Grass snakes are widely distributed across the Western Palearctic. Recent phylogeographic studies provided evidence that three distinct parapatric species exist. Two of these occur in Italy, Natrix helvetica and N. natrix, and a contact zone between both taxa has been suggested for north‐eastern Italy. Moreover, previous investigations revealed for the Italian Peninsula a complex phylogeographic structure. Using mtDNA sequences and microsatellite loci, we examined the situation for mainland Italy, Sicily, Sardinia, and Corsica. Our study confirmed the occurrence of N. natrix in north‐eastern Italy. Cline analyses revealed limited gene flow between N. helvetica and N. natrix across a narrow hybrid zone. Within N. helvetica, conflicting patterns of mitochondrial and nuclear genomic differentiation were revealed. Three nuclear genomic clusters were found; one of them corresponded to no fewer than five distinct and, in part, deeply divergent and ancient mitochondrial lineages from mainland Italy and Sicily. This cluster was paraphyletic with respect to the two remaining mitochondrial lineages, each of which matched with another nuclear genomic cluster (one from Corsica plus Sardinia and another one from western Europe north of the Alps). This unexpected pattern most likely results from mainly male‐mediated gene flow and female philopatry combined with population‐density‐dependent processes such as ‘high‐density blocking’. With respect to taxonomy, we propose to synonymize N. h. lanzai Kramer, 1970 with N. h. sicula (Cuvier, 1829), acknowledging their lacking nuclear genomic differentiation. The studied hybrid zone of N. h. helvetica and N. h. sicula in Italy is wide, with a smooth cline for nuclear markers, supporting their subspecies status. We found no evidence for the distinctiveness of the two subspecies from Corsica (N. h. corsa) and Sardinia (N. h. cetti), suggesting their synonymy, but refrain from taxonomic conclusions because of small sample sizes and the endangered status of the Sardinian taxon.

Using two mitochondrial DNA fragments and 13 microsatellite loci, we examined the phylogeographic structure and taxonomy of two codistributed snake species (Natrix natrix, N. tessellata) in their eastern distribution area, with a focus on Turkey. We found evidence for frequent interspecific hybridization, previously thought to be extremely rare, and for backcrosses. This underscores that closely related sympatric species should be studied together because otherwise the signal of hybridization will be missed. Furthermore, the phylogeographic patterns of the two species show many parallels, suggestive of a shared biogeographic history. In general, the phylogeographies follow the paradigm of southern richness to northern purity, but the dice snake has some additional lineages in the south and east in regions where grass snakes do not occur. For both species, the Balkan Peninsula and the Caucasus region served as glacial refugia, with several mitochondrial lineages occurring in close proximity. Our results show that the mitochondrial divergences in both species match nuclear genomic differentiation. Yet, in the former glacial refugia of grass snakes there are fewer nuclear clusters than mitochondrial lineages, suggesting that Holocene range expansions transformed the glacial hotspots in melting pots where only the mitochondrial lineages persisted, bearing witness of former diversity. On the other hand, the deep mitochondrial divergences in N. tessellata across its entire range indicate that more than one species could be involved, even though lacking microsatellite data outside of Turkey prevent firm conclusions. On the contrary, our microsatellite and mitochondrial data corroborate that N. megalocephala is invalid and not differentiated from sympatric populations of N. natrix. For Cypriot grass snakes, our analyses yielded conflicting results. A critical assessment of the available evidence suggests that N. natrix is a genetically impoverished recent invader on Cyprus and taxonomically not distinct from a subspecies also occurring in western Anatolia and the southern Balkans. Based on combined mitochondrial and nuclear genomic evidence we propose that for grass snakes the following subspecies should be recognized in our study region: (1) Natrix natrix vulgaris Laurenti, 1768, southeastern Central Europe and northern Balkans; (2) Natrix natrix moreoticus (Bedriaga, 1882), southern Balkans, western Anatolia, and Cyprus; and (3) Natrix natrix scutata (Pallas, 1771), eastern Anatolia, Caucasus region, Iran, northeastern distribution range (from eastern Poland and Finland to Kazakhstan and the Lake Baikal region). Thus, Natrix natrix cypriaca (Hecht, 1930) becomes a junior synonym of N. n. moreoticus and Natrix natrix persa (Pallas, 1814) becomes a junior synonym of N. n. scutata. Due to insufficient material, we could not resolve the status of Natrix natrix syriaca (Hecht, 1930) from the Gulf of İskenderun, southeastern Turkey.

We examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most likely the result of human-mediated long-distance dispersal. For N. helvetica, we identified a southern and a northern population cluster, connected by broad-scale gene flow in a unimodal hybrid zone running across France. This pattern either reflects genetic divergence caused by allopatry in two microrefuges and subsequent secondary contact or introgression of foreign alleles into the southern cluster.

Based on 1031 samples of grass snakes from Central Europe, we examine the recently reported occurrence of the southern subspecies of the barred grass snake (Natrix helvetica sicula) in southern Bavaria, Germany. Using 13 microsatellite loci and mtDNA coding for the cytb gene and the partial ND4 gene plus adjacent tRNAs, we show that N. h. sicula is restricted to a few river valleys (Inn, Isar, Loisach) in southernmost Bavaria and adjacent Tyrol, Austria. At the widening of the river valleys into the pre‐Alpine plains, N. h. sicula hybridizes locally with the common grass snake (Natrix natrix) in a bimodal hybrid zone. Our study provides evidence that Central Europe was colonized by Natrix helvetica over two distinct immigration routes. In addition to the previously known western route of the nominotypical subspecies, leading to the colonization of the Rhine region, N. h. sicula crossed the Alps, most likely using the Brenner Pass and/or the Reschen Pass. Our study underlines that the Alps are not an impermeable biogeographic barrier, as often assumed. North of the Alps, the combination of geographic setting (occurrence of N. h. sicula in sheltered Alpine valleys) and population‐density‐dependent blocking of immigrants by the resident species (N. natrix), acting in concert with intrinsic genetic factors, prevented the formation of a geographically more extended hybrid zone. Unlike N. helvetica, the two subspecies of N. natrix hybridize north of the Alps broadly, in accordance with their better genetic compatibility. Many populations of the resident Central European subspecies (Natrix natrix natrix) have been “genetically swamped” by Natrix natrix vulgaris immigrating from the Balkans. This led to the complete replacement of N. n. natrix by N. n. vulgaris in some regions, where today only the mtDNA of the nominotypical subspecies persists.

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) is presented in a digital form. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed as part of a project to link phenotypic differences between mammals to differences in their genomes using Forward Genomics. Apart from genomes this approach requires information on homologous phenotypes that are numerically encoded (presence-absence; multistate character coding*) in a matrix. MaTrics provides these data, links them to at least one reference (e.g., literature, photographs, histological sections, CT-scans, or museum specimens) and makes them available in a machine actionable NEXUS-format. By making the data computer readable, MatTrics opens a new way for digitizing collections. Currently, MaTrics covers 147 mammalian species and includes 207 characters referring to structure, morphology, physiology, ecology and ethology. Researching these traits revealed substantial knowledge gaps, highlighting the need for substantial phenotyping efforts in the genomic era. Using the trait information documented in MaTrics, previous Forward Genomics screens identified changes in genes that are associated with various phenotypes, ranging from fully-aquatic lifestyle to dietary specializations. These results motivate the continuous expansion of phenotype information, both by filling research gaps or by adding additional taxa and traits. MaTrics is digitally available online within the data repository Morph·D·Base (www.morphdbase.de).

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We examined the mitochondrial identity of Aegean Natrix natrix moreotica representing different morphotypes, with a focus on new material from Milos and Skyros. We found no correlation between distinct morphotypes and mitochondrial identity. Our results support that grass snake populations are polyphenetic and that southern subspecies, including island populations, show a higher variability than northern ones.