The Effect of Climate Change on Marine Brachyurans and The
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The effect of climate change on marine brachyurans and the implication of shell disease Von der Fakultät für Mathematik und Naturwissenschaften der Carl von Ossietzky Universität Oldenburg zur Erlangung des Grades und Titels eines Doktors der Naturwissenschaften Dr. rer. nat. angenommene Dissertation von Herrn Philipp Krämer geboren am 02.01.1982 in Salzkotten 1. Gutachterin: Frau Prof. Gabriele Gerlach 2. Gutachter: Herr Prof. Meinhard Simon 3. Gutachter: Herr Prof. Dirk Albach Tag der Disputation: 23.09.2015 Contents Summary 1 Zusammenfassung 3 Aims of the thesis 5 1 Shell disease in marine decapods 7 1.1 Introduction . 8 1.1.1 Shell disease syndrome in crustaceans . 8 1.1.2 Bacterial biofilms as a source of shell disease . 8 1.1.3 Effect of shell disease syndrome in crustacean populations . 10 1.2 Summary Manuscript I/II . 11 Manuscript I: Bacterial biofilms on Cancer pagurus and its implication for future shell disease prevalence . 13 Manuscript II: Shell disease in crabs in the North Sea: Native Carcinus maenas and Cancer pagurus suffer but bioinvasive Hemigrapsus penicillatus flourishes . 39 2 Population genetics 52 2.1 Introduction . 53 2.1.1 Allele diversity in demes . 53 2.1.2 Allele diversity between demes . 54 2.2 Summary Manuscript III/IV . 59 Manuscript III: Demerelate: an R package to calculate inter-individual relatedness for kinship analysis based on codominant diploid genetic markers . 60 Manuscript IV: Calculations of population differentiation based on GST and D: forget GST but not all of statistics! . 71 3 Population structures in crustaceans 80 3.1 Introduction . 81 3.1.1 Population genetics in marine crustaceans . 81 3.1.2 Processes under selection in marine crustaceans . 81 3.2 Summary Manuscript V . 83 Manuscript V: Characterization of transcripts of Cancer pagurus acclimatized to different temperature regimes and the population structure on a latitudinal gradient . 84 Synthesis 109 References 114 Abbreviations 122 Danksagung 123 Annex 124 Curriculum Vitae 158 Erklärungen gemäß §10 der Promotionsordnung 161 1 Summary In the marine ecosystem climate change is a major threat to crustacean biodiversity. Altered environmental conditions will physiologically challenge eukaryotes and prokaryotes. The micro- biotic origin of crustacean shell disease and its dependence on the interaction of environmental factors with host susceptibility and local pathogens serves as a good model studying the response and potential resilience of crustaceans towards environmental alterations by climate change. De- spite the broad distribution and long knowledge of shell disease as a syndrome, detailed current information are scarce for the North Atlantic. In my thesis I contribute to understand the effect of shell disease on the level of inter- as well as intra-specific interactions by using state of the art genetic methods combined with ecological data. I focus on the brown crab Cancer pagurus Linnaeus, 1758 as a species of high commercial value and ecological importance with generally high susceptibility to environmental factors and shell disease. In chapter I, I study on the interaction of C. pagurus and its bacterial biofilm. I analyze whether temperature alone may alter bacterial communities in biofilms and whether long term differences in environmental factors between different populations may play a role in shell dis- ease susceptibility and bacterial biofilm composition. I figure out that both temperature and population specific conditions may have an effect on bacterial biofilms. However, bacterial biofilms are relatively specific for individuals and stable for short term temperature alterations. I present the first broad overview of the bacterial community structure in C. pagurus biofilms. I detect many bacterial strains similar to those playing a role in shell disease inflammation in the American lobster Homarus americanus Milne Edwards, 1837. This shows the large geo- graphic impact of those bacteria. The biofilm communities includes obligate anoxic and aerobic bacteria. Anoxic conditions may arise in biofilm communities in micro-habitats and may serve obligate anoxic pathogens as well as chitinolytic bacteria as starting point for lesion formation. To test for the prevalence of shell disease in other crustaceans I compare shell disease in three decapod crabs of the North Sea. I discover differences between species which might have an effect on community structure in local marine benthic communities. A recent invaded species Hemigrapsus penicillatus (De Haan, 1835) seems to be more resistant to shell disease syndromes and may thus benefit in inter-specific competition with native crabs such as Carcinus maenas (Linnaeus, 1758) or C. pagurus. Body size of the host is a major factor influencing shell disease prevalence. This may lead to negative selective pressure for, not only large species, but also bigger sized individuals within species. To study shell disease on the intra-specific level, population genetics is used as a tool to search for genetic signatures of adaptation on the distributional range of C. pagurus. In chapter II, I present two different approaches to understand local adaptation based on population ge- netics. I describe how population genetics data may be used to analyze relatedness structures in local populations. This is necessary to differentiate between local adaptation of populations and physiological similarities merely due to close relatedness of con-specifics. I used the R pro- gramming language to implement different statistics for this purpose and published the code in the R Network. Furthermore, population genetics can be used to understand structures among populations. Summary 2 I contribute to the recent discussion, which estimate, GˆST or DEST , best describes population structure by modeling migration and mutation in an island population situation. Both estima- tors produce similar results in statistics, i.e. significance is congruent for both estimates. While Gˆst is heavily influenced by mutation, DEST calculations are more robust in this situation. In chapter III, I use a population genetics approach to analyze the genetic profile of different populations of C. pagurus on a latitudinal gradient from Norway to Spain. Variable sites in annotated genes of different populations were identified by 454 full transcriptomics. I find low differentiation among populations by neutral simple sequence repeat (SSR) markers implying high connectivity between different areas. Similarly, genetic markers derived from different expressed sequence tag (EST) sequences show weak structuring between populations. To find genes, which may be source for adaptation, two populations at environmental extreme positions are compared. Individuals in northern Norway are experimentally stressed with temperature conditions equivalent to the southern North Sea. Similarity in relative gene expression between populations suggests that similar high temperature conditions will be tolerated. Severity of shell disease is not increased by the treatment. Decreased transcripts during warm conditions are immune or metabolism related such as hemocyanines or gamma-butyrobetaine. Those genes may be important for acclimation over longer periods. Gene expression and population genetics showed a high degree of similarity implying a common gene pool among populations. High migration distance by larvae and adults connect populations over long distances and will help C. pagurus to persist during climate change induced environmental changes. Changes in population size during the last years especially at the edges of their distribution indicate that this species arlready underwent a northward shift. This may obscure former population structures. Significant differentiation between shell diseased and non shell diseased individuals are found in Northern Norway. A high degree of population admixture in shell diseased individuals in contrast to healthy individuals might suggest that diseased animals may originate from different populations. This indicates a subgroup of migrants in Northern Norway. The high degree of connectivity may be beneficial for migrants to invade into northern habitats. Being better adapted to more southern populations, they may more often develop shell disease in newly invaded habitats. This is also supported by two transcripts belonging to the hemocyanines, which show evidence for differences in expression between populations in contrast to ≈13,000 other transcripts studied. These transcripts will be promising to study to see if high connectivity and potential to shift already skews locally adapted populations in the wild and will further change the population structure of C. pagurus with climate change induced altered temperature conditions in the future. 3 Zusammenfassung Die durch den Klimawandel verursachten Veränderungen von Umweltfaktoren im Ökosystem Meer bedrohen die Vielfalt der Krebse und wirken sich auf die Physiologie von Eukaryoten und Bakterien aus. Solche Veränderungen von Umweltbedingungen stehen in einigen Fällen in einem direkten Zusammenhang mit dem Auftreten der Schwarzfleckkrankheit. In meiner Doktorarbeit untersuche ich das Auftreten der Schwarzfleckkrankheit in lokalen Krebspopulationen, sowie die Konsequenzen auf ihre zukünftige Verbreitung. Der mikrobielle Ursprung dieser Krankheit und das übergreifende Auftreten bei verschiedenen Krebsen bieten ein gutes Modell, um die Reaktion und die potentielle Widerstandsfähigkeit des Ökosystems am Beispiel der Krebse auf zukünftige Klimaveränderungen abschätzen zu können. Obwohl die Schwarzfleckkrankheit