Mitochondrial markers are widely used as a first approach in determining evolutionary relationships among vertebrate taxa at different hierarchical scales. Cytochrome b and cytochrome oxidase I are among the most common markers; they are particularly useful in phylogeography and species delineation studies. Simulation and empirical studies show that increasing the taxon sampling has a clear and strong effect on the accuracy of the inferred trees and therefore on hypothesized phylogenetic relationships (and eventually in new taxonomic rearrangements); this should be considered in the design of studies. The lizard genus Liolaemus is widely distributed in southern South America and includes more than 250 described species. The number of taxa and the distribution of Liolaemus species/populations makes them a good model for testing different hypotheses in systematics. We studied two Liolaemus species, Liolaemus nigroviridis and L. monticola as focal species to evaluate their monophyly and the influence of adding new samples from related taxa in the resulting phylogenies. We performed phylogenetic analyses (maximum likelihood and Bayesian inference) using 141 sequences of the mitochondrial DNA Cytochrome b (cyt-b) of 11 Liolaemus species. Our study show that using intensive taxon sampling for phylogenetic reconstructions, two species (L. uniformis and L. nitidus) are placed within the clades of the two focal species (L. nigroviridis and L. monticola, respectively). Our study confirms the importance of taxon sampling to infer more accurate phylogenetic relationships, particularly to reveal hidden polyphyly or paraphyly, which may have a strong impact on taxonomic proposals and/or inferring cryptic diversity.
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