DOI: 10.5061/dryad.91867
title: Data from: Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards

description: Accurate gene tree inference is an important aspect of species tree
 estimation in a summary-coalescent framework. Yet, in empirical studies,
 inferred gene trees differ in accuracy due to stochastic variation in
 phylogenetic signal between targeted loci. Empiricists should, therefore,
 examine the consistency of species tree inference, while accounting for
 the observed heterogeneity in gene tree resolution of phylogenomic data
 sets. Here, we assess the impact of gene tree estimation error on
 summary-coalescent species tree inference by screening ${\sim}2000$ exonic
 loci based on gene tree resolution prior to phylogenetic inference. We
 focus on a phylogenetically challenging radiation of Australian lizards
 (genus Cryptoblepharus, Scincidae) and explore effects on topology and
 support. We identify a well-supported topology based on all loci and find
 that a relatively small number of high-resolution gene trees can be
 sufficient to converge on the same topology. Adding gene trees with
 decreasing resolution produced a generally consistent topology, and
 increased confidence for specific bipartitions that were poorly supported
 when using a small number of informative loci. This corroborates
 coalescent-based simulation studies that have highlighted the need for a
 large number of loci to confidently resolve challenging relationships and
 refutes the notion that low-resolution gene trees introduce phylogenetic
 noise. Further, our study also highlights the value of quantifying changes
 in nodal support across locus subsets of increasing size (but decreasing
 gene tree resolution). Such detailed analyses can reveal anomalous
 fluctuations in support at some nodes, suggesting the possibility of model
 violation. By characterizing the heterogeneity in phylogenetic signal
 among loci, we can account for uncertainty in gene tree estimation and
 assess its effect on the consistency of the species tree estimate. We
 suggest that the evaluation of gene tree resolution should be incorporated
 in the analysis of empirical phylogenomic data sets. This will ultimately
 increase our confidence in species tree estimation using
 summary-coalescent methods and enable us to exploit genomic data for
 phylogenetic inference.
description: concatenated dataset
 used for RAxML analysisConcatenated alignment
 of the complete dataset (1361 loci) and the inferred maximum likelihood
 RAxML tree (100 tree searches, 1000 bootstrap
 replicates)RAxML.tar.gzAlignmentsAll 1852 loci (contains both complete and incomplete, up to 1 species missing, alignments)1852_exon_cap_alignments.tar.gzASTRAL complete dataset, random locus subsetsThe ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were randomly (i.e. not ranked by Tree Certainty score) selected.ASTRAL_0_indiv_miss_allowed_RANDOM.tar.gzASTRAL complete dataset, ranked locus subsetsThe ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were ranked (i.e. ranked by Tree Certainty score) selected.ASTRAL_0_indiv_miss_allowed_RANKED.tar.gzASTRAL incomplete dataset, random locus subsetsThe ASTRAL input and output for the summary-coalescent species tree analysis based on the incomplete dataset. Locus subsets were randomly (i.e. not ranked by Tree Certainty score) selected.ASTRAL_1_indiv_miss_allowed_RANDOM.tar.gzASTRAL incomplete dataset, ranked locus subsetsThe ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were ranked (i.e. ranked by Tree Certainty score) selected.ASTRAL_1_indiv_miss_allowed_RANKED.tar.gzSupplementary_Table_1Information on individuals used in the study and sequencing successSupplementary figuresSupplementary figures in order and as described in manuscriptsupp_figures_V2.pdf