Refining the evolutionary time machine: an assessment of whole genome amplification using single historical Daphnia eggs

Christopher James O’Grady, Vignesh Dhandapani, John K. Colbourne, Dagmar Frisch*

*Corresponding author for this work

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Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.

Original languageEnglish
Number of pages16
JournalMolecular ecology resources
Early online date20 Oct 2021
Publication statusPublished - 20 Oct 2021

Bibliographical note

Funding Information:
D.F. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie grant agreement No. 658714 and NERC Biomolecular Analysis Facility Pilot Project Grant NBAF998. C.O.G. received funding from the Midlands Integrative Biosciences Training Partnership (MIBTP). We are grateful to Stephen Kissane for preparation and sequencing of SE libraries, and to Caroline Sewell for supplying ephippia from the facility, University of Birmingham. PE library preparation and sequencing were carried out by Edinburgh Genomics, the University of Edinburgh, which is partly supported with core funding from NERC (UKSBS PR18037). D. magna Daphnia

Publisher Copyright:
© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.


  • ancient DNA
  • Daphnia
  • population genomics
  • SNP analysis
  • whole genome sequencing

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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