cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/fkvcgdw9j6.1
title: LHC collider phenomenology of minimal universal extra dimensions

description: We discuss the collider phenomenology of the model of Minimal Universal Extra Dimensions (MUED) at the Large hadron Collider (LHC). We derive analytical results for all relevant strong pair-production processes of two level 1 Kaluza–Klein partners and use them to validate and correct the existing MUED implementation in the fortran version of the Pythia event generator. We also develop a new implementation of the model in the C++ version of Pythia. We use our implementations in conjunction with the Checkmate package to derive the LHC bounds on MUED from a large number of published experimental analyses from Run 1 at the LHC. The previous version of this program (ACTU_v2_1) may be found at http://dx.doi.org/10.1016/j.cpc.2009.08.008.
DOI: 10.5061/dryad.085dd/10
title: 10-75p-Concatenated-ExaBayes-Analyses.tar

description: ExaBayes analysis files for the 75% (75p) complete data set.  Includes unpartitioned and partitioned analyses.
DOI: 10.5061/dryad.085dd/11
title: 11-75p-Astral-Analyses.tar

description: Astral analysis files for the 75% (75p) complete data set.
DOI: 10.5061/dryad.085dd/2
title: 2-Assembled-Contigs-That-Are-UCEs.tar

description: Of the assembled contigs in 1-All-Assembled-Contigs.tar.gz, these are the loci, for each species, that are targeted UCE loci.
DOI: 10.5061/dryad.085dd/3
title: 3-All-Alignments-Untrimmed.tar

description: These are all alignments generated as part of this manuscript.  Manuscripts in this archive are UNTRIMMED (we used TRIMMED alignments in the manuscript - see 4-95p-Trimmed-Alignments.tar.gz and 5-75p-Trimmed-Alignments.tar.gz for those).
DOI: 10.5061/dryad.085dd/4
title: 4-95p-Trimmed-Alignments.tar

description: These are the trimmed alignments used in analyses of the 95% complete (95p) data set.
DOI: 10.5061/dryad.085dd/5
title: 5-75p-Trimmed-Alignments.tar

description: These are the trimmed alignments used in analyses of the 75% complete (75p) data set.
DOI: 10.5061/dryad.085dd/6
title: 6-95p-Concatenated-Alignment-For-Analysis.tar

description: Contains the concatenated loci from the 95% (95p) complete data set.
DOI: 10.5061/dryad.085dd/7
title: 7-75p-Concatenated-Alignment-For-Analysis.tar

description: Contains the concatenated loci from the 75% (75p) complete data set.
DOI: 10.5061/dryad.085dd/8
title: 8-75p-Concatenated-RAxML-Analyses.tar

description: RAxML Analysis files for the 75% (75p) complete data set.  Includes unpartitioned, partitioned, and RY-coded analyses.
DOI: 10.5061/dryad.085dd/9
title: 9-95p-Concatenated-ExaBayes-Analyses.tar

description: ExaBayes analysis files for the 95% (95p) complete data set.  Includes unpartitioned and partitioned analyses.
DOI: 10.5061/dryad.2434f/1
title: Citrullus_matrix_for_Taxon_paper_20Nov2017

description: DNA alignment, 47 taxa, NCHAR=9224
DOI: 10.5061/dryad.67nd5/1
title: Seedling regeneration

description: Data were collected in a subtropical evergreen broad-leaved forest in eastern China between 2011 and 2014. The zip file contains five xlsx files, of which "Recruits between 2011 and 2014.xlsx" contains the number of deciduous (DBL) and evergreen (EBL) broad-leaved seedlings recruited into each 1 m2 seedling quadrat between 2011 and 2014. The other four xlsx files each contain two datasheets, one is "community", represents the community data; the other is "sparseMatrix", represents the inverse phylogenetic covariance matrix of the species present in the community data, for performing generalised linear mixed models with correlated random effect arising from phylogeny. Specifically, "Survival.across.All.Habitats.xlsx" and "Survival.in.Canopy.Gaps.xlsx" contains the survival status in 2014 of seedlings recorded in the 2011 census across all habitats and only in canopy gaps, respectively. "RGR.across.All.Habitats.xlsx" and "RGR.in.Canopy.Gaps.xlsx" contain the height relative growth rate of seedlings alive both in the 2011 and 2014 censuses across all habitats and only in canopy gaps, respectively. 
      Abbreviated headlines are as follows: "canopy.gap.size"= the size of canopy gap, in m2; "survival" = survival status in 2014, of which "0" means death and "1" means alive; "canopy.status" = the status of canopy, can be "gap" or "understory"; "DBL. number"=the number of deciduous broad-leaved seedlings recruited into a 1 m2 seedling quadrat between 2011 and 2014; "EBL. number"=the number of evergreen broad-leaved seedlings recruited into a 1 m2 seedling quadrat between 2011 and 2014; "leaf.habit"= leaf habit, can be deciduous (DBL) or evergreen (EBL) broad-leaved; "quadrat"= 1 m2 seedling quadrat; "RGR"= seedling height relative growth rate between 2011 and 2014; "seedling.height"= seedling height recorded in the 2011 census, in cm; "site"= sampling gap site; "species"= species; "topographic.habitat"= habitat classified according to topographic condition, can be "valley" or "ridge".
DOI: 10.5061/dryad.c76pf34.1
title: Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird
DOI: 10.5061/dryad.c76pf34.1/1.1
title: 2012-2016 MSAT Genotypes

description: Microsatellite genotypes of offspring and adult variegated fairy-wrens
DOI: 10.5061/dryad.c76pf34/10
title: popmap_1

description: Popmap file for Index 1 (Group A) assembly
DOI: 10.5061/dryad.c76pf34/11
title: popmap_9

description: Popmap file for Index 9 (Group B) assembly
DOI: 10.5061/dryad.c76pf34/13
title: popmap_11v2

description: Popmap file for Index 11 (Group D) assembly
DOI: 10.5061/dryad.c76pf34/14
title: popmap_12v2

description: Popmap file for Index 12 (Group E) assembly
DOI: 10.5061/dryad.c76pf34/3
title: post_rxstacks_assembly_all

description: RAD loci from de novo assembly in Stacks for Indexes 1-8 (Group All)
DOI: 10.5061/dryad.c76pf34/4
title: post_rxstacks_assembly_1

description: RAD loci from de novo assembly in Stacks for Index 1 (Group A)
DOI: 10.5061/dryad.c76pf34/6
title: post_rxstacks_assembly_10

description: RAD loci from de novo assembly in Stacks for Index 10 (Group C)
DOI: 10.5061/dryad.c76pf34/8
title: post_rxstacks_assembly_12

description: RAD loci from de novo assembly in Stacks for Index 12 (Group E)
DOI: 10.5061/dryad.cc8834s/1
title: Drought intensities

description: List of drought intensity (DI) values for all of the mesocosm channels
DOI: 10.5061/dryad.dq70c/1
title: README

description: README file to describe all data files to accompany the publication Dool et al. Variable molecular markers for the order Mantophasmatodea (Insecta) published in Journal of Heredity.
DOI: 10.5061/dryad.dq70c/2
title: COI_tree
DOI: 10.5061/dryad.dq70c/4
title: Microsatellite Sequences_KB1_KB50
DOI: 10.5061/dryad.gm1td/1
title: Genbank-mtDNA-accessions

description: Accession IDs for all DNA sequences uploaded to Genbank for this project
DOI: 10.5061/dryad.gm1td/10
title: ABC input file: Gmi, Pacific

description: DIYABC input file for G. mirabilis Pacific populations
DOI: 10.5061/dryad.gm1td/2
title: allelic-richness-test-steep-broad

description: Data used for linear mixed model to test whether populations on broad coasts have higher allelic richness than narrow coasts  (they do).
DOI: 10.5061/dryad.gm1td/3
title: Mol_Ecol_Allelic_Richness_Broad-steep-results

description: Results in HTML format from linear mixed model run in JMP showing that allelic richness is higher on broad coasts than narrow coasts.
DOI: 10.5061/dryad.gm1td/4
title: Refugia-geospatial-size-data

description: This is all the attribute data used for discriminant function analyses and generalized linear models to determine: 1) the predictors of present-day species distributions; 2) whether lowstand size attributes were similar to present-day size attributes; 3) relative size of habitats on steep versus broad coasts.
DOI: 10.5061/dryad.gm1td/5
title: Sample sites

description: Google Earth file of sampling localities
DOI: 10.5061/dryad.gm1td/6
title: Microsat data: Fundulus parvipinnis

description: Full microsatellite dataset in STRUCTURE format for F. parvipinnis
DOI: 10.5061/dryad.gm1td/7
title: Microsat data: Gillichthys mirabilis

description: Full microsatellite dataset in STRUCTURE format for G. mirabilis
DOI: 10.5061/dryad.gm1td/8
title: Microsat data: Quietula y-cauda

description: Full microsatellite dataset in STRUCTURE format for Quietula y-cauda
DOI: 10.5061/dryad.gm1td/9
title: ABC input file: Fpa

description: Input file for DIYABC2 for F. parvipinnis
DOI: 10.5061/dryad.j0j2b70/1
title: Gehyra_data

description: This file includes measurements of a capture-mark-recapture field study of Gehyra variegata over the course of 30 years (1986-2016). In comprises three tables: body temperatures during the day measured with RFID tags; body temperatures during the night measured with an IR thermometer; and individual capture-recapture data including exact time and location, lengths and mass measures, sexing and aging. For more detail, please refer to Grimm-Seyfarth et al., 2018, Ecological Monographs.
DOI: 10.5061/dryad.mb342.1
title: Data from: Macronutrient signature of dietary generalism in an ecologically diverse primate in the wild
DOI: 10.5061/dryad.mb342.1/1.1
title: % of 3 year mean in AP, NP and TE

description: Percentage of 3-year means for protein, non-protein energy and total energy intake in spring
DOI: 10.5061/dryad.mb342.1/2.1
title: Non-nutritional factors

description: Spring intakes of non-digestible fiber and tannin
DOI: 10.5061/dryad.mb342.1/3.1
title: Nutrients and energy intake in spring ACROSS 3 YEARS

description: Absolute macronutrient and energy spring intakes in 2013, 2014 and 2015
DOI: 10.5061/dryad.mb342.1/4.1
title: Seeds density and contributions to diets on a dry metters basis

description: Availability estimates and intake measures of seeds over 24 months
DOI: 10.5061/dryad.mb342.2/1.2
title: % of 3 year mean in AP, NP and TE

description: Percentage of 3-year means for protein, non-protein energy and total energy intake in spring
DOI: 10.5061/dryad.mb342.2/2.2
title: Non-nutritional factors

description: Spring intakes of non-digestible fiber and tannin
DOI: 10.5061/dryad.mb342.2/3.2
title: Nutrients and energy intake in spring ACROSS 3 YEARS

description: Absolute macronutrient and energy spring intakes in 2013, 2014 and 2015
DOI: 10.5061/dryad.mb342.2/4.2
title: Seeds density and contributions to diets on a dry metters basis

description: Availability estimates and intake measures of seeds over 24 months
DOI: 10.5061/dryad.p6qb650/1
title: database vfan
DOI: 10.5061/dryad.p6qb650/2
title: household questionnaire
DOI: 10.5061/dryad.p6qb650/3
title: individual questionnaire
DOI: 10.5061/dryad.ph3h8/1
title: Raw data- adult cognitive testing

description: Results of adult cognitive tests
DOI: 10.5061/dryad.ph3h8/2
title: Raw data- juvenile cognitive testing

description: Results of juvenile cognitive tests
DOI: 10.5061/dryad.ph3h8/3
title: Raw data- reproductive success

description: Female reproductive success data, and general cognitive performance scores.
DOI: 10.17632/dx65syc4p4.1
title: Data for: The impacts of the global financial crisis on hospitalizations due to depressive illnesses in Taiwan: A prospective nationwide population-based study

description: The technical appendix for details of model specification, model diagnosis, and parameter estimation.
DOI: 10.17632/zngwxgg5wm.1
title: Data for: Early Short-term Intensive Multidisciplinary Diabetes Care: A Ten-Year Follow-up of Outcomes

description: Early Short-term Intensive Multidisciplinary Diabetes Care: A Ten-Year Follow-up of Outcomes
DOI: 10.5061/dryad.085dd/12
title: 12-All-Phylo-Trees.tar

description: All phylogenetic trees from this manuscript, in a variety of formats.
DOI: 10.5061/dryad.085dd/13
title: 13-95p-Rate-Based-Partition-For-PAML.tar

description: Files used for rate-based partitioned of the 95% complete (95p) concatenated data, prior to analysis using PAML.
DOI: 10.5061/dryad.085dd/14
title: 14-PAML-Inputs.tar

description: Input files (alignments, guide trees, control files) for all PAML dating analyses (baseml and mcmctree).
DOI: 10.5061/dryad.085dd/15
title: 15-Dated-Tree.tar

description: The dated tree resulting from mcmctree analysis.
DOI: 10.5061/dryad.085dd/16
title: 16-Dating-Figures-Inputs.tar

description: Tabular (CSV) output from mcmctree analyses that form the basis of Figures 5, S7, and S8, along with a description of steps used in R to plot the figures.
DOI: 10.5061/dryad.085dd/17
title: README-Data-Processing-Analysis-Steps

description: A description of the steps used to assemble the data, prepare them for phylogenetic analysis, and run analyses.
DOI: 10.5061/dryad.085dd/18
title: README-Tree-Figure-Formatting-for-Supplement

description: A description of the steps used to format trees for the Supplement (specifically, Figures S1-S5).
DOI: 10.5061/dryad.085dd/19
title: fish-uce-1k-probes.MyBaits.UCE-Acanthomorphs.1Kv1.fasta

description: Design file for Acanthomorph baits.  Also available as bait set from Arbor Biosciences (UCE-Acanthomorphs 1Kv1).  Additionally same as bait set design file used in https://doi.org/10.5061/dryad.9pg8d.
DOI: 10.5061/dryad.3vb73/1
title: Proboscis lengths for hawkmoth species

description: A two-column data frame containing species names and the proboscis length corresponding to each species. These data are drawn from https://doi.org/10.5061/dryad.qn83r and the original publication should be cited when referring to this data. In cases where a species occurred in more than one network in the aforementioned paper, the mean proboscis length is given in this file.
DOI: 10.5061/dryad.3vb73/2
title: Hawkmoth phylogeny

description: The dated phylogeny used for this study. Tree was compiled from the species presence data of: http://dx.doi.org/10.5061/dryad.qn83r. Nodes were dated with the phylogeny of: http://dx.doi.org/10.5061/dryad.3450r
DOI: 10.5061/dryad.3vb73/3
title: Hawkmoth proboscis length optima

description: The optima calculated based on selective regimes, pollination interactions, and plant corolla lengths. Original trait and interaction data can be found at: http://dx.doi.org/10.5061/dryad.qn83r
DOI: 10.5061/dryad.3vb73/4
title: Supplementary Material

description: Additional analyses including model-fits where EIT is not weighted by interaction frequency, output of SURFACE, and comparisons to the SLOUCH model.
DOI: 10.5061/dryad.3vb73/5
title: Model implementation example

description: Two R scripts. One containing the functions that implement the model and one containing a short script to run the model.
DOI: 10.5061/dryad.623hq/1
title: 0 initial n=100 lambda=1-5

description: Mathematica code used to generate Tables 1, 2 and Figure 4
DOI: 10.5061/dryad.623hq/2
title: stationarity initial n=100 lambda=5

description: Mathematica code used to generate Figure 5
DOI: 10.5061/dryad.74839/1
title: Code for survival distributions, creation of Figure 2

description: Script used with accompanying datasets to derive survival distributions, infectious distributions, and to create Figure 2.
DOI: 10.5061/dryad.74839/2
title: Numerical Data Underlying Figure Creation

description: Supplement that shows numerical data for figure creation throughout manuscript.
DOI: 10.5061/dryad.76tk7/4
title: AppendixS3

description: AFLP data has been exported as a presence/absence (1/0) matrix. The reproducibility was estimated based on 12 replicated samples. Information regarding the included populations can be found in the main article text (see Table 1).
DOI: 10.5061/dryad.7b92c/1
title: Simulations

description: Simulation files examining ESS and CSS
DOI: 10.5061/dryad.7b92c/2
title: Model_solve_final_Dryad

description: Parameter file
DOI: 10.5061/dryad.7b92c/3
title: fitevictplasticitycomp

description: Equations
DOI: 10.5061/dryad.7b92c/4
title: Model output
DOI: 10.5061/dryad.875257v/1
title: geral
DOI: 10.5061/dryad.8t026/1
title: Data_OuedraogoEtAl2017_Biotropica

description: We provide a zip file containing three txt files and one R script file used in the analyses presented in the article assessing the size at reproduction of 31 major timber species in central Africa. The ReproductiveSize_DATA.txt file contains the list of trees monitored for reproductive phenology in three central African countries (Cameroon, Congo, and Central African Republic) in 11 sites, with their species names, diameter, crown exposure index, and phenological status. The ReproductiveSize_TRAITS.txt file contains the list of the 31 studied species with their traits (regeneration guild, leaf habit, wood density, maximum diameter and height, dispersal mode, and maximum growth rate). The ReproductiveSize_MCDL.txt file contains the list of the 31 studied species with their minimum cutting diameter limits in the three studied contries. The ReproductiveSize_SCRIPT.r file contains the code used to perform the analyses and make the figures.
DOI: 10.5061/dryad.bn7p2f5/1
title: JAPPL-2017-01144_Data

description: Included is the data that went in to each of our models described in the manuscript. Included in data are: counts of bobwhite, aggregated densities of conservation fields without specific spatial information (i.e., no x y coordinates), and distance sampling metrics needed to run the model.
DOI: 10.5061/dryad.cc8834s/2
title: Presence-absence data

description: Presence-absence matrix listing the macroinvertebrate taxa (columns) recorded in each mesocosm channel (rows); 1=present, 0=absent
DOI: 10.5061/dryad.cc8834s/3
title: Fuzzy coded trait data

description: Values of 49 fuzzy-coded macroinvertebrate traits (columns) for the taxa recorded in the mesocosm channels (rows)
DOI: 10.5061/dryad.d8ts9/1
title: Supporting Table S1

description: Line mean, standard error and number of replicates per trait for all DGRP lines
DOI: 10.5061/dryad.d8ts9/2
title: Supporting Table S4

description: Top SNPs associated with V(plast), V(v.plast), V(WE), and V(AE)
DOI: 10.5061/dryad.dq70c/3
title: Dool_SupplTable 1_2_4_5_JHeredity
DOI: 10.5061/dryad.dq70c/5
title: PrimerNote_FSTAT
DOI: 10.5061/dryad.dq70c/6
title: PrimerNote_FSTAT-POPULATION NAMES
DOI: 10.5061/dryad.dq70c/7
title: Supp_Table3_Genotypes
DOI: 10.5061/dryad.gm1td/11
title: ABC input file: Gmi, Gulf

description: DIYABC input file for G. mirabilis Gulf samples
DOI: 10.5061/dryad.gm1td/12
title: ABC input file: Qyc, Pacific

description: DIYABC input file for Q. y-cauda Pacific samples
DOI: 10.5061/dryad.gm1td/13
title: ABC input file: Qyc, Gulf

description: DIYABC input file for Q. y-cauda Gulf samples
DOI: 10.5061/dryad.m96r3/1
title: Supplemental Figure 4

description: The ability to correctly recover trees simulated under a time-dependent model or temperature-dependent model where the dependence is on extinction. Columns in each plot show the percentage of trees recovered (A,B) or Akaike weights (C,D) for constant-rate (black), time-dependent (light blue), or temperature-dependent extinction (brown) models for a set of trees simulated under (A,C) time-dependence or (B,D) temperature-dependence. Trees simulated under time-dependent extinction (B,D) were also fit with time-dependent speciation models (grey). The x-axis shows the strength of the dependencies (i.e., $\alpha$ value) used to simulate each set of trees. Akaike weights are averaged over all trees simulated with the same $\alpha$.}
DOI: 10.5061/dryad.m96r3/14
title: Supplemental Figure 1

description: Recovered parameter estimates for trees simulated with a constant λ and an exponential dependency of μ on temperature. Simulations with: (A) varying λ0, constant μ0, and constant αμ; (B) constant λ0, varying μ0, and constant αμ; and (C) constant λ0, constant μ0, and varying αμ. Dashed red lines mark the simulated parameter value.
DOI: 10.5061/dryad.m96r3/15
title: Supplemental Figure 2

description: Recovered parameter estimates for trees simulated with an exponential dependency of λ and μ on temperature. Dashed red lines mark the simulated parameter value.
DOI: 10.5061/dryad.m96r3/17
title: Supplemental Figure 3

description: The effect of undersampling on parameter estimation. Parameter estimates for trees simulated with (a) a positive exponential dependency of λ on temperature and constant extinction (μ = 0.05) and (b) a positive exponential dependency of μ on temperature with constant speciation (λ = 0.5) by fitting the temperature-dependent model. Parameter estimates are shown for trees with increasingly smaller sampling fractions, which were achieved by jackknifing the simulated trees by a fixed % and then fitting the environment-dependent model. Simulated parameters are marked by dashed red lines. Model selection determined by (c) AICc and (d) Akaike weights for trees simulated with a positive exponential dependency of λ on temperature and constant extinction (grey, temperature- dependent model; light blue, time-dependent model; black, constant-rate model). In (d), weights are averaged across all trees within each undersampled bracket.
DOI: 10.5061/dryad.m96r3/19
title: Supplemental Figure 6

description: Parameter estimates for (a) λ0, (b) μ0, (c) αμ for trees simulated with a positive exponential dependency of μ on temperature by fitting the temperature- dependent model. Parameter estimates are shown for trees with different species richness. Simulated parameters are marked by dashed red lines. (c, inset) A magnified plot of αμ estimates. (d) Akaike weights averaged over all trees for each species richness cohort for models fitted with temperature-dependent models (grey), time-dependent models (light blue), and constant-rate models (black).
DOI: 10.5061/dryad.m96r3/2
title: Supplemental Figure 5

description: Parameter estimates for trees simulated with a positive (left) and negative (right) exponential dependency of $\lambda$ on temperature by fitting the temperature-dependent model. Parameter estimates are shown for trees with different species richness. Simulated parameters are marked by dashed red lines. Akaike weights are shown for trees fitted with temperature-dependent models (grey), time-dependent models (light blue), and constant-rate models (black). Weights are averaged across all trees within each species richness bracket.
DOI: 10.5061/dryad.m96r3/20
title: Supplemental Figure 7

description: Model selection and parameter estimation in temperature- dependent trees under various spline smoothings in the fitted model. (a) Plots of temperature curve splines smoothed by different degrees of freedom. The time-series of temperature data are shown in grey dots and the smoothed curves in black lines. (b,c) Parameter estimates for trees simulated with an exponential dependency of speciation on temperature (b, λ = 0.2e0.05·T(t); C, λ = 0.3e−0.05·T(t)) with temperature curves determined using generalized cross-validation (degrees of freedom=208), where the fitted temperature-dependent models have temperature curve splines smoothed by different degrees of freedom. Simulated parameters are marked by dashed red lines. (d) The percentage of temperature-dependent trees, simulated with a temperature curve determined using generalized cross-validation, best sup- ported by models fit with temperature curve splines smoothed by different degrees of freedom versus constant-rate models and time-dependent models with an exponential dependence on speciation.
DOI: 10.5061/dryad.pq3376q/1
title: GP_755SNP_wild_turbot

description: Genepop input file created by Populations including all the locations and markers used in the study (755 markers). Location codes are shown in Table 1 of the manuscript.
DOI: 10.5061/dryad.pq3376q/2
title: GP_513NeutralSNP_wild_turbot

description: Genepop input file created by Populations. Only markers included in neutral dataset (513 markers). Location codes are shown in Table 1 of the manuscript.
DOI: 10.5061/dryad.pq3376q/3
title: MAFTur_def

description: Vegan input file including genetic information (i.e. minimum allele frequency within each location for 755 markers) for all the studied locations. Location codes are shown in Table 1 of the manuscript.