Coastal environmental gradients – Key to reproduction habitat mapping of freshwater fish in the Baltic Sea

Habitat requirements of fish are most strict during the early life stages, and the quality and quantity of reproduction habitats lays the basis for fish production. A considerable number of fish species in the northern Baltic Sea reproduce in the shallow coastal areas, which are also the most heavily exploited parts of the brackish marine area. However, the coastal fish reproduction habitats in the northern Baltic Sea are poorly known. The studies presented in this thesis focused on the influence of environmental conditions on the distribution of coastal reproduction habitats of freshwater fish. They were conducted in vegetated littoral zone along an exposure and salinity gradient extending from the innermost bays to the outer archipelago on the south-western and southern coasts of Finland, in the northern Baltic Sea. Special emphasis was placed on reed-covered Phragmites australis shores, which form a dominant vegetation type in several coastal archipelago areas. The main aims of this research were to (1) develop and test new survey and mapping methods, (2) investigate the environmental requirements that govern the reproduction of freshwater fish in the coastal area and (3) survey, map and model the distribution of the reproduction habitats of pike (Esox lucius) and roach (Rutilus rutilus). The white plate and scoop method with a standardized sampling time and effort was demonstrated to be a functional method for sampling the early life stages of fish in dense vegetation and shallow water. Reed-covered shores were shown to form especially important reproduction habitats for several freshwater fish species, such as pike, roach, other cyprinids and burbot, in the northern Baltic Sea. The reproduction habitats of pike were limited to sheltered reed- and moss-covered shores of the inner and middle archipelago, where suitable zooplankton prey were available and the influence of the open sea was low. The reproduction habitats of roach were even more limited and roach reproduction was successful only in the very sheltered reed-covered shores of the innermost bay areas, where salinity remained low (< 4‰) during the spawning season due to freshwater inflow. After identifying the critical factors restricting the reproduction of pike and roach, the spatial distribution of their reproduction habitats was successfully mapped and modelled along the environmental gradients using only a few environmental predictor variables. Reproduction habitat maps are a valuable tool promoting the sustainable use and management of exploited coastal areas and helping to maintain the sustainability of fish populations. However, the large environmental gradients and the extensiveness of the archipelago zone in the northern Baltic Sea demand an especially high spatial resolution of the coastal predictor variables. Therefore, the current lack of accurate large-scale, high-resolution spatial data gathered at exactly the right time is a considerable limitation for predictive modelling of shallow coastal waters.

Phylogeography and Adaptive Divergence of Three-spined Stickleback Populations

Genetic studies on phylogeography and adaptive divergence in Northern Hemisphere fish species such as three-spined stickleback (Gasterosteus aculeatus) provide an excellent opportunity to investigate genetic mechanisms underlying population differentiation. According to the theory, the process of population differentiation results from a complex interplay between random and deterministic processes as well historical factors. The main scope in this thesis was to study how historical factors like the Pleistocene ice ages have shaped the patterns molecular diversity in three-spined stickleback populations in Europe and how this information could be utilized in the conservation genetic context. Furthermore, identifying footprints of natural selection at the DNA level might be used in identifying genes involved in evolutionary change. Overall, the results from phylogeographic studies indicate that the three-spined stickleback has colonized the Atlantic basin relatively recently but constitutes three major evolutionary lineages in Europe. In addition, the colonization of freshwater appears to result from multiple and independent invasions by the marine conspecifics. Molecular data together with morphology suggest that the most divergent freshwater populations are located in the Balkan Peninsula and these populations deserve a special conservation genetic status without warranting further taxonomical classification. In order to investigate the adaptive divergence in Fennoscandian three-spined stickleback populations several approaches were used. First, sequence variability in the Eda-gene, coding for the number of lateral plates, was concordant with the previously observed global pattern. Full plated allele is in high frequencies among marine populations whereas low plated allele dominates in the freshwater populations. Second, a microsatellite based genome scan identified both indications of balancing and directional selection in the three-spined stickleback genome, i.e. loci with unusually similar or unusually different allele frequencies over populations. The directionally selected loci were mainly associated with the adaptation to freshwater. A follow up study conducting a more detailed analysis in a chromosome region containing a putatively selected gene locus identified a fairly large genomic region affected by natural selection. However, this region contained several gene predictions, all of which might be the actual target of natural selection. All in all, the phylogeographic and adaptive divergence studies indicate that most of the genetic divergence has occurred in the freshwater populations whereas the marine populations have remained relatively uniform.

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.