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Fig. S1 Maximum likelihood (ML) phylogenetic tree on 239 Hemidactylus specimens based on 667 bp of one nuclear (mc1r) loci.

Fig. S2 Statistical parsimony nuclear allele networks of prdx4 and mc1r loci with colors corresponding to TCS mitochondrial lineages.

Fig. S3 Ultrametric gene tree based on the mitochondrial data from Hemidactylus.

Fig. S4 Bayesian species delimitation results for Hemidactylus from Socotra assuming 13 putative species for clade I, and 6 species for clades II and III.

Table S1. Details of the 144 Hemidactylus from the Socotra Archipelago included in the present study (25 H. pumilio, 35 H. inintellectus, 22 H. dracaenacolus, 14 H. granti, 9 H. forbesii, 19 H. oxyrhinus and 20 H. homoeolepis).

Table S2. Hemidactylus specimens from mainland Africa (Somalia and Egypt) and southwest Asia (Arabia and Iran) belonging to the Arid Clade plus two specimens of H. flaviviridis from the Asian Clade (Carranza & Arnold 2006).

Table S3. Amplification conditions and information on markers used in this study.

Table S4. Datasets, models and parameter setting for each particular analysis performed.

Table S5. Divergence time estimates (in Ma) for Socotran Hemidactylus derived from the BEAST and *BEAST analyses (see Figs. 2 and 3).

Table S6. Pairwise ΦST mtDNA divergences among lineages within: H. inintellectus, H. homoeolepis and H. pumilio.

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