Genetic diversity among horse populations with a special focus on the Franches-Montagnes breed

Genetic characterization helps to assure breed integrity and to assign individuals to defined populations. The objective of this study was to characterize genetic diversity in six horse breeds and to analyse the population structure of the Franches-Montagnes breed, especially with regard to the degree of introgression with Warmblood. A total of 402 alleles from 50 microsatellite loci were used. The average number of alleles per locus was significantly lower in Thoroughbreds and Arabians. Average heterozygosities between breeds ranged from 0.61 to 0.72. The overall average of the coefficient of gene differentiation because of breed differences was 0.100, with a range of 0.036-0.263. No significant correlation was found between this parameter and the number of alleles per locus. An increase in the number of homozygous loci with increasing inbreeding could not be shown for the Franches-Montagnes horses. The proportion of shared alleles, combined with the neighbour-joining method, defined clusters for Icelandic Horse, Comtois, Arabians and Franches-Montagnes. A more disparate clustering could be seen for European Warmbloods and Thoroughbreds, presumably from frequent grading-up of Warmbloods with Thoroughbreds. Grading-up effects were also observed when Bayesian and Monte Carlo resampling approaches were used for individual assignment to a given population. Individual breed assignments to defined reference populations will be very difficult when introgression has occurred. The Bayesian approach within the Franches-Montagnes breed differentiated individuals with varied proportions of Warmblood.

A common ancestral glycoprotein (GP) 9 1828A>G (Asn45Ser) gene mutation occurring in European families from Australia and Northern Europe with Bernard-Soulier Syndrome (BSS)

Bernard-Soulier syndrome (BSS) is an extremely rare hereditary bleeding disorder, caused by mutations occurring in the Glycoprotein (GP) Ibalpha, GPIbbeta and GP9 genes that encode for the corresponding subunits of platelet GPIb-V-IX adhesion receptor complex. BSS has been reported in many populations, mostly behaving in an autosomal-recessive manner.While the great majority of BSS mutations are unique to a single individual or family, the GP9 1828A>G Asn45Ser mutation, which we have identified in an undocumented Australian Caucasian, has already been reported in multiple unrelated Caucasian families from various Northern and Central European countries. Haplotype analysis of 19 BSS patients from 15 unrelated Northern European families (including 2 compound heterozygote siblings from a British family previously published, and 17 1828A>G Asn45Ser homozygotes), showed that 14 of these BSS patients from 11 of the 1828A>G Asn45Ser homozygote families share a common haplotype at the chromosomal region 3' to the GP9 gene. Hence, the results suggest that the GP9 1828A>GAsn45Ser mutation in these families is ancient, and its frequent emergence in the European population is the result of a founder effect rather than recurrent mutational events. Association of the 1828A>G Asn45Ser mutation with variant haplotypes in 4 other Northern European BSS families raised the possibility of a second founder event, or rare recombinations in these families. Additional members from these 'atypical' lineages would need to be screened to resolve this question.

Invasion patterns of emerald ash borer and European earthworms in forested ecosystems

Invasive and exotic species present a serious threat to the health and sustainability of natural ecosystems. These species often benefit from anthropogenic activities that aid their introduction and dispersal. This dissertation focuses on invasion dynamics of the emerald ash borer, native to Asia, and European earthworms. These species have shown detrimental impacts in invaded forest ecosystems across the Great Lakes region, and continue to spread via human-assisted long distance dispersal and by natural modes of dispersal into interior forests from areas of introduction. Successful forest management requires that the impact and effect of invasive species be considered and incorporated into management plans. Understanding patterns and constraints of introduction, establishment, and spread will aid in this effort. To assist in efforts to locate introduction points of emerald ash borer, a multicriteria risk model was developed to predict the highest risk areas. Important parameters in the model were road proximity, land cover type, and campground proximity. The model correctly predicted 85% of known emerald ash borer invasion sites to be at high risk. The model’s predictions across northern Michigan can be used to focus and guide future monitoring efforts. Similar modeling efforts were applied to the prediction of European earthworm invasion in northern Michigan forests. Field sampling provided a means to improve upon modeling efforts for earthworms to create current and future predictions of earthworm invasion. Those sites with high soil pH and high basal area of earthworm preferred overstory species (such as basswood and maples) had the highest likelihood of European earthworm invasion. Expanding beyond Michigan into the Upper Great Lakes region, earthworm populations were sampled across six National Wildlife Refuges to identify potential correlates and deduce specific drivers and constraints of earthworm invasion. Earthworm communities across all refuges were influenced by patterns of anthropogenic activity both within refuges and in surrounding ecoregions of study. Forest composition, soil pH, soil organic matter, anthropogenic cover, and agriculture proximity also proved to be important drivers of earthworm abundance and community composition. While there are few management options to remove either emerald ash borer or European earthworms from forests after they have become well established, prevention and early detection are important and can be beneficial. An improved understanding the factors controlling the distribution and invasion patterns of exotic species across the landscape will aid efforts to determine their consequences and generate appropriate forest management solutions to sustain ecosystem health in the presence of these invaders.

Survey of public knowledge about Echinococcus multilocularis in four European countries: Need for proactive information

Background Public information about prevention of zoonoses should be based on the perceived problem by the public and should be adapted to regional circumstances. Growing fox populations have led to increasing concern about human alveolar echinococcosis, which is caused by the fox tapeworm Echinococcus multilocularis. In order to plan information campaigns, public knowledge about this zoonotic tapeworm was assessed. Methods By means of representative telephone interviews (N = 2041), a survey of public knowledge about the risk and the prevention of alveolar echinococcosis was carried out in the Czech Republic, France, Germany and Switzerland in 2004. Results For all five questions, significant country-specific differences were found. Fewer people had heard of E. multilocularis in the Czech Republic (14%) and France (18%) compared to Germany (63%) and Switzerland (70%). The same effect has been observed when only high endemic regions were considered (Czech Republic: 20%, France: 17%, Germany: 77%, Switzerland: 61%). In France 17% of people who knew the parasite felt themselves reasonably informed. In the other countries, the majority felt themselves reasonably informed (54–60%). The percentage that perceived E. multilocularis as a high risk ranged from 12% (Switzerland) to 43% (France). In some countries promising measures as deworming dogs (Czech Republic, Switzerland) were not recognized as prevention options. Conclusion Our results and the actual epidemiological circumstances of AE call for proactive information programs. This communication should enable the public to achieve realistic risk perception, give clear information on how people can minimize their infection risk, and prevent exaggerated reactions and anxiety.

Associations of Forest Type, Parasitism and Body Condition of Two European Passerines, Fringilla coelebs and Sylvia atricapilla

Human-induced forest modification can alter parasite-host interactions and might change the persistence of host populations. We captured individuals of two widespread European passerines (Fringilla coelebs and Sylvia atricapilla) in southwestern Germany to disentangle the associations of forest types and parasitism by haemosporidian parasites on the body condition of birds. We compared parasite prevalence and parasite intensity, fluctuating asymmetries, leukocyte numbers, and the heterophil to lymphocyte ratio (H/L-ratio) among individuals from beech, mixed-deciduous and spruce forest stands. Based on the biology of bird species, we expected to find fewer infected individuals in beech or mixed-deciduous than in spruce forest stands. We found the highest parasite prevalence and intensity in beech forests for F. coelebs. Although, we found the highest prevalence in spruce forests for S. atricapilla, the highest intensity was detected in beech forests, partially supporting our hypothesis. Other body condition or health status metrics, such as the heterophil to lymphocyte ratio (H/L-ratio), revealed only slight differences between bird populations inhabiting the three different forest types, with the highest values in spruce for F. coelebs and in mixed-deciduous forests for S. atricapilla. A comparison of parasitized versus non-parasitized individuals suggests that parasite infection increased the immune response of a bird, which was detectable as high H/L-ratio. Higher infections with blood parasites for S. atricapilla in spruce forest indicate that this forest type might be a less suitable habitat than beech and mixed-deciduous forests, whereas beech forests seem to be a suboptimal habitat regarding parasitism for F. coelebs.

Prognostic implications of the seventh edition of the international union against cancer classification for patients with gastric cancer: the Western experience of patients treated in a single-center European institution

PURPOSE Validity of the seventh edition of the American Joint Committee on Cancer/International Union Against Cancer (AJCC/UICC) staging systems for gastric cancer has been evaluated in several studies, mostly in Asian patient populations. Only few data are available on the prognostic implications of the new classification system on a Western population. Therefore, we investigated its prognostic ability based on a German patient cohort. PATIENTS AND METHODS Data from a single-center cohort of 1,767 consecutive patients surgically treated for gastric cancer were classified according to the seventh edition and were compared using the previous TNM/UICC classification. Kaplan-Meier analyses were performed for all TNM stages and UICC stages in a comparative manner. Additional survival receiver operating characteristic analyses and bootstrap-based goodness-of-fit comparisons via Bayesian information criterion (BIC) were performed to assess and compare prognostic performance of the competing classification systems. RESULTS We identified the UICC pT/pN stages according to the seventh edition of the AJCC/UICC guidelines as well as resection status, age, Lauren histotype, lymph-node ratio, and tumor grade as independent prognostic factors in gastric cancer, which is consistent with data from previous Asian studies. Overall survival rates according to the new edition were significantly different for each individual's pT, pN, and UICC stage. However, BIC analysis revealed that, owing to higher complexity, the new staging system might not significantly alter predictability for overall survival compared with the old system within the analyzed cohort from a statistical point of view. CONCLUSION The seventh edition of the AJCC/UICC classification was found to be valid with distinctive prognosis for each stage. However, the AJCC/UICC classification has become more complex without improving predictability for overall survival in a Western population. Therefore, simplification with better predictability of overall survival of patients with gastric cancer should be considered when revising the seventh edition.

A linguistically informed autosomal STR survey of human populations residing in the Greater Himalayan Region

The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and Indo-European. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas.

Spatial Distribution of Cryptic Species Diversity in European Freshwater Amphipods (Gammarus fossarum) as Revealed by Pyrosequencing

In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C). We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany). A clear transition is observed from type A in the east (Danube and Po drainages) to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems). Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present.

Pinus nigra (European black pine) as the dominant species of the last glacial pinewoods in south-western to central Iberia: a morphological study of modern and fossil pollen

Aim Our aim was to discriminate different species of Pinus via pollen analysis in order to assess the responses of particular pine species to orbital and millennial-scale climate changes, particularly during the last glacial period. Location Modern pollen grains were collected from current pine populations along transects from the Pyrenees to southern Iberia and the Balearic Islands. Fossil pine pollen was recovered from the south-western Iberian margin core MD95-2042. Methods We measured a set of morphological traits of modern pollen from the Iberian pine species Pinus nigra, P. sylvestris, P. halepensis, P. pinea and P. pinaster and of fossil pine pollen from selected samples of the last glacial period and the early to mid-Holocene. Classification and regression tree (CART) analysis was used to establish a model from the modern dataset that discriminates pollen from the different pine species and allows identification of fossil pine pollen at the species level. Results The CART model was effective in separating pollen of P. nigra and P. sylvestris from that of the Mediterranean pine group (P. halepensis, P. pinea and P. pinaster). The pollen of Pinus nigra diverged from that of P. sylvestris by having a more flattened corpus. Predictions using this model suggested that fossil pine pollen is mainly from P. nigra in all the samples analysed. Pinus sylvestris was more abundant in samples from Greenland stadials than Heinrich stadials, whereas Mediterranean pines increased in samples from Greenland interstadials and during the early to mid-Holocene. Main conclusions Morphological parameters can be successfully used to increase the taxonomic resolution of fossil pine pollen at the species level for the highland pines (P. nigra and P. sylvestris) and at the group of species level for the Mediterranean pines. Our study indicates that P. nigra was the dominant component of the last glacial south-western/central Iberian pinewoods, although the species composition of these woodlands varied in response to abrupt climate changes.

Hybrid ‘superswarm’ leads to rapid divergence and establishment of populations during a biological invasion

Understanding the genetic background of invading species can be crucial information clarifying why they become invasive. Intraspecific genetic admixture among lineages separated in the native ranges may promote the rate and extent of an invasion by substantially increasing standing genetic variation. Here we examine the genetic relationships among threespine stickleback that recently colonized Switzerland. This invasion results from several distinct genetic lineages that colonized multiple locations and have since undergone range expansions, where they coexist and admix in parts of their range. Using 17 microsatellites genotyped for 634 individuals collected from 17 Swiss and two non-Swiss European sites, we reconstruct the invasion of stickleback and investigate the potential and extent of admixture and hybridization among the colonizing lineages from a population genetic perspective. Specifically we test for an increase in standing genetic variation in populations where multiple lineages coexist. We find strong evidence of massive hybridization early on, followed by what appears to be recent increased genetic isolation and the formation of several new genetically distinguishable populations, consistent with a hybrid ‘superswarm’. This massive hybridization and population formation event(s) occurred over approximately 140 years and likely fuelled the successful invasion of a diverse range of habitats. The implications are that multiple colonizations coupled with hybridization can lead to the formation of new stable genetic populations potentially kick-starting speciation and adaptive radiation over a very short time.

Tracing reinforcement through asymmetrical partner preference in the European common vole Microtus arvalis

Background The mechanistic basis of speciation and in particular the contribution of behaviour to the completion of the speciation process is often contentious. Contact zones between related taxa provide a situation where selection against hybridization might reinforce separation by behavioural mechanisms, which could ultimately fully isolate the taxa. One of the most abundant European mammals, the common vole Microtus arvalis, forms multiple natural hybrid zones where rapidly diverging evolutionary lineages meet in secondary contact. Very narrow zones of hybridization spanning only a few kilometres and sex-specific gene flow patterns indicate reduced fitness of natural hybrids and incipient speciation between some of the evolutionary lineages. In this study, we examined the contribution of behavioural mechanisms to the speciation process in these rodents by fine-mapping allopatric and parapatric populations in the hybrid zone between the Western and Central lineages and experimental testing of the partner preferences of wild, pure-bred and hybrid female common voles. Results Genetic analysis based on microsatellite markers revealed the presence of multiple parapatric and largely non-admixed populations at distances of about 10 km at the edge of the area of natural hybridization between the Western and Central lineages. Wild females from Western parapatric populations and lab-born F1 hybrids preferred males from the Western lineage whereas wild females of Central parapatric origin showed no measurable preference. Furthermore, wild and lab-born females from allopatric populations of the Western or Central lineages showed no detectable preference for males from either lineage. Conclusions The detected partner preferences are consistent with asymmetrical reinforcement of pre-mating reproductive isolation mechanisms in the European common vole and with earlier results suggesting that hybridization is more detrimental to the Western lineage. As a consequence, these differences in behaviour might contribute to a further geographical stabilization of this moving hybrid zone. Such behavioural processes could also provide a mechanistic perspective for frequently-detected asymmetrical introgression patterns in the largely allopatrically diversifying Microtus genus and other rapidly speciating rodents.

Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits

Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species – the great tit Parus major – at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (< 50 km), using 22 microsatellite markers. Overall we found a low but significant genetic differentiation among sites (FST = 0.008). Genetic differentiation was higher, and genetic diversity lower, in south-western Europe. These regional differences were statistically best explained by winter temperature. Overall, our results suggest that great tits form a single patchy metapopulation across Europe, in which genetic differentiation is independent of geographical distance and gene flow may be regulated by environmental factors via movements related to winter severity. This might have important implications for the evolutionary trajectories of sub-populations, especially in the context of climate change, and calls for future investigations of local differences in costs and benefits of philopatry at large scales.

A picture of trends in Aujeszky's disease virus exposure in wild boar in the Swiss and European contexts.

BACKGROUND In parallel to the increase of wild boar abundance in the past decades, an increase of exposure to the Aujeszky's disease virus (ADV) has been reported in wild boar in several parts of Europe. Since high animal densities have been proposed to be one of the major factors influencing ADV seroprevalence in wild boar populations and wild boar abundance has increased in Switzerland, too, a re-evaluation of the ADV status was required in wild boar in Switzerland. We tested wild boar sera collected from 2008-2013 with a commercial ELISA for antibodies against ADV. To set our data in the European context, we reviewed scientific publications on ADV serosurveys in Europe for two time periods (1995-2007 and 2008-2014). RESULTS Seven out of 1,228 wild boar sera were positive for antibodies against ADV, resulting in an estimated seroprevalence of 0.57% (95% confidence interval CI: 0.32-0.96%). This is significantly lower than the prevalence of a previous survey in 2004-2005. The literature review revealed that high to very high ADV seroprevalences are reported from Mediterranean and Central-eastern countries. By contrast, an "island" of low to medium seroprevalences is observed in the centre of Europe with few isolated foci of high seroprevalences. We were unable to identify a general temporal trend of ADV seroprevalence at European scale. CONCLUSIONS The seroprevalence of ADV in wild boar in Switzerland belongs among the lowest documented in Europe. Considering the disparity of seroprevalences in wild boar in Europe, the fact that seroprevalences in Switzerland and other countries have decreased despite increasing wild boar densities and the knowledge that stress leads to the reactivation of latent ADV with subsequent excretion and transmission, we hypothesize that not only animal density but a range of factors leading to stress - such as management - might play a crucial role in the dynamics of ADV infections.

Cryptic invasion drives phenotypic changes in central European threespine stickleback

Cryptic invasions are commonly associated with genetic changes of the native species or genetic lineage that the invaders replace. Phenotypic shifts resulting from cryptic invasions are less commonly reported given the relative paucity of historical specimens that document such phenotypic changes. Here, I study such a case in two populations of threespine stickleback from central Europe, comparing contemporary patterns of gene flow with phenotypic changes between historical and contemporary population samples. I find gene flow from an invasive lineage to be associated with significant phenotypic changes, where the degree of phenotypic change corresponds with the level of gene flow that a population receives. These findings underline the utility of combining genetic approaches with phenotypic data to estimate the impact of gene flow in systems where anthropogenic alterations have removed former geographic barriers promoting cryptic invasions.