Unveiling patterns of genetic differentiation across insular distributions is relevant for biogeographic and conservation reasons. In the Indian Ocean, surprisingly, little is known regarding the genetic structure of many taxa across the Seychelles Islands, despite their importance as old Gondwanic islands, part of the western Indian Ocean biodiversity hotspot. In recent molecular studies, a northeastern–southwestern subdivision pattern across the granitic islands has been uncovered within some species. Pamelaescincus gardineri, a Seychelles endemic skink and possibly one of the deepest lineages of Afro-Malagasy ‘scincines’, is another species widespread across these islands, within which undescribed variation may occur. Both nuclear (c-mos and MC1R) and mitochondrial (Cyt-b) DNA data were used to address this issue. Mitochondrial DNA shows a marked northeastern–southwestern structure of two highly divergent clades, similar to the pattern previously described in other reptile species. Nuclear DNA seems to corroborate this pattern, although these markers were much less informative. Migration between the two island groups was identified, and gene flow between the two mtDNA lineages is likely, the extent of which remains to be fully explored. This will require more variable nuclear markers and more detailed sampling across the island of Mahé. A suitable assessment of morphological variation is also needed prior to any taxonomic revision of this species. From a conservation point of view, however, these lineages should already be treated as two distinct evolutionary units.

citb_pam_outgroup_haps.nex.conconsensus tree file from mrbayes phylogenetic analyses (BI)citb_pam_outgroup_haps_phy_phyml_treetree file from maximum likelihood analysis with bootstrapscmos_inferred_haplotypesNuclear haplotypes from C-mos gene fragment inferred using PHASE (see details in article) and used for haplotype network constructionmc1r_inferred_haplotypesNuclear haplotypes inferred using PHASE (see details in publication) for the MC1R dataset and used for haplotype network construction