Publikationen

@article{b057aa2decfc4247b7c3f4b8109e2a49,

title = "The cuticle proteome of a planktonic crustacean",

abstract = "The cuticles of arthropods provide an interface between the organism and its environment. Thus, the cuticle's structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the moulted cuticle of the aquatic crustacean Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology. We detected a total of 278 high-confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin-modifying enzymes as the most abundant protein groups in the cuticle proteome. Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle. Finally, cuticle protein genes were also clustered as tandem gene arrays in the D. magna genome. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing genome annotations and investigations on diverse topics such as the genetic basis of interactions with predators and parasites.",

keywords = "arthropods, cuticle, Daphnia, label-free quantification proteomics, mass spectrometry",

author = "Otte, {Kathrin A.} and Maridel Fredericksen and Peter Fields and Thomas Fr{\"o}hlich and Christian Laforsch and Dieter Ebert",

note = "Publisher Copyright: {\textcopyright} 2024 The Authors. Proteomics published by Wiley-VCH GmbH.",

year = "2024",

doi = "10.1002/pmic.202300292",

language = "English",

journal = "Proteomics",

issn = "1615-9853",

publisher = "Wiley-VCH Verlag",

@article{51ef024f1a3f4fbca9227809683a15f9,

title = "A window into local adaptation",

abstract = "How organisms adapt to their environment is not only a central topic of evolutionary biology but also a pressing question in the light of recent global change. Unravelling the genetic basis of these local adaptations can help to predict the response of a population to an increase in temperature or the more frequent occurrence of droughts. A popular approach to study the genes that drive local adaptation is the analysis of genotype–environment associations (GEA), testing the correlation of genomic features (typically single-nucleotide polymorphisms, SNPs) and environmental conditions. In this issue of Molecular Ecology Resources, Booker et al. (Molecular Ecology Resources, 2023) present a new approach to GEA, introducing genomic window analysis. They combine the information of neighbouring SNPs instead of analysing each SNP independently, therefore gaining power for detecting genomic signals of environmental adaptation. Using simulations of local adaptation to a heterogeneous environment as well as previously published real data from a natural population of lodgepole pine, they prove the superiority of their method over several established GEA approaches, especially in the case of small sample sizes. Leveraging the information present in closely linked genomic sites, Booker et al. (Molecular Ecology Resources, 2023) take genotype–environment association studies to the next level.",

keywords = "adaptation, ecological genetics, genomics, landscape genetics",

author = "Otte, {Kathrin A.}",

year = "2023",

month = sep,

day = "29",

doi = "10.1111/1755-0998.13872",

language = "English",

volume = "24",

journal = "Molecular Ecology Resources",

issn = "1755-098X",

publisher = "Wiley-Blackwell Publishing Ltd",

number = "2",

@article{6c498915d04d480c9bc2efeb66ee63e6,

title = "Effects of larval crowding on the transcriptome of Drosophila simulans",

abstract = "Larval crowding is one common ecological stressor for many insect species. In Drosophila, high larval density alters multiple widely-studied phenotypes including life-history traits, morphology and behavior. Nevertheless, we still miss a holistic view of the full range of phenotypic changes and the underlying molecular mechanisms. In this study, we analyzed the adult transcriptomes of high and low larval density fly cohorts, and highlighted the molecular basis of the plastic traits. Increased cellular energy metabolism and locomotion, along with reduced reproductive investment, are key responses to high larval density. Moreover, we compared the expression changes among cohorts with different developmental delays caused by larval crowding. The majority of genes induced by larval crowding showed the strongest expression alterations in cohorts with intermediate delay. Furthermore, linear expression changes were observed in genes related to nutrition and detoxification. Comparing different high-density cohorts could provide insights into the varied responses to distinct larval crowding-induced stresses such as space competition, food degradation and waste accumulation.",

author = "Stephan Buchner and Sheng-Kai Hsu and Viola Nolte and Otte, {Kathrin A} and Christian Schl{\"o}tterer",

year = "2023",

month = sep,

day = "27",

doi = "10.1111/eva.13592",

language = "English",

journal = "Evolutionary Applications",

issn = "1752-4571",

publisher = "Wiley-Blackwell",

@article{1190aeb74b864ecd852c7c07ec3bcb1c,

title = "Evolution of Metabolome and Transcriptome Supports a Hierarchical Organization of Adaptive Traits",

abstract = "Most organismal phenotypes have a polygenic basis, which enables adaptive phenotypic responses on ecological time scales. While adaptive phenotypic changes are highly parallel in replicate populations, this does not apply to the contributing loci. In particular for small populations, the same phenotypic shift can be fueled by different sets of alleles at alternative loci (genetic redundancy). Although this phenomenon is empirically well supported, the molecular basis of the genetic redundancy is not yet understood. To fill this gap, we compared the heterogeneity of the evolutionary transcriptomic and metabolomic response in ten Drosophila simulans populations which evolved parallel high-level phenotypic changes in a novel temperature environment but used different allelic combinations of alternative loci. We showed that the metabolome evolved more parallel than the transcriptome, confirming a hierarchical organization of molecular phenotypes. Different sets of genes responded in each evolved population but led to the enrichment of similar biological functions and a consistent metabolic profile. Since even the metabolomic response was still highly heterogeneous across evolved populations, we propose that selection may operate on pathways/networks.",

keywords = "Animals, Biological Evolution, Drosophila simulans, Gene Expression Profiling, Metabolome, Phenotype, Transcriptome",

author = "Wei-Yun Lai and Otte, {Kathrin A} and Christian Schl{\"o}tterer and Toni Gossmann",

year = "2023",

month = may,

day = "26",

doi = "10.1093/gbe/evad098",

language = "English",

volume = "15",

journal = "Genome biology and evolution",

issn = "1759-6653",

publisher = "Oxford University Press",

number = "6",

@article{91867f2c622547d0ac0a8291269d943d,

title = "Population-wide differentiation of tolerance to microcystins and other cyanobacterial nonmicrocystin effects in Daphnia",

abstract = "Cyanobacteria cause major concern due to toxic secondary metabolites, especially microcystins. Adaptation of Daphnia populations to these toxic cyanobacteria has repeatedly been shown; however, it remains unclear if this adaptation indeed reflects increased tolerance to microcystins or to other cyanobacterial metabolites. To shed light on this question, we compared the response of Daphnia to a toxic cyanobacterium and to its microcystin-free mutant. We analysed clones originating from an experienced Daphnia magna population that coexists with toxic cyanobacteria as well as from a naive population. Diets containing 10 % and 20 % of either cyanobacterium resulted in stronger relative reduction of somatic growth in animals exposed to the toxic cyanobacterium. These effects did not differ among Daphnia populations. Contrastingly, tolerance to the mutant cyanobacterium was higher in the experienced population. This indicates that adaptation to cyanobacterial non-microcystin effects in Daphnia populations is possible and that the molecular mechanisms of tolerance are different for microcystins and other non-microcystin effects. Finally, a connection of high tolerance to microcystins and low somatic growth tentatively points at trade-offs of microcystin tolerance, which might constrain evolutionary adaptation of Daphnia to microcystins.",

keywords = "Daphnia, Microcystis, cyanobacteria, microcystin, toxin",

author = "{von Elert}, Eric and Otte, {Kathrin A.}",

year = "2022",

month = jul,

day = "8",

doi = "10.1127/fal/2022/1452",

language = "English",

volume = "196",

pages = "267--278",

journal = "Fundamental and Applied Limnology",

issn = "1863-9135",

publisher = "Schweizerbart Science Publishers",

number = "3-4",

@article{d3078a078e014579bacce616298dd99a,

title = "Phenotypic convergence in a natural Daphnia population acclimated to low temperature",

abstract = "Fluidity of a given membrane decreases at lower ambient temperatures, whereas it rises at increasing temperatures, which is achieved through changes in membrane lipid composition. In consistence with homeoviscous adaptation theory, lower temperatures result in increased tissue concentrations of polyunsaturated fatty acids (PUFAs) in Daphnia magna, suggesting a higher PUFA requirement at lower temperatures. However, so far homeoviscous adaptation has been suggested for single or geographically separated Daphnia genotypes only. Here, we investigated changes in relative fatty acid (FA) tissue concentrations in response to a lower temperature (15°C) within a D. magna population. We determined juvenile growth rates (JGR) and FA patterns of 14 genotypes that were grown on Chlamydomonas klinobasis at 15°C and 20°C. We report significant differences of JGR and the relative body content of various FAs between genotypes at either temperature and between temperatures. Based on slopes of reaction norms, we found genotype-specific changes in FA profiles between temperatures suggesting that genotypes have different strategies to cope with changing temperatures. In a hierarchical clustering analysis, we grouped genotypes according to differences in direction and magnitude of changes in relative FA content, which resulted in three clusters of genotypes following different patterns of changes in FA composition. These patterns suggest a lower importance of the PUFA eicosapentaenoic acid (EPA, C20:5ω3) than previously assumed. We calculated an unsaturation index (UI) as a proxy for membrane fluidity at 15°C, and we neither found significant differences for this UI nor for fitness, measured as JGR, between the three genotype clusters. We conclude that these three genotype clusters represent different physiological solutions to temperature changes by altering the relative share of different FAs, but that their phenotypes converge with respect to membrane fluidity and JGR. These clusters will be subjected to different degrees of PUFA limitation when sharing the same diet.",

keywords = "Daphnia, PUFA, intraspecific competition, membrane fluidity, polyunsaturated fatty acid",

author = "Christian Werner and Otte, {Kathrin A.} and Elert, {Eric von}",

year = "2021",

month = nov,

doi = "10.1002/ece3.8217",

language = "English",

volume = "11",

pages = "15312--15324",

journal = "Ecology and evolution",

issn = "2045-7758",

publisher = "John Wiley and Sons Ltd",

number = "21",

@article{8474399d7d4d47fdb8763ad46109a14f,

title = "The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime",

abstract = "Background: Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence, which combines advantages of experimental evolution such as time series, replicate populations, and controlled environmental conditions, with whole genome sequencing. Recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures—either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Results: Here, we expose the founder population from Portugal to a cold temperature regime. Although almost no selection targets are shared between the hot and cold selection regime, the adaptive architecture was similar. We identify a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. Conclusions: These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations.",

keywords = "Adaptive architecture, Experimental evolution, Temperature adaptation",

author = "Otte, {Kathrin A.} and Viola Nolte and Fran{\c c}ois Mallard and Christian Schl{\"o}tterer",

year = "2021",

month = jul,

day = "16",

doi = "10.1186/s13059-021-02425-9",

language = "English",

volume = "22",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "1",

@article{79c151fb12d342f7bbd2f82cc031cd72,

title = "Detecting selected haplotype blocks in evolve and resequence experiments",

abstract = "Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of evolve and resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool-seq data need a variety of data-specific parameters that are typically defined ad hoc and require haplotype sequences for validation. Here, we introduce haplovalidate, a tool which detects selected haplotypes in Pool-seq time series data without the need for sequenced haplotypes. Haplovalidate makes data-driven choices of two key parameters for the clustering procedure, the minimum correlation between SNPs constituting a cluster and the window size. Applying haplovalidate to simulated E&R data reliably detects selected haplotype blocks with low false discovery rates. Importantly, our analyses identified a restriction of the haplotype block-based approach to describe the genomic architecture of adaptation. We detected a substantial fraction of haplotypes containing multiple selection targets. These blocks were considered as one region of selection and therefore led to underestimation of the number of selection targets. We demonstrate that the separate analysis of earlier time points can significantly increase the separation of selection targets into individual haplotype blocks. We conclude that the analysis of selected haplotype blocks has great potential for the characterization of the adaptive architecture with E&R experiments.",

keywords = "data-driven parameter choices, evolve and resequence, experimental evolution, haplotype reconstruction, replicated time series data, selection, sequencing of pooled individuals",

author = "Otte, {Kathrin A.} and Christian Schl{\"o}tterer",

year = "2020",

month = sep,

day = "6",

doi = "10.1111/1755-0998.13244",

language = "English",

volume = "21",

pages = "93--109",

journal = "Molecular Ecology Resources",

issn = "1755-098X",

publisher = "Wiley-Blackwell Publishing Ltd",

number = "1",

@article{ae4abe56605540d1806f85fe5069e8c9,

title = "Neuronal Function and Dopamine Signaling Evolve at High Temperature in Drosophila",

abstract = "Neuronal activity is temperature sensitive and affects behavioral traits important for individual fitness, such as locomotion and courtship. Yet, we do not know enough about the evolutionary response of neuronal phenotypes in new temperature environments. Here, we use long-term experimental evolution of Drosophila simulans populations exposed to novel temperature regimes. Here, we demonstrate a direct relationship between thermal selective pressure and the evolution of neuronally expressed molecular and behavioral phenotypes. Several essential neuronal genes evolve lower expression at high temperatures and higher expression at low temperatures, with dopaminergic neurons standing out by displaying the most consistent expression change across independent replicates. We functionally validate the link between evolved gene expression and behavioral changes by pharmacological intervention in the experimentally evolved D. simulans populations as well as by genetically triggered expression changes of key genes in D. melanogaster. As natural temperature clines confirm our results for Drosophila and Anopheles populations, we conclude that neuronal dopamine evolution is a key factor for temperature adaptation.",

keywords = "Behavior, Dopamine, Drosophila, Experimental evolution, Gene expression",

author = "Jak{\v s}i{\'c}, {Ana Marija} and Julia Karner and Viola Nolte and Sheng-Kai Hsu and Neda Barghi and Fran{\c c}ois Mallard and Otte, {Kathrin Anna} and Lidija Sve{\v c}njak and Kirsten-Andr{\'e} Senti and Christian Schl{\"o}tterer and Jian Lu",

year = "2020",

month = sep,

day = "1",

doi = "10.1093/molbev/msaa116",

language = "English",

volume = "37",

pages = "2630--2640",

journal = "Molecular Biology and Evolution",

issn = "0737-4038",

publisher = "Oxford University Press",

number = "9",

@article{a0998fed6ac4406d950d1c48a222498d,

title = "Genetic redundancy fuels polygenic adaptation in Drosophila",

abstract = "The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic—i.e., result from selection on a large number of genetic loci—but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes (AFCs) across many contributing loci. To resolve this, we use laboratory natural selection to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among beneficial alleles. We observed convergent responses for several phenotypes—e.g., fitness, metabolic rate, and fat content—and a strong polygenic response (99 selected alleles; mean s = 0.059). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. We discerned different evolutionary paradigms based on the heterogeneous genomic patterns among replicates. Redundancy and quantitative trait (QT) paradigms fitted the experimental data better than simulations assuming independent selective sweeps. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses using multiple alternative genetic pathways converging at a new phenotypic optimum. This key property of beneficial alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.",

keywords = "Adaptation, Physiological/genetics, Alleles, Animals, Biological Evolution, Drosophila simulans/genetics, Genetic Fitness, Genetic Heterogeneity, Genome, Insect, Haplotypes/genetics, Multifactorial Inheritance/genetics, Phenotype, Polymorphism, Single Nucleotide/genetics, Quantitative Trait Loci/genetics",

author = "Neda Barghi and Raymond Tobler and Viola Nolte and Jak{\v s}i{\'c}, {Ana Marija} and Fran{\c c}ois Mallard and Otte, {Kathrin Anna} and Marlies Dolezal and Thomas Taus and Robert Kofler and Christian Schl{\"o}tterer",

year = "2019",

month = feb,

day = "4",

doi = "10.1371/journal.pbio.3000128",

language = "English",

volume = "17",

journal = "PLoS Biology ",

issn = "1544-9173",

publisher = "Public Library of Science",

number = "2",