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Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.

Cystic echinococcosis is a socioeconomically important parasitic disease caused by the larval stage of the canid tapeworm Echinococcus granulosus, afflicting millions of humans and animals worldwide. The development of a vaccine (called EG95) has been the most notable translational advance in the fight against this disease in animals. However, almost nothing is known about the genomic organisation/location of the family of genes encoding EG95 and related molecules, the extent of their conservation or their functions. The lack of a complete reference genome for E. granulosus genotype G1 has been a major obstacle to addressing these areas. Here, we assembled a chromosomal-scale genome for this genotype by scaffolding to a high quality genome for the congener E. multilocularis, localised Eg95 gene family members in this genome, and evaluated the conservation of the EG95 vaccine molecule. These results have marked implications for future explorations of aspects such as developmentally-regulated gene transcription/expression (using replicate samples) for all E. granulosus stages; structural and functional roles of non-coding genome regions; molecular ‘cross-talk’ between oncosphere and the immune system; and defining the precise function(s) of EG95. Applied aspects should include developing improved tools for the diagnosis and chemotherapy of cystic echinococcosis of humans.

BackgroundReduction of genetic diversity can lead to reduced fitness of species, such as the loss of adaptability to changing environments. The native Eurasian beaver (Castor fiber) was hunted to extinction from Finland and many other countries in Europe in the nineteenth century. In Finland, the species was re-introduced in the 1930s with only a few individuals from Norway. Re-introductions were performed also in other countries of northern Europe and as a result, Eurasian beaver populations have undergone population bottlenecks leading to low levels of genetic diversity.Materials and MethodsHere, 200 Eurasian beaver samples from Finland, Estonia, Lithuania, and Russian Karelia were investigated using 12 microsatellite markers to examine the level of genetic diversity and relationship between the populations.ResultsWhile Russian and Estonian populations were genetically the closest, the Finnish population was clearly distinct from all others and had the lowest genetic variability among the study populations. This may be deleterious to the population especially in a changing environment.ConclusionsGenetic rescue could be the best solution to increase the genetic diversity and improve the future prospects of the population, although more studies are required to resolve the optimal source population.

By the beginning of the twentieth century, many brown bear populations in Europe were on the brink of extinction due to relentless hunting pressure and habitat loss. The situation was critical also in Estonia, where in the 1920s the population went through a severe demographic bottleneck. Thanks to the protective measures implemented in the 1930s, the population started to recover. However, the process has been slow, especially in the western and southern areas of the country. To study the effects of the demographic bottleneck, we analysed 216 brown bear samples from throughout their main range in Estonia. In combination with widely used methods of population genetics, a recently developed spatially explicit analysis (distribution of residual dissimilarity, DResD) was also applied. Three genetic clusters were revealed, of which two were most likely founded by the survivors of the bottleneck. The DResD analysis revealed several contact zones near the Estonian-Russian border, suggesting that the third cluster was influenced by gene flow from the neighbouring population in Russia. The DResD analysis revealed also a male biased movement corridor along the forested south-north axis in the central part of Estonia. In comparison to other European populations, the genetic diversity of the Estonian population is relatively low and is comparable with other populations that have gone through a severe bottleneck. This work has important implications for brown bear conservation and highlights once again the dangers of excessive hunting.

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

Predation on livestock is a cause of serious and long-lasting conflict between farmers and wildlife, promoting negative public attitudes and endangering conservation of large carnivores. However, while large carnivores, especially the grey wolf (Canis lupus), are often blamed for killing sheep and other farm animals, free-ranging dogs may also act as predators. To develop appropriate measures for livestock protection, reliable methods for identifying predator species are critical. Identification of predators from visual examination of livestock wounds can be ambiguous and genetic analysis is strongly preferable for accurate species determination. To estimate the proportion of wolves and dogs implicated in sheep predation, we developed a sensitive genetic assay to distinguish between wolves and domestic dogs. A total of 183 predator saliva samples collected from killed sheep in Estonia were analysed. The assay identified the predator species in 143 cases (78%). Sheep were most often killed by wolves (81%); however, predation by dogs was substantial (15%). We compared the molecular results with field observations conducted by local environmental officials and recorded some disagreement, with the latter underestimating the role of dogs. As predator saliva samples collected from prey are often of poor quality, we suggest using mitochondrial DNA as a primary tool to maximise the number of successfully analysed samples. We also suggest adopting forensic DNA analysis more widely in livestock predation assessments as a legislative measure since misidentification that is biased against wolves can be counterproductive for conservation by enhancing conflict with society and leading to increased culling and poaching.

Protecting animal aggregation sites is intuitively an efficient conservation approach, particularly for threatened species in fragmented landscapes. However, the appropriate scale of protection depends on accompanying threats, such as predator attraction to the same aggregation sites, to which the target species may need to respond by moving to alternative habitat patches. We performed experiments using artificial ground nests around protected capercaillie leks in commercially managed forest landscape in Estonia. We considered two scales: the landscape up to 3 km from the lek centre, and among 10–30-ha forest compartments, which differed in predator abundance. We found that nest predation significantly declined with distance from the lek. Nests were depredated by multiple mammalian and avian predator species and total predator abundance explained most of the between-forest variation in predation rate. Our results indicate that, in this hemiboreal area, (i) ground nest predation is largely determined by landscape-scale distribution of predators and (ii) predators can aggregate at capercaillie leks. The implication is that lek-centred habitat protection used for the capercaillie and other grouse may be ineffective unless the peripheral habitat quality and predator abundance are specifically addressed. More generally, predation pressure can be a serious problem in small set-asides within hostile landscapes for threatened ground-nesting birds.

We have studied in vivo the phenotypes of 23S rRNA mutations G2582A, G2582U, G2583C, and U2584C, which are located at the A site of Escherichia coli 50S ribosomal subunit. All mutant rRNAs incor- porated into 50S ribosomal subunits. Upon sucrose gradient fractionation of cell lysates, 23S rRNAs mutated at G2582 to A and G2583 to C accumulated in the 50S and 70S fractions and were underrepresented in the poly- some fraction. Induction of 23S rRNAs mutated at G2582 and G2583 lead to a drastic reduction in cell growth. In addition, mutations G2582A and G2583C reduced to one-third the total protein synthesis but not the RNA synthesis. Finally, we show that 23S rRNA mutations G2582A, G2582U, and G2583C cause a significant increase in peptidyl-tRNA drop-off from ribosomes, thereby reducing translational processivity. The results clearly show that tRNA-23S rRNA interaction has an essential role in maintaining the processivity of transla- tion.