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.

Struggles over resources and representations in territorial conflicts in the Northern Autonomous Atlantic Region (RAAN), Nicaragua

Territoriality is a central issue in indigenous peoples struggles. The territorial struggles involve struggles over the control of natural resources and over political participation and representation, but also over the perception of territorial rights and the symbolic representation of the territory. These struggles are carried through both in material and symbolic ways through recurring to different discourses and representations that provide legitimation for the territorial claims of the group. The study is located in the Northern Autonomous Atlantic Region of Nicaragua. The study concerns the territorial strategies, conceptions and practices of the indigenous people and other actors. Territorial conflicts exist between the autonomous region and the central government of Nicaragua, between mestizo settlers and indigenous people, between different indigenous groups, and between these and development agents such as conservation projects. The study focuses on how territorial discourses and representations are used to legitimate territorial control. Environmental, historical and cartographical discourses are the most important discourses recurred to. The influence of discourses and representations on the territorial practices and policies of the different actors, the links between the local struggles and global processes, and the broader structural factors impacting on the territorial struggles are also analysed. Among the structural factors are the problems related to land tenure and management and the use of natural resources, the advance of the agricultural frontier, the institutional weaknesses of the central and regional governments and the legislative processes. The territorial discourses are both recurred to in a strategic way and also grounded in local ideals and practices. The discourses have produced real effects for example in legislation, land tenure systems, political representation and environmental practices. Although the use of discourses and representations are an important power tool in territorial struggles, territorial control cannot be effectively accomplished merely through representing territorial claims in a legitimate way or through reforming legislation, as the conflicts are also largely a result of structural factors affecting the region. The fieldwork was carried out during a total of twelve months between 2000 and 2002. The research methods used were semi-structured interviews, participant observation and participatory research methods. A broad range of literary sources were also used to collect data. The study is located within the field of critical political geography with a discursive political ecology approach. It can be called a critical realist approach to the discursive analysis of indigenous territoriality.

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.

Conservation of Atlantic salmon by supplementary stocking of juvenile fish

Wild salmon stocks in the northern Baltic rivers became endangered in the second half of the 20th century, mainly due to recruitment overfishing. As a result, supplementary stocking was widely practised, and supplementation of the Tornionjoki salmon stock took place over a 25 year period until 2002. The stock has been closely monitored by electrofishing, smolt trapping, mark-recapture studies, catch samples and catch surveys. Background information on hatchery-reared stocked juveniles was also collected for this study. Bayesian statistics was applied to the data as this method offers the possibility of bringing prior information into the analysis and an advanced ability for incorporating uncertainty, and also provides probabilities for a multitude of hypotheses. Substantial divergences between reared and wild Tornionjoki salmon were identified in both demographic and phenological characteristics. The divergences tended to be larger the longer the duration spent in hatchery and the more favourable the hatchery conditions were for fast growth. Differences in environment likely induced most of the divergences, but selection of brood fish might have resulted in genotypic divergence in maturation age of reared salmon. Survival of stocked 1-year old juveniles to smolt varied from about 10% to about 25%. Stocking on the lower reach of the river seemed to decrease survival, and the negative effect of stocking volume on survival raises the concern of possible similar effects on the extant wild population. Post-smolt survival of wild Tornionjoki smolts was on average two times higher than that of smolts stocked as parr and 2.5 times higher than that of stocked smolts. Smolts of different groups showed synchronous variation and similar long-term survival trends. Both groups of reared salmon were more vulnerable to offshore driftnet and coastal trapnet fishing than wild salmon. Average survival from smolt to spawners of wild salmon was 2.8 times higher than that of salmon stocked as parr and 3.3 times higher than that of salmon stocked as smolts. Wild salmon and salmon stocked as parr were found to have similar lifetime survival rates, while stocked smolts have a lifetime survival rate over 4 times higher than the two other groups. If eggs are collected from the wild brood fish, stocking parr would therefore not be a sensible option. Stocking smolts instead would create a net benefit in terms of the number of spawners, but this strategy has serious drawbacks and risks associated with the larger phenotypic and demographic divergences from wild salmon. Supplementation was shown not to be the key factor behind the recovery of the Tornionjoki and other northern Baltic salmon stocks. Instead, a combination of restrictions in the sea fishery and simultaneous occurrence of favourable natural conditions for survival were the main reasons for the revival in the 1990 s. This study questions the effectiveness of supplementation as a conservation management tool. The benefits of supplementation seem at best limited. Relatively high occurrences of reared fish in catches may generate false optimism concerning the effects of supplementation. Supplementation may lead to genetic risks due to problems in brood fish collection and artificial rearing with relaxed natural selection and domestication. Appropriate management of fisheries is the main alternative to supplementation, without which all other efforts for long-term maintenance of a healthy fish resource fail.

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.