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Hybrid zones are natural laboratories allowing insights in genetic processes like lineage diversification, speciation and introgression. Using large sampling, 15 microsatellite loci and a mitochondrial marker, we examined the Pyrenean contact zone of three pond turtle taxa (Emys orbicularis orbicularis, E. o. galloitalica, E. o. occidentalis). The Pyrenees are a biogeographically important region separating many lineages endemic to the Iberian Peninsula from their Western European counterparts. We discovered limited admixture, reflecting a complex biogeographic scenario. Simulations using Approximate Bayesian Computing supported that E. o. orbicularis invaded the Iberian Peninsula in the Holocene, circumventing the Pyrenees along the Mediterranean coast, and hybridized in the northern peninsula with the local coastal subspecies galloitalica, and to a lesser extent, with occidentalis. While E. o. occidentalis, and in particular E. o. orbicularis, expanded their ranges considerably during Holocene warming, E. o. galloitalica remained largely confined to its former Iberian refuge. Admixture among the three taxa is surprisingly low, and a future taxonomic investigation that includes the unstudied subspecies of E. orbicularis from North Africa, Eastern Europe and Asia has to determine whether their current status properly reflects their evolutionary divergence or whether certain taxa should be regarded as full species.

Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.