Data from: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data

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.