Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)

 

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Title Alignment of cyt b
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Description Text file in nexus format containing the alignment of cytochrome b mtDNA data of the Liolaemus darwinii complex (77 taxa, 713 bp)
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Title Alignment of A1D
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Description Text file in nexus format containing the alignment of the anonymous nuclear locus A1D of the Liolaemus darwinii complex (80 taxa, 700 bp)
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Title Alignment of A9C
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Description Text file in nexus format containing the alignment of the anonymous nuclear locus A9C of the Liolaemus darwinii complex (80 taxa, 481 bp)
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Title Alignment of B6B
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Description Text file in nexus format containing the alignment of the anonymous nuclear locus B6B of the Liolaemus darwinii complex (80 taxa, 415 bp)
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Title Simulation code for evaluation of species delimitation methods
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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
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Title Input and output of SpeDeSTEM analyses
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Description Compressed file containing the input and output files of SpeDeSTEM analyses based on the empirical data from the Liolaemus darwinii complex
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Title Input and output of BPP analyses
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Description Compressed file containing input and output files of BPP analyses based on empirical data from the Liolaemus darwinii complex
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Title Input and output of ABC analyses
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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
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Title Table S1
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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.
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Title Table S2
Downloaded 23 times
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.
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Title Table S3
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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.
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Title Figure S1
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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.
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Title Appendix 1
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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).
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Title Appendix S1
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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".
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When using this data, please cite the original publication:

Camargo A, Morando M, Avila LJ, Sites JWJ (2012) Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution 66(9): 2834–2849. http://dx.doi.org/10.1111/j.1558-5646.2012.01640.x

Additionally, please cite the Dryad data package:

Camargo A, Morando M, Avila LJ, Sites Jr. JW (2012) Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4409k652
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