DOI: 10.5061/dryad.8m8c0
title: 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)

description: Molecular phylogenetics has entered a new era in which species trees are
 estimated from a collection of gene trees using methods that accommodate
 their heterogeneity and discordance with the species tree. Empirical
 evaluation of species trees is necessary to assess the performance (i.e.,
 accuracy and precision) of these methods with real data, which consist of
 gene genealogies likely shaped by different historical and demographic
 processes. We analyzed 20 loci for 16 species of the South American
 lizards of the Liolaemus darwinii species group and reconstructed a
 species tree with *BEAST, then compared the performance of this method
 under different sampling strategies of loci, individuals, and sequence
 lengths. We found an increase in the accuracy and precision of species
 trees with the number of loci, but for any number of loci, accuracy
 decreased when using only one individual per species or 25% of the full
 sequence length. In addition, locus 'informativeness' was an
 important factor in the accuracy/precision of species trees when using a
 few loci, but it became increasingly irrelevant with additional loci. Our
 empirical results combined with previous simulation studies suggest that
 there is an optimal range of sampling effort of loci, individuals, and
 sequence lengths for a given speciation history and information content of
 the data. Future studies should be directed towards further assessment of
 other factors that can impact performance of species trees, including gene
 flow, data 'informativeness', tree shape, missing data, and
 uncertain species boundaries.
description: Alignments of unphased
 DNA sequencesConcatenated text files
 in nexus format of DNA sequences from 20 loci of 16 species of the
 Liolaemus darwinii groupdatasets.txtOutput files from Phase analysesConcatenated 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 groupphase_output.txtAlignments of phased DNA sequencesConcatenated text files in nexus format of phased DNA sequences from 19 nuclear loci of 16 species of the Liolaemus darwinii groupphase_nexus.txtInput files for BEAST analysesCompressed 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 groupxml_files.tgzSimulated gene trees for MesquiteInput 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.simulations.nexAppendix 2Sequence alignments of unphased data for 20 lociAppendix2.docxAppendix 3Plots of regression analyses between proportion of variable sites, proportion of informative sites, clade support index, level of discordance, and precision of species trees.Appendix3.docxAppendix 4Gene trees estimated in *BEAST using the full data set. Branch lengths are in units of substitutions per site.Appendix4.docxAppendix 5Species 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.Appendix5.docxAppendix 6Species trees estimated in *BEAST with variable numbers of loci using phased and unphased data.Appendix6.docxAppendix 7Simulation 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.Appendix7.docxAppendix 8Phylogenetic trees estimated in previous studies of the Liolaemus darwinii group.Appendix8.docx