Using DNA from formaldehyde-preserved Daphnia to reconstruct past populations
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.
KeywordsAncient 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.
- 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
- 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
- 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
- Thermofischer, 2000. ABI PRISM® SNaPshot™ Multiplex Kit. https://tools.thermofisher.com/content/sfs/manuals/cms_041203.pdf