Regulatory control of phenotypic plasticity: Analysis of the molecular basis of stressor-induced adaptation processes in the aquatic keystone species Daphnia
Animal Physiology and Biochemistry
Evolution, Anthropology
Evolutionary Cell and Developmental Biology (Zoology)
Final Report Abstract
The funded project aimed at understanding how the environment interacts with (and shapes) genomes, and how genome regulation and variation are linked to phenotypic plasticity and phenotypic evolution. Specifically, my research focused on the stage-dependent, tissue-specific and reversible morphological development of traits that are induced, in the new model organism, "Daphnia pulex", by chemical signals from their environment. So far, our understanding of the mechanistic basis of common morphological variation such as phenotypic plasticity is only fragmentary as there has been relatively little success at identifying empirical patterns of cellular control mechanisms governing phenotypic variation. This is predominantly due to the fact that determining the genetic architecture of complex traits is challenging since plastic development typically does not rely on a few plasticity or robustness genes but rather arises from interactions between multiple environmentally sensitive components and pathways that might be controlled by many loci. In order to elucidate the cellular machineries that drive the expression of plastic responses at the molecular level, I have employed a unique combination of state-of-the-art ‘omic methodologies and "in silico" approaches, using the genomic model organism Daphnia pulex. In response to chemical cues released by predators (i.e., kairomones) this species exhibits an astonishing repertoire of inducible defences including developmental, stage dependent, tissue-specific and reversible de novo morphological formations. During the course of my fellowship, I have been able to quantify the natural variation in life-history and phenotypic reaction norms in response to the applied environmental risk conditions in a number of different Daphnia genotypes that originate from ponds across the UK. Obtained data clearly indicate clonespecific (morphological) plasticity under the applied environmental risk conditions. Application of another risk factor - copper - in single and combined exposure with predation risk, offered an additional manipulation of the stress environment, which in combination with some knowledge about the mode of action of copper allowed more effective dissection of the processes underpinning the response to predation. Data analyses included the use of response surface regression models - a classic ecological design. The use of these models has advantages in that there is no need to collect data at every point along each axis or their combinations to estimate features about the interaction between the applied stressors. Combined with the use of high and non-responding genotypes, it is a very powerful design. In order to identify genomic elements that are differentially regulated in stressor exposed Daphnia withreference to its developmental transcriptome, I have employed state-of-art RNA-Seq technology. Obtained data revealed significant differences in the enrichment of distinct functional gene categories and pathways between the different treatments and genotypes. Considering the fact that some (molecular) responses may be caused (or accompanied) by changes in co-regulation of genes that are invisible to single gene-based analyses, I have also established a weighted gene correlation network analysis that allowed me to identify key nodes in the gene regulatory network patterning the plastic responses in question during development and in response to the applied environmental risk exposure(s). These analyses also included the identification of potential cis-dependent regulation mechanisms via the use of a promoter analysis tool that had specifically been modified for the Daphnia system. In addition to the original focus on transcriptional regulation mechanisms, I have been able to add a second layer of ‘omics data (i.e., application of high-resolution mass spectrometry technology) to the project. While preliminary analyses of the metabolomics data indicate a clear separation of some of the tested groups (i.e., developmental stages) across the investigated conditions and genotypes, further analyses are currently aimed at identifying distinct chemical fingerprints that reflect the functional, phenotypic response of D. pulex to the applied combination of risk(s). Applying functional genomic assays across genotypes and developmental stages that differ in expression of the adaptive and plastic traits that I have examined in this research project, I am convinced that this study will ultimately provide genuine insights into how organisms can and do respond to environmental challenges, and by that, improve our understanding of organisms as integrated units of biological organization. By bridging the gap between genotype and phenotype in an ecologically relevant framework, results from this innovative investigation are hence expected to have great impact in the field of ecological and evolutionary genomics, for they will provide a radically new perspective on the nature of genetic constraints and the evolution of adaptation and speciation processes. Because Daphnia is a keystone species of ponds and lakes, this study will furthermore transform our current understanding of the buffering capacity of populations and ecosystems in response to environmental change.
Publications
- (2015). Differential transcriptomic responses of ancient and modern Daphnia genotypes to phosphorus supply. Mol Ecol, 24, 123-135
Roy Chowdhury, P., D. Frisch, D. Becker, L.J. Weider, J.A. Lopez, J.K. Colbourne, and P.D Jeyasingh
(See online at https://doi.org/10.1111/mec.13009) - (2016). Adjustments of the serine proteases of Daphnia pulex in response to temperature changes. Comp Biochem Physiol Part B, 194-195: 1:10
Dölling, R., D. Becker, S. Hawat, M. Koch, A. Schwarzenberger, and B. Zeis
(See online at https://doi.org/10.1016/j.cbpb.2016.01.001)
