Striking Suture Zone Mismatch Between Nuclear and Mitochondrial Markers in North African Chalcides ocellatus (Squamata: Scincidae)

Linnaean and Wallacean shortfalls remain pervasive even among common and widespread Mediterranean taxa, limiting our understanding of evolutionary history and species boundaries. The Ocellated Skink Chalcides ocellatus complex illustrates this issue, with disputed subspecific taxonomy and deep mitochondrial divergences across North Africa and the Middle East. We combined mitochondrial (cytochrome b; 189 individuals) and nuclear markers (four loci; 2339 bp concatenated; 44 individuals) to test whether mitochondrial lineages reflect independently evolving units and to assess gene flow across contact zones. Both nuclear and mitochondrial DNA analyses recovered four clades and haplogroups, respectively. While deeper relationships among these lineages remained unresolved in both phylogenies precluding potential topological comparisons, geographical comparisons revealed marked cytonuclear discordances. In the Maghreb, the mitochondrial contact zone between Western and Eastern haplogroups occurs in Kabylia (eastern Algeria), whereas the nuclear transition between corresponding subtypicus and tiligugu subspecies lies ~650 km further west near the Morocco—Algeria border. Most individuals across this region carry Western mtDNA haplotypes within an ‘eastern’ tiligugu nuclear background, indicating extensive mitochondrial introgression. Similar discordance was also observed in Egypt between C. humilis and C. o. ocellatus . Nuclear data supports the evolutionary distinctiveness of the four main lineages but provide limited resolution regarding their deeper relationships. The large geographic displacement between mitochondrial and nuclear suture zones strongly suggests historical introgression rather than incomplete lineage sorting. Our results confirm the reproductive isolation of C. humilis , highlight the independence of both Maghreb ( subtypicus and tiligugu ) lineages, and demonstrate that mtDNA alone is unreliable for delimiting taxa in this complex, calling for genome‐wide reassessment of species boundaries.