cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rm5v5/7
title: Supplemental Figure 7: Z-score values of ILs relative to cv. M82.

description: Supplemental Figure 7: Z-score values of ILs relative to cv. M82: Z-score values of ILs (mean centered relative to cv. M82) for leaf development traits. Values are directional; yellow indicates standard deviations from cv. M82 towards S. pennellii, blue indicates transgressive standard deviations beyond cv. M82. Traits exhibit either broad deviation from cv. M82 towards S. pennellii values (e.g., leaf complexity traits) or more balanced deviation in both directions (e.g., cellular and stomatal traits, and leaflet AR and Roundness).
DOI: 10.5061/dryad.rm5v5/8
title: Supplemental Figure 8: Correlation between leaf developmental traits.

description: Supplemental Figure 8: Correlation between leaf developmental traits: Shown is a matrix of correlation coefficient values between leaf development traits as measured in the ILs. Traits are arranged by similarity using absolute correlation from hierarchical clustering (bottom). Major groups of traits that vary similarly across the ILs include 1) leaflet size and leaf complexity traits, 2) pavement cell and stomatal patterning traits, and 3) traits relating to leaflet shape, serration, and flowering time. Developmentally relevant correlations include the negative correlation between leaflet size and leaf complexity and between pavement cell size and absolute stomatal density (Supplemental Figure 9 online). Blue indicates negative Pearson correlation coefficient values and yellow positive.
DOI: 10.5061/dryad.rp5tt780/1
title: Buzatto et al 2012

description: This file contains the body weight of quiescent tritonymphs (QTW, see text) that developed into fighter or scrambler males of the bulb mite Rhizoglyphus echinopus. Males were either from one of eight inbred lines (L10, L18, L19, L27, L29, L30, L36 and L38) or from the base population from which the inbred lines were derived.
DOI: 10.5061/dryad.th08v/1
title: WellerEtAl_Data

description: Number of Townsend’s big-eared bats (Corynorhinus townsendii) counted in 52 individual caves during each year from 1991 – 2012 at Lava Beds National Monument, Siskiyou County, California.
DOI: 10.5061/dryad.v64q8/1
title: S7_alignment
DOI: 10.5061/dryad.v64q8/2
title: ND2 alignment
DOI: 10.5061/dryad.1529d/1
title: Golden_Jackal_Genotypes

description: Genotypes table at 15 canine microsatellites. The first column includes the sample identifiers, the second column the country of origin of samples.
DOI: 10.5061/dryad.157d7/1
title: Datasets from Salichos & Rokas (2013)

description: The files include individual gene (protein) alignments for the 1070 genes as well as RAxML gene trees
DOI: 10.5061/dryad.157d7/2
title: Binned_Data

description: Binned data: alignment and tree files
DOI: 10.5061/dryad.157d7/3
title: List_Genes_260C_131S

description: List of genes in the 260C and 131S sets
DOI: 10.5061/dryad.157d7/4
title: Supplementary Figure 1

description: Molecular properties for the 260 most conserved (260C) genes and the 131 genes with strongest phylogenetic signal (131S). ***U test P &lt; 0.00001.
DOI: 10.5061/dryad.1vb63/1
title: Morphological & environmental dataset
DOI: 10.5061/dryad.1vb63/2
title: Myobatrachidae phylogeny
DOI: 10.5061/dryad.246pr/1
title: XML of Eurasian AIV

description: XML were created in BEAUti v1.6.2 for analysis in BEAST v1.7.3 (Drummond & Rambaut, 2007, Drummond et al. 2012).  For each file, one internal segment of the same 344 subsampled Eurasian AIV (specified with subtype, host, location and isolate dates) was used as input data, labelled with the segment name. Files labelled with “original” represent the original time-scaled phylogenies of different segments. The substitution, clock and coalescent models are provided along with the priors placed on the model parameters. The other files labelled “empirical” and “H, N or HN” were generated to estimate the transition rate among discrete subtypes (HA, NA or HA-NA combined), with the implementation of a discrete trait model and BSSVS (Lemey et al. 2009) using empirical trees for each segment. These other files contain additional XML code not generated by BEAUTi in order to allow the re-use of the previously generated empirical tree sets.
DOI: 10.5061/dryad.2qp1v/1
title: Jordan et al Am Nat 2013 data

description: Coordinate data for all males and females at time 1 and time 2, along with measurements of weight, length, and death.
DOI: 10.5061/dryad.33tb2/1
title: Teeth character coding

description: Character states and character coding of a dentition-based datamatrix/supermatrix including 60 nonavian theropod taxa and 4 isolated teeth from the collection of the Museum of Lourinhã.
DOI: 10.5061/dryad.33tb2/2
title: Morphometric graphs on nonavian theropod teeth

description: Morphometric data on nonavian theropod teeth
DOI: 10.5061/dryad.33tb2/3
title: Dentition-based datamatrix

description: Tnt files including the dentition-based datamatrix coded in 60 nonavian theropod teeth and four isolated tooth from the collection of the Museum of Lourinhã.
DOI: 10.5061/dryad.33tb2/4
title: Dentition-based supermatrix

description: Tnt files including the dentition-based datamatrix combined to six datasets (Xu et al. 2009; Brusatte et al. 2010; Martinez et al. 2011; Senter 2011; Pol & Rauhut 2012; Carrano et al. 2012) and coded in 60 nonavian theropod teeth and four isolated tooth from the collection of the Museum of Lourinhã.
DOI: 10.5061/dryad.40gg7/1
title: Raw Data for submission
DOI: 10.5061/dryad.465v3/1
title: ann_arg_fst_map

description: Contains: all SNPs kept in the H. annuus - H. argophyllus comparison, name of reference gene, position of SNP in gene, genotypes of all individuals, Fst, Fit, Fis, name, linkage group, position in centimorgan, unique position on map, number of nucleotides in gene, boolean value whether SNP is in the top5% most divergent.
DOI: 10.5061/dryad.55c2f/1
title: Genotypes

description: SSR genotypes from 6 loci for progeny arrays (sheet1) and for adult trees (shhet 2) from CL (Clonee) and K (Kildalkey) sites. The location of the mother trees  are also indicated: Native or Plantation.  Numbers are allele size. 0 = missing value
DOI: 10.5061/dryad.6nm40/1
title: Microsatellite data from parasites

description: This data consists genotypes obtained from Schistosoma mansoni parasites that were type at nine microsatellite markers. Each locus (e.g. L46951) is coded by 6 digits (e.g. 169175). Each allele is coded by 3 digits (e.g. 169).
DOI: 10.5061/dryad.6nm40/2
title: Human host data

description: Village: location where human host lived. Host: population number that was assigned to the human host. HostIdentifier: code that is linked with that host. SamplingTime: time when parasites were sampled (e.g. Aug-09 or 09-Aug means that parasites were sampled from this host in August 2009. Age: age of the human host. EPG: eggs per gram of feces, i.e. a measure of infection intensity. CoInfectionWithShaematobium: 1 = when human host was coinfected with Schistosoma haematobium, 0 = when human host was NOT coinfected.
DOI: 10.5061/dryad.6nm40/3
title: R script written for some of the analyses

description: This is an R script that was written for some of the analysis, namely: 1) hierarchical f-statistics 2) tests for inbreeding with multilocus heterozygosity and 3) tests for family structure with relatedness estimates
DOI: 10.5061/dryad.7dp5v/1
title: Appendix 1

description: Means of morphometric measurements for each specimen. Missing measurement indicators (?) were retained for cladistic analysis whereas species’ means were substituted for missing measurements (bold) for phenetic analyses. BSLC and BSLZ were removed from analyses because missing values substantially outnumbered measurements.
DOI: 10.5061/dryad.7dp5v/10
title: Appendix 10

description: Integer codes for 21 characters used in cladistic analysis. Characters are defined in Table 1, original measurement means are in Appendix 1, and gap-coding intervals, character weighting factors, and final character weights are listed in Table 2. Missing codes (not measureable) indicated by question marks.
DOI: 10.5061/dryad.7dp5v/2
title: Appendix 2

description: Summary statistics for morphological characters measured in Strotopora compressa. Characters are defined in Table 1. N = number of measurements. Means for each measured specimen are listed in Appendix 3.
DOI: 10.5061/dryad.7dp5v/3
title: Appendix 3

description: Character means for specimens of Strotopora compressa. Characters are defined in Table 1. Ten replicate measurements were collected for each quantity unless indicated by a superscript value. Missing values indicated by dashes. All specimens are from the UMMP; UMMP 6547G has been selected as the lectotype, with UMMP 6547A-F, and H designated as paratypes.
DOI: 10.5061/dryad.7dp5v/4
title: Appendix 4

description: Summary statistics for morphological characters of Strotopora foveolata. Characters are defined in Table 1. N = number of measurements. Character means for each specimen are listed in Appendix 5.
DOI: 10.5061/dryad.7dp5v/5
title: Appendix 5

description: Character means for specimens of Strotopora foveolata. Characters are defined in Table 1. Ten replicate measurements were collected for each quantity unless indicated by a superscript value. Missing values indicated by dashes. All specimens are from the USNM with accession numbers indicated for individual specimens.
DOI: 10.5061/dryad.7dp5v/6
title: Appendix 6

description: Summary statistics for morphological characters of Strotopora dermata. Characters are defined in Table 1. N = number of measurements Character means for each specimen are listed in Appendix 7.
DOI: 10.5061/dryad.7dp5v/7
title: Appendix 7

description: Character means for specimens of Strotopora dermata. Characters are defined in Table 1. Ten replicate measurements were collected for each quantity unless indicated by a superscript value. Missing values indicated by dashes; all specimens are from the USNM.
DOI: 10.5061/dryad.7dp5v/8
title: Appendix 8

description: Summary statistics for morphological characters of Cliotrypa ramosa. Characters are defined in Table 1. N = number of measurements. Character means for each specimen are listed in Appendix 9.
DOI: 10.5061/dryad.7dp5v/9
title: Appendix 9

description: Character means for specimens of Cliotrypa ramosa. Characters are defined in Table 1. Ten replicate measurements were collected for each quantity unless indicated by a superscript value. Missing values indicated by dashes. All specimens are from the USNM with accession numbers indicated for individual specimens. The holotype is USNM 92133.
DOI: 10.5061/dryad.7j504/3
title: Sequence alignments

description: Sequence alignments of malaria lineages identified in pied and collared flycatchers
DOI: 10.5061/dryad.7j504/4
title: MARK-CF_analysis

description: MARK code for general analysis (CF, collared flycatchers)
DOI: 10.5061/dryad.7j504/5
title: MARK-PF_analysis

description: MARK code for general analysis (PF, pied flycatchers)
DOI: 10.5061/dryad.7j504/6
title: MARK-CF-recapture_data

description: MARK (input) recapture data (CF, collared flycatchers)
DOI: 10.5061/dryad.7j504/7
title: MARK-PF-recapture_data

description: MARK (input) recapture data (PF,  pied flycatchers)
DOI: 10.5061/dryad.7j504/8
title: GLMM_input_data
DOI: 10.5061/dryad.7nk1nc63/1
title: BEAST nex files

description: The ZIP folder contains all nex files used for the single gene BEAST analyses according to dataset numbers in the publication
DOI: 10.5061/dryad.8m0t6/1
title: Microsatellite and sex data
DOI: 10.5061/dryad.8n776/1
title: Pomacea_proteins

description: Protein sequences translated from the assembled unigenes
DOI: 10.5061/dryad.8n776/2
title: Pomacea_unigenes

description: Unigenes assembled from the Illumina raw reads
DOI: 10.5061/dryad.8n776/3
title: Pomacea_SNP

description: SNP information deduced from the unigenes
DOI: 10.5061/dryad.8n776/4
title: Protein identified by LC-MS/MS

description: A list of 878 proteins identified by LC-MS/MS.
DOI: 10.5061/dryad.cd168nj1/1
title: Norwegian_porps_8loci

description: North Sea and Norwegian Sea harbour porpoises genotype data for 8 microsatellite loci.
DOI: 10.5061/dryad.cp2vn740/3
title: ParentExp

description: Time spent shoaling for families raised by different fathers.
DOI: 10.5061/dryad.f8539/1
title: pollinators_all

description: This file shows pollinator visitation rates to single focal plants across nine common gardens.  It includes two rainy and two dry seasons.
DOI: 10.5061/dryad.f8539/2
title: FruitSet

description: This file shows the number of flowers marked and the number that developed into fruits for plants in nine common gardens over two rainy and two dry seasons.
DOI: 10.5061/dryad.f8539/3
title: abortion_data_2011

description: This file shows the days to abscission for marked flowers of self-compatible and self-incompatible plants.
DOI: 10.5061/dryad.f8539/4
title: paternity

description: This file shows genotypes at microsatelliite loci for parental plants and their progeny formed in seven common gardens.
DOI: 10.5061/dryad.j42c6/1
title: BAGpipe Alignments

description: Mafft Alignments of psbA-trnH sequences produced by the BAGpipe.
DOI: 10.5061/dryad.j42c6/2
title: Nicaraguan SDTF Database psbA-trnH Sequences

description: A fasta file containing psbA-trnH sequences of 450 angiosperm samples from the Nicaraguan Seasonally Dry Tropical Forest, with taxonomic and geographic information
DOI: 10.5061/dryad.jd8vg.1
title: Data from: Standard sister-clade comparison fails when testing derived character states
DOI: 10.5061/dryad.jd8vg.2
title: Data from: Standard sister clade comparison fails when testing derived character states
DOI: 10.5061/dryad.jr421/7
title: aflp_profiles_by_species_genalex

description: This file contains scored AFLP profiles used in all downstream analyses in GenAlEx format.
DOI: 10.5061/dryad.kt540/1
title: Mistletoe-infected and non-infected hosts and dispersers niche models and environmental data

description: ASCII files of niche models and environmental data of mistletoe-infected and non-infected hosts and dispersers (year-round and winter).
DOI: 10.5061/dryad.m0r5qv24/1
title: Gene expression levels in fire ants

description: Analysis of gene expression levels in workers, queens and males of the fire ants S. invicta, S. richteri and their hybrids, at the larval, pupal and adult stages (see also Ometto et al. 2011 Mol Biol Evol 28:1381–1392). Samples were collected in the field in 2005 and 2007. All collected colonies were returned to the laboratory and maintained in a rearing room under standard conditions. Gene expression of each sample (n=140) was measured through microarray hybridizations. Next, we estimated the relative expression of each clone for each node (caste/species/stage; n = 27), and the significance of the differential expression of such clones among nodes, using the Bayesian approach implemented in the program Bayesian Analysis of Gene Expression Levels (BAGEL;  Meiklejohn and  Townsend 2006 Brief Bioinformatics 6:318–330). Three-letter labels (one for each node) identify species (i = S. invicta; r = S. richteri; h = S. invicta X S. richteri), caste (W = workers; Q = queens; M = males), and developmental stage (l = larvae; p = pupae; a = adults).
DOI: 10.5061/dryad.mm11q/11
title: envsamples

description: Environmental data sampled from specimens across the Ctenophorus maculatus complex. Data were sourced from databases as listed in the published manuscript. Email author for further information.
DOI: 10.5061/dryad.mp40j/1
title: Early Triassic ecosystems of the Western U.S.

description: Data file containing full sample and abundance list of benthic macrofossils of the Thaynes Group and the Sinbad Formation (Lower Triassic), benthic associations, and alpha and beta diversity calculations.
DOI: 10.5061/dryad.q3ng0/2
title: CBSilveira el al 2012

description: The file contains data from 295 individuals genotyped for 13 microsatellite (127 Microtus duodecimcostatus MD), 104 Microtus lusitanicus (ML) and 52 individuals for which assignment to either species based on morphology was difficult here termed Microtus sp (M)). First line contains microsatellite names. Each microsatellite has two columns one for each allele genotyped. Empty cell represents no data.
DOI: 10.5061/dryad.r0056/20
title: OSRE.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample OSRE.
DOI: 10.5061/dryad.r0056/21
title: Ta.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample Ta.
DOI: 10.5061/dryad.r0056/22
title: TaRE.Equus_cab_nucl
DOI: 10.5061/dryad.r0056/23
title: TP3.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample TP3.
DOI: 10.5061/dryad.r0056/24
title: TP3RE.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample TP3RE.
DOI: 10.5061/dryad.r0056/25
title: Tu.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample Tu.
DOI: 10.5061/dryad.r0056/26
title: TuRE.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample TuRE.
DOI: 10.5061/dryad.r0056/27
title: Ty.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample Ty.
DOI: 10.5061/dryad.r0056/28
title: TyRE.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample TyRE.
DOI: 10.5061/dryad.r17n5/1
title: Case study data on field voles

description: This file is an ASCII text representation of an R list object created by the ‘dput’ function in R. It can be read into R by the ‘dget’ function. Please see the README.txt file for a description of the list elements.See Appendix S2 of the paper for detailed information about the data.The data have the same structure as the data that can be simulated and fit to the RD-SCR model provided in Appendix S3 of the paper.
DOI: 10.5061/dryad.r84n5/1
title: MicroSatResults

description: Symbiodinium genotypes associated with Aiptasia. Genotypes were determined using 18S RFLP, ITS2 DGGE, and 6 microsatellite markers specific to Symbiodinium Clade B. The spreadsheets provide sample location, sample ID, RFLP and DGGE proflies, as well as the allele sizes for each microsatellite. The data are presented on two worksheets within the file. The first worksheet includes samples in which Clade B was detected according to the 18S RFLP. The second worksheet includes samples from Florida in which only Clade A was detected according to the 18S RFLP, but the samples were screened with the Clade B-specific microsatellites to determine whether low levels of Clade B (i.e., "background" or "cryptic" populations)  could be detected.
DOI: 10.5061/dryad.rm5v5/10
title: Supplemental Figure 10: Detected leaf development QTLs.

description: Supplemental Figure 10: Detected leaf development QTLs: p-values, as calculated from mixed-effect linear models for deviation of ILs from cv. M82. Shown are only those QTL with a significance value &lt; 0.05. Yellow indicates deviation towards S. pennellii and blue indicates transgressive deviation beyond cv. M82. In total, 1035 QTL for leaf developmental traits were detected; 826 towards S. pennellii and 209 transgressive beyond cv. M82.
DOI: 10.5061/dryad.rm5v5/11
title: Supplemental Figure 11: Leaflet shape QTL.

description: Supplemental Figure 11: Leaflet shape QTL: A) Mean terminal and distal lateral leaflet shapes for parents and ILs. Mean cv. M82 leaflet shapes are indicated in light gray, and mean shapes of S. pennellii, intermediate shape ILs towards S. pennellii (IL4-3 and IL5-4), and transgressive ILs beyond cv. M82 (IL2-1 and IL9-1-2) are shown as superimposed black outlines. S. pennellii leaflets exhibit an inverted length-to-width orientation relative to cv. M82; ILs 4-3 and 5-4 are similarly wider than cv. M82; and ILs 2-1 and 9-1-2 are significantly narrower than cv. M82. B) Shape QTL vary distinctly in the way they alter leaflet length-to-width ratios. Superimposed are the outlines of two intermediate, wider ILs (4-3 and 5-4) and two transgressive, narrower ILs (9-1-2 and 2-1). Note the distinctness of the tip and wider base of IL5-4 relative to IL4-3, and the more lanceolate shape of IL2-1 relative to IL9-1-2. C) PCs 1 and 4 (the most heritable PCs) differentiate the distinctness of shape ILs. PC1 explains variance due to length-to-width ratio differences, whereas PC4 explains the distribution of blade outgrowth along the proximal-distal axis of leaflet. ILs 2-1 and 5-4 vary most strongly with respect to PC4 (especially in the lateral leaflets), whereas ILs 4-3 and 9-1-2 are separated by PC1.
DOI: 10.5061/dryad.rm5v5/12
title: Supplemental Figure 12: IL10-3 exhibits QTL affecting pavement cell size and stomatal density.

description: Supplemental Figure 12: IL10-3 exhibits QTL affecting pavement cell size and stomatal density. A) Images of epidermal peels from the adaxial side of mature leaves and cotyledons are shown. S. pennellii has larger pavement cells and decreased stomatal density relative to cv. M82, perhaps an adaptive feature to its native arid environment. IL10-3 exhibits decreased stomatal density on the adaxial side of mature leaves relative to cv. M82, and increased pavement cell size and decreased stomatal density on the adaxial side of cotyledons. B) IL10-3 is consistently one of the most extreme ILs for a suite of related traits, including adaxial leaf stomatal density, adaxial cotyledon stomatal density, and adaxial cotyledon pavement cell size. One perspective is that, because stomatal patterning in IL10-3 relative cv. M82 is not significantly changed, increases in pavement cell size decrease stomatal density.
DOI: 10.5061/dryad.rm5v5/13
title: Supplemental Figure 13: Developmentally insightful correlations between leaf development traits.

description: Supplemental Figure 13: Developmentally insightful correlations between leaf development traits. A) Pairwise correlations between leaf size (“TermLfSize” and “LatLfSize”) and leaf complexity (“CompPri,” “CompInt,” “CompSec,” “CompRachis,” and “CompAll”). Besides the high correlations within leaf size and leaf complexity traits, there is significant negative correlation between size and complexity. The least significant negative correlation (LatLfSize x CompPri, r = -0.33) is significant at a level of p = 0.0046 (two-tailed, n = 72). The correlation suggests that overall blade area in a leaf is not modulated through complexity, as any additional leaflets are on average smaller. This has implications for resource allocation at the level of the leaf, but also between different parts of the plant, as complexity only modulates the dissection of the leaf rather than its overall blade area. B) Pairwise correlations between absolute stomatal density on the adaxial side of the cotyledon (“CotStom”) and epidermal pavement cell size (“CotPaveArea”) and count (“CotPaveCnt”). The negative correlation between CotStom and CotPaveArea, and the positive correlation between CotStom and CotPaveCnt, suggests that as pavement cell size increases, stomatal density decreases. The least significant correlation between two traits of each class (CotPaveArea x CotStom, r = -0.44) is significant at a level of p = 0.00011 (two-tailed, n = 72). This has implications for mechanisms by which stomatal spacing is modulated in this population, which may not be directly through stomatal patterning, but rather changes in epidermal pavement cell size.