The Supercomputer MACH-2: Use Cases

Use Case: Processing whole genome time series data from resting egg banks of the microcrustacean Daphnia to investigate evolutionary consequences of recent anthropogenic change.

• Department of Ecology, University of Innsbruck.

Whole-genome time series from resting egg stages, deposited in lake sediments, provide a unique opportunity to investigate the evolutionary consequences of recent anthropogenic change (1,2). Here, we make use of whole genome resequencing data from resting stages of the microcrustacean Daphnia to reconstruct secondary contact and hybridization events in peri-Alpine lakes and their putative evolutionary consequences. To achieve this, we isolated and sequenced DNA of Daphnia resting stages from the sediment cores of two large European peri-alpine lakes. Finally, we processed our whole genome resequencing data using Snakemake (3), a flexible and automatic Python-based workflow.

Figure: Overview of workflow for processing whole genome time series data from Daphnia resting stages. A. Isolation of Daphnia resting stages from several layers of a sediment core. B. DNA extraction of single resting eggs. C. Snakemake workflow and principal component analysis (PCA).

References

1. Jana Nickel, Tilman Schell, Tania Holtzem, Anne Thielsch, Stuart R Dennis, Birgit C Schlick-Steiner, Florian M Steiner, Markus Möst, Markus Pfenninger, Klaus Schwenk, Mathilde Cordellier, Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome, Genome Biology and Evolution, Volume 13, Issue 12, December 2021, evab267, https://doi.org/10.1093/gbe/evab267
2. Nora Brede, Christoph Sandrock, Dietmar Straile, Piet Spaak, Thomas Jankowski, Bruno Streit, Klaus Schwenk, The impact of human-made ecological changes on the genetic architecture of Daphnia species, PNAS, Volume 106, Issue 12, March 2009, https://doi.org/10.1073/pnas.0807187106
3. Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J., 2021. Sustainable data analysis with Snakemake. F1000Res 10, 33.