| Abstract |
Podarcis wall-lizards are included phylogenetically into the Balkan species group and into the “P. tauricus” species subgroup that consists of P. gaigeae, P. melisellensis, P. milensis and P. tauricus. This subgroup is distributed in the western and south Balkans, an area that is considered as an herpetofauna biodiversity hotspot. A plethora of endemic species can be found closely to the external Hellenides (Pindos mountain range) that comprise one of the most important biogeographic barriers in the Balkan Peninsula. The four focal species are characterized by obscure phylogenetic relationships among them, as well as among their populations. The general scope of the present thesis is to investigate the evolutionary history of the “P. tauricus” species subgroup by using a dataset containing samples from the entire species distribution and by producing different types of genetic and genomic data (Sanger sequencing, Next Generation Sequencing, Microsatellites). In order to achieve the above goal a large variety of analyses were performed that includes phylogenetic analyses (Second Chapter), phylogenomic analyses (Third Chapter), population structure analyses (Forth Chapter), species delimitation (Fifth Chapter), species distribution modelling (Fifth Chapter), divergence time estimations (Sixth Chapter), construction of mitochondrial haplotype networks (Sixth Chapter), and demographic analyses (Sixth Chapter). According to the results of the phylogenetic and phylogenomic analyses the “P. tauricus” species subgroup consists of five major phylogenetic clades that correspond to the taxa (in an order of evolutionary diversification) P. melisellensis, P. milensis, P. gaigeae, P. t. ionicus and P. t. tauricus/P. t. thasopulae. The taxon of P. t. ionicus displays hidden genetic diversity, comprising of five geographically isolated phylogenetic subclades with genetic distances of species level among them. In the context of taxonomical revision within the “P. tauricus” species subgroup and in congruence with the results of the species delimitation we propose the synonymy between some of the subspecies and the existence of a distinct Greek-Albanian species (or species complex) with the provisional name P. ionicus. The relationships among the subclades (a – e) of P. ionicus are resolved with the help of the genomic data in the following order of evolutionary diversification: subclade α (south Ionian islands), subclade e (southwestern Albania, northwestern Greece and western Peloponnisos), subclade c (northeastern Peloponnisos) and subclade d (central and southeastern Peloponnisos). Subclade b (western central Greece) is either a sister subclade to subclade a (Sanger sequencing), or closely related to subclade d (ddRADseq data). The results of population structure analyses shown that there is a general concordance between the revealed clusters and the phylogenetic clades and subclades (or group of them). Most of the resulted clusters consisted of pure individuals (>90% assignment probability), however in some cases it was observed that the daughter clusters of a parental one (e.g. the case of P. t. tauricus) contained also a small percentage of non-pure individuals originated from a different geographic area. Furthermore, there were cases in which individuals originated from the same geographic locality were grouping within different clusters. The species distribution analyses revealed that, in general, there are distinct putative distributions based on the environmental data among the taxa of the focal species subgroup. Finally, taking into account all the above data and analyses and in combination with the existing knowledge on the Paleogeography and the Paleoclimatology of the Balkans a phylogeographic scenario is proposed, which is taking place in several main stages. Before ~14-9 my the ancestral of “P. tauricus” species subgroup started to colonize the Balkan peninsula. The first divergence event happened at ~8-7 with the ancestror of P. melisellensis being isolated south of the Dinarides. Before ~7-6 my ago the distribution of the ancestor of the rest of the species includes the eastern and western to the External Hellenides continental Greece, Peloponnisos, central Greece, Skyros area, and Milos area. At ~5-4 mya the end of the Messinian salinity crisis caused the isolation of the aforementioned areas and the diversification of the isolated populations inhabiting these areas led to the forming of P. milensis, P. gaigeae, P. t. ionicus and P. t. tauricus / P. t. thasopulae. Before ~4-3 my the diversification of P. melisellensis and P. ionicus into their subclades is happening and during the time period of ~2,5-0,018 mya the populations were experienced the affection of the glacial and inter-glacial cycles of Pleistocene that formed in a great manner the current genetic diversity of the species. After the end of the last glacial period (~18.000 years ago) and until today the populations started to expand gradually, especially at their northern distribution limits.
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