@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{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}
}
@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}
}