Genetic diversity of Atlantic salmon (Salmo salar) and European whitefish (Coregonus lavaretus) in the Baltic Sea

We described the patterns and extent of microsatellite DNA variation in historical and present-day Atlantic salmon (Salmo salar L.) stocks in the Baltic Sea and neighbouring areas, and in European whitefish (Coregonus lavaretus) ecotypes, populations and run-timing types in Finland. Moreover, the amount and pattern of genetic diversity in historical salmon populations before human impact were described, and the proportion of diversity maintained in the present hatchery stocks evaluated. Salmon populations in the Baltic Sea were, on average, significantly less variable than eastern Atlantic populations, and the diversity of landlocked populations (Lakes Vänern, Saimaa, Onega and Ladoga) was in turn significantly lower than that of anadromous salmon populations in the Baltic Sea populations. Within the Baltic Sea, the anadromous populations of Atlantic salmon formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin) and southern (western Baltic Main Basin) regions. Based on microsatellite data, three salmon population groups in the Baltic Sea were considered potentially different colonization lineages. In short- and long-term breeding programmes of Atlantic salmon, the average observed rate of loss of alleles was 4.9% and 2.0% per generation and the average rate of loss of heterozygosity was 1.4% and 1% per generation, respectively. When comparing the genetic parameters of stocks before and after hatchery breeding of several successive generations (Rivers Iijoki and Oulujoki), statistically significant changes in allele frequencies were common, while large wild stock in the Teno River has remained temporally very stable over 56 years. Despite the observed losses of genetic diversity in broodstock breeding, a large proportion of the genetic resources of the extirpated stocks are still conserved in the broodstocks. Genetic differentiation among European whitefish ecotypes was generally low, thus giving support to the hypothesis of one native European whitefish species in Fennoscandia. Among the ecotypes, the northern, large sparsely rakered, bottom-dwelling whitefish was the most unique. The known genetic differences in quantitative traits have thus either developed independently of potential phylogenetic lineages, or the lineages have mixed and the quantitative traits of the ecotypes, like gill-raker number, have later changed according to environment and selection pressures. Overall, genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Wild whitefish populations studied had slightly higher allelic diversity than hatchery-reared populations in corresponding rivers.

Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Optimal management of conflicting species: Grey seal (Halichoerus grypus) and Atlantic salmon (Salmo salar) in the Baltic Sea

The objective of this thesis is to examine the economic effects in the conflict between grey seal population and the salmon fishery in the Baltic Sea. We will formulate a bioeconomic model which provides new insights on the optimal management of Atlantic salmon with respect to the effects brought about by the grey seal population. As the catch losses caused by seals have an effect on salmon fishery in Baltic, we will study how seal population affects the present value of the salmon fishery. The study considers the Finnish coastal trap net fishery. The bioeconomic model considers a scenario of sole salmon fishery and a scenario of salmon fishery affected by the grey seal population. On the basis of these scenarios, a seal compensation scheme is introduced. We can observe a significant economic seal-induced effect on the salmon fishery. The results suggest that the present seal compensation scheme emploid by the Finnish government is suboptimal. This thesis is part of the TARMO –project, in which the conflict between grey seal population and salmon fishery is studied using the methods of environmental economics.

From the river to the open sea - a critical life phase of young Atlantic salmon migrating from the Simojoki river

Long-term monitoring data collected from wild smolts of Atlantic salmon (Salmo salar) in the Simojoki river, northern Finland, were used in studying the relationships between the smolt size and age, smolt and postsmolt migration, environmental conditions and postsmolt survival. The onset of the smolt run was significantly dependent on the rising water temperature and decreasing discharge of the river in the spring. The mean length of smolts migrating early in the season was commonly higher and the mean age always older than among smolts migrating later. Many of the smolts migrating early in the season and almost all smolts migrating later had started their new growth in spring in the river before their sea entry. Among postsmolts, the time required for emigration from the estuary was dependent on the sea surface temperature (SST) off the river, being significantly shorter in years with warm than cold sea temperatures. After leaving the estuary, the postsmolts migrated southwards along the eastern coast of the northern Gulf of Bothnia, the geographical distribution of the tag recoveries coinciding with the warm thermal zone in spring in the coastal area. After arriving in the southern Gulf of Bothnia in late summer the postsmolts mostly migrated near the western coast, reaching the Baltic Main Basin in late autumn. Until the early 1990s there was only a weak positive association between smolt length and postsmolt survival. However, following a subsequent decrease in the mean smolt size, a significant positive dependence was observed between smolt size and the reported recapture rate of tagged salmon. The differences in recapture rates between smolts tagged during the first and second half of the annual migration season were insignificant, indicating that the seasonal variation in smolt size and age seem to be too small to affect survival. Among the climatic factors examined, the summer SST in the Gulf of Bothnia was most clearly related to the survival of the wild postsmolts. Postsmolt survival appeared to be highest in years when the SST in June in the Bothnian Bay varied between 9 and 12 ºC. In addition, the survival of wild postsmolts showed a significant positive dependence on the SST in July in the Bothnian Sea, but not on the abundance of the prey fish (0+ herring, Clupea harengus and sprat, Sprattus sprattus) in the Bothnian Sea and in the Baltic Main Basin. The results suggest, that if the incidence of extreme weather conditions were to increase due to climatic changes, it would probably reduce the postsmolt survival of wild salmon populations. For improving the performance of hatchery-reared smolts, it could be useful to examine opportunities to produce smolts that are in their smolt traits and abilities more similar to the wild smolts described in this thesis.

Environmental factors and uncertainty in fisheries management in the northern Baltic Sea

The Baltic Sea is a geologically young, large brackish water basin, and few of the species living there have fully adapted to its special conditions. Many of the species live on the edge of their distribution range in terms of one or more environmental variables such as salinity or temperature. Environmental fluctuations are know to cause fluctuations in populations abundance, and this effect is especially strong near the edges of the distribution range, where even small changes in an environmental variable can be critical to the success of a species. This thesis examines which environmental factors are the most important in relation to the success of various commercially exploited fish species in the northern Baltic Sea. It also examines the uncertainties related to fish stocks current and potential status as well as to their relationship with their environment. The aim is to quantify the uncertainties related to fisheries and environmental management, to find potential management strategies that can be used to reduce uncertainty in management results and to develop methodology related to uncertainty estimation in natural resources management. Bayesian statistical methods are utilized due to their ability to treat uncertainty explicitly in all parts of the statistical model. The results show that uncertainty about important parameters of even the most intensively studied fish species such as salmon (Salmo salar L.) and Baltic herring (Clupea harengus membras L.) is large. On the other hand, management approaches that reduce uncertainty can be found. These include utilising information about ecological similarity of fish stocks and species, and using management variables that are directly related to stock parameters that can be measured easily and without extrapolations or assumptions.

Kannan, kasvatusympäristön ja ehdollistamisen vaikutus lohenpoikasten pedonvälttämiskäyttäytymiseen

Istutetut kalat selviävät luonnonoloissa usein huomattavasti luonnossa kasvaneita lajikumppaneitaan heikommin. Laitosten kasvatusaltaissa kasvavilla kaloilla ei ole ennen istutusta tarvetta oppia luonnossa välttämättömiä taitoja. Jos istutuskalat ovat sukupolvi sukupolven jälkeen laitoskalojen jälkeläisiä, voi myös kalojen perimä laitostua, kun perimään kertyy luonnossa selviytymisen kannalta haitallisia ja laitosoloissa hyödyllisiä ominaisuuksia. Suomessa hyvä esimerkkilaji istutuskaloista ja niiden ongelmista on lohi (Salmo salar). Yksi istutusten tuloksellisuudelle merkityksellisistä kalojen taidoista on pedonvälttämiskäyttäytyminen eli se, kuinka hyvin kalat välttävät saaliksi jäämistä. Sekä laitosoloissa kasvamisen että perimän laitostumisen on todettu voivan muuttaa kalojen pedonvälttämiskäyttäytymiseen liittyviä käyttäytymispiirteitä. On myös saatu näyttöä perimältään laitostuneiden kalojen luonnonkantaisia kaloja suuremmasta riskistä jäädä petojen saaliiksi. Luonnonkalojen ja laitoskalojen väliset erot sopeutuvuudessa luonnonoloihin ovat poikineet runsaasti tutkimuksia, joissa on selvitetty, miten laitoskalojen pedonvälttämiskäyttäytyminen saataisiin muistuttamaan enemmän luonnonkalojen käyttäytymistä. Tärkeimpiä samankaltaistamiskeinoja ovat laitosten kasvatusaltaiden muuttaminen virikkeellisiksi eli enemmän luonnonoloja vastaaviksi ja laitoskalojen kouluttaminen ennen istutusta. Tutkin kokeissani perimän laitostumisen, virikkeellisen kasvatusympäristön ja klassisen ehdollistamisen vaikutuksia yksivuotiaiden lohenpoikasten pedonvälttämiskäyttäytymiseen. Käytössäni oli Simojoen populaation lohenpoikasia neljästä eri kanta-kasvatusympäristö-käsittelystä: perinteisissä kasvatusaltaissa kasvatettuja luonnonkannan kaloja, virikkeellisissä kasvatusaltaissa kasvatettuja luonnonkannan kaloja, perinteisissä kasvatusaltaissa kasvatettuja laitostuneen kannan kaloja ja virikkeellisissä kasvatusaltaissa kasvatettuja laitostuneen kannan kaloja. Ensimmäisessä kokeessani vertailin eri käsittelyjen kalojen poistumisnopeutta ns. lähtölaatikosta sekä uintikäyttäytymistä kaukalossa, jossa ne eivät olleet aiemmin olleet. Toisessa kokeessa tarkkailin, miten ns. hälyaine vaikutti rohkeuskokeessa olleiden kalojen käyttäytymiseen, kun niitä uitettiin uudestaan samoissa kaukaloissa. Kolmannessa kokeessa ehdollistin molempien laitoskantaisten käsittelyjen kaloja hauen hajulle hälyaineen avulla. Ehdollistamisen jälkeen tarkkailin, kuinka poikaset käyttäytyvät kaukaloissa, joihin johdettiin hauen hajua. Tein myös selviytymiskokeen, jossa vapautin saman ehdollistamiskäsittelyn läpikäyneitä kaloja altaisiin, joissa hauet saivat saalistaa poikasia ja joihin oli kasattu poikasille suojapaikaksi kiviröykkiö. Odotin luonnonkantaisten, virikkeellisesti kasvatettujen ja ehdollistettujen kalojen olevan muita varovaisempia ja hauilta paremmin selviytyviä. Virikkeellinen kasvatus lisäsi monella käyttäytymismuuttujalla mitattuna kalojen varovaisuutta tai arkuutta. Joillain muuttujilla mitattuna virikkeellisyys vaikutti varovaisuutta tai arkuutta lisäten vain luonnonkantaisiin kaloihin Siten myös kalan kannalla oli merkitystä. Yhdessä käyttäytymismuuttujassa kannalla oli lisäksi kasvatusympäristöstä riippumatonkin vaikutus. Hälyaine vaikutti kaloihin lähinnä niiden liikkumista vähentäen. Ehdollistamisen vaikutus kaukalomuuttujiin riippui kasvatusympäristöstä: ehdollistaminen lisäsi virikkeellisissä oloissa kasvatettujen ja vähensi tavallisissa altaissa kasvatettujen uimista. Ehdollistamisella tai kasvatusympäristöllä ei ollut vaikutusta kalojen selviytymiseen haukien saalistukselta. Tulokset herättivät myös mahdollisia uusia tutkimuskysymyksiä. Tulosten perusteella voin sanoa, että kasvatuksessa käytetyt yksinkertaiset ja edulliset virikkeet ja ehdollistamismenetelmät voivat vaikuttaa kalojen käyttäytymiseen muuttamalla sitä varovaisemmaksi ja sopeutuvammaksi eli mahdollisesti joiltain osin luonnonmukaisemmaksi tai luonnossa selviytymistä auttavaksi. Erot virikkeellisen kasvatuksen vaikutuksissa luonnonkantaisiin ja laitoskantaisiin kaloihin voivat kertoa siitä, kuinka tärkeää oli, että kokeissa oli mukana molempien kantojen kaloja. Tulosten soveltamismahdollisuudet ovat lupaavat, koska tämä oli yksi ensimmäisistä koejärjestelyistä, joissa virikkeellistettyjen kasvatusaltaiden kalatiheydet olivat samaa luokkaa kuin kalankasvatuslaitoksissa tavallisesti käytetyt tiheydet.