Evolutionary Genetics in the WIld : from Populations to Individuals

Predicting evolutionary outcomes and reconstructing past evolutionary transitions are among the main goals of evolutionary biology. Ultimately, understanding the mechanisms of evolutionary change will also provide answers to the timely question of whether and how organisms will adapt to changing environmental conditions. In this thesis, I have investigated the relative roles of natural selection, random genetic drift and genetic correlations in the evolution of complex traits at different levels of organisation from populations to individuals. I have shown that natural selection has been the driving force behind body shape divergence of marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations, while genetic drift may have played a significant role in the more fine scale divergence among isolated freshwater populations. These results are concurrent with the patterns that have emerged in the published studies comparing the relative importance of natural selection and genetic drift as explanations for population divergence in different traits and taxa. I have also shown that body shape and armour divergence among threespine stickleback populations is likely to be biased by the patterns of genetic variation and covariation. Body shape and armour variation along the most likely direction of evolution the direction of maximum genetic variance reflects the general patterns of variation observed wild populations across the distribution range of the threespine stickleback. Conversely, it appears that genetic correlations between the sexes have not imposed significant constraints on the evolution of sexual dimorphism in threespine stickleback body shape and armour. I have demonstrated that the patterns of evolution seen in the wild can be experimentally recreated to tease out the effects of different selection agents in detail. In addition, I have shown how important it is to take into account the correlative nature of traits, when making interpretations about the effects of natural selection on individual traits. Overall, this thesis provides a demonstration of how considering the relative roles of different mechanism of evolutionary change at different levels of organisation can aid in an emergence of a comprehensive picture of how adaptive divergence in wild populations occurs.

The ecology of the mountain hare (Lepus timidus L.) in managed boreal forests: habitat associations at different forest scales

Aims of this thesis This study is part of a larger hare project in Finland, which provides answers to basic ecological questions regarding the mountain hare. This study of the ecology of the mountain hare focuses in particular on different levels of managed boreal forest. The feeding habits and intensity of mountain hares in winter are explored, and the connections between mountain hares versus the forest structure are also studied (e.g. habitat use and the importance of different forest layers for hares). The use of the environment by hares at the landscape level was examined (forest patch structures), and the home ranges of mountain hares were studied. Finally, the productivity and survival rate of mountain hare populations were also studied (discussion e.g. predator effects on hare populations). Conclusions Feeding intensity seemed to be highest in the spring-winter, when home ranges were also largest. Favourable food species are covered by snow in winter and the mobility of hares is highest during late winter. A shortage of suitable food species may be problematic for hares, especially during the winter period. In this study mountain hares preferred a dense shrub layer at local level and deciduous and mixed tree forest over coniferous forest at the landscape level. Food and shelter are vital for hares and the preference for particular habitats may also affect the population dynamics of the mountain hare. It would be possible to improve the quality of food and shelter or at least prevent the most negative habitat changes through forest management. At a local level it is also possible to add supplementary food for hares through the winter period. The intensive clearing of young sapling stands and especially the removal of deciduous shrubs and trees reduces the quality of habitats for the mountain hare. Mountain hares primarily live in forest habitat and it is possible that changes in the forest structure play a crucial role in mountain hare habitat preference. Ecological knowledge of the mountain hare is vital to create habitat structure more suitable for the species. More deciduous trees should be saved in managing forests and the mechanical clearing of the shrub layer should be done carefully.

Microbial communities in Pb contaminated boreal forest soil

Lead contamination in the environment is of particular concern, as it is a known toxin. Until recently, however, much less attention has been given to the local contamination caused by activities at shooting ranges compared to large-scale industrial contamination. In Finland, more than 500 tons of Pb is produced each year for shotgun ammunition. The contaminant threatens various organisms, ground water and the health of human populations. However, the forest at shooting ranges usually shows no visible sign of stress compared to nearby clean environments. The aboveground biota normally reflects the belowground ecosystem. Thus, the soil microbial communities appear to bear strong resistance to contamination, despite the influence of lead. The studies forming this thesis investigated a shooting range site at Hälvälä in Southern Finland, which is heavily contaminated by lead pellets. Previously it was experimentally shown that the growth of grasses and degradation of litter are retarded. Measurements of acute toxicity of the contaminated soil or soil extracts gave conflicting results, as enchytraeid worms used as toxicity reporters were strongly affected, while reporter bacteria showed no or very minor decreases in viability. Measurements using sensitive inducible luminescent reporter bacteria suggested that the bioavailability of lead in the soil is indeed low, and this notion was supported by the very low water extractability of the lead. Nevertheless, the frequency of lead-resistant cultivable bacteria was elevated based on the isolation of cultivable strains. The bacterial and fungal diversity in heavily lead contaminated shooting sectors were compared with those of pristine sections of the shooting range area. The bacterial 16S rRNA gene and fungal ITS rRNA gene were amplified, cloned and sequenced using total DNA extracted from the soil humus layer as the template. Altogether, 917 sequenced bacterial clones and 649 sequenced fungal clones revealed a high soil microbial diversity. No effect of lead contamination was found on bacterial richness or diversity, while fungal richness and diversity significantly differed between lead contaminated and clean control areas. However, even in the case of fungi, genera that were deemed sensitive were not totally absent from the contaminated area: only their relative frequency was significantly reduced. Some operational taxonomic units (OTUs) assigned to Basidiomycota were clearly affected, and were much rarer in the lead contaminated areas. The studies of this thesis surveyed EcM sporocarps, analyzed morphotyped EcM root tips by direct sequencing, and 454-pyrosequenced fungal communities in in-growth bags. A total of 32 EcM fungi that formed conspicuous sporocarps, 27 EcM fungal OTUs from 294 root tips, and 116 EcM fungal OTUs from a total of 8 194 ITS2 454 sequences were recorded. The ordination analyses by non-parametric multidimensional scaling (NMS) indicated that Pb enrichment induced a shift in the EcM community composition. This was visible as indicative trends in the sporocarp and root tip datasets, but explicitly clear in the communities observed in the in-growth bags. The compositional shift in the EcM community was mainly attributable to an increase in the frequencies of OTUs assigned to the genus Thelephora, and to a decrease in the OTUs assigned to Pseudotomentella, Suillus and Tylospora in Pb-contaminated areas when compared to the control. The enrichment of Thelephora in contaminated areas was also observed when examining the total fungal communities in soil using DNA cloning and sequencing technology. While the compositional shifts are clear, their functional consequences for the dominant trees or soil ecosystem remain undetermined. The results indicate that at the Hälvälä shooting range, lead influences the fungal communities but not the bacterial communities. The forest ecosystem shows apparent functional redundancy, since no significant effects were seen on forest trees. Recently, by means of 454 pyrosequencing , the amount of sequences in a single analysis run can be up to one million. It has been applied in microbial ecology studies to characterize microbial communities. The handling of sequence data with traditional programs is becoming difficult and exceedingly time consuming, and novel tools are needed to handle the vast amounts of data being generated. The field of microbial ecology has recently benefited from the availability of a number of tools for describing and comparing microbial communities using robust statistical methods. However, although these programs provide methods for rapid calculation, it has become necessary to make them more amenable to larger datasets and numbers of samples from pyrosequencing. As part of this thesis, a new program was developed, MuSSA (Multi-Sample Sequence Analyser), to handle sequence data from novel high-throughput sequencing approaches in microbial community analyses. The greatest advantage of the program is that large volumes of sequence data can be manipulated, and general OTU series with a frequency value can be calculated among a large number of samples.

The visual preferences for forest regeneration and field afforestation - four case studies in Finland

The overall aim of this dissertation was to study the public's preferences for forest regeneration fellings and field afforestations, as well as to find out the relations of these preferences to landscape management instructions, to ecological healthiness, and to the contemporary theories for predicting landscape preferences. This dissertation includes four case studies in Finland, each based on the visualization of management options and surveys. Guidelines for improving the visual quality of forest regeneration and field afforestation are given based on the case studies. The results show that forest regeneration can be connected to positive images and memories when the regeneration area is small and some time has passed since the felling. Preferences may not depend only on the management alternative itself but also on the viewing distance, viewing point, and the scene in which the management options are implemented. The current Finnish forest landscape management guidelines as well as the ecological healthiness of the studied options are to a large extent compatible with the public's preferences. However, there are some discrepancies. For example, the landscape management instructions as well as ecological hypotheses suggest that the retention trees need to be left in groups, whereas people usually prefer individually located retention trees to those trees in groups. Information and psycho-evolutionary theories provide some possible explanations for people's preferences for forest regeneration and field afforestation, but the results cannot be consistently explained by these theories. The preferences of the different stakeholder groups were very similar. However, the preference ratings of the groups that make their living from forest - forest owners and forest professionals - slightly differed from those of the others. These results provide support for the assumptions that preferences are largely consistent at least within one nation, but that knowledge and a reference group may also influence preferences.

Behavioural and physiological responses to predators of captive-bred Arctic charr: significance of genetics, learning and ontogeny

Predation forms one of the main selective forces in nature and in a vast number of prey species the behavioural responses form the main way to avoid predation. World wide numerous captive breeding programs are used to produce fish and other animal species for conservational reintroductions. However, rearing animals in the absence of predators in captivity has been shown to weaken their predator avoidance skills and lead to behavioural divergence between wild and captive-bred populations. In my thesis I studied the effects of predator odour exposures on antipredator behavioural and physiological responses of captive reared Saimaa Arctic charr. This charr population is the most endangered fish population in Finland and a sample of the remaining population has been taken to captive breeding and used for an extensive reintroduction program. Lowered responsiveness to predators is probably one of the major reasons for the poor survival probability of the charr after release into the wild. The main aims of my thesis were to explore the reasons for behavioural phenotypic variation in this charr population and whether naïve charr young could be trained to recognise their natural predators. The predator species in my thesis were burbot (Lota lota) and pikeperch (Sander lucioperca). In my thesis I showed that the captive-bred charr responded to chemical cues from burbot and pikeperch, but the magnitude of responses was linked to the predator species. The burbot odour increased the spatial odour avoidance of the charr young. On the other hand, in the pikeperch treatment charr reduced their relative swimming activity and tended to show more freezing behaviour relative to the burbot treatment. It seems evident that these different responses are related to the different hunting tactics of predator species. Furthermore, I detected wide between-family differences in antipredator responsiveness (i.e. inherited variation in antipredator behaviours) in this captive stock. Detected differences were greater in the response towards burbot than towards pikeperch. These results, in addition to predator-specific antipredator responses, suggest that there is a clear inherited component in antipredator responsiveness in Saimaa charr population and that the detected inherited differences could explain a part of the behavioural phenotypic variation in this population. In my thesis I also found out that both social learning and direct exposure to live predators enhance the antipredator responsiveness of charr young. In addition, I obtained indications that predator odour exposures (i.e. life-skills training) in alevin and fry stages can fine-tune the innate antipredator responsiveness of charr. Thus, all these methods have the potential to enhance the innate antipredator responsiveness of naïve charr young, possibly also improving the post-release survival of these trained individuals in the wild. However, the next logical phase would be to carry out large scale survival studies in the wild to test this hypothesis. Finally, the results of my thesis emphasize that possible long-term life-skills training methods should take into account not only the behavioural but also the physiological effects of training.

The Emerging Phenotype: Ecological Genetics of Color, Form and Sex in the Common Frog

One of the main aims of evolutionary biology is to explain why organisms vary phenotypically as they do. Proximately, this variation arises from genetic differences and from environmental influences, the latter of which is referred to as phenotypic plasticity. Phenotypic plasticity is thus a central concept in evolutionary biology, and understanding its relative importance in causing the phenotypic variation and differentiation is important, for instance in anticipating the consequences of human induced environmental changes. The aim of this thesis was to study geographic variation and local adaptation, as well as sex ratios and environmental sex reversal, in the common frog (Rana temporaria). These themes cover three different aspects of phenotypic plasticity, which emerges as the central concept for the thesis. The first two chapters address geographic variation and local adaptation in two potentially thermally adaptive traits, namely the degree of melanism and the relative leg length. The results show that although there is an increasing latitudinal trend in the degree of melanism in wild populations across Scandinavian Peninsula, this cline has no direct genetic basis and is thus environmentally induced. The second chapter demonstrates that although there is no linear, latitudinally ordered phenotypic trend in relative leg length that would be expected under Allen s rule an ecogeographical rule linking extremity length to climatic conditions there seems to be such a trend at the genetic level, hidden under environmental effects. The first two chapters thus view phenotypic plasticity through its ecological role and evolution, and demonstrate that it can both give rise to phenotypic variation and hide evolutionary patterns in studies that focus solely on phenotypes. The last three chapters relate to phenotypic plasticity through its ecological and evolutionary role in sex determination, and consequent effects on population sex ratio, genetic recombination and the evolution of sex chromosomes. The results show that while sex ratios are strongly female biased and there is evidence of environmental sex reversals, these reversals are unlikely to have caused the sex ratio skew, at least directly. The results demonstrate that environmental sex reversal can have an effect on the evolution of sex chromosomes, as the recombination patterns between them seem to be controlled by phenotypic, rather than genetic, sex. This potentially allows Y chromosomes to recombine, lending support for the recent hypothesis suggesting that sex-reversal may play an important role on the rejuvenation of Y chromosomes.

Molecular genetics of RECQL4 syndromes

RAPADILINO syndrome is an autosomally resessively inherited condition that belongs to a group of rare syndromes more common in Finland than in other parts of the world. RAPADILINO is characterized by pre- and postnatal growth retardation, radial ray defects, diarrhoea of unknown aetiology during chilhood, a facial resemblance with other patients and normal intelligence. In Finland, 15 patients with this condition have been found which compares with only five patients in other parts of the world. We found RECQL4 gene mutations in RAPADILINO patients and proved this syndrome to be allelic with a subgroup of Rothmund-Thomson syndrome (RTS). Later we found RECQL4 mutations in patients with Baller-Gerold syndrome (BGS). These three syndromes share clinical findings and differential diagnostics rely on poikiloderma and craniosynostosis not seen in RAPADILINO syndrome. We found five different mutations in the Finnish RAPADILINO patients. The g.2545delT mutation is the founder mutation in the Finnish population as all the patients are either homozygotes or compound heterozygotes for it. This mutation leads to the inframe skipping of exon seven from mRNA. The protein encoded by this mutant mRNA lacks the nuclear retention signal and thus leads to the mislocalization of the mutant protein. The genotype-phenotype correlation is not straightforward but it seems that RAPADILINO could be due to alteration in protein function and truncating mutations in both alleles are more common among RTS patients. RTS patients with RECQL4 mutations have an elevated risk for osteosarcoma, but their risk to develop other types of malignancies is not increased.Two Finnish RAPADILINO patients have been diagnosed with osteosarcoma, but in addition to this we have found an excess of lymphoma cases among the Finnish RAPADILINO patients. This difference between cancer types could be due to different mutations found in these syndromes. The mutation screening of the patients will help to differentiate patients who have RECQL4 mutations and thus the elevated cancer risk. Patients will benefit from the follow up since early detection of malignancies is important for the treatment.

Expression, Enzymatic Activities and Subcellular Localization of Hepatitis E Virus and Semliki Forest Virus Replicase Proteins

Viruses are submicroscopic, infectious agents that are obligate intracellular parasites. They adopt various types of strategies for their parasitic replication and proliferation in infected cells. The nucleic acid genome of a virus contains information that redirects molecular machinery of the cell to the replication and production of new virions. Viruses that replicate in the cytoplasm and are unable to use the nuclear transcription machinery of the host cell have developed their own transcription and capping systems. This thesis describes replication strategies of two distantly related viruses, hepatitis E virus (HEV) and Semliki Forest virus (SFV), which belong to the alphavirus-like superfamily of positive-strand RNA viruses. We have demonstrated that HEV and SFV share a unique cap formation pathway specific for alphavirus-like superfamily. The capping enzyme first acts as a methyltransferase, catalyzing the transfer of a methyl group from S-adenosylmethionine to GTP to yield m7GTP. It then transfers the methylated guanosine to the end of viral mRNA. Both reactions are virus-specific and differ from those described for the host cell. Therefore, these capping reactions offer attractive targets for the development of antiviral drugs. Additionally, it has been shown that replication of SFV and HEV takes place in association with cellular membranes. The origin of these membranes and the intracellular localization of the components of the replication complex were studied by modern microscopy techniques. It was demonstrated that SFV replicates in cytoplasmic membranes that are derived from endosomes and lysosomes. According to our studies, site for HEV replication seems to be the intermediate compartment which mediates the traffic between endoplasmic reticulum and the Golgi complex. As a result of this work, a unique mechanism of cap formation for hepatitis E virus replicase has been characterized. It represents a novel target for the development of specific inhibitors against viral replication.

Disturbance in boreal spruce forest - immediate dynamics from stand to understorey level

The immediate effects of two human-related vegetation disturbances, (1) green tree retention (GTR) patch felling and scarification by harrowing and (2) experimental understorey vegetation layer removal, were examined in boreal forest stands in Finland. Effects of GTR patch felling and scarification on tree uprootings, on coarse woody debris (CWD) and on epixylic plant community were followed in upland and in paludified forest types. Uprootings increased considerably during 2-3 years after the fellings and were more frequent (47%) in the paludified than in the upland forest (13%). Scarification reduced 68% of the CWD in the felling area. Cover and especially species richness of epixylics declined in the both areas during 1-2 years after the felling. The increasing size of GTR patch correlated positively with the species richness. Regeneration of understorey vegetation community and Vaccinium myrtillus and Vaccinium vitis-idaea after different removals of vegetation layers in an old-growth forest took four years. The regeneration occurred mainly by vegetative means and it was faster in the terms of species richness than in the cover. In the most severe treatment, recovery occurred merely by sexual reproduction. V. myrtillus recovered mainly by producing new shoots. V. vitis-idaea recovered faster than V. myrtillus, mainly by increasing length growth. For ecological reasons, use of larger GTR patches on paludified biotope would be recommendable. In felling areas, scarification by harrowing could be replaced with some other spot-wise method. After moderate intensity level disturbance, recovery occurs rapidly by vegetative regrowth of the dominating species. High level of intensity may prevent the recovery of vegetation community for years, while enabling also the genetic regeneration of the initial species. Local anthropogenic-related disturbances are currently increasing and they can interact during temporally short times, which should be taken in to account in the future forest management plans.

Molecular genetics of X-linked cone-rod dystrophy and Åland Island eye disease

Inherited retinal diseases are the most common cause of vision loss among the working population in Western countries. It is estimated that ~1 of the people worldwide suffer from vision loss due to inherited retinal diseases. The severity of these diseases varies from partial vision loss to total blindness, and at the moment no effective cure exists. To date, nearly 200 mapped loci, including 140 cloned genes for inherited retinal diseases have been identified. By a rough estimation 50% of the retinal dystrophy genes still await discovery. In this thesis we aimed to study the genetic background of two inherited retinal diseases, X-linked cone-rod dystrophy and Åland Island eye disease. X-linked cone-rod dystrophy (CORDX) is characterized by progressive loss of visual function in school age or early adulthood. Affected males show reduced visual acuity, photophobia, myopia, color vision defects, central scotomas, and variable changes in fundus. The disease is genetically heterogeneous and two disease loci, CORDX1 and CORDX2, were known prior to the present thesis work. CORDX1, located on Xp21.1-11.4, is caused by mutations in the RPGR gene. CORDX2 is located on Xq27-28 but the causative gene is still unknown. Åland Island eye disease (AIED), originally described in a family living in Åland Islands, is a congenital retinal disease characterized by decreased visual acuity, fundus hypopigmentation, nystagmus, astigmatism, red color vision defect, myopia, and defective night vision. AIED shares similarities with another retinal disease, congenital stationary night blindness (CSNB2). Mutations in the L-type calcium channel α1F-subunit gene, CACNA1F, are known to cause CSNB2, as well as AIED-like disease. The disease locus of the original AIED family maps to the same genetic interval as the CACNA1F gene, but efforts to reveal CACNA1F mutations in patients of the original AIED family have been unsuccessful. The specific aims of this study were to map the disease gene in a large Finnish family with X-linked cone-rod dystrophy and to identify the disease-causing genes in the patients of the Finnish cone-rod dystrophy family and the original AIED family. With the help of linkage and haplotype analyses, we could localize the disease gene of the Finnish cone-rod dystrophy family to the Xp11.4-Xq13.1 region, and thus establish a new genetic X-linked cone-rod dystrophy locus, CORDX3. Mutation analyses of candidate genes revealed three novel CACNA1F gene mutations: IVS28-1 GCGTC>TGG in CORDX3 patients, a 425 bp deletion, comprising exon 30 and flanking intronic regions in AIED patients, and IVS16+2T>C in an additional Finnish patient with a CSNB2-like phenotype. All three novel mutations altered splice sites of the CACNA1F gene, and resulted in defective pre-mRNA splicing suggesting altered or absent channel function as a disease mechanism. The analyses of CACNA1F mRNA also revealed novel alternative wt splice variants, which may enhance channel diversity or regulate the overall expression level of the channel. The results of our studies may be utilized in genetic counseling of the families, and they provide a basis for studies on the pathogenesis of these diseases. In the future, the knowledge of the genetic defects may be used in the identification of specific therapies for the patients.