Broad whitefish, Coregonus nasus, is an important subsistence fish species in Arctic North America, yet virtually nothing is known regarding the genetic population structure of Nearctic populations of this species. In this thesis, microsatellite DNA variation was assayed among 1213 broad whitefish from 47 localities throughout North America, with emphasis on the Mackenzie River system, Northwest Territories. Specifically, I examined geographic variation in allele frequencies to assess how historical factors (Pleistocene glaciations) have shaped the current structuring of genetic variability and population differentiation. Microsatellite data was also used to resolve the relative contributions of broad whitefish populations to subsistence fisheries in the Mackenzie River system. Overall, broad whitefish exhibit relatively high intrapopulation microsatellite variation (average 12.29 alleles/locus, average HE = 0.58) and there were declines in these measures of genetic diversity with distance from putative refugia suggesting historical factors, namely post-glacial dispersal, have influenced current microsatellite variation. Interpopulation divergence was low (overall FST = 0.07), but the main regions assayed in this study (Russia, Alaska, Mackenzie River and Travaillant Lake systems) are genetically differentiated. Strong isolation-by-distance among samples was resolved when including only those populations occupying former Beringia, but not when assaying those at the periphery of the range in the Mackenzie River system, suggesting that broad whitefish in the Mackenzie system have not occupied the region long enough since their invasion post-glacially to have approached equilibrium between gene flow and drift. Mixture analysis indicated that most fish from the lower Mackenzie River subsistence fishery originated from the Peel River, highlighting the importance of this tributary. Additionally the mixture analysis provides evidence for a putative riverine life history form in the Mackenzie River. My results indicate that glaciation and post-glacial colonization have been important in shaping the current genetic population structure of North American broad whitefish. They also illustrate the utility of microsatellite DNA to delineate population structure and patterns of genetic diversity in recently founded populations in addition to resolving contributions to fisheries. My data also support the hypothesis that there are several designatable units of conservation among broad whitefish populations and that management strategies should be implemented accordingly.

The persistence of a species in the face of environmental change is a function of the extent to which populations respond differently to changes in their environment and the spatial correspondence between the scale of disturbance and the scale of adaptation. The pattern by which a population, or genotype, expresses a range of phenotypes across an environmental gradient is called a norm of reaction. The level of phenotypic plasticity displayed within a population (i.e. the slope of the reaction norm) reflects the short-term response of a population to environmental change while variation in reaction norm slopes among populations reflects the spatial scale of variation in these responses. Using a reaction norm framework, I examined the spatial scale of genetic variation in plasticity for life-history traits in Atlantic cod (Gadus morhua), a marine fish of global biological and socioeconomic importance. Through common-garden experiments, I found evidence of both adaptive and non-adaptive plasticity for larval growth rate and survival in two cod populations that experience contrasting thermal environments in nature. A comparison of these reaction norms with those of four cod populations studied previously revealed significant genetic divergence in adaptive traits at a smaller spatial scale than has previously been shown for a marine fish with no apparent physical barriers to gene flow (<250 km). This fine-scale genetic structure is likely the result of populations being locally adapted to seasonal changes in temperature during the larval stage caused by differences in spawning times and may be maintained by behavioural barriers to gene flow. Implications of variation in life-history trait plasticity to fisheries management in the face of predicted changes in climate are discussed.

Šiame darbe buvo tiriamas Lietuvoje gyvenančių jerubių genetinis variabilumas panaudojant mikrosatelitinių pradmenų analizės metodus. Pavyzdžiai buvo surinkti iš Rietavo savivaldybėje, Ukmergės, Trakų, Vilniaus, Šakių ir Telšių rajonuose esančių miškų. DNR buvo išskiriama iš neinvaziniu būdu surinktų pavyzdžių, iškritusių plunksnų bei surinktų ekskrementų. Kadangi specialių mikrosatelitinių pradmenų jerubių rūšiai dar nėra sukurta, šiame darbe buvo panaudotos trys žvyrėms (Lagopus lagopus) specifiški mikrosatelitinių lokusų pagausinimui skirti pradmenys. Buvo apskaičiuoti alelių, genotipų ir heterozigotiškumo dažniai, ir individai iš Ukmergės MU pasižymėjo žemu alelių dažniu ir aukštu homozigotų dažniu. Mitochondrinės DNR analizė parodė, kad tarp 12 Lietuvos populiacijai priklausančių jerubių sekų, net 8 buvo skirtingos ir dėl to priskirtinos 8 skirtingiems haplotipais. Mitochondrinės DNR sekų filogenetiniai ryšiai parodė, kad Lietuvos jerubių populiacijoje aptikti haplotipai formuoja dvi filogenetiškai tolimas šakas, tuo tarpu Lenkijos haplotipų įvairovė gerokai didesnė. Tikėtina, kad šiuos skirtumus labiausiai įtakoja nevienodi lyginamų imčių dydžiai. / Non-invasively collected samples of feathers and faeces of Hazel Grouse (Tetrastes bonasia) were collected in different parts of Lithuania and covered several local populations of Rietavas, Ukmergė, Trakai, Vilnius, Šakiai and Telšiai districts. Three primer pairs of microsatellite loci, designed for taxonomically related Red Grouse (Lagopus lagopus scoticus), were used to verify their suitability for evaluation of genetic structure. Allele and genotype frequencies as well as heterozygosity were calculated and individuals from Ukmergė showed low frequency of allele, and high in homozigosity. Mitochondrial DNA analysis showed that in 12 sequences from Lithuanian population, 8 of them were different and could be assigned to 8 different haplotypes. Neighbour joining tree showed that haplotypes in Lithuanian population forms two branches with high distance. While variability of Poland haplotypes, obtained from Gene Bank was bigger. That could be affected by different compared samples sizes.

Post-zygotic genetic variation has previously been shown in healthy individuals and linked to various disorders. The definition of post-zygotic or somatic variation is the existence of genetically distinct populations of cells in a subject derived from a single zygote. Structural changes in the human genome are a major type of inter-individual genetic variation and copy number variation (CNV), involving changes in the copy number of genes, are one of the best studied category of structural genetic changes. In paper I we reported a pair of healthy female monozygotic (MZ) twins discordant for aneuploidy of chromosomes X and Y, contributing to the delineation of the frequency of somatic variation in MZ twins. It also illustrates the plasticity of the genome for tolerating large aberrations in healthy subjects. In paper II we showed age-related accumulation of copy number variation in the nuclear genomes in vivo for both megabase- and kilobase-range variants. Using age-stratified MZ twins and single-born subjects, we detected megabase-range aberrations in 3.4% of people ≥60 years old but not in individuals younger than 55 years. Moreover, the longitudinal analysis of subjects with aberrations suggests that the aberrant cell clones are not immortalized and disappear from circulation. We also showed that sorted blood cells display different genomic profiles.  The detected recurrent rearrangements are candidates for common age-related defects in blood cells. This work might help to describe the cause of an age-related decline in the number of cell clones in the blood, which is one of the hallmarks of immunosenescence. In paper III we described a variable number tandem repeat (VNTR) ~4 kb upstream of the IFNAR1 gene, which was somatically variable.  We detected 14 alleles displaying inter- and intra-individual variation. Further analyses indicated strong clustering of transcription factor binding sites within this region, suggesting an enhancer. This putative VNTR-based enhancer might influence the transcriptional regulation of neighboring cytokine receptor genes and the pathways they are involved in. These three studies stress the importance of research on post-zygotic variation in genetics. Furthermore, they emphasize that biobanks should consider sampling of multiple tissues to better address this issue in the genetic studies.

The aim of the research. To evaluate the genetic diversity in sweet and sour cher-ry populations, to characterize the injuries to blossoms and fruits caused by blossom blight brown rot, to identify the species composition of Monilinia patho-gens and to analyse the DNA polymorphism within and among pathogens popula-tions. Main tasks: 1. To analyse the genetic diversity of sweet and sour cherry cultivars and wild cherry population, growing in west Lithuania, using molecular marker methods (AFLP and SSR). 2. To determine factors affecting injuries caused by blossom blight. 3. To investigate characteristics of brown rot agent M. fructigena development in sweet and sour cherry cultivars differing in resistance to brown rot. 4. To identify species composition of Monilinia spp. in IH LRCAF stone fruit collection based on PCR methood and to evaluate inter- and intraspecific DNA polymorphism of Monilinia spp. based on AFLP method. / Tyrimų tikslas. Įvertinti trešnės ir paprastosios vyšnios populiacijų ge-netinę įvairovę, ištirti trešnės ir paprastosios vyšnios žiedų bei vaisių užsikrėtimo kaulavaisinių monilioze mechanizmus, nustatyti šios ligos sukėlėjų Monilinia rūšinę sudėtį bei išanalizuoti jų tarprūšinį ir vidurūšinį DNR polimorfizmą. Tyrimų uždaviniai: 1. Išanalizuoti skirtingų pagal atsparumą moniliozinei degligei LAMMC SDI kaulavaisinių kolekcijoje augančių trešnės ir vyšnios veislių ir Vakarų Lietuvo-je augančios laukinės trešnės populiacijos genetinę įvairovę, naudojant molekuli-nius metodus (SSR ir PFIP) bei palyginti PFIP pradmenų kombinacijų informaty-vumo rodiklius. 2. Nustatyti žiedų pažeidimo moniliozine deglige (M. laxa) veiksnius: ištirti žiedo da¬lių atsparumą moniliozinei degligei, nustatyti kuriame žiedo raidos tarpsnyje jie yra jautriausi, įvertinti, ar kuokelių mechaninis pašalinimas (kastravimas) turi įtakos užsikrėtimui moniliozine deglige ir nustatyti ar žiedų ap-dulkinimas gali aktyvuoti augalo imunines reakci¬jas ir užkirsti kelią patogenui patekti į žiedo vidų. 3. Ištirti rudojo puvinio sukėlėjo M. fructigena vystymosi ypatumus kontrastinėse pa¬gal atsparumą rudajam puviniui trešnės ir vyšnios veislėse. Nusta-tyti, ar vaisiai jautresni patogenui yra nokimo pradžioje ar techninės brandos (skynimo) metu, įvertinti vaisių mechani¬nio pažeidimo poveikį užsikrėtimui ruduo-ju puviniu. 4. Identifikuoti Monilinia spp. LAMMC SDI kaulavaisinių kolekcijos augyne rūšinę sudėtį PGR... [toliau žr. visą tekstą]

The study of genetic variation in populations is of great interest for the study of the evolutionary history of humans and other species. Improvement in sequencing technology has resulted in the availability of many large datasets of genetic data. Computational methods have therefore become quite important in analyzing these data. Two important problems that have been studied using genetic data are population stratification (modeling individual ancestry with respect to ancestral populations) and genetic association (finding genetic polymorphisms that affect a trait). In this thesis, we develop methods to improve our understanding of these two problems. For the population stratification problem, we develop hierarchical Bayesian models that incorporate the evolutionary processes that are known to affect genetic variation. By developing mStruct, we show that modeling more evolutionary processes improves the accuracy of the recovered population structure. We demonstrate how nonparametric Bayesian processes can be used to address the question of choosing the optimal number of ancestral populations that describe the genetic diversity of a given sample of individuals. We also examine how sampling bias in genotyping study design can affect results of population structure analysis and propose a probabilistic framework for modeling and correcting sample selection bias. Genome-wide association studies (GWAS) have vastly improved our understanding of many diseases. However, such studies have failed to uncover much of the variation responsible for a number of common multi-factorial diseases and complex traits. We show how artificial selection experiments on model organisms can be used to better understand the nature of genetic associations. We demonstrate using simulations that using data from artificial selection experiments improves the performance of conventional methods of performing association. We also validate our approach using semi-simulated data from an artificial selection experiment on Drosophila Melanogaster.

Broad whitefish, Coregonus nasus, is an important subsistence fish species in Arctic North America, yet virtually nothing is known regarding the genetic population structure of Nearctic populations of this species. In this thesis, microsatellite DNA variation was assayed among 1213 broad whitefish from 47 localities throughout North America, with emphasis on the Mackenzie River system, Northwest Territories. Specifically, I examined geographic variation in allele frequencies to assess how historical factors (Pleistocene glaciations) have shaped the current structuring of genetic variability and population differentiation. Microsatellite data was also used to resolve the relative contributions of broad whitefish populations to subsistence fisheries in the Mackenzie River system. Overall, broad whitefish exhibit relatively high intrapopulation microsatellite variation (average 12.29 alleles/locus, average HE = 0.58) and there were declines in these measures of genetic diversity with distance from putative refugia suggesting historical factors, namely post-glacial dispersal, have influenced current microsatellite variation. Interpopulation divergence was low (overall FST = 0.07), but the main regions assayed in this study (Russia, Alaska, Mackenzie River and Travaillant Lake systems) are genetically differentiated. Strong isolation-by-distance among samples was resolved when including only those populations occupying former Beringia, but not when assaying those at the periphery of the range in the Mackenzie River system, suggesting that broad whitefish in the Mackenzie system have not occupied the region long enough since their invasion post-glacially to have approached equilibrium between gene flow and drift. Mixture analysis indicated that most fish from the lower Mackenzie River subsistence fishery originated from the Peel River, highlighting the importance of this tributary. Additionally the mixture analysis provides evidence for a putative riverine life history form in the Mackenzie River. My results indicate that glaciation and post-glacial colonization have been important in shaping the current genetic population structure of North American broad whitefish. They also illustrate the utility of microsatellite DNA to delineate population structure and patterns of genetic diversity in recently founded populations in addition to resolving contributions to fisheries. My data also support the hypothesis that there are several designatable units of conservation among broad whitefish populations and that management strategies should be implemented accordingly.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2008. / Härtill 5 uppsatser.

Diss. (sammanfattning) Alnarp : Sveriges lantbruksuniversitet, 2005. / Härtill 4 uppsatser.

Diss. (sammanfattning). Alnarp : Sveriges lantbruksuniversitet, 2005. / Härtill 4 uppsatser.