@phdthesis{Westbury2018, author = {Westbury, Michael V.}, title = {Unraveling evolution through Next Generation Sequencing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409981}, school = {Universit{\"a}t Potsdam}, pages = {129}, year = {2018}, abstract = {The sequencing of the human genome in the early 2000s led to an increased interest in cheap and fast sequencing technologies. This interest culminated in the advent of next generation sequencing (NGS). A number of different NGS platforms have arisen since then all promising to do the same thing, i.e. produce large amounts of genetic information for relatively low costs compared to more traditional methods such as Sanger sequencing. The capabilities of NGS meant that researchers were no longer bound to species for which a lot of previous work had already been done (e.g. model organisms and humans) enabling a shift in research towards more novel and diverse species of interest. This capability has greatly benefitted many fields within the biological sciences, one of which being the field of evolutionary biology. Researchers have begun to move away from the study of laboratory model organisms to wild, natural populations and species which has greatly expanded our knowledge of evolution. NGS boasts a number of benefits over more traditional sequencing approaches. The main benefit comes from the capability to generate information for drastically more loci for a fraction of the cost. This is hugely beneficial to the study of wild animals as, even when large numbers of individuals are unobtainable, the amount of data produced still allows for accurate, reliable population and species level results from a small selection of individuals. The use of NGS to study species for which little to no previous research has been carried out on and the production of novel evolutionary information and reference datasets for the greater scientific community were the focuses of this thesis. Two studies in this thesis focused on producing novel mitochondrial genomes from shotgun sequencing data through iterative mapping, bypassing the need for a close relative to serve as a reference sequence. These mitochondrial genomes were then used to infer species level relationships through phylogenetic analyses. The first of these studies involved reconstructing a complete mitochondrial genome of the bat eared fox (Otocyon megalotis). Phylogenetic analyses of the mitochondrial genome confidently placed the bat eared fox as sister to the clade consisting of the raccoon dog and true foxes within the canidae family. The next study also involved reconstructing a mitochondrial genome but in this case from the extinct Macrauchenia of South America. As this study utilised ancient DNA, it involved a lot of parameter testing, quality controls and strict thresholds to obtain a near complete mitochondrial genome devoid of contamination known to plague ancient DNA studies. Phylogenetic analyses confidently placed Macrauchenia as sister to all living representatives of Perissodactyla with a divergence time of ~66 million years ago. The third and final study of this thesis involved de novo assemblies of both nuclear and mitochondrial genomes from brown and striped hyena and focussed on demographic, genetic diversity and population genomic analyses within the brown hyena. Previous studies of the brown hyena hinted at very low levels of genomic diversity and, perhaps due to this, were unable to find any notable population structure across its range. By incorporating a large number of genetic loci, in the form of complete nuclear genomes, population structure within the brown hyena was uncovered. On top of this, genomic diversity levels were compared to a number of other species. Results showed the brown hyena to have the lowest genomic diversity out of all species included in the study which was perhaps caused by a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. The studies within this thesis show the power NGS sequencing has and its utility within evolutionary biology. The most notable capabilities outlined in this thesis involve the study of species for which no reference data is available and in the production of large amounts of data, providing evolutionary answers at the species and population level that data produced using more traditional techniques simply could not.}, language = {en} } @article{SteinertCassouHirschfeld2013, author = {Steinert, Bastian and Cassou, Damien and Hirschfeld, Robert}, title = {CoExist overcoming aversion to change preserving immediate access to source code and run-time information of previous development states}, series = {ACM SIGPLAN notices}, volume = {48}, journal = {ACM SIGPLAN notices}, number = {2}, publisher = {Association for Computing Machinery}, address = {New York}, issn = {0362-1340}, doi = {10.1145/2480360.2384591}, pages = {107 -- 117}, year = {2013}, abstract = {Programmers make many changes to the program to eventually find a good solution for a given task. In this course of change, every intermediate development state can of value, when, for example, a promising ideas suddenly turn out inappropriate or the interplay of objects turns out more complex than initially expected before making changes. Programmers would benefit from tool support that provides immediate access to source code and run-time of previous development states of interest. We present IDE extensions, implemented for Squeak/Smalltalk, to preserve, retrieve, and work with this information. With such tool support, programmers can work without worries because they can rely on tools that help them with whatever their explorations will reveal. They no longer have to follow certain best practices only to avoid undesired consequences of changing code.}, language = {en} } @article{SmithDupontMcCarthyetal.2019, author = {Smith, Sarah R. and Dupont, Chris L. and McCarthy, James K. and Broddrick, Jared T. and Obornik, Miroslav and Horak, Ales and F{\"u}ssy, Zolt{\´a}n and Cihlar, Jaromir and Kleessen, Sabrina and Zheng, Hong and McCrow, John P. and Hixson, Kim K. and Araujo, Wagner L. and Nunes-Nesi, Adriano and Fernie, Alisdair R. and Nikoloski, Zoran and Palsson, Bernhard O. and Allen, Andrew E.}, title = {Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-12407-y}, pages = {14}, year = {2019}, abstract = {Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.}, language = {en} } @misc{SicardLenhard2011, author = {Sicard, Adrien and Lenhard, Michael}, title = {The selfing syndrome a model for studying the genetic and evolutionary basis of morphological adaptation in plants}, series = {Annals of botany}, volume = {107}, journal = {Annals of botany}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-7364}, doi = {10.1093/aob/mcr023}, pages = {1433 -- 1443}, year = {2011}, abstract = {Background In angiosperm evolution, autogamously selfing lineages have been derived from outbreeding ancestors multiple times, and this transition is regarded as one of the most common evolutionary tendencies in flowering plants. In most cases, it is accompanied by a characteristic set of morphological and functional changes to the flowers, together termed the selfing syndrome. Two major areas that have changed during evolution of the selfing syndrome are sex allocation to male vs. female function and flower morphology, in particular flower (mainly petal) size and the distance between anthers and stigma. Scope A rich body of theoretical, taxonomic, ecological and genetic studies have addressed the evolutionary modification of these two trait complexes during or after the transition to selfing. Here, we review our current knowledge about the genetics and evolution of the selfing syndrome. Conclusions We argue that because of its frequent parallel evolution, the selfing syndrome represents an ideal model for addressing basic questions about morphological evolution and adaptation in flowering plants, but that realizing this potential will require the molecular identification of more of the causal genes underlying relevant trait variation.}, language = {en} } @phdthesis{Schuette2011, author = {Sch{\"u}tte, Moritz}, title = {Evolutionary fingerprints in genome-scale networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57483}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Mathematical modeling of biological phenomena has experienced increasing interest since new high-throughput technologies give access to growing amounts of molecular data. These modeling approaches are especially able to test hypotheses which are not yet experimentally accessible or guide an experimental setup. One particular attempt investigates the evolutionary dynamics responsible for today's composition of organisms. Computer simulations either propose an evolutionary mechanism and thus reproduce a recent finding or rebuild an evolutionary process in order to learn about its mechanism. The quest for evolutionary fingerprints in metabolic and gene-coexpression networks is the central topic of this cumulative thesis based on four published articles. An understanding of the actual origin of life will probably remain an insoluble problem. However, one can argue that after a first simple metabolism has evolved, the further evolution of metabolism occurred in parallel with the evolution of the sequences of the catalyzing enzymes. Indications of such a coevolution can be found when correlating the change in sequence between two enzymes with their distance on the metabolic network which is obtained from the KEGG database. We observe that there exists a small but significant correlation primarily on nearest neighbors. This indicates that enzymes catalyzing subsequent reactions tend to be descended from the same precursor. Since this correlation is relatively small one can at least assume that, if new enzymes are no "genetic children" of the previous enzymes, they certainly be descended from any of the already existing ones. Following this hypothesis, we introduce a model of enzyme-pathway coevolution. By iteratively adding enzymes, this model explores the metabolic network in a manner similar to diffusion. With implementation of an Gillespie-like algorithm we are able to introduce a tunable parameter that controls the weight of sequence similarity when choosing a new enzyme. Furthermore, this method also defines a time difference between successive evolutionary innovations in terms of a new enzyme. Overall, these simulations generate putative time-courses of the evolutionary walk on the metabolic network. By a time-series analysis, we find that the acquisition of new enzymes appears in bursts which are pronounced when the influence of the sequence similarity is higher. This behavior strongly resembles punctuated equilibrium which denotes the observation that new species tend to appear in bursts as well rather than in a gradual manner. Thus, our model helps to establish a better understanding of punctuated equilibrium giving a potential description at molecular level. From the time-courses we also extract a tentative order of new enzymes, metabolites, and even organisms. The consistence of this order with previous findings provides evidence for the validity of our approach. While the sequence of a gene is actually subject to mutations, its expression profile might also indirectly change through the evolutionary events in the cellular interplay. Gene coexpression data is simply accessible by microarray experiments and commonly illustrated using coexpression networks where genes are nodes and get linked once they show a significant coexpression. Since the large number of genes makes an illustration of the entire coexpression network difficult, clustering helps to show the network on a metalevel. Various clustering techniques already exist. However, we introduce a novel one which maintains control of the cluster sizes and thus assures proper visual inspection. An application of the method on Arabidopsis thaliana reveals that genes causing a severe phenotype often show a functional uniqueness in their network vicinity. This leads to 20 genes of so far unknown phenotype which are however suggested to be essential for plant growth. Of these, six indeed provoke such a severe phenotype, shown by mutant analysis. By an inspection of the degree distribution of the A.thaliana coexpression network, we identified two characteristics. The distribution deviates from the frequently observed power-law by a sharp truncation which follows after an over-representation of highly connected nodes. For a better understanding, we developed an evolutionary model which mimics the growth of a coexpression network by gene duplication which underlies a strong selection criterion, and slight mutational changes in the expression profile. Despite the simplicity of our assumption, we can reproduce the observed properties in A.thaliana as well as in E.coli and S.cerevisiae. The over-representation of high-degree nodes could be identified with mutually well connected genes of similar functional families: zinc fingers (PF00096), flagella, and ribosomes respectively. In conclusion, these four manuscripts demonstrate the usefulness of mathematical models and statistical tools as a source of new biological insight. While the clustering approach of gene coexpression data leads to the phenotypic characterization of so far unknown genes and thus supports genome annotation, our model approaches offer explanations for observed properties of the coexpression network and furthermore substantiate punctuated equilibrium as an evolutionary process by a deeper understanding of an underlying molecular mechanism.}, language = {en} } @misc{SchippersNguyenLuetal.2012, author = {Schippers, Jos H. M. and Nguyen, Hung M. and Lu, Dandan and Schmidt, Romy and M{\"u}ller-R{\"o}ber, Bernd}, title = {ROS homeostasis during development: an evolutionary conserved strategy}, series = {Cellular and molecular life sciences}, volume = {69}, journal = {Cellular and molecular life sciences}, number = {19}, publisher = {Springer}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-012-1092-4}, pages = {3245 -- 3257}, year = {2012}, abstract = {The balance between cellular proliferation and differentiation is a key aspect of development in multicellular organisms. Recent studies on Arabidopsis roots revealed distinct roles for different reactive oxygen species (ROS) in these processes. Modulation of the balance between ROS in proliferating cells and elongating cells is controlled at least in part at the transcriptional level. The effect of ROS on proliferation and differentiation is not specific for plants but appears to be conserved between prokaryotic and eukaryotic life forms. The ways in which ROS is received and how it affects cellular functioning is discussed from an evolutionary point of view. The different redox-sensing mechanisms that evolved ultimately result in the activation of gene regulatory networks that control cellular fate and decision-making. This review highlights the potential common origin of ROS sensing, indicating that organisms evolved similar strategies for utilizing ROS during development, and discusses ROS as an ancient universal developmental regulator.}, language = {en} } @misc{RomeroMujalliJeltschTiedemann2018, author = {Romero-Mujalli, Daniel and Jeltsch, Florian and Tiedemann, Ralph}, title = {Individual-based modeling of eco-evolutionary dynamics}, series = {Regional environmental change}, volume = {19}, journal = {Regional environmental change}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1436-3798}, doi = {10.1007/s10113-018-1406-7}, pages = {1 -- 12}, year = {2018}, abstract = {A challenge for eco-evolutionary research is to better understand the effect of climate and landscape changes on species and their distribution. Populations of species can respond to changes in their environment through local genetic adaptation or plasticity, dispersal, or local extinction. The individual-based modeling (IBM) approach has been repeatedly applied to assess organismic responses to environmental changes. IBMs simulate emerging adaptive behaviors from the basic entities upon which both ecological and evolutionary mechanisms act. The objective of this review is to summarize the state of the art of eco-evolutionary IBMs and to explore to what degree they already address the key responses of organisms to environmental change. In this, we identify promising approaches and potential knowledge gaps in the implementation of eco-evolutionary mechanisms to motivate future research. Using mainly the ISI Web of Science, we reveal that most of the progress in eco-evolutionary IBMs in the last decades was achieved for genetic adaptation to novel local environmental conditions. There is, however, not a single eco-evolutionary IBM addressing the three potential adaptive responses simultaneously. Additionally, IBMs implementing adaptive phenotypic plasticity are rare. Most commonly, plasticity was implemented as random noise or reaction norms. Our review further identifies a current lack of models where plasticity is an evolving trait. Future eco-evolutionary models should consider dispersal and plasticity as evolving traits with their associated costs and benefits. Such an integrated approach could help to identify conditions promoting population persistence depending on the life history strategy of organisms and the environment they experience.}, language = {en} } @phdthesis{RomeroMujalli2019, author = {Romero Mujalli, Daniel}, title = {Ecological modeling of adaptive evolutionary responses to rapid climate change}, doi = {10.25932/publishup-43062}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430627}, school = {Universit{\"a}t Potsdam}, pages = {167}, year = {2019}, abstract = {A contemporary challenge in Ecology and Evolutionary Biology is to anticipate the fate of populations of organisms in the context of a changing world. Climate change and landscape changes due to anthropic activities have been of major concern in the contemporary history. Organisms facing these threats are expected to respond by local adaptation (i.e., genetic changes or phenotypic plasticity) or by shifting their distributional range (migration). However, there are limits to their responses. For example, isolated populations will have more difficulties in developing adaptive innovations by means of genetic changes than interconnected metapopulations. Similarly, the topography of the environment can limit dispersal opportunities for crawling organisms as compared to those that rely on wind. Thus, populations of species with different life history strategy may differ in their ability to cope with changing environmental conditions. However, depending on the taxon, empirical studies investigating organisms' responses to environmental change may become too complex, long and expensive; plus, complications arising from dealing with endangered species. In consequence, eco-evolutionary modeling offers an opportunity to overcome these limitations and complement empirical studies, understand the action and limitations of underlying mechanisms, and project into possible future scenarios. In this work I take a modeling approach and investigate the effect and relative importance of evolutionary mechanisms (including phenotypic plasticity) on the ability for local adaptation of populations with different life strategy experiencing climate change scenarios. For this, I performed a review on the state of the art of eco-evolutionary Individual-Based Models (IBMs) and identify gaps for future research. Then, I used the results from the review to develop an eco-evolutionary individual-based modeling tool to study the role of genetic and plastic mechanisms in promoting local adaption of populations of organisms with different life strategies experiencing scenarios of climate change and environmental stochasticity. The environment was simulated through a climate variable (e.g., temperature) defining a phenotypic optimum moving at a given rate of change. The rate of change was changed to simulate different scenarios of climate change (no change, slow, medium, rapid climate change). Several scenarios of stochastic noise color resembling different climatic conditions were explored. Results show that populations of sexual species will rely mainly on standing genetic variation and phenotypic plasticity for local adaptation. Population of species with relatively slow growth rate (e.g., large mammals) - especially those of small size - are the most vulnerable, particularly if their plasticity is limited (i.e., specialist species). In addition, whenever organisms from these populations are capable of adaptive plasticity, they can buffer fitness losses in reddish climatic conditions. Likewise, whenever they can adjust their plastic response (e.g., bed-hedging strategy) they will cope with bluish environmental conditions as well. In contrast, life strategies of high fecundity can rely on non-adaptive plasticity for their local adaptation to novel environmental conditions, unless the rate of change is too rapid. A recommended management measure is to guarantee interconnection of isolated populations into metapopulations, such that the supply of useful genetic variation can be increased, and, at the same time, provide them with movement opportunities to follow their preferred niche, when local adaptation becomes problematic. This is particularly important for bluish and reddish climatic conditions, when the rate of change is slow, or for any climatic condition when the level of stress (rate of change) is relatively high.}, language = {en} } @phdthesis{RianoPachon2008, author = {Ria{\~n}o-Pach{\´o}n, Diego Mauricio}, title = {Identification of transcription factor genes in plants}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-27009}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {In order to function properly, organisms have a complex control mechanism, in which a given gene is expressed at a particular time and place. One way to achieve this control is to regulate the initiation of transcription. This step requires the assembly of several components, i.e., a basal/general machinery common to all expressed genes, and a specific/regulatory machinery, which differs among genes and is the responsible for proper gene expression in response to environmental or developmental signals. This specific machinery is composed of transcription factors (TFs), which can be grouped into evolutionarily related gene families that possess characteristic protein domains. In this work we have exploited the presence of protein domains to create rules that serve for the identification and classification of TFs. We have modelled such rules as a bipartite graph, where families and protein domains are represented as nodes. Connections between nodes represent that a protein domain should (required rule) or should not (forbidden rule) be present in a protein to be assigned into a TF family. Following this approach we have identified putative complete sets of TFs in plant species, whose genome is completely sequenced: Cyanidioschyzon merolae (red algae), Chlamydomonas reinhardtii (green alga), Ostreococcus tauri (green alga), Physcomitrella patens (moss), Arabidopsis thaliana (thale cress), Populus trichocarpa (black cottonwood) and Oryza sativa (rice). The identification of the complete sets of TFs in the above-mentioned species, as well as additional information and reference literature are available at http://plntfdb.bio.uni-potsdam.de/. The availability of such sets allowed us performing detailed evolutionary studies at different levels, from a single family to all TF families in different organisms in a comparative genomics context. Notably, we uncovered preferential expansions in different lineages, paving the way to discover the specific biological roles of these proteins under different conditions. For the basic leucine zipper (bZIP) family of TFs we were able to infer that in the most recent common ancestor (MRCA) of all green plants there were at least four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. Currently, following the approach described above, up to 57 TF and 11 TR families can be identified, which are among the most numerous transcription regulatory families in plants. Three families of putative TFs predate the split between rhodophyta (red algae) and chlorophyta (green algae), i.e., G2-like, PLATZ, and RWPRK, and may have been of particular importance for the evolution of eukaryotic photosynthetic organisms. Nine additional families, i.e., ABI3/VP1, AP2-EREBP, ARR-B, C2C2-CO-like, C2C2-Dof, PBF-2-like/Whirly, Pseudo ARR-B, SBP, and WRKY, predate the split between green algae and streptophytes. The identification of putative complete list of TFs has also allowed the delineation of lineage-specific regulatory families. The families SBP, bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA significantly differ in size between algae and land plants. The SBP family of TFs is significantly larger in C. reinhardtii, compared to land plants, and appears to have been lost in the prasinophyte O. tauri. The families bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA preferentially expanded with the colonisation of land, and might have played an important role in this great moment in evolution. Later, after the split of bryophytes and tracheophytes, the families MADS, AP2-EREBP, NAC, AUX/IAA, PHD and HRT have significantly larger numbers in the lineage leading to seed plants. We identified 23 families that are restricted to land plants and that might have played an important role in the colonization of this new habitat. Based on the list of TFs in different species we have started to develop high-throughput experimental platforms (in rice and C. reinhardtii) to monitor gene expression changes of TF genes under different genetic, developmental or environmental conditions. In this work we present the monitoring of Arabidopsis thaliana TFs during the onset of senescence, a process that leads to cell and tissue disintegration in order to redistribute nutrients (e.g. nitrogen) from leaves to reproductive organs. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. 76\% of these TFs are down-regulated during senescence, the remaining are up-regulated. The identification of TFs in plants in a comparative genomics setup has proven fruitful for the understanding of evolutionary processes and contributes to the elucidation of complex developmental programs.}, language = {en} } @article{ParaskevopoulouDennisWeithoffetal.2020, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Tiedemann, Ralph}, title = {Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-020-70173-0}, pages = {15}, year = {2020}, abstract = {Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.}, language = {en} } @misc{ParaskevopoulouDennisWeithoffetal.2020, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Tiedemann, Ralph}, title = {Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {1012}, issn = {1866-8372}, doi = {10.25932/publishup-48228}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-482280}, pages = {17}, year = {2020}, abstract = {Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.}, language = {en} } @phdthesis{Lamanna2015, author = {Lamanna, Francesco}, title = {Adaptive radiation and speciation in African weakly-electric fish}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-80097}, school = {Universit{\"a}t Potsdam}, pages = {114}, year = {2015}, abstract = {The rise of evolutionary novelties is one of the major drivers of evolutionary diversification. African weakly-electric fishes (Teleostei, Mormyridae) have undergone an outstanding adaptive radiation, putatively owing to their ability to communicate through species-specific Electric Organ Discharges (EODs) produced by a novel, muscle-derived electric organ. Indeed, such EODs might have acted as effective pre-zygotic isolation mechanisms, hence favoring ecological speciation in this group of fishes. Despite the evolutionary importance of this organ, genetic investigations regarding its origin and function have remained limited. The ultimate aim of this study is to better understand the genetic basis of EOD production by exploring the transcriptomic profiles of the electric organ and of its ancestral counterpart, the skeletal muscle, in the genus Campylomormyrus. After having established a set of reference transcriptomes using "Next-Generation Sequencing" (NGS) technologies, I performed in silico analyses of differential expression, in order to identify sets of genes that might be responsible for the functional differences observed between these two kinds of tissues. The results of such analyses indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ; ii) the metabolic activity of the electric organ might be specialized towards the production and turnover of membrane structures; iii) several ion channels are highly expressed in the electric organ in order to increase excitability, and iv) several myogenic factors might be down-regulated by transcription repressors in the EO. A secondary task of this study is to improve the genus level phylogeny of Campylomormyrus by applying new methods of inference based on the multispecies coalescent model, in order to reduce the conflict among gene trees and to reconstruct a phylogenetic tree as closest as possible to the actual species-tree. By using 1 mitochondrial and 4 nuclear markers, I was able to resolve the phylogenetic relationships among most of the currently described Campylomormyrus species. Additionally, I applied several coalescent-based species delimitation methods, in order to test the hypothesis that putatively cryptic species, which are distinguishable only from their EOD, belong to independently evolving lineages. The results of this analysis were additionally validated by investigating patterns of diversification at 16 microsatellite loci. The results suggest the presence of a new, yet undescribed species of Campylomormyrus.}, language = {en} } @article{HillLeowBleidornetal.2013, author = {Hill, Natascha and Leow, Alexander and Bleidorn, Christoph and Groth, Detlef and Tiedemann, Ralph and Selbig, Joachim and Hartmann, Stefanie}, title = {Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information}, series = {Theory in biosciences}, volume = {132}, journal = {Theory in biosciences}, number = {2}, publisher = {Springer}, address = {New York}, issn = {1431-7613}, doi = {10.1007/s12064-012-0173-0}, pages = {93 -- 104}, year = {2013}, abstract = {Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary.}, language = {en} } @article{HebigGiese2017, author = {Hebig, Regina and Giese, Holger}, title = {On the complex nature of MDE evolution and its impact on changeability}, series = {Software and systems modeling}, volume = {16}, journal = {Software and systems modeling}, publisher = {Springer}, address = {Heidelberg}, issn = {1619-1366}, doi = {10.1007/s10270-015-0464-2}, pages = {333 -- 356}, year = {2017}, language = {en} } @phdthesis{GuedesCorrea2009, author = {Guedes Corr{\^e}a, Luiz Gustavo}, title = {Evolutionary and functional analysis of transcription factors controlling leaf development}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40038}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Leaves are the main photosynthetic organs of vascular plants, and leaf development is dependent on a proper control of gene expression. Transcription factors (TFs) are global regulators of gene expression that play essential roles in almost all biological processes among eukaryotes. This PhD project focused on the characterization of the sink-to-source transition of Arabidopsis leaves and on the analysis of TFs that play a role in early leaf development. The sink-to-source transition occurs when the young emerging leaves (net carbon importers) acquire a positive photosynthetic balance and start exporting photoassimilates. We have established molecular and physiological markers (i.e., CAB1 and CAB2 expression levels, AtSUC2 and AtCHoR expression patterns, chlorophyll and starch levels, and photosynthetic electron transport rates) to identify the starting point of the transition, especially because the sink-to-source is not accompanied by a visual phenotype in contrast to other developmental transitions, such as the mature-to-senescent transition of leaves. The sink-to-source transition can be divided into two different processes: one light dependent, related to photosynthesis and light responses; and one light independent or impaired, related to the changes in the vascular tissue that occur when leaves change from an import to an export mode. Furthermore, starch, but not sucrose, has been identified as one of the potential signalling molecules for this transition. The expression level of 1880 TFs during early leaf development was assessed by qRTPCR, and 153 TFs were found to exhibit differential expression levels of at least 5-fold. GRF, MYB and SRS are TF families, which are overrepresented among the differentially expressed TFs. Additionally, processes like cell identity acquisition, formation of the epidermis and leaf development are overrepresented among the differentially expressed TFs, which helps to validate the results obtained. Two of these TFs were further characterized. bZIP21 is a gene up-regulated during the sink-to-source and mature-to-senescent transitions. Its expression pattern in leaves overlaps with the one observed for AtCHoR, therefore it constitutes a good marker for the sink-to-source transition. Homozygous null mutants of bZIP21 could not be obtained, indicating that the total absence of bZIP21 function may be lethal to the plant. Phylogenetic analyses indicate that bZIP21 is an orthologue of Liguleless2 from maize. In these analyses, we identified that the whole set of bZIPs in plants originated from four founder genes, and that all bZIPs from angiosperms can be classified into 13 groups of homologues and 34 Possible Groups of Orthologues (PoGOs). bHLH64 is a gene highly expressed in early sink leaves, its expression is downregulated during the mature-to-senescent transition. Null mutants of bHLH64 are characterized by delayed bolting when compared to the wild-type; this indicates a possible delay in the sink-to-source transition or the retention of a juvenile identity. A third TF, Dof4, was also characterized. Dof4 is neither differentially expressed during the sink-to-source nor during the senescent-to-mature transition, but a null mutant of Dof4 develops bigger leaves than the wild-type and forms a greater number of siliques. The Dof4 null mutant has proven to be a good background for biomass accumulation analysis. Though not overrepresented during the sink-to-source transition, NAC transcription factors seem to contribute significantly to the mature-to-senescent transition. Twenty two NACs from Arabidopsis and 44 from rice are differentially expressed during late stages of leaf development. Phylogenetic analyses revealed that most of these NACs cluster into three big groups of homologues, indicating functional conservation between eudicots and monocots. To prove functional conservation of orthologues, the expression of ten NAC genes of barley was analysed. Eight of the ten NAC genes were found to be differentially expressed during senescence. The use of evolutionary approaches combined with functional studies is thus expected to support the transfer of current knowledge of gene control gained in model species to crops.}, language = {en} } @book{GieseBecker2013, author = {Giese, Holger and Becker, Basil}, title = {Modeling and verifying dynamic evolving service-oriented architectures}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-246-9}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-65112}, publisher = {Universit{\"a}t Potsdam}, pages = {97}, year = {2013}, abstract = {The service-oriented architecture supports the dynamic assembly and runtime reconfiguration of complex open IT landscapes by means of runtime binding of service contracts, launching of new components and termination of outdated ones. Furthermore, the evolution of these IT landscapes is not restricted to exchanging components with other ones using the same service contracts, as new services contracts can be added as well. However, current approaches for modeling and verification of service-oriented architectures do not support these important capabilities to their full extend.In this report we present an extension of the current OMG proposal for service modeling with UML - SoaML - which overcomes these limitations. It permits modeling services and their service contracts at different levels of abstraction, provides a formal semantics for all modeling concepts, and enables verifying critical properties. Our compositional and incremental verification approach allows for complex properties including communication parameters and time and covers besides the dynamic binding of service contracts and the replacement of components also the evolution of the systems by means of new service contracts. The modeling as well as verification capabilities of the presented approach are demonstrated by means of a supply chain example and the verification results of a first prototype are shown.}, language = {en} } @article{FerTietjenJeltschetal.2017, author = {Fer, Istem and Tietjen, Britta and Jeltsch, Florian and Trauth, Martin H.}, title = {Modelling vegetation change during Late Cenozoic uplift of the East African plateaus}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {467}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2016.04.007}, pages = {120 -- 130}, year = {2017}, abstract = {The present-day vegetation in the tropics is mainly characterized by forests worldwide except in tropical East Africa, where forests only occur as patches at the coast and in the uplands. These forest patches result from the peculiar aridity that is linked to the uplift of the region during the Late Cenozoic. The Late Cenozoic vegetation history of East Africa is of particular interest as it has set the scene for the contemporary events in mammal and hominin evolution. In this study, we investigate the conditions under which these forest patches could have been connected, and a previous continuous forest belt could have extended and fragmented. We apply a dynamic vegetation model with a set of climatic scenarios in which we systematically alter the present-day environmental conditions such that they would be more favourable for a continuous forest belt in tropical East Africa. We consider varying environmental factors, namely temperature, precipitation and atmospheric CO2 concentrations. Our results show that all of these variables play a significant role in supporting the forest biomes and a continuous forest belt could have occurred under certain combinations of these settings. With our current knowledge of the palaeoenvironmental history of East Africa, it is likely that the region hosted these conditions during the Late Cenozoic. Recent improvements on environmental hypotheses of hominin evolution highlight the role of periods of short and extreme climate variability during the Late Cenozoic specific to East Africa in driving evolution. Our results elucidate how the forest biomes of East Africa can appear and disappear under fluctuating environmental conditions and demonstrate how this climate variability might be recognized on the biosphere level.}, language = {en} } @misc{EtteKnoblochSchwarzetal.2014, author = {Ette, Ottmar and Knobloch, Eberhard and Schwarz, Oliver and Werner, Petra and Suckow, Christian and Jobst, Anne and Schmuck, Thomas and Ringmacher, Manfred and Tintemann, Ute and Leitner, Ulrike and Holl, Frank and Panwitz, Sebastian and P{\´e}aud, Laura and Holtz, B{\"a}rbel and Folkerts, Menso and P{\"a}ßler, Ulrich and Roba, Bill}, title = {HiN : Alexander von Humboldt im Netz = Ingo Schwarz zum 65. Geburtstag}, series = {HIN : Alexander von Humboldt im Netz ; international review for Humboldtian studies}, volume = {XV}, journal = {HIN : Alexander von Humboldt im Netz ; international review for Humboldtian studies}, number = {29}, editor = {Ette, Ottmar and Knobloch, Eberhard}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {1617-5239}, doi = {10.18443/hinvol15iss292014}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-85033}, pages = {201}, year = {2014}, abstract = {Inhalt: Alexander von Humboldt-Forschungsstelle: Ingo Schwarz zum 65. Geburtstag Ottmar Ette: Findung und Erfindung einer Leserschaft. Neuere Editionsprojekte zu Alexander von Humboldt als Grundlage und Herausforderung k{\"u}nftigen Forschens Eberhard Knobloch: Alexandre de Humboldt et le Marquis de Laplace Oliver Schwarz: Alexander von Humboldt als astronomischer Arbeiter, Diskussionspartner und Ideengeber Petra Werner: Innenwelten und bleiche G{\"a}rten. Alexander von Humboldt untertage und in der Caripe-H{\"o}hle Christian Suckow: Alexander von Humboldt in Ust'-Kamenogorsk Anne Jobst: Neue Briefe Christian Gottfried Ehrenbergs an Alexander von Humboldt Thomas Schmuck: Humboldt, Baer und die Evolution Manfred Ringmacher: Zwei Briefe auf Guaran{\´i} in Alexander von Humboldts Handschrift Ute Tintemann: Julius Klaproths Mithridates-Projekt, Alexander von Humboldt und das Verlagshaus Cotta Ulrike Leitner: „Ja! Wenn Berlin Bonn w{\"a}re!" Friedrich R{\"u}ckerts Berufung nach Berlin Frank Holl: „Zur Freiheit bestimmt" - Alexander von Humboldts Blick auf die Kulturen der Welt Sebastian Panwitz: Das Humboldt-Mendelssohn-Haus J{\"a}gerstraße 22. Ein Quellenfund Laura P{\´e}aud: Du Mexique {\`a} l'Oural : l'expertise humboldtienne au service du politique B{\"a}rbel Holtz: „Cicerone" des K{\"o}nigs? Alexander von Humboldt und Friedrich Wilhelm III. Menso Folkerts: Ein unerwartetes Zusammentreffen in Sanssouci. Alexander von Humboldt und Karl Ludwig Hencke an der Tafel Friedrich Wilhelms IV. Ulrich P{\"a}ßler: Preußens Mann in Washington. F{\"u}nf Briefe Friedrich von Gerolts an Alexander von Humboldt (1858/1859) Bill Roba: German-Iowan Strategies in Celebrating the Centennial of Alexander von Humboldt's Birth Regina Mikosch: Ingo Schwarz' Ver{\"o}ffentlichungen zur Alexander von Humboldt {\"U}ber die Autoren}, language = {mul} } @phdthesis{CastroPrieto2011, author = {Castro Prieto, Aines del Carmen}, title = {Immunogenetics of free-ranging felids on Namibian farmlands}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-55505}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Genetic variation is crucial for the long-term survival of the species as it provides the potential for adaptive responses to environmental changes such as emerging diseases. The Major Histocompatibility Complex (MHC) is a gene family that plays a central role in the vertebrate's immune system by triggering the adaptive immune response after exposure to pathogens. MHC genes have become highly suitable molecular markers of adaptive significance. They synthesize two primary cell surface molecules namely MHC class I and class II that recognize short fragments of proteins derived respectively from intracellular (e.g. viruses) and extracellular (e.g. bacteria, protozoa, arthropods) origins and present them to immune cells. High levels of MHC polymorphism frequently observed in natural populations are interpreted as an adaptation to detect and present a wide array of rapidly evolving pathogens. This variation appears to be largely maintained by positive selection driven mainly by pathogenic selective pressures. For my doctoral research I focused on MHC I and II variation in free-ranging cheetahs (Acinonyx jubatus) and leopards (Panthera pardus) on Namibian farmlands. Both felid species are sympatric thus subject to similar pathogenic pressures but differ in their evolutionary and demographic histories. The main aims were to investigate 1) the extent and patterns of MHC variation at the population level in both felids, 2) the association between levels of MHC variation and disease resistance in free-ranging cheetahs, and 3) the role of selection at different time scales in shaping MHC variation in both felids. Cheetahs and leopards represent the largest free-ranging carnivores in Namibia. They concentrate in unprotected areas on privately owned farmlands where domestic and other wild animals also occur and the risk of pathogen transmission is increased. Thus, knowledge on adaptive genetic variation involved in disease resistance may be pertinent to both felid species' conservation. The cheetah has been used as a classic example in conservation genetics textbooks due to overall low levels of genetic variation. Reduced variation at MHC genes has been associated with high susceptibility to infectious diseases in cheetahs. However, increased disease susceptibility has only been observed in captive cheetahs whereas recent studies in free-ranging Namibian cheetahs revealed a good health status. This raised the question whether the diversity at MHC I and II genes in free-ranging cheetahs is higher than previously reported. In this study, a total of 10 MHC I alleles and four MHC II alleles were observed in 149 individuals throughout Namibia. All alleles but one likely belong to functional MHC genes as their expression was confirmed. The observed alleles belong to four MHC I and three MHC II genes in the species as revealed by phylogenetic analyses. Signatures of historical positive selection acting on specific sites that interact directly with pathogen-derived proteins were detected in both MHC classes. Furthermore, a high genetic differentiation at MHC I was observed between Namibian cheetahs from east-central and north-central regions known to differ substantially in exposure to feline-specific viral pathogens. This suggests that the patterns of MHC I variation in the current population mirrors different pathogenic selective pressure imposed by viruses. Cheetahs showed low levels of MHC diversity compared with other mammalian species including felids, but this does not seem to influence the current immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease susceptibility. However, it cannot be ruled out that the low MHC variation might limit a prosperous immunocompetence in the case of an emerging disease scenario because none of the remaining alleles might be able to recognize a novel pathogen. In contrast to cheetahs, leopards occur in most parts of Africa being perhaps the most abundant big cat in the continent. Leopards seem to have escaped from large-scale declines due to epizootics in the past in contrast to some free-ranging large carnivore populations in Africa that have been afflicted by epizootics. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, I characterized genetic variation at MHC I and MHC II genes in free-ranging leopards from Namibia. A total of six MHC I and six MHC II sequences were detected in 25 individuals from the east-central region. The maximum number of sequences observed per individual suggests that they likely correspond to at least three MHC I and three MHC II genes. Hallmarks of MHC evolution were confirmed such as historical positive selection, recombination and trans-species polymorphism. The low MHC variation detected in Namibian leopards is not conclusive and further research is required to assess the extent of MHC variation in different areas of its geographic range. Results from this thesis will contribute to better understanding the evolutionary significance of MHC and conservation implications in free-ranging felids. Translocation of wildlife is an increasingly used management tool for conservation purposes that should be conducted carefully as it may affect the ability of the translocated animals to cope with different pathogenic selective pressures.}, language = {en} } @phdthesis{Borghi2021, author = {Borghi, Gian Luca}, title = {Evolution and diversity of photosynthetic metabolism in C3, C3-C4 intermediate and C4 plants}, doi = {10.25932/publishup-52220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522200}, school = {Universit{\"a}t Potsdam}, pages = {163}, year = {2021}, abstract = {In C3 plants, CO2 diffuses into the leaf and is assimilated by the Calvin-Benson cycle in the mesophyll cells. It leaves Rubisco open to its side reaction with O2, resulting in a wasteful cycle known as photorespiration. A sharp fall in atmospheric CO2 levels about 30 million years ago have further increased the side reaction with O2. The pressure to reduce photorespiration led, in over 60 plant genera, to the evolution of a CO2-concentrating mechanism called C4 photosynthesis; in this mode, CO2 is initially incorporated into 4-carbon organic acids, which diffuse to the bundle sheath and are decarboxylated to provide CO2 to Rubisco. Some genera, like Flaveria, contain several species that represent different steps in this complex evolutionary process. However, the majority of terrestrial plant species did not evolve a CO2-concentrating mechanism and perform C3 photosynthesis. This thesis compares photosynthetic metabolism in several species with C3, C4 and intermediate modes of photosynthesis. Metabolite profiling and stable isotope labelling were performed to detect inter-specific differences changes in metabolite profile and, hence, how a pathway operates. The results obtained were subjected to integrative data analyses like hierarchical clustering and principal component analysis, and were deepened by correlation analyses to uncover specific metabolic features and reaction steps that were conserved or differed between species. The main findings are that Calvin-Benson cycle metabolite profiles differ between C3 and C4 species and between different C3 species, including a very different response to rising irradiance in Arabidopsis and rice. These findings confirm Calvin-Benson cycle operation diverged between C3 and C4 species and, most unexpectedly, even between different C3 species. Moreover, primary metabolic profiles supported the current C4 evolutionary model in the genus Flaveria and also provided new insights and opened up new questions. Metabolite profiles also point toward a progressive adjustment of the Calvin-Benson cycle during the evolution of C4 photosynthesis. Overall, this thesis point out the importance of a metabolite-centric approach to uncover underlying differences in species apparently sharing the same photosynthetic routes and as a valid method to investigate evolutionary transition between C3 and C4 photosynthesis.}, language = {en} } @phdthesis{Becker2013, author = {Becker, Basil}, title = {Architectural modelling and verification of open service-oriented systems of systems}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70158}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {Systems of Systems (SoS) have received a lot of attention recently. In this thesis we will focus on SoS that are built atop the techniques of Service-Oriented Architectures and thus combine the benefits and challenges of both paradigms. For this thesis we will understand SoS as ensembles of single autonomous systems that are integrated to a larger system, the SoS. The interesting fact about these systems is that the previously isolated systems are still maintained, improved and developed on their own. Structural dynamics is an issue in SoS, as at every point in time systems can join and leave the ensemble. This and the fact that the cooperation among the constituent systems is not necessarily observable means that we will consider these systems as open systems. Of course, the system has a clear boundary at each point in time, but this can only be identified by halting the complete SoS. However, halting a system of that size is practically impossible. Often SoS are combinations of software systems and physical systems. Hence a failure in the software system can have a serious physical impact what makes an SoS of this kind easily a safety-critical system. The contribution of this thesis is a modelling approach that extends OMG's SoaML and basically relies on collaborations and roles as an abstraction layer above the components. This will allow us to describe SoS at an architectural level. We will also give a formal semantics for our modelling approach which employs hybrid graph-transformation systems. The modelling approach is accompanied by a modular verification scheme that will be able to cope with the complexity constraints implied by the SoS' structural dynamics and size. Building such autonomous systems as SoS without evolution at the architectural level --- i. e. adding and removing of components and services --- is inadequate. Therefore our approach directly supports the modelling and verification of evolution.}, language = {en} } @phdthesis{Autenrieth2020, author = {Autenrieth, Marijke}, title = {Population genomics of two odontocetes in the North Atlantic and adjacent waters}, school = {Universit{\"a}t Potsdam}, pages = {IX, 110}, year = {2020}, abstract = {Due to continuously intensifying human usage of the marine environment worldwide ranging cetaceans face an increasing number of threats. Besides whaling, overfishing and by-catch, new technical developments increase the water and noise pollution, which can negatively affect marine species. Cetaceans are especially prone to these influences, being at the top of the food chain and therefore accumulating toxins and contaminants. Furthermore, they are extremely noise sensitive due to their highly developed hearing sense and echolocation ability. As a result, several cetacean species were brought to extinction during the last century or are now classified as critically endangered. This work focuses on two odontocetes. It applies and compares different molecular methods for inference of population status and adaptation, with implications for conservation. The worldwide distributed sperm whale (Physeter macrocephalus) shows a matrilineal population structure with predominant male dispersal. A recently stranded group of male sperm whales provided a unique opportunity to investigate male grouping for the first time. Based on the mitochondrial control region, I was able to infer that male bachelor groups comprise multiple matrilines, hence derive from different social groups, and that they represent the genetic variability of the entire North Atlantic. The harbor porpoise (Phocoena phocoena) occurs only in the northern hemisphere. By being small and occurring mostly in coastal habitats it is especially prone to human disturbance. Since some subspecies and subpopulations are critically endangered, it is important to generate and provide genetic markers with high resolution to facilitate population assignment and subsequent protection measurements. Here, I provide the first harbour porpoise whole genome, in high quality and including a draft annotation. Using it for mapping ddRAD seq data, I identify genome wide SNPs and, together with a fragment of the mitochondrial control region, inferred the population structure of its North Atlantic distribution range. The Belt Sea harbors a distinct subpopulation oppose to the North Atlantic, with a transition zone in the Kattegat. Within the North Atlantic I could detect subtle genetic differentiation between western (Canada-Iceland) and eastern (North Sea) regions, with support for a German North Sea breading ground around the Isle of Sylt. Further, I was able to detect six outlier loci which show isolation by distance across the investigated sampling areas. In employing different markers, I could show that single maker systems as well as genome wide data can unravel new information about population affinities of odontocetes. Genome wide data can facilitate investigation of adaptations and evolutionary history of the species and its populations. Moreover, they facilitate population genetic investigations, providing a high resolution, and hence allowing for detection of subtle population structuring especially important for highly mobile cetaceans.}, language = {en} }