Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem

Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.

A multidisciplinary approach to tackling invasive species: barcoding, morphology, and metataxonomy of the leafhopper Arboridia adanae

The leafhopper genus Arboridia includes several species that feed on Vitis vinifera and cause leaf chlorosis. We report the first alien Arboridia infestation in Italy in 2021 in an Apulian vineyard. To confirm the taxonomic status of the species responsible for crop damage, and reconstruct its demographic history, we barcoded individuals from Apulia together with Arboridia spp. from Crete (Greece), A. adanae from Central Turkey and other specimens of the presumed sister species, A. dalmatina from Dalmatia (Croatia). Molecular phylogenies and barcoding gap analysis identified clades not associated with sampling locations. This result is incongruent with classical specimen assignment and is further supported by morphological analyses, which did not reveal significant differences among the populations. Therefore, we propose A. dalmatina as a junior synonym of A. adanae, which would become the only grapevine-related Arboridia species in the eastern Mediterranean. To further characterise A. adanae evolution, we performed a molecular clock analysis that suggested a radiation during the Pleistocene glaciations. Finally, to assess whether the Apulian individuals carried microorganisms of agricultural relevance, we sequenced their bacterial microbiota using 16S rRNA amplicon sequencing identifying three phytopathogens not generally associated with Arboridia activities as well as Wolbachia in one Apulian haplogroup. We discuss the agricultural implications of this infestation.

Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance

Although male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi (gut microbiota) in relation to habitat type has not been fully examined. To understand whether the combination of sex and habitat affects gut microbiota variation, we analyzed 40 fecal samples of wild yellow baboons (Papio cynocephalus) living in contrasting habitat types (intact, well-protected vs. fragmented, less protected forests) in the Udzungwa Mountains of Tanzania. Sex determination was performed using the marker genes SRY (Sex-determining Region Y) and DDX3X-DDX3Y (DEAD-Box Helicase 3). Samples were attributed to 34 individuals (19 females and 15 males) belonging to five social groups. Combining the results of sex determination with two amplicon sequencing datasets on bacterial (V1-V3 region of the 16S rRNA gene) and fungal (ITS2) gut communities, we found that overall, baboon females had a significantly higher gut bacterial richness compared to males. Beta diversity estimates indicated that bacterial composition was significantly different between males and females, and this was true for individuals from both well- and less protected forests. Our results highlight the combined role of sex and habitat type in shaping variation in gut microbial communities in wild non-human primates.

A multidisciplinary approach to estimating wolf population size for long-term conservation

The wolf (Canis lupus) is among the most controversial of wildlife species. Abundance estimates are required to inform public debate and policy decisions, but obtaining them at biologically relevant scales is challenging. We developed a system for comprehensive population estimation across the Italian alpine region (100,000 km2 ), involving 1513 trained operators representing 160 institutions. This extensive network allowed for coordinated genetic sample collection and landscape-level spatial capture-recapture analyses that transcended administrative boundaries to produce the first estimates of key parameters for wolf population status assessment. Wolf abundance was estimated at 952 individuals (95% credible interval 816-1120) and 135 reproductive units (i.e., packs) (95% credible interval 112-165). We also estimated that mature individuals accounted for 33-45% of the entire population. The monitoring effort was spatially estimated thereby overcoming an important limitation of citizen science data. This is an important approach for promoting wolf-human coexistence based on wolf abundance monitoring and an endorsement of large-scale harmonized conservation practices.

Current and future distribution of a parasite with complex life cycle under global change scenarios: Echinococcus multilocularis in Europe

Global change is expected to have complex effects on the distribution and transmission patterns of zoonotic parasites. Modelling habitat suitability for parasites with complex life cycles is essential to further our understanding of how disease systems respond to environmental changes, and to make spatial predictions of their future distributions. However, the limited availability of high quality occurrence data with high spatial resolution often constrains these investigations. Using 449 reliable occurrence records for Echinococcus multilocularis from across Europe published over the last 35 years, we modelled habitat suitability for this parasite, the aetiological agent of alveolar echinococcosis, in order to describe its environmental niche, predict its current and future distribution under three global change scenarios, and quantify the probability of occurrence for each European country. Using a machine learning approach, we developed large-scale (25 × 25 km) species distribution models based on seven sets of predictors, each set representing a distinct biological hypothesis supported by current knowledge of the autecology of the parasite. The best-supported hypothesis included climatic, orographic and land-use/land-cover variables such as the temperature of the coldest quarter, forest cover, urban cover and the precipitation seasonality. Future projections suggested the appearance of highly suitable areas for E. multilocularis towards northern latitudes and in the whole Alpine region under all scenarios, while decreases in habitat suitability were predicted for central Europe. Our spatially explicit predictions of habitat suitability shed light on the complex responses of parasites to ongoing global changes.

Tracking Chromosomal Origins in the Northern Italy System of Metacentric Races of the House Mouse

The Western European house mouse is chromosomally diverse, with diploid karyotypes ranging from the standard 40 telocentric chromosomes down to 22 chromosomes. Karyotypes are modified through Robertsonian (Rb) fusion of 2 telocentrics into a single metacentric, occurring repeatedly with fixation, and whole-arm reciprocal translocations (WARTs) generating additional novel karyotypes. Over 100 metacentric populations (chromosomal races) have been identified, geographically clustered into “systems.” Chromosomal races within systems often hybridise, and new races may emerge through this hybridisation (“zonal raciation”). We wished to determine the degree to which chromosomal races in a system have evolved independently or share common ancestry. Recombination between chromosomes from hybridising chromosomal races can erase the signals associated with a particular metacentric of interest, making inferences challenging. However, reduced recombination near the centromeres of chromosomal race-specific metacentrics makes centromere-adjacent markers ideal for solving this problem. For the Northern Italy System (NIS), we used microsatellite markers near the centromere to test previous hypotheses about evolutionary relationships of 5 chromosomal races. We chose markers from chromosomes 1, 3, 4, and 6, all of which comprise one arm of a metacentric in at least 2 of these NIS metacentric populations. We used estimates of F_ST and R_ST, as well as principal components analyses and neighbour-joining phylogenetic analyses, to infer evolutionary relationships between these 5 chromosomal races and neighbouring mice with the standard karyotype. We showed that the metacentric populations form a single grouping distinct from the standard populations, consistent with their common origin and consistent with a parsimonious sequence of chromosomal rearrangements to explain the relationship of the chromosomal races. That origin and evolution of the chromosomal races in the system would have involved Rb fusions, explaining the occurrence of chromosomal races with diploid numbers as low as 22. However, WARTs and zonal raciation have also been inferred, and the rare occurrence of chromosome 1 in different metacentrics in closely related chromosomal races is almost certainly explained by a WART. Our results with centromeric microsatellites are consistent with the above scenarios, illustrating, once again, the value of markers in the centromeric region to test evolutionary hypotheses in house mouse chromosomal systems.

Microsatellite Characterization and Panel Selection for Brown Bear (Ursus arctos) Population Assessment

An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human-wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10-5), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10-11) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations.

Interactions between parasitic helminths and gut microbiota in wild tropical primates from intact and fragmented habitats

The mammalian gastrointestinal tract harbours a highly complex ecosystem composed of a variety of micro- (bacteria, fungi, viruses, protozoans) and macro-organisms (helminths). Although most microbiota research focuses on the variation of single gut components, the crosstalk between components is still poorly characterized, especially in hosts living under natural conditions. We investigated the gut micro-biodiversity (bacteria, fungi and helminths) of 158 individuals of two wild non-human primates, the Udzungwa red colobus (Procolobus gordonorum) and the yellow baboon (Papio cynocephalus). These species have contrasting diets and lifestyles, but live sympatrically in both human-impacted and pristine forests in the Udzungwa Mountains of Tanzania. Using non-invasive faecal pellets, helminths were identified using standard microscopy while bacteria and fungi were characterized by sequencing the V1–V3 variable region of the 16S rRNA gene for bacteria and the ITS1–ITS2 fragment for fungi. Our results show that both diversity and composition of bacteria and fungi are associated with variation in helminth presence. Although interactions differed by habitat type, in both primates we found that Strongyloides was negatively associated and Trichuris was positively associated with bacterial and fungal richness. To our knowledge, this is one of the few studies demonstrating an interaction between helminth and gut microbiota communities in wild non-human primates.

Geographical Distribution and Genetic Diversity of Bank Vole Hepaciviruses in Europe

The development of new diagnostic methods resulted in the discovery of novel hepaciviruses in wild populations of the bank vole (Myodes glareolus, syn. Clethrionomys glareolus). The naturally infected voles demonstrate signs of hepatitis similar to those induced by hepatitis C virus (HCV) in humans. The aim of the present research was to investigate the geographical distribution of bank vole-associated hepaciviruses (BvHVs) and their genetic diversity in Europe. Real-time reverse transcription polymerase chain reaction (RT-qPCR) screening revealed BvHV RNA in 442 out of 1838 (24.0%) bank voles from nine European countries and in one of seven northern red-backed voles (Myodes rutilus, syn. Clethrionomys rutilus). BvHV RNA was not found in any other small mammal species (n = 23) tested here. Phylogenetic and isolation-by-distance analyses confirmed the occurrence of both BvHV species (Hepacivirus F and Hepacivirus J) and their sympatric occurrence at several trapping sites in two countries. The broad geographical distribution of BvHVs across Europe was associated with their presence in bank voles of different evolutionary lineages. The extensive geographical distribution and high levels of genetic diversity of BvHVs, as well as the high population fluctuations of bank voles and occasional commensalism in some parts of Europe warrant future studies on the zoonotic potential of BvHVs.

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet

The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.

Geographical Distribution of Ljungan Virus in Small Mammals in Europe

Ljungan virus (LV), which belongs to the Parechovirus genus in the Picornaviridae family, was first isolated from bank voles (Myodes glareolus) in Sweden in 1998 and proposed as a zoonotic agent. To improve knowledge of the host association and geographical distribution of LV, tissues from 1685 animals belonging to multiple rodent and insectivore species from 12 European countries were screened for LV-RNA using reverse transcriptase (RT)-PCR. In addition, we investigated how the prevalence of LV-RNA in bank voles is associated with various intrinsic and extrinsic factors. We show that LV is widespread geographically, having been detected in at least one host species in nine European countries. Twelve out of 21 species screened were LV-RNA PCR positive, including, for the first time, the red vole (Myodes rutilus) and the root or tundra vole (Alexandromys formerly Microtus oeconomus), as well as in insectivores, including the bicolored white-toothed shrew (Crocidura leucodon) and the Valais shrew (Sorex antinorii). Results indicated that bank voles are the main rodent host for this virus (overall RT-PCR prevalence: 15.2%). Linear modeling of intrinsic and extrinsic factors that could impact LV prevalence showed a concave-down relationship between body mass and LV occurrence, so that subadults had the highest LV positivity, but LV in older animals was less prevalent. Also, LV prevalence was higher in autumn and lower in spring, and the amount of precipitation recorded during the 6 months preceding the trapping date was negatively correlated with the presence of the virus. Phylogenetic analysis on the 185 base pair species-specific sequence of the 5' untranslated region identified high genetic diversity (46.5%) between 80 haplotypes, although no geographical or host-specific patterns of diversity were detected.

Altitude and human disturbance are associated with helminth diversity in an endangered primate, Procolobus gordonorum

Gastrointestinal parasites colonizing the mammalian gut influence the host immune system and health. Parasite infections, mainly helminths, have been studied intensively in both humans and non-human animals, but relatively rarely within a conservation framework. The Udzungwa red colobus monkey (Procolobus gordonorum) is an endangered endemic primate species living in the Udzungwa Mountains of Tanzania, a global biodiversity hotspot. Since this endemic primate species is highly sensitive to human disturbance, here we investigate whether habitat type (driven by natural and human-induced factors) is associated with helminth diversity. Using standard flotation and sedimentation techniques, we analyzed 251 fecal samples belonging to 25 social groups from four different forest blocks within the Udzungwa Mountains. Five parasitic helminth taxa were recovered from Udzungwa red colobus, including Trichuris sp., Strongyloides fulleborni, S. stercoralis, a strongylid nematode and Colobenterobius sp. We used Generalized Linear Mixed Models to explore the contribution of habitat type, altitude and fecal glucocorticoid levels (as biomarkers of stress) in predicting gut parasite variation. Although some parasites (e.g., Trichuris sp.) infected more than 50% of individuals, compared to others (e.g., Colobenterobius sp.) that infected less than 3%, both parasite richness and prevalence did not differ significantly across forests, even when controlling for seasonality. Stress hormone levels also did not predict variation in parasite richness, while altitude could explain it resulting in lower richness at lower altitudes. Because human activities causing disturbance are concentrated mainly at lower altitudes, we suggest that protection of primate forest habitat preserves natural diversity at both macro- and microscales, and that the importance of the latter should not be underestimated.

A49 Emerging rodent-borne viral pathogens in Italy: Overview of seroprevalence and genomic investigations

Rodents play a key role as reservoirs of many zoonotic pathogens which represent an emerging public health threat worldwide. Among these, Dobrava-Belgrade virus (DOBV) is the most pathogenic hantavirus in Europe with a case-fatality rate of up to 12 per cent, while Lymphocytic choriomeningitis virus (LCMV) has a mortality rate below 1 per cent. Both viruses are predominantly transmitted to humans through the inhalation of infected particles in aerosolized urine, feces, or saliva that are shed in the environment by chronically infected hosts, such as the yellow-necked mouse Apodemus flavicollis. Although no human cases of DOBV or LCMV have been reported in the Province of Trento (northeastern Italy) thus far, in order to evaluate the human hazard for these viruses, the prevalence of antibodies to DOBV and LCMV has been monitored using a specific immunofluorescence assay test in a wild population of A. flavicollis since 2000. These investigations have shown that the two RNA viruses circulate silently in this species in the study area. In particular, a sudden increase (up to 12.5%) in DOBV seroprevalence was observed in this rodent species between 2010 and 2012. Several efforts have been undertaken to isolate these viruses and characterize their genomes, but it has not yet been possible to detect viral RNA from seropositive mice using traditional methods such as RT-PCR. Since RNA viruses are very diverse and often difficult to isolate, innovative molecular methods based on viral targeted enrichment and high-throughput sequencing have been applied. We intend to report on this long-term seroprevalence study and provide an overview of the molecular approaches adopted in the attempt to confirm the presence of these viruses, and identify which variants are circulating in the region, as well as their pathogenicity.

Global change-driven use of onshore habitat impacts polar bear faecal microbiota

The gut microbiota plays a critical role in host health, yet remains poorly studied in wild species. Polar bears (Ursus maritimus), key indicators of Arctic ecosystem health and environmental change, are currently affected by rapid shifts in habitat that may alter gut homeostasis. Declining sea ice has led to a divide in the southern Beaufort Sea polar bear subpopulation such that an increasing proportion of individuals now inhabit onshore coastal regions during the open-water period ('onshore bears') while others continue to exhibit their typical behaviour of remaining on the ice ('offshore bears'). We propose that bears that have altered their habitat selection in response to climate change will exhibit a distinct gut microbiota diversity and composition, which may ultimately have important consequences for their health. Here, we perform the first assessment of abundance and diversity in the faecal microbiota of wild polar bears using 16S rRNA Illumina technology. We find that bacterial diversity is significantly higher in onshore bears compared to offshore bears. The most enriched OTU abundance in onshore bears belonged to the phylum Proteobacteria, while the most depleted OTU abundance within onshore bears was seen in the phylum Firmicutes. We conclude that climate-driven changes in polar bear land use are associated with distinct microbial communities. In doing so, we present the first case of global change mediated alterations in the gut microbiota of a free-roaming wild animal.

The evolution of transmission mode

This article reviews research on the evolutionary mechanisms leading to different transmission modes. Such modes are often under genetic control of the host or the pathogen, and often in conflict with each other via trade-offs. Transmission modes may vary among pathogen strains and among host populations. Evolutionary changes in transmission mode have been inferred through experimental and phylogenetic studies, including changes in transmission associated with host shifts and with evolution of the unusually complex life cycles of many parasites. Understanding the forces that determine the evolution of particular transmission modes presents a fascinating medley of problems for which there is a lack of good data and often a lack of conceptual understanding or appropriate methodologies. Our best information comes from studies that have been focused on the vertical versus horizontal transmission dichotomy. With other kinds of transitions, theoretical approaches combining epidemiology and population genetics are providing guidelines for determining when and how rapidly new transmission modes may evolve, but these are still in need of empirical investigation and application to particular cases. Obtaining such knowledge is a matter of urgency in relation to extant disease threats.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.

Seroprevalence of lymphocytic choriomeningitis virus and Ljungan virus in Finnish patients with suspected neurological infections

Directly-transmitted rodent-borne zoonotic viruses, such as lymphocytic choriomeningitis virus (LCMV) can cause nervous system infections. Rodent-borne Ljungan virus (LV) is considered potentially zoonotic possibly causing neurological symptoms. Our objective was to understand the role of these two viruses compared to other pathogens in causing neurological infections in Finnish patients. Routine screening data were available for 400 patients aged 5-50 years, collected from December 2013 to December 2014 with suspected neurological infection. Depending on symptoms, patients were variously tested for herpesviruses, enteroviruses, varicella zoster virus, and Mycoplasma pneumoniae, while those suspected of tick bite were further tested for Borrelia spp. and tick-borne encephalitis virus using antibody and/or nucleic acid tests. For 380 patients, we also screened the RNA and antibody prevalence of LCMV and LV in order to test if either of these viruses were the causative agent. Data collected indicated that the causative microbial agent was confirmed in only 15.5% of all Finnish patients with neurological symptoms, with M. pneumoniae (26 cases) being the most common causative agent found in sera, whereas Borrelia spp. (15), herpes simplex viruses (7), and enteroviruses (5) were the most common agents confirmed in the CSF. The seroprevalences for LV and LCMV were 33.8% and 5.0%, respectively, but no samples were PCR-positive. In this study, M. pneumoniae and Borrelia spp. were the most common causative agents of neurological infections in Finland. No LCMV or LV infections were detected. We conclude there was no association of LV with neurological diseases in this patient cohort.

Tick-borne pathogens and their reservoir hosts in northern Italy

The aim of this study was to determine the occurrence of Anaplasma phagocytophilum, Rickettsia spp., Babesia spp., and Candidatus Neoehrlichia mikurensis in Ixodes spp. ticks removed from wildlife, domestic animals and humans in the Province of Trento (northern Italy) in order to better understand their ecology and provide public health professionals with an updated list of pathogens which should be considered during their diagnostic procedures after a tick bite. During 2011-2012, 848 feeding ticks at all life stages (adults, nymphs and larvae) from various hosts (wild ungulates, birds and rodents; domestic sheep, dogs and humans) were collected. The highest prevalences of A. phagocytophilum and Rickettsia spp. were detected in adult and nymphal tick stages feeding on wild ungulates (11.4% prevalence for both pathogens), while the Babesia spp. prevailed in nymphal and larval ticks feeding on wild birds (7.7%). A wide spectrum of tick-borne agents was present in larval ticks: those detached from wild ungulates were positive for A. phagocytophilum, B. venatorum, R. helvetica, R. monacensis and R. raoultii, while those removed from wild rodents were positive for B. venatorum, R. helvetica, R. monacensis and Ca. N. mikurensis, and ticks from wild birds carried A. phagocytophilum, B. venatorum, B. capreoli and R. helvetica. This study provides evidence of circulation of five tick-borne pathogens not reported in this region before, specifically R. raoultii, R. monacensis, B. venatorum, B. capreoli and B. microti. Furthermore, it discusses the epidemiological role of the animal species from which the ticks were collected highlighting the needs for more experimental studies especially for those pathogens where transovarial transmission in ticks has been demonstrated.

Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies

A wealth of human studies have demonstrated the importance of gut microbiota to health. Research on non-human animal gut microbiota is now increasing, but what insight does it provide? We reviewed 650 publications from this burgeoning field (2009-2016) and determined that animals driving this research were predominantly 'domestic' (48.2%), followed by 'model' (37.5%), with least studies on 'wild' (14.3%) animals. Domestic studies largely experimentally perturbed microbiota (81.8%) and studied mammals (47.9%), often to improve animal productivity. Perturbation was also frequently applied to model animals (87.7%), mainly mammals (88.1%), for forward translation of outcomes to human health. In contrast, wild animals largely characterised natural, unperturbed microbiota (79.6%), particularly in pest or pathogen vectoring insects (42.5%). We used network analyses to compare the research foci of each animal group: 'diet' was the main focus in all three, but to different ends: to enhance animal production (domestic), to study non-infectious diseases (model), or to understand microbiota composition (wild). Network metrics quantified model animal studies as the most interdisciplinary, while wild animals incorporated the fewest disciplines. Overall, animal studies, especially model and domestic, cover a broad array of research. Wild animals, however, are the least investigated, but offer under-exploited opportunities to study 'real-life' microbiota.

Anticipating species distributions: Handling sampling effort bias under a Bayesian framework

Anticipating species distributions in space and time is necessary for effective biodiversity conservation and for prioritising management interventions. This is especially true when considering invasive species. In such a case, anticipating their spread is important to effectively plan management actions. However, considering uncertainty in the output of species distribution models is critical for correctly interpreting results and avoiding inappropriate decision-making. In particular, when dealing with species inventories, the bias resulting from sampling effort may lead to an over- or under-estimation of the local density of occurrences of a species. In this paper we propose an innovative method to i) map sampling effort bias using cartogram models and ii) explicitly consider such uncertainty in the modeling procedure under a Bayesian framework, which allows the integration of multilevel input data with prior information to improve the anticipation species distributions.

Population dynamics of wild rodents induce stochastic fadeouts of a zoonotic pathogen

Stochastic processes play an important role in the infectious disease dynamics of wildlife, especially in species subject to large population oscillations. Here, we study the case of a free ranging population of yellow-necked mice (Apodemus flavicollis) in northern Italy, where circulation of Dobrava-Belgrade hantavirus (DOBV) has been detected intermittently since 2001, until an outbreak emerged in 2010. We analysed the transmission dynamics of the recent outbreak using a computational model that accounts for seasonal changes of the host population and territorial behaviour. Model parameters were informed by capture-mark-recapture data collected over 14 years and longitudinal seroprevalence data from 2010 to 2013. The intermittent observation of DOBV before 2010 can be interpreted as repeated stochastic fadeouts after multiple introductions of infectious rodents migrating from neighbouring areas. We estimated that only 20% of introductions in a naïve host population results in sustained transmission after 2 years, despite an effective reproduction number well above the epidemic threshold (mean 4·5, 95% credible intervals, CI: 0·65-15·8). Following the 2010 outbreak, DOBV has become endemic in the study area, but we predict a constant probability of about 4·7% per year that infection dies out, following large population drops in winter. In the absence of stochastic fadeout, viral prevalence is predicted to continue its growth to an oscillating equilibrium around a value of 24% (95% CI: 3-57). We presented an example of invasion dynamics of a zoonotic virus where stochastic fadeout have played a major role and may induce future extinction of the endemic infection.

A Half-Century of Studies on a Chromosomal Hybrid Zone of the House Mouse

The first natural chromosomal variation in the house mouse was described nearly 50 years ago in Val Poschiavo on the Swiss side of the Swiss-Italian border in the Central Eastern Alps. Studies have extended into neighboring Valtellina, and the house mice of the Poschiavo-Valtellina area have been subject to detailed analysis, reviewed here. The maximum extent of this area is 70 km, yet it has 4 metacentric races and the standard 40-chromosome telocentric race distributed in a patchwork fashion. The metacentric races are characterized by highly reduced diploid numbers (2n = 22-26) resulting from Robertsonian fusions, perhaps modified by whole-arm reciprocal translocations. The races hybridize and the whole Poschiavo-Valtellina area can be considered a "hybrid zone." The studies of this area have provided insights into origin of races within hybrid zones, gene flow within hybrid zones and the possibility of speciation in hybrid zones. This provides a case study of how chromosomal rearrangements may impact the genetic structure of populations and their diversification.

Lymphocytic choriomeningitis, Ljungan and orthopoxvirus seroconversions in patients hospitalized due to acute Puumala hantavirus infection

BACKGROUND

The emergence and re-emergence of zoonotic and vector-borne diseases are increasing in Europe. Prominent rodent-borne zoonotic viruses include Puumala hantavirus (PUUV; the causative agent of nephropathia epidemica, NE), lymphocytic choriomeningitis virus (LCMV), and orthopoxviruses (OPV). In addition, Ljungan virus (LV) is considered a potentially zoonotic virus.

OBJECTIVE

The aim of this study was to compare clinical picture between acute PUUV patients with and without additional rodent-borne viral infections, to investigate if concurrent infections influence disease severity.

STUDY DESIGN

We evaluated seroprevalence of and seroconversions to LCMV, LV and OPV in 116 patients hospitalized for NE. Clinical and laboratory variables were closely monitored during hospital care.

RESULTS

A total of five LCMV, 15 LV, and one OPV seroconversions occurred. NE patients with LCMV seroconversions were younger, and had lower plasma creatinine concentrations and platelet counts than patients without LCMV seroconversions. No differences occurred in clinical or laboratory findings between patients with and without seroconversions to LV and OPV. We report, for the first time, LCMV seroprevalence in Finland, with 8.5% of NE patients seropositive for this virus. Seroprevalences for LV and OPV were 47.8% and 32.4%, respectively.

CONCLUSION

Cases with LCMV seroconversions were statistically younger, had milder acute kidney injury and more severe thrombocytopenia than patients without LCMV. However, the low number of seroconversion cases precludes firm conclusions. Concurrent LV or OPV infections do not appear to influence clinical picture for NE patients.

Empirical demonstration of hybrid chromosomal races in house mice

Western house mice (Mus musculus domesticus) and common shrews (Sorex araneus) are important models for study of chromosomal speciation. Both had ancestral karyotypes consisting of telocentric chromosomes, and each is subdivided into numerous chromosomal races many of which have resulted from fixation of new mutations (Robertsonian fusions and whole-arm reciprocal translocations). However, some chromosomal races in both species may alternatively have originated through hybridization, with particular homozygous recombinant products reaching fixation. Here, we demonstrate the process of generation of hybrid chromosomal races for the first time in either species using molecular markers. Analysis of centromeric microsatellite markers show that the Mid Valtellina (IMVA) and Upper Valtellina (IUVA) chromosomal races of the house mouse are recombinant products of hybridization of the Lower Valtellina (ILVA) and Poschiavo (CHPO) chromosomal races, supporting earlier theoretical analysis. IMVA and IUVA occupy a small area of the Italian Alps where ILVA makes contact with CHPO. IUVA and CHPO have previously been shown to be reproductively isolated in one village, emphasizing that hybrid chromosomal races in small mammals, as in plants, have the potential to be part of the speciation process.

Interactions between multiple helminths and the gut microbiota in wild rodents

The gut microbiota is vital to host health and, as such, it is important to elucidate the mechanisms altering its composition and diversity. Intestinal helminths are host immunomodulators and have evolved both temporally and spatially in close association with the gut microbiota, resulting in potential mechanistic interplay. Host–helminth and host–microbiota interactions are comparatively well-examined, unlike microbiota–helminth relationships, which typically focus on experimental infection with a single helminth species in laboratory animals. Here, in addition to a review of the literature on helminth–microbiota interactions, we examined empirically the association between microbiota diversity and composition and natural infection of multiple helminth species in wild mice (Apodemus flavicollis), using 16S rRNA gene catalogues (metataxonomics). In general, helminth presence is linked with high microbiota diversity, which may confer health benefits to the host. Within our wild rodent system variation in the composition and abundance of gut microbial taxa associated with helminths was specific to each helminth species and occurred both up- and downstream of a given helminth's niche (gut position). The most pronounced helminth–microbiota association was between the presence of tapeworms in the small intestine and increased S24–7 (Bacteroidetes) family in the stomach. Helminths clearly have the potential to alter gut homeostasis. Free-living rodents with a diverse helminth community offer a useful model system that enables both correlative (this study) and manipulative inference to elucidate helminth–microbiota interactions.

Genetic differentiation within and away from the chromosomal rearrangements characterising hybridising chromosomal races of the western house mouse (Mus musculus domesticus)

The importance of chromosomal rearrangements for speciation can be inferred from studies of genetic exchange between hybridising chromosomal races within species. Reduced fertility or recombination suppression in karyotypic hybrids has the potential to maintain or promote genetic differentiation in genomic regions near rearrangement breakpoints. We studied genetic exchange between two hybridising groups of chromosomal races of house mouse in Upper Valtellina (Lombardy, Italy), using microsatellites. These groups differ by Robertsonian fusions and/or whole-arm reciprocal translocations such that F1 hybrids have a chain-of-five meiotic configuration. Previous studies showed genetic differentiation in two chromosomes in the chain-of-five (10 and 12) close to their centromeres (i.e. the rearrangement breakpoints); we have shown here that the centromeric regions of the other two chromosomes in the chain (2 and 8) are similarly differentiated. The internal chromosomes of the chain (8 and 12) show the greatest differentiation, which may reflect pairing and recombination properties of internal and external elements in a meiotic chain. Importantly, we found that centromeric regions of some non-rearranged chromosomes also showed genetic differentiation between the hybridising groups, indicating a complex interplay between chromosomal rearrangements and other parts of the genome in maintaining or promoting differentiation and potentially driving speciation between chromosomal races.

R2d2 Drives Selfish Sweeps in the House Mouse

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2^HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2^HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2^HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.

Chromosomal speciation in mice: a cytogenetic analysis of recombination

Within species, populations differing by chromosomal rearrangements ("chromosomal races") may become reproductively isolated in association with reduced hybrid fertility due to meiotic aberrations. Speciation is also possible if hybridizing chromosomal races accumulate genetic differences because of reduced meiotic recombination in the heterozygous configuration in hybrids. Here, we examine recombination in pure races and hybrids within a model system for chromosomal speciation: the hybridization of the Poschiavo (CHPO) and Upper Valtellina (IUVA) chromosomal races of house mouse in Upper Valtellina, Italy. These races differ by Robertsonian fusions/whole-arm reciprocal translocations, such that hybrids produce a pentavalent meiotic configuration. We determined the number and position of the recombination points (using an antibody against the MutL homolog 1 [MLH1] protein) on synaptonemal complexes at pachytene in laboratory-reared CHPO, IUVA, and hybrid males, analyzing at least 112 spermatocytes per karyotypic group, up to a total of 534 spermatocytes. The mean ± standard deviation numbers of MLH1 foci per spermatocyte were 22.2 ± 3.2, 20.1 ± 2.9, 20.7 ± 2.3, and 21.9 ± 2.9 for CHPO, IUVA, CHPO × IUVA, and IUVA × CHPO, respectively. Altogether, 10,146 chromosome arms were examined, allowing multiple comparisons. Overall, recombination events were more frequently distal than proximal or interstitial. The average number of proximal MLH1 foci per chromosome arm decreased going from telocentric to metacentric bivalents to pentavalents (when present), which (together with other factors) influenced the average number of MLH1 foci per cell between CHPO, IUVA, and hybrid mice. The low frequency of proximal recombination in pentavalents of CHPO-IUVA hybrids may promote reproductive isolation between the CHPO and IUVA races, when coupled with reduced hybrid unfitness.

Evidence of Ljungan virus specific antibodies in humans and rodents, Finland

Ljungan virus (LV, genus Parechovirus, family Picornaviridae) is considered currently to be a rodent-borne virus. Despite suggested human disease associations, its zoonotic potential remains unclear. To date, LV antibody prevalence in both humans and rodents has not been studied. In this study, two different LV immunofluorescence assays (LV IFAs) were developed with LV genotypes 1 (LV strain 87-012G) and 2 (LV strain 145SLG), and cross-neutralization and -reaction studies were carried out with LV strain 145SLG. Finally, a panel of 37 Finnish sera was screened for anti-LV antibodies using two different LV IFAs (LV 145SLG and LV 87-012G) and a neutralization (NT) assay (LV 145SLG), and 50 samples from Myodes glareolus by LV IFA (LV 145SLG). The LV seroprevalence study showed 38% and 18% positivity in humans and M. glareolus, respectively. LV IFAs and NT assays were compared, and the results were in good agreement. The data are the first evidence of humans and rodents coming into contact with LV in Finland. Additional studies are required in order to acquire a better understanding of the prevalence, epidemiological patterns and possible disease association of LV infections.

Understanding the basis of diminished gene flow between hybridizing chromosome races of the house mouse

Speciation may be promoted in hybrid zones if there is an interruption to gene flow between the hybridizing forms. For hybridizing chromosome races of the house mouse in Valtellina (Italy), distinguished by whole-arm chromosomal rearrangements, previous studies have shown that there is greater interruption to gene flow at the centromeres of chromosomes that differ between the races than at distal regions of the same chromosome or at the centromeres of other chromosomes. Here, by increasing the number of markers along race-specific chromosomes, we reveal a decay in between-race genetic differentiation from the centromere to the distal telomere. For the first time, we use simulation models to investigate the possible role of recombination suppression and hybrid breakdown in generating this pattern. We also consider epistasis and selective sweeps as explanations for isolated chromosomal regions away from the centromere showing differentiation between the races. Hybrid breakdown alone is the simplest explanation for the decay in genetic differentiation with distance from the centromere. Robertsonian fusions/whole-arm reciprocal translocations are common chromosomal rearrangements characterizing both closely related species and races within species, and this fine-scale empirical analysis suggests that the unfitness associated with these rearrangements in the heterozygous state may contribute to the speciation process.

Saturation deficit and deer density affect questing activity and local abundance of Ixodes ricinus (Acari, Ixodidae) in Italy

The wood tick Ixodes ricinus, one of the most common arthropod-borne disease vectors, is of increasing relevance for human and animal health in Europe. The aim of this study was to determine the relative contribution of several abiotic and biotic factors potentially affecting questing activity and local abundance of I. ricinus in Italy, considering the scale at which these factors interact with the host-seeking ticks. Within EDEN, a large-scale EU collaborative project on eco-epidemiology of vector-borne diseases, we collected questing ticks for three consecutive years using a standard protocol at eleven sites in the Italian Alps and Apennines. A total of 25 447 I. ricinus were collected. All sites showed the same annual pattern of tick activity (bimodal for nymphs and unimodal for larvae and adults), although the abundance of nymphs was statistically different between sites and years. A Generalized Linear Mixed Model and a Linear Mixed Model fitted to data for nymphs, showed that while the principal variables affecting the local abundance of questing ticks were saturation deficit (an index combining temperature and relative humidity) and red deer density, the most important variable affecting questing nymph activity was saturation deficit. As for the timing of seasonal emergence, we confirmed that the threshold temperature at this latitude for larvae is 10°C (mean maximum) while that for nymphs is 8°C.

Lyme borreliosis in Europe

Despite improvements in prevention, diagnosis and treatment, Lyme borreliosis (LB) is still the most common arthropod-borne disease in temperate regions of the northern hemisphere, with risk of infection associated with occupation (e.g. forestry work) and certain outdoor recreational activities (e.g. mushroom collecting). In Europe, LB is caused by infection with one or more pathogenic European genospecies of the spirochaete Borrelia burgdorferi sensu lato, mainly transmitted by the tick Ixodes ricinus. Recent surveys show that the overall prevalence of LB may be stabilising, but its geographical distribution is increasing. In addition, much remains to be discovered about the factors affecting genospecific prevalence, transmission and virulence, although avoidance of tick bite still appears to be the most efficient preventive measure. Uniform, European-wide surveillance programmes (particularly on a local scale) and standardisation of diagnostic tests and treatments are still urgently needed, especially in the light of climate change scenarios and land-use and socio-economic changes. Improved epidemiological knowledge will also aid development of more accurate risk prediction models for LB. Studies on the effects of biodiversity loss and ecosystem changes on LB emergence may identify new paradigms for the prevention and control of LB and other tick-borne diseases.

Staggered chromosomal hybrid zones in the house mouse: relevance to reticulate evolution and speciation

In the house mouse there are numerous chromosomal races distinguished by different combinations of metacentric chromosomes. These may come into contact with each other and with the ancestral all-acrocentric race, and form hybrid zones. The chromosomal clines that make up these hybrid zones may be coincident or separated from each other (staggered). Such staggered hybrid zones are interesting because they may include populations of individuals homozygous for a mix of features of the hybridising races. We review the characteristics of four staggered hybrid zones in the house mouse and discuss whether they are examples of primary or secondary contact and whether they represent reticulate evolution or not. However, the most important aspect of staggered hybrid zones is that the homozygous populations within the zones have the potential to expand their distributions and become new races (a process termed 'zonal raciation'). In this way they can add to the total 'stock' of chromosomal races in the species concerned. Speciation is an infrequent phenomenon that may involve an unusual set of circumstances. Each one of the products of zonal raciation has the potential to become a new species and by having more races increases the chance of a speciation event.

New metacentric population of the house mouse (Mus musculus domesticus) found in Valchiavenna, Northern Italy

Although the standard karyotype of the western house mouse (Mus musculus domesticus) consists entirely of telocentric chromosomes, there are over 100 populations across western Europe and North Africa characterized by different sets of metacentrics formed by Robertsonian fusions and whole-arm reciprocal translocations. Here we report the discovery of a new metacentric population from Valchiavenna, northern Italy, that we have named the 'Lower Valchiavenna population' (abbreviated as ILVC). This metacentric population is found in villages and on farms over a 10-kilometer stretch comprising the southern half of Valchiavenna. ILVC is characterized by the metacentrics 1.18, 2.4, 3.8, 5.15, 6.7, 9.14, 10.12, 11.13 and 16.17, and appears to be closely related to the Chiasso population (CHCH), which possesses the same set of metacentrics except 1.18. We discuss the evolutionary origin of ILVC in relation to human occupation of the region. We also suggest that the geographical position of ILVC between 2 other metacentric populations with entirely different sets of metacentrics (Chiavenna, ICHI, and lower Valtellina, ILVA) may provide 2 additional chromosomal hybrid zones for the study of speciation.

Spatial and temporal dynamics of lymphocytic choriomeningitis virus in wild rodents, northern Italy

Prevalence of virus infection was higher in areas of greater rodent density.

We determined the prevalence of infection with lymphocytic choriomeningitis virus (LCMV) among small mammals in northern Italy and analyzed long-term dynamics of LCMV in a rodent population in the province of Trento. LCMV is circulating among the most widespread and common wild rodent species in this area (Apodemus flavicollis, Myodes glareolus, and Microtus arvalis); overall prevalence is 6.8%. During 2000–2006, intensive monitoring of LCMV in a population of yellow-necked mice (A. flavicollis) showed a positive correlation between prevalence of infection and rodent density. At the individual level, weight and sex appeared to correlate with antibody prevalence, which suggests that horizontal transmission of LCMV occurs principally among heavier, older males and occurs during fighting. Isolation and genetic characterization of this virus will be the crucial next steps for a better understanding of its ecology.

The genetic impact of translocations and habitat fragmentation in chamois (Rupicapra) spp

The chamois is a useful species with which to investigate the combined genetic impact of habitat fragmentation, over hunting, and translocations. Genetic variation within and between chamois (genus Rupicapra) populations was analyzed in 259 individuals from 16 sampling sites located in Italy, Spain, Slovakia, and the Czech Republic. Two mitochondrial DNA markers (control region and cytochrome b) and 11 nuclear microsatellites were typed. The principal results of this study can be summarized as follows: 1) high and significant differentiation between almost all chamois populations is observed even on a microgeographical scale, probably caused by the patchy distribution of this species, sharp geographical barriers to gene flow, and drift effects related to recent bottlenecks; 2) historical translocation events have left a clear genetic signature, including interspecific hybridization in some Alpine localities; 3) the Apennine subspecies of chamois, Rupicapra pyrenaica ornata, shows a high and similar level of divergence (about 1.5 My) from the Pyrenean (Rupicapra pyrenaica pyrenaica) and the Alpine (Rupicapra rupicapra) chamois; therefore, the specific status of these taxa should be revised. These results confirm the potential of population genetic analyses to dissect and interpret complex patterns of diversity in order to define factors important to conservation and management.

Forest structure and roe deer abundance predict tick-borne encephalitis risk in Italy

Background

The Western Tick-borne encephalitis (TBE) virus often causes devastating or lethal disease. In Europe, the number of human TBE cases has increased dramatically over the last decade, risk areas are expanding and new foci are being discovered every year. The early localisation of new TBE foci and the identification of the main risk factors associated with disease emergence represent a priority for the public health community. Although a number of socio-economic parameters have been suggested to explain TBE upsurges in eastern Europe, the principal driving factors in relatively stable western European countries have not been identified.

Methodology/Principal Findings

In this paper, we analyse the correlation between the upsurge of TBE in 17 alpine provinces in northern Italy from 1992 to 2006 with climatic variables, forest structure (as a proxy for small mammal reservoir host abundance), and abundance of the principal large vertebrate tick host (roe deer), using datasets available for the last 40 years. No significant differences between the pattern of changes in climatic variables in provinces where TBE has emerged compared to provinces were no clinical TBE cases have been observed to date. Instead, the best model for explaining the increase in TBE incidence in humans in this area include changes in forest structure, in particular the ratio of coppice to high stand forest, and the density of roe deer.

Conclusion/Significance

Substantial changes in vegetation structure that improve habitat suitability for the main TBE reservoir hosts (small mammals), as well as an increase in roe deer abundance due to changes in land and wildlife management practices, are likely to be among the most crucial factors affecting the circulation potential of Western TBE virus and, consequently, the risk of TBE emergence in humans in western Europe. We believe our approach will be useful in predicting TBE risk on a wider scale.

Development of unique house mouse resources suitable for evolutionary studies of speciation

Two house mouse subspecies, Mus musculus domesticus and Mus musculus musculus, form a hybrid zone in Europe and represent a suitable model for inferring the genes contributing to isolation barriers between parental taxa. Despite long-term intensive studies of this hybrid zone, we still know relatively little about the causes and mechanisms maintaining the 2 taxa as separate subspecies; therefore, to gain insight into this process, we developed 8 wild-derived inbred house mouse strains. In order to produce strains as pure domesticus or musculus genomes as possible, the individuals used to establish the breeding colony for the 3 domesticus and 2 of the musculus strains were captured in the Czech Republic from wild populations at extreme western and eastern edges of the subspecific contact zone, respectively. The remaining 3 musculus strains were bred from mice captured about 250 km east of the hybrid zone. Genetic analysis based on 361 microsatellite loci showed that 82% of these markers are diagnostic for either the musculus or the domesticus strains. In order to demonstrate the potential utility of this genetic differentiation in such strains, phenotypic variation was scored for 2 strains from opposite edges of the hybrid zone and significant differences in morphology, reproductive performance, in vitro immune responses, mate choice based on urinary signals, and aggressiveness were found. In addition, the 3 strains derived from musculus populations far from the hybrid zone display significant differences in polymorphism in hybrid male sterility when crossed with the laboratory strains C57BL/6 or C57BL/10, which have a predominantly domesticus genome. Although further studies will be necessary to demonstrate intersubspecific differences, all analyses presented here indicate that these newly developed house mouse strains represent a powerful tool for elucidating the genetic basis of isolation barriers in hybrid zones and for studying speciation in general.