Gene flow and evolutionary divergence between lineages of the Lacerta viridis complex

The European green lizards of the Lacerta viridis complex consist of two closely related species, L. viridis and L. bilineata. A recent study indicated that their split occurred less than 3 million years ago and are experiencing gene flow. Recently, a third lineage, referred to as the “Adriatic” lineage was described within the L. viridis complex distributed from Slovenia to Greece. However, it is currently unknown whether there is gene flow between the Adriatic lineage with L. viridis or L. bilineata and the evolutionary processes involved in their speciation. We hypothesized that their divergence occurred in the presence of gene flow between multiple lineages and tissue-specific factors are involved in their divergence. In this study we sequenced the whole genome of an Adriatic lineage individual and tested for the presence of gene flow amongst the three lineages (L. viridis, L. bilineata and Adriatic). Additionally, we sequenced transcriptomes from multiple tissues to understand tissue-specific divergence. We detected the presence of gene flow between the Adriatic lineage and L. bilineata, and the Adriatic lineage was deeply branched and seems to be positioned closer to L. viridis. Ovary specific expressed genes experience accelerated evolution contributing to their divergence. Ongoing gene flow, assortative mating, and tissue-specific evolution seem to play a major role in driving their speciation.