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Using DNA from formaldehyde-preserved Daphnia to reconstruct past populations

  • Patrick Turko
  • Justyna Wolinska
  • Christoph Tellenbach
  • Marcin Krzysztof Dziuba
  • Marie-Eve Monchamp
  • Piet SpaakEmail author
Primary Research Paper

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 genotyping panel of short SNP-bearing amplicons and, to facilitate screening, we developed a multiplex genotyping 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-genotyping was more efficient than microsatellites on sedimentary eggs, and was more sensitive for hybrid detection. In conclusion, the SNP-based genotyping panel presented here enables to study the genetic structure of past populations from common formaldehyde-preserved collections. It is also promising for genotyping old dormant eggs, which can extend the temporal range of Daphnia community reconstructions.

Keywords

Ancient DNA Archive Formaldehyde SNaPshot SNP 

Notes

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.

Supplementary material

10750_2019_4015_MOESM1_ESM.pdf (281 kb)
Supplementary material 1 (PDF 281 kb)

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Aquatic EcologyEawag, Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
  2. 2.Institute of Integrative BiologyETH ZürichZurichSwitzerland
  3. 3.Department of Ecosystem ResearchLeibniz-Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
  4. 4.Department of Biology, Chemistry, Pharmacy, Institute of BiologyFreie Universität BerlinBerlinGermany
  5. 5.Department of Hydrobiology, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
  6. 6.Department of DermatologyUniversity of Zürich HospitalZurichSwitzerland
  7. 7.Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagen KDenmark

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