Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae)

Camargo A, Avila LJ, Morando M, Sites JWJ

Date Published: February 3, 2012

DOI: http://dx.doi.org/10.5061/dryad.8m8c0

 

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Title Alignments of unphased DNA sequences
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Description Concatenated text files in nexus format of DNA sequences from 20 loci of 16 species of the Liolaemus darwinii group
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Title Output files from Phase analyses
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Description Concatenated output files in text format of analyses with the software Phase to phase DNA sequence data from 19 nuclear loci of 16 species of the Liolaemus darwinii group
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Title Alignments of phased DNA sequences
Downloaded 39 times
Description Concatenated text files in nexus format of phased DNA sequences from 19 nuclear loci of 16 species of the Liolaemus darwinii group
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Title Input files for BEAST analyses
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Description Compressed file containing input files in xml format for estimating species trees with the software *BEAST using DNA sequence data from 20 loci of 16 species of the Liolaemus darwinii group
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Title Simulated gene trees for Mesquite
Downloaded 41 times
Description Input file for Mesquite in nexus format containing 100 simulated gene trees for a species tree of 8 species and 3 sequences/species. The number of deep coalescences for each gene tree was calculated in Mesquite to group gene trees in three categories of discordance with the species tree. See more details in online Appendix 7.
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Title Appendix 2
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Description Sequence alignments of unphased data for 20 loci
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Title Appendix 3
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Description Plots of regression analyses between proportion of variable sites, proportion of informative sites, clade support index, level of discordance, and precision of species trees.
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Title Appendix 4
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Description Gene trees estimated in *BEAST using the full data set. Branch lengths are in units of substitutions per site.
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Title Appendix 5
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Description Species trees estimated in *BEAST using: phased data, variable population size and tree priors, and 200 million generations. Species tree estimated with BEST using the full data set.
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Title Appendix 6
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Description Species trees estimated in *BEAST with variable numbers of loci using phased and unphased data.
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Title Appendix 7
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Description Simulation of 100 gene trees from a pre-specified species tree to analyze the relationship between accuracy of species-tree estimation and the distribution of gene-tree discordance.
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Title Appendix 8
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Description Phylogenetic trees estimated in previous studies of the Liolaemus darwinii group.
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When using this data, please cite the original publication:

Camargo A, Avila LJ, Morando M, Sites JW Jr (2011) Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae). Systematic Biology 61(2): 272-288. http://dx.doi.org/10.1093/sysbio/syr105

Additionally, please cite the Dryad data package:

Camargo A, Avila LJ, Morando M, Sites JWJ (2011) Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8m8c0
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