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The papers II and III of this thesis are not available in Munin. Paper II : Bhat, S., Bernatchez, L., Amundsen, P. –A., Fevolden, S. –E., Benestan, L., Præbel, K.: «Speciation reversal leads to unpredictable genomic outcomes in European whitefish”. (Manuscript). Paper III: Bhat, S., Lamaze, F. C., Bernatchez, L., Præbel, K.: “Effect of speciation reversal on genomic introgression in sympatric whitefish eco-morphs.” (Manuscript). Anthropogenic activities, such as introduction of non-native species, is considered as one of the most significant causes for declining biodiversity, since such introduction may destabilise ecological barriers to gene flow between native populations. In the 1960s a salmonid fish, vendace, was introduced to the upper parts of Pasvik watercourse and during the early 1990s it invaded the entire watercourse, including the lakes studied in this project/thesis. These lakes harbour an eco-morph pair of European whitefish that has diverged in sympatry in post-glacial times. The vendace, being a competitively superior planktivore to the densely rakered eco-morph, relegated this eco-morph from its native pelagic habitat into the non-native littoral habitat, which is mainly occupied by the large sparsely rakered eco-morph. These observations have inspired this PhD thesis to study the phenotypic, genetic, and genomic consequences of the vendace invasion on native sympatric European whitefish eco-morphs. Using neutral microsatellite markers, the study documented that the introduction and invasion of vendace have induced speciation reversal in the eco-morph pair. The comparison of the number of gill rakers from the pre- and post-invasion periods revealed merging of two peaks of distribution of number of gill rakers following the invasion suggesting reduction in discreteness of phenotypes. Population genomic analyses, using genome-wide coverage of SNP markers obtained by sequencing of restriction site associated DNA libraries (RADseq), revealed an unpredicted outcome of speciation reversal at the genomic and functional phenotypic levels. This was attributed to a change in the selective forces during speciation reversal. The introgression patterns at genomic regions of adaptive importance, showed that speciation reversal have unpredictable consequences on introgression. Overall, this PhD study concludes that anthropogenic activities have wide-ranging and stochastic effects for species undergoing speciation reversal.

The lumpfish (Cyclopterus lumpus Linnaeus, 1758) has for many years been an attractive target for the roe fisheries in Norway and has more recently become an important cleanerfish in the salmonid farming industry for the control of salmon lice (Copepoda: Caligidae). Despite this, there is a lack of knowledge about several life aspects of the species and studies on its genetic structure have been inconsistent. It is therefore uncertain how scenarios involving, for instance, overfishing or escaping of lumpfish from the fish farms might affect the natural stocks genetically and biologically. To initiate the investigations of how human activities might affect lumpfish in nature, this project aimed to clarify the genetic structure and reveal potential signatures of local adaptation in juvenile lumpfish in Norway. Whole genome sequencing was performed for 30 individuals from three different locations and a set of 607,663 SNPs were selected for downstream genetic structure analyses. Significant genetic differentiation was detected between the northern and southern parts of Norway, with further discrimination of two populations within one location in the north. Lumpfish separated by long geographical distances showed greater differentiation than those collected at locations more proximate to each other, but no significant correlation was detected. Loci putatively under selection were identified and revealed population structure at smaller geographical scales. These findings suggest that multiple driving forces may have contributed to population structuring in lumpfish. The study presents evidence for genetic structuring of Norwegian juvenile lumpfish and discriminate at least three populations, and further studies should therefore contribute to establishing sustainable management practices for the species. Keywords: Lumpfish, Cyclopterus lumpus, population genetics, whole genome sequencing, SNPs, genetic structure

Salmon louse (Lepeophtheirus salmonis) is a parasitic copepod that causes significant damage to Atlantic salmon (Salmo salar) and incurs significant costs to the salmonid aquaculture industry. In Norway, the industry has been coping with salmon lice issues with various methods such as chemical treatments, but it has resulted in an acquisition of resistance in salmon lice towards the existing delousing treatments. In order to maximize the effectiveness of the treatments, it is important to understand population structuring of salmon lice, and factors that are driving the structure, since recent studies suggested that several Atlantic salmon lice populations are sharing genetic materials coding for resistance toward delousing treatments. The objective of this study was to investigate whether salmon lice in northern Norway display population structure and differentiation at small geographical scales. We identified 25,795 robustly supported SNPs among salmon lice from 8 different locations in northern Norway. While only very weak structure was observed based on the full SNP dataset (25,795 SNPs), relatively weak, but highly significant, population structure was observed using 303 important SNPs identified using a random forest classification approach. No significant correlation between genetic differentiation and geographical distance was observed. To our knowledge, it was the first study to reveal the significant population structure of salmon lice at such small spatial scales. Our results suggested that the observed population structure was a result of dispersal and mixing of salmon lice, as well as selective pressure such as delousing treatments and local environment. Our results are potentially helpful to make population specific delousing treatments, where the treatments are designed depending on the genetic characteristics of the targeted salmon lice population.