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The theory of "genomic islands of speciation" has been extensively debated during the last decade. This thesis not only supports this theory, but provides evidence that challenges previous beliefs on the level of admixture between species. The recently published Heliconius melpomene genome project reported apparent genomic paraphyly of H. pardalinus with regard to H. elevatus (Heliconius Genome Consortium 2012). Here, we investigate this pair of butterfly species more fully, firstly by using whole-genome resequence data, and secondly by analyzing additional geographic populations of both species, as well as outgroup taxa. Using a nuclear whole-genome phylogenetic analysis we also confirm that H. elevatus is paraphyletic. The genome-wide phylogenetic signal in H. pardalinus and H. elevatus does not indicate expected mutual monophyly of each species as it seems strongly distorted by a high level of admixture. However, several regions of the genome remain differentiated and do show the presumably original phylogenetic signal with mutual monophyly of H. pardalinus and H. elevatus. The genomic background is so homogenized that its level of differentiation (FST ~ 0.03) virtually implies panmixia. The pattern of a high level of homogenization across the genome with several regions of differentiation was consistent with a number of other statistics such as absolute divergence Dxy, nucleotide polymorphism π, number of fixed differences and with a sliding window phylogeny. The identified genomic islands of divergence comprise genes responsible for wing-patterning and chemosensation in Heliconius and some of these genes are found to be under positive selection, suggesting possible candidates of speciation.

abstract: Building mathematical models and examining the compatibility of their theoretical predictions with empirical data are important for our understanding of evolution. The rapidly increasing amounts of genomic data on polymorphisms greatly motivate evolutionary biologists to find targets of positive selection. Although intensive mathematical and statistical studies for characterizing signatures of positive selection have been conducted to identify targets of positive selection, relatively little is known about the effects of other evolutionary forces on signatures of positive selection. In this dissertation, I investigate the effects of various evolutionary factors, including purifying selection and population demography, on signatures of positive selection. Specifically, the effects on two highly used methods for detecting positive selection, one by Wright's Fst and its analogues and the other by footprints of genetic hitchhiking, are investigated. In Chapters 2 and 3, the effect of purifying selection on Fst is studied. The results show that purifying selection intensity greatly affects Fst by modulating allele frequencies across populations. The footprints of genetic hitchhiking in a geographically structured population are studied in Chapter 4. The results demonstrate that footprints of genetic hitchhiking are significantly influenced by geographic structure, which may help scientists to infer the origin and spread of the beneficial allele. In Chapter 5, the stochastic dynamics of a hitchhiking allele are studied using the diffusion process of genetic hitchhiking conditioned on the fixation of the beneficial allele. Explicit formulae for the conditioned two-locus diffusion process of genetic hitchhiking are derived and stochastic aspects of genetic hitchhiking are investigated. The results in this dissertation show that it is essential to model the interaction of neutral and selective forces for correct identification of the targets of positive selection. / Dissertation/Thesis / Ph.D. Biology 2011

The suggester functionality is an important feature of modern search engines. The aim of the thesis is to implement it for the OpenGrok project. The OpenGrok search engine is based on Apache Lucene and supports its query syntax. Presented suggester implementation supports this query syntax and provides suggestions not only for prefixes but also for wildcards, regular expressions, or phrases. The implementation also takes into account the possibility of grouping queries. That means, if one query is already specified and user is typing another query, then the first query will restrict the suggestions for the second query. The promotion of specific suggestions is based on the underlying Lucene index data structure and previous searches of the users.

In the Western United States, the Great Basin is a geographic feature that is home to a variety of unique species, including Great Basin bristlecone pine (Pinus longaeva, PILO). P. longaeva is well known for the age of some of the trees, some of which are over 4000 years old. In this study 17 microsatellite markers (simple sequence repeat, SSR) are identified and used to genotype a selection of 480 individuals spread across 24 PILO populations and 60 individuals divided equally between 2 outgroup species, Pinus aristata and Pinus flexilis. One population of PILO, HMW, shows more genetic similarity with P. aristata, and is included with outgroup species in the analysis. The population structure of PILO is examined and found to be weakly related to the geographic distance between populations. The population statistics Fst, Gst, Rst, Dest and an AMOVA analysis suggest that there is a substantial amount of admixture at the individual level, similar to some other species of pines. Phylogenetic trees computed using the neighbor-joining method based on the average population genetic distance and based on individual genetic distance support the population structure results and show further evidence that most of the species variation is concentrated at the individual level, rather than inside of or between species. It is possible that gene flow is still occurring, or that gene flow has occurred recently enough that the separated populations have not yet diverged from each other in a measurable way.

The aim of the thesis is to examine the power of organized composers of art music in interwar Sweden and their development of areas of interest 1919-1939. The period is chosen due to the 1918 founding of the Society of Swedish Composers (the FST). Although of significant value, most of the previous research on the subject has focused on individual composers. The thesis, instead, combines concepts of Pierre Bourdieu’s theory of cultural fields with power theories of Steven Lukes and Walter Korpi to investigate access to power resources and exercise of power within the field of music by the FST and its members 1919-1939. The results show that the FST of 1939 had greater access to economic capital, which correlated with the expansion of the FST’s exercise of power and areas of interest concerning the whole field of Swedish music, rather than exclusively the field of art music. Social networks tied to the FST, however, never ceased to be an important factor influencing the operations of the FST.

This study is exploring the possibilities of automatic morphological analysis of L-verbs in the Palula language by the help from Finite-state technology and two-level morphology along with supervised machine learning. The type of machine learning used are neural Sequence to Sequence models. A morphological transducer is made with the Helsinki Finite-State Transducer Technology, HFST, toolkit covering the L-verbs of the Palula Language. Several Sequence to Sequence models are trained on sets of L-verbs along with morphological tagging annotation. One model is trained with a small amount of manually annotated data and four models are trained with different amounts of training examples generated by the Finite-State Transducer. The efficiency and accuracy of these methods are investigated. The Sequence to Sequence model trained on solely manually annotated data did not perform as well as the other models. A Sequence to Sequence model trained with training examples generated by the transducer performed the best recall, accuracy and F1-score, while the Finite-State Transducer performed the best precision score. / Denna studie undersöker möjligheterna för en automatisk morfologisk analys av L-verb i språket Palula med hjälp av finit tillståndsteknik och två-nivå-morfologi samt övervakad maskininlärning. Den typ av maskininlärning som används i studien är neurala Sekvens till Sekvens-modeller. En morfologisk transduktor är skapad med verktyget Helsinki Finite-State Transducer Technology, HFST, som täcker L-verben i Palula. Flera Sekvens till Sekvens-modeller tränas på set av L-verb med morfologisk taggningsannotation. En modell tränas på ett litet set av manuellt annoterade data och fyra modeller tränas på olika mängder träningsdata som genererats av den finita tillstånds-transduktorn. Effektiviteten och noggrannheten för dessa modeller undersöks. Sekvens till Sekvens-modellen som tränats med bara manuellt annoterade data presterade inte lika bra som de andra modellerna i studien. En Sekvens till Sekvens-modell tränad med träningsdata bestående av genereringar producerade av transduktorn gav bästa svarsfrekvens, noggrannhet och F1-poäng, medan den finita tillstånds-transduktorn gav bästa precision.

A key component to conservation is an accurate understanding of genetic subdivision within a species. Despite their ecological and economic importance, relatively little is understood about the genetic structuring of Yellowstone cutthroat trout in Yellowstone National Park. Here, we use traditional (Fst, Rst, Nm, and AMOVA) and modern (Bayesian assignment tests, coalescent theory, and nested clade analysis) analytical approaches to describe the population genetic subdivision of cutthroat trout spawning populations in Yellowstone Lake and to identify genetically distinct population segments throughout Yellowstone National Park. Evidence for restricted gene flow between spawning populations within Yellowstone Lake was detected using nested clade analysis. This is the first molecular evidence for restricted gene flow between spawning populations in Yellowstone Lake. In contrast, traditional methods such as Fst and Rst as well as the Bayesian clustering program STRUCTURE v2.0 failed to detect evidence for restricted gene flow. Across our sampling range within Yellowstone National Park, eleven genetically distinct cutthroat trout population segments were detected. These showed a general pattern of small, isolated populations with low genetic diversity in headwater streams and wide-spread, genetically diverse populations in higher-order rivers. We recommend populations be managed to maintain current levels of genetic diversity and gene flow. Based on the recent decline of and distinct morphological, behavioral, and genetic nature of cutthroat trout in Yellowstone Lake, we recommend the Yellowstone Lake spawning populations collectively be recognized as an evolutionarily significant unit.

<p>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 (<i>Rana temporaria</i>) populations along a 1600 km transect from southern Sweden to northern Finland.</p><p>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.</p><p>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 (F_ST) and quantitative characters (Q_ST) revealed that although both estimates of divergence were relatively high, estimates of Q_ST was generally higher than those of F_ST, 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</p>

QC 20110926