The Wall Lizards of the Balkan Peninsula: Tackling Questions at the Interphase of Phylogenomics and Population Genomics

[Abstract] Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of “P. tauricus” consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of “P. erhardii” comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis’ species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.This study was funded by NSFR 2007-2013 programme for development, European Social Fund, Operational Programme, Education and Lifelong Learning investing in knowledge society, Ministry of Education and Religious Affairs, Managing Authority, Co-financed by Greece and the European Union. Part of this work was funded by the Klaus Tschira Foundation, by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 / AEI / 10.13039/501100011033), and by the Xunta de Galicia and FEDER funds of the EU under the Centro de Investigación de Galicia accreditation 2019-2022 (ED431G 2019/01)Xunta de Galicia; ED431G 2019/0