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.

Tenojoen pääuoman habitaattien määrä ja merkitys lohen (Salmo salar) poikastuotannolle

Atlantin lohen (Salmo salar) kannanhoidollisia toimenpiteitä varten vaaditaan tietoa lisääntymisjoissa olevien habitaattien määrästä ja laadusta. Tässä tutkielmassa selvitettiin Tenojoen pääuoman erilaisten habitaattien määrää ja niiden merkitystä lohen poikashabitaatteina. Tenojoen pääuoma kartoitettiin lohen habitaattien kartoitukseen kehitetyllä mesohabitaatti-luokittelulla, jossa joki kartoitetaan havainnoimalla sen hydromorfologisia piirteitä, virtausnopeutta, syvyyttä ja pohjan raekokoa. Lisäksi mitattiin suojakolojen määrää ja syvyysluokkaa erilaisilla substraateilla, ja tämän perusteella arvioitiin pohjan raekoon vaikutusta suojakolojen määriin ja syvyyteen. Lohenpoikasten esiintyvyyttä erilaisilla mesohabitaateilla, syvyyksillä ja substraateilla selvitettiin koekalastamalla laajoja alueita erityisvalmisteisella sähkökoekalastusveneellä. Raekoon, syvyyden ja suojakolojen vaikutusta lohenpoikastiheyksiin testattiin lisäksi tilastollisin menetelmin käyttämällä Luonnonvarakeskuksen tekemiä sähkökoekalastuksia. Mesohabitaattikartoituksen ja veneellä tehtyjen sähkökoekalastuksien aikana virtaama Tenojoessa oli lähellä vuosittaista minimiä. Mesohabitaattikartoituksesta selvisi, että Tenojoesta valtaosa (67 %) kuului hiekkapohjaiseen ja >50 cm/s virtaavaan mesohabitaattiin. Veneellä tehdyissä sähkökoekalastuksissa näiltä hiekka-alueilta saatiin vain vähäisiä määriä lohenpoikasia, ja nekin rantavyöhykkeiltä, joilla oli kivien ja lohkareiden muodostamia suojapaikkoja. Noin 32 % Tenojoesta on pienen virtaaman aikana lohen poikashabitaattina merkittäviä, nivamaisia tai koskimaisia alueita, jotka voidaan luokitella syvyyden ja virtausnopeuden mukaan eri mesohabitaattiluokkiin. Suojakolomittauksien perusteella vallitseva raekoko vaikuttaa merkitsevästi suojakolojen määrään ja syvyyteen. Kesän vanhat (0+) ja vanhemmat (>0+) poikaset suosivat eri syvyisiä suojakoloja, ja etenkin >0+ poikasten määrä ja >10 cm syvien suojakolojen määrän välillä oli voimakas positiivinen korrelaatio (p = 0,01). Ympäristöparametrien (syvyys, virtausnopeus ja raekoko) ja poikastiheyksien välinen suhde vastasi hyvin aiempia tutkimuksia, mutta sekä kesän vanhoja (0+) ja vanhempia (>0+) poikasia havaittiin aikaisempien tutkimuksien preferenssiarvoja syvemmillä alueilla. Veneellä tehdyissä sähkökoekalastuksissa havaittiin suurempia poikastiheyksiä rannanläheisillä linjoilla verrattuna joen keskellä tehtyihin koekalastuslinjoihin, kun vertailtiin habitaattiolosuhteiltaan samankaltaisia linjoja, jotka olivat ainakin osittain joen pituussuunnassa päällekkäin.

From genotype to phenotype : diversity and population structure of Flavobacterium psychrophilum

Flavobacterium psychrophilum is the etiological agent of bacterial cold-water disease (BCWD) causing high fish mortalities and significant economic losses to the freshwater salmonid aquaculture industry around the world. Today BCWD outbreaks are mainly treated with environmentally hazardous antimicrobial agents and alternative preventative measures are urgently needed in order to ensure the well-being of animals and the sustainability of aquaculture. The diversity of pathogenic bacteria challenges the development of universal control strategies and in many cases the pathogen population structure, i.e. the total genetic diversity of the species must be taken into account. This work integrates the tools of modern molecular biology and conventional phenotypic microbiology to gain knowledge about the diversity and population structure of F. psychrophilum. The present work includes genetic characterization of a large collection of isolates collected from diverse origins and years, from aquaculture in a whole region including different countries, and provides the first international validation of a universal multilocus sequence typing (MLST) approach for unambiguous genetic typing of F. psychrophilum. Population structure analyses showed that the global F. psychrophilum population is subdivided into pathogenic species-specific clones, of which one particular genetic lineage, clonal complex CC-ST2, has been responsible for the majority of BCWD outbreaks in rainbow trout (Oncorhynchus mykiss) in European aquaculture facilities over several decades. Genotypic and phenotypic population heterogeneity affecting antimicrobial resistance in F. psychrophilum within BCWD outbreaks was discovered. Specific genotypes were associated with severe infections in farmed rainbow trout and Atlantic salmon (Salmo salar), and in addition to high adherence, antimicrobial resistance was strongly associated with outbreak strains. The study brought additional support for the hypothesis of an epidemic F. psychrophilum population structure, where recombination is an important force for the generation and maintenance of genetic diversity, and a significant contribution towards mapping the genetic diversity of this important fish pathogen. Evidence indicating dissemination of virulent strains with commercial movement of fish and fish products was strengthened.

Annotation of Gyrodactylus salaris transcriptome

Relationship between organisms within an ecosystem is one of the main focuses in the study of ecology and evolution. For instance, host-parasite interactions have long been under close interest of ecology, evolutionary biology and conservation science, due to great variety of strategies and interaction outcomes. The monogenean ecto-parasites consist of a significant portion of flatworms. Gyrodactylus salaris is a monogenean freshwater ecto-parasite of Atlantic salmon (Salmo salar) whose damage can make fish to be prone to further bacterial and fungal infections. G. salaris is the only one parasite whose genome has been studied so far. The RNA-seq data analyzed in this thesis has already been annotated by using LAST. The RNA-seq data was obtained from Illumina sequencing i.e. yielded reads were assembled into 15777 transcripts. Last resulted in annotation of 46% transcripts and remaining were left unknown. This thesis work was started with whole data and annotation process was continued by the use of PANNZER, CDD and InterProScan. This annotation resulted in 56% successfully annotated sequences having parasite specific proteins identified. This thesis represents the first of Monogenean transcriptomic information which gives an important source for further research on this specie. Additionally, comparison of annotation methods interestingly revealed that description and domain based methods perform better than simple similarity search methods. Therefore it is more likely to suggest the use of these tools and databases for functional annotation. These results also emphasize the need for use of multiple methods and databases. It also highlights the need of more genomic information related to G. salaris.