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Simplified human Y-chromosome tree. Haplogroups specific to Aboriginal Australia and Melanesia are shown in details, also shown hg C5-M356 found among populations of South Asia. Haplogroup geographical origin is color-coded according to the legend. Modified from Karafet et al. (2008).
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Analysis of genetic variation in modern human populations has become a valuable tool for the study of the prehistory of our species. Recent genetic work has offered new insights into various evolutionary processes, including peopling of the world by anatomically modern humans, but also allowed for better characterization of diverse adaptive process...
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... overall Y- chromosome heterogeneity there appears to be smaller than that of mtDNA: Aboriginal Australians are represented by two main NRY clades: K-M9 and M- M130 (for review see Kayser 2010), with hg C-M130 bearing the Australian- specific DYS390.1 deletion (C-DYS390.1del) reaching up to 69% of the total variation ( Figure 3) ( Kayser et al. 2001). The spread of hg C-DYS390.1del ...
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... the occurrence of different paternal lineages varies substantially between populations of New Guinea, the following haplogroups can be noted: C2-M38, including C2a-M208, M1-M4, S-M230, and sub-branches of hg O- M175 ( Figure 3) ( Karafet et al. 2010;Kayser 2010). Hg C2a-M208 has northern Melanesian ancestry; C2-M38, M1-M4 and S-M230 were also detected in eastern Indonesia, pointing to either a more westward origin or gene flow from Near Oceania towards eastern Indonesia, probably the same process that might have introduced the Melanesian-specific mitochondrial hg Q to the ISEA region. ...
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... The geographical distribution, diversity and age estimates of different E sub-clades suggest their in situ origin in Island Southeast Asia, either on the northeastern coast of Sundaland or in the neigh- boring northwestern Wallacea (northern Sulawesi) (Figure 3 in ref. II), whereas the unusually high frequency of hg E and its spotty distribution in Near Oceania can be explained by the extreme level of genetic drift among insular populations ( Friedlaender et al. 2007). ...
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... additional non-synonymous polymorphisms that were detected have low frequency: two are singletons (one in the African and another in the European sample) and one is a doubleton found in Europe. The ancestral recombination graph shows that the majority of non-synonymous polymorphisms are centered in Europe or North Africa: 72% of total non-synonymous variation was confined to these two populations (Figure 3 in ref. III). ...
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... contrast, on a genome-wide scale, populations from the African continent usually possess higher diversity estimates. Secondly, sub-Saharan Africans almost totally lack non-synonymous alleles in the tyrosinase gene likely because of purifying selection (Figure 3 in ref. III). ...
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... Thirdly, lightly pig- mented East Asian individuals are virtually depleted for non-synonymous variants (Figure 3 in ref. III). ...
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... a similar pattern of diversity has previously been observed in pigmentation associated MC1R loci ( Rana et al. 1999;Harding et al. 2000). The lack of non-synonymous allele sharing between lightly pigmented Europeans and East Asians should not be surprising (Figure 3 in ref. III). ...
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... alleles are common in Europe and North Africa. The first and the most frequent cluster, referred to as hg B1 in the ancestral recombination graph (Figure 3 in ref. III), coalesces at 6,100±3,600 years BP as estimated by rho and 15,600 years BP (95%CI=400-46,600) as estimated by Bayesian coalescent approach. ...
Citations
Fungi represent one of the largest and diverse kingdoms of eukaryotes, and Basidiomycota is the second most species-rich group within Fungi. Despite the ecological importance of basidial fungi, i.e., their leading role in decomposition of wood in terrestrial ecosystems, their diversity and taxonomy are insufficiently known. Fulfilling this knowledge gap, the thesis presents taxonomic studies in a class of basidal fungi called Dacrymycetes. Dacrymycetes occur only on dead wood and produce either of the two types of fruitbodies: gelatinous voluminous yellow or dry flat bleak-coloured. The latter type, also called corticioid fruitbodies, is the primary focus of this thesis. Traditionally, such corticioid fruitbodies in dacrymycetes were strictly associated with the family Cerinomycetaceae and its only genus Cerinomyces. This emphasis on a single character led to inclusion of dissimilar species into Cerinomyces, and over the time the genus became overly broad and polyphyletic. Thus, aim of the present thesis was to revise Cerinomyces and related taxa on a basis of DNA sequence-based phylogenetic analyses and morphological studies. As a result, Cerinomyces was reshaped to a more natural scope and became monophyletic. Priority for the corticioid morphology was abandoned, and gelatinous members were introduced to the genus. Instead of fruitbody type, the genus is now united by a set of microscopic characters: simple clamps, thin-walled aseptate basidiospores, and low amount of carotenoid pigments. Moreover, investigating taxa morphologically similar to Cerinomyces, the rest of dacrymycetes was partially revised. Special attention was paid to notable morphological structures called “dendrohyphidia” that are common in Cerinomyces, but were also found in other dacrymycetes. To accommodate such taxa in the Dacrymycetaceae family, a new genus Dendrodacrys was raised. In total, the thesis proposes 42 nomenclatural novelties to science, including one new genus, 27 new species, and 14 new combinations.
Modern day human genomes are mixtures of ancient components. Thanks to advancements in ancient DNA (aDNA) research, we can detect the origins of these components and study them. However, aDNA might either not be available or be of low quality in many situations due to DNA structure being subject to degradation related to time and different environmental factors. Thankfully, we can identify and extract these ancient layers also from contemporary human genomes with local ancestry inference methods. With this approach, we can study admixed populations, which have highly divergent ancestral components, in terms of demography and functional analyses. This thesis particularly focuses on two such groups: South Asian populations, which are composed of West Eurasian and South Asian ancestries, and Ethiopian populations, which are composed of Eurasian and African ancestries. In the first part, past demographic events, diverse genomic variation and post-admixture natural selection in South Asia are investigated by generating surrogates for the two main ancestral components of contemporary South Asian genomes. In the second part, a local ancestry inference-based method is evaluated for improving selection detection in ancestral components of admixed genomes and it is applied on South Asian genomes. In the third and the last part, a similar approach to the first part is conducted for Ethiopian genomes to pinpoint the source of Eurasian ancestry in contemporary Ethiopians.
Eurasian wild boar is the most widespread species of the Suidae family and its populations increased significantly in the second half of the 20th century – a change that has been largely associated with the continuing spread of agriculture, as well as the widespread practice of supplementary feeding. However, due to its omnivorous diet, high population density of wild boar can have disastrous effects on other animals, particularly on ground-nesting birds, whose populations have suffered from loss of habitat as well as predation.Wild boar can also play an important role in disease outbreaks as a reservoir of various pathogens shared between wildlife and domestic animals. The purpose of this thesis was to examine the potential consequences of supplementary feeding of wild boar for ground-nesting birds and wild boar infection with endoparasites, because increased overall abundance of wild boar and increased contact rates at feeding sites can promote the spread of various diseases.
In this study, supplementary feeding had a key role in determining wild boar abundance and grain from feeding sites constituted a major food category even in the warm season, when food availability was not hindered by low temperatures and deep snow. However, despite having access to supplemental food, wild boar acted as a predator of nests and chicks of forest grouse and the concentration of wild boar and other predators near feeding sites resulted in locally increased predation risk for ground-nesting birds. What is more, the novel molecular method applied in this study revealed that faecal diet analysis based on morphology, which is still a popular method in diet studies, underestimates the proportion of bird in wild boar diet, indicating that previous studies might suffer from the same error. In addition to its contribution to increased predation of ground-nesting birds, supplementary feeding was shown to influence endoparasite infection in wild boar both directly and indirectly through increased abundance. Supplementary feeding sites had become hot-spots for acquiring lungworm infection and parasites with a direct life cycle benefited from the overall high host abundance. These unwanted effects should be reckoned with in wild boar management.
Forests provide habitat for a huge variety of fungi that, in turn, play key roles in several forest ecosystem processes. The fungal biota is increasingly affected by human-caused transformation of forests, i.a., significant declines in the amount of coarse dead wood and large old trees. My thesis concentrates on fungi inhabiting such structures. My main focus is on polypores that belong to the dominant dead-wood composers in the forests, but I also explore lichenised fungi. Many polypores and lichens are nowadays found mainly in the remaining old-forest patches, and the occurrence of several species is thought to indicate ecological value of a forest. My general aim was to assess the forest conservation and management practices from the perspective of the fungi inhabiting dead wood and old living trees. The main method in polypore studies was fruit-body based species-inventory. In the stand scale, I found this method efficient: while all polypore species inhabiting a tree-trunk (as revealed by their DNA in the wood samples) may not produce fruit-body on the same tree, conspecific fruit-bodies can be usually found on other trunks in close vicinity. Differently from the intensively managed Fennoscandia, the old-forest associations of polypores were relatively weak in Estonia, as revealed by a comparison of old-growth, mature managed and harvested forests. Thus, fungal habitat associations and indicator value depend on regional landscape context. For the few species that were confined to old -growths, specific substrate requirements (notably large spruce trunks) were the reason. I also show that interpreting species habitat associations may me confused by “cryptic species” that have similar morphology, but differ by genetics and ecology. Thus, conservation practices might benefit from fewer, but better supported, fungal indicators. I demonstrate that fungi inhabiting dead wood and old living trees (including putative old-forest specialists) may form species-rich assemblages also in managed forests. This is possible if these forests are diverse in terms of tree species, dead-wood structures, and successional stages, including old stands. My general conclusion is that there are many possibilities for adjusting forest management to better address the fungal diversity that depends on dead wood and old living trees.
Air pollution is a consequential global threat to overall biodiversity, affecting different biological levels – from cellular to ecosystem level. The dust pollution has always been essential environmental issue in Estonia since over the years the large part of industrial pollution was formed by alkaline dust. The current thesis is focused on alkaline coarse dust particles, which are released to the environment through cement industry, limestone quarries and directly from unpaved gravel roads by traffic. In order to monitor and mitigate damages caused by dust pollution, the influence of pollution on different levels of biodiversity should be estimated and the potential sources of pollution and their extension detected. Therefore, the aim of the thesis was to study the response of pine forest ecosystems, epiphytic communities (algae, lichens, bryophytes) on pines, and genetic diversity of populations of a common lichen-forming fungus to changed environmental conditions induced by a long-term alkaline pollution. The results showed that long-term dust pollution had a neutralizing effect on soil properties, pine and spruce barks: the pH value of soil and tree barks decreased along an increasing distance from the sources of pollution. The alkaline pollution has caused destruction of natural communities and formation of novel communities in the vicinity of pollution sources, for example invasion of non-typical and pollution-tolerant species for local communities occurred, including calcicolous species and species characteristic for nutrient-rich habitats. Interestingly, dust pollution revealed a kind of ‘parapositive’ impact on natural communities, suggesting that pollution might, besides disturbing communities, temporarily also contribute to the distribution of rare and protected species. Finally, alkaline pollution had a negative impact on the genetic variation of Usnea subfloridana populations, a common species of lichen-forming fungi.
