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


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.


Ancient DNA Archive Formaldehyde SNaPshot SNP 



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)


  1. Billiones, R., M. Brehm, J. Klee & K. Schwenk, 2004. Genetic identification of Hyalodaphnia species and interspecific hybrids. Hydrobiologia 526: 43–53.CrossRefGoogle Scholar
  2. Brede, N., A. Thielsch, C. Sandrock, P. Spaak, B. Keller, B. Streit & K. Schwenk, 2006. Microsatellite markers for European Daphnia. Molecular Ecology Notes 6: 536–539.CrossRefGoogle Scholar
  3. Brede, N., C. Sandrock, D. Straile, T. Jankowski, P. Spaak, B. Streit & K. Schwenk, 2009. The impact of human-made ecological changes on the genetic architecture of Daphnia species. Proceedings of the National Academy of Sciences of the United States of America 106: 4758–4763.CrossRefGoogle Scholar
  4. Brody, J. R. & S. E. Kern, 2004. Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques 36: 214–217.CrossRefGoogle Scholar
  5. Bürgi, H. R., P. Weber & H. Bachman, 1985. Seasonal variations in the trophic structure of phyto- and zooplankton communities in lakes in different trophic states. Schweizerische Zeitschrift für Hydrologie 47: 197–224.CrossRefGoogle Scholar
  6. Bürgi, H. R., H. Bührer & B. Keller, 2003. Long-term changes in functional properties and biodiversity of plankton in Lake Greifensee (Switzerland) in response to phosphorus reduction. Aquatic Ecosystem Health & Management 6: 147–158.CrossRefGoogle Scholar
  7. Fox, C. H., F. B. Johnson, J. Whiting & P. P. Roller, 1985. Formaldehyde fixation. Journal of Histochemistry & Cytochemistry 33: 845–853.CrossRefGoogle Scholar
  8. Frisch, D., P. K. Morton, P. R. Chowdhury, B. W. Culver, J. K. Colbourne, L. J. Weider & P. D. Jeyasingh, 2014. A millennial-scale chronicle of evolutionary responses to cultural eutrophication in Daphnia. Ecology Letters 17: 360–368.CrossRefGoogle Scholar
  9. Guichoux, E., L. Lagache, S. Wagner, P. Chaumeil, P. Léger, O. Lepais, C. Lepoittevin, T. Malausa, E. Revardel, F. Salin & R. J. Petit, 2011. Current trends in microsatellite genotyping. Molecular Ecology Resources 11: 591–611.CrossRefGoogle Scholar
  10. Hann, J., 1984. Influence of temperature on life-history characteristics of two sibling species of Eurycercus (Cladocera, Chydoridae). Canadian Journal of Zoology 63: 891–898.CrossRefGoogle Scholar
  11. Ishida, S. & D. J. Taylor, 2007. Quaternary diversification in a sexual Holarctic zooplankter, Daphnia galeata. Molecular Ecology 16: 569–582.CrossRefGoogle Scholar
  12. Keller, B. & P. Spaak, 2004. Nonrandom sexual reproduction and diapausing egg production in a Daphnia hybrid species complex. Limnology and Oceanography 49: 1393–1400.CrossRefGoogle Scholar
  13. Keller, B., J. Wolinska, C. Tellenbach & P. Spaak, 2007. Reproductive isolation keeps hybridizing Daphnia species distinct. Limnology and Oceanography 52: 984–991.CrossRefGoogle Scholar
  14. Kerfoot, W. C. & L. J. Weider, 2004. Experimental paleoecology (resurrection ecology): chasing Van Valen’s Red Queen hypothesis. Limnology and Oceanography 49: 1300–1316.CrossRefGoogle Scholar
  15. Lack, J. B., L. J. Weider & P. D. Jeyasingh, 2017. Whole genome amplification and sequencing of a Daphnia resting egg. Molecular Ecology Resources. Scholar
  16. Ma, X., J. Wolinska, A. Petrusek, S. Gießler, W. Hu & M. Yin, 2016. The phenotypic plasticity in Chinese populations of Daphnia similoides sinensis: recurvate helmeted forms are associated with the presence of predators. Journal of Plankton Research 38: 855–864.CrossRefGoogle Scholar
  17. Ma, X., W. Hu, P. Smilauer, M. Yin & J. Wolinska, 2019. Daphnia galeata and D. dentifera are geographically and ecologically separated whereas their hybrids occur in intermediate habitats: survey of 44 Chinese lakes. Molecular Ecology 28: 785–802.CrossRefGoogle Scholar
  18. Mergeay, J., D. Verschuren, L. Van Kerckhoven & L. De Meester, 2004. Two hundred years of a diverse Daphnia community in Lake Naivasha (Kenya): effects of natural and human-induced environmental changes. Freshwater Biology 49: 998–1013.CrossRefGoogle Scholar
  19. Monchamp, M. E., J. C. Walser, F. Pomati & P. Spaak, 2016. Sedimentary DNA reveals cyanobacteria community diversity over 200 years in two peri-alpine lakes. Applied and Environmental Microbiology 82: 6472–6482.CrossRefGoogle Scholar
  20. Monchamp, M.-E., I. Enache, P. Turko, F. Pomati, G. Rîşnoveanu & P. Spaak, 2017. Sedimentary and egg-bank DNA from 3 European lakes reveal concurrent changes in the composition and diversity of cyanobacterial and Daphnia communities. Hydrobiologia 800: 155–172.CrossRefGoogle Scholar
  21. Montero-Pau, J., A. Gómez & J. Muñoz, 2008. Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs. Limnology and Oceanography: Methods 6: 218–222.Google Scholar
  22. Möst, M., S. Oexle, S. Markova, D. Aidukaite, L. Baumgartner, H. B. Stich, M. Wessels, D. Martin-Creuzburg & P. Spaak, 2015. Population genetic dynamics of an invasion reconstructed from the sediment egg bank. Molecular Ecology 24: 4074–4093.CrossRefGoogle Scholar
  23. Orsini, L., K. Schwenk, L. De Meester, J. K. Colbourne, M. E. Pfrender & L. J. Weider, 2013. The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments. Trends in Ecology & Evolution 28: 274–282.CrossRefGoogle Scholar
  24. Ortells, R., A. Gómez & M. Serra, 2003. Coexistence of cryptic rotifer species: ecological and genetic characterisation of Brachionus plicatilis. Freshwater Biology 48: 2194–2202.CrossRefGoogle Scholar
  25. Palero, F., S. Hall, P. F. Clark, D. Johnston, J. Mackenzie-Dodds & S. Thatje, 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina 74: 465–470.CrossRefGoogle Scholar
  26. Parducci, L., T. Jorgensen, M. M. Tollefsrud, E. Elverland, T. Alm, S. L. Fontana, K. D. Bennett, J. Haile, I. Matetovici, Y. Suyama, M. E. Edwards, K. Andersen, M. Rasmussen, S. Boessenkool, E. Coissac, C. Brochmann, P. Taberlet, M. Houmark-Nielsen, N. K. Larsen, L. Orlando, M. T. Gilbert, K. H. Kjaer, I. G. Alsos & E. Willerslev, 2012. Glacial survival of boreal trees in northern Scandinavia. Science 335: 1083–1086.CrossRefGoogle Scholar
  27. Rusek, J., G. Ayan, P. Turko, C. Tellenbach, S. Giessler, P. Spaak & J. Wolinska, 2015. New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data. Journal of Plankton Research 37: 626–635.CrossRefGoogle Scholar
  28. Spaak, P. & J. R. Hoekstra, 1995. Life history variation and the coexistence of a Daphnia hybrid with its parental species. Ecology 76: 553–564.CrossRefGoogle Scholar
  29. Spaak, P. & B. Keller, 2004. No evidence for adaptive micro-evolution to a decrease in phosphorus-loading of a Daphnia population inhabiting a pre-alpine lake. Hydrobiologia 526: 15–21.CrossRefGoogle Scholar
  30. Thermofischer, 2000. ABI PRISM® SNaPshot™ Multiplex Kit.
  31. Thielsch, A., E. Voelker, R. H. S. Kraus & K. Schwenk, 2012. Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia. Molecular Ecology Resources 12: 697–705.CrossRefGoogle Scholar
  32. Weider, L. J., P. D. Jeyasingh & D. Frisch, 2018. Evolutionary aspects of resurrection ecology: progress, scope, and applications–An overview. Evolutionary Applications 11: 3–10.CrossRefGoogle Scholar
  33. Wolinska, J., K. Bittner, D. Ebert & P. Spaak, 2006. The coexistence of hybrid and parental Daphnia: the role of parasites. Proceedings of the Royal Society B-Biological Sciences 273: 1977–1983.CrossRefGoogle Scholar
  34. Yin, M., J. Wolinska & S. GießLer, 2010. Clonal diversity, clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex. Molecular Ecology 19: 4168–4178.CrossRefGoogle Scholar

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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