{
  "abstract": "Comparative genomics has traditionally relied on sequence-based markers, yet the global evolutionary landscape of protein architecture remains largely unexplored. We present the Structural History of Eukarya (SHE), a structural similarity-derived phylogeny from all-vs-all structural comparisons on the proteome level of 1542 eukaryotic species, encompassing nearly 300 trillion pairwise protein alignments. This proteome-scale analysis reveals a bipartite model of eukaryotic evolution: a rigid Strict Core dominated by cytoskeletal architecture, supporting a more plastic Operational Engine centered on translational machinery. We identify lineage-specific accelerations of structural evolution in species such as birds and ants that are decoupled from proteome expansion. Finally, we demonstrate that proteome-wide structural fidelity enables the functional annotation of uncharacterized proteins and a data-driven framework for model organism selection, replacing heuristic choices with quantitative matching to human biological processes. SHE is freely accessible as an interactive portal.",
  "abstract_shown": true,
  "affiliations": [
    "The Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Svante Arrhenius väg 20C, 114 18 Stockholm.",
    "Science for Life Laboratory, Solna 171 65, Sweden."
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  "author_total": 3,
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      "name": "Diandra Daumiller",
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      "name": "Qiuzhen Li",
      "orcid": "0009-0009-2913-4786"
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    {
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        1
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      "name": "Patrick Bryant",
      "orcid": "0000-0003-3439-1866"
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  "doi": "10.1126/sciadv.aeh2524",
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  "pmcid": "PMC13715714",
  "pmid": "42950045",
  "published": "2026-10-28",
  "publisher": "American Association for the Advancement of Science (AAAS)",
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  "subjects": [
    {
      "field": "biology",
      "origin": "heading:Computational Biology",
      "subfield": "bioinformatics"
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  "title": "The structural history of Eukarya",
  "title_text": "The structural history of Eukarya",
  "type": "peer-reviewed",
  "updated_at": "2026-11-01T12:22:56Z",
  "url": "https://research.draconitic.com/paper/3rzyrsp12tdzr",
  "venue": "Science Advances",
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}