Species with wide‐range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single‐nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.

Snake genomes attract significant attention from multiple disciplines, including medicine, drug bioprospection, and evolutionary biology. However, genomic research within the Viperidae family has mostly focused on the subfamily Crotalinae, while the true vipers (Viperinae) have largely been overlooked. European vipers ( Vipera ) have been the subject of extensive research due to their phylogeographic and ecological diversification, as well as their venoms. Nevertheless, phylogeography and systematics in this genus have primarily relied on biased information from mitochondrial genes, which fail to capture the likely effects of introgression and are prone to biases. On the other hand, venom research in this group has been conducted predominantly through proteomics alone. In this study, we generated chromosome‐level genome assemblies for three Vipera species and whole‐genome sequencing data for 94 samples representing 15 Vipera lineages. This comprehensive dataset allowed us to disentangle the phylogenomic relationships of this genus, affected by mito‐nuclear discordance and pervaded by ancestral introgression. Population‐level analyses in the Iberian Peninsula, where the three oldest lineages within Vipera meet, revealed signals of recent adaptive introgression between old‐diverged and ecologically dissimilar species, whereas chromosomal rearrangements isolate species occupying similar niches. Finally, using transcriptomic and proteomic data, we characterised the Vipera toxin‐encoding genes, in which opposing selective forces were unveiled as common drivers of the evolution of venom as an integrated phenotype.

A global genome database of all of Earth's species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ~1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 34 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.

Semi-natural environments within cities can provide habitats for vulnerable reptile species. Better understanding of their habitat use and home range sizes is important for their conservation. We investigated the spatial ecology of Caspian whipsnakes (Dolicophis caspius) in a peri-urban habitat in Budapest, Hungary. We used radiotelemetry to track five adult snakes and analyzed their microhabitat preferences, home range sizes and daily movements. The Caspian whipsnakes intensively utilized areas covered with woody vegetation, with a high density of hibernacula. The tracked snakes used an area of 40.15 ha during the activity period from spring to autumn, but for the winter, they withdrew to a central area of 1.75 ha, abundant in hibernacula. During the activity period the individual home range sizes varied between 6.1 and 15.5 ha, estimated using the minimum convex polygon (MCP); however, for the entire datasets of the individuals, the adaptive kernel method gave the highest mean (13.8 ha), while the LoCoH-R yielded the smallest home ranges (5.19 ha). We found that the average daily displacement for the different individuals ranged between 12.6 and 36.6 m during their main activity season. In the study area, the whipsnakes currently have enough space for foraging, but the restricted spatial distribution of hibernacula, which is mainly available in the central dry rocky forest and partly in the shrubby areas, can limit the extent of the suitable habitat. Human activities and anthropogenic disturbances, especially around hibernacula, may exert pressure on this peri-urban snake population.