Climatic influences on the genetic structure and distribution of the common vole and field vole in Europe

Shrew Communities in Mediterranean Agro-Ecosystems of Central Greece: Associations with Crop Types, Land Uses, and Soil Parameters

Shrew communities play a crucial role in a diverse range of natural, urban, and agricultural ecosystems. We used Barn owl diet analysis as the ideal proxy to assess small-mammal distribution patterns on large spatial scales. More than 10,000 pellets were analyzed from Thessaly, the largest agricultural prefecture located in central Greece. A total of more than 29,000 prey items were identified, one of the largest datasets used in similar analyses in Europe. Three discrete shrew species were present in Thessaly agricultural plains, central Greece (Güldenstädt's shrew Crocidura gueldenstaedtii, Bi-coloured shrew Crocidura leucodon, and Pygmy white-toothed shrew Suncus etruscus), which comprised a total of 7452 shrews, representing 25.64% of the total small-mammals' dataset. C. gueldenstaedtii and S. etruscus demonstrated strong associations with heavy argillaceous-clay soils and Vertisol soil types, whereas S. etruscus was also associated with non-irrigated land and non-intensive cultivated plots. C. leucodon demonstrated no significant associations to any environmental gradient and demonstrated habitat plasticity, most possibly shaped by existing resources and competition. Our study highlights the important insights gained from Barn owl diet analysis in respect of small-mammal assemblages on broad geographical scales, and the inclusion of soil parameters as drivers of habitat suitability and distribution patterns for small-mammal responses.

Genetic footprints of a rapid and large-scale range expansion: the case of cyclic common vole in Spain

In the Anthropocene, many species are rapidly shifting their ranges in response to human-driven habitat modifications. Studying patterns and genetic signatures of range shifts helps to understand how species cope with environmental disturbances and predict future shifts in the face of global environmental change. We investigated the genetic signature of a contemporary wide-range expansion observed in the Iberian common vole Microtus arvalis asturianus shortly after a colonization event. We used mtDNA and microsatellite data to investigate patterns of genetic diversity, structure, demography, and gene flow across 57 localities covering the historical range of the species and the newly colonized area. The results showed a genetic footprint more compatible with a true range expansion (i.e. the colonization of previously unoccupied areas), than with a model of "colonization from within" (i.e. local expansions from small, unnoticed populations). Genetic diversity measures indicated that the source population was likely located at the NE of the historical range, with a declining gradient of genetic diversity towards the more recently invaded areas. At the expansion front, we observed the greatest gene flow and smallest pairwise differences between nearby localities. Both natural landscape features (rivers) and recent anthropogenic barriers (roads, railways) explained a large proportion of genetic variance among populations and had a significant impact on the colonization pathways used by voles.

Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland

Previous studies indicated that in some species phylogeographic patterns obtained in the analysis of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check whether there was any discordance between mtDNA and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in the analysis of other genetic markers and functional genes. However, genome-wide SNP analyses revealed the more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as recognised previously in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for insufficient amount of time to develop significant genetic differentiation.

Seasonal Adaptation: Geographic Photoperiod-Temperature Patterns Explain Genetic Variation in the Common Vole Tsh Receptor

The vertebrate photoperiodic neuroendocrine system uses the photoperiod as a proxy to time the annual rhythms in reproduction. The thyrotropin receptor (TSHR) is a key protein in the mammalian seasonal reproduction pathway. Its abundance and function can tune sensitivity to the photoperiod. To investigate seasonal adaptation in mammals, the hinge region and the first part of the transmembrane domain of the Tshr gene were sequenced for 278 common vole (Microtus arvalis) specimens from 15 localities in Western Europe and 28 localities in Eastern Europe. Forty-nine single nucleotide polymorphisms (SNPs; twenty-two intronic and twenty-seven exonic) were found, with a weak or lack of correlation with pairwise geographical distance, latitude, longitude, and altitude. By applying a temperature threshold to the local photoperiod-temperature ellipsoid, we obtained a predicted critical photoperiod (pCPP) as a proxy for the spring onset of local primary food production (grass). The obtained pCPP explains the distribution of the genetic variation in Tshr in Western Europe through highly significant correlations with five intronic and seven exonic SNPs. The relationship between pCPP and SNPs was lacking in Eastern Europe. Thus, Tshr, which plays a pivotal role in the sensitivity of the mammalian photoperiodic neuroendocrine system, was targeted by natural selection in Western European vole populations, resulting in the optimized timing of seasonal reproduction.

Distribution of Four Vole Species through the Barn Owl Tyto alba Diet Spectrum: Pattern Responses to Environmental Gradients in Intensive Agroecosystems of Central Greece

Voles are the most common vertebrate pests in European agriculture. Identifying their distribution and abundance patterns provides valuable information for future management. Barn Owl diet analysis is one of the optimum methods used to record small mammal distribution patterns on large spatial scales. From 2003 to 2005, a total of 10,065 Barn Owl pellets were collected and analyzed from 31 breeding sites in the largest agroecosystem in Greece, the Thessaly plains. A total of 29,061 prey items were identified, offering deep insight into small mammal distribution, specifically voles. Four discrete vole species (Harting's vole Microtus hartingi, East European vole Microtus levis, Thomas's pine vole Microtus thomasi, and Grey dwarf hamster Cricetulus migratorius) comprised 40.5% (11,770 vole prey items) of the total Barn Owl prey intake. The presence and abundance of the voles varied according to underlying environmental gradients, with soil texture and type playing a major role. M. levis showed no significant attachments to gradients, other than a mild increase in Mollisol soils. It was syntopic in all sites with M. hartingi, which was the dominant and most abundant small mammal species, preferring non-arable cultivated land, natural grasslands, set-aside fields, and fallow land. M. thomasi was strictly present in western Thessaly and strongly associated with a sandy-clay soil texture and Alfisol soils. C. migratorius was the least represented vole (162 items), exclusively present in eastern Thessaly and demonstrating a stronger association with cereals, Mollisol soils, and an argillaceous-clay soil texture. This is the first study in Greece at such a large spatial scale, offering insights for pest rodents' distribution in intensive agroecosystems and their response to environmental gradients including soil parameters.

The effect of habitat and climatic on microsatellite diversity and allele length variation

Microsatellite loci have been shown to vary according to environment. We studied allelic length variation and diversity in eight microsatellite loci along a sharp climatic and habitat gradient in Israel, using the eastern spadefoot toad (Pelobates syriacus) as our model system. We found a gradual increase in allele lengths from north to south. We used a distance-based redundancy analysis (dbRDA) to associate between allele length and habitat and climatic measures and found that geography and annual climate explained the significant variation in allele length. We also used additional measurements pertaining to demography, heterozygosity and allelic diversity to explore four different hypotheses that might explain the variations in allele length. Our results suggest that the changes we observed in allele lengths may not be purely random but could be influenced by the differential mutation rate and/or local environmental conditions operating at the different locations.

Pan‐European phylogeography of the European roe deer ( Capreolus capreolus )

To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.

Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

Phylogeographical structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe

Southern and northern glacial refugia are considered paradigms that explain the complex phylogeographical patterns and processes of European biota. Here, we provide a revisited statistical phylogeographical analysis of the pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae), examining its genetic diversity, genetic differentiation and demographic history in the Mediterranean peninsulas and in Western and Central Europe. The results showed support for genetically distinct and diverse phylogeographical groups consistent with southern and northern glacial refugia, as expected from previous studies. We also identified geographical barriers concordant with glaciated mountain ranges during the Last Glacial Maximum (LGM), early diversification events dated between the Late Pleistocene and Early Holocene for the main phylogeographical groups, and recent (post-LGM) patterns of demographic expansions. This study is the most comprehensive investigation of this species to date, and the results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.

Geographical distribution and hosts of the cestode Paranoplocephala omphalodes (Hermann, 1783) Lühe, 1910 in Russia and adjacent territories

Paranoplocephala omphalodes is a widespread parasite of voles. Low morphological variability within the genus Paranoplocephala has led to erroneous identification of P. omphalodes a wide range of definitive hosts. The use of molecular methods in the earlier investigations has confirmed that P. omphalodes parasitizes four vole species in Europe. We studied the distribution of P. omphalodes in Russia and Kazakhstan using molecular tools. The study of 3248 individuals of 20 arvicoline species confirmed a wide distribution of P. omphalodes. Cestodes of this species were found in Microtus arvalis, M. levis, M. agrestis, Arvicola amphibius, and also in Chionomys gud. Analysis of the mitochondrial gene cox1 variability revealed a low haplotype diversity in P. omphalodes in Eurasia.