An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data

In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F_ST statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.     

A new mitochondrial haplotype confirms the distinctiveness of the Italian wolf (Canis lupus) population

In the past century the Italian wolf has been repeatedly indicated as a distinct subspecies, Canis lupus italicus, due to its unique morphology and its distinctive mtDNA control region (CR) monomorphism. However, recent studies on wolf x dog hybridization in Italy documented the presence of a second mtDNA CR haplotype (W16), previously found only in wolves from Eastern Europe, casting doubts on the genetic uniqueness of the Italian wolves. To test whether this second haplotype belongs to the Italian wolf population, we genotyped 92 wolf DNA samples from Italy, Slovenia, Greece and Bulgaria at four mtDNA regions (control-region, ATP6, COIII and ND4 genes) and at 39 autosomal microsatellites. Results confirm the presence of two mtDNA multi-fragment haplotypes (WH14 and WH19) in the Italian wolves, distinct from all the other European wolves. Network analyses of the multi-fragment mtDNA haplotypes identified two strongly differentiated clades, with the Italian wolf WH14 and WH19 multi-fragment haplotypes rooted together. Finally, Bayesian clustering clearly assigned all the wolves sampled in Italy to the Italian population, regardless of the two different multi-fragment haplotypes. These results demonstrate that the W16 CR haplotype is part of the genetic pool of the Italian wolf population, reconfirming its distinctiveness from other European wolves. Overall, considering the presence of unique mtDNA and Y-linked haplotypes, the sharply different frequencies of genome-wide autosomal alleles and the distinct morphological features of Italian wolves, we believe that this population should be considered a distinct subspecies.     

Grey squirrels in central Italy: a new threat for endemic red squirrel subspecies

A new population of the invasive American Eastern grey squirrel (Sciurus carolinensis) has recently settled in central Italy from an accidental release in Perugia, Umbria in the early 2000s. The grey squirrel is known to compete with and exclude native red squirrels (S. vulgaris) in the British Isles and Northern Italy, so it represents a potentially important new conservation threat to the red squirrel subspecies of south and central Italy, S. vulgaris italicus and S. v. meridionalis, which are endemic to peninsular Italy. The grey squirrel population range in Perugia is currently expanding at a rate of about 0.29 km/year (SD 0.19), slower than grey squirrel invasions elsewhere in Europe. Nuclear DNA analysed at 12 different microsatellite loci revealed that the grey squirrels in Perugia have extremely low genetic diversity, consistent with a small founder size. Genetic assignment tests indicate that the Perugia population was founded by translocations from an established population in Piedmont, Italy. No genetic substructure is evident yet in the Perugia population. These results together have serious consequences for the management of the grey squirrel invasion in Perugia and the conservation of the red squirrel subspecies: the Perugia grey squirrel population should be eradicated if politically feasible; otherwise new releases of grey squirrels, especially from sources other than the Piedmont population, should be prevented because such introductions could increase genetic diversity, thereby potentially increasing population range expansion rate to the much higher levels seen for more diverse grey squirrel populations elsewhere in Europe.     

Effects of an exceptionally snowy winter on chamois survival

Although weather-induced mass mortalities of wild ungulates have been reported, no study has quantified how these episodes may affect the survival of prime-aged adults. Long-term studies of marked ungulates have instead consistently found very weak or no effects of weather on the survival of this age class, particularly for females. We report on the effects of the exceptionally snowy winter of 2008–2009 on three populations of chamois in the western Alps: two in Italy, one in France. In the Alpi Marittime Natural Park in Italy, mortality of prime-aged females (aged 2–9 years) was 43%, about five times higher than reported by previous studies of chamois. Just across the continental divide in the adjacent Mercantour National Park (PNM) in France, however, prime-aged female mortality was only 6%. Senescent females suffered very high mortality in both populations (100% and 56%). In the Gran Paradiso National Park in Italy and in the Alpi Marittime Natural Park, adult male mortality rate was respectively of 81% and 44%, whereas in the PNM, it was only 10%. A recent reduction in population density in the French population, or lower absolute snowfall than in Italy, may explain the difference in survival. Survival of males and prime-aged females can be affected by exceptional weather events, possibly in combination with high population density. Adult chamois of both sexes appeared to show elevated mortality in response to harsh winter conditions. Our results underline the importance of considering sex and age classes in evaluating the impacts of population density in wild ungulates.     

Effects of range position,inter-annual variation and density on demographic transition rates of <Emphasis Type="Italic">Hornungia petraea</Emphasis> populations

The central-marginal model assumes unfavourable and more variable environmental conditions at the periphery of a species’ distribution range to negatively affect demographic transition rates, finally resulting in reduced population sizes and densities. Previous studies on density-dependence as a crucial factor regulating plant population growth have mainly focussed on fecundity and survival. Our objective is to analyse density-dependence in combination with the effect of inter-annual variation and range position on all life stages of an annual plant species, Hornungia petraea, including germination and seed incorporation into the seed bank. As previous studies on H. petraea had revealed a pattern opposite to existing theory with lower population densities at the distribution centre in Italy than at the periphery in Germany, we hypothesised that (1) demographic transition rates are lower, (2) the inter-annual variation in demographic transition rates is higher and (3) the intensity of density-dependence is weaker in Italy than in Germany. To analyse demographic transition rates, we used an autoregressive covariance strategy for repeated measures including density and inter-annual variation. All the three hypotheses were confirmed, but the impact of range position, density-dependence and inter-annual variation differed among the transition steps. All transition rates except fecundity were higher in the German populations than in the Italian populations. Germination rate and incorporation rate into the seed bank were strongly density-dependent. Central populations showed a larger inter-annual variation in fecundity and winter survival rate. Winter survival rate was the only transition step with a stronger density-dependence in peripheral populations. In most cases, these differences between distribution centre and periphery would not have emerged without taking density-dependence and inter-annual variation into account. We conclude that including range position, inter-annual variation and density-dependence in one single statistical model is an important tool for the interpretation of demographic patterns regarding the central-marginal model. Electronic Supplementary Material Supplementary material is available for this article at     

Evidence of genetic distinction and long-term population decline in wolves (Canis lupus) in the Italian Apennines

Historical information suggests the occurrence of an extensive human-caused contraction in the distribution range of wolves (Canis lupus) during the last few centuries in Europe. Wolves disappeared from the Alps in the 1920s, and thereafter continued to decline in peninsular Italy until the 1970s, when approximately 100 individuals survived, isolated in the central Apennines. In this study we performed a coalescent analysis of multilocus DNA markers to infer patterns and timing of historical population changes in wolves surviving in the Apennines. This population showed a unique mitochondrial DNA control-region haplotype, the absence of private alleles and lower heterozygosity at microsatellite loci, as compared to other wolf populations. Multivariate, clustering and Bayesian assignment procedures consistently assigned all the wolf genotypes sampled in Italy to a single group, supporting their genetic distinction. Bottleneck tests showed evidences of population decline in the Italian wolves, but not in other populations. Results of a Bayesian coalescent model indicate that wolves in Italy underwent a 100- to 1000-fold population contraction over the past 2000-10,000 years. The population decline was stronger and longer in peninsular Italy than elsewhere in Europe, suggesting that wolves have apparently been genetically isolated for thousands of generations south of the Alps. Ice caps covering the Alps at the Last Glacial Maximum (c. 18,000 years before present), and the wide expansion of the Po River, which cut the alluvial plains throughout the Holocene, might have provided effective geographical barriers to wolf dispersal. More recently, the admixture of Alpine and Apennine wolf populations could have been prevented by deforestation, which was already widespread in the fifteenth century in northern Italy. This study suggests that, despite the high potential rates of dispersal and gene flow, local wolf populations may not have mixed for long periods of time.     

Estimation of population density of European pine marten in central Italy using camera trapping

Evaluating presence and abundance of small carnivores is essential for their conservation. In Italy, there is scarce information on European pine marten distribution, and no data are published on its abundance. Camera traps have been widely used to estimate population density applying capture–recapture models for species in which individual recognition is possible. Here we estimate the abundance of European pine martens in central Italy using camera trapping and a model that allows the estimation of population density without the need for individual recognition Rowcliffe et al. (Anim Conserv 11:185–186, 2008). Camera trapping was also used to evaluate habitat use patterns by martens. Fifteen camera traps were deployed in 90 placements for 15 days each, for a total of 1,334 camera days. Pine martens were captured in 24% of camera trap placements with a mean trap success rate of 0.33 photographs per camera placement. Estimated pine marten population density in the study area was 0.34 individuals km⁻². Marten trap rate was not strongly associated with any habitat type, although there were trends towards lower probability of records at locations with high coverage of cultivated fields and higher probability of records at locations with high coverage of human-made woodland. The results suggest that pine martens in this area are not confined to wooded habitat. To our knowledge, this study is the first application of the Rowcliffe et al. (Anim Conserv 11:185–186, 2008) method to a wild carnivore population and, furthermore, the first estimation of population density of pine martens in Italy.     

Postglacial dispersal of Phlebotomus perniciosus into France

Phlebotomus perniciosus was identified morphologically in samples from France and northeast Spain, and individuals were then characterized at three polymorphic isoenzyme loci (by isoelectrofocusing) and at the mitochondrial DNA locus (by comparative DNA sequence analysis of a fragment of the Cytochrome b gene). The four polymorphic loci gave conflicting patterns of population relationships, which can be explained by hypothesizing different amounts of gene introgression at each locus when two distinctive lineages met in southern France or northeast Spain after isolation in southern Italy and Spain during the Pleistocene Ice Ages. P. perniciosus is an important vector of leishmania infantum and so these population differentiation studies are relevant for predicting the emergence and spread of leishmaniasis in relation to environmental changes, including climate.     

Duplication polymorphism at MHC class II DRB1 locus in the wild boar (<Emphasis Type="Italic">Sus scrofa</Emphasis>)

The origin of allelic polymorphism in genes of the major histocompatibility complex represents a central topic in evolutionary genetics as it is probably the most polymorphic region in the nuclear genome of vertebrates. Accordingly, the analyses of genetic variability at these loci provide evidence complementary to the population genetics studies based on neutral loci. In this study, four wild boar populations, two from Italy (Florence region and Castelporziano Presidential Reserve, outside Rome) and one each from Hungary and Poland, were characterized at a highly polymorphic fragment including part of intron 1 and exon 2 of swine leukocyte antigen (SLA) class II DRB1 gene by direct sequencing and by cloning. Excluding the false alleles, a total of 18 different sequences were observed in 57 individuals. The high ratio of nonsynonymous (dN) vs synonymous (dS) substitution rates in the peptide-binding region supports the hypothesis that balancing selection is operating at this locus. A duplication event at the DRB1 gene was documented only in one Italian population with both copies being putatively active. This is the first evidence of a polymorphism for the number of copies of an SLA gene.     

Migratory flows in apulia: Preliminary studies on some samples

The aim of this study is to analyse the structural characteristics, educational level, professed religion, composition of the family nucleus in Italy and in the home country, and work conditions in Italy and in the home country, in order to describe the anthropological stress of the sample of immigrants examined. A series of questions was given to Albanian population immigrating to the province of Bari after 1991, Albanian refugees of 1997, Chinese population resident in Bari, and a sample of immigrants in Metaponto, regarding their specific motives for immigration.     

Seroprevalence study of Tick-borne encephalitis, Borrelia burgdorferi, Dengue and Toscana virus in Turin Province

Tick borne encephalitis virus (TBEV) is present in some European countries and it is transmitted by a tick bite. Ixodes ricinus is the main vector of the infection in Italy, where fortunately clinical neurological manifestations, typical of the more serious phase of the disease, are very rarely observed. This behaviour is different from other endemic Euroasiatic areas where numerous cases of encephalitis are described. However TBE transmission has not been widely investigated in Italy and available epidemiological data have been obtained only by studies performed in Central and Northern Regions of the country. In addition seroepidemiological researches were made prevalently on subjects at high risk of tick bite, such as hunters or forest guards from Trentin and Central Italy. No precise information about TBE virus diffusion was available in the Piedmont before our investigations. We found that hunters and wild boar breeders seem to be particularly exposed to the risk of TBE virus infection in Turin Province and in particular in the Susa valley, although no neurological involvement was observed in our population. In particular a seroprevalence of about 5% was detected by the use of purified antigens ELISA test, amongst the subjects at high risk of tick bite. Moreover low risk individuals showed a seroprevalence of below 2%. In addition a parallel seroepidemiological study was performed in Turin Province for Borrelia burgdorferi, the aetiological agent of Lyme disease, also transmitted by tick bite (e.g. Ixodes ricinus), for Dengue and Toscana (TOS) arboviruses, respectively transmitted by Aedes mosquitoes and phlebotomes. Data reported here demonstrate only a sporadic presence in our population of antibodies against Borrelia and Dengue infection. Moreover using an ELISA test performed with viral purified nucleoprotein, we reported a total percentage of about 3% of subjects positive for TOSV.     

Secondary Contact and Admixture between Independently Invading Populations of the Western Corn Rootworm,Diabrotica virgifera virgifera in Europe

The western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is one of the most destructive pests of corn in North America and is currently invading Europe. The two major invasive outbreaks of rootworm in Europe have occurred, in North-West Italy and in Central and South-Eastern Europe. These two outbreaks originated from independent introductions from North America. Secondary contact probably occurred in North Italy between these two outbreaks, in 2008. We used 13 microsatellite markers to conduct a population genetics study, to demonstrate that this geographic contact resulted in a zone of admixture in the Italian region of Veneto. We show that i) genetic variation is greater in the contact zone than in the parental outbreaks; ii) several signs of admixture were detected in some Venetian samples, in a Bayesian analysis of the population structure and in an approximate Bayesian computation analysis of historical scenarios and, finally, iii) allelic frequency clines were observed at microsatellite loci. The contact between the invasive outbreaks in North-West Italy and Central and South-Eastern Europe resulted in a zone of admixture, with particular characteristics. The evolutionary implications of the existence of a zone of admixture in Northern Italy and their possible impact on the invasion success of the western corn rootworm are discussed.     

Modelling the amphibian chytrid fungus spread by connectivity analysis: towards a national monitoring network in Italy

The emerging amphibian disease, Batrachochytrium dendrobatidis (Bd), is driving population declines worldwide and even species extinctions in Australia, South and Central America. In order to mitigate effects of Bd on amphibian populations, high-exposed areas should be identified at the local scale and effective conservation measures should be planned at the national level. This assessment is actually lacking in the Mediterranean basin, and in particular in Italy, one of the most relevant amphibian diversity hotspots in the entire region. In this study, we reviewed the available information on Bd in Italy, and conducted a 5-year molecular screening on 1274 individual skin swabs belonging to 18 species. Overall, we found presence of Bd in 13 species and in a total of 56 known occurrence locations for peninsular Italy and Sardinia. We used these occurrence locations and climate data to model habitat suitability of Bd for current and future climatic scenarios. We then employed electric circuit theory to model landscape permeability to the diffusion of Bd, using a resistance map. With this procedure, we were able to model, for the first time, the diffusion pathways of Bd at the landscape scale, characterising the main future pathways towards areas with a high probability of Bd occurrence. Thus, we identified six national protected areas that will become pivotal for a nationally-based strategic plan in order to monitor, mitigate and possibly contrast Bd diffusion in Italy.

     

Telomere shortening in women resident close to waste landfill sites

Several studies demonstrate links between environmental stress and index of reduced health, including risk factors for cardiovascular disease, reduced immune function and cancer risks. We investigated the hypothesis that pollution, as an environmental stress, impacts health by modulating the rate of cellular aging in healthy pregnant women. Our research looked at the effects that illegal waste sites have on the localized population of pregnant women in Campania, Italy. As is often the case in illegal dumping, the effects on the population are often seen well before knowing what specific agents in the soil and water are responsible. Here we provide evidence that the pollution in this region is significantly associated with higher oxidative stress, shorter telomere length and lower telomerase activity, which are known determinants of cell senescence and aging-related meiotic dysfunction in women, in peripheral blood mononuclear cells from healthy pregnant women, subjected to therapeutic abortion in the second trimester of pregnancy. These findings may have implications for understanding how, at the cellular level, environmental stress may promote earlier onset of age-related diseases.     

The HLA system in Italy

4,902 Italians were typed for HLA-A antigens, 4,721 for HLA-B and 1,503 for HLA-C. The samples, which were composed of unrelated, healthy individuals born in Italy, were used for estimating HLA-A, HLA-B and HLA-C gene frequencies with the maximum-likelihood method. Different Italian regions showed significant differences in the HLA alleles, providing further evidence for the genetic heterogeneity of the Italian population. HLA gene frequencies place continental Italy and Sicily in a position which is similar to that of other Mediterranean populations, whereas the genetic isolation of Sardinia is quite evident. The most significant linkage disequilibrium values found in the Italian population (except for Sardinia) were in agreement with those observed in other Caucasian populations. The difference between Northern and Southern Italy and between continental Italy and Sardinia was emphasized by the linkage disequilibrium values and by the principal-component analysis as well.     

Range and local population densities of brown bear Ursus arctos in Slovenia

Solid understanding of species’ range and local population densities is important for successful wildlife management and research. Specific behavioral and ecological characteristics make brown bear Ursus arctos a difficult species to study. We present a map of range and local population densities of brown bears in Slovenia, made with the use of a new approach similar to voting classifications based on a combination of four datasets: Global Positioning System telemetry data, records of bear removals, systematic and opportunistic direct observations and signs of bear presence, and noninvasive genetic samples. Results indicate that the majority of bears in Slovenia live in Dinaric Mountains in the southern part of the country where local bear population densities exceed 40 bears/100 km². This is one of the highest population densities reported so far for this species worldwide. Population densities decrease towards the north (Alpine region) and are very low along the border with Italy and Austria where almost no females are present. This explains slow past and present expansion of this transboundary bear population into the Alps and should be considered in future bear re-colonization management strategies. Results also showed that data from observations and removals overestimate bear population densities at low values, while mortality and genetic data overestimate population densities in areas with more people. Nevertheless, all data types appeared useful for describing the general bear distribution patterns. Similar approach could be applied to studies of other charismatic or game species, for which several types of data are often available.     

Bone-fracture incidence rate in two Italian regions with different fluoride concentration levels in drinking water.

The effect of the fluoride concentration in drinking water on the prevention of fractures related to osteoporosis has been questioned or contradicted in several recent studies. These studies have been mostly performed using water with artificially added fluoride, at the optimum level of about 1 mg/l. In the present study authors have investigated the effect of equal or greater fluoride concentrations (mean 1.45 mg/l) naturally present in waters supplied for human consumption to a population of 72.756 (Bracciano county), in comparison with a population of 126.189 (Avezzano county), supplied with low fluoride concentration water (mean 0.05 mg/l). The incidence of fractures in the years 1990 and 1991 was evaluated in the two areas (Bracciano and Avezzano), which are located in central Italy and where population have a similar life style, economic and social level and employment structure. The incidence data were obtained from the registers of the public hospital taken as a reference in each district. The authors noticed a significantly greater rate of fracture incidence at several parts of the body, in particular femur fractures (relative risks for males 4.28 and for females 2.64), in the population of the district of Avezzano than in the population of Bracciano. The greater concentration of fluoride in waters distributed for human consumption in Bracciano district seems to have the effect of protecting its inhabitants against fractures.     

Protostrongylus pulmonalis from hares (Lepus europaeus) in Italy

Protostrongylus (Pulmostrongylus) pulmonalis from Lepus europaeus in Italy (Alto Adige) was studied. Most of the parasite population showed the typical morphology described for this species. Variations observed in the morphological features of gubernaculum, antero-lateral ray and telamon are considered to lie within the range of variability of the species. This is the first record of Protostrongylus (Pul.) pulmonalis in hares in Italy.     

Latitude-correlated genetic polymorphisms: selection or gene flow?

Latitude-correlated polymorphisms can be due to either selection-driven evolution or gene flow. To discriminate between them, we propose an approach that studies subpopulations springing from a single population that have lived for generations at different latitudes and have had a low genetic admixture. These requirements are fulfilled to a large extent by Ashkenazi and Sephardi Jews. The original population lived at a latitude of 35 degrees N, where the Sephardis still live. The Ashkenazis, however, moved to a latitude of 50 degrees N, starting about 10 centuries ago. The present study examines 3 latitude-correlated polymorphisms: PGP, PGM1, and AHSG. We found that PGP*2 and AHSG*2 alleles most likely underwent selection-driven evolution, but that PGM1*ts allele was not similarly affected. Since temperature might have been considered a reasonable selective factor, we also studied a population living at >800 m above sea level from Aosta Valley (Italy).