cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r634p/1
title: Secretary Island & mainland stoat haplotypes

description: Microsatellite genotypes of the Secretary Island stoat population over time.  This is formatted to be used as an input for the GeneChart R code.  Column 1 = sample id, column 2 = population, subsequent columns are the loci with microsatellite sizes.  Population codes are: "Mainland" = mainland, y2005 = Secretary Island captures in 2005, y2006 = Secretary Island captures in 2006, etc.  Missing values = 0.  Allele names at the top of each column.  Each locus has two columns, one for each allele, and the names are the locus name followed by .a1 and .a2 for allele one and allele two.
DOI: 10.5061/dryad.r634p/2
title: GeneChart R code

description: This is the R code for the GeneChart assignment used in the paper.  The main commands are at the top.  Select the Secretary-Genechart.input.csv as stoat.dat.  Read in this R code using source(file.choose()).  Plot the chart using the command:  chart.func(stoat.dat, refpopnames=c("Mainland", "y2005"), include.pops=c("y2006", "y2007", "y2008","y2009")) title(main="...").  This code will then produce a GeneChart assignment using the Mainland and Secretary Island 2005 captures as reference populations, and attempt to assign subsequent Secretary Island captures (from 2006 - 2009) onto this chart. The reference populations and additional included populations can be modified in the command.
DOI: 10.5061/dryad.rm5v5/44
title: Supplemental Figure 44: Bin mapping results for TermPC1.

description: Supplemental Figure 44: Bin mapping results for TermPC1. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend.
DOI: 10.5061/dryad.rm5v5/45
title: Supplemental Figure 45: Bin mapping results for TermPC3.

description: Supplemental Figure 45: Bin mapping results for TermPC3. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend.
DOI: 10.5061/dryad.rm5v5/46
title: Supplemental Figure 46: Bin mapping results for TermPC4.

description: Supplemental Figure 46: Bin mapping results for TermPC4. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend.
DOI: 10.5061/dryad.rm5v5/47
title: Supplemental Figure 47: Bin mapping results for TermPC5.

description: Supplemental Figure 47: Bin mapping results for TermPC5. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend.
DOI: 10.5061/dryad.rm5v5/48
title: Supplemental Figure 48: Significant correlations between leaf complexity and shape with fruit sugar levels.

description: Supplemental Figure 48: Significant correlations between leaf complexity and shape with fruit sugar levels. The traits Brix (BX), glucose, maltose, fructose, sucrose, and glucose_e were graphed as a function of the leaf morphology traits A) CompAll, a measure of overall leaf complexity, B) LatPC4 (PC4 values for lateral leaflets), and C) TermPC4 (PC4 values for terminal leaflets). Trait values are given as averaged z-scores, mean-centered on the cv. M82 value. To aid the visualization of the correlations, fitted linear (yellow) and LOESS (blue) models are provided. p-values, multiple test adjusted for all trait x trait correlations, are given. D) Examples of differences in leaf complexity, with which fruit sugar levels positively correlate with, amongst ILs. Shown are ILs with significantly decreased (IL7-4-1) and increased (IL8-2) complexity relative to cv. M82. CompAll values are the sum of primary, intercalary (purple), and secondary (orange) leaflet counts. E) Examples of differences in PC4-related leaflet shape variance, with which fruit sugar levels negatively correlate. Shown are ILs with significantly decreased (IL1-1) and increased (IL8-1-1) PC4 values.
DOI: 10.5061/dryad.rm5v5/49
title: Supplemental Figure 49: Network analysis reveals a relationship between leaf complexity and shape with sugars, Brix, and biomass.

description: Supplemental Figure 49: Network analysis reveals a relationship between leaf complexity and shape with sugars, Brix, and biomass. A) Hive plot axis with significant correlations (after multiple test adjustment) between DEV traits and traits from other classes arranged by -log10(p-value). Each edge represents such a correlation, and is colored by -log10(p-value): ≥ 3.0 black, ≥ 2.0 blue, &lt; 2.0 yellow. B) The other hive plot axis, in which nodes correspond to traits from the MET, ENZ, MOR, and SEED trait classes, arranged by the overall connectivity of the trait. Additionally, the size of the terminal end of each edge is proportional to the trait connectivity. Note that the most significant correlations tend to involve traits with high connectivity. C) Traits with the highest connectivities along the axis in (B) are shown. Adjacent to each trait is a dot representing the trait class (MOR magenta, MET blue, ENZ yellow, and SEED orange). The traits with the highest connectivity include traits associated with either vegetative biomass or fruit mono- and disaccharide levels. D) Traits representing the most significant correlations are shown. There is an abundance of correlations between leaf complexity traits (“Comp” traits) and PC4 with biomass and mono- and disaccharide level traits. The correlations of interest are denoted by an asterisk.
DOI: 10.5061/dryad.rm5v5/50
title: Supplemental Figure 50: Hierarchical clustering of traits analyzed in this study.

description: Supplemental Figure 50: Hierarchical clustering of traits analyzed in this study. Hierarchical clustering of leaf development traits with other previously studied traits. Hierarchical clustering is based on absolute correlation values. This figure complements Figure 4 to show trait names. Traits are represented by their class followed by their name. Trait classes are represented by color: Black, “DEV”; magenta, “MOR”; blue, “MET”; yellow, “ENZ”; orange, “SEED”. The group of traits, including PW, BX, EA, glucose, galactose, fructose, sucrose, mannose, and trehalose, that are mentioned in the text can be found in the uppermost cluster indicated by the red dotted box. The groups of traits corresponding to the upper right hand dotted box in Fig. 4A are indicated in the lower part of this figure, also with a dotted, black box. This constellation of traits negatively correlates with harvest index (HI), many of which involve amino acid metabolism (indicated by asterisk).
DOI: 10.5061/dryad.rm5v5/51
title: Supplemental Figure 51: Jackknifing results indicate stable correlations between leaf complexity and shape with sugar metabolism and yield traits.

description: Supplemental Figure 51: Jackknifing results indicate stable correlations between leaf complexity and shape with sugar metabolism and yield traits. A) Visualization of a sampling of jackknifing results (from Supplemental Dataset 12 online) for significant correlations between leaf complexity and shape traits with yield-associated and sugar metabolite traits. The small black dot represents the actual value of the Pearson correlation coefficient between the two traits indicated on the x-axis. Bars represent the standard error of jackknifing results. The larger, transparent orange dot represents the actual r value plus the calculated jackknifed bias. B) The same results indicated in (A), but showing individual calculated r values from the removal of each IL. Large black dot represents the actual r value, the large transparent orange dot represents r plus the jackknife bias, and the small blue dots represent individual jackknifed values that were used to calculate standard error and jackknifed bias. Note the relative stability of r values to the removal of IL values calculating the correlation between traits, indicating that significant r values do not represent undue bias from a few ILs.
DOI: 10.5061/dryad.s44gk/1
title: Characteristic flying squirrel vocalizations

description: A set of 4 different high frequency vocalizations made by southern flying squirrels, stored in a zip archive as wav files. Type 1 vocalizations are broadband bursts; Type 2 vocalizations are frequency modulated, varying from about 27 to about 19 kHz, and contain higher frequency harmonics; Type 3 vocalizations are pure ultrasound exceeding 50 kHz; and Type 4 vocalizations are frequency modulated between about 51 kHz and 28 kHz. Types 1-3 were recorded from captive squirrels in a sound lab at McMaster University, and Type 4 was recorded in the field at Trent University's Oliver Research Centre near Bobcaygeon, Ontario.
DOI: 10.5061/dryad.t3b18/1
title: COLONIES 1

description: Original data used in analyses for this paper.
DOI: 10.5061/dryad.vb131/2
title: Pinus halepensis__KEGG_annotation

description: Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway annotations of the assembled transcripts.
DOI: 10.5061/dryad.vb131/3
title: Pinus halepensis transcriptome sequence

description: Assembled sequence of Pinus halepensis transcriptome
DOI: 10.5061/dryad.vf1ms/1
title: stomach_content_analysis

description: data from the stomach content analyses
DOI: 10.5061/dryad.vf1ms/2
title: qPCR1

description: raw data from the qPCR analyses
DOI: 10.5061/dryad.vf1ms/3
title: qPCR2

description: data from the quantitative real-time experiments
DOI: 10.5061/dryad.vf1ms/4
title: Amphilophus
DOI: 10.5061/dryad.vf1ms/5
title: Tropheini
DOI: 10.5061/dryad.0179t/11
title: Alignment of merged reads for modern-2

description: Merged reads that aligned to the reference sequences for sample modern-2. Use with file 'Reference sequences for modern-2'.
DOI: 10.5061/dryad.0179t/13
title: Alignment of merged reads for modern-1

description: Merged reads that aligned to the reference sequences for sample modern-1. Use with file 'Reference sequences for modern-1'.
DOI: 10.5061/dryad.0179t/15
title: Alignment of merged reads for ancient-1

description: Merged reads that aligned to the reference sequences for sample ancient-1. Use with file 'Reference sequences for ancient-1'.
DOI: 10.5061/dryad.0179t/17
title: Alignment of merged reads for ancient-2

description: Merged reads that aligned to the reference sequences for sample ancient-2. Use with file 'Reference sequences for ancient-2'.
DOI: 10.5061/dryad.0179t/7
title: Alignment of merged reads for museum-1

description: Merged reads that aligned to the reference sequences for sample museum-1. Use with file 'Reference sequences for museum-1'.
DOI: 10.5061/dryad.0179t/9
title: Alignment of merged reads for museum-2

description: Merged reads that aligned to the reference sequences for sample museum-2. Use with file 'Reference sequences for museum-2'.
DOI: 10.5061/dryad.23j8n/1
title: Ego-depletion meta-analysis raw data

description: Raw data from our meta-analysis of the ego depletion effect. Columns are: (1) Ego-depletion effect size for each study in Cohen's d (standardized mean difference between experimental and control group); (2) Experimental group sample size; (3) Control group sample size; (4) Depleting task domain code, CA = controlling attention, CI = controlling impulses, CV = choice and volition, CE = controlling emotions, CT = controlling thoughts, SP = social processing, CP = cognitive processing; (5) Study authors, year and (if applicable) experiment/sample number within study. For details see: Hagger, M. S., Wood, C., Stiff, C., & Chatzisarantis, N. L. D. (2010). Ego depletion and the strength model of self-control: A meta-analysis. Psychological Bulletin, 136(4), 495-525. doi: 10.1037/a0019486
DOI: 10.5061/dryad.2656v/1
title: Hibiscus meyeri growth, survival, and reproduction

description: repeated measurements of height, basal area, reproductive structure number (allrep), fruit, between 2011 and 2012, for Hibiscus meyeri plants subject to either neighbor removal treatments (NR) or unmanipuated control (control; indicated in the trmtAL column), at a variety of aridity levels (N, arid; S, mesic; indicated in the level column) and herbivore exclosure treatments (open control, "CONT" and full exclosure, "LMH"; indicated in the trmtUHURU column).
DOI: 10.5061/dryad.28kh9/1
title: Trees, seeds and pollen genotypic data
DOI: 10.5061/dryad.2rm60/2
title: Cymbid GB and vouchers MASTER

description: Table of voucher specimens and GenBank numbers for Cymbidieae analysis.
DOI: 10.5061/dryad.3kn08/1
title: Alignments of DNA sequences, input file for GeoDis, formatted MSN from Network software, and output from IM, IMa2

description: The archive contain the README.txt file describing each file in detail
DOI: 10.5061/dryad.425rs/1
title: Statistical models

description: R script used to run all statistical models included in the manuscript
DOI: 10.5061/dryad.425rs/2
title: Onset of activity

description: Dataframe for the analyses of the onset of activity data
DOI: 10.5061/dryad.425rs/3
title: Offset of activity

description: Dataframe for the analyses of the offset of activity
DOI: 10.5061/dryad.425rs/4
title: raw activity
DOI: 10.5061/dryad.504636cd/10
title: ALN2_NS3

description: Alignment derived from ALN2.fas that corresponds to the NS3-gene region.
DOI: 10.5061/dryad.504636cd/11
title: ALN2_NS4A

description: Alignment derived from ALN2.fas that corresponds to the NS4A-gene region.
DOI: 10.5061/dryad.504636cd/12
title: ALN2_NS4B

description: Alignment derived from ALN2.fas that corresponds to the NS4B-gene region.
DOI: 10.5061/dryad.504636cd/13
title: ALN2_NS5

description: Alignment derived from ALN2.fas that corresponds to the NS5-gene region.
DOI: 10.5061/dryad.504636cd/14
title: ALN2_PrM

description: Alignment derived from ALN2.fas that corresponds to the PrM-gene region.
DOI: 10.5061/dryad.504636cd/8
title: ALN2_NS2A

description: Alignment derived from ALN2.fas that corresponds to the NS2A-gene region.
DOI: 10.5061/dryad.504636cd/9
title: ALN2_NS2B

description: Alignment derived from ALN2.fas that corresponds to the NS2B-gene region.
DOI: 10.5061/dryad.522cm/1
title: Data file: Fst values by species

description: Fst values used as estimates of population genetic structure. File formatted for input into R.
DOI: 10.5061/dryad.522cm/2
title: Data file: Species richness in reef fish families

description: Species richness values used as estimates of diversity. File formatted for input into R.
DOI: 10.5061/dryad.522cm/3
title: Database of Fst data for benthic fishes

description: This is the full database used by Riginos et al. 2011 (Ecography). The records omitted in the 2014 Am Nat study are indicated. References to original genetic source materials are indicated.
DOI: 10.5061/dryad.522cm/4
title: Tree1: Constrained_chronogram

description: Nexus file of chronogram based on a constrained tree as described in text.
DOI: 10.5061/dryad.656gf/1
title: SRL original genotype data

description: The Microsoft excel file 'SRL original genotype data' lists the important data for each individual scored in this study. By column, data includes an ID code relative to the individual lobster sampled, the site the lobster was taken from, the latitude and longitude location of this site, the site code used in analysis, the phenotype of the individual, and a list of the 8 microsatellite genotypes scored for the individual. In columns G to V are featured the 8 microsatellite loci, with two columns each indicating each allele for the microsatellite. There are 6 sites total sampled across Southern Tasmania, and one site sampled in New Zealand (latitude and longitude not given for this area).
DOI: 10.5061/dryad.656gf/2
title: SRL adjusted genotype data

description: The Microsoft excel file 'SRL adjusted genotype data' features the same data as that of the original file 'SRL original genotype data', excepting that the microsatellite data is now represented as it was when adjusted (using the number 999) for null alleles. This method involved replacing an established number of false homozygote genotypes with the assigned heterozygote number of 999. This data set has been indicated as being used in some statistical tests, hence may be useful when testing in programs that are not robust to the level of null alleles as found in the original data set.
DOI: 10.5061/dryad.6j777/1
title: Callitris_nSSR_genotype

description: The microsatellite genotype data of Callitris columellaris species complex (Cupressaceae), analysed in the MS (RSPB-2013-2182).
DOI: 10.5061/dryad.6rd6f/1
title: Phenotypic data

description: This file includes for each tree an identifier, two population structure coefficients (q1 and q2), 11 wood traits and tree height data.
DOI: 10.5061/dryad.6rd6f/2
title: Genotypic data file

description: This file contains for each of the 1694 trees used in this study the genotype of 6385 SNP markers. Tree identifiers can be found in the first column white the name of the SNPs can be found in the first line.
DOI: 10.5061/dryad.7b87b/1
title: Plastid DNA sequence alignment (non-coding regions rpl32-trnL and rps12-rpl20) of Ranunculus glacialis s.l.

description: The file contains the alignment of sequences used for the BEAST analysis of plastid DNA variation (concatenated sequences of non-coding regions rpl32-trnL and rps12-rpl20)in Ranunculus glacialis s.l.
DOI: 10.5061/dryad.7b87b/2
title: Nuclear ribosomal ITS DNA sequence alignment of Ranunculus glacialis s.l.

description: The file contains the alignment of sequences used for the BEAST analysis of nuclear ribosomal ITS (Internal transcribed Spacer region containing ITS1, 5.8S gene and ITS 2) DNA variation in Ranunculus glacialis s.l.
DOI: 10.5061/dryad.7j9t5/1
title: Expression Data

description: These files contain expression data, both in its pre-processed form and the actual data we used to generate the results. We've also included the scripts used to process the Illumina data as described in the supplementary materials.
DOI: 10.5061/dryad.7j9t5/3
title: Morphology Data

description: These folders contain text versions of the morphology data (morphological landmark locations) as well scripts used to transform these data into length data used in the analyses. The file "allResults_26Aug.csv" contains the final transformed data (the location in space of each morphological landmark). "AveMeasures_aveCulture.txt" has averaged data that was used in the 2B-PLS analyses. Due to size restrictions, we cannot upload the raw images, however we are happy to provide them on request.
DOI: 10.5061/dryad.96pr7/1
title: Cooper_et_al_FE_data

description: Sheet one contains the full data set from Cooper et al. Sheet two contains a key that matches the lipid identifiers (l1 to l23) to the actual lipids. Any questions about these data should be sent to Brandon S. Cooper (brandonscooper@gmail.com).
DOI: 10.5061/dryad.9kh1b/1
title: IMa2 input file (2 populations, mtDNA)

description: Input file used in the simulations of the Isolation-with-Migration (IM) model with 2 populations (D. yakuba and D. santomea) performed with the program IMa2 and the dataset of complete mitochondrial DNA sequences
DOI: 10.5061/dryad.9kh1b/2
title: IMa2 input file (3 populations, mtDNA)

description: Input file used in the simulations of the Isolation-with-Migration (IM) model with 3 populations (D. yakuba mainland, D. yakuba island and D. santomea) performed with the program IMa2 and the dataset of complete mitochondrial DNA sequences
DOI: 10.5061/dryad.9kh1b/3
title: IMa2 input file (2 populations, mtDNA and Y chromosome)

description: Input file used in the simulations of the Isolation-with-Migration (IM) model with 2 populations (D. yakuba and D. santomea) performed with the program IMa2 and the dataset of complete mitochondrial and partial Y chromosome DNA sequences
DOI: 10.5061/dryad.9kh1b/4
title: Gene tree file

description: Input file in MEGA format used to obtain the gene tree shown in Fig. 3
DOI: 10.5061/dryad.cm61n/1
title: InterIntraCompSoftStrSeln-Data

description: Shows the number of surviving adults (wild-type and mutants) for each treatment of the experiment.
DOI: 10.5061/dryad.dp17k/1
title: Data set_Marie-Orleach et al
DOI: 10.5061/dryad.fn2rg/26
title: bluedevil_settings

description: The configuration file for BlueDevil.py
DOI: 10.5061/dryad.fn2rg/27
title: DomainDivider_phot

description: A Python scripts to build phototropin alignment based on conserved domains (i.e. LOV1, LOV2 and STK). The search results from NCBI Conserved Domain Database is parsed to identify domain boundaries and extract domain sequences. Each domain is separately aligned (based on the amino acid sequences) using Muscle, and then concatenated.
DOI: 10.5061/dryad.fn2rg/28
title: DomainDivider_phy

description: A Python scripts to build phytochrome alignment based on conserved domains (i.e. PAS, GAF, PHY, PAS repeats, HisKA and HATPase). The search results from NCBI Conserved Domain Database is parsed to identify domain boundaries and extract domain sequences. Each domain is separately aligned (based on the amino acid sequences) using Muscle, and then concatenated.
DOI: 10.5061/dryad.fn2rg/29
title: DomainDivider_neo

description: A Python scripts to extract conserved domains in neochrome (i.e. PAS, GAF, PHY, LOV1, LOV2, and STK). The search results from NCBI Conserved Domain Database is parsed to identify domain boundaries and extract domain sequences.
DOI: 10.5061/dryad.fn2rg/30
title: Readme
DOI: 10.5061/dryad.fn2rg/31
title: NEO_MLBS_tree_raxml

description: The maximum likelihood bootstrapping trees from "NEO_alignment.fas", using RAxML (1000 replicates). We partitioned the data by codon position, and GTR+Γ+I, GTR+Γ+I, GTR+I models were applied to each codon position respectively. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.kg45v/4
title: individual survival data

description: This file contains simulation data from individuals listing that state, optimal behavior and optimal reallocation to maintenance and repair decision. Data is listed dependent on year (only 1), time in the year, patch quality (pq, 0=good, 1=bad), individual number (ind), fat (fat), abdomen (abd) and thorax (tho) weight, fecundity (fec), age in number of days (age), biological age (bdamage), optimal behavior decision (beh), optimal reallocation strategy (real), proportion of fat used for repair (rfat), absolute fat used for repair (ufat) and generation of which the adult belongs to. This all is used for figure 3G.
DOI: 10.5061/dryad.kg45v/5
title: thorax ratio and abdomen weight

description: File is the summary of thorax weight and fecundity data from both model and earlier performed experiment. Source (lab experiment or model simulation), food treatment (ad libitum or restricted), trait (thorax ratio or fecundity in experiment and abdomen weight in model) and mean and standard deviation (sd) of these variables are listed. This data is used for figure 4 of the paper.
DOI: 10.5061/dryad.kg45v/6
title: data experiment PAR

description: Summarizing data from an experiment in which larvae and adults were stressed and optmally treated from both a laboratory experiment and a model simulation. Source indicates where data is from (lab experiment, 1st, 2nd or 3rd generation butterfly simulation), which trait is measured (trait), larval and flight stress treatments and means and standard deviations of the measurements. This data is used for figure 5 of the paper
DOI: 10.5061/dryad.kg45v/7
title: pupal weight data

description: This file contains the individual pupal weight data at the initiation of pupation from simulations. Listed are the individual number (ind), time, patch quality (pq, 0=good, 1=bad) and actual pupal weight in mgs.
DOI: 10.5061/dryad.kg45v/8
title: allocation strategy pupae

description: This file lists data from allocation strategies of pupae from the simulations. Columns list indvidual number (ind), time, generation the individual belongs to, allocation to fat (fat), abdomen (abd) and thorax (tho) and patch quality (pq, 0=good, 1=bad). This data was used to produce figure A4.
DOI: 10.5061/dryad.n1506/1
title: Microsatellite data

description: Microsatellite genotypes for 371 individuals and 27 loci. Island abbreviations as in the manuscript.
DOI: 10.5061/dryad.n1506/2
title: Morphometric data

description: Morphometric traits for all Berthelot's pipits from 2005/2006. Individual codes as in the microsatellite file. Island codes as in the manuscript.