Abstract The evolution of microsatellites was studied within and between the pine species. Sequences showed that microsatellites do not necessarily mutate in a stepwise fashion and that size homoplasy is common due to flanking sequence and repeat area changes within and between the species. Thus, some assumptions of statistical methods based on changes in repeat numbers may not hold. Sequences from cross-species amplifications revealed evidence of duplications of microsatellite loci in pines. On two independent occasions, the repeat area of the microsatellite had undergone a rapid expansion during the last 10-25 million of years. Microsatellite markers were used together with other molecular markers (allozymes, RFLPs, RAPDs, rDNA RFLPs) and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (Pinus sylvestris) in Finland. All molecular markers showed high level of within population variation, while differentiation among populations was low (FST = 0.02). Of the total variation in bud set, 36.4 % was found among the populations which experience a steep climatic gradient. Thus, the markers applied were poor predictors of population differentiation of the quantitative trait studied The distribution of genetic variation was studied in five natural populations of radiata pine (Pinus radiata), species which has gone through bottlenecks in the past. Null allele frequencies were estimated and used in later analyses. Microsatellites showed high level of variability within populations (He = 0.68-0.77). Allele length distributions and average number of alleles per locus showed some traces of bottlenecks. Instead, comparison of observed genetic diversities and expected diversities suggested post-bottleneck expansion of populations. Genetic differentiation (FST and RST) among populations was over 10 %, reflecting situation in the isolated radiata pine populations. Using microsatellites and a newly developed Bayesian method, individual inbreeding coefficients were estimated in five populations of radiata pine. Most individuals were outbred while some were selfed. Presumably, in ancestral radiata pine populations the recessive deleterious alleles have been eliminated after bottlenecks and the mating system has changed as a consequence.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / Tomopterna delalandii occurs throughout the west coast, Western Cape and south coast of South Africa. This range stretches across three distinct biogeographical assemblages. Based on historical records and the fact that Tomopterna is a genus of cryptic frogs, it is possible that there are unknown genetic variations within the species. To investigate whether population structure is present within T. delalandii a mitochondrial gene and nuclear gene, 16S and Tyrosinase, was sequenced from across the range. Haplotype networks and cladograms were constructed to look at the relationship between the genetic samples. This revealed definite population structuring between samples from the western edge of the range and samples from the eastern edge of the range. It also revealed that samples taken from the northern edge of the range, while matching general T. delalandii tadpole morphology, are genetically different. Further study needs to be made into the identity of this new form. This study shows that by using both mitochondrial and nuclear DNA patterns can be discovered about the genetic structure of a species as well as revealing a new one.

The sperm whale is the largest of the toothed whales (Odontoceti), and inhabits deep waters from equatorial to Polar Regions. Sperm whales are social and commonly l r . found in small groups. However, sociality varies according to sex and age. Immature males form bachelor groups that disperse as they mature, mature males are frequently encountered alone. Sperm whales are renowned for their diving capabilities. Therefore, surface observations are only possible for 10 to 15 minutes every hour. Consequently, the sperm whale is an ideal candidate for investigation using genetic markers. Genetic variation can reveal information on geographical structuring of populations and, on a finer scale, the social organisation within these groups. The focus of this thesis is an investigation into the structure of populations around the Azores. To date, this work represents the most comprehensive molecular investigation into North Atlantic sperm whales. Since 1988 sloughed skin samples have been collected from the Azores but, to facilitate the comparison between local and global structuring, samples were also obtained from a number of geographically distinct regions. Twelve microsatellite loci and a marker to indicate sex were selected for screening. Genetic variation was sufficient to allow identification of individuals with a high degree of accuracy. A system of scoring the amplification quality was found to be both a simple and accurate method of determining the reliability of a genotype. Errors were found to arise infrequently, hence their influence in the final dataset was considered negligible. Of the 467 sloughed skin samples collected from the Azores, 102 individuals were identified. The majority of these samples had been collected from groups. As groups are presumed to be matrilineal, the identification of mother calf pairs was anticipated. However the samples revealed few parent offspring combinations. Within a group the majority of whales were related at the level of half )siblings. This indicates that I I Azorean groups comprise of individuals related through either the maternal or paternal lineage. Full siblings were also identified, which suggests that a degree of mate choice can occur. The first insight into the relationships within bachelor groups arose when two such groups, stranded off the coast of Scotland, were examined. Individuals within the groups were predominantly unrelated to each other. However, potential half/sibling relationships within the groups were identified. A mother offspring pair was identified between an Azorean whale and one of the stranded whales. Microsatellite data from Atlantic (n=I32) and Pacific (n=I59) sperm whales revealed low, but significant, inter-ocean variation. However, examinations of populations structuring on a finer scale (geographic regions) failed to reveal any consistent pattern of differentiation. This lack of differentiation is surprising when compared with other cetaceans, all of which show increased genetic differentiation with distance.

Understanding whether groups of individuals represent a single panmictic gene pool, or multiple genetically structured populations across a species range should aid in predicting whether specific conservation strategies would be more or less effective for species preservation. Further, contrasting the population structures of multiple coexisting taxa could foster an even deeper understanding of evolutionary divergence among demes and potentially even suggest local adaptation in the form of tight coevolutionary relationships. Finally, the analysis of population dynamics within small and isolated populations could improve our understanding of the relative importance that different evolutionary mechanisms have in predicting population persistence in the wild. Using microsatellite markers I characterized the population genetic structure in the critically endangered Cyclura cychlura cychlura iguanas on Andros Island. I found significant differences between inferred and realized rates of gene flow. This finding demonstrates that evolutionarily independent populations can occur even with high rates of dispersal. In the second and third study I contrasted patterns of genetic variability in Cyclura cychlura cychlura iguanas, ticks in the genus Amblyomma parasitizing these iguanas, and Rickettsia spp., potential pathogens transmitted by these ticks. I determined that genetic differences among Rickettsia samples and Amblyomma samples are highly concordant with genetic divergence among iguana populations. This finding suggests largely vertical dispersal of ticks and their super-parasite, a high specificity of this reptile-tick interaction, and historically low rates of dispersal in iguanas. This finding also indicates that island populations of iguanas may be locally adapted due to tight coevolutionary relationships. Finally, I investigated the mechanisms that eliminate harmful mutations in small isolated and natural populations of the critically endangered Cyclura cychlura cychlura iguanas. Using molecular tools I found indirect evidence suggesting that small natural populations can maintain significant levels of genetic variation in spite of strong selection acting against harmful mutations. Under regimes of random mating, the buildup of harmful mutations in small populations may result in a large number of inviable young. However, harmful mutations may also be eliminated when exposed to natural selection through increased competition, as population density increases. However, quantification of the relative role of competition was not feasible in this study.

No description available.

The genus Populus consists of many ecologically and economically important forest tree species. Their rapid growth makes them one of the most productive hardwoods growing in temperate latitudes. Populus spp. frequently hybridize where their ranges overlap, and poplar hybrids are the most frequently planted genotypes for fiber production. To better understand the genomics of hybridization in Populus, we sampled and sequenced the genome of 574 poplar trees from six east-west transects across the hybrid zone between Populus trichocarpa and Populus balsamifera in western North America. I used these data to characterize population structure within and between transects, and hybridization between the species. There was a consistent transition from greater P. balsamifera ancestry in the north and east to greater P. trichocarpa ancestry in the south and west. Hybridization between the species was common across each of the six transects, though more common in colder climates. The results also showed that both latitude and longitude affect the genetic structure of this species complex, and that subtle introgression from P. balsamifera may facilitate adaptation of P. trichocarpa to colder climates. / Master of Science / The genus Populus has many ecologically and economically important forest tree species. Balsam poplar (Populus balsamifera) and black cottonwood (Populus trichocarpa) are two such species, both for fiber production and models for understanding tree biology and adaptation. Whereas black cottonwood is distributed close to the west coast of North America from California through Alaska, balsam poplar mostly occurs across the interior of Canada from Newfoundland through Alberta. Where their ranges overlap, the species often hybridize. In this study, we used genome sequencing of trees collected across six east-west transects from Washington state through British Columbia, Canada, and Alaska to understand genetic variation and the geography of hybridization. I found evidence of widespread hybridization across all transects. While the influence of P. balsamifera was extensive in northern populations, a large number of pure P. trichocarpa were found in southern populations. The transition from P. trichocarpa to P. balsamifera was also steeper in the south than the north, with a narrower hybrid zone in the south. Additionally, I found that gene flow among some populations was limited by temperature and geographical barriers. Taken together, my results suggest genetic structure and hybridization within and between these species is driven by climate variation, and that P. balsamifera ancestry may help northern P. trichocarpa populations adapt to their local environments.

The fossil population structure of the gastropod Neptunea angulata from the late Pliocene and Early Pleistocene was investigated in this project in order to contribute to a wider study on the influence of predation on populations and the evolutionary history of organisms. Over time, predator-prey relationships can drive evolution in a way similar to the Red Queen Hypothesis. However, before the effects of predation can be understood one must determine how the population dynamics functioned without the influence of predation. There are a number of problems that arise when determining population dynamics for fossil assemblages. These are usually caused by missing fossil data and the uncertain nature of their absence. Bias is rife within fossils at various stages from post-portem processes to when they are present in museum collections. One way to estimate these biases is to investigate the population structures of the fossils both directly from the fossil record and from museum collections. The variation in oxygen istopes found in N. angulata shells corresponded to yearly cycles which then were counted to determine the age of the specimen at time of death. Measuring the length of the spiral at yearly intervals provided the growth rate for the organism while it was alive. The growth rates were then used to determine the ages of specimens based on their size. The resulting ages were organized into an age distribution graph which was used to determine any museum bias. Bias in the preservation was also investigated by measuring the taphonomic damage of organisms of different size and then determine the distributions of size vs taphonomy. The ages of three specimens were found to differ even though the organisms had similar whorl lengths. As a result the growth equations differed and so different age distributions were calculated from each growth equation. All the age distributions demonstrated that the museum collections did show some bias against the smaller sized and thus younger specimens. There also appeared to be a size bias towards small N. angulata within the fossil record, with the extremely small individuals missing. The majority of the smallest specimens found in the field collections were not actually N. angulata specimens. A major problem with the results was a lack of data and a small sample size and it is highly recommended that an extensive collection and review of material be undertaken to fully determine the population structure present in the fossil assemblages. Other parts of the study, for example, the growth rates also require larger data sets in order for the confidence of the data to be improved. / I detta projekt studerades snäckpopulationer (Neptunea angulata) från Pliocen och Pleistocen för att besvara bredare frågeställningar om predation och dess inflytande på populationer och evolution. Innan man kan fastställa effekten av predation så behöver man förstå hur populationen betedde sig utan predationstryck. Flertalet problem uppstår när man studerar fossila populationer: tillgången på data kan vara begränsad och det kan vara svårt att se vad som saknas och varför. Information från fossil förloras från tiden som organismen dör fram till att de återfinns i museisamlingar. Ett sätt att uppskatta informationsförlusten är att studera fossil såväl i fossilbäddar som i museisamlingar. Genom att använda sig av den observerade cykliska skillnaden i stabila syreisotoper mellan olika tillväxtzoner i skalen av Neptunea angulata var det möjligt att uppskatta åldern på en organism vid en viss längd. Hastigheten med vilken snäckan växte beräknades genom att mäta förändringen i längd mellan olika åldrar. Genom att beräkna hur snabbt en snäcka växte så var det möjligt att använda storleken på fossilerna för att uppskatta dess ålder då den dog. Fossilen organiserades efter ålder för att visa populationsstrukturer. Förluster av fossil efter deposition uppskattades undersöktes genom att bestämma om mindre storleksgrupper var mer skadad än större storleksgrupper . Den varierade tillväxten hos olika snäckor användes för att beräkna dess åldrar. Det upptäcktes att museisamlingar tenderade att inneha större och äldre individer. Det tycktes också finnas färre små fossil av Neptunea angulata inom opartisk samling. Några av de extrement små individerna saknades helt och majoriteten av de minsta fossilen var inte ens Neptunea angulata. Skador på fossilen var större ju mindre individerna var. Mängden data inverkade negativt på denna studie och därför rekommenderas en omfattande genomgång av de tillgängliga samlingarna för att bättre kunna besvara frågor kring denna population i framtiden.

Landscape genetics is an emerging field that seeks to understand how specific landscape features and microevolutionary processes such as gene flow, genetic drift, and selection interact to shape the amount and spatial distribution of genetic variation. This study explores, through agent based simulations, how the specific mating and social system of tamarin primates (genus Saguinus) influences population genetic structure and patterns of relatedness within and among groups of this primate species, which might affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. I use a spatially-explicit agent-based population genetics simulation model (GENESYS) configured to reflect the particular social system of tamarin monkeys (i.e. small group size, limited numbers of breeders per group, frequent twin births, and short dispersal distances) to assess whether the isolation by distance model of genetic differentiation expected in an unfragmented landscape can be distinguished from the isolation by barrier model expected in a fragmented landscape. GENESYS allows a user to explore the effects of social structure and landscape features on the population genetic structure of social animals, such as primates. I simulated two different landscapes containing an otherwise equivalent population of tamarins. In the first setup I simulated a homogeneous landscape unconstrained by any barriers to gene flow, while for the second setup, a barrier to gene flow restricted dispersal from one half of the landscape to the other. I found that the particular mating system of tamarin results in the rapid genetic differentiation of its social groups and consequently its populations. Social groups in the continuous landscape indeed revealed an isolation by distance pattern, while social groups on the fragmented landscape yielded instead an isolation by barrier model, where the barrier rather than geographic distance per se influenced the spatial genetic structure of the population. The results from this study suggest that features of the tamarin social system influence population genetic structure, which could affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. To more fully address that issue, future studies should focus on a range of different primate social systems. / text

Transforming the composition of families and households in the 19th and 20th centuries in a selected area of the Czech Lands Abstract The aim of this work is to analyze changes in the size and composition of families and households in the 19th and 20th centuries in the South Bohemian town of Soběslav. The research is based on a comparison of data obtained excerption of census in 1869, 1880 and 1910. The first part of the demographic analysis focuses on the assessment of the size and structure of the population by age, sex, family status and nationality. In the second part the survey data from individual census are processed for individual households and families. The notion of familly and household is based on the basis of cohabitation. The division of households by the P. Laslett was used.

Rice blast disease is caused by the ascomycete fungus Magnaporthe oryzae and is of economic importance worldwide, due to its wide geographical distribution and the severe yield losses it causes on cultivated rice. Understanding the population structure of M. oryzae is key to sustainable management of blast disease. In this study, a total of 290 M. oryzae isolates were collected from rice growing regions in Kenya including Central Kenya (Mwea irrigation scheme), Western Kenya (Ahero and Maugo irrigation schemes in Ahero and Homa-Bay respectively) and Coastal Kenya (Kwale). Initially, I undertook genotyping of a subset of Kenyan isolates by DNA sequence analysis of the internal transcribed spacer regions (ITS 1 and ITS 2) of the rRNA-encoding gene unit and by DNA fingerprinting using the Pot2 repetitive DNA element. Phylogenetic analyses based on ITS sequences clustered together isolates from Western and Coastal Kenya which were distinct from Central Kenya isolates. Cluster analysis based on 80% DNA fingerprint similarity, identified five clonal lineages designated KL1, KL2, KL3, KL4 and KL5 with most isolates belonging to lineages KL2, KL3, KL4. The clustering of isolates was region specific with Western and Coastal isolates closely related to each other and distinct from Central Kenya isolates. Distribution of mating type gene loci (MAT1.1 and MAT1.2) was determined using mating type gene specific primers. My results indicate that MAT1.1 is the predominant mating type and is distributed in all the rice growing regions of Kenya. MAT1.2 isolates were identified only in Coastal Kenya. I further undertook high throughput next-generation DNA sequencing of the genomes of 27 M. oryzae isolates from sub-Saharan Africa (SSA), including Kenya, Uganda, Tanzania, Benin, Togo, Nigeria and Burkina Faso and compared them to other sequenced strains from China, India, USA, Philippines, Thailand, Korea, Japan, France and French Guiana. Single nucleotide polymorphisms (SNPs) indicated that majority of East African isolates of M. oryzae clustered separately from West African isolates. African isolates clustered with isolates from India and China, indicating that rice blast in SSA may have originated from Asia. Pathotype analysis of Kenyan isolates was undertaken using a set of monogenic differential rice varieties, collectively harbouring 24 disease resistance genes. Rice blast resistance gene Pi-z5 conferred resistance to all the isolates tested. Other resistance genes that conferred resistance to majority of isolates tested include Pi-9, Pi-12(t), Pi-ta, Pi-ta2 and Pi-z. These resistance genes are suitable candidates for introgressing into commercially grown varieties in Kenya in combinations. I also investigated the population of M. oryzae isolates to identify cognate avirulence gene loci, including novel genes not yet reported. Finally, I evaluated rice varieties grown in Kenya for resistance to indigenous rice blast isolates under laboratory conditions. Rice variety Basmati 370 was susceptible to rice blast with varieties IR2793-80-1, BW 196, NERICA 1, NERICA 4, NERICA 10, and NERICA 11 showing some disease resistance. Varieties ITA 310 and Duorado Precoce were moderately tolerant to rice blast. This information is being used to develop a durable blast resistance strategy in sub-Saharan Africa.