The Mediterranean Basin has been the stage of various paleogeographical events that have helped shape the genetic diversity and phylogeographic patterns of numerous taxa. In particular, the connection between the Mediterranean Sea and the Atlantic Ocean closed about 5.96 million years ago (Mya) causing the Mediterranean Sea to desiccate during the Messinian Salinity Crisis, an event that ended 5.33 Mya, with the formation of the Strait of Gibraltar [1–3]. The opening of the Strait led to the separation of terrestrial faunal elements in the region into allopatric units , as in the cases of the spiny-footed lizards Acanthodactylus erythrurus , or the West Mediterranean newts of the genus Pleurodeles . Regarding the study performed on the spiny-footed lizards, the Iberian Acanthodactylus e. erythrurus apparently became separated from its North African relatives around 5 Mya , and it was also the refilling of the Strait of Gibraltar that may have led to the separation between Pleurodeles waltl and the North African newts Pleurodeles nebulosus and Pleurodeles poireti . Another extremely influential event occurred during the Pleistocene when sea level and climate oscillations led to repeated isolation and connection of taxa [6, 7], and consequent population differentiation [e.g. [8, 9]]. At a more local scale, the Atlas Mountains originated during the mid- to late Miocene as a consequence of the impact between the Eurasian and African plates , and seem to have been an important barrier for allopatric speciation [e.g. [11, 12]]. All these events have made the Mediterranean Basin a centre for genetic differentiation that, in some cases, has led to vicariant speciation, partially explaining the observed high levels of biodiversity [13, 14].
Tarentola geckos are members of the Family Phyllodactylidae , and the genus is currently comprised of 21 different species [16–20]. Tarentola is distributed across the Mediterranean Basin and on many Macaronesian islands, including Madeira, the Selvages, the Canary and Cape Verde islands [21, 22]. On the other side of the Atlantic Ocean, three species are accepted: T. americana, from Cuba and the Bahamas; the recently described T. crombiei  endemic to Cuba; and the probably extinct T. albertschwartzi , known from a single specimen allegedly from Jamaica. Since all the Macaronesian islands are volcanic, and therefore have never been connected to the mainland , the most likely hypothesis is that these geckos reached these islands by transmarine dispersal [21, 22]. Regarding the Neotropical members of Tarentola, these also seem to be the result of a post-Gondwanan dispersal from the Old World [21, 24, 25].
The Mediterranean Basin harbours nine different species of Tarentola, namely T. mauritanica, T. chazaliae, T. deserti, T. boehmei, T. annularis, T. neglecta, T. mindiae, T. ephippiata, and T. fascicularis, a former subspecies of T. mauritanica recently elevated to the species level . Although several molecular studies have been published for some of these species, these have always been focused on one [26–30] or a few taxa [17, 19, 21, 24, 25]. Moreover, all species of Mediterranean Tarentola have never been assembled into a phylogenetic context using a multilocus approach. The majority of the studies have been focused on the phylogeographic patterns of the Moorish gecko T. mauritanica. This species is characterized by an extremely high mitochondrial genetic variation in North Africa, which led to the hypothesis that this taxon could be, in fact, a species complex [29, 30]. In contrast, the European populations of the Moorish gecko have very low mitochondrial diversity, initially thought to be the result of a recent introduction [21, 28–30], probably human-mediated. However, a recent study  has demonstrated that this low mtDNA variability that characterizes the European populations of T. mauritanica could be the result of genetic hitch-hiking, and not solely due to a recent colonization event.
Additionally, several studies have demonstrated the paraphyly of T. mauritanica with respect to T. angustimentalis from the Canary Islands [21, 26–30]. A recent study  concluded that populations of T. fascicularis from Libya and central Tunisia constitute a monophyletic lineage and, together with T. mindiae and T. neglecta, represent the sister group of T. deserti. On the other hand, previous mtDNA studies indicated that T. fascicularis is paraphyletic with respect to T. deserti [26–30], although sampling was limited in all cases.
Therefore, in order to estimate an evolutionary hypothesis able to explain the previously mentioned patterns we have increased the taxonomic and geographic sampling in this study. Further, we used two mitochondrial, and four nuclear markers in order to better evaluate the inter- and intraspecific relationships within the genus Tarentola from the Mediterranean Basin.