioning of total live-dead compositional variation among multiple living (individuals sampled alive) and death assemblages (individuals collected as dead) into variation caused by (1) sampling and biological variation among living assemblages and (2) new variation that arises from postmortem taphonomic processes. The balanced design is required, i.e., the same number of living and death assemblages sampled in the same (homogeneous) habitat.
DOI: 10.5061/dryad.1637/2
title: Counts of living individuals in subtidal habitats off San Juan Islands

description: Counts of mollusk individuals sampled alive by dredge in 2002 at several subtidal stations off San Juan Islands. The source of data and description of sampling and counting methods is in: Kowalewski M., Carroll M., Casazza L., Gupta N., Hannisdal B., Hendy A., Krause R. A. Jr., LaBarbera M., Lazo D.G., Messina C., Puchalski S., Rothfus T. A., Sälgeback J., Stempien J., Terry R.C., Tomašových A. 2003, Quantitative fidelity of brachiopod-mollusk assemblages from modern subtidal environments of San Juan Islands, USA. Journal of Taphonomy 1, 43-65
DOI: 10.5061/dryad.8309/4
title: Hs_La_Lm_Microsats.xls

description: Hs_La_Lm_Microsats.xls has all the microsatellite data for the paper in a spreadsheet. For each species there is a tab.
DOI: 10.5061/dryad.8309/5
title: Hsub_MtDNA_IBDWS_format

description: H sublaevis MtDNA data in IBDWS format.
DOI: 10.5061/dryad.8309/6
title: Hsub_MtDNA_Pops.nex

description: H sublaevis MtDNA sequences in nexus format with population information.
DOI: 10.5061/dryad.8309/7
title: Hsub_MtDNA_haplotypefile_Pops.nex

description: H sublaevis MtDNA sequences in nexus haplotype format with population information.
DOI: 10.5061/dryad.8797/1
title: Mapsamplingsites

description: Geographic location of sampling sites and islands
DOI: 10.5061/dryad.8991/1
title: MunshiSouth.Loxodonta.cyclotis.genotypes

description: GENEPOP file containing unique eight-locus microsatellite genotypes identified for 162 forest elephant individuals in SW Gabon, central Africa.  Genotypes were generated from fecal DNA collected from dung piles at two locations in the wild (the Industrial Corridor of the Gamba Complex of Protected Areas; sample names begin with 'R' or 'T'; and Loango National Park; sample names begin with 'L').
DOI: 10.5061/dryad.vh3dm/1
title: alignment_human_mouse

description: The file involves the pairwise alignments in 5'UTRs of human and mouse genomes. The alignments were downloaded from the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/). The versions of the human and mouse genomes (hg18 and mm9, respectively) correspond to Ensembl release 54. The Ensembl IDs of genes, transcripts, and proteins were listed. Noted that unalignable regions between human and mouse have been excluded in the file. Noted that the Ensembl IDs include both human (the first 61592 rows) and mouse (after row no. 61592).
DOI: 10.5061/dryad.1455/1
title: Fur seal genotypes

description: Multilocus genotypes of 84 dead male Antarctic fur seals
DOI: 10.5061/dryad.1468/1
title: TsetseJerCoordGeo&Trap&SexMaleHomozXLinked.xls
DOI: 10.5061/dryad.1472/1
title: A cristatellus microsatellite data.txt
DOI: 10.5061/dryad.1476/1
title: AliceDennis_sequences.zip

description: Alignment files in FASTA format.  There are 4 species and three genes, each in an individual file.  The 4 species are: (1) Melampus coffeus, (2) Melampus bidentatus cryptic species NORTH, (3) Melampus bidentatus cryptic species SOUTH, (4) Melampus bidentatus cryptic species GULF.  The 3 genes are: (1) Histone H3 (2) Cytochrome oxidase I (CO1) and (3) MCP, which has been Probable mitochondrial phosphate carrier protein.
DOI: 10.5061/dryad.1480/1
title: Biomphalaria glabrata sample data for Bateman gradient analysis

description: Details of sampling procedures and calculations performed with this sample dataset are available in Online Appendix B of the corresponding publication
DOI: 10.5061/dryad.1484/1
title: Genotypes of contents of queen cells
DOI: 10.5061/dryad.1492/1
title: File of individual observations from published studies

description: These data were collected from the original publications.
DOI: 10.5061/dryad.1637/3
title: Counts of all dead individuals in subtidal habitats off San Juan Islands

description: Counts of dead mollusk individuals sampled by dredge in 2002 at several subtidal stations off San Juan Islands. This is exhaustive dataset - includes all fragments and is not corrected for disarticulated elements. The source of data and description of sampling and counting methods is in: Kowalewski M., Carroll M., Casazza L., Gupta N., Hannisdal B., Hendy A., Krause R. A. Jr., LaBarbera M., Lazo D.G., Messina C., Puchalski S., Rothfus T. A., Sälgeback J., Stempien J., Terry R.C., Tomašových A. 2003, Quantitative fidelity of brachiopod-mollusk assemblages from modern subtidal environments of San Juan Islands, USA. Journal of Taphonomy 1, 43-65
DOI: 10.5061/dryad.1637/4
title: Counts of complete dead individuals in subtidal habitats off San Juan Islands

description: Counts of dead mollusk individuals sampled by dredge in 2002 at several subtidal stations off San Juan Islands. This is restrictive dataset - includes complete individuals and is corrected for disarticulated elements. The source of data and description of sampling and counting methods is in: Kowalewski M., Carroll M., Casazza L., Gupta N., Hannisdal B., Hendy A., Krause R. A. Jr., LaBarbera M., Lazo D.G., Messina C., Puchalski S., Rothfus T. A., Sälgeback J., Stempien J., Terry R.C., Tomašových A. 2003, Quantitative fidelity of brachiopod-mollusk assemblages from modern subtidal environments of San Juan Islands, USA. Journal of Taphonomy 1, 43-65
DOI: 10.5061/dryad.8378/2
title: P_element_probe_labels_illumina

description: Probe information for microarray data
DOI: 10.5061/dryad.8378/3
title: sd_illumina

description: Microarray data set for "test" comparison for the scalloped (sd) mutant VS. wild-type
DOI: 10.5061/dryad.8378/4
title: partial_warps_wings_For_PLS

description: line "means" for partial warps and uniform components for wing shape used for the Partial Least Squares. See readme file.
DOI: 10.5061/dryad.8433/1
title: genotype data in CONVERT format
DOI: 10.5061/dryad.8633/1
title: rundle_data

description: See readme.txt
DOI: 10.5061/dryad.n40h2/1
title: ST1

description: Genotyped individuals
DOI: 10.5061/dryad.n40h2/2
title: ST2 3 & 4

description: Supplementary Table 2: Mitochondrial sequence alignment showing variable sites. Supplementary Table 3: Synopsis alignment of Felis silvestris phylogenetically informative mitochondrial sites. Supplementary Table 4: Primer sequences for mitochondrial amplification of F. silvestris ssp. informative sites.
DOI: 10.5061/dryad.n40h2/3
title: ST5

description: Supplementary Table 5: STR genotypes ascertained in range-wide survey.
Header rows indicate cat chromosome location of  STR loci with distances given according to conventions used in PHASE (STEPHENS 2004). Alleles are indicated by base-pair length. Missing data is denoted by -9. Individual cats are listed by LGD code in column one. Refer to Supplemental Table 1 for additional information regarding provenance and taxonomic assignment. Data is provided for 77 loci, however only the 36 that amplified most completely across different runs were further characterized and used in published analysis (DRISCOLL et al. 2007). A limited examination of alternative locus combinations (data not shown) that include loci other than the published 36 indicates similar levels of performance. For future studies requiring the greatest genetic resolution these additional data could be considered.
DOI: 10.5061/dryad.1500/1
title: DUN x IM RIL M. guttatus genotype and linkage map data.xls

description: This file includes the genotype data for EST markers, as described in Lowry et al. (2009) New Phytologist 183:776-788. These markers were genotyped in 191 recombinant inbred lines (RILs) from IM & DUN parents of Mimulus guttatus. Marker genotypes are: a=IM/IM homozygote, h=IM/DUN heterozygote, b=DUN/DUN homozygote. The markers are ordered by linkage group (1-14) and include distances (cM) between markers.