Assessing the performance of statistical classifiers to discriminate fish stocks using Fourier analysis of otolith shape

The assignment of individual fish to its stock of origin is important for reliable stock assessment and fisheries management. Otolith shape is commonly used as the marker of distinct stocks in discrimination studies. Our literature review showed that the application and comparison of alternative statistical classifiers to discriminate fish stocks based on otolith shape is limited. Therefore, we compared the performance of two traditional and four machine learning classifiers based on Fourier analysis of otolith shape using selected stocks of Atlantic cod (Gadus morhua) in the southern Baltic and Atlantic herring (Clupea harengus) in the western Norwegian Sea, Skagerrak and the southern Baltic Sea. Our results showed that the stocks can be successfully discriminated based on their otolith shapes. We observed significant differences in the accuracy obtained by the tested classifiers. For both species, support vector machines (SVM) resulted in the highest classification accuracy. These findings suggest that modern machine learning algorithms, like SVM, can help to improve the accuracy of fish stock discrimination systems based on the otolith shape.Assessing the performance of statistical classifiers to discriminate fish stocks using Fourier analysis of otolith shapesubmittedVersio

Leben im globalen Wandel: Anpassungsmechanismen des marinen Dreistachligen Stichlings Gasterosteus aculeatus

Due to ongoing increases in carbon dioxide (CO2) concentrations in the atmosphere, the world’s climate is changing at an unprecedented rate, leading to rising global mean air and water temperatures. When atmospheric CO2 dissolves in seawater, ocean pH declines, causing an acidification of the ocean. These altered environmental conditions are highly probable to have severe impacts on marine organisms by affecting their performance and survival. When environmental stress is increasing, some species can migrate to habitats with more favourable conditions, others have to adapt to changing conditions. Whether species will be able to adapt fast enough to keep pace with changing environments will be one decisive factor for population persistence. In this thesis, a prime model organism, the three-spined stickleback Gasterosteus aculeatus, was used to study ecological and evolutionary effects of rising water temperatures and ocean acidification on marine fish populations. Rising temperatures are likely to stress marine species, dependent on their thermal tolerance. Thermal stress can alter immune functions of organisms, thereby increasing the susceptibility to infectious diseases. By combining the effects of elevated temperature and bacterial infection in a common garden experiment, the influence of thermal stress on evolutionary trajectories of disease resistance in three-spined stickleback populations could be investigated (chapter II). Environmental stress negatively impacted life-history traits and pathogen resistance of sticklebacks. Furthermore, thermal stress reduced genetic differentiation between populations by releasing cryptic within-population variation. While life-history traits showed positive genetic correlations between temperatures and genotype by environment interactions (GxE), thermal stress led to negative genetic correlations in disease resistance, showing that evolutionary responses in altered environments can be hard to predict from prevailing conditions. Rising temperatures, on the other hand, promote the development of many parasites and pathogenic bacteria, increasing the risk of infection and diseases during summer. To understand infection patterns in relation to water temperature, the parasite and bacterial communities of marine fish species were investigated over a period of two years (chapter I). Temporarily elevated water temperatures resulted in increased macroparasite and bacterial diversities in marine fish species. In addition, some parasite groups showed a forward shift and extension in infection peaks, following warmer spring seasons. This shows that even subtle changes in seasonal temperatures can have an effect on the epidemiology and phenology of parasites as well as opportunistic pathogens. Increased virulence of pathogens at higher temperatures in combination with immune-compromised hosts can have far fetching consequences for marine ecosystems. Next to rising ocean temperatures, marine organisms have to cope with ocean acidification. It has been shown, that elevated CO2 concentrations negatively impacted fish development and survival, particularly in early developmental stages. A powerful mechanism to mediate the effects of global change is transgenerational acclimation. By acclimating parents and offspring to different CO2 concentrations, within- and transgenerational effects of ocean acidification on life-history traits of marine sticklebacks were studied (chapter III). Exposure to elevated CO2 concentrations led to an increase in clutch size in adults as well as increased juvenile survival and growth rates. Transgenerational effects could be found for juvenile growth and for otolith characteristics, suggesting that parental acclimation can modify ocean acidification effects. To summarize, three-spined sticklebacks cope better with ocean acidification than with rising ocean temperatures. Transgenerational acclimation enables sticklebacks to respond quickly to environmental changes and provides time for genetic evolution, as long-term adaptive mechanism, to catch up. The high tolerance to fluctuations in water chemistry and temperature as well as the substantial amount of standing genetic variation suggest that stickleback populations can adapt fast enough to changing environmental conditions.Durch stetig ansteigende Kohlenstoffdioxid-Konzentrationen (CO2) ändert sich das weltweite Klima mit rasanter Geschwindigkeit und Luft- und Wassertemperaturen steigen. Wenn sich atmosphärisches CO2 im Meerwasser löst, sinkt der pH-Gehalt des Meeres und führt zu einer Versauerung des Ozeans. Diese veränderten Umweltbedingungen können schwerwiegende Folgen für die Leistungsfähigkeit und das Überleben von Meeresbewohner haben. Wenn der Umweltstress ansteigt, können einige Arten in Habitate mit geeigneteren Bedingungen ausweichen, andere wiederum müssen sich an die veränderten Umweltbedingungen anpassen. Ob Lebewesen in der Lage sind, sich schnell genug an die sich ändernde Umwelten anzupassen, wird ein entscheidender Faktor für das Bestehen von Populationen sein. Um ökologische und evolutionäre Effekte des globalen Wandels auf marine Fischpopulationen zu untersuchen, wurde ein hervorragend geeigneter Modellorganismus, der Dreistachlige Stichling Gasterosteus aculeatus, für diese Arbeit verwendet. Abhängig von der thermalen Toleranz, können ansteigende Temperaturen Stress in marinen Lebewesen hervorrufen. Thermaler Stress kann Immunfunktionen von Organismen beeinflussen und dadurch die Anfälligkeit für Infektionskrankheiten erhöhen. Durch die kombinierten Effekte von erhöhter Temperatur und bakterieller Infektion in einem „common garden“ Experiment, konnte der Einfluss von thermalem Stress auf evolutionäre Mechanismen der Pathogenresistenz bei Stichlings-populationen untersucht werden (Kapitel II). Umweltstress beeinträchtigte Fitnesskomponenten und Pathogenresistenzen bei Stichlingen. Zudem führte thermaler Stress zu reduzierter genetischer Differenzierung zwischen Populationen. Während Fitnesskomponenten eine positive genetische Korrelation zwischen Temperaturen zeigten, führte thermaler Stress zu einer negativen genetischen Korrelation für Krankheitsresistenz. Ausgehend von vorherrschenden Bedingungen scheinen evolutionäre Antworten auf veränderte Umwelten schwer vorhersagbar. Ansteigende Temperaturen begünstigen andererseits die Entwicklung von vielen Parasiten und pathogenen Bakterien und erhöhen dadurch das Risiko für Infektionen und Krankheiten während des Sommers. Um temperaturbedingte Infektionsmuster zu verstehen, wurden die Parasiten- und Bakteriengemeinschaften von marinen Fischarten in einem Zeitraum von zwei Jahren untersucht. Kurzzeitig ansteigende Wassertemperaturen verursachten erhöhte Makroparasiten- und Bakteriendiversitäten in marinen Fischarten. Zusätzlich zeigten einige Parasitengruppen eine Verschiebung und Ausdehnung des Infektionshöhepunkts durch wärmere Frühlingsmonate. Bereits kleine Änderungen in saisonalen Temperaturen können die Epidemiologie und die Phänologie von Parasiten, als auch von opportunistischen Pathogenen, beeinflussen. Erhöhte Pathogenvirulenz durch ansteigende Temperaturen kombiniert mit immungeschwächten Wirten kann zu weitreichenden Konsequenzen für marine Ökosysteme führen. Neben ansteigenden Wassertemperaturen, müssen marine Lebewesen auch mit Ozeanversauerung umgehen. Es wurde bewiesen, dass erhöhte CO2 Konzentrationen die Entwicklung und das Überleben von Fischen beeinträchtigt. Ein wirkungsvoller Mechanismus, um die Effekte des globalen Wandels zu mildern, ist transgenerationale Akklimatisierung. Durch das Akklimatisieren von Eltern und Nachwuchs an verschiedene CO2 - Konzentrationen, konnten inner- und trans-generationale Effekte von Ozeanversauerung auf marine Stichlinge untersucht werden (Kapitel III). Erhöhte CO2 - Konzentrationen führten zu vergrößerten Eigelegen bei den Eltern, als auch zu erhöhten Überlebens- und Wachstumsraten bei den Juvenilen. Transgenerationale Effekte konnten für juveniles Wachstum und für Otolithencharakteristiken bestätigt werden und lassen darauf schließen, dass elterliche Akklimatisierung die Auswirkungen von Ozeanversauerung verändern können. Zusammenfassend ist zu erwähnen, dass der Dreistachlige Stichling mit Ozeanversauerung besser umgehen kann, als mit ansteigenden Meerestemperaturen. Zudem ermöglicht transgenerationale Akklimatisierung, Stichlingen auf Umweltveränderungen schnell zu reagieren, bevor genetische Evolution, als Langzeitanpassungsmechanismus, übergreift. Die hohe Toleranz für schwankende Wasserchemie und Temperatur, als auch die erhebliche Menge an dauerhafter genetischer Varianz ermöglicht Stichlingspopulationen sich schnell genug an die sich verändernde Umweltbedingungen anzupassen

Living apart together: Long-term coexistence of Baltic cod stocks associated with depth-specific habitat use

Coexistence of fish populations (= stocks) of the same species is a common phenomenon. In the Baltic Sea, two genetically divergent stocks of Atlantic cod (Gadus morhua), Western Baltic cod (WBC) and Eastern Baltic cod (EBC), coexist in the Arkona Sea. Although the relative proportions of WBC and EBC in this area are considered in the current stock assessments, the mixing dynamics and ecological mechanisms underlying coexistence are not well understood. In this study, a genetically validated otolith shape analysis was used to develop the most comprehensive time series of annual stock mixing data (1977–2019) for WBC and EBC. Spatio-temporal mixing analysis confirmed that the two stocks coexist in the Arkona Sea, albeit with fluctuating mixing proportions over the 43-year observation period. Depth-stratified analysis revealed a strong correlation between capture depth and stock mixing patterns, with high proportions of WBC in shallower waters (48–61% in <20m) and increasing proportions of EBC in deeper waters (50–86% in 40-70m). Consistent depth-specific mixing patterns indicate stable differences in depth distribution and habitat use of WBC and EBC that may thus underlie the long-term coexistence of the two stocks in the Arkona Sea. These differences were also reflected in significantly different proportions of WBC and EBC in fisheries applying passive gears in shallower waters (more WBC) and active gears in deeper waters (more EBC). This highlights the potential for fishing gear-specific exploitation of different stocks, and calls for stronger consideration of capture depth and gear type in stock assessments. This novel evidence provides the basis for improved approaches to research, monitoring and management of Baltic cod stocks

Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod

Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology

Seasonal variation in parasite infection patterns of marine fish species from the Northern Wadden Sea in relation to inter annual temperature fluctuations

Marine environmental conditions are naturally changing throughout the year, affecting life cycles of hosts aswell as parasites. In particular,water temperature is positively correlatedwith the development ofmany parasites and pathogenic bacteria, increasing the risk of infection and diseases during summer. Interannual temperature fluctuations are likely to alter host?parasite interactions, which may result in profound impacts on sensitive ecosystems. In this context we investigated the parasite and bacterial Vibrionaceae communities of four common small fish species (three-spined stickleback Gasterosteus aculeatus, Atlantic herring Clupea harengus, European sprat Sprattus sprattus and lesser sand eel Ammodytes tobianus) in the Northern Wadden Sea over a period of two years. Overall, we found significantly increased relative diversities of infectious species at higher temperature differentials. On the taxon-specific level some macroparasite species (trematodes, nematodes) showed a shift in infection peaks that followed the water temperatures of preceding months, whereas other parasite groups showed no effects of temperature differentials on infection parameters. Our results show that even subtle changes in seasonal temperatures may shift and modify the phenology of parasites as well as opportunistic pathogens that can have far reaching consequences for sensitive ecosystems