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.
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.tre
ASTRAL-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.tre
ASTRAL-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.tre
ASTRAL-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.tre
ASTRAL-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.nwk
ASTRAL-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.nwk
ASTRAL-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.tree
ASTRAL-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.tre
Input 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.nex
Input 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.nex
Input 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.nex
Input 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.nex
SVDquartets 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.tre
SVDquartets 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.tre
SVDquartets 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.tre
SVDquartets 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.tre
IQTREE Partitions for the full data set with Liolaemus tenuis tenuis
IQTREE Partitions (input) in nexus format for the full data set with Liolaemus tenuis tenuis.
IQTRE_Partitions_ucesPC_withtenuis.nex
IQTREE Partitions for the protein-coding data set with Liolaemus tenuis tenuis
IQTREE Partitions (input) in nexus format for the protein-coding data set with Liolaemus tenuis tenuis
IQTREE_Partitions_PC_withtenuis.nex
IQTREE Partitions for the ultraconserved elements data set with Liolaemus tenuis tenuis
IQTREE Partitions (input) in nexus format for the ultraconserved elements (UCEs) data set with Liolaemus tenuis tenuis.
IQTREE_Partitions_uces_withtenuis.nex
IQTREE Partitions for the full data set without Liolaemus tenuis tenuis
IQTREE Partitions (input) in nexus format for the full data set excluding Liolaemus tenuis tenuis.
IQTREE_Partitions_ucesPC_withouttenuis.nex
IQTREE 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.nex
IQTREE 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.nex
IQTREE 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.nex
IQTREE 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.nex
IQTREE Results, protein-coding dataset, with Liolaemus tenuis tenuis.
IQTREE Results (phylogenetic tree), protein-coding dataset, with Liolaemus tenuis tenuis.
Results_IQTREE__PC_withtenuis.nwk
IQTREE Results, ultraconserved elements dataset, with Liolaemus tenuis tenuis.
IQTREE Results (phylogenetic tree), ultraconserved elements (UCEs) dataset, with Liolaemus tenuis tenuis.
Results_IQTREE_uces_withtenuis.nwk
IQTREE Results, full dataset, without Liolaemus tenuis tenuis.
IQTREE Results (phylogenetic tree), full dataset, excluding Liolaemus tenuis tenuis.
Results_IQTREE_ucesPC_withouttenuis.nwk
IQTREE Results, full dataset, with Liolaemus tenuis tenuis.
IQTREE Results (phylogenetic tree), full dataset, with Liolaemus tenuis tenuis.
Results_IQTREE_ucesPC_withtenuis.nwk