Population genetic structure of the bank vole Myodes glareolus within its glacial refugium in peninsular Italy

Unveiling a hotspot of genetic diversity in southern Italy for the endangered Hermann’s tortoise Testudo hermanni

Background

Hotspots of intraspecific genetic diversity represent invaluable resources for species to cope with environmental changes, and their identification is increasingly recognized as a major goal of conservation ecology research. However, even for iconic and endangered species, conservation strategies are often planned without thorough information on the geographic patterns of genetic variation. Here, we investigated the spatial patterns of genetic variation of the endangered Hermann’s tortoise Testudo hermanni in the Italian Peninsula by genotyping 174 individuals at 7 microsatellite loci, with the aim to contribute to planning effective conservation strategies.

Results

Ordination-based and Bayesian clustering analyses consistently identified three main genetic clusters, one spread in the central and northern part of the peninsula, and two restricted to southern Italy and Sicily, respectively. The highest levels of genetic diversity were found in populations of the southern cluster and, in particular, at the northern edges of its distribution (He > 0.6, Ar > 2.8 ), that correspond to areas of putative secondary contact and admixture between distinct lineages. Our results clearly identify a hotspot of genetic diversity for the Hermann’s tortoise in southern Italy.

Conclusion

We inferred the evolutionary history and the spatial patterns of genetic variation of the Hermann’s tortoise in the Italian Peninsula. We identified three main genetic clusters along the peninsula and a hotspot of intraspecific diversity in southern Italy. Our results underline the urgent need for conservation actions to warrant the long-term persistence of viable tortoise populations in this area. Furthrmore, these data add further evidence to the role of southern Italy as a biodiversity hotspot for temperate fauna, claiming for higher consideration of this area in large scale conservation programs.

Distribution and conservation status of threatened endemic amphibians within the Aspromonte mountain region, a hotspot of Mediterranean biodiversity

Amphibian biodiversity loss in recent years has exceeded that of all other groups of vertebrates. In this context, biodiversity hotspots represent priority targets for conservation in amphibian populations. However, little information is available on the distribution and conservation status of amphibian species within most biodiversity hotspots. Here, we characterized the distribution and conservation status of four threatened endemic amphibians (Bombina pachypus, Salamandra salamandra gigliolii, Salamandrina terdigitata, and Rana italica) in the Aspromonte Mountain region, a biodiversity hotspot in southern Italy where the conservation status of amphibians is almost unexplored. We conducted an intensive field survey of 507 potential breeding sites spanning over 2,326 km2. We found that all four species were widespread in the study area. We observed 337 species occurrences: 63 for S. s. gigliolii, 29 for S. terdigitata, 84 for B. pachypus, and 161 for R. italica. Species distribution analysis revealed that S. s. gigliolii and R. italica populations had an extended and homogenous distribution. Conversely, S. terdigitata showed a dispersed pattern, with long distances among breeding sites, and B. pachypus an aggregated pattern, associated with the availability of suitable artificial habitats. On the other hand, we reported a decrease in B. pachypus occurrence in its natural habitats, which reflects a negative trend of its populations. Overall, our results provide an encouraging framework for the conservation of amphibian populations in this area, but highlight the low coverage of threatened amphibian populations in protected areas, highlighting the need for a reassessment of conservation policies and spatial conservation planning for the Aspromonte region.

Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe

The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3D^pol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5' untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission.

Characterizing the demographic history and prion protein variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)

Assessments of the adaptive potential in natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. Species face a range of stressors in human-dominated landscapes, often with contrasting effects. White-tailed deer (Odocoileus virginianus; deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability. Chronic wasting disease (CWD), a prion disease affecting deer, is likewise expanding and represents a major threat to deer and other cervids. We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada, which has yet to detect CWD in wild populations. We used high-throughput sequencing to assess neutral genomic variation and variation in the prion protein gene (PRNP) that is partly responsible for the protein misfolding when deer contract CWD. Neutral variation revealed a high number of rare alleles and no population structure, and demographic models suggested a rapid historical population expansion. Allele frequencies of PRNP variants associated with CWD susceptibility and disease progression were evenly distributed across the landscape and consistent with deer populations not infected with CWD. We estimated the selection coefficient of CWD, with simulations showing an observable and rapid shift in PRNP allele frequencies that coincides with the start of a novel CWD outbreak. Sustained surveillance of genomic and PRNP variation can be a useful tool for guiding management practices, which is especially important for CWD-free regions where deer are managed for ecological and economic benefits.

A dynamic history of admixture from Mediterranean and Carpathian glacial refugia drives genomic diversity in the bank vole

Understanding the historical contributions of differing glacial refugia is key to evaluating the roles of microevolutionary forces, such as isolation, introgression, and selection in shaping genomic diversity in present-day populations. In Europe, where both Mediterranean and extra-Mediterranean (e.g., Carpathian) refugia of the bank vole (Clethrionomys glareolus) have been identified, mtDNA indicates that extra-Mediterranean refugia were the main source of colonization across the species range, while Mediterranean peninsulas harbor isolated, endemic lineages. Here, we critically evaluate this hypothesis using previously generated genomic data (>6,000 SNPs) for over 800 voles, focusing on genomic contributions to bank voles in central Europe, a key geographic area in considering range-wide colonization. The results provide clear evidence that both extra-Mediterranean (Carpathian) and Mediterranean (Spanish, Calabrian, and Balkan) refugia contributed to the ancestry and genomic diversity of bank vole populations across Europe. Few strong barriers to dispersal and frequent admixture events in central Europe have led to a prominent mid-latitude peak in genomic diversity. Although the genomic contribution of the centrally located Carpathian refugium predominates, populations in different parts of Europe have admixed origins from Mediterranean (28%-47%) and the Carpathian (53%-72%) sources. We suggest that the admixture from Mediterranean refugia may have provisioned adaptive southern alleles to more northern populations, facilitating the end-glacial spread of the admixed populations and contributing to increased bank vole diversity in central Europe. This study adds critical details to the complex end-glacial colonization history of this well-studied organism and underscores the importance of genomic data in phylogeographic interpretation.

Unveiling cryptic diversity among Müllerian co-mimics: insights from the Western Palaearctic Syntomis moths (Lepidoptera: Erebidae: Arctiinae)

Accurate species delimitation is of primary importance in biodiversity assessments and in reconstructing patterns and processes in the diversification of life. However, the discovery of cryptic species in virtually all taxonomic groups unveiled significant gaps in our knowledge of biodiversity. Mimicry complexes are good candidates to source for cryptic species. Indeed, members of mimicry complexes undergo selective pressures on their habitus, which results in strong resemblance even between distantly related species. In this study, we used a multi-locus genetic approach to investigate the presence of cryptic diversity within a group of mimetic day-flying moths whose systematics has long been controversial, the Euro-Anatolian Syntomis. Results showed incongruence between species boundaries and the currently accepted taxonomy of this group. Both mitochondrial and nuclear markers indicate the presence of four, well-distinct genetic lineages. The genetic distance and time of divergence between the Balkan and Italian populations of S. marjana are the same as those found between S. phegea and S. ragazzii, the last two being well-distinct, broadly sympatrically occurring species. The divergence between the two lineages of S. marjana dates back to the Early Pleistocene, which coincided with substantial changes in climatic conditions and vegetation cover in Southern Europe that have likely induced geographic and ecological vicariance. Syntomis populations belonging to the taxa kruegeri (s. str.), albionica and quercii are now considered a separate species from marjana s. str. and are thus distinguished as Syntomis quercii Verity, 1914, bona sp., stat. nov. Our results show that the species richness of mimicry complexes inhabiting temperate regions might still be severely underestimated.

Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.