Abstract
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.
Highlights
Lizards of the genus Liolaemus Wiegmann 1834 are widely distributed throughout temperate South America, occurring mainly in Argentina and Chile, and in Bolivia, Brazil, Paraguay, Peru and Uruguay (Abdala & Quinteros, 2013)
Our final incomplete dataset yielded a total of 581 loci, which consisted of 538 ultra-conserved elements (UCEs) and 43 protein-coding genes
We focused on the subgenus Liolaemus by studying a sample of species allocated to its two sections, the nigromaculatus and chiliensis sections, and to seven species groups
Summary
Lizards of the genus Liolaemus Wiegmann 1834 are widely distributed throughout temperate South America, occurring mainly in Argentina and Chile, and in Bolivia, Brazil, Paraguay, Peru and Uruguay (Abdala & Quinteros, 2013). They cover a wide range of climatic regimes, from the Atacama Desert to the Valdivian rainforest, and from Mediterranean shrublands to Patagonian steppes (Donoso-Barros, 1966; Cei, 1986; Cei, 1993). Liolaemus has a long evolutionary history dating back to 18–22 million years ago (Schulte II et al, 2000; Fontanella et al, 2012). Phylogenetic relationships among species of Liolaemus have been difficult to resolve, due in part to the incomplete taxon sampling of most studies (but see Olave et al, 2014), the discordance between inferences based on molecular and morphological data (Schulte II et al, 2000; Lobo, 2001; Lobo, 2005; Vidal & Labra, 2008), and to the incongruences between nuclear and mitochondrial gene trees caused by, likely, incomplete lineage sorting and hybridization (e.g., Olave et al, 2011)
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