cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.42f2q/1
title: Diet & phylogeny shape Antarctic seal gut microbiota

description: Faecal samples were collected from southern elephant seals (n=24) and leopard seals (n=12) in the western Antarctic using rectal swabs. Sterile swabs (Oxoid Australia Pty, SA, Australia)were used and samples were frozen after collection. Faecal samples were collected opportunistically after defecation from captive leopard seals (n=2) housed at Taronga Zoo, Sydney, NSW, Australia. Total genomic DNA was extracted using QIAamp Stool DNA Mini Kit (Qiagen Pty, Vic., Australia) following the manufacturers protocol.Pyrosequencing of the16S rRNA gene was carried out at the Research and Testing Laboratory (Lubbock, TX, USA). Primers 27F 5′-AGAGTTTGATCCTGGCTCAG-3′ and 519R 5′-GTATTACCGCGGCTGCTG-3′ were used (Lane et al., 1985, PNAS USA, 82(20):6955-6959). PCR reactions were carried out individually for each sample using ~ 10 ng of template DNA. Tagged primer pairs and PCR reaction conditions followed the protocol of Dowd et al., 2008 (Foodborne Pathogens & Disease, 5(4):459-472). Sequencing was carried out on a Roche 454 titanium sequencer. Sequence data were trimmed to between 200 and 600 bp and labelled using the Mothur v.1.13.0 suite of programs (Schloss et al., 2009, Applied & Environmental Microbiology, 75(23):7357-7541).
DOI: 10.5061/dryad.46h6j/1
title: DemogDatabase_Km23

description: Capture records and demographic data for site Km23
DOI: 10.5061/dryad.5fs6j/1
title: Appendix II
DOI: 10.5061/dryad.5fs6j/2
title: Appendix 1
DOI: 10.5061/dryad.7bc88/1
title: Nexus file of Caryophylloideae

description: Nexus file of the phylogenetic relationships among the investigated Caryophylloideae. Our analyses were based on an unresolved phylogeny constructed using published molecular phylogenies and taxonomic groupings. The file was used in MESQUITE for further analyses.
DOI: 10.5061/dryad.7bc88/2
title: Figure 1 - model (as MS powerpoint file)

description: Figure 1. Factors that might affect evaporation of water from nectar. (A) Flower nectar depth (nectar is hidden in long-tubed flowers), (B) hydrolyis of sucrose by invertase into hexoses (increase in osmolality), (C) Relation between activity time of flowers (diurnal vs. nocturnal) and temperature (higher during the day) and humidity (higher during the night), (D) features of the anthophore (an elongated internodium above the calyx found in some Caryophylloideae) like its length and hairs. Note: While for hypotheses (A) and (B) evidence can be found in the literature (see text), (C & D) has been tested in this study.
DOI: 10.5061/dryad.7bc88/3
title: Figure 2 - flower morphology (as Ms powerpoint file)

description: Figure 2. Floral features in Silene: A. Half-drawing of a hypothetical female Silene flower (with sterile anthers and nectar along the anthophore) illustrating where nectar is located and how flower structure (here the protruding corona scales) may affect the functional flower length for flower visiting insects. B. Silene colorata; showing how the petal claws and corona scales may increase the functional flower length. C. Anthophore of Silene dichotoma with nectar.
DOI: 10.5061/dryad.7bc88/4
title: Figure 3 - phylogeny (CorelDRAW file)

description: Figure 3. Phylogenetic distribution of nectar sugar composition, flower tube length and pollination modes in 78 Caryophylloideae. Nectar sugar composition according to the classification system of Baker & Baker (1983); Flower tube length data (gray box; according to Jürgens (2006) and this study. Pollination modes: blue = day-flowering, black = night-flowering, white = self-pollination.
DOI: 10.5061/dryad.7fj1k/85
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_01

description: First salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/86
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_02

description: Second salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/87
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_03

description: Third salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/88
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_04

description: Fourth salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/89
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_05

description: Fifth salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/90
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_06

description: Sixth salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/91
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_07

description: Seventh salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/92
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_08

description: Eighth salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.7fj1k/93
title: Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_09

description: Ninth salt pulse for ceca 12, run 5
DOI: 10.5061/dryad.81m7r/1
title: Table A1

description: Data used to parameterise the two-sex model  for bulb mites, coho salmon and bullhorned dung beetles. All data are taken from published studies and references can be found in the footnotes of the Table.
DOI: 10.5061/dryad.8883h/1
title: dryad_LG

description: This data file contains the microsatellite (STR) genotypes for 176 Pristionchus pacificus strains collected from La Reunion Island.These strains were genotyped at 19 loci (which included 14 di-nucleotide, four tri-nucleotide, one tetra-nucleotide and one penta-nucleotide repeat), using the primer pairs, protocol and cycling conditions detailed in (Morgan et al., 2012).
DOI: 10.5061/dryad.8h154h65/10
title: kin_melpPHASED

description: DNA sequence data for the gene kinesin for multiple individuals for multiple races of Heliconius melpomene. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/11
title: kineratoPHASED

description: DNA sequence data for the gene kinesin for multiple individuals for multiple races of Heliconius erato. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/12
title: mterato

description: DNA sequence data for a sequenced fragment including mitochondrial COI-tRNALeu-COII for multiple individuals for multiple races of Heliconius erato. The data is derived from direct sequencing. Sequences can also be obtained in Genbank. Phylogenetic trees from neighbor-joining and Bayesian analyses are attached as a treeblock.
DOI: 10.5061/dryad.8h154h65/13
title: mtmelpomene

description: DNA sequence data for a sequenced fragment including mitochondrial COI-tRNALeu-COII for multiple individuals for multiple races of Heliconius melpomene. The data is derived from direct sequencing. Sequences can also be obtained in Genbank. Phylogenetic trees from neighbor-joining and Bayesian analyses are attached as a treeblock.
DOI: 10.5061/dryad.8h154h65/14
title: SUMOHeratoPHASED

description: DNA sequence data for the gene SUMO-1 activating enzyme (sae-1) for multiple individuals for multiple races of Heliconius erato. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/15
title: SUMOHmelpomenePHASED

description: DNA sequence data for the gene SUMO-1 activating enzyme (sae-1) for multiple individuals for multiple races of Heliconius melpomene. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/16
title: Suz12eratoPHASED

description: DNA sequence data for the gene Su(z)12 for multiple individuals for multiple races of Heliconius erato. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/17
title: Suz12melpomenePHASED

description: DNA sequence data for the gene Su(z)12 for multiple individuals for multiple races of Heliconius melpomene. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/18
title: VanGogheratoPHASED

description: DNA sequence data for the gene VanGogh for multiple individuals for multiple races of Heliconius erato. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.8h154h65/7
title: GPCReratoPHASED

description: DNA sequence data for a partial protein-coding sequence of the gene G protein coupled receptor for multiple individuals for multiple races of Heliconius erato. The data is derived from direct sequencing, inferring polymorphisms from double peaks in the chromatograms. Haplotypes were determined by analytically phasing the data across all sequences using the program PHASE. Inferred sequence before phasing can be obtained in Genbank. The file includes a treeblock containing a neighbor-joining tree constructed from this data using PAUP* and used in the study.
DOI: 10.5061/dryad.d9b2t/1
title: antenna runs

description: This Matlab struct includes all subject ID and condition info, as well as video tracking and scoring data.
DOI: 10.5061/dryad.f1c11/1
title: Abundance data

description: Count data of Odax pullus and Notolabrus fucicola at three locations across New Zealand: the Hauraki Gulf, D'Urville Island and Stewart Island. Count data was obtained from 30x10m belt transects.
DOI: 10.5061/dryad.f1c11/2
title: Ovary weight vs body size

description: Ovary weight data of Odax pullus in the Hauraki Gulf and at Stewart Island (New Zealand). Ovary weight is wet weight of whole gonads.
DOI: 10.5061/dryad.f1c11/3
title: Sea surface temperature data

description: Satellite-derived sea surface temperature data retrieved for the Hauraki Gulf, D'Urville Island, and Stewart Island (New Zealand). Temperature data presented is mean monthly sea surface temperature from January 1985 to December 2007, and was retrieved from the National Oceanographic and Atmospheric Administration (NOAA) CoastWatch Program.
DOI: 10.5061/dryad.f1c11/4
title: Size and age data

description: Size and age data of Odax pullus and Notolabrus fucicola individuals sampled in the Hauraki Gulf, D'Urville Island, and Stewart Island (New Zealand). Age was estimated from sectioned sagittal otoliths, and size was measured as Fork Length.
DOI: 10.5061/dryad.f1c11/5
title: Size- and age-at-maturity data

description: Size, age, and sexual maturity (immature / mature) of females Odax pullus and Notolabrus fucicola in the Hauraki Gulf and at Stewart Island. Size was measured as Fork Length, age was estimated from sectioned sagittal otoliths, and sexual maturity was established from gonad histology.
DOI: 10.5061/dryad.g42qs/1
title: Supl. Table S1
DOI: 10.5061/dryad.g42qs/2
title: Supl. Table S2
DOI: 10.5061/dryad.h6pf365t/11
title: README

description: This file describes the contents of the supplementary data package for Stotlzfus, et al, Sharing Phylogenetic Trees.  The package includes this README file, a PDF file with user stories, and 4 spreadsheets (for 3 literature samples plus 1 quick analysis of Dryad content): * LitSample1_Apr2011_AmJBot_Evol.csv - all pubs from 2 April issues* LitSample2_40RecentPhylogenInDepth.csv - sample of 40 recent phylogen* pubs* LitSample3_100RandomPhylogen2010.csv - random sample of 2010 phylogen* pubs* ArchiveSample_AllDryad_2010_Phylogen.csv* UserStories_BarriersToReUse.pdf - user stories and taxonomy of barriers* README = this file |This README file is Unicode (UTF-8) with Unix/Linux file endings.The .csv files are also in Unicode (UTF-8), with field delimiter symbol , (comma) and text delimiter symbol " (double quote mark)
DOI: 10.5061/dryad.h6pf365t/5
title: Literature Sample1: conducted in April 2011, journals: American Journal of Botany & Evolution

description: LitSample1.  To get a sense of current practices, AS and BO picked 2 journals, Evolution and Am J Bot, and looked at every one of the 32 regular articles in the April 2011 issues.  Evolution is the premier trade journal for organismal evolutionary biologists.  American Journal of Botany is a frequent venue for phylogenetic systematics.
DOI: 10.5061/dryad.h6pf365t/6
title: Literature Sample2: 40 recently published phylogeny-related articles

description: We searched Thomson Reuters Web of Science (WoS) in May of 2011 for articles matching 'phylogen*' in title or 'topic'.  WoS sorted the results by 'relevance', and we picked 40 articles from the top of the list.  We deliberately chose this approach to focus on articles likely to focus on phylogeny, rather than to mention it peripherally.  However, because we do not know exactly what 'topic' and 'relevance' mean in this case (and WoS does not make its methodology clear to users), we cannot be certain what kind of a sample this represents.  Of the 40 articles, 38 report new trees, considerably more than the 27/40 expected by chance for an article that matches 'phylogen*' anywhere (see below).   The file "LitSample2_40RecentPhylogenInDepth.csv" contains extensive notes on the 40 articles.  This spreadsheet was populated by an online fillable form that is available from the authors on request (in case any reader would like to analyze their own literature sample).
DOI: 10.5061/dryad.h6pf365t/7
title: Literature Sample3: 100 randomly-selected 'phylogen*' articles published in 2010

description: The sole purpose of this survey was to estimate the frequency of reports of new trees among 2010 publications.  We first searched Web of Science for 2010 papers that matched 'phylogen*' in any field.  Many of the 11,664 matching publications might be false positives, i.e., papers that refer to 'phylogen*' in some way, but do not report a new tree.  To estimate this fraction, we picked 100 papers at random.  Each paper was assigned to BO, AS or RM for individual evaluation, with the result that 66 of the 100 papers reported a new tree.  

The file "LitSample3_100RandomPhylogen2010.csv" contains results of the analysis of the sample of 100 publications.  There is not much in this spreadsheet other than a determination of whether it has a new tree or not.  This spreadsheet was populated by an online fillable form that is available from the authors on request (in case any reader would like to analyze their own literature sample).  

We also considered false negatives due to papers that report a new phylogeny, but avoid the term 'phylogen*', using instead some term such as  'dendrogram', 'cladogram' or 'tree'.   Because 'tree' has many non-phylogenetic uses, we used a restricted search methodology based on other terms associated with phylogenies, such as 'SSU' or 'cytb' and so on.  By comparing matches to 'SSU + tree -phylogeny' to those for 'SSU + phylogeny', we can estimate how often authors use 'tree' as a synonym while avoiding 'phylogeny'.  We got only about 1/100 as many hits, and many of these referred to "trees" that were not phylogenetic trees.  Thus, the results suggest that phylogeny synonyms would increase the yield by less than 1 %.

We did not estimate false negatives due to poor indexing, or non-indexing, in Web of Science.  Web of Science may contain information on articles that are indexed very incompletely, e.g., articles for which only the citation information is available, without keywords or abstract.  A poorly indexed article that reports a phylogeny will only be found if 'phylogen*' appears in the title.  

We also did not estimate the number of false negatives due to phylogeny reports that are not indexed at all in Web of Science.  It is difficult to see how this could be done.  However, one way to do it would be to take a very carefully researched review article, e.g., on phylogeny of major reptile groups, and then assess what fraction of cited phylogeny articles can be found in WoS.  Apropos, TimeTree has nearly a thousand articles in its database, and a substantial fraction are not indexed in PubMed.
DOI: 10.5061/dryad.h6pf365t/8
title: Archive Sample Analysis of All Dryad 2010 studies matching keyword: 'phylogen*'

description: All TreeBASE entries have trees, but not all Dryad packages for phylogeny papers have decodable (i.e., not graphic) trees.  Using the Dryad search interface in August, 2011, AS found 32 entries for 2010 studies in Dryad that match "phylogen". In this group, AS found one server error:.Among the remainder, there were 24 packages without any phylogeny in decodable form, and 7 packages with one or more phylogenies in decodable form. Note that most of the NEXUS files do not have trees, and that there are trees in non-NEXUS formats, e.g., some are just Newick strings in text files (e.g., http://datadryad.org/handle/10255/dryad.1965). The file "ArchiveSample_AllDryad_2010_Phylogen.csv" is a spreadsheet with the results of this very brief analysis.
DOI: 10.5061/dryad.h6pf365t/9
title: User stories of barriers to data re-use encountered

description: As part of a MIAPA exercise we gathered and analyzed stories of phylogeny use & re-use, based on our own experiences, and those of colleagues who are sharing this information as a personal communication.  This material provides a basis for many aspects of the barriers to re-use taxonomy in the text, and for individual comments about problems that users experience, such as inconsistent names, re-doing analyses, etc.
DOI: 10.5061/dryad.hr768/1
title: KnotweedHybridisation
DOI: 10.5061/dryad.r1hk5/1
title: MCC and Posterior Trees - output from BEAST

description: This compressed file contains the posterior distribution of trees as well as the MCC tree (with mean node heights) for each clade.
DOI: 10.5061/dryad.r1hk5/2
title: Trees pruned of extraneous taxa for diversification analyses

description: These are the MCC and posterior trees of each clade that have been pruned of inappropriate taxa for the diversification analyses.  Pruned tips are not from Madagascar, are intraspecific samples, and/or are not valid species.
DOI: 10.5061/dryad.r1hk5/3
title: Model fitting results and summaries

description: This file contains the results of the HMM model fits for each clade.  Each clade was analyzed at two levels of taxonomic sampling completeness - 100% and 50%.  Thus, the files that include "_1_Complete" or "_0.5_Complete" refer to 100% or 50% complete respectively.  The files with "AnalyzedTrees" in their names are the randomly selected trees from the posterior distributions that were analyzed.  Note that in producing these lists, the MCC tree was placed on top of all posterior trees.  Thus, the first row in all refers to the MCC tree (1), and the remaining 49 rows are the number of the randomly selected posterior tree plus 1.
DOI: 10.5061/dryad.r1hk5/4
title: R code and functions to run this analysis

description: This contains relevant functions and the code I used to collect these data.  See the README within for more details.
DOI: 10.5061/dryad.r3r60/2
title: Biorhiza_pallida.meta-assembly.fa

description: Biorhiza pallida combined assembly using clc bio v4.0.3
DOI: 10.5061/dryad.r3r60/5
title: tar archive of alignment summaries for mathematica

description: Contains 4 files each summarizing one of the 2kb alignments used as mathematica input
DOI: 10.5061/dryad.r3r60/6
title: scripts_for_Hearn_et_al

description: Tar archive of custom scripts referred to in Hearn et al 2013. Includes a document summarising each script
DOI: 10.5061/dryad.r3r60/7
title: Bpal.BLAST_and_Coverage_filtered_noINDELS_2609.vcf

description: VCF file for Biorhiza pallida ingroup individuals created using samtools. Contaminant and high coverage sequences have been removed from this file. The VCF_haploif_parser.pl script was run on this file.
DOI: 10.5061/dryad.r3r60/8
title: Bgib.BLAST_and_Coverage_filtered_noINDELS_2609.vcf

description: VCF file of the outgroup Belizinella gibbera, contaminant and high coverage contigs removed. Produced using samtools mpileup.
DOI: 10.5061/dryad.r90j0/1
title: Pygospio_genotype_data

description: The 'Pygospio_genotype_data.txt' file contains microsatellite genotype data of 765 P. elegans individuals used in the study. There is 2 to 3 temporal samples collected from 7 different European collection sites.
DOI: 10.5061/dryad.rk836/1
title: The dynamics of niche evolution upon abrupt environmental change

description: In this excel files, 1. we describe our data on the "Readme" sheet, and 2. show the raw data used in our article. On the "relative fitness" sheet, the data used for our estimation of selection coefficients (s) are presented. On the "rmax" sheet, the data used for the estimation of maximal growth rate are shown.
DOI: 10.5061/dryad.t6j52/2
title: Allele size data Floreana Tree Finches 2005 & 2010

description: Allele size data for tree finches on Floreana Island, Galapagos. "Year" refers to whether an individual was sampled in 2005 or 2010. "FTA" is a unique number that was given to the blood sample of each sampled individual (this number was written next to blood samples stored on FTA paper). "Ring number" refers to the identifier inscribed on an aluminum band around a bird's tarsus.  "Pop" refers to the species category given to each individual in the field: small tree finch=1, medium tree finch=2, large tree finch=3. Remaining information refers to allele size (maximum height at peak of allele) at each of 10 microsatellite loci (Gf01, Gf03, Gf04, Gf05, Gf06, Gf07, Gf09, Gf11, Gf12, Gf13)
DOI: 10.5061/dryad.26qt6/3
title: Supplementary Material: Cox et al.

description: Supplementary text and figures.
DOI: 10.5061/dryad.2g9p0/1
title: mtDNA haplotype sequences

description: DNA sequences of each of the haplotypes identified in this study. This file, in conjunction with the haplotypes, can be used to estimate population genetic parameters.
DOI: 10.5061/dryad.2g9p0/2
title: Individual mtDNA haplotypes

description: For each individual, the first column provides field id number (including location and date), second column provides lab id (sorted by year), and the third column identifies the haplotype.