Conclusions
The Balearic lizard P. lilfordi has recently entered the genomic era, offering a new interesting insular system to explore trends in vertebrate genome evolution. Our study presents a first use of theP. lilfordi genome to reliably mapped extensive SNP data. Comparative analysis using independent methods and datasets provided robustness to our findings. We found support for the origin of this species colonization in the Mallorca Island, confirming previous proposals and providing a framework for future studies of the evolutionary trajectories in genome diversification for this insular species. The substantial genetic diversity observed in these effectively closed populations suggest that they have potential mechanisms to partially counteract genetic drift and inbreeding depression that are worth further investigation by genome resequencing and inclusion of additional populations. Furthermore, integration of population demographic data (ongoing) and collection of detailed phenotypic data, still scarce for this species, will be critical to evaluate the genomic plasticity and ability to persist of these insular populations.