Insight into the last eukaryotic common ancestor (LECA) is central to any phylogeny-based reconstruction of early eukaryotic evolution. Increasing amounts of data enable such reconstructions, without necessarily providing further insight into what LECA actually was. We consider four possible concepts of LECA: an abstract phylogenetic state, a single cell, a population, and a consortium of organisms. We argue that the view most realistically underlying work in the field is that of LECA as a population. Drawing on recent findings of genomically heterogeneous populations in eukaryotes (‘pangenomes’), we examine the evolutionary implications of a pangenomic LECA population. For instance, how does this concept affect standard expectations about the ecology, geography, fitness, and diversification of LECA? Does it affect evolutionary interpretations of LECA’s cellular functions? Finally, we examine whether this novel pangenomic concept of LECA has implications for phylogenetic reconstructions of early eukaryote evolution. Our aim is to add to the conceptual toolkit for developing theories of LECA and interpreting genomic datasets.

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We gratefully acknowledge S. Muñoz-Gómez for several thoughtful discussions and the inspiration for Fig. 2. We also thank W. F. Doolittle and A. J. Roger for insightful comments on earlier drafts of this paper. For views on the conceptual continuum of LECA, we are grateful to anonymous attendees at the 2017 EMBO workshop on Comparative Genomics of Eukaryotic Microbes, and members of the Dalhousie University Centre for Comparative Genomics and Evolutionary Bioinformatics. M.A.O.’s research is supported by the French government via the ‘Investments for the future’ Programme, IdEx Bordeaux (ANR-10-IDEX-03-02). M.M.L. is supported by a Marie Skłodowska-Curie Individual Fellowship under the EU Framework Programme for Research and Innovation Horizon 2020 (Project ID 747789). J.G.W. was supported by a College for Life Sciences Fellowship at the Wissenschaftskolleg zu Berlin. I.R.-T. was supported by a European Research Council Consolidator Grant (ERC-2012-Co -616960) grant and funding (BFU2017-90114-P) from Ministerio de Economía y Competitividad (MINECO), Agencia Estatal de Investigación (AEI), and Fondo Europeo de Desarrollo Regional (FEDER).

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Author notes

  1. These authors contributed equally: Maureen A. O’Malley, Michelle M. Leger.


  1. LaBRI, University of Bordeaux, Talence, France

    • Maureen A. O’Malley
  2. HPS, University of Sydney, Sydney, New South Wales, Australia

    • Maureen A. O’Malley
  3. Institute of Evolutionary Biology, UPF-CSIC Barcelona, Barcelona, Spain

    • Michelle M. Leger
    •  & Iñaki Ruiz-Trillo
  4. Wissenschaftskolleg zu Berlin, Berlin, Germany

    • Jeremy G. Wideman
  5. Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

    • Jeremy G. Wideman
  6. Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain

    • Iñaki Ruiz-Trillo
  7. ICREA, Barcelona, Spain

    • Iñaki Ruiz-Trillo


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All authors jointly conceived and wrote the paper.

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Correspondence to Maureen A. O’Malley or Iñaki Ruiz-Trillo.

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