Phylogeography and population genetics of north European Atlantic salmon (Salmo salar L.)

Although abundant in the number of individuals, the Atlantic salmon may be considered as a threatened species in many areas of its native distribution range. Human activities such as building of power plant dams, offshore overfishing, pollution, clearing of riverbeds for timber floating and badly designed stocking regimes have diminished the distribution of Atlantic salmon. As a result of this, many of the historical populations both in Europe and northern America have gone extinct or are severely depressed. In fact, only 1% of Atlantic salmon existing today are of natural origin, the rest being farmed salmon. All of this has lead to a vast amount of research and many restoration programmes aiming to bring Atlantic salmon back to rivers from where it has vanished. However, many of the restoration programmes conducted thus far have been unsuccessful due to inadequate scientific research or lack of its implementation, highlighting the fact that more research is needed to fully understand the biology of this complex species. The White and Barents Seas in northwest Russia are among the last regions in Europe where Atlantic salmon populations are still stable, thus forming an important source of biodiversity for the entire European region. Salmon stocks from this area are also of immense economic and social importance for the local people in the form of fishing tourism. The main aim of this thesis was to elucidate the post-glacial history and population genetic structure of north European and particularly northwest Russian Atlantic salmon, both of which are aspects of great importance for the management and conservation of the species. Throughout the whole thesis, these populations were studied by utilizing microsatellites as the main molecular tool. One of the most important discoveries of the thesis was the division of Atlantic salmon from the White and Barents Seas into four separate clusters, which has not been observed in previous studies employing nuclear markers although is supported by mtDNA studies. Populations from the western Barents Sea clustered together with the northeast Atlantic populations into a clearly distinguishable group while populations from the White Sea and eastern Barents Sea were separated into three additional groups. This has important conservation implications as this thesis clearly indicates that conservation of populations from all of the observed clusters is warranted in order to conserve as much of the genetic diversity as possible in this area. The thesis also demonstrates how differences in population life histories within a species, migratory behaviour in this case, and in their phylogeographic origin affect the genetic characteristics of populations, namely diversity and divergence levels. The anadromous populations from the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than the anadromous populations form the Baltic Sea basin. Among the non-anadromous populations the result was the opposite: the Baltic freshwater populations were more variable. This emphasises the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash and thus deserve a high conservation status. In the last chapter of this thesis immune relevant marker loci were developed and screened for signatures of natural selection along with loci linked to genes with other functions or no function at all. Also, a novel landscape genomics method, which combines environmental information with molecular data, was employed to investigate whether immune relevant markers displayed significant correlations to various environmental variables more frequently than other loci. Indications of stronger selection pressure among immune-relevant loci compared to non-immune relevant EST-linked loci was found but further studies are needed to evaluate whether it is a common phenomenon in Atlantic salmon.

The genetics of behaviour and other adaptive traits in nine-spined sticklebacks (Pungitius pungitius)

One of the main goals in current evolutionary biology research is to identify genes behind adaptive phenotypic variations. The advances in genomic technologies have made it possible to identify genetic loci behind these variations, also concerning non-model species. This thesis investigates the genetics of the behaviour and other adaptive traits of the nine-spined stickleback (Pungitius pungitius) through the application of different genetic approaches. Fennoscandian nine-spined stickleback populations express large phenotypical differences especially in behaviour, life –history traits and morphology. However the underlying genetic bases for these phenotypical differences have not been studied in detail. The results of the project will lay the foundation for further genetics studies and provide valuable information for our understanding of the genetics of the adaptive divergence of the nine-spined stickleback. A candidate gene approach was used to develop microsatellite markers situating close to candidate genes for behaviour in the nine-spined stickleback. Altogether 13 markers were developed and these markers were used in the subsequent studies with the anonymous random markers and physiologically important gene markers which are already currently available for nine-spined sticklebacks. It was shown that heterozygosity correlated with behaviour in one of the marine nine-spined stickleback populations but with contrasting effects: correlations with behaviour were negative when using physiological gene markers and positive with random markers. No correlation was found between behavioural markers and behaviour. From the physiological gene markers, a strong correlation was found between osmoregulation-related gene markers and behaviour. These results indicate that both local (physiological) and general (random) effects are important in the shaping of behaviour and that heterozygosity– behaviour correlations are population dependent. In this thesis a second linkage map for nine-spined sticklebacks was constructed. Compared to the earlier nine-spined stickleback linkage map, genomic rearrangements were observed between autosomal (LG7) and sex-determing (LG12) linkage groups. This newly constructed map was used in QTL mapping studies in order to locate genomic regions associated with pelvic structures, behaviour and body size/growth. One major QTL was found for pelvic structures and Pitx1 gene was related to these traits as was predicted from three-spined stickleback studies, but this was in contrast to earlier nine-spined stickleback study. The QTL studies also revealed that behaviour and body size/growth were genetically more complex by having more QTL than pelvic traits. However, in many cases, pelvic structure, body size/growth and behaviour were linked to similar map locations indicating possible pleiotropic effects of genes locating in these QTL regions. Many of the gene related markers resided in the QTL area. In the future, studying these possible candidate genes in depth might reveal the underlying mechanism behind the measured traits.

Macro- and Microevolution of Languages: Exploring Linguistic Divergence with Approaches from Evolutionary Biology

There are more than 7000 languages in the world, and many of these have emerged through linguistic divergence. While questions related to the drivers of linguistic diversity have been studied before, including studies with quantitative methods, there is no consensus as to which factors drive linguistic divergence, and how. In the thesis, I have studied linguistic divergence with a multidisciplinary approach, applying the framework and quantitative methods of evolutionary biology to language data. With quantitative methods, large datasets may be analyzed objectively, while approaches from evolutionary biology make it possible to revisit old questions (related to, for example, the shape of the phylogeny) with new methods, and adopt novel perspectives to pose novel questions. My chief focus was on the effects exerted on the speakers of a language by environmental and cultural factors. My approach was thus an ecological one, in the sense that I was interested in how the local environment affects humans and whether this human-environment connection plays a possible role in the divergence process. I studied this question in relation to the Uralic language family and to the dialects of Finnish, thus covering two different levels of divergence. However, as the Uralic languages have not previously been studied using quantitative phylogenetic methods, nor have population genetic methods been previously applied to any dialect data, I first evaluated the applicability of these biological methods to language data. I found the biological methodology to be applicable to language data, as my results were rather similar to traditional views as to both the shape of the Uralic phylogeny and the division of Finnish dialects. I also found environmental conditions, or changes in them, to be plausible inducers of linguistic divergence: whether in the first steps in the divergence process, i.e. dialect divergence, or on a large scale with the entire language family. My findings concerning Finnish dialects led me to conclude that the functional connection between linguistic divergence and environmental conditions may arise through human cultural adaptation to varying environmental conditions. This is also one possible explanation on the scale of the Uralic language family as a whole. The results of the thesis bring insights on several different issues in both a local and a global context. First, they shed light on the emergence of the Finnish dialects. If the approach used in the thesis is applied to the dialects of other languages, broader generalizations may be drawn as to the inducers of linguistic divergence. This again brings us closer to understanding the global patterns of linguistic diversity. Secondly, the quantitative phylogeny of the Uralic languages, with estimated times of language divergences, yields another hypothesis as to the shape and age of the language family tree. In addition, the Uralic languages can now be added to the growing list of language families studied with quantitative methods. This will allow broader inferences as to global patterns of language evolution, and more language families can be included in constructing the tree of the world’s languages. Studying history through language, however, is only one way to illuminate the human past. Therefore, thirdly, the findings of the thesis, when combined with studies of other language families, and those for example in genetics and archaeology, bring us again closer to an understanding of human history.