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The smooth snake Coronella austriaca (Laurenti, 1768) is distributed across the western Palearctic throughout north‐central, southern Europe and western Asia. So far, only few phylogenetic studies, based on mitochondrial DNA, have been carried out on this species focusing mainly on the Iberian Peninsula and northern Europe, leaving unstudied some of important areas of its distribution. This study aims to cover this gap and to explore the phylogenetic relationships between the populations of in the Eastern Mediterranean and to detect possible historical refugia. With this objective, total genomic DNA was extracted from samples originated from the Balkans, Anatolia and a large part of Europe. Two mitochondrial (cyt b, 16S) and six nuclear (BDNF, NKTR, RAG1, RAG2, MC1R and PRLR) markers were combined for phylogenetic and chronophylogenetic analyses. The different analyses confirmed previous phylogeographic hypothesis showing the presence of several well‐supported clades distributed in Anatolia, Central Europe, Eastern Europe, Western Europe, the Balkans and the Iberian Peninsula and cryptic diversity within Anatolia and the Balkans. Moreover, dating analysis confirmed the diversification of the species during the Pleistocene, as well as the role of the Southern Balkans and Anatolia region as refugia during this period. [ABSTRACT FROM AUTHOR]

Lacerta pamphylica and Lacerta trilineata are two currently recognized green lizard species with a historically problematic taxonomy. In cases of tangled phylogenies, next‐generation sequencing and double‐digest restriction‐site‐associated DNA protocols can provide a wealth of genomic data and resolve difficult taxonomic issues. Here, we generated genome‐wide SNPs and mitochondrial sequences, and applied molecular species delimitation approaches to provide a stable taxonomy for the Aegean green lizards. Mitochondrial gene trees, genetic cluster delimitation and population structure analyses converged into recognizing the populations of (a) L. pamphylica, (b) east Aegean islands, Anatolia and Thrace (diplochondrodes lineage), (c) central Aegean islands (citrovittata), and (d) remaining Balkan populations and islands (trilineata), as separate clusters. Phylogenomic analyses revealed a split into two major clades, east and west of the Aegean Barrier, unambiguously showing a sister–clade relationship between pamphylica and diplochondrodes, rendering L. trilineata paraphyletic. Species delimitation models were tested in a Bayesian framework using the genomic SNPs: lumping all populations into a single 'species' had the lowest likelihood but the current taxonomy was also outperformed by all other models. All lines of evidence support the Pamphylian green lizard as a valid species; thus, east Aegean L. trilineata should also be considered a distinct species under the name Lacerta diplochondrodes. Finally, evidence from the mitochondrial and nuclear genomes is overwhelmingly in favour of recognizing the morphologically distinct Cycladian green lizards as a distinct species. We propose their elevation to full species under the name Lacerta citrovittata. All remaining insular and continental populations of the Balkan Peninsula represent the species L. trilineata. [ABSTRACT FROM AUTHOR]