Through genomic phylogeography, previously unrecognised biodiversity can be revealed. The alpine newt serves as a case in point: this taxon carries highly distinct mtDNA clades and has a severely fragmented range. We obtain genome-wide data with target enrichment by sequence capture to delineate cryptic species and disentangle their phylogenetic relationships. Furthermore, we explore potential niche divergence and glaciation-driven distribution dynamics. On the basis of the uncovered genetic structure, we distinguish five main groups that we propose should be treated as distinct species. Limited interspecific genetic admixture often occurs away from current contact zones between these species, in line with a scenario of current range reduction, compared to the Last Glacial Maximum. A decline in suitable habitat also explains the fragmented nature of current species ranges. We uncover pronounced mito-nuclear discordance. We show that an ancient mtDNA lineage endemic to the Vlasina Plateau on the border between Serbia and Bulgaria, previously interpreted to be a 'ghost lineage', in fact represents a distinct species. However, it is nested considerably deeper inside the alpine newt species complex than mtDNA suggests. Our study illustrates how genomic phylogeography allows intricate evolutionary histories to be untangled.

Genetically determined color morphs are found in many animals. Polymorphism can be maintained by social selection if competitive interactions allow each morph to increase in frequency when rare. This reliance on negative frequency-dependent selection should make color polymorphism vulnerable to the appearance of novel phenotypes that disrupt competitive interactions among morphs. We show that the origin and adaptive spread of a sexually selected syndrome in common wall lizards (Podarcis muralis) selectively eliminates alleles coding for alternative color morphs that have been maintained for millions of years. The results demonstrate how the arrival of a novel phenotype can disrupt balancing selection, providing a link between rapid phenotypic evolution and the loss of color polymorphisms.

The Mediterranean Sea is a major hotspot of non-indigenous species, many of which arrive through the Suez Canal and spread via vessel-mediated transport. Among them, the tropical oyster Dendostrea cf. crenulifera has long been affected by taxonomic uncertainty. By integrating morphological characters with mitochondrial cox1 sequences from 38 specimens collected in nine localities of Greece, Croatia and Italy, we provide the first molecularly validated evidence of its occurrence outside the Levantine basin. New records from the Aegean Sea, Libyan Sea, Ionian Sea, Adriatic Sea and southern Tyrrhenian Sea extend the known range by more than 1000 km westwards. Specimens from Crete were found on natural rocky substrates, whereas those from all western localities occurred exclusively on artificial structures in harbours and marinas, supporting hull fouling as the primary vector of spread. The ability of this tropical oyster to establish in environmentally diverse basins, including areas where native oysters occur, suggests the potential for spatial overlap and competitive interactions. The early detection of this range expansion offers opportunities for monitoring and for the assessment of its ecological implications.

The European leaf-toed gecko ( Euleptes europaea ) is a small, nocturnal gecko endemic to the western Mediterranean. As a phylogenetically distinctive member of the Gondwanan family Sphaerodactylidae, it represents an important species for studying Mediterranean island biogeography, adaptation, and reptile genome evolution. The species also occupies a key position for investigating the evolution of sex chromosomes, as geckos exhibit remarkable diversity and frequent transitions in sex-determination systems. We present a chromosome-level genome assembly of Euleptes europaea generated as part of the Vertebrate Genomes Project. The 1.8 Gb assembly has a scaffold N50 of 102.3 Mb (contig N50 27 Mb), with 21 chromosome-scale scaffolds corresponding to the known karyotype (2n = 42). The primary assembly has a BUSCO completeness of 97.80% (95.60% as single-copy), a k-mer completeness of 96.00%, and a k-mer quality value (QV) of 61.20. Repetitive elements account for 53.20% of the genome and genome annotation identified 18,633 protein-coding genes. This high-quality reference genome will facilitate studies of genome evolution, island adaptation, and sex chromosome evolution across geckos and other reptiles.

The Central Apennines host a taxonomically complex scenario within the genus Psylliodes. Building on previous molecular evidence, we conducted a detailed morphological and morphometric investigation of Psylliodes biondii, P. picipes, and P. springeri to clarify the taxonomic status of the Maiella population previously attributed to P. biondii. Our results support the description of Psylliodes carolisp. nov., excluding the hypothesis that the Maiella population represents a disjunct population of P. picipes. We provide a comprehensive assessment of the distinctiveness of each species within the Psylliodes picipes species group, and present a diagnostic key based on external morphological characters, as well as the median lobe of the aedeagus, and spermatheca.

Invasive alien lizards are among the most frequently introduced reptiles worldwide, yet their management remains fragmented, underreported, and comparatively overlooked in invasion science. Here, we present the first global, practitioner-informed synthesis focused specifically on the management of invasive lizards, integrating evidence from the scientific literature with the outcomes of an international workshop held in 2025 that brought together 42 experts from 10 countries involved in detection, control, health surveillance, policy, and biosecurity. Our review shows that introductions are driven primarily by the pet trade and unintentional transport pathways, while impacts extend far beyond simple establishment success. Invasive lizards can disrupt native communities through predation, competition, behavioural interference, hybridisation, and pathogen transmission, with consequences for biodiversity, ecosystem functioning, public health, agriculture, and infrastructure. Management responses are highly context-dependent, but a consistent pattern emerges globally: prevention and early detection and rapid response (EDRR) are far more effective than reactive intervention once populations are established. A key original contribution of this synthesis is the identification of recurrent barriers that cut across taxa and regions. These include low detectability, high reproductive potential, taxonomic and biogeographic uncertainty, limited availability of species-specific control tools, chronic underfunding, inconsistent reporting of management outcomes, and major socio-political constraints such as public resistance, stakeholder conflict, and legislative misalignment. The review also highlights a substantial implementation gap between scientific knowledge and management practice, with many projects remaining undocumented or poorly evaluated. By combining global case studies with on-the-ground management experience, this review provides a rare “from practice to synthesis” perspective. We argue that effective invasive lizard management requires a shift towards proactive prevention, stronger governance and pathway regulation, improved knowledge circulation, and closer integration of ecological, health, and socio-economic dimensions within adaptive management frameworks.

Small populations face high extinction risks. This can be explained by several non-genetic and genetic factors, the latter including the loss of genetic diversity and evolutionary potential, as well as the accumulation of harmful mutations (genetic load). Using whole-genome data from island populations with different effective sizes, we estimated genetic variation and load and explored the relationship between these quantities. An extremely small population of the Aeolian wall lizard, Podarcis raffonei, likely isolated for tens of thousands of years, shows the lowest genome-wide heterozygosity observed in wild eukaryotes (one polymorphic site every 300 kb on average). Despite this, its realized genetic load is comparable to that observed in another larger and more genetically variable population. Both populations have lower variation and higher load than the much more abundant sister species, the Sicilian wall lizard. These observations are consistent with the hypothesis that populations experiencing severe bottlenecks may persist for extended periods with extremely low genomic variation, provided that their burden of deleterious mutations remains within tolerable bounds.

Aim: Quaternary climatic oscillations have profoundly shaped the genetic structure and geographic distributions of alpine biotas. Understanding how cold-adapted taxa responded to past climatic shifts is essential for unravelling the processes shaping mountain biodiversity, yet cold-adapted taxa may have followed divergent refugial histories. We compared two co-distributed, high-altitude endemic beetles to test two alternative biogeographic models: (1) persistence in nunatak (i.e., ice-free mountain peaks) and (2) survival in peripheral glacial refugia. Location: Central Apennines, Italy. Taxon: The high-altitude (1700-2700 m a.s.l.) endemic flea-beetles Longitarsus springeri and Psylliodes biondii. Methods: We sampled 112 individuals across 21 mountain sites and integrated mitochondrial and nuclear markers with phylogenetic tree (ML), haplotype-network, divergence-time (BEAST), demographic (EBSP) and spatial genetic (SAMOVA) analyses. Results: The two species exhibited sharply contrasting patterns of divergence, historical demography and migration. L. springeri showed deep phylogeographic structure with 11 mountain-specific lineages and demographic stability, consistent with long-term persistence in isolated nunatak-like refugia. In contrast, P. biondii displayed shallower genetic structure, highest diversity in the Gran Sasso massif, and a demographic expansion pre-dating the LGM (similar to 300 kya, MIS 7), consistent with survival in a peripheral refugium followed by range expansion. This pre-LGM expansion extends the temporal scope of the classical peripheral-refugia model. Main Conclusions: Even ecologically similar, sympatric endemics can follow divergent responses to climatic and environmental shifts. The contrasting histories of L. springeri and P. biondii demonstrate how topographic complexity and glacial dynamics in the central Apennines shaped lineage persistence, range dynamics and genetic structure in alpine biotas and how spatial and temporal dimensions of refugial dynamics can decouple within the same landscape. The central Apennines sky-island system thus emerges as both a long-term macro-refugium and a fine-scale network of microrefugia driving lineage diversification. A comparative phylogeographic framework offers a powerful approach to understanding how sky-island systems generate and maintain biodiversity in southern European mountains.

Abstract Snakes introduced outside their native range are an emerging conservation concern because unnoticed populations may establish and impact native vertebrate communities. Here, we investigate two recent extra-range records of the western whip snake ( Hierophis viridiflavus ) in south-western Germany using mitochondrial DNA, phylogeographic network analyses, and local contextual information. Five samples from a waste dump population in Zweibrücken shared the same ND4 haplotype, belonging to a widespread Italian lineage, whereas a road-killed individual from Saarbrücken carried a previously undescribed haplotype of the western lineage. These results indicate two distinct origins. The Zweibrücken population is consistent with human-mediated introduction via long-distance waste transport from Italy, whereas the Saarbrücken record may reflect arrival from the nearby French range margin. Preliminary surveys suggest possible local impacts on native lizards. This case highlights waste movement as a potentially overlooked pathway for snake introductions, with ecological and sanitary implications.

The oyster traditionally referred to as Booneostrea subucula (Jousseaume in Lamy, 1925) exemplifies persistent generic instability in Ostreinae, driven by misidentified type material and debated synonymies spanning multiple genera, subfamilies and even families. We reassessed the identity of Ostrea subucula and the validity of Booneostrea Harry, 1985 using an integrative approach that combined shell morphology, anatomy and multilocus phylogenetic data. Phylogenetic analyses reveal two deeply divergent, reciprocally monophyletic lineages. The Western Indian Ocean lineage corresponds to O. subucula sensu stricto and ranges from Rodrigues to Yemen and Oman. By contrast, the northern Arabian-Persian Gulf lineage represents a distinct species, here described as Ostrea sorosubucula sp. nov. Despite substantial genetic divergence, morphological differences are subtle, mainly in the adductor muscle scar. Re-examination of historical material reveals that the type concept of Booneostrea is based on misidentified or now-untraceable shells. Ostrea subucula and Ostrea setoensis Habe, 1958 are morphologically and genetically distinct, and O. subucula does not conform to the shell features historically used to define Booneostrea. We conclude that Booneostrea cannot be applied in a taxonomically consistent and meaningful way and should be treated as a nomen dubium. By resolving this long-standing confusion and documenting an endemic Gulf lineage, this study significantly contributes to stabilising generic concepts in Ostreinae and demonstrates the power of integrating molecular and morphological evidence in oyster systematics. ZooBank: urn:lsid:zoobank.org:pub:ECDB3E11-0C17-4EE9-A253-36EC59B28DD8.

Aim: Mediterranean peninsulas typically harbour high intraspecific genetic diversity associated with long-term persistence in multiple glacial refugia. However, some widespread taxa show unexpectedly shallow phylogeographic structure. Here, we investigate which historical processes can generate a pattern of strong genetic depletion within a classic southern European refugial region. Location: Iberian Peninsula and southern France. Taxon: A widespread Mediterranean colubrid snake (Zamenis scalaris). Methods: We combined range-wide multilocus genetic data (mitochondrial and nuclear markers) with coalescent-based demographic inference, species distribution modelling under present and Last Glacial Maximum climatic conditions, and Pliocene-Pleistocene fossil evidence. This integrative framework was used to reconstruct refugial history, post-glacial expansion dynamics, and spatial patterns of genetic diversity. Results: Both mitochondrial and nuclear markers indicate very low genetic variation across most of the species' range, with rare, derived haplotypes geographically clustered in southeastern and eastern Iberia. This pattern, combined with demographic reconstructions, indicates persistence through the Late Pleistocene in a single, spatially restricted refugium with reduced effective population size, followed by rapid post-glacial expansion around similar to 20 ka. Climatic suitability models and fossil records independently support this scenario, showing persistent suitable conditions confined to eastern-southeastern Iberia during glacial phases and a broad east-to-west temporal gradient of fossil occurrences consistent with long-term eastern persistence and subsequent westward expansion. Main Conclusions: Despite its long-term presence in Iberia, Zamenis scalaris lacks the multilayered phylogeographic structure typical of many Mediterranean vertebrates. Its genetic legacy is consistent with strong Late Pleistocene contraction that overrode deeper evolutionary history. This study highlights how glacial dynamics can erode genetic complexity even in widespread taxa within classical refugial regions, with broader implications for comparative phylogeography and the interpretation of genetic diversity patterns in southern Europe.

The Tyrrhenian tree frog (Hyla sarda) is a small cryptically coloured amphibian found in Corsica, Sardinia, and the Tuscan Archipelago. Investigation into the species’ evolutionary history has revealed phenotypic changes triggered by glaciation-induced range expansion, but understanding the genetic basis of this trait variation has been hampered by the lack of a reference genome. To address this, we assembled a chromosome-level genome of Hyla sarda using PacBio HiFi long reads, Bionano optical maps, and Hi-C data. The assembly comprises 13 assembled chromosomes, spanning a total length of 4.15 Gb with a scaffold N50 of 385 Mb, a BUSCO completeness of 94.60%, and a k-mer completeness of 98.30%. Approximately 75% of the genome consists of repetitive elements. We annotated 22,847 protein-coding genes with a BUSCO completeness of 94.60% and an OMArk completeness of 93.74%. This high-quality assembly provides a valuable resource for studying phenotypic evolution and its genomic basis during range expansion, and will assist future investigations into the population and conservation genomics of Hyla sarda.

The Manabí oyster (Crassostrea sp.) is considered a potential emerging aquaculture species for estuarine environments in the Tropical American Pacific, particularly in equatorial regions. While preliminary studies on its biological feasibility for cultivation are underway and although its mitochondrial genome has been recently described, its taxonomic identity has remained unclear until now. Here we conducted a comparative morphological study of natural and cultured Manabí oysters with Crassostrea corteziensis from Boca de Camichín, Nayarit, Mexico, and performed molecular identification using mitochondrial DNA genes (cytochrome c oxidase subunit I and 16S ribosomal RNA) to construct phylogenetic trees. Although evident morphological differences exist between the Manabí oyster—primarily a protuberance on the right valve of natural Manabí oysters and a blackish color in both natural and cultured Manabí oysters—and the oyster from Boca de Camichín, their phylogenetic analysis provides conclusive evidence that the Manabí oyster from the Chone River in Ecuador is conspecific with Crassostrea corteziensis. This clarification has direct implications for aquaculture planning and policy.

Repeated adaptation provides valuable insights into the predictability of evolution. Population history, selection and stochastic processes can concur to generate a continuum from distinct to highly parallel evolutionary trajectories across replicate populations. Yet, the role of genetic and environmental factors in shaping this continuum remains underexplored. We quantified repeated genetic adaptation in lizards that colonised multiple islands with comparable environmental gradients, investigating whether environmental-dependent and divergence-dependent processes can explain the degree of repeated adaptation (genetic reuse and trajectory similarity). We found 149 genes exhibiting repeated adaptation in multiple islands, some of which are likely involved in thermal physiology and developmental processes. Genetic reuse was stronger at the functional level than at the mutation level and exceeded random expectations, highlighting that different genetic combinations can generate similar functional outcomes. Adaptive trajectories were more similar between islands with low genetic differentiation and similar environmental conditions, but the effects of genetic and environmental factors varied across the diverse facets of repeatability. Overall, our findings reveal the extent and conditions under which local adaptation is, in part, predictable.

Since the opening of the Suez Canal in 1869, hundreds of Indo-Pacific species have rapidly colonised the Mediterranean. Understanding the spatial and temporal patterns of this biological invasion is crucial for assessing its ecological impact. A notable example is the non-indigenous oyster Dendostrea sp., first discovered in Türkiye in 1998 and later found throughout the easternmost Mediterranean, though its identity remained uncertain. This study clarifies the taxonomic identity and the introduction pathways of Dendostrea sp. using molecular analyses. Over 100 specimens from 25 sites in the eastern Mediterranean, as well as Île d’Ambre and Rodrigues in the Mauritius Archipelago (the native range), were sequenced for mitochondrial DNA (COI) and compared to 422 sequences from GenBank. Phylogenetic and species delimitation analyses identified the Mediterranean oysters as D. cf. crenulifera, conspecific with oysters from Rodrigues. The Mediterranean populations exhibited high genetic diversity, lack of phylogeographic structure and showed no evidence of a founder effect. These findings suggest that D. cf. crenulifera entered the Mediterranean over two decades ago through multiple shipping-mediated introductions from its native range and successfully established, likely aided by the decline of native biodiversity. The observed genetic diversity pattern across the Mediterranean indicates high propagule pressure driving the species’ invasion history, which likely underpins its establishment success by reducing the deleterious consequences of population bottlenecks and overcoming the so-called genetic paradox. This study underscores the value of molecular surveys in identifying taxonomically challenging non-indigenous species and uncovering their invasion histories.

Molecular and morphological data suggest that the Mediterranean populations of the non-indigenous genus Dendostrea are part of a single clade. This clade includes oysters from Rodrigues but is distinct from oysters from Hawaii and Mauritius. Based on morphology and sequence data, the Hawaiian and Mauritian oysters can be referred to as Dendostreasandvichensis Sowerby, 1871. The Mediterranean/Rodrigues clade, although morphologically very similar to D.sandvichensis, is significantly genetically distant from it and from D.frons and D.folium. As a result, the Mediterranean/Rodrigues clade cannot be assigned to any currently accepted nominal species. However, the statuses of the junior synonyms of D.sandvichensis are based on morphology and are therefore reconsidered with the result that D.crenulifera Sowerby, 1871 is shown to be morphologically very similar to the Mediterranean/Rodrigues clade. Given that the type locality of D.crenulifera is the Red Sea, and that Mediterranean populations are considered tropical invaders, D.crenulifera is a likely candidate name. However, without supporting sequence data from the type locality in the Red Sea, we conservatively conclude that the most appropriate name for the Mediterranean/Rodrigues clade is Dendostreacf.crenulifera (Sowerby, 1871).

Cave crickets of the genus Dolichopoda (Orthoptera; Rhaphidophoridae) represent a key component of cave ecosystems. In Italy, nine species are currently known, distributed from the northwestern regions to the southernmost Apennines, with occurrences also along various Tyrrhenian coastal areas and islands, including Sardinia. In this study, we focus on the Apennine region, where we sampled 18 populations of Dolichopoda spp. and sequenced mitochondrial markers (cox1 and 16S) from newly collected individuals to investigate their distribution and genetic diversity. Our analyses identified two previously unrecognized lineages within D. geniculata. Moreover, the sampled caves in the northern Apennines allowed us to refine the distributional ranges of D. geniculata, D. letitiae, and D. schiavazzii. Finally, we provide comments to support a future taxonomic revision of the group.

ABSTRACTEctotherms are particularly threatened by climate change because they are strictly reliant on environmental conditions for homeostasis. Increasing environmental temperatures may approach the species' critical thermal maximum, with deleterious effects on individual thermoregulation capacities. This study tests the hypothesis developed in a recent work that under ongoing global warming populations living in sites at the warm edge of the species' thermal niche will suffer a disruption of the thermoregulation process, with detrimental effects at the individual and population level. We collected individual measurements and temperature data for Mediterranean endemic rock lizards, across the entire distribution range of the species and during two different sampling periods ~20 years apart to compare thermoregulation coefficient (C), body condition index (BCI) and population size under different climatic conditions. We found that C and BCI vary across space and time following a linear pattern along the thermal niche gradient (Niche Margin Effect, NME) until a threshold temperature, beyond which the NME is disrupted. This threshold temperature indicates the warm edge of the species' thermal niche. A slightly higher temperature marks the threshold at which we observed significant population declines over the 20‐year study period in the warmest sites. This suggests a lagged response of population trends to climate warming. This study suggests a mechanism of disruption of homeostatic processes when the warm margin of the thermal niche is reached and indicates that individual parameters such as thermoregulation coefficient and body condition, rather than demographic trends, are key indicators for an early detection of population extinction risk. The multipopulation approach implemented in our study allows to identify the niche edge that underlies species' vulnerability to global warming, and to identify populations suffering negative effects of climate change before demographic collapse. This might allow to plan appropriate mitigation measures and management strategies to avoid local extinctions.

We present a genome assembly from an individual female Podarcis tiliguerta (Tyrrhenian Wall Lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1 462.31 megabases and 1 394.94 megabases. Most of haplotype 1 (99.26%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Most of haplotype 2 (99.2%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.19 kilobases.

High-altitude environments on isolated mountain peaks harbor unique biodiversity, offering natural laboratories to study past climate change impacts on speciation. In Europe, the Italian Apennines stand out for their high insect endemism, including the micro-endemic flea beetles Psylliodes springeri Leonardi, 1975and the more widely distributed P. biondii Leonardi, 1975, which shows a morphologically distinct population on the Maiella Massif. Using species delimitation methods, multispecies coalescent models, and a multilocus molecular approach, we identified key phylogenetic lineages and estimated the timing of cladogenetic events shaping this diversity. Phylogenetic analysis confirmed the monophyly of the springeri species complex, consistent with their morphological and ecological similarities. Large genetic distances and lineage sorting in both mitochondrial and nuclear gene trees distinguish the Maiella population as a separate lineage from P. biondii. Genetic differentiation between these 2 lineages matches the interspecific distance observed between P. biondii and P. springeri. Molecular dating places their divergence in a short time frame during the Early Pleistocene, approximately 2 million years ago, likely driven by glacial-interglacial cycles, which isolated populations and triggered divergence. While P. springeri and the Maiella lineage remained confined to their respective single massifs, P. biondii exhibited a broader distribution, suggesting distinct ecological responses to climate fluctuations. This study underscores how climate-driven isolation has fueled rapid speciation in the Sky Island beetles of the central Apennines, shedding light on the evolutionary history of the largely unexplored biodiversity of high-altitude southern European ecosystems. Future studies may offer further insight into the evolutionary and taxonomic status of the Maiella lineage.