Inference of natural selection from ancient DNA

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  • Marianne Dehasque
    Stockholm University
  • María C Ávila-Arcos
    International Laboratory for Human Genome Research (LIIGH), Mexico
  • David Díez‐del‐Molino
    Stockholm University
  • Matteo Fumagalli
    Imperial College London
  • Katerina Guschanski
    Uppsala University
  • Eline Lorenzen
    University of Copenhagen
  • Anna-Sapfo Malaspinas
    University of Lausanne
  • Tomas Marques-Bonet
    Barcelona Institute of Science and Technology
  • Michael D. Martin
    Norwegian University of Science and Technology
  • Gemma Murray
    University of Cambridge
  • Alexander S. T. Papadopulos
  • Nina Overgaard Therkildsen
    Cornell University
  • Daniel Wegmann
    Fribourg University
  • Love Dalén
    Swedish Museum of Natural History, Stockholm
  • Andrew Foote
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.

Keywords

  • Adaptation, ancient DNA, natural selection, paleogenomics, time series
Original languageEnglish
Pages (from-to)94-108
JournalEvolution Letters
Volume4
Issue number2
Early online date18 Mar 2020
DOIs
Publication statusPublished - Apr 2020

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