cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.744p394/2
title: 2_recombination_maps_mimicrEE_ZIP

description: Recombination map files for D. simulans and D. melanogaster, at different smoothing resolutions. This set of files is the same as the CSV files, except that they formatted for use with MimicrEE simulation software. Also, we provide  “Dsim_recombination_map_LOESS_100kb_1.txt”, in which LOESS smoothing equivalent to 100 kb windows is applied through an alternative R algorithm. The standard files provided are, again, the moving median and LOESS smoothed maps. For Dsim, moving median files are provided at resolutions: 5, 25, 101, 501, and 2501 kb. For Dmel, the moving median files are provided at resolutions: 501, and 2501 kb, due to a lower resolution initial map. For Dsim the LOESS files are at 0.001, 0.005, 0.02, 0.10. These levels are equivalent to moving median windows of 25, 101, 501, and 2501 kb. For Dmel, the LOESS smoothing parameter is set at: 0.02, 0.10. A raw recombination map is provided for Dsim, in 1 kb windows and for Dmel in 101 kb windows. Details for how this raw map was produced can be found in our paper, Howie et et al. 2019. The R script used to produce differently smoothed recombination maps is provided as an R-Markdown file.
DOI: 10.5061/dryad.744p394/3
title: 3_dmel-fimo_ZIP.tsv

description: Motif density files for D. melanogaster, which are output from FIMO. These can be used to plot motif density along the genome or, in combination with the recombination maps, to test the relationship between recombination rates and motif density. The script is provided in the R Markdown file.
DOI: 10.5061/dryad.744p394/4
title: 4-dsim-fimo_ZIP.tsv

description: Motif density files for D. simulans, which are output from FIMO. These can be used to plot motif density along the genome or, in combination with the recombination maps, to test the relationship between recombination rates and motif density. The script is provided in the R Markdown file.
DOI: 10.5061/dryad.744p394/5
title: 5_figures+mapfiles

description: R-Markdown file. This contains the in house scripts used to process raw data files and run all downstream analyses reported in our paper. The script includes code to smooth recombination maps, generate motif density files, test correlations and and fit linear models to examine the relationship between motif density and recombination rate, at different smoothing scales, in Dmel and Dsim. Details can be found in our paper.
DOI: 10.5061/dryad.744p394/6
title: 6_PrepareFasta_X

description: Phased Haplotypes - that is, SNP and genomic location - used to produce the Dsim Recombination Map, for the X chromosome. We crossed focal males from 189 isofemale lines, from Florida, to virgin “reference” females, and then individually sequenced the F1 progeny. From the raw BAM files, we produced phased haplotype files, in which reference alleles are removed and SNPs called. This was done in FreeBayes: segment size 1kb, alpha 0.05, theta 0.04. Full details are provided in our paper. Here, we provide 189 phased haplotypes for the X chromosome. This is essentially information about SNPs and their genomic positions.
DOI: 10.5061/dryad.744p394/7
title: 7_PrepareFasta

description: Phased Haplotypes - that is, SNP and genomic location - used to produce the Dsim Recombination Map, for the main autosomes, 2L, 2R, 3L, 3R. We crossed focal males from 189 isofemale lines, from Florida, to virgin “reference” females, and then individually sequenced the F1 progeny. From the raw BAM files, we produced phased haplotype files, in which reference alleles are removed and SNPs called. This was done in FreeBayes: segment size 1kb, alpha 0.05, theta 0.04. Full details are provided in our paper. Here, we provide 189 phased haplotypes for the autosome arms 2L, 2R, 3L, 3R. This is essentially information about SNPs and their genomic positions.
DOI: 10.5061/dryad.7d028rp/1
title: Egg investment, female breeder survival and reproductive success

description: Data used to analyse egg investment and its consequences on female breeder's fitness in cooperatively breeding Ground tits on the Tibetan plateau, China.
DOI: 10.5061/dryad.8tp4q6d/1
title: programs

description: zipped file of all the programs
DOI: 10.5061/dryad.9pv5625/2
title: CANINE_DATA_LABELS_2018-12-07 public deidentified V2

description: Data used for manuscript
DOI: 10.5061/dryad.ct7dg14/1
title: Affinity DATA
DOI: 10.5061/dryad.d6f6q7p/1
title: tseng-et-al-algae-evolution-dryad-2019-04-15

description: Raw data for the algae evolution component of the paper
DOI: 10.5061/dryad.d6f6q7p/2
title: tseng-et-al-daphnia-evolution-dryad-2019-04-15

description: Raw data for the Daphnia evolution component of the study
DOI: 10.5061/dryad.f9s73ms/1
title: Q.humilis_seed_production

description: site - site ID; treeid - tree ID; acorns - acorn count
DOI: 10.5061/dryad.f9s73ms/2
title: Q.ilex_seed_production

description: site - site ID; treeid - tree ID; acorns - acorn count
DOI: 10.5061/dryad.f9s73ms/3
title: S.aucuparia_fruit_production

description: treeid - treeID; fruits - fruit count
DOI: 10.5061/dryad.f9s73ms/4
title: P.albicaulis_cone_production

description: TreeName - treeID; site - site ID; cones - cone count
DOI: 10.5061/dryad.fc75292/1
title: Khelifa_et_al_Anim.Ecol.Data

description: TPC Data: Provides the development rates for all temperature treatments and all species Temperature fluctuations: Provides the development rates derived from the temperature fluctuation experiment Predicted vs. observed rate: Provides the data for development rate derived from the TPC (predicted) and observed in the experiment Ratios and chilling: Provides data for the ratio between predicted and observed development rates and the number of days below the critical minimal temperature
DOI: 10.5061/dryad.ff11k13/8
title: Herbivore-induced glucosinolates

description: Constitutive and herbivore-induced amounts of glucosinolates produced by Arabis alpina plants from six populations in a common greenhouse environment.
DOI: 10.5061/dryad.g7s0hk3/2
title: Supplementary Figure 2

description: Median age estimates and 95% HPDs for Hymenoptera obtained using a range of approaches to constructing a subsample of fossil occurrences and constraining their placement. These approaches consist of: a uniform subsample of occurrences with and without topological constraints, a uniform subsample of occurrences supplemented with the oldest unequivocal members of clades which were then constrained to their respective crown groups, a subsample consisting of only the oldest unequivocal members of clades with and without topological constraints applied to constrain them to their respective crown groups.
DOI: 10.5061/dryad.g7s0hk3/3
title: Supplementary Figure 3

description: The accuracy and precision of estimated node ages obtained from subsamples of 100 replicate fossil occurrence datasets after the addition of the oldest occurrences for each clade to the subsample. These occurrences were then topologically constrained to lineages that descend from the node either 1, 2, or 4 nodes below the direct ancestor of the occurrence. Each point represents the median posterior age estimate of one clade, with grey bars representing the 95% HPD for that node age estimate. When occurrences are placed one node below their direct ancestor an approach in which the rate of fossil sampling is estimated produces the greatest accuracy. When occurrences are placed with reduced accuracy then the accuracy of age estimates when sampling rate is an estimated parameter of the FBD process decreases. Conversely, fixing the rate of fossil sampling or placing an informed prior on this parameter improves the accuracy as fossils are placed with reduced accuracy. For all cases in which fossils occurrences are placed at a node that is lower than their true ancestral fossil the 95% HPDs of age estimates extend to ages that violate the minimum age of the clade, as implied by the complete sample of fossil occurrences.
DOI: 10.5061/dryad.j0k8370/1
title: Supplementary Tables 1-8

description: Supplementary Tables 1-8 which includes (1) systematic list of megafloral morphotypes from the San Juan Basin, (2) stratigraphic position, depositional facies, location, and morphotype tallies for all floral sites, (3) megafloral census data, (4) megafloral presence-absence data, (5) total Ojo Alamo Sandstone and facies mean physiognomic variables using the DiLP paleoclimate calculation, (6) measured leaf physiognomy values for all measureable specimens/morphotypes, (7) regional diversity comparison, and (8) - calculated p-values for Margalef Index, Pielou's Evenness, and Berger-Parker Index for all San Juan Basin, Denver Basin, and Williston Basin diversity indice comparison.
DOI: 10.5061/dryad.j0k8370/2
title: Appendix 1 - Morphotype Catalog

description: Ojo Alamo Sandstone Morphotype Catalog Morphological descriptions, botanical affinities, photographs, and line drawings of all identified Ojo Alamo Sandstone megafloral morphotypes. All dicotyledonous angiosperm leaf morphotypes were described using the Manual of Leaf Architecture (Ellis et al. 2009). Each dicotyledonous angiosperm leaf morphotype description contains leaf architecture description, margin classification, and Raunkiaer-Webb (Webb 1959) size classification. All other groups (i.e. dicotyledonous angiosperm reproductive structures, pteridophytes, monocotyledonous angiosperms, and conifers) were described based on their gross morphology. Botanical affinities of morphotypes were determined after comparison with previously published taxonomy. Each morphotype also has a specimen number which corresponds with the morphotype exemplar. See Supplementary Table 1 for detailed systematic morphotype list and Supplementary Table 2 for morphotype abundance by fossil locality.
DOI: 10.5061/dryad.j0k8370/3
title: Supplementary Figure 1 - Facies and Formation Photos Small

description: Generalized latest Cretaceous and earliest Paleocene stratigraphic units and Ojo Alamo Sandstone lithofacies.  A:  contact between the Maastrichtian Naashoibito Member of the Kirtland/Fruitland Formation and the overlying earliest Paleocene Ojo Alamo Sandstone.  B: the contact between the earliest Paleocene Ojo Alamo Sandstone and overlying early Paleocene Nacimiento Formation.  C: representative overbank leaf Locality AF1409D in the Ojo Alamo Sandstone.  D: closeup of the overbank flora deposits which are interbedded siltstone and medium to coarse grained sandstone and have been interpreted to represent downstream accretionary bars.  E: is a coarse grained cross-bedded sandstone with occasional gravel lag deposits which account for the majority of the Ojo Alamo Sandstone.  F: representative pond/swamp floral locality AF1407 and the contact between earliest Paleocene Ojo Alamo Sandstone and early Paleocene Nacimiento Formation.  G: close up of pond/swamp leaf locality AF1407 showing fine grained carbonaceous shales typical of pond/swamp floral facies.
DOI: 10.5061/dryad.j0k8370/4
title: Supplementary Figure 2 - Digital Leaf Physiognomy Examples

description: Examples of the 4 different types of leaves prepared for digital leaf physiognomy (DiLP) following the protocol of Peppe et al. 2011.  All digital preparation was done using Adobe Photoshop.
DOI: 10.5061/dryad.jc5745v/1
title: Centroid Data for high speed images of jumps: csvstoanalyze

description: These data track the centroid of each jump and are read by the R files to gather scaling information about image, frame rate, etc.
DOI: 10.5061/dryad.jc5745v/2
title: Animal sizes and IDs: IDsandsizesforcsvstoanalyze

description: This spreadsheet includes the necessary information about individual sizes to be used by the R code to calculate energetics, etc.
DOI: 10.5061/dryad.jc5745v/6
title: Rcode with ballistics equation: ballisticequationformidgejumps_043019

description: This Rcode takes the midge data and applies the ballistics equation to back out takeoff speed, as well as calculate cost of transport.
DOI: 10.5061/dryad.jc5745v/7
title: MidgeTabletopJumpDistances

description: This spreadsheet includes the data from horizontal jump distance experiments.
DOI: 10.5061/dryad.jc5745v/8
title: LoadingPhaseData

description: This spreadsheet includes the data taken from high speed videos to calculate loading phases prior to gall midge jumps.
DOI: 10.5061/dryad.jc5745v/9
title: Gallmidge_dataanalysiscode

description: This R code includes all of the kinematic and statistical analyses used in this study. The code pulls the data files also included in this repository and automatically analyzes the raw kinematic and body size datasets.
DOI: 10.5061/dryad.r58d342/1
title: Supplementary_Revised

description: eMethods, eTables (Table e1, Table e2, Table e3, Table e4), eFigures (Figure e1, Figure e2), eReferences (1)
DOI: 10.5061/dryad.s90b488/1
title: Tree stem growth rates (DBH growth rate, basal area growth rate and wood growth rate) in natural mangrove forests across the world

description: We collected DBH growth rate data from published literature and unpublished data of co-authors. Data of basal area growth was calculated from initial DBH and DBH growth rate. Aboveground wood growth rate was calculated from allometric equations.
DOI: 10.5061/dryad.s90b488/2
title: Stand aboveground wood production in natural mangrove forests across the world.

description: Data were collected from published literature.
DOI: 10.5061/dryad.s90b488/3
title: Stand mean DBH growth rate and stand wood production in mangrove plantations across the world

description: Data were collected from published literature.
DOI: 10.5061/dryad.s90b488/4
title: Literature

description: The literature used for data collection
DOI: 10.5061/dryad.t7m9806/1
title: Spider_Abundance_Data

description: Spider species absolute abundances (i.e., individuals) of 85 spider species collected in original open-forest stands and transformed closed-forest stands in the Bavarian Forest National Park (Thorn et al. 2016). See the main text and Appendix S3 of Chao et al. (2019) for analysis details.
DOI: 10.17632/n2tjbnv9hb.1
title: Data for: iTRAQ-based quantitative proteomic analysis provides insights into strong broodiness in Muscovy duck (Cairina moschata) combined with metabolomics analysis

description: Raw data on proteomics and metabolomics sequencing.
DOI: 10.17632/w9km8shjt7.1
title: Data for: Molecular features of organic matter in anthropogenic earthen mounds, canals and lagoons in the Pago Lindo archaeological complex (Tacuarembó, Uruguayan lowlands) are controlled by pedogenetic processes and fire practices

description: The data files contain the original Pyrolysis-GC-MS data of the study on organic matter composition in earthen mounds, lagoons and canals at the archaeological site of Pago Lindo (Uruguay). The first sheet contain the relative proportions of the pyrolysis products (% of total quantified peak area), whereas the second and third slides present the results of the Principal Component Analysis (PCA) performed on the Py-GC-MS data.
DOI: 10.5061/dryad.14qd4q6/1
title: Functional groups of soil fauna in rainforest, rubber and oil palm plantations

description: The dataset contains supplementary data of the article and consists of four data spreadsheets, an R script and a description. The main spreadsheet gives density, biomass and taxa richness of soil invertebrates from different functional groups (decomposers, herbivores, omnivores (ants) and predators) in rainforest, jungle rubber agroforest, rubber monoculture and oil palm monoculture. Additional spreadsheets provide information on density of different size classes, energy fluxes between functional groups and proportion of energy, used by earthworms. R script describes energy flux calculations. More details are given in the description and in the article.
DOI: 10.5061/dryad.18j0j5q/1
title: Genome-wide data in nonoverlapping 500kb windows

description: This file includes population genetic statistics, measures of genomic features, and estimates of phylogenetic concordance in 500kb nonoverlapping windows across the bush monkeyflower genome, which were used in analyses of genomic landscape evolution. Fst and dxy are included for 36 pairwise comparisons between taxa, and nucleotide diversity is included for all 9 taxa. These statistics were calculated using python scripts downloaded from https://github.com/simonhmartin/genomics_general. PC1 Fst, PC1 dxy, and PC1 nucleotide diversity for each window are obtained by performing a PCA using the 36 comparisons (fst or dxy) or 9 taxa (nucleotide diversity) as variables, and provide a summary of variation across taxa or taxon comparisons in each of these statistics. Gene count is obtained from the genome annotation, recombination rate (cM/Mb) is based on the genetic map, and tree concordance is obtained by taking the correlation coefficient between the window based tree and the whole genome ‘species tree.’
DOI: 10.5061/dryad.18j0j5q/2
title: Genome-wide data in nonoverlapping 100kb windows

description: This file includes population genetic statistics, measures of genomic features, and estimates of phylogenetic concordance in 100kb nonoverlapping windows across the bush monkeyflower genome, which were used in analyses of genomic landscape evolution. Fst and dxy are included for 36 pairwise comparisons between taxa, and nucleotide diversity is included for all 9 taxa. These statistics were calculated using python scripts downloaded from https://github.com/simonhmartin/genomics_general. PC1 Fst, PC1 dxy, and PC1 nucleotide diversity for each window are obtained by performing a PCA using the 36 comparisons (fst or dxy) or 9 taxa (nucleotide diversity) as variables, and provide a summary of variation across taxa or taxon comparisons in each of these statistics. Gene count is obtained from the genome annotation, recombination rate (cM/Mb) is based on the genetic map, and tree concordance is obtained by taking the correlation coefficient between the window based tree and the whole genome ‘species tree.’
DOI: 10.5061/dryad.18j0j5q/3
title: Genome-wide fd statistic in 500kb windows

description: This file contains estimates of admixture (fd) calculated in 500kb non-overlapping windows across the genome, for 48 different four taxon comparisons. Fd was calculated using a python script download from https://github.com/simonhmartin/genomics_general.
DOI: 10.5061/dryad.18j0j5q/4
title: Genotypes file for genetic map

description: This file is the input data file used for map construction in joinmap format (.loc) produced by the program Stacks 1.3.5 assuming a cp cross design. The first column gives the locus ID assigned to each marker by the program Stacks 1.3.5. The next column gives the segregation type code for each marker using the joinmap 4 convention. Each subsequent column provides the genotypes for an individual for all 9029 markers. Missing data is coded as “--“. The ID for each individual is given as a list in the first column underneath the last locus ID.
DOI: 10.5061/dryad.18j0j5q/5
title: Genetic map

description: This file contains the full genetic map used to estimate recombination rates and scaffold the genome. ‘LG’ is the linkage group identifier, which ranges from 1 – 10. The stacks_id field contains the locus ID allocated to each marker by the program Stacks 1.3.5 (Catchen et al. 2013). bp is the base-pair position of the marker within the M. aurantiacus assembly at the chromosome scale. Contig is the assembly contig (scaffold) that each marker is associated with. cM gives the sex-averaged map position estimated for each marker.
DOI: 10.5061/dryad.18j0j5q/6
title: Genomic location of mapped markers

description: This file, which is in standard SAM format, contains the genomic position of each of the mapped markers. The ID for each locus is the ID allocated to each marker by the program Stacks 1.3.5. The sequence in the SEQ field is the consensus tag sequence for each marker, exported from Stacks 1.3.5. Mapping was performed with bowtie 2.2.6.
DOI: 10.5061/dryad.18j0j5q/7
title: Tree topologies in 500kb non-overlapping windows

description: This file contains ML trees estimated by RAxML using MVFtools in 500kb non-overlapping windows. These were used to calculate the estimate of tree concordance based on the correlation with the species tree topology.
DOI: 10.5061/dryad.18j0j5q/8
title: Tree topologies in 100kb non-overlapping windows

description: This file contains ML trees estimated by RAxML using MVFtools in 100kb non-overlapping windows. These were used to calculate the estimate of tree concordance based on the correlation with the species tree topology.
DOI: 10.5061/dryad.18j0j5q/9
title: Genome-wide variant calls

description: This file contains the genome-wide variant calls (SNPs) for all 37 individuals included in the study. Variants were called with GATK v3.8 using UnifiedGenotyper and following the best practices work flow.
DOI: 10.5061/dryad.2444ck7/1
title: Yellow Perch Eastern Lake Michigan Microsatellite Genotypes

description: Microsatellite genotypes of yellow perch in near-shore Eastern Lake Michigan and connected drowned river mouth lakes. Data organization: first column = sample id, second column = location where sample was collected, columns 3-30 = locus1_allele1, locus1_allele2, locus2_allele1....
DOI: 10.5061/dryad.295h8km/1
title: Supl. Dataset 1_Raw Data
DOI: 10.5061/dryad.295h8km/2
title: Supl. Dataset 2_Experimental data
DOI: 10.5061/dryad.295h8km/3
title: Supl. Dataset 3_Relationship between no-choice vs. male-choice court preferences
DOI: 10.5061/dryad.295h8km/4
title: Supl. Dataset 4_Stocks used in experiments
DOI: 10.5061/dryad.295h8km/5
title: Supl. Dataset 5_Relationship between exper. and lit. mate preferences
DOI: 10.5061/dryad.295h8km/6
title: Supl. Dataset 6_Phylog. Corrected Data
DOI: 10.5061/dryad.3hv2826/1
title: Metabolic data

description: Body mass and metabolic rate (MR) data of A. iberica ants from different elevations collected for this study. Units are as follows: elevation (m.a.s.l.), Temp TRT (15, 20, 25, 30, 32 C), Temperature (empirically measured temperature values C), Wet mass and Dry mass (mg), MR ((CO2 µL-1 hr-1), Mass-spec MR (mass-specific MR; CO2 µL-1 mg-1 hr-1, where mg is in dry mass).
DOI: 10.5061/dryad.65f22d6/2
title: Supplemental Fig 2a
DOI: 10.5061/dryad.65f22d6/3
title: Supplemental Fig 2b
DOI: 10.5061/dryad.65f22d6/4
title: Supplemental Fig 2c
DOI: 10.5061/dryad.65f22d6/5
title: Supplemental Fig 3a
DOI: 10.5061/dryad.65f22d6/6
title: Supplemental Fig 3b
DOI: 10.5061/dryad.65f22d6/7
title: Supplemental Fig 3c
DOI: 10.5061/dryad.96096t0/1
title: Schumm_etal_PRSLB_data

description: Please refer to README