Molecular characterization of Fasciola hepatica from Sardinia based on sequence analysis of genomic and mitochondrial gene markers

The aim of the present study is to investigate for the first time the genetic diversity of samples identified morphologically as Fasciola hepatica (Platyhelminthes: Trematoda: Digenea) (n = 66) from sheep and cattle from two localities of Sardinia and to compare them with available data from other localities by partial sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes, the mitochondrial cytochrome c oxidase subunit I (COI), and nicotinamide adenine dinucleotide dehydrogenase subunit I (ND1) genes. Comparison of the sequences from Sardinia with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. hepatica. The nucleotide sequencing of ITS rDNA showed no nucleotide variation in the ITS-1, 5.8S and ITS-2 rDNA sequences among all Sardinian samples, comparing with two ITS-2 haplotypes in standard F. hepatica, showing a substitution C/T in 20 position 859, reported previously from Tunisia, Algeria, Australia, Uruguay and Spain. The present study shows that in Sardinian sheep and cattle there is the most frequent haplotype (FhITS-H1) of F. hepatica species from South Europe. Considering NDI sequences, the phylogenetic trees showed reliable grouping among the haplotypes of F. hepatica from Sardinia and the mitochondrial lineage I, including the main N1 haplotype, observed previously from Europe (Russia, Belarus, Ukraine and Bulgaria), Armenia, West Africa (Nigeria), America (Uruguay and USA), Asia (Turkey, Japan, and China), Georgia, Turkmenistan, Azerbaijan and Australia. Furthermore, common haplotypes FhCOI-H1 and FhCOI-H2 of F. hepatica from Sardinia also corresponded mostly to the first lineage including the main C1 haplotype reported previously from Eastern European and Western Asian populations, they belonged just to a phylogenically distinguishable clade, as F. hepatica from Australia, France, Turkey, Uruguay, Russia, Armenia, Ukraine, Belarus, Turkmenistan, USA, Tunisia and Algeria, indicating that this is the main haplotype involved in the spread of F. hepatica throughout all continents.     

Phylogeography of the common vole (Microtus arvalis) with particular emphasis on the colonization of the Orkney archipelago

To investigate the human introduction of the common vole Microtus arvalis onto the Orkney islands, the complete cytochrome b gene was sequenced in 41 specimens from both Orkney (four localities) and elsewhere in their range (26 localities). Orkney voles belonged to the same phylogenetic lineage, 'Western', as individuals from France and Spain indicating southwestern Europe as the most likely source area for the islands. This result is of interest with respect to the movement and trading links of the Neolithic people who likely transported the voles. As well as the Western lineage, our phylogenetic trees revealed three other purely European lineages: the 'Italian' (single specimen from N. Italy), the 'Central' (Germany, Netherlands, Denmark) and the 'Eastern' (Hungary, Slovakia, Poland, Ukraine, Finland, European Russia). Individuals from European Russia, W. Siberia, Georgia, Ukraine and Armenia formed a fifth distinct lineage coinciding with the distribution of the 'obscurus' chromosomal form of M. arvalis. These phylogeographical data suggest that M. arvalis occupied multiple refugia during the last glaciation.     

Molecular biogeography of red deer Cervus elaphus from eastern Europe: insights from mitochondrial DNA sequences

European red deer are known to show a conspicuous phylogeographic pattern with three distinct mtDNA lineages (western, eastern and North-African/Sardinian). The western lineage, believed to be indicative of a southwestern glacial refuge in Iberia and southern France, nowadays covers large areas of the continent including the British Isles, Scandinavia and parts of central Europe, while the eastern lineage is primarily found in southeast-central Europe, the Carpathians and the Balkans. However, large parts of central Europe and the whole northeast of the continent were not covered by previous analyses. To close this gap, we produced mtDNA control region sequences from more than 500 red deer from Denmark, Germany, Poland, Lithuania, Belarus, Ukraine and western Russia and combined our data with sequences available from earlier studies to an overall sample size of almost 1,100. Our results show that the western lineage extends far into the European east and is prominent in all eastern countries except for the Polish Carpathians, Ukraine and Russia where only eastern haplotypes occurred. While the latter may actually reflect the natural northward expansion of the eastern lineage after the last ice age, the present distribution of the western lineage in eastern Europe may in large parts be artificial and a result of translocations and reintroduction of red deer into areas where the species became extinct in historical times.     

Bees of the genus <Emphasis Type="Italic">Rophites</Emphasis> Spinola (Hymenoptera,Halictidae, Rophitinae) of Russia and adjacent territories

An illustrated key to Rophites species and an annotated list of 9 species from Russia and adjacent territories are given. Rophites clypealis stepposus subsp. n. and the female of R. schoenitzeri Dubitzky, 2004 are described. Lectotypes of Rhophites caucasicus Morawitz, 1876 and Rh. mandibularis Morawitz, 1891 are designated. Rophites algirus is recorded for the first time from Armenia; R. caucasicus, from Azerbaijan; R. clypealis, from Bulgaria, Russia, and Kazakhstan; R. foveolatus, from Georgia; R. quinquespinosus, from Armenia and Uzbekistan; R. schoenitzeri, from Azerbaijan and Iran.     

Chalcids of the subfamily Pteromalinae (Hymenoptera,Pteromalidae) as parasitoids of the bark beetles (Coleoptera,Scolytidae) in the fauna of Russia and adjacent territories

Eighteen species of ten genera of bark beetle parasitoids were found in the fauna of Russia and adjacent countries. Sixteen species of the parasitoids are recorded as new to the faunas of Belarus, Ukraine, Azerbaijan, Kazakhstan, Tajikistan, Uzbekistan, Kyrgyzstan, and regions of Russia. An annotated list of nineteen species of pteromalids, with data on the material examined, geographic distribution, and hosts is given. New hosts are reported for five species of the bark beetle ectoparasitoids. An original key to eighteen species and ten genera of Pteromalidae parasitizing bark beetles is provided.     

Multiple origins of European populations of the giant liver fluke Fascioloides magna (Trematoda: Fasciolidae), a liver parasite of ruminants

The giant liver fluke, Fascioloides magna, a liver parasite of free-living and domestic ruminants of Europe and North America, was analysed in order to determine the origin of European populations and to reveal the biogeography of this originally North American parasite on the European continent. The variable fragments of the mitochondrial cytochrome c oxidase subunit I (cox1; 384bp) and nicotinamide dehydrogenase subunit I (nad1; 405bp) were used. Phylogenetic trees and haplotype networks were constructed and the level of genetic structuring was evaluated using population genetic tools. In F. magna individuals originating from all European foci of infection (Italy, Czech Republic and Danube floodplain forests involving the territories of Slovakia, Hungary and Croatia) and from four of five major North American enzootic areas, 16 cox1 and 18 nad1 haplotypes were determined. The concatenated sequence set produced 22 distinct haplotypes. The European fluke populations were less diverse than those from North America in that they contained proportionately fewer haplotypes (eight), while a more substantial level of genetic diversity and a greater number of haplotypes (15) were recorded in North America. Only one haplotype was shared between the European (Italy) and North American (USA/Oregon and Canada/Alberta) flukes, supporting a western North American origin of the Italian F. magna population. Haplotypes found in Italy were distinct from those determined in the remaining European localities which indicates that introduction of F. magna to the European continent occurred more than once. In the Czech focus of infection, a south-eastern USA origin was revealed. Identical haplotypes, common to parasites from the Czech Republic and from an expanding focus in Danube floodplain forests, implies that the introduction of F. magna to the Danube region came from an already established Czech focus of infection.     

Spatial patterns and intraspecific diversity of the glacial relict legume species <Emphasis Type="Italic">Vavilovia formosa</Emphasis> (Stev.) Fed. in Eurasia

Vavilovia formosa is one of five genera in tribe Fabeae, (Fabaceae, Leguminosae) with close phylogenetic relationships to Pisum. It grows in subalpine and alpine levels in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia and Turkey and is recognized as an endangered and protected plant. This study was conducted to reveal its intraspecific variability, as well as to predict the past, extant and future species distribution range. We analysed 51 accessions with common phylogenetic markers (trnF-trnL, trnS-trnG, matK, rbcL, psbA-trnH and ITS). These represent in total up to 2551 bp of chloroplast and 664 bp of nuclear sequences per sample. Two populations from Turkey and Armenia were analysed for genetic diversity by AFLP. Leaf morphometry was conducted on 1457 leaflets from 43 specimens. Extracted bioclimatic parameters were used for niche-modelling approach. Analysis of cpDNA revealed two haplotypes, 12 samples from Armenia, Daghestan, Nakhichevan and Iran belonged to H1 group, while 39 samples of all Turkish and part of Armenian were in H2 group. The mean intrapopulation diversity based on AFLP was low (H _E = 0.088) indicating limited outcrossing rate. A significantly positive correlation between geographical latitude and leaf area (\(\rho\) = 0.527, p < 0.05) was found. Niche modelling has shown temporal variation of predicted occurrence across the projected time periods. Vavilovia formosa has suffered a range reduction following climate warming after last glacial maximum, which classify this species as cold-adapted among the Fabeae species as well as a glacial relict.     

Spread of mitochondrial DNA haplotypes in population of scots pine (Pinus sylvestris L.) in northern European Russia

The variability of the first intron of the nad7 gene of Scots pine mitochondrial DNA was investigated in 15 populations in northeast of European Russia and in three populations in Belarus, Sweden, and the Voronezh region. Restriction Fragments Length Polymorphism of the PCR product (PCR-RFLP) and sequencing were used. The investigated samples were compared with the populations studied previously [1, 2]. The haplotype, which is absolutely dominant in the eastern part of the Scots pine range [1, 2], was fixed in the Kirov, Arkhangelsk, and Kostroma regions; Komi; and Chuvashia. The extreme northeastern discovery of an alternative haplotype that is present in most European populations and occurs the most frequently in eastern Scandinavia was made in the Vologda region. These results support the hypothesis that the population of Scots pine in northeast Russia and Fennoscandia originated from different glacial refugia.     

Polymorphism of the ND1 and CO1 mitochondrial genes in populations of liver fluke Fasciola hepatica

Polymorphism of fragments of the ND1 and CO1 mitochondrial genes was for the first time found in four liver fluke Fasciola hepatica samples from Ukraine, Belarus, Moscow region, and Mordovia. The ND1 and CO1 fragments were respectively 292 and 433 bp in size, with polymorphic sites accounting for 2.7 and 0.9% of the total sequence. Seven haplotypes were found in the four samples; two haplotypes (A and B) were most common (29.1 and 45.8%, respectively) in the pooled sample. The haplotype frequency distribution differed among the four populations. Haplotype B prevailed in the Mordovian and Moscow region samples. In addition, these samples had a higher number of unique haplotypes (A2, A3, B2). The results testify to genetic divergence of the four geographically distant populations of F. hepatica.     

Mitochondrial DNA divergence in populations of the tapeworm Diphyllobothrium nihonkaiense and its phylogenetic relationship with Diphyllobothrium klebanovskii

Diphyllobothrium nihonkaiense [Y. Yamane, H. Kamo, G. Bylund, J.P. Wilkgren. Diphyllobothrium nihonkaiense sp. nov (Cestoda: Diphyllobothriidae)- revised identification of Japanese broad tapeworm. Shimane J Med Sci 1986;10:29-48.] and Diphyllobothrium klebanovskii [I.V. Muratov, P.S. Posokhov. Causative agent of human diphyllobothriasis - Diphyllobothrium klebanovskii sp. n. Parazitologiia. 1988;22:165-170.] are two major species of human diphyllobothriasis in Japan and Far East Russia, respectively, but their taxonomical relationship remains unclear. In this study, we analysed the DNA sequences of 16 clinical isolates of D. nihonkaiense from Japanese people, 3 isolates of D. klebanovskii from a bear in Kamchatka, and 4 clinical isolates of D. klebanovskii from native Udygeyci people in Russia, as well as 4 plerocercoids from Oncorhynchus spp. 18S rDNA and internal transcribed spacer 1 (ITS1) sequences from D. nihonkaiense and D. klebanovskii showed a high level of similarity, indicating synonymy of the two species. Analyses of mitochondrial DNA (mtDNA) sequence polymorphisms in the cox1 and nad3 genes of D. nihonkaiense (D. klebanovskii) revealed two deeply divergent lineages, A and B, with genetic distances (Kimura-2 parameter) of 0.018-0.022. Furthermore, the distinct monophyletic groupings of cox1 haplotypes corresponded to the distinct monophyletic groupings of nad3 haplotypes. The two lineages were neither distinguished by morphological features nor defined by the localities of the samples. These results suggest that the two morphologically cryptic lineages have diverged and coexisted over a long period of time.     

Polymorphism of the STR-locus of Y chromosomes in Eastern Slavs in three populations from Belorussia, Russia and the Ukraine

Allelic polymorphism of five microsatellite loci of the human Y chromosome (DYS19, DYS390, DYS391, DYS392, and DYS393) was analyzed in samples of male populations from Ukraine, Russia, and Belarus (152 subjects in total). The allelic diversity indices (Dg) were determined for all loci; they varied from 0.23 to 0.72. The mean values of this parameter in the Ukrainian, Russian, and Belarussian populations were 0.45, 0.47, and 0.52, respectively. A total of 53 different haplotypes were found in 152 subjects from three populations. The most frequent haplotype was found in 14.5% of the subjects, whereas 35 haplotypes (23%) were each found in only one person. The haplotypic diversity index (Dhp) was 0.94. The genetic distances between the populations studied and some populations of Western and Central Europe were estimated. These data were used to construct a phylogram (tree) of genetic similarity between the populations, which demonstrated that the three Eastern Slavic populations are genetically close to one another and remote from Western European populations.     

Phylogenetic relationships of Eurasian Nuthatches (Sitta europaea Linnaeus, 1758) from the Alborz and Zagros Mountains,Iran

The Eurasian Nuthatch (Sitta europaea Linnaeus, 1758) is a resident bird in the Alborz and Zagros deciduous forests. We investigated the phylogenetic relationships and the taxonomic position of the Eurasian Nuthatch among other separated lineages of Eurasia with the help of blood samples collected from 19 individuals belonging to four populations in the Eastern and Western Alborz, as well as in the Northern and Southern Zagros forests. Genetic variation was then analysed using complete ND2 gene sequence (1041?bp) and phylogenetic analysis was done using Bayesian and maximum likelihood inference. Additionally, a median-joining algorithm was used to reveal the relationships among haplotypes. The results of the phylogenetic and haplo-type network analyses indicated that Eurasian Nuthatch haplotypes from the Alborz and Zagros Mountains form lineages distinct from the Asian, Caucasian and European haplotypes. Furthermore, an analysis of molecular variance (AMOVA) detected significant (P<0.001) genetic structure among the lineages. The Asian, European, Caucasian and Alborz lineages diverged from one another by an uncorrected genetic distance ranging from 0.029 to 0.039, while the Zagros lineage showed a slightly lower genetic divergence from the Caucasian lineage (0.006), but it did not share any haplotype with the Caucasian lineage. Thus, we suggest considering five Conservation Significant Units (CSU) for the Eurasian Nuthatches as the result of used dataset.     

The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa

The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to other Metazoa. The genome has an overall AT richness of 59.4%. We found seven regions of overlaps between tRNAs and protein-coding genes ranging from 2 to 11 nt, and seven regions of overlap between tRNAs, ranging from 1 to 8 nt, resulting in a total number of 46 overlapping nucleotides. Genes nad4, cox2, atp8, and nad3 are terminated by the abbreviated stop codon T and cytb is suggested to terminate on (ACT)AA; we postulate that mRNA editing is required to remove AC for TAA to be functional in terminating translation. Phylogenetic analysis of nucleotide and amino acid data place Flustrellidra in the Lophotrochozoa. DNA for this study originated from two populations resulting in a contig consisting of multiple haplotypes. Twenty-seven SNP sites were detected, the majority occurring in cox1 and nad5. With cox1 already established as a marker in bryozoan studies, we advocate the further testing of nad5.     

Mitochondrial DNA sequence variation among geographical isolates of Opisthorchis viverrini in Thailand and Lao PDR, and phylogenetic relationships with other trematodes

The present study compared the genetic variation among 14 different geographical isolates of Opisthorchis viverrini sensu lato from Thailand and Lao PDR using sequence data for 2 mitochondrial DNA genes, the subunit 1 of NADH dehydrogenase gene (nad1) and cytochrome c oxidase gene (cox1). Four different nad1 haplotypes were detected among isolates, all of which were identical at the amino acid sequence level. Nucleotide sequence variation among 14 isolates ranged from 0 to 0.3% for nad1. Two different cox1 haplotypes were detected among isolates. These two haplotypes differed at 2 nucleotide positions, one of which resulted in a change in the amino acid sequence. Nucleotide sequence variation among isolates for cox1 ranged from 0 to 0.5%. Comparison of cox1 sequences of O. viverrini to those of other trematodes revealed nucleotide differences of 13-31%. A phylogenetic analysis of the cox1 sequence data revealed strong statistical support for a clade containing O. viverrini and 2 other species of opisthorchid trematodes; O. felineus and Clonorchis sinsensis.     

Deep amplicon sequencing highlights low intra-host genetic variability of Echinococcus multilocularis and high prevalence of the European-type haplotypes in coyotes and red foxes in Alberta,Canada

Echinococcus multilocularis (Em) is a zoonotic parasite considered a global emergent pathogen. Recent findings indicate that the parasite is expanding its range in North America and that European-type haplotypes are circulating in western Canada. However, genetic analyses are usually conducted only on a few parasites out of thousands of individuals within each definitive host, likely underestimating the prevalence of less common haplotypes. Moreover, mixed infections with several mtDNA haplotypes in the same host have been reported, but their relative abundance within the host was never estimated. We aimed to 1) estimate the frequency of co-infections of different Em haplotypes in coyotes (Canis latrans) and red foxes (Vulpes vulpes) from western Canada and their relative abundance within the definitive hosts, 2) detect less prevalent haplotypes by sampling a larger proportion of the parasite subpopulation per host, and 3) investigate differences in the distribution of Em haplotypes in these main definitive hosts; foxes and coyotes. We extracted DNA from ~10% of the worm subpopulation per host (20 foxes and 47 coyotes) and used deep amplicon sequencing (NGS technology) on four loci, targeting the most polymorphic regions from the mitochondrial genes cox1 (814 bp), nad1 (344 bp), and cob (387 bp). We detected the presence of mixed infections with multiple Em haplotypes and with different Echinococcus species including Em and E. granulosus s.l. genotypes G8/G10, low intraspecific diversity of Em, and a higher abundance of the European-type haplotypes in both hosts. Our results suggest a population expansion of the European over the North American strain in Alberta and a limited distribution of some European-type haplotypes. Our findings indicate that deep amplicon sequencing represents a valuable tool to characterize Em in multiple hosts, to assess the current distribution and possible origins of the European strain in North America. The potential use of next-generation sequencing technologies is particularly important to understand the patterns of geographic expansion of this parasite.     

Polymorphism of STR Loci of the Y Chromosome in Three Populations of Eastern Slavs from Belarus,Russia, and Ukraine

Allelic polymorphism of five microsatellite loci of the human Y chromosome (DYS19, DYS390, DYS391, DYS392, and DYS393) was analyzed in samples of male populations from Ukraine, Russia, and Belarus (152 subjects in total). The allelic diversity indices (D _g) were determined for all loci; they varied from 0.23 to 0.72. The mean values of this parameter in the Ukrainian, Russian, and Belarussian populations were 0.45, 0.47, and 0.52, respectively. A total of 53 different haplotypes were found in 152 subjects from three populations. The most frequent haplotype was found in 14.5% of the subjects, whereas 35 haplotypes (23%) were each found in only one person. The haplotypic diversity index (D _hp) was 0.94. The genetic distances between the populations studied and some populations of Western and Central Europe were estimated. These data were used to construct a phylogram (tree) of genetic similarity between the populations, which demonstrated that the three Eastern Slavic populations are genetically close to one another and remote from Western European populations.     

Polymorphism of the ND1 and CO1 Mitochondrial Genes in Populations of Liver Fluke Fasciola hepatica

Polymorphism of fragments of the ND1 and CO1 mitochondrial genes was for the first time found in four liver fluke Fasciola hepatica samples from Ukraine, Belarus, Moscow region, and Mordovia. The ND1 and CO1fragments were respectively 292 and 433 bp in size, with polymorphic sites amounting to 2.7 and 0.9% of the total sequence. Seven haplotypes were found in the four samples; two haplotypes (A and B) were most common (29.1 and 45.8%, respectively) in the pooled sample. The haplotype frequency distribution differed among the four populations. Haplotype B prevailed in the Mordovian and Moscow region samples. In addition, these samples had a higher number of unique haplotypes (A2, A3, B2). The results testify to genetic differences of the four geographically distant populations of F. hepatica.     

The gene pool of Belgorod oblast population: study of biochemical gene markers in populations of Ukraine and Belarus and the position of the Belgorod population in the Eastern Slavic gene pool system

The characteristics of the gene pools of indigenous populations of Ukraine and Belarus have been studied using 28 alleles of 10 loci of biochemical gene markers (HP, GC, TF, PI, C'3, ACP1, GLO1, PGM1, ESD, and 6-PGD). The gene pools of the Russian and Ukrainian indigenous populations of Belgorod oblast (Russia) and the indigenous populations of Ukraine and Belarus have been compared. Cluster analysis, multidimensional scaling, and factor analysis of the obtained data have been used to determine the position of the Belgorod population gene pool in the Eastern Slavic gene pool system.     

The gene pool of Belgorod oblast population: Study of biochemical gene markers in populations of Ukraine and Belarus and the position of the Belgorod population in the Eastern Slavic gene pool system

The characteristics of the gene pools of indigenous populations of Ukraine and Belarus have been studied using 28 alleles of 10 loci of biochemical gene markers (HP, GC, TF, PI, C′3, ACP1, GLO1, PGM1, ESD, and 6-PGD). The gene pools of the Russian and Ukrainian indigenous populations of Belgorod oblast (Russia) and the indigenous populations of Ukraine and Belarus have been compared. Cluster analysis, multidimensional scaling, and factor analysis of the obtained data have been used to determine the position of the Belgorod population gene pool in the Eastern Slavic gene pool system.     

Loneliness: Its Correlates and Association with Health Behaviours and Outcomes in Nine Countries of the Former Soviet Union

Background

Research suggests that the prevalence of loneliness varies between countries and that feeling lonely may be associated with poorer health behaviours and outcomes. The aim of the current study was to examine the factors associated with loneliness, and the relationship between feeling lonely and health behaviours and outcomes in the countries of the former Soviet Union (FSU) – a region where loneliness has been little studied to date.

Methods

Using data from 18,000 respondents collected during a cross-sectional survey undertaken in nine FSU countries – Armenia, Azerbaijan, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Moldova, Russia and Ukraine – in 2010/11, country-wise logistic regression analysis was conducted to determine: the factors associated with feeling lonely; the association between feeling lonely and alcohol consumption, hazardous drinking and smoking; and whether feeling lonely was linked to poorer health (i.e. poor self-rated health and psychological distress).

Results

The prevalence of loneliness varied widely among the countries. Being divorced/widowed and low social support were associated with loneliness in all of the countries, while other factors (e.g. living alone, low locus of control) were linked to loneliness in some of the countries. Feeling lonely was connected with hazardous drinking in Armenia, Kyrgyzstan and Russia but with smoking only in Kyrgyzstan. Loneliness was associated with psychological distress in all of the countries and poor self-rated health in every country except Kazakhstan and Moldova.

Conclusions

Loneliness is associated with worse health behaviours and poorer health in the countries of the FSU. More individual country-level research is now needed to formulate effective interventions to mitigate the negative effects of loneliness on population well-being in the FSU.