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In this study, we include 207 specimens belonging to all 12 recognized species of the genus<jats:italic>Stenodactylus<\/jats:italic>. Molecular phylogenies inferred using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (c-<jats:italic>mos<\/jats:italic>and<jats:italic>RAG<\/jats:italic>-2) markers are employed to obtain a robust time-calibrated phylogeny, as the base to investigate the inter- and intraspecific relationships and to elucidate the biogeographical history of<jats:italic>Stenodactylus<\/jats:italic>, a genus with a large distribution range including the arid and hyper-arid areas of North Africa and Arabia.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The phylogenetic analyses of molecular data reveal the existence of three major clades within the genus<jats:italic>Stenodactylus<\/jats:italic>, which is supported by previous studies based on morphology. Estimated divergence times between clades and sub-clades are shown to correlate with major geological events of the region, the most important of which is the opening of the Red Sea, while climatic instability in the Miocene is hypothesized to have triggered diversification. High genetic variability is observed in some species, suggesting the existence of some undescribed species. The<jats:italic>S. petrii<\/jats:italic>-<jats:italic>S. stenurus<\/jats:italic>species complex is in need of a thorough taxonomic revision. New data is presented on the distribution of the sister species<jats:italic>S. sthenodactylus<\/jats:italic>and<jats:italic>S. mauritanicus<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The phylogenetic hypothesis for the genus<jats:italic>Stenodactylus<\/jats:italic>presented in this work permits the reconstruction of the biogeographical history of these common desert dwellers and confirms the importance of the opening of the Red Sea and the climatic oscillations of the Miocene as major factors in the diversification of the biota of North Africa and Arabia. Moreover, this study traces the evolution of this widely distributed and highly specialized group, investigates the patterns of its high intraspecific diversity and elucidates its systematics.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2148-12-258","type":"journal-article","created":{"date-parts":[[2013,9,17]],"date-time":"2013-09-17T10:41:45Z","timestamp":1379414505000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":80,"title":["Conquering the Sahara and Arabian deserts: systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae)"],"prefix":"10.1186","volume":"12","author":[{"given":"Margarita","family":"Metallinou","sequence":"first","affiliation":[]},{"given":"Edwin Nicholas","family":"Arnold","sequence":"additional","affiliation":[]},{"given":"Pierre-Andr\u00e9","family":"Crochet","sequence":"additional","affiliation":[]},{"given":"Philippe","family":"Geniez","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 Carlos","family":"Brito","sequence":"additional","affiliation":[]},{"given":"Petros","family":"Lymberakis","sequence":"additional","affiliation":[]},{"given":"Sherif","family":"Baha El Din","sequence":"additional","affiliation":[]},{"given":"Roberto","family":"Sindaco","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Robinson","sequence":"additional","affiliation":[]},{"given":"Salvador","family":"Carranza","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,12,31]]},"reference":[{"key":"2260_CR1","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1016\/j.jafrearsci.2005.07.020","volume":"43","author":"W Bosworth","year":"2005","unstructured":"Bosworth W, Huchon P, McClay K: The Red Sea and Gulf of Aden Basins. 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