cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.308g1h54/1
title: Plethodontid salamanders shotgun reads

description: The uploaded zip file contains the 454 shotgun reads (in fasta format) for six species of plethodontid salamanders: Aneides flavipunctatus, Batrachoseps nigriventris, Bolitoglossa occidentalis, Bolitoglossa rostrata, Desmognathus ochrophaeus, and Eurycea tynerensis.
DOI: 10.5061/dryad.4409k652/1
title: Alignment of cyt b

description: Text file in nexus format containing the alignment of cytochrome b mtDNA data of the Liolaemus darwinii complex (77 taxa, 713 bp)
DOI: 10.5061/dryad.4409k652/2
title: Alignment of A1D

description: Text file in nexus format containing the alignment of the anonymous nuclear locus A1D of the Liolaemus darwinii complex (80 taxa, 700 bp)
DOI: 10.5061/dryad.4409k652/3
title: Alignment of A9C

description: Text file in nexus format containing the alignment of the anonymous nuclear locus A9C of the Liolaemus darwinii complex (80 taxa, 481 bp)
DOI: 10.5061/dryad.4k1v5/1
title: JEB-2012-00598_Data_Elytra

description: Family = F0 family; SCP = Sex and condition of parent (F1); Repl = Replicate; Sex = Sex of offspring (F2); CondOff = Condition of offspring (F2); Ind = Individual (5 Individuals per treatment combination were measured); Elytra = Length of Elytra; Data were collected in the laboratory.
DOI: 10.5061/dryad.4k1v5/2
title: JEB-2012-00598_Data_Abdomensegment

description: Family = F0 family; SCP = Sex and condition of parent (F1); Repl = Replicate; Sex = Sex of offspring (F2); CondOff = Condition of offspring (F2); Ind = Individual (5 Individuals per treatment combination were measured); Abdomen = Length of Abdomen segment; Data were collected in the laboratory
DOI: 10.5061/dryad.59gp4/1
title: Morphospecies abundance per moss patch & species information

description: Please note file has multiple worksheets. Moss patches (Dicranoloma sp.) were collected in the Yarra Ranges National Park, Victoria, Australia (37°29'13"S, 145°49'59"E, 800 m, permit 10004595 of the Department of Sustainability and Environment, State Government of Victoria). Moss patches were subjected to Tullgren funnel extraction. Microarthropods (&lt; 2 mm) were sorted to morphospecies on the basis of morphological features. See paper for details.
DOI: 10.5061/dryad.6kb0v/1
title: Summary Bone Data and Charts August 2010

description: Excel file with data derived from CT scans indicated in manuscript showing values of individual species for each measure. Summary charts included.
DOI: 10.5061/dryad.6s146/1
title: Morphological and phylogenetic data for Poseidonamicus populations
DOI: 10.5061/dryad.6s146/2
title: R functions used for model fitting
DOI: 10.5061/dryad.78vr9/1
title: Raw data
DOI: 10.5061/dryad.78vr9/2
title: R scripts
DOI: 10.5061/dryad.78vr9/3
title: Data files for R
DOI: 10.5061/dryad.7qr3f154/1
title: Data for CDL study Bean et al
DOI: 10.5061/dryad.93f1r/1
title: Reflectance_and_carotenoids
DOI: 10.5061/dryad.d56g84n5/1
title: mating

description: The "Year" column refers to the year in which experiments were performed. "Small" and "Large" refer to the size of the experimental females.
DOI: 10.5061/dryad.m827p/1
title: Abundance of amoA and amoB genes in soils from Stipa tenacissima grasslands along an aridity gradient in the Mediterranean

description: Data on the abundance of amoA and amoB genes in soils from Stipa tenacissima grasslands along a Mediterranean aridity gradient (from Spain to Tunisia). The database also includes information about different soil variables and the abiotic characteristics of the sites surveyed. All the units and information about the variables are included in the "Metadata" spreadsheet.
DOI: 10.5061/dryad.v5007p45/2
title: Final Tree used

description: The phylogenetic tree used in our analysis. This tree is fully dichotomous, includes branch lengths, and has no non-zero branch-lengths. Tree structure and branch lengths were collected from the literature and estimated as described in the methods. The tree was edited in R and Notepad.
DOI: 10.5061/dryad.v5007p45/3
title: Final data used

description: The data used for the phylogenetic meta-analysis in Phylometa. The data file is formatted in accordance with the instructions in the Phylometa manual: it is tab-delimited and the columns are taxon name, taxon-specific effect size, effect size variance, and moderator grouping. In moderator grouping, 0=arachnid, lizard or fish, 1=mammal, 2=bird, and 3=insect.
DOI: 10.5061/dryad.v5007p45/4
title: Supplementary methods

description: Describes statistical methods omitted from paper because they were not relevant to the results presented.
DOI: 10.5061/dryad.vk7t0/1
title: R script for methods comparison simulations under budding

description: This R script will execute the methods comparison simulations shown in the paper under budding differentiation, given that appropriate libraries are installed.
DOI: 10.5061/dryad.vk7t0/2
title: R script for methods comparison simulations under terminal-taxon differentiation

description: This R script will execute the methods comparison simulations shown in the paper under terminal-taxon differentiation, given that appropriate libraries are installed.
DOI: 10.5061/dryad.vk7t0/3
title: R Workspace for methods comparisons with budding

description: Workspace file containing methods comparison simulation data generated under budding differentiation.
DOI: 10.5061/dryad.vk7t0/4
title: R Workspace for methods comparisons with terminal-taxon differentiation

description: Workspace file containing methods comparison simulation data generated under terminal-taxon differentiation.
DOI: 10.5061/dryad.vk7t0/5
title: R script for plotting methods comparison figures

description: This R script, when executed with the two R workspace files for methods comparisons (see first few lines) will recreate the various methods comparison plots from the paper. Note that the figure numbers in the actual paper have shifted since this script was written, with one figure even being moved to the supplement.
DOI: 10.5061/dryad.vk7t0/6
title: R script for testing Ps derivation with simulations

description: R script for simulating Ps under various rates to compare to the value calculated by the solved derivation.
DOI: 10.5061/dryad.1pd2j/1
title: Sequence alignment of fourfold degenerate sites of the 2L chromosome arm

description: We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns &lt; 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
DOI: 10.5061/dryad.1pd2j/2
title: Sequence alignment of fourfold degenerate sites of the 2R chromosome arm

description: We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns &lt; 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
DOI: 10.5061/dryad.1pd2j/3
title: Sequence alignment of fourfold degenerate sites of the 3L chromosome arm

description: We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns &lt; 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
DOI: 10.5061/dryad.1pd2j/4
title: Sequence alignment of fourfold degenerate sites of the 3R chromosome arm

description: We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns &lt; 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
DOI: 10.5061/dryad.21nf3/20
title: Cox1-alnFLYTREE

description: Alignment of dipteran mitochondrial CO1 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/21
title: Cox2-alnFLYTREE

description: Alignment of dipteran mitochondrial COII (cox2) gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/22
title: Cox3-alnFLYTREE

description: Alignment of dipteran mitochondrial CO-III (Cox3) gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/23
title: Cytb-alnFLYTREE

description: Alignment of dipteran mitochondrial cyt-b gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/24
title: Large_rRNA16S-alnFLYTREE

description: Alignment of dipteran mitochondrial 16S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.4409k652/10
title: Table S2

description: Summary statistics (SuSt) of the prior, the observed data, and the posterior of ABC analyses for parameter estimation. Observed SuSt were obtained from the sequence data of four loci for the L. darwinii complex. Mean and standard deviation (StDv) of SuSt were calculated across simulated or observed loci. Abbreviations: π = mean of pairwise differences, MFS = mutation frequency spectrum, NmS = Nm-like based on the number of segregating sites, privS = number of private segregating sites, 25%Q = 25% quartile, 75%Q = 75% quartile.
DOI: 10.5061/dryad.4409k652/11
title: Table S3

description: Model selection with AIC criteria of alternative demographic models estimated with IMa2. Models are nested within the full migration model and are ranked based on AIC values. Best model is bolded. AIC = Akaike information criterion, k = number of parameters, Δi = AIC - AICmin, ωi = model probability. Subscripts of M (migration) parameters represent the directionality of gene flow between populations going backwards in time: 0 = L. darwinii-N, 1= L. darwinii-S, 2 = L. laurenti, and 3 = L. grosseorum. Parameters values constrained in nested models are enclosed in squared brackets.
DOI: 10.5061/dryad.4409k652/4
title: Alignment of B6B

description: Text file in nexus format containing the alignment of the anonymous nuclear locus B6B of the Liolaemus darwinii complex (80 taxa, 415 bp)
DOI: 10.5061/dryad.4409k652/5
title: Simulation code for evaluation of species delimitation methods

description: Compressed file containing a Perl script (speciation.pl), associated files, and executables for simulating sequence data and summary statistics used as input of species delimitation methods
DOI: 10.5061/dryad.4409k652/6
title: Input and output of SpeDeSTEM analyses

description: Compressed file containing the input and output files of SpeDeSTEM analyses based on the empirical data from the Liolaemus darwinii complex
DOI: 10.5061/dryad.4409k652/7
title: Input and output of BPP analyses

description: Compressed file containing input and output files of BPP analyses based on empirical data from the Liolaemus darwinii complex
DOI: 10.5061/dryad.4409k652/8
title: Input and output of ABC analyses

description: Compressed file containing simulation code for generating summary statistics used in ABC analyses, observed summary statistics for species delimitation (obs12sust_SD) and parameter estimation (obs44sust_PE) based on empirical data from the Liolaemus darwinii complex, and output of ABC analyses (R_output_SD and R_output_PE) in R
DOI: 10.5061/dryad.4409k652/9
title: Table S1

description: Summary statistics (SuSt) of the priors, the observed data, and the posterior of ABC analyses for species delimitation. Observed SuSt were obtained from the sequence data of four loci for the L. darwinii complex. Mean and standard deviation (StDv) of SuSt were calculated across simulated or observed loci. Abbreviations: π = mean of pairwise differences, S = number of segregating sites, MFS = mutation frequency spectrum. Details about the computation of these SuSt are given in user guide of the program popABC.
DOI: 10.5061/dryad.6d86v/1
title: Schilthuizen ALL

description: Raw data for each of the sample sites, with absolute and relative frequencies of morph categories (as well as bar and pie graphs of the same), photographs of the habitat and maps of the exact locations of the study sites, summaries of the vegetation, sampling dates, coordinates, and other field notes.
DOI: 10.5061/dryad.mn11k/1
title: Eider

description: Field data on eider group formation behaviour.
DOI: 10.5061/dryad.n710v/1
title: Source data for paper
DOI: 10.5061/dryad.sv37s/1
title: Konrad_etal_2012_Figure 1
DOI: 10.5061/dryad.sv37s/2
title: Konrad_etal_2012_Figure 2
DOI: 10.5061/dryad.vk7t0/10
title: R script for simulating cap-delta distributions (Budding, set B)

description: This R script, when executed, generates simulated phylogenies and fossil records under a budding scenario with branching and extinction rates greater than sampling rates, saving the cap-delta values at the root (as defined in the manuscript).
DOI: 10.5061/dryad.vk7t0/11
title: R script for simulating cap-delta distributions (Budding, set C)

description: This R script, when executed, generates simulated phylogenies and fossil records under a budding scenario with branching and extinction rates less than sampling rates, saving the cap-delta values at the root (as defined in the manuscript).
DOI: 10.5061/dryad.vk7t0/12
title: R script for simulating cap-delta distributions (Bifurcation)

description: This R script, when executed, generates simulated phylogenies and fossil records under a bifurcating cladogenesis scenario with equal branching, extinction and sampling rates, saving the cap-delta values at the root (as defined in the manuscript).
DOI: 10.5061/dryad.vk7t0/13
title: R workspace for simulated cap-delta distributions (Budding, set A)

description: This contains simulated cap-delta values generated under a budding scenario with equal branching, extinction and sampling rates.
DOI: 10.5061/dryad.vk7t0/14
title: R workspace for simulated cap-delta distributions (Budding, set B)

description: This contains simulated cap-delta values generated under a budding scenario with branching and extinction rates greater than the sampling rates.
DOI: 10.5061/dryad.vk7t0/15
title: R workspace for simulated cap-delta distributions (Budding, set C)

description: This contains simulated cap-delta values generated under a budding scenario with branching and extinction rates less than the sampling rates.
DOI: 10.5061/dryad.vk7t0/7
title: R Workspace for testing Ps

description: Workspace file that contains all the simulation data necessary for creating the figure showing the comparison of simulated and calculated values of Ps.
DOI: 10.5061/dryad.vk7t0/8
title: R script for plotting Ps comparison figure

description: R script which, given the workspace file that contains all the simulation data from the Ps comparison, will create the figure showing the comparison of simulated and calculated values of Ps.
DOI: 10.5061/dryad.vk7t0/9
title: R script for simulating cap-delta distributions (Budding, set A)

description: This R script, when executed, generates simulated phylogenies and fossil records under a budding scenario with branching, extinction and sampling rates equal, saving the cap-delta values at the root (as defined in the manuscript).
DOI: 10.5061/dryad.21nf3/25
title: Small_rRNA12S-alnFLYTREE

description: Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/26
title: Nad1-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH1 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/27
title: Nad2-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH2 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/28
title: Nad3-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH3 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/29
title: Nad4-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH4 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/30
title: Nad4L-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH4L gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/31
title: Nad5-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH5 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/32
title: Nad6-alnFLYTREE

description: Alignment of dipteran mitochondrial NADH6 gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/33
title: Small_rRNA12S-alnFLYTREE

description: Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
DOI: 10.5061/dryad.21nf3/34
title: Textnames

description: This file resolves the identity of taxon name codes used in the phylogenetic data sets below.  You can also find information about all of these name codes at :http://www.inhs.uiuc.edu/research/flytreephp/flytree/index.php
DOI: 10.5061/dryad.4409k652/12
title: Figure S1

description: Species tree of the L. darwinii complex based on a Bayesian analysis in *BEAST. Numbers above branches are posterior probabilities of clades. The scale bar represents substitutions per site.
DOI: 10.5061/dryad.4409k652/13
title: Appendix 1

description: List of specimens sequenced for this study. Code represents the numbers used to identify sampled localities in Fig. 1. GenBank accession numbers are given for each locus; italicized numbers indicate sequences used in species-tree analysis. Acronyms: BYU = Bean Life Science Museum, Brigham Young University (USA); FML = Fundación Miguel Lillo (Argentina); IMCN = Instituto y Museo de Ciencias Naturales, Universidad Nacional de San Juan (Argentina); LJAMM-CNP = herpetological collection of the Centro Nacional Patagónico (CENPAT-CONICET, Argentina); and MLP S. = herpetological collection of the Museo de La Plata (Argentina).
DOI: 10.5061/dryad.4409k652/14
title: Appendix S1

description: Figure 1. Number of references published between 1981 and 2010 retrieved from the ISI Web of Science that contained the keyword "species delimitation". Figure 2. Number of references published between 1992 and 2010 retrieved from the ISI Web of Science that contained the keyword "approximate bayesian computation".
DOI: 10.5061/dryad.7bp771n4/1
title: all B virility

description: The file contains male virility for 1000 fruitflies as a function of age. An "NA" in the age-at-death field (death) indicates the fly was accidently killed or escaped. These flies were not used in the anlaysis.
DOI: 10.5061/dryad.8gv43s53/1
title: Supplementary Figures & Tables

description: Saturation curves of pairwise genetic distances calculated in GenClone. Graphs of log-likelihood and delta K across varying numbers of genetic clusters, from STRUCTURE. Supplementary tables 1 & 2 showing results when all but one one copy of each identical genotype was removed from the data set.
DOI: 10.5061/dryad.d6n271pv/1
title: Archiving data

description: Each sheet of the Excel file contains each measured variable (survival to herbicide, aphid herbivory, plant yield and endophyte transmission) in the two experiments. The logic is easy to understand since the nomenclature is the same used in the article.
DOI: 10.5061/dryad.ft5v0/1
title: sum

description: Data for Figure 3
DOI: 10.5061/dryad.g2b10/1
title: Genotype data

description: Allele sizes at each locus for all sampled individuals. Genepop format.
DOI: 10.5061/dryad.g2b10/2
title: DIYABC input file
DOI: 10.5061/dryad.kr006cf0/1
title: CAGO AP management plan March 2008 Final

description: The management plan created by the Atlantic Flyway to manage the Atlantic Population of Canada Geese.
DOI: 10.5061/dryad.p462j4f3/1
title: Data Davidowitz Evolution 2012

description: data of all offspring and parents analyzed. see ReadMe file for key.
DOI: 10.5061/dryad.s2np7/1
title: Auger et al F1 digit length and ratio input file

description: All basic measurements on digit length and ratio according to exposures conditions; from semi automatic image analysis of forepaw X-rays.
DOI: 10.5061/dryad.s2np7/2
title: Auger et al F2 digit length and ratio input file

description: All basic measurements on digit length and ratio in the progeny according to exposures conditions in fathers; from semi automatic image analysis of forepaw X-rays in the second unexposed generation sired by exposed fathers and unexposed mothers.
DOI: 10.5061/dryad.s2np7/3
title: Auger et al F1 2D4D vs AGD input file

description: 2D to 4D digit ratio measured by semi-automatic image analysis vs relative anogenital distance (AGD) measured by a standardized method according to exposure conditions in the F1 generation
DOI: 10.5061/dryad.s5573/1
title: Dryad Greenbulls - Vangestel Carl

description: Microsatellite data (10 loci) of 362 birds (Phyllastrephus cabanisi) sampled in the Taita Hills, Kenya during 2 periods (first period (1996-2000), second period (2006-2010)).
DOI: 10.5061/dryad.sv37s/10
title: Konrad_etal_2012_Spatial separation experiment
DOI: 10.5061/dryad.sv37s/3
title: Konrad_etal_2012_Figure 3
DOI: 10.5061/dryad.sv37s/4
title: Konrad_etal_2012_Figure 4
DOI: 10.5061/dryad.sv37s/5
title: Konrad_etal_2012_Figure 5AB
DOI: 10.5061/dryad.sv37s/6
title: Konrad_etal_2012_Figure 5CD
DOI: 10.5061/dryad.sv37s/7
title: Konrad_etal_2012_Figure 6
DOI: 10.5061/dryad.sv37s/8
title: Konrad_etal_2012_Figure 7
DOI: 10.5061/dryad.sv37s/9
title: Konrad_etal_2012_Figure S4
DOI: 10.5061/dryad.t749b/1
title: pleuroProtGenes.123

description: Nexus alignment file with character sets and export block. Includes sequences generate for this study and those retrieved from GenBank.