cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5418t/10
title: MrBayes_consensus_tree

description: Nanos-Apotolamprus consensus tree obtained in MrBayes.
DOI: 10.5061/dryad.5418t/11
title: Maximum_Likelihood_best_tree

description: Nanos-Apotolamprus tree obtained with GARLI (Maximum Likelihood approach).
DOI: 10.5061/dryad.57n57/5
title: nodIJ_tree_smaller_data_set_nonhomogeneous_ML
DOI: 10.5061/dryad.5c88j/1
title: Aspen epiphytes Davies_et_al (1)

description: Frequency of occurrence of epiphyte species on clones of aspen replicated in blocks at two sites. Data are from  5 cm x 25 cm quadrats divided into sub-quadrats of 5 cm x 5 cm, each with 1 cm x 1 cm subunits. Quadrats were place at cardinal points on the bole at a height of 1.3 m..
DOI: 10.5061/dryad.6356f/17
title: R Code for the CO2 dataset
DOI: 10.5061/dryad.85pr1/1
title: Microsatellite genotypes and mitochondrial D-loop haplogroups dataset

description: The file includes microsatellite genotypes (12 markers) and mitochondrial D-loop haplogroups of Bufo viridis/balearicus green toads sampled in the Po valley. "NA" indicates missing data. Microsatellites null alleles (estimated with MICROCHECKER) are indicated as "0". For details on the mitochondrial D-loop haplogroups, please refer to the paper.
DOI: 10.5061/dryad.866j4/1
title: single resource sibling competition experiment
DOI: 10.5061/dryad.866j4/2
title: two_resource_compeition_exp
DOI: 10.5061/dryad.86p42/1
title: Romano_et_al

description: Data on begging behaviour of nestling barn swallow. See README.txt for details.
DOI: 10.5061/dryad.876dn/1
title: AFLP and phenotypic trait allele table

description: Allele table for 106 AFLP loci and two phenotypic traits (bands and stripes) for 224 ground snakes from central North America. Column headings are locus/trait names and rows labels are individual specimens. Datfile created and saved as .csv file in Microsoft Excel.
DOI: 10.5061/dryad.876dn/2
title: Age-class, color pattern, and geographic location

description: Specimen information (Specimen number,Year Collected,Country,State,County,Morph,Age Class) for 2380 ground snakes (Sonora semiannulata) from across central and western North America. In the Specimen number column, the letters that begin each specimen number indicate the natural history collection that the snake is from : Arizona State University (ASU), California Academy of Sciences (CAS), Museum of Southwestern Biology at the University of New Mexico (MSB), Museum of Vertebrate Zoology at the University of California (MVZ), New Mexico State University (NMSU), Sam Noble Museum at the University of Oklahoma (OMNH), San Diego Natural History Museum (SDNHM), University of Arizona (UAZ), University of Kansas (KU), , University of Texas – Arlington (UTA), the University of Texas - El Paso (UTEP), and the North American Field Herping Association (NAFHA). All other acronyms represent individual collector numbers for specimens that are not housed in natural history collections.  In the Morph column, B=black-banded, M= red-striped and black-banded or mimetic, S=striped and U=uniform. In the Age-class column, J=juvenile and A=adult.
DOI: 10.5061/dryad.878m3/1
title: ColauttiBarrett

description: Data (.csv) and analysis (.R) files. Can be run in order (S1-S8) or see Science online supplementary materials for more detail.
DOI: 10.5061/dryad.89jd5/1
title: mcomp-main
DOI: 10.5061/dryad.89jd5/2
title: aggrredlendiffs
DOI: 10.5061/dryad.89jd5/3
title: mcompbytank
DOI: 10.5061/dryad.8b490/1
title: Amphiacusta sanctaecrucis morphological and microsatellite data
DOI: 10.5061/dryad.8mn44/1
title: Alldata_Benadi_JAE_2013
DOI: 10.5061/dryad.94tr3/1
title: Bokma_Suppl_Mat

description: Data on taxonomic membership of biological species, word frequencies in the U.S. declaration of independence, and Finnish car sales.
DOI: 10.5061/dryad.c03c2/1
title: Jaffe et al-Interspecific sims Sall by superfamily

description: Sampling protocol and simulations used to construct the null hypothesis under random paternity allocation. Interspecific simulations based on the entire data set (Sall, n = 72 species), performed within ants, bees and wasps.
DOI: 10.5061/dryad.c03c2/5
title: Jaffe et al-Intraspecific simulations

description: Sampling protocol and simulations used to construct the null hypothesis under random paternity allocation. Intraspecific simulations.
DOI: 10.5061/dryad.dk712/1
title: set31.Zupdated.autoANDchrZ.union.SNP.Fst.w100m2.5s20.csv

description: Pairwise Fst values for 100 kb sliding windows, sliding in increments of 20 kb. Fst for each pair of populations, for each window was calculated using the EGGLIB Python library.
DOI: 10.5061/dryad.dk712/2
title: PANAMA.ALLSHARED.w100.rerooted

description: Maximum likelihood trees for all non-overlapping 100 kb windows for the cydno-melpomene data set. Genomic locations of trees, and the designated topologies are given by the file PANAMA.ALLSHARED.w100.topology.csv.
DOI: 10.5061/dryad.dk712/3
title: PERU.ALLSHARED.w100.rerooted

description: Maximum likelihood trees for all non-overlapping 100 kb windows for the timareta-melpomene data set. Genomic locations of trees, and the designated topologies are given by the file PERU.ALLSHARED.w100.topology.csv.
DOI: 10.5061/dryad.dk712/4
title: PANAMA.ALLSHARED.w100.topology

description: Genomic locations of non-overlapping 100 kb windows and topologies supported by the corresponding maximum likelihood tree in the cydno-melpomene dataset. The full newick trees are given in the file PANAMA.ALLSHARED.w100.nwk.
DOI: 10.5061/dryad.dk712/5
title: PERU.ALLSHARED.w100.topology

description: Genomic locations of non-overlapping 100 kb windows and topologies supported by the corresponding maximum likelihood tree in the timareta-melpomene dataset. The full newick trees are given in the file PERU.ALLSHARED.w100.nwk.
DOI: 10.5061/dryad.dk712/6
title: set31.Zupdated.autoANDchrZ.ALLSHARED.SNP.derFreqs.csv

description: Derived allele frequencies for each population sample at each variable site for which there was a high-quality genotype call for all 31 individuals, and the outgroup species were fixed for the ancestral state. Columns with the suffixes "_1" and "_2" give the allele frequencies for sample subsets of two individuals, used for calculating the denominator of the fraction introgression f statistic. Values were calculated using the script freq.py. Values for Z and autosomes were calculated separately due to ploidy differences between the sexes, and then the outputs were combined.
DOI: 10.5061/dryad.dk712/7
title: Hmel1-1_Scaff-Chrom_Zcorrected_20120730

description: Chromosomal assignments of scaffolds and scaffold fragments. This file builds upon the chromosomal assignments provided by Dasmahapatra et al. 2012 doi:10.1038/nature11041, based on our read-depth analysis described in the supplementary information. Each scaffold is assigned to one or more scaffold "fragments", which are each assigned to a chromosome. Most scaffolds correspond to a single fragment that spans the length of the scaffold, but those that were found to be chimeric were split into 2 or 3 fragments, each of which then received a chromosomal assignment.
DOI: 10.5061/dryad.ds6c4/1
title: Columbia River steelhead trout SNP data

description: These data are genotypes for biallelic SNPs (two alleles). Data is formatted for the program GENALEX: (Peakall, R., and P. E. Smouse. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295. Program note available from: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2005.01155.x). The first row in the file contains: #loci, total#samples, #populations, and #samples/population. Row two has the data set title in column A, followed by two empty cells, then the name or designation of each population beginning in column D.In row three, column A is the header “sample ID” followed by “popID” in column B, and then a list of locus names.  Between each locus name is an empty cell (every other column).Raw genotypic data begins on row four, column C. Individuals are sequential in column A, and genotypes for 180 SNP are in columns C-MX. Each three digit allele appears in its own column.Populations designations, POP1-POP145 correspond with population reference numbers in the manuscript supplemental 1.
DOI: 10.5061/dryad.gf3qp/1
title: Results Diffusion Model

description: Range connectivity (Bayes Factors) and ancestral location probabilities among nine discrete geographical regions in Saxifraga oppositifolia inferred using reversible and non-reversible models of geographic diffusion of plastid DNA sequences
DOI: 10.5061/dryad.hb87k/1
title: thyroid data for DuRant et al.
DOI: 10.5061/dryad.j15q6/1
title: IMa2

description: IMa2 file used for analyses of isolation with migration. Data includes DNA sequences from 15 nuclear introns and 1 mtDNA locus.
DOI: 10.5061/dryad.j15q6/2
title: BEAST_mtDNA

description: mtDNA xml file used for phylogenetic analyses in BEAST.
DOI: 10.5061/dryad.j15q6/3
title: BEAST_15-nuclear-introns

description: XML file for *BEAST (Species Tree) analyses using 15 nuclear intronic markers.
DOI: 10.5061/dryad.j15q6/4
title: STRUCTURE_Tam-huds_15Introns

description: Multilocus genotype dataset from 15 nuclear introns from samples of Tamiasciurus hudsonicus. Dataset was used in population structure/assignment analysis using STRUCTURE.
DOI: 10.5061/dryad.j15q6/5
title: STRUCTURE_Tam-doug_15Introns

description: Multilocus genotype dataset from 15 nuclear introns from samples of Tamiasciurus douglasii. Dataset was used in population structure/assignment analysis using STRUCTURE.
DOI: 10.5061/dryad.j16p2/3
title: carnivores.multi.scaled.functions.setup.final

description: FINAL VERSIONS OF R CODE FROM START TO FINISH, WITH DOCUMENTATION
DOI: 10.5061/dryad.j16p2/4
title: carnivores.multi.scaled.graphs.runfile.final

description: R code for graphs shown in this publication
DOI: 10.5061/dryad.j16p2/5
title: carnivores.multi.scaled.runcode.final

description: simulation distributions and family-space analyses in R.
DOI: 10.5061/dryad.j16p2/6
title: new pretty histograms nov2013

description: Histogram code for R and rough simulations of raw data for R
DOI: 10.5061/dryad.js88n/1
title: Etienne et al - Evolution 2014 - supporting data
DOI: 10.5061/dryad.nf7697j6/4
title: Ord_TJ-2011-0215R1_birds-close
DOI: 10.5061/dryad.nf7697j6/5
title: Ord_TJ-2011-0215R1_birds-distant
DOI: 10.5061/dryad.nf7697j6/6
title: Ord_TJ-2011-0215R1_frogs
DOI: 10.5061/dryad.nf7697j6/7
title: Ord_TJ-2011-0215R1_lizards-close
DOI: 10.5061/dryad.nf7697j6/8
title: Ord_TJ-2011-0215R1_lizards-distant-dich
DOI: 10.5061/dryad.nh3d2/2
title: Geographic_localities_Runemark_et_al

description: GPS coordinates for field sites.
DOI: 10.5061/dryad.pj891/1
title: Figure 2, Panels A,B,C: Response of mule deer females to infant distress vocalizations and selected control stimuli.

description: Data in this file represent the response of mule deer females (panels A, B, C) to infant distress vocalizations of diverse mammalian species and selected control stimuli. Female responses to narrow band white noise (white noise NB, 400-1500 Hz) are included in the data set, but are not shown in fig. 2 due to the lack of a mean F0 for that stimulus. Data columns include:Column A: Species & call type: This column includes the species name and the type of stimulus including unmanipulated (UM) distress calls, F0-shifted distress calls (F0S, F0 manipulated by multiplying F0 by a certain factor)) and RS distress calls (distress calls with the F0 manipulated by overriding the sampling frequency).Column B: Species & Call Type lumped: When certain species were pooled in figure 2, this column shows the lumped category including “other ungulates” for ungulates except for mule deer and eland; and “pinniped” for fur seal and sea lions.Column C. Individual: This column lists the identity of the animal producing the sound stimulus.Column D. Mean F0: The mean fundamental frequency (mean F0) of the call in Hz.Column E. Jitter: due to overlapping values, it was necessary to jitter the data on the x-axis so that the overlapping calls would be visible in figure 2. This column shows the specific extent to which values were jittered. Data are represented on a log scale, making it necessary to apply a larger numerical ‘jitter’ when the mean F0 was higher. Values were not jittered on the y-axis.Column F. Mean F0 jittered (x): Mean F0 in Hz once jitter is taken into account. This column shows data for the x-axis.Column G. Female response (y): This column shows data for the y-axis. See corresponding publication for details on the response scale.For MD (mule deer) 0.2 to 1.8-F0S entries (see Columns A and B), median values for female responses to manipulated mule deer calls were obtained from Teichroeb, L. J., T. Riede, R. Kotrba, and S. Lingle. 2013. Fundamental frequency is key to response of female deer to juvenile distress calls. Behavioural Processes 92:15– 23.
DOI: 10.5061/dryad.pj891/2
title: Figure 2, Panel D: Response of white-tailed deer females to infant distress vocalizations and selected control stimuli.

description: Data in this file represent the response of white-tailed deer females (fig 2, D) to infant distress vocalizations of diverse mammalian species and selected control stimuli. Data columns include:Column A: Species & call type: This column includes the species name and the type of stimulus including unmanipulated (UM) distress calls, F0-shifted distress calls (F0S, F0 manipulated by multiplying F0 by a certain factor), RS distress calls (distress calls with the F0 manipulated by overriding the sampling frequency) and certain control stimuli (meadowlark song).Column B. Individual: This column lists the identity of the animal producing the sound stimulus.Column C. Mean F0: The mean fundamental frequency (mean F0) of the call in Hz.Column D. Jitter: due to overlapping values, it was necessary to jitter the data on the x-axis so that the overlapping calls would be visible in figure 2. This column shows the specific extent to which values were jittered. Data are represented on a log scale, making it necessary to apply a larger numerical ‘jitter’ when the mean F0 was higher. Values were not jittered on the y-axis.Column E. Mean F0 jittered (x): Mean F0 in Hz once jitter is taken into account. This column shows data for the x-axis.Column G. Female response (y): This column shows data for the y-axis. See corresponding publication for details on the response scale.For WT (white-tailed deer) 0.2 to 2.0-F0S entries (see Column A), median values for female responses to manipulated white-tailed deer calls were obtained from Teichroeb, L. J., T. Riede, R. Kotrba, and S. Lingle. 2013. Fundamental frequency is key to response of female deer to juvenile distress calls. Behavioural Processes 92:15– 23.
DOI: 10.5061/dryad.pj891/3
title: Figure 4: Response of mule deer females to natural mule deer distress calls, synthesized mule deer distress calls and sine wave stimuli.

description: We (Tobias Riede and Susan Lingle) modeled synthesized mule deer (MD) distress calls using parameters measured from natural distress calls (described in publication). We created sine wave stimuli that had the same mean F0 as the natural and synthesized distress calls. The sine wave stimuli had no additional harmonics and were longer (5 s in length). These stimuli were played to mule deer mothers in the field in summer 2013.  Data were collected by video and audio-recording female responses. Data were transcribed from video and audio and entered into an excel spreadsheet.Data columns represent:Column A: Type of call = Natural MD (mule deer), Synthesized MD or Sine MDColumn B: Specific call refers to the individual producing the call or upon which the stimulus was prepared.Column C: Mean fundamental frequency (mean F0) for the sound stimulus.Column D: Distance between female and speaker at the start of the trial.Column E: Closest distance the female came to the speaker, for females that approached the speaker (na or not applicable if a female did not approach).Column F: Basic response of female. Possibilities include: Retreat; No response; Intermittent alert, Continual alert, Approach.Column G: Female’s ehaviour close to speaker. If a female approached within 10 m of the speaker, did she remain within that distance for at least 10 s? Yes (y), No, or na (not applicable).Column H: Mule deer response coded. The number is based on the general response, the distance to which the female approached, and whether she remained close to the speaker if she came within 10 m. See corresponding publication for details.
DOI: 10.5061/dryad.pj891/4
title: Data used for logistic regression analyses (female response relative to acoustic traits) shown in Table B2, in the main text and figure 3.

description: This excel file includes data used for logistic regression analyses of the relationship between acoustic traits, starting distance to speaker, number of females per group, and the female’s response.  Rows 1-63 (Row number as per Column A) show responses of mule deer females to distress vocalizations made by species other than mule deer.  Rows 96-100 present data for mule deer responses to natural mule deer distress calls. Rows 64-95 and to mule deer calls for which the F0 was manipulated. Data in rows are from Teichroeb, L. J., T. Riede, R. Kotrba, and S. Lingle. 2013. Fundamental frequency is key to response of female deer to juvenile distress calls. Behavioural Processes 92:15– 23. Mean F0, female starting distance and female response, but no other predictor variables, were included for data from Teichroeb et al. (2013). Column A: Row number to identify each trial.Column B: Taxonomic order of the animal producing the sound used in the trial.Column C: Species of the animal producing the sound used in the trial.Column D: Call type. UM = unmanipulated calls; F0S = calls for which the F0 was shifted by multiplying the mean F0 by a certain factor; RS = calls for which the F0 was shifted by overriding the sampling frequency.Column E: Caller ID. Identity of individual producing the call.Colume F: No. Females. Number of females in the subject’s group at the start of the trial.Column G: Starting distance, code. Distance between female and speaker at the start of the trial, identified as a code. 2 = 50 -75 m; 3 = 75-100 m; 4 = 100-125 m; 5 = 125-150 m; 6 = 150-200 m; 7 = 200-250; 8 = &gt;250 m.Column H: Mean F0 (kHz)Column I: Maximum F0 (kHz)Column J: Range F0/Mean F0Column K: Call duration (s)Column L: Max dominant harmonic (Hz)Column M: Lowest of the three dominant harmonics (Hz), ranked by frequencyColumn N: Middle of the three dominant harmonics (Hz), ranked by frequencyColumn O: Highest of the three dominant harmonics (Hz), ranked by frequencyColumn P: Maximum dominant harmonic (kHz)Column Q: A principal component formed by the three dominant harmonics (columns M, N, O).Column R: Noise scored as a binary variable, showing presence or absence.Column S: Female response scored as a binary variable. Responses of 5 through 9 were considered moderate to strong responses and scored as “1”. Alert behaviour and approaches &lt;25 m were scored as 0. See corresponding publication for details.
DOI: 10.5061/dryad.pv6df/1
title: real_alignments

description: Alignments constructed using MUSCLE and GBLOCKS for 1099 cyanobacterial gene families with from version 5 of the HOGENOM database.
DOI: 10.5061/dryad.pv6df/2
title: real_trees

description: For each cleaned alignment an MCMC sample was obtained using PhyloBayes. For each family we subsequently sampled reconciled gene trees using ALEsample. For each ALEsample sample we computed "real" trees for each gene family by finding the tree that maximised conditional clade probabilities based on the sample.
DOI: 10.5061/dryad.pv6df/3
title: real_ale

description: .ale files based on PhyloBayes samples for real alignments.
DOI: 10.5061/dryad.pv6df/4
title: real_mlrec

description: ALEml output for real ales.
DOI: 10.5061/dryad.pv6df/5
title: sequence_mlrec

description: ALEml output fro PhyML trees based on real alignments.
DOI: 10.5061/dryad.pv6df/6
title: simulated_alignments

description: Simulated alignments based on real trees.
DOI: 10.5061/dryad.pv6df/7
title: simulated_ale

description: .ale files based on PhyloBayes samples using the SIMPLE sequnce evolution model for simulated alignments.
DOI: 10.5061/dryad.pv6df/8
title: simulated_mlrec

description: ALEml output for simulated ales.
DOI: 10.5061/dryad.r20t0/1
title: Read length simulations without sequencing errors

description: Sequences of uniform length at each of 100, 150, 200, 250, 300, 350, 400, 500, 600, 700, 800, 1000 and 1200 bp were drawn at random from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) using 0.1x coverage. Simulations were conducted using Grinder v0.5.3 without the inclusion of sequencing errors.
DOI: 10.5061/dryad.r20t0/2
title: Read length simulations with sequencing errors

description: Sequences of uniform length at each of 100, 150, 200, 250, 300, 350, 400, 500, 600, 700, 800, 1000 and 1200 bp were drawn at random from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) using 0.1x coverage. Simulations were conducted using PBSIM v1.0.3 with built-in PacBio CCS error profiles (substitutions/insertions/deletions ratio of 6:21:73; read accuracy of 98 ± 2%).
DOI: 10.5061/dryad.r20t0/3
title: Sequencing error simulations

description: Sequencing errors of substitutions and indels (insertions and deletions) were introduced to reads of uniformly 350 bp simulated from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) at 0.1x coverage using Grinder v0.5.3. In terms of sequencing error type, simulations included substitution-biased (substitutions/indels ratio of 90:10) and indel-biased (substitutions/indels ratio of 10:90) sequencing errors. In terms of sequencing error rate distribution, we assumed that sequencing errors occurred either uniformly or linearly from the 5′ end to 3′ end of each read. With uniformly distributed sequencing errors, reads were simulated with an error rate of 0, 0.01%, 0.1%, 0.5%, 1%, 2%, 3%, and 5%. With linearly distributed errors, the error rate doubled from the 5′ end to 3′ end: 0, 0.01–0.02%, 0.1–0.2%, 0.2–0.4%, 0.5–1%, 1–2%, and 2–4%. For the file name of each simulation, the first three letters reflect the error rate distribution (e.g. Lin for linear error rate distribution, Uni for uniform distribution); the following 4 digits represent the sequencing error type (e.g. 9010 for substitutions/indels ratio of 90:10); the remaining digits indicate the error rate (e.g. 0.1%). When error rate was 0, the simulation was designated as ErrorRate_0.
DOI: 10.5061/dryad.s7d2d/1
title: Data for Dryad version 1

description: Excel Spreadsheet,four sheets of data
DOI: 10.5061/dryad.v2t58/1
title: Butterfly and plant raw data

description: This excel file contains three tabs. Tab 1 includes data for the monarch rearing experiment including sex (males, females), rearing treatment (roadside collected milkweed or prairie collected milkweed), wing length (the measure of body size), thoracic protein, dry thoracic weight and the width of each eye (note the final analyses used log transformed values of several metrics as described in the methods). Tab 2 includes data for the cabbage white butterfly rearing experiment, including sex (males, females), rearing treatment (low sodium or medium sodium artificial diet), wing length (the measure of body size), thoracic protein, dry thoracic weight and brain volume of a subset of specimens (note that the final analysis used log transformed values of several metrics as described in the methods). Tab 3 includes element measurements of leaf tissue of plants collected from along roadsides and in control sites &gt;100 m from the road. Our analyses focused on sodium and nitrogen (note that sodium values were log transformed for normality in statistical analyses). Here we also include values of other elements that are measured in a standard ICP-AES analysis; N values came from a separate analysis of the same samples (using the Dumas method).