The research conducted for this thesis has produced quantitative data on the biology and population genetic structure of the Mulloway Argyrosomus japonicus in Western Australia, where this sciaenid is recreationally and commercially fished. These data were used 1) to test various hypotheses regarding the relationship between key biological characteristics of A. japonicus and both latitude and environmental variables, 2) to investigate the population structure and genetic characteristics of populations of A. japonicus on the west and south coasts of Western Australia and to assess the relationships between these populations and those of A. japonicus in eastern Australia and South Africa, and 3) to consider the implications of the biological and genetic results for management.

The Atlantic cod (Gadus morhua L.) fishery is of great economic importance to the Faroese economy. There are two separately managed cod stocks around the Faroe Islands, the Faroe Plateau and the Faroe Bank cod. Both have experienced dramatic decreases in size and informed management decisions are vital for both stock viability and exploitation. The stocks are geographically isolated by an 800 m deep channel and water temperatures are on average 1 – 2 ºC higher on the Faroe Bank than on the Faroe Plateau. There are clear phenotypic differences between the stocks; in particular, the markedly higher growth rate for the Faroe Bank cod has caught public and scientific attention. There is continuing debate regarding the relative importance of genetics and environmental contributions to the contrasting phenotypes. Analyses of reproductive parameters (field data and experimental captive spawnings) as well as analyses of microsatellite and single nucleotide polymorphism (SNP) markers were undertaken to better resolve the issue. Field data as well as data from experimental captive spawnings provided evidence of reproductive differences between Faroe Plateau and Faroe Bank cod. Peak spawning occurred earlier on the Faroe Plateau than on the Faroe Bank and this difference in timing of spawning was maintained in captivity. In particular, differences in sizes of eggs (average diameters of 1.40 and 1.30 mm for Faroe Plateau and Faroe Bank cod eggs, respectively) and indirect evidence of greater volumes spawned by the Faroe Bank females suggested stock differences with respect to egg size – egg number trade-off. It was hypothesised that the strategy adopted by cod on the Faroe Bank, with a higher number of smaller eggs, evolved in response to a more hostile environment (bare seabed and higher exposure to predators) experienced by early life stages in this area. Experimental captive spawnings with Faroe Bank cod showed a large interfamily skew in survival rates of cod eggs and fry. Egg size was identified as a useful indicator of survival rates in the egg stage, but egg survival rates could not be used to predict viability in later developmental stages, thus highlighting the importance of employing some sort of genetic monitoring of cod fry to ensure sufficient family representation in the progeny. While no tank effect was evident concerning fry survival, a significant tank effect was identified concerning body sizes of fry. Microsatellite data were analysed using large sample sizes of Faroe Plateau and Faroe Bank cod with the Faroe Plateau divided into two locations, Faroe Plateau North-East and Faroe Plateau West (cod from each of the two were known to belong to separate spawning grounds). Two Norwegian coastal cod samples were included as outlier populations. While no genetic differentiation was detected between the two Faroe Plateau locations, these analyses revealed a detectable, albeit relatively modest, degree of genetic differentiation between cod from the Faroe Plateau and the Faroe Bank (FST = 0.0014 and 0.0018; DJost_EST = 0.0027 and 0.0048; P < 0.0001 and P < 0.001 for the Faroe Plateau North-East – Faroe Bank and the Faroe Plateau West – Faroe Bank comparisons). These values were several times smaller than those between Faroese and Norwegian coastal cod (pairwise FST and DJost_EST values in the range of 0.0061 – 0.0137 and 0.0158 – 0.0386, respectively). Despite recent reductions in census population sizes for Faroe Plateau and, particularly, Faroe Bank cod, genetic diversity estimates were comparable to the ones observed for Norwegian coastal cod and there was no evidence of significant genetic bottlenecks. Lastly, data for one of the markers (Gmo132) indicated genotype-dependent vertical distribution of cod (as investigated for Faroe Plateau North-East cod). Contrary to some previously published studies, analysis of SNPs of two candidate genes for adaptive divergence, the hemoglobin gene Hb-ß1 and the transferrin gene Tf1, failed to detect differentiation between samples of Faroe Plateau and Faroe Bank cod analysed in this thesis. Of 3533 novel SNPs simultaneously discovered and genotyped by restriction-site associated DNA (RAD) sequencing, 58 showed evidence of genetic differentiation between Faroe Plateau North-East and Faroe Bank cod (P < 0.05). No single locus was fixed for different alleles between Faroe Plateau and Faroe Bank cod. A set of eight informative SNPs (FST values between Faroe Plateau and Faroe Bank samples > 0.25; P < 0.0005) were selected for validation in larger samples, that included cod from both Faroe Plateau areas and the Faroe Bank as well as Norwegian coastal and White Sea cod. Six out of the eight loci amplified successfully with a PCR-based method and there was 100 % concordance between genotypes of individuals screened by both techniques. Due to ascertainment bias, the SNPs should only be applied with caution in a broader geographical context. Nonetheless, these SNPs did confirm the genetic substructure suggested for Faroese cod by microsatellite analyses. While no genetic differentiation was evident between the two Faroe Plateau locations, significant genetic differentiation was evident between Faroe Plateau and Faroe Bank cod at five of the SNPs (FST values in the range of 0.0383 – 0.1914). This panel of five SNPs could confidently be used to trace groups of Faroe Plateau and Faroe Bank cod to their population of origin. In conclusion, multiple lines of evidence demonstrate that Faroe Plateau and Faroe Bank cod are truly two genetically distinct populations. While the findings contribute to a broader understanding of the biology and the genetics of Faroe Plateau and Faroe Bank cod, the novel SNPs developed may provide a valuable resource for potential future demands of i.e. genetic stock identification methods.

Vattenkraftens påverkan på rinnande vatten är välbeskriven i litteraturen. Med ökat intresse för vindkraft och andra energislag med begränsad klimatpåverkan, ökar även behovet av reglerkraft. Effekten av korttidsreglerad vattenkraft på ekosystem är ett aktuellt ämne med kunskapsluckor i stort behov av fler studier. Indalsälven passerar Järkvissle kraftverk några mil norr om Sundsvall. Den lokala harrpopulationen har minskat kraftigt och misstankar finns om kopplingar till korttidsregleringen i Järkvissle kraftverk. Vid förvaltning av ekosystem och djuren i dem är kunskapen om interaktioner och beteenden bland det viktigaste att etablera. Detta för att kunna avgöra om artens beteende påverkas av korttidsreglering. Bristande kunskap om lokala lekbeteenden innebar således att harren nedan Järkvissle kraftverk studerades inför förväntad lekperiod. Studien baserades på två antaganden 1) harr förflyttar sig uppströms mot grundområden, lämpade för lek, när vattentemperaturen ökar. 2) harr är mer aktiv när flödesvariationen är hög, eftersom lekplatsernas beskaffenhet påverkas av flödesförhållanden. Harr (n = 20) från sträckan nedan Järkvissle kraftverk märktes med radiosändare, för att studera rörelsemönster och beteenden i anslutning till lek under perioden 28 april till 29 maj 2022. Vid 24 handpejlingstillfällen registrerades de märkta individernas position och djup. En Multipel linjär regression med bakåtvänd eliminering gav tre signifikanta resultat. Det observerades en ökad aktivitet i form av euklidisk förflyttning vid höga flöden motsvarande en förflyttning om 1,0 m (± 1 m) för varje 1,0 m3 s-1 ökat flöde. Det observerades även ett temperaturberoende val av ståndplats där en ökning om 1,0 ºC resulterade i en förflyttning till en ståndplats som var 0,21 ± 0,03 m grundare, på ett avstånd som var 65,2 ± 12,5 m längre bort från dammen. Studien bör kompletteras med kartläggning av optimala värden för flödesförändring som gynnar harr, samt om det finns andra variabler som bättre kan förutse tidpunkt och plats för lek. Om avsikten är att stoppa minskandet av harrbeståndet i Järkvissle, bör Järkvissle kraftstation övervaka vattentemperatur och anpassa sin flödesregim. Detta för mjukare övergångar mellan högt och lågt flöde samt att flödet hålls stabilt under lek med fyra extra veckors utrymme för inkubering. / The effect of hydroelectric powerplants (HEP) on waterways is extensive and has been well documented in the literature. But with an increased interest in wind power and other green alternatives, a higher demand for regulated hydroelectric power has emerged, so as not to put stress on the electric grid. Hydropeaking and its effect on ecosystems are a hot topic with gaps in knowledge calling for more research. Indalsälven runs through Järkvissle HEP a few miles north of Sundsvall. The local grayling population has seen a large decline and there are suspicions of a connection to the hydropeaking at Järkvissle HEP. When managing ecosystems and the animals within them it is vital to establish a firm understanding of interactions and behaviour. This can be used to determine the effect of hydropeaking on the behaviours of grayling. A lack in knowledge of local spawning behaviour thus led to a study of the grayling2population below Järkvissle HEP leading up to the expected spawning period. The study was based around two assumptions: 1) grayling move upstream towards shallower areas suitable for spawning as the temperature in the water rises, and 2) grayling are more active when the variation in flow is high, because the number of suitable spawning grounds are limited by flow. Graylings (n = 20) in the area below the Järkvissle HEP were tagged with radio transmitters, to study the movement and behaviour exhibited before the expected spawning period between April 28th and May 29th, 2022. On 24 occasions hand tracking was performed and position and depth of the marked individuals were recorded. Through a multiple linear regression with backwards stepwise elimination three significant results were found. There was an observed increase in activity in the form of Euclidean movement represented by a 1,0 m (± 1 m) movement for every 1,0 m3 s-1 of increased flow. We also observed a temperature dependency when it came to habitat choice, where an increase of 1,0 ºC in water temperature resulted in a movement to an area 0,21 ± 0,03 m shallower, at a distance that was 65,2 ± 12,5 m further from the dam. The findings of this study should be expanded upon with further research into optimal values for flow variation that best suit grayling, and additionally explore whether there are other variables to better predict time and place for spawning. If the intention is to stop the decline of the grayling population, Järkvissle HEP should monitor the water temperature and adapt their flow regime to make softer transitions between high and low flow and keeping the flow at a stable interval during spawning and an additional four weeks to leave room for incubation.