First report of highly pathogenic Echinococcus granulosus genotype G1 in dogs in a European urban environment

BACKGROUND: Echinococcus granulosus and E. multilocularis are tapeworm parasites of major medical and veterinary importance, causing cystic and alveolar echinococcosis, respectively. Both diseases are listed among the most severe parasitic diseases in humans, representing 2 of the 17 neglected diseases prioritised by the World Health Organisation. However, little is known about the role of urban animals in transmission of both parasite species. FINDINGS: A sensitive non-invasive genetic method was used to monitor E. granulosus and E. multilocularis infection among dog faecal samples collected from an urban area in Estonia in 2012–13. Out of 181 dog faecal samples analysed, 2.2% tested positive for E. granulosus, determined by sequencing as genotype G1. None of the samples tested positive for E. multilocularis. CONCLUSIONS: We report contamination of an urban environment with highly pathogenic E. granulosus G1 disseminated by dogs, and a potential risk to human health

Pruunkaru (Ursus arctos) fülogeograafia Põhja-Euraasias

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Fülogeograafia on valdkond, mis on keskendunud liigisiseste ja lähiliikidevaheliste geneetiliste liinide ruumilist paiknemist mõjutavate seaduspärasuste ja protsesside uurimisele. Looduslike imetajaliikide hulgas on seni olnud üheks mudelliigiks pruunkaru, seda eelkõige tänu laiale levikule, arvukatele luuleidudele ja emakarude filopatrilisusele. Käesolev doktoritöö vaatleb pruunkaru emaliini fülogeograafiat (analüüsides mitokondriaalse DNA (mtDNA) järjestusi) Põhja-Euraasias, pöörates erilist tähelepanu Loode-Euraasia populatsioonile. Hoolimata asjaolust, et see piirkond moodustab enamiku antud liigi tänapäevasest levikualast ning hõlmab suure osa maailma karupopulatsioonist, oli Põhja-Euraasia kohta käiv fülogegraafiline informatsioon seni puudulik. Antud töö tulemused viitavad, et tänapäeval on kõik pruunkaruliinid Põhja-Euraasias suhteliselt lähedalt seotud ja peale viimase jääaja maksimumi toimus tugev demograafiline ekspansioon ning ükski geograafiline tõke ei olnud piisavaks takistuseks pruunkarude migratsioonile üle Mandri-Euraasia põhjaosa. Loode-Euraasia pruunkaru populatsiooni detailne analüüs mitokondri genoomi täisjärjestuste alusel selgitas välja viis selgesti eristatavat, geograafiliselt piiritletud ja ainult osaliselt kattuvat haplogruppi. Analüüsid näitasid, et need viis haplogruppi moodustusid jääajajärgsel perioodil ning peegeldavad seega kombinatsiooni jääajajärgsest migratsioonimustrist ja hilisemast demograafilisest ajaloost. Et selles töös sekveneeriti 95 mitogenoomi, siis võimaldas see esimest korda analüüsida ka pruunkaru mitokondri genoomide liigisisest variatsiooni. Positiivne evolutsiooniline valik tuvastati valgugeenile ND6. Antud töö tulemused pakuvad olulist baasinformatsiooni pruunkaru efektiivsete majandamis- ja kaitsestrateegiate väljatöötamiseks Euraasias.Phylogeography is a discipline that focuses on the principles and processes affecting the spatial distribution of genetic lineages, within and among closely related species. Among wild mammals, the brown bear (Ursus arctos) has become a model species for phylogeographic analysis, due to wide distribution, the availability of numerous subfossils and its female philopatry. Current thesis examined brown bear matrilineal phylogeography (by analysing mitochondrial DNA (mtDNA) sequences) in northern Eurasia with particular focus on the population in north-west Eurasia. Prior to the studies performed in the frame of this thesis, information on brown bear phylogeography was largely lacking for northern Eurasia, which nonetheless constitutes a major part of the species’ current distribution and contains the majority of the world’s brown bear population. The results suggest that all contemporary brown bears in northern Eurasia are relatively closely related and after the Last Glacial Maximum, brown bears underwent a sudden demographic expansion and no significant geographic barrier was found to restrict migration across northern continental Eurasia. Detailed analysis of the north-west Eurasian brown bear population using complete mitochondrial sequences revealed five divergent, geographically confined and only partially overlapping haplogroups. Our analysis demonstrated that these five haplogroups formed during the post-glacial period and thus reflect a combination of postglacial migration patterns and more recent demographic history. Ninety-five complete mitogenomes, sequenced during this study, allowed us to make the first analysis of intra-specific variation among brown bear mitogenomes. Positive selection was found to act on the gene ND6. The results of this study provide scientific data that is potentially very useful for the development of effective management and conservation strategies for Eurasian brown bears in the near future

Wolves Recolonizing Islands: Genetic Consequences and Implications for Conservation and Management.

After a long and deliberate persecution, the grey wolf (Canis lupus) is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country's two largest islands, Saaremaa and Hiiumaa. The main objective of this study was to analyse wolf population structure and processes in Estonia, with particular attention to the recolonization of islands. Fifteen microsatellite loci were genotyped for 185 individuals across Estonia. As a methodological novelty, all putative wolf-dog hybrids were identified and removed (n = 17) from the dataset beforehand to avoid interference of dog alleles in wolf population analysis. After the preliminary filtering, our final dataset comprised of 168 "pure" wolves. We recommend using hybrid-removal step as a standard precautionary procedure not only for wolf population studies, but also for other taxa prone to hybridization. STRUCTURE indicated four genetic groups in Estonia. Spatially explicit DResD analysis identified two areas, one of them on Saaremaa island and the other in southwestern Estonia, where neighbouring individuals were genetically more similar than expected from an isolation-by-distance null model. Three blending areas and two contrasting transition zones were identified in central Estonia, where the sampled individuals exhibited strong local differentiation over relatively short distance. Wolves on the largest Estonian islands are part of human-wildlife conflict due to livestock depredation. Negative public attitude, especially on Saaremaa where sheep herding is widespread, poses a significant threat for island wolves. To maintain the long-term viability of the wolf population on Estonian islands, not only wolf hunting quota should be targeted with extreme care, but effective measures should be applied to avoid inbreeding and minimize conflicts with local communities and stakeholders

Principal component analysis (PCA) of Estonian wolves (n = 168) representing four genetic groups (G1–G4) as suggested by STRUCTURE.

<p>Points represent individual genotypes; genetic groups are labelled inside their 95% inertia ellipses. Note that only individuals with a membership coefficient <i>q</i> > 0.7 are shown. Inset figure shows a bar chart of the eigenvalues with corresponding components filled in black.</p

Locations of four genetic groups in the Estonian wolf population (n = 168) according to STRUCTURE (admixture model; 15 autosomal microsatellite loci).

<p>Colored dots denote the sample locations and groups are colored as follows: G1 (green), G2 (blue), G3 (red), and G4 (yellow). Individuals are placed into a particular genetic group based on their highest membership coefficient. The background map was downloaded from an Open Access database of the Estonian Land Board (<a href="http://www.maaamet.ee" target="_blank">www.maaamet.ee</a>; download date: 1. Nov. 2014).</p

Spatial distribution of local average heterozygosity in Estonian wolf population.

<p>Based on the proportion of heterozygous loci at individual level, statistically interpolated across the study area using procedure of universal kriging. The full colored areas represents statistically significant deviation from global median (0.67); <i>p</i> ≤ 0.05 according to 499 bootstrap iterations. The dots represent sample locations.</p

Changes in numbers of wolf packs and hunted wolves in Estonia during the last fifteen years (2000–2014; data from the Estonian Environment Agency).

<p>Inset figure represents the age structure of analysed wolves (n = 138, the age estimation was not available for all wolves) during the hunting seasons of 2011–2012 to 2014–2015 in Estonia.</p

Putative elements of the genetic structure and dynamics in Estonian wolf population during 2011–2015.

<p>The conclusion is based on the analysis of placement of genetic groups (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158911#pone.0158911.g002" target="_blank">Fig 2</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158911#pone.0158911.s002" target="_blank">S2 Fig</a>), DResD (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158911#pone.0158911.g004" target="_blank">Fig 4</a>), and heterozygosity distribution (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158911#pone.0158911.g005" target="_blank">Fig 5</a>). The dots represent sample locations.</p

Spatial distribution of local genetic differentiation in the Estonian wolf population.

<p>In the DResD analysis, neighbouring individual pairs are used in distance range 17–33 km. The pairwise IBD corrected genetic distance (Nei’s D) was interpolated across the study area using the procedure of universal kriging. The full coloured areas represent statistically significant deviation from the global model of IBD; <i>p</i> ≤ 0.05 according to 499 bootstrap iterations; median IBD residual = 0.12. The large points represent sample locations and the small dots denote midpoint locations of sample pairs.</p