The main aim of this work was to identify local adaptation processes in amphibian populations, thereby improving the general understanding of genetics and mechanisms behind the evolution and maintenance of biological diversity. Phenotypic and genetic variation in life-history traits was studied within and between populations common frog (Rana temporaria) populations along a 1600 km transect from southern Sweden to northern Finland. Embryonic and larval development and growth was investigated both under field and laboratory conditions. The results suggest ample genetic diversity in larval life-history traits among Fennoscandian common frog populations. Larval developmental rate along the gradient has evolved a countergradient variation pattern of genotypes and phenotypes as indicated by the positive relationship between developmental rate and latitude under laboratory conditions and the lack of such a relationship in the field. The data suggest that this pattern has evolved because of time constraints due to decreasing length of growth season with latitude. Neither field-caught adults nor laboratory raised larvae displayed a linear latitudinal size cline as expected from the so called Bergmanns rule. Rather, size increased towards the mid-latitude populations and decreased thereafter, indicating that body size is a product of direct environmental induction or a trade-off with other life-history characters. Age and size at hatching showed no consistent latitudinal pattern, indicating that the embryonic stage is not as time constrained as the larval stage. A large part of the variation in age and size at metamorphosis among populations was due to additive genetic effects. However, small, but significant maternal effects, mostly due to variation in egg size and non-additive genetic effects also contributed to among population variation. A comparison of divergence in presumably neutral molecular genetic markers (FST) and quantitative characters (QST) revealed that although both estimates of divergence were relatively high, estimates of QST was generally higher than those of FST, indicating that the genetic variation observed in larval traits is primarily a result of natural selection rather than genetic drift. Hence, our results reinforce the conclusion that intraspecific genetic heterogeneity in the young northern European ecosystems may be more widespread than previously anticipated

The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.

In the present study / ten autosomal human-specific Alu insertion polymorphisms / ACE, APO, A25, B65, D1, FXIIIB, HS4.32, HS4.69, PV92 and TPA25 were analyzed in approximately 100 unrelated individuals from Anatolia. Alu insertion polymorphisms offer several advantages over other nuclear DNA polymorphisms for human evolution studies. The frequencies of the ten biallelic Alu insertions in Anatolians were calculated and all systems were found to be in Hardy-Weinberg equilibrium (p&gt / 0.05). By combining the results of this study with results of previous studies done on worldwide populations, the genetic distance (Nei&rsquo / s DA) between each pair of populations was calculated and neighbor joining trees were constructed. In general, geographically closer populations were found to be also genetically similar. Principal component analysis (PCA) was performed and Anatolia was found to be in the European cluster. As a result of PCA / it was concluded that FXIIIB, PV92 and ACE were the variables contributing the most to the explanation of the variation between the populations. Additionally / canonical variates analysis (CVA) concluded that the most discriminative markers for the groups of populations were PV92, D1, ACE and HS4.32. Pair-wise Fst values were also calculated between Anatolians and some of the populations for which the data was available. It was concluded that, Anatolians have non-significant pair-wise Fst values with Swiss and French Acadian populations. Lastly, heterozygosity vs. distance from centroid graph was constructed and it was found that Anatolians and India-Hindu had exactly the expected heterozygosity value predicted by the model of Harpending and Ward (1982).

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2016-04-18T10:48:49Z No. of bitstreams: 2 Tese - Marcelo Corrêa da Silva - 2015.pdf: 7209207 bytes, checksum: c24f13fb20a00a3bc5b7d242ee956d69 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-04-18T10:51:37Z (GMT) No. of bitstreams: 2 Tese - Marcelo Corrêa da Silva - 2015.pdf: 7209207 bytes, checksum: c24f13fb20a00a3bc5b7d242ee956d69 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-04-18T10:51:37Z (GMT). No. of bitstreams: 2 Tese - Marcelo Corrêa da Silva - 2015.pdf: 7209207 bytes, checksum: c24f13fb20a00a3bc5b7d242ee956d69 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-09-21 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Livestock production has played a major role in social-economic aspects of rural development worldwide. In South America the introduction of domestic breeds such as cows, sheep and goats occurred during Spanish and Portuguese colonization expeditions over five hundred years ago. The Pantaneiro and Curraleiro Pé-Duro cattle breeds originate from this exact context and resemble historic, cultural and ecological aspects of traditional cattle farming in Brazil. This is characterized by rough and extensive breeding systems placed in many ecosystems of this country. Small population sizes and severe loss of genetic diversity in livestock breeds are of great concern regarding the scenario of global warming, emphasis on the sustainability of farming activities, the need of alternatives to attend market trends and promote rural development in a local perspective. This study was undertaken to explore patterns of genetic diversity in Pantaneiro e Curraleiro Pé-Duro cattle, aiming to identify differences between groups reared in several regions of Central-West, Central, North and Northeast of Brazil. Animals were genotyped using a SNP (single nucleotide polymorphism) chip containing over fifty thousand markers. Different analytical procedures were carried out using differentiation index, estimates of common ancestry, simple and multivariate clustering, inbreeding coefficients, genetic and also geographical distances. Spatial analysis was developed to allow the identification of patterns of genetic variation, specific geographical regions and herds of greater genetic differentiation. The results furnish insights in order to develop strategies to preserve genetic variability in Pantaneiro and Curraleiro Pé-Duro cattle. / Os bovinos são tradicionalmente utilizados como fonte de proteína animal na alimentação humana em diversas regiões do mundo. Na América do Sul esta espécie foi introduzida por colonizadores espanhóis e portugueses e há mais de 500 anos tem sido disseminada no Brasil com importância alimentar e socioeconômica. Bovinos Pantaneiros e Curraleiro Pé-Duro são remanescentes de bovinos trazidos da região ibero-americana por meio de navios. Atualmente são considerados patrimônios históricos e culturais do país, com destaque à pecuária extensiva e tradicional que é praticada em diversos biomas do interior do Brasil, como o Pantanal, o Cerrado e a Caatinga. O baixo número de indivíduos existente, a demanda por uma produção animal mais competitiva e economicamente viável, com potencial de agregação de valor ou diferencial em termos de rusticidade, tem sido favoráveis para a discussão da conservação e maior utilização de raças localmente adaptadas. Isso tem tido maior destaque também em função do advento do aquecimento global e maior valorização de especificidades que caracterizam circunstâncias sociais, ecológicas e produtivas em escala local. Assim, este estudo foi desenvolvido a fim de explorar e compreender padrões de diversidade genética em populações de bovinos Pantaneiros e Curraleiro Pé-Duro, investigando-se diferenças e semelhanças genéticas entre indivíduos e rebanhos amostradas em diferentes biomas das regiões centro oeste, norte e nordeste do Brasil. Bovinos foram amostrados e genotipados com uso de um chip contendo mais de 50 mil marcadores polimórficos de base única (single nucleotide polymorphism, SNP). Diferentes técnicas de análise genética foram realizadas como o uso de distância genéticas, índices de diferenciação genética, estimativas de ancestralidade comum, endogamia e análises de dispersão e agrupamento uni e multivariados. Foram utilizados métodos de estatística espacial, que possibilitaram a identificação de padrões de variabilidade genética em função de distâncias geográficas e a identificação de descontinuidades genéticas, revelando uma compreensão inédita acerca da diferenciação entre grupos formados com base em um critério geopolítico ou com base em similaridade genética. Os resultados obtidos fornecem subsídios para a formação de grupos experimentais, a troca de material genético entre criadores, planejamentos participativos para a preservação e gestão sustentável desses bovinos junto às associações de criadores, entidades de pesquisa e demais atores envolvidos.

Although spoken dialogue systems have greatly improved, they still cannot handle communications involving unknown topics. One of the problems is, that they experience difficulties when they should pronounce unknown words. We will investigate methods that can improve spoken dialogue systems by correcting the pronunciation of unknown words. This is a crucial step to provide a better user experience, since for example mispronounced proper nouns are highly undesirable. Incorrect pronunciation is caused by imperfect phonetic representation of the word. We aim to detect incorrectly pronounced words, use knowledge about the pronunciation and user's feedback and correct the transcriptions accordingly. Furthermore, the learned phonetic transcriptions can be added to the speech recognition module's vocabulary. Thus extracting correct pronunciations benefits both speech recognition and text-to-speech components of the dialogue systems.

<p> Although historically treated as separate systems, there is considerable interaction between the immune system and brain. It has become increasingly clear that immunebrain communication is important to both health and disease. An immunogenic challenge given during the first postnatal week in rodents impacts the developing central nervous system (CNS) leading to long-term behavioural and molecular alterations reflective of enhanced stress-reactivity. Anxiety and depression are stress-related pathologies with a proposed neurodevelopmental origin suggesting that perturbation to neonatal immunebrain signalling may contribute to psychopathology. The current body of work examined the long-term impact of an early immune challenge on behavioural and molecular phenotypes associated with anxiety and depression. Mice were administered lipopolysaccharide (LPS) on postnatal days three and five. The emergence of anxietyrelated behaviour was characterized along the developmental trajectory of LPS-mice concurrent with changes to serotonergic neurocircuitry. Adult depressive-related behaviour was assessed in the forced swim test (FST) along with hippocampal neurogenesis as revealed by immunoreactivity for bromodeoxyuridine (BrdU) and doublecortin (DCX). The results demonstrated a sex-specific alteration in both the temporal emergence and phenotypic variant of anxiety-related behaviours displayed by LPS-mice. This was accompanied by changes to CNS serotonergic-related gene expression that coincided with a critical developmental time window essential to the establishment of emotionality. Adult LPS-mice exhibited hyperactivity during the FST that was accompanied by increased doublecortin immunoreactivity in the dorsal and ventral hippocampus, reflecting enhanced immature neuronal differentiation. The current results demonstrate that an early immune challenge impacts the developing CNS leading to enhanced emotional-reactivity. Altered serotonergic neurocircuitry and adult hippocampal neurogenesis may underlie behavioural abnormalities. The current body of work demonstrates a preeminent role for early-life immune disturbance in psychopathology and advances understanding of how immune-brain signalling impacts the developing CNS and confers risk for later disease. </p> / Thesis / Doctor of Philosophy (PhD)

Selection and genetic drift are often competing forces in shaping genetic structure in populations. Genetic drift will often effectively cancel out the effect of selection when population sizes are small, such as in colonizing island populations. On a small island in the Skeppsvik Archipelago in northern Sweden, a newly founded population of Silene dioica has been monitored since it first established around 1993. Though inhabiting an area of merely 173 m2, the population has been shown to exhibit a genetically differentiated patch structure where closely related individuals are tightly grouped, distanced from other family groups. In this study, the effect of selection was evaluated as compared to that of genetic drift. Variation in phenotypic traits in flowers, leaves and stalks were compared to that of neutral markers, in the form of PST and FST measures, to assess a measure of what proportion of differentiation among patches in phenotypic traits could not be attributed to genetic drift. Males and females were analysed separately to obtain measures of sex specific selection. Signs of divergent and stabilizing selection were found in several traits in both males and females despite the small spatial scale and short time since colonization. Further analysis is needed to assess explanations for trait divergence among patches and direction of selection.