cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7q0nq/1
title: Scripts

description: Scripts used to calculate average pairwise differences between all 6 pairwise combinations along the XR chromosome between Drosophila pseudoobscura, Drosophila persimilis, Sex-Ratio Drosophila persimilis, and Drosophila miranda. These output file can then be used to calculate RND betweenD pseudoobscura, D persimilis, and SR D persimilis in another program such as Microsoft Excel. All scripts are written in Perl. Author: Kenneth Hoehn. Date: May-5-2011. Sections: 1. Constructing the combined, raw input file from PILEUP outputs (skip if combined input file is provided); 2. Necessary input files for final analysis; 3. Editing combined input file and calculating average pairwise differences; 4. Calculating RND; 5. Double checking output; 6. Simple window writing script. See README.txt for more details.
DOI: 10.5061/dryad.7q0nq/6
title: Multiple genome alignment of XR

description: This document contains the multiple genome alignment file associated with this publication. A total of four XR chromosome sequences were used for this study – one D. miranda, one D. pseudoobscura, and two D. persimilis.
DOI: 10.5061/dryad.s1m9h/1
title: Hekkalaetal_MolEcol_2011_12s

description: Nexus file containing sequence data for the 12S rRNA mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/2
title: Hekkalaetal_MolEcol_2011_16s

description: Nexus file containing sequence data for the 16S rRNA mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/3
title: Hekkalaetal_MolEcol_2011_dloop

description: Nexus file containing sequence data for the control region/dloop mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/4
title: Hekkalaetal_MolEcol_2011_ND4

description: Nexus file containing sequence data for the NADH dehydrogenase subunit 4 mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/5
title: Hekkalaetal_MolEcol_2011_wancy

description: Nexus file containing sequence data for the WANCY tRNA cluster from the ND2-flanking region including tRNA_Trp, tRNA_Ala, tRNA_Asn, tRNA_Cys, and part of tRNA_Tyr mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/6
title: Hekkalaetal_MolEcol_2011_rag1

description: Nexus file containing sequence data for the rag-1 recombination activating gene-1 nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/7
title: Hekkalaetal_MolEcol_2011_S6

description: Nexus file containing sequence data for the ribosomal protein S6 nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.s1m9h/8
title: Hekkalaetal_MolEcol_2011_Trop

description: Nexus file containing sequence data for the tropomyosin intron nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.bt760/1
title: Multiple sequence alignment

description: Multiple sequence alignment of DNA sequence data for mitochondrial 16S ribosomal RNA gene.
DOI: 10.5061/dryad.cg1jv/2
title: Henk_Fleming_Penicillium_data

description: Location, allelic profiles, and species assignment in a single datasheet. A second datasheet contains allelic size information.
DOI: 10.5061/dryad.p71fk/1
title: Ketchum_&_Benson_data_files
DOI: 10.5061/dryad.s1m9h/10
title: Hekkalaetal_MolEcol_2011_12s_museumdataONLY

description: Nexus file containing sequence data for the 12s rRNA mitochondrial gene region. Sequences listed here are the "short 12s" sequences for the museum and mummy specimens only. Please refer to the associated manuscript Table 2, and Methods, for further specimen information.
DOI: 10.5061/dryad.s1m9h/12
title: Hekkalaetal_MolEcol_2011_dloop_museumdataONLY

description: Nexus file containing sequence data for the control region/dloop mitochondrial gene region. Sequences listed here are the "short dloop" sequences for the museum and mummy specimens only. Please refer to the associated manuscript Table 2, and Methods, for further specimen information.
DOI: 10.5061/dryad.s1m9h/9
title: Hekkalaetal_MolEcol_2011_OD

description: Nexus file containing sequence data for the ornithine decarboxylase intron nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.
DOI: 10.5061/dryad.181v0/1
title: PCareFinal

description: See ReadMe file
DOI: 10.5061/dryad.4qr34/1
title: Elnagdy et al 2011 data

description: Survival data for three experiments to investigate resource reallocation in coccinellids (Coleoptera: Coccinellidae) infected with male-killing bacteria
DOI: 10.5284/1000411
title: The BTC Pipeline Archaeological Excavations in Azerbaijan

description: The Baku-Tbilisi-Ceyhan and South Caucasus Pipelines (BTC) were constructed through Azerbaijan, Georgia and Turkey during the period 2003-5. The project was accompanied by a 5 phase archaeological project intended to investigate and mitigate the effects of this construction. The project grew from small beginnings in 2001 to include a continuously operating team of around 80 staff during 2005 that included members of the Institute of Archaeology and Ethnography (IoAE) in Baku, international archaeologists and local labourers. This project was the largest archaeological enterprise in Azerbaijan for many years prior to the end of the USSR.

Archaeological results of the project included over 40 excavations on sites of varying date, surveys of different pipeline route options and the study of numerous sites while crossing the country. The project coincided with the introduction of GPS measuring equipment and the use of available satellite imagery and mapping, some of which was prepared specifically for the project. This meant that for the first time local archaeologists could record geographical information to a level that had previously been a state secret. Novel techniques were introduced such as aerial archaeology, digital images and the collection of over 50 radiocarbon dates.

The archaeological sites covered a range of periods and types from Chalcolithic settlements and cemeteries, Bronze Age settlements and cemeteries and Antique cemeteries. Medieval sites were represented by a potential Christian chapel and associated cemetery and a number of rural settlements of varying complexity. A key result of this project was the appearance of the Chalcolithic sites that dramatically extended the limited corpus of known sites in Azerbaijan; the almost non-visibility of evidence for the Kura Araz culture and the excavation of the rural medieval sites that would previously have been ignored in favour of the more interesting and finds-rich urban sites.
DOI: 10.5061/dryad.6t94p/1
title: scientists survey data
DOI: 10.5061/dryad.dm690/2
title: ML_analyses

description: This zip directory gives the BiSSE maximum likelihood analyses reported in Table S3.
DOI: 10.5061/dryad.585qk/1
title: Metamorphic success, post-metamorphic survival and post-metamorphic size
DOI: 10.5061/dryad.585qk/2
title: Overyielding analyses for each trait
DOI: 10.5061/dryad.585qk/3
title: Overyielding for overall performance full-sibling vs half-sibling
DOI: 10.5061/dryad.585qk/4
title: Overyielding for overall performance full-sibling vs unrelated
DOI: 10.5061/dryad.989d0/2
title: urocotyledon_citb_haplotypes

description: nexus file of haplotypes of cytochrome-b used to phylogenetic analysis (figure 2). Whole alignments of unphased sequences can be obtained from public genbank database (acession numbers given in the manuscript). Only further sequence alignment files used for analyses are provided here. All "specimen" codes in the files are as given in Appendix S1 of manuscript ("a" and "b" added when needed to represent the different haplotypes of the same individual.
DOI: 10.5061/dryad.989d0/3
title: urocotyledon_cmos

description: fasta file of haplotypes for the fragment of c-mos gene for all individuals (note that no heterozygous individuals were observed, so for this gene both haplotypes for each individual are identical). This is the alignment used for the MJ networks and all further analysis.
DOI: 10.5061/dryad.dm690/1
title: Onagraceae TREEBASE file
DOI: 10.5061/dryad.dm690/3
title: MCMC_analyses

description: This zip directory gives the full MCMC results and the R code that generated the data underlying Figure 3, Figure S1, Figure S3, Table 1, and Table S2.
DOI: 10.5061/dryad.989d0/10
title: urocotyledon_reln_phases08_ambiguities

description: fasta file of haplotypes infered for reln dataset for all individuals but where positions whose phases were resolved with &lt; 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP.
DOI: 10.5061/dryad.989d0/11
title: urocotyledon_reln_phased08_bestguesses

description: fasta file of haplotypes infered for reln dataset for all individuals, where positions whose phases were resolved with &lt; 0.8 posterior probability are nevertheless coded with the respective best guesses for each base. (as in this dataset the different runs of PHASE (Stephens et al., 2001 - to be fund on manuscript references) were inconsistent at some positions we used results of the run with the highest likelihood score, whose seed (and command line) is given bellow. The known haplotypes used (uro_reln.known) were those read directly from sequences heterozigous for indels, and that can be found on genbank - accession numbers given in the paper). [phase comand line: ./PHASE -MS -p0.8 -q0.8 -d1 -s48993 -kuro_reln.known uro_reln.inp uro_reln.out 10000 1 100]
DOI: 10.5061/dryad.989d0/4
title: urocotyledon_pdc_phased

description: fasta file of haplotypes from the pdc fragment for all individuals (note that no multiple heterozigous were observed, so all haplotypes - phases - are determined with certainty)
DOI: 10.5061/dryad.989d0/5
title: urocotyledon_rag2_phased08_network

description: fasta file of haplotypes infered for the rag2 dataset for all individuals. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3), summary statistics, and IMa analysis.
DOI: 10.5061/dryad.989d0/6
title: urocotyledon_rag2_phased08_ambiguities

description: fasta file of haplotypes infered for rag2 dataset for all individuals but where positions whose phases were resolved with &lt; 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP / species-tree analyses.
DOI: 10.5061/dryad.989d0/7
title: urocotyledon_mc1R_phased08_network

description: fasta file of haplotypes infered for the mc1r dataset for all individuals. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3), summary statistics and IMa analysis.
DOI: 10.5061/dryad.989d0/8
title: urocotyledon_mc1R_phased08_ambiguities

description: fasta file of haplotypes infered for mc1r dataset for all individuals but where positions whose phases were resolved with &lt; 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP / species-tree analyses.
DOI: 10.5061/dryad.989d0/9
title: urocotyledon_reln_phased08_network

description: fasta file of haplotypes infered for the reln dataset for all individuals. Here, positions were phases were resolved with &lt; 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3) and summary statistics.
DOI: 10.5061/dryad.989d0/12
title: urocotyledon_reln_imgc_Cw03

description: fasta file resulting from the trimming of the file "urocotyledon_reln_phased08_network.fas" to the maximum block free of evidence of recombination, using the program IMgc (Woerner et al., 2007 - reference to be found in the ms) with a chromosome copy weight of 0.3 (the value chosen as it maximized the sequence lenght keeping all needed populations represented). Used for IMa and species-tree analyses (that assume no recombination within each sequence fragment)
DOI: 10.5061/dryad.989d0/13
title: urocotyledon_reln_bestguesses_imgc_Cw03

description: fasta file resulting from the trimming of the file "urocotyledon_reln_phased08_bestguesses.fas" to the maximum block free of evidence of recombination, using the program IMgc (Woerner et al., 2007 - reference to be found in the ms) with a chromosome copy weight of 0.3 (the value chosen as it maximized the sequence lenght keeping all needed populations represented). Used for IMa and species-tree analyses (that assume no recombination within each sequence fragment)
DOI: 10.5061/dryad.jb314/1
title: brood mass d2 data

description: Data on the average mass (g) of wild blue tit broods at two days of age, collected during three years in south central Sweden. Treatment categories: H = 38.0 C; M = 36.5 C; L = 35.0 C
DOI: 10.5061/dryad.jb314/2
title: incubation period and hatching success data

description: Data on length of the incubation period and hatching success in experimental blue tit nests. Data also includes reference information from unmanipulated nests in the field. Data were collected over three years in south central Sweden. Treatment categories: H = 38.0 C; M = 36.5 C; L = 35.0 C; C = Reference nests.
DOI: 10.5061/dryad.jb314/3
title: nestling biometric data

description: Biometric measurements (mass, tarsus and wing length) on experimental blue tit nestlings at 6 and 14 days of age, collected over three years in south central Sweden. Treatment categories: H = 38.0 C; M = 36.5 C; L = 35.0 C. 'NA' = missing data.
DOI: 10.5061/dryad.jb314/4
title: nest provisioning data

description: Data on parental nest provisioning rates (as feedings / h / chick) in experimental blue tit nests. Data was collected by means of PIT-tags during nestlings days 8-10, during three years in south central Sweden. Treatment categories: H = 38.0 C; M = 36.5 C; L = 35.0 C. 'NA' = missing data.
DOI: 10.5061/dryad.vd0m7/1
title: amphibian sequence data

description: A phylip-format file containing the sequence data (12712 bp from 12 genes for 2871 amphibians and one outgroup) used in the analyses.
DOI: 10.5061/dryad.vd0m7/3
title: amphibian model file

description: Text file containing partition information for phylip-format DNA sequence data.
DOI: 10.5061/dryad.2m7b0/1
title: Lazarus_2012_Paleobiology_Appendices

description: Appendices 1 and 2.  1-tabular data extracted from or calculated from the Neptune database for Cenozoic radiolarian occurrences.  2-histograms (pdf plates) of occurences in time and effects of pacman data trimming for selected species of radiolarians. Details of table formats in readme.txt file included.  File is zip archive, created with OS X 10.6 system 'compress'.
DOI: 10.5061/dryad.69g7p/1
title: Lee_ATPase_DATA_ALL
DOI: 10.5061/dryad.jb314/5
title: nestling rmr data

description: Data on resting metabolic rate (RMR; ml O2 / min) in experimental blue tit nestlings. Data was collected by means of flow through respirometry in the darkness in thermoneutrality during the night between nestlings days 14-15, during three years. Treatment categories: H = 38.0 C; M = 36.5 C; L = 35.0 C. 'Channel' = Respirometer channel.
DOI: 10.5061/dryad.63kf4/1
title: Snakes_All_Leaved_1

description: XML file for first independent run of the 29-gene dataset in BEAST
DOI: 10.5061/dryad.63kf4/2
title: Snakes_All_Leaved_2

description: XML file for second independent run of 29-gene dataset in BEAST.
DOI: 10.5061/dryad.99qj3/1
title: Table S1

description: Crown morphometrics for Varanus komodoensis dry skull specimens
DOI: 10.5061/dryad.99qj3/2
title: Table S2

description: Skull and body measurements for ziphodont specimens of Varanus komodoensis and theropods.
DOI: 10.5061/dryad.99qj3/3
title: Table S3

description: Dental crown morphometrics for theropod fossil specimens
DOI: 10.5061/dryad.99qj3/4
title: Table S4

description: A listing of all Varanus komodoensis striated tooth marks collected.
DOI: 10.5061/dryad.1dv51/1
title: JN1-top

description: Ancient DNA sequences extracted from sediment sample 'JN1-top' from J.A.D. Jensen's Nunataks (Greenland). Sequences are amplified with the trnL g and h primers and sequenced on the Roche 454 Sequencing Platform. The results are trimmed for primers and tags, and only sequences found in more than 5 copies per amplicon are included.
DOI: 10.5061/dryad.1dv51/2
title: JN1_low

description: Ancient DNA sequences extracted from sediment sample 'JN1-low' from J.A.D. Jensen's Nunataks (Greenland). Sequences are amplified with the trnL g and h primers and sequenced on the Roche 454 Sequencing Platform. The results are trimmed for primers and tags, and only sequences found in more than 5 copies per amplicon are included.
DOI: 10.5061/dryad.1dv51/3
title: JN2-top

description: Ancient DNA sequences extracted from sediment sample 'JN2-top' from J.A.D. Jensen's Nunataks (Greenland). Sequences are amplified with the trnL g and h primers and sequenced on the Roche 454 Sequencing Platform. The results are trimmed for primers and tags, and only sequences found in more than 5 copies per amplicon are included.
DOI: 10.5061/dryad.63kf4/3
title: Snakes_All_Time

description: Resulting time-tree from two independent BEAST runs.
DOI: 10.5061/dryad.67529/1
title: Microsatellite Data Medusagyne oppositifolia

description: The data file contains alleleic information for 13 microsatellites from Medusagyne oppositifolia individuals from the Seychelles.
DOI: 10.5061/dryad.8cn82/1
title: Genotypes 2006-2007

description: 19 loci genotypes of the individuals in the study.
DOI: 10.5061/dryad.1dv51/4
title: JN2-low

description: Ancient DNA sequences extracted from sediment sample 'JN2-low' from J.A.D. Jensen's Nunataks (Greenland). Sequences are amplified with the trnL g and h primers and sequenced on the Roche 454 Sequencing Platform. The results are trimmed for primers and tags, and only sequences found in more than 5 copies per amplicon are included.
DOI: 10.5061/dryad.1dv51/5
title: JN3-low

description: Ancient DNA sequences extracted from sediment sample 'JN3-low' from J.A.D. Jensen's Nunataks (Greenland). Sequences are amplified with the trnL g and h primers and sequenced on the Roche 454 Sequencing Platform. The results are trimmed for primers and tags, and only sequences found in more than 5 copies per amplicon are included.
DOI: 10.5061/dryad.1dv51/6
title: Blank Controls

description: Blank controls sequences, amplified with the trnL g and h primers and sequenced on the Roche 454 Sequencing Platform. The results are trimmed for primers and tags, and only sequences found in more than 5 copies per amplicon are included.
DOI: 10.5061/dryad.7vg42/1
title: Ms 10045 data Salvatteci et al
DOI: 10.5061/dryad.h6t7g/1
title: AlatesxSize

description: Data on the number of alate queens found in myrmecophytic plants of different sizes, where size is the number of domatia a plant has.
DOI: 10.5061/dryad.h6t7g/2
title: EstablishedColonies_9haPlot

description: X-Y locations of all established ant colonies found,i.e., the location of all myrmecophytic plants in a 9-ha study plot in the central Amazon and the identity of the ant resident.
DOI: 10.5061/dryad.h6t7g/3
title: ExperimentalSeedlings_9haPlot

description: Data on the experimental seedlings used in our experiment, including size, location, and colonization history.
DOI: 10.5061/dryad.3s92c/1
title: Dryad_info

description: Explanation of files
DOI: 10.5061/dryad.3s92c/2
title: IM_clivii_small

description: "Small" IMa2 input file for X. clivii with non-neutral loci removed
DOI: 10.5061/dryad.505dp/1
title: zfsnp_ped_zv9_dryad
DOI: 10.5061/dryad.505dp/2
title: zfsnp_map_zv9
DOI: 10.5061/dryad.pk7v8/1
title: 2011 data Dryad Prunus S-allele Stoeckel et al.

description: Observed Parents-offspring S-allele frequencies within populations of wild cherry trees
DOI: 10.5061/dryad.3s92c/10
title: larg_struct.in

description: Structurama input file for X. largeni
DOI: 10.5061/dryad.3s92c/3
title: IM_clivii

description: IMa2 input file for X. clivii
DOI: 10.5061/dryad.3s92c/4
title: IM_largeni

description: IMa2 input file for X. largeni
DOI: 10.5061/dryad.3s92c/5
title: clivii_in

description: MIMAR input file for X. clivii
DOI: 10.5061/dryad.3s92c/6
title: largeni_IN

description: MIMAR input file for X. largeni
DOI: 10.5061/dryad.3s92c/7
title: xen12s16s_MrBayes

description: Mitochondrial DNA sequence alignment for MrBayes
DOI: 10.5061/dryad.3s92c/8
title: cliv_struct_reduce

description: Structurama input file for X. clivii with some individuals with lots of missing data removed.
DOI: 10.5061/dryad.3s92c/9
title: cliv_struct.in

description: Structurama input file for X. clivii
DOI: 10.5061/dryad.3s92c/11
title: cliv_struct_reduce

description: Structure input file for X. clivii with some individuals with lots of missing data removed
DOI: 10.5061/dryad.vd094/1
title: Clustered_OTUdata

description: Processed raw data clustered into Operational Taxonomic units in the QIIME, OCTUPUS, and AmpliconNoise pipelines.  Contains OTU representative sequences (FASTA files), BLAST-derived taxonomy (tab-delimited text files), and OTU mapping file displaying the site distribution within OTUs (tab-delimited text files).
DOI: 10.5061/dryad.p72p0/1
title: Plant AFLP patterns

description: This file contains the normalized AFLP patterns of the Galega accessions from Caucasus, created with BioNumerics. These patterns functioned as the basis for the curve-based analysis, used to construct the similarity matrix.
DOI: 10.5061/dryad.p72p0/2
title: Rhizobium AFLP patterns

description: This file contains the normalized gel picture of the AFLP patterns for the Rhizobium galegae strains representing the R. galegae population in Caucasus. The file was created with BioNumerics and used in the curve-based analysis to construct the similarity matrix of the rhizobial AFLP analysis.
DOI: 10.5061/dryad.p72p0/3
title: Galega AFLP similarity matrix

description: The similarity matrix obtained from the BioNumerics analysis of the Galega AFLP data.
DOI: 10.5061/dryad.p72p0/4
title: Rhizobium AFLP similarity matrix

description: The similarity matrix obtained from the BioNumerics analysis of the Rhizobium galegae AFLP data.
DOI: 10.5061/dryad.p72p0/5
title: NORK neighbor-joining tree of complete dataset

description: The neighbor-joining tree used for the codeml analyses of the NORK gene. The tree was constructed in MEGA 4, with the substitution model of Tamura-Nei + gamma 1.0 and complete deletion of gaps. Bootstrap values &gt; 70 % are shown.
DOI: 10.5061/dryad.p72p0/6
title: Nfr5 neighbor-joining tree of complete dataset

description: The neighbor-joining tree used for the codeml analyses of the Nfr5 gene. The tree was constructed in MEGA 4, with the substitution model of Tamura-Nei + gamma 1.0 and pairwise deletion of gaps and missing data. Bootstrap values &gt; 70 % are shown.
DOI: 10.5061/dryad.vd094/2
title: Raw 454 Data

description: Raw sequence reads and associated quality file (~1.2 million sequences averaging 350-450 bp in length) generated on a GS FLX Titanium platform in August 2009.
DOI: 10.5061/dryad.t46v2/1
title: C2TotalsDataForArchiving

description: "C2" data, lifetime offspring production
DOI: 10.5061/dryad.t46v2/2
title: C3TotalsDataForArchiving

description: "C3" data, lifetime total offspring production
DOI: 10.5061/dryad.t46v2/3
title: C2DataByAgeForArchiving

description: "C2" data, offspring produced by age
DOI: 10.5061/dryad.t46v2/4
title: C3DataByAgeForArchiving

description: "C3" data, offspring produced by age