DOI: 10.5061/dryad.35q4h
title: Data from: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data

description: The genus Liolaemus is one of the most ecologically diverse and
 species-rich genera of lizards worldwide. It currently includes more than
 250 recognized species, which have been subject to many ecological and
 evolutionary studies. Nevertheless, Liolaemus lizards have a complex
 taxonomic history, mainly due to the incongruence between morphological
 and genetic data, incomplete taxon sampling, incomplete lineage sorting
 and hybridization. In addition, as many species have restricted and remote
 distributions, this has hampered their examination and inclusion in
 molecular systematic studies. The aims of this study are to infer a robust
 phylogeny for a subsample of lizards representing the Chilean clade
 (subgenus Liolaemus sensu stricto), and to test the monophyly of several
 of the major species groups. We use a phylogenomic approach, targeting 541
 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa.
 We conduct a comparison of phylogenetic analyses using maximum-likelihood
 and several species tree inference methods. The UCEs provide stronger
 support for phylogenetic relationships compared to the protein-coding
 genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On
 average, the protein-coding genes contain over twice the number of
 informative sites. Based on our phylogenomic analyses, all the groups
 sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in
 the phylogeny, because only a few loci (nine) were recovered for this
 species. Topologies or support values did not change dramatically upon
 exclusion of L. t. tenuis from analyses, suggesting that missing data did
 not had a significant impact on phylogenetic inference in this data set.
 The phylogenomic analyses provide strong support for sister group
 relationships between L. fuscus, L. monticola, L. nigroviridis and L.
 nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling,
 we have provided a reliable starting hypothesis for the relationships
 among many major groups of the Chilean clade of Liolaemus that will help
 future work aimed at resolving the Liolaemus phylogeny.
description: ASTRAL-II input
 (protein-coding data set) with Liolaemus tenuis tenuis.File containing gene
 trees estimated by RaxML (which are the input for ASTRAL-II).
 Protein-coding genes data set, including Liolaemus tenuis
 tenuis.Input_ASTRAL_PC_withtenuis.treASTRAL-II input (UCEs data set) with Liolaemus tenuis tenuis.File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Ultraconserved elements (UCEs) data set, including Liolaemus tenuis tenuis.Input_ASTRAL_uces_withtenuis.treASTRAL-II input (full data set) with Liolaemus tenuis tenuis.File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Protein-coding genes + ultraconserved elements data set (full data set), including Liolaemus tenuis tenuis.Input_ASTRAL_ucesPC_withtenuis.treASTRAL-II input (full data set) without Liolaemus tenuis tenuis.File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Full data set, excluding Liolaemus tenuis tenuis.Input_ASTRAL_ucesPC_withouttenuis.treASTRAL-II inferred tree using the protein-coding data set with Liolaemus tenuis tenuis.Results of ASTRAL-II: inferred tree using the protein-coding data set with Liolaemus tenuis tenuis.Results_ASTRAL_PC_withtenuis.nwkASTRAL-II inferred tree using the UCEs data set with Liolaemus tenuis tenuis.Results of ASTRAL-II: inferred tree using the ultraconserved elements (UCEs) data set with Liolaemus tenuis tenuis.Results_ASTRAL_uces_withtenuis.nwkASTRAL-II inferred tree using the full data set with Liolaemus tenuis tenuis.Results of ASTRAL-II: inferred tree using the full data set with Liolaemus tenuis tenuis.Results_ASTRAL_ucesPC_withtenuis.treeASTRAL-II inferred tree using the full data set without Liolaemus tenuis tenuis.Results of ASTRAL-II: inferred tree using the full data set excluding Liolaemus tenuis tenuis.Results_ASTRAL_ucesPC_withouttenuis.treInput for SVDquartets, full dataset, with Liolaemus tenuis tenuis.Input sequences in nexus format for SVDquartets, full dataset, with Liolaemus tenuis tenuis.Input_SVDquartets_fulldataset_with_tenuis.nexInput for SVDquartets, full dataset, without Liolaemus tenuis tenuis.​Input sequences in nexus format for SVDquartets, full dataset, excluding Liolaemus tenuis tenuis.Input_SVDquartets_fulldataset_without_tenuis.nexInput for SVDquartets, protein-coding dataset, with Liolaemus tenuis tenuis.​​Input sequences in nexus format for SVDquartets, protein-coding dataset, with Liolaemus tenuis tenuis.Input_SVDquartets_protein-codingdataset_with_tenuis.nexInput for SVDquartets, ultraconserved elements dataset, with Liolaemus tenuis tenuis.​​Input sequences in nexus format for SVDquartets, ultraconserved elements (UCEs) dataset, with Liolaemus tenuis tenuis.Input_SVDquartets_UCEdataset_with_tenuis.nexSVDquartets output for the full data set with Liolaemus tenuis tenuis.SVDquartets output (phylogenetic tree) for the full data set with Liolaemus tenuis tenuis.Output_SVDquartets_fulldataset_with_tenuis.treSVDquartets output for the full data set without Liolaemus tenuis tenuis.SVDquartets output (phylogenetic tree) for the full data set excluding Liolaemus tenuis tenuis.Output_SVDquartets_fulldataset_without_tenuis.treSVDquartets output for the protein-coding data set with Liolaemus tenuis tenuis.SVDquartets output (phylogenetic tree) for the protein-coding data set with Liolaemus tenuis tenuis.Output_SVDquartets_protein-codingdataset_with_tenuis.treSVDquartets output for the ultraconserved elements data set with Liolaemus tenuis tenuis.SVDquartets output (phylogenetic tree) for the ultraconserved elements (UCEs) data set with Liolaemus tenuis tenuis.Output_SVDquartets_UCEdataset_with_tenuis.treIQTREE Partitions for the full data set with Liolaemus tenuis tenuisIQTREE Partitions (input) in nexus format for the full data set with Liolaemus tenuis tenuis.IQTRE_Partitions_ucesPC_withtenuis.nexIQTREE Partitions for the protein-coding data set with Liolaemus tenuis tenuisIQTREE Partitions (input) in nexus format for the protein-coding data set with Liolaemus tenuis tenuisIQTREE_Partitions_PC_withtenuis.nexIQTREE Partitions for the ultraconserved elements data set with Liolaemus tenuis tenuisIQTREE Partitions (input) in nexus format for the ultraconserved elements (UCEs) data set with Liolaemus tenuis tenuis.IQTREE_Partitions_uces_withtenuis.nexIQTREE Partitions for the full data set without Liolaemus tenuis tenuisIQTREE Partitions (input) in nexus format for the full data set excluding Liolaemus tenuis tenuis.IQTREE_Partitions_ucesPC_withouttenuis.nexIQTREE Sequences, protein-coding data set, with Liolaemus tenuis tenuis.IQTREE Sequences (input) in nexus format, protein-coding data set, with Liolaemus tenuis tenuis.IQTREE_Sequences_PC_withtenuis.nexIQTREE Sequences, ultraconserved elements data set, with Liolaemus tenuis tenuis.IQTREE Sequences (input) in nexus format, ultraconserved elements (UCEs) data set, with Liolaemus tenuis tenuis.IQTREE_Sequences_uces_withtenuis.nexIQTREE Sequences, full data set, without Liolaemus tenuis tenuis.IQTREE Sequences (input) in nexus format, full data set, excluding Liolaemus tenuis tenuis.IQTREE_Sequences_ucesPC_withouttenuis.nexIQTREE Sequences, full data set, with Liolaemus tenuis tenuis.IQTREE Sequences (input) in nexus format, full data set, with Liolaemus tenuis tenuis.IQTREE_Sequences_ucesPC_withtenuis.nexIQTREE Results, protein-coding dataset, with Liolaemus tenuis tenuis.IQTREE Results (phylogenetic tree), protein-coding dataset, with Liolaemus tenuis tenuis.Results_IQTREE__PC_withtenuis.nwkIQTREE Results, ultraconserved elements dataset, with Liolaemus tenuis tenuis.IQTREE Results (phylogenetic tree), ultraconserved elements (UCEs) dataset, with Liolaemus tenuis tenuis.Results_IQTREE_uces_withtenuis.nwkIQTREE Results, full dataset, without Liolaemus tenuis tenuis.IQTREE Results (phylogenetic tree), full dataset, excluding Liolaemus tenuis tenuis.Results_IQTREE_ucesPC_withouttenuis.nwkIQTREE Results, full dataset, with Liolaemus tenuis tenuis.IQTREE Results (phylogenetic tree), full dataset, with Liolaemus tenuis tenuis.Results_IQTREE_ucesPC_withtenuis.nwk