Hidden diversity in the driest desert on Earth: genomics unveils cryptic diversity in an ancient South American gecko lineage (Phyllodactylidae, Garthia)

Quantifying and delimiting biodiversity is a critical challenge in modern biology, particularly in taxa where species boundaries are unclear or poorly defined. In many cases, traditional morphological approaches are insufficient or even misleading when delimiting taxonomic units. Modern genomic methods offer a powerful tool to gain an in-depth perspective of evolutionary history and genetic variation across populations. The Chilean Marked Geckos (genus Garthia) currently comprise two species, G. gaudichaudii and G. penai, endemic to the semi-arid coastal regions of North-Central Chile. Although additional species/subspecies have been proposed, a recent study went so far as to suggest that just one species should be recognized. However, no study to date has evaluated their diversity using genetic tools. For the first time, we used phylogenomic and population genetic methods to better understand diversity across the entire distribution of Garthia. Using both mtDNA and nDNA data, we reconstruct the phylogeny, assess population structure, and delimit species. Our phylogenetic analyses reveal deep evolutionary divergence strongly supporting the existence of at least the two nominate species. However, our species delimitation and population structure analyses suggest alpha-level diversity could be even higher, with evidence supporting a cryptic species complex of between three and eleven species, including deep divergences between geographically proximate populations. We discuss the impact these findings have on our understanding of Chilean gecko diversity and biogeographic patterns in the world's driest desert.