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Using DNA from formaldehyde-preserved Daphnia to reconstruct past populations

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Abstract

We compared taxon composition of the Daphnia longispina hybrid community, as reconstructed from dormant eggs (retrieved from sediment samples) and the pelagic population (retrieved from formaldehyde-preserved zooplankton samples), from the same lake and of the same time period. As microsatellite markers do not work on largely fragmented DNA, such as of formaldehyde-preserved samples, both types of samples (dormant eggs and pelagic Daphnia) were screened with single-nucleotide polymorphism (SNP) markers. Here, we designed a genoty** panel of short SNP-bearing amplicons and, to facilitate screening, we developed a multiplex genoty** protocol. The results of this comparison confirmed differences between dormant and pelagic samples. Specifically, D. galeata was overrepresented in the sedimentary egg bank in comparison to the pelagic population, indicating that this taxon is more involved in sexual reproduction than other taxa. In addition to being successfully applied on formaldehyde-preserved samples, SNP-genoty** was more efficient than microsatellites on sedimentary eggs, and was more sensitive for hybrid detection. In conclusion, the SNP-based genoty** panel presented here enables to study the genetic structure of past populations from common formaldehyde-preserved collections. It is also promising for genoty** old dormant eggs, which can extend the temporal range of Daphnia community reconstructions.

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Acknowledgements

We thank Esther Keller for help in the lab and in the field and Markus Möst for help with the microsatellite analysis. This work was supported by two joint “lead agency” grants from the Swiss National Science Foundation (310030L 135750 and 310030L 166628 to P.S.) and German Science Foundation (WO 1587/3-1 and WO 1587/6-1 to J.W.). M.K.D. was supported by a scholarship of the Adam Mickiewicz University Foundation for the school year 2018/2019. We thank two anonymous reviewers for their constructive comments on an earlier draft.

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Author notes

  1. Marie-Eve Monchamp

    Present address: Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark

Authors and Affiliations

  1. Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland

    Patrick Turko, Christoph Tellenbach, Marie-Eve Monchamp & Piet Spaak

  2. Institute of Integrative Biology, ETH Zürich, 8092, Zurich, Switzerland

    Patrick Turko, Marie-Eve Monchamp & Piet Spaak

  3. Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587, Berlin, Germany

    Justyna Wolinska

  4. Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-5, 14195, Berlin, Germany

    Justyna Wolinska

  5. Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland

    Marcin Krzysztof Dziuba

  6. Department of Dermatology, University of Zürich Hospital, 8952, Zurich, Switzerland

    Patrick Turko

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Correspondence to Piet Spaak.

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Turko, P., Wolinska, J., Tellenbach, C. et al. Using DNA from formaldehyde-preserved Daphnia to reconstruct past populations. Hydrobiologia 841, 153–161 (2019). https://doi.org/10.1007/s10750-019-04015-0

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