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Mol Biol Evol. 2017 Jan 12. pii: msw284. doi: 10.1093/molbev/msw284. [Epub ahead of print]

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution.

Author information

  • 1Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, 10002 Zagreb, Croatia
  • 2Catholic University of Croatia, Ilica 242, 10000 Zagreb, Croatia.
  • 3Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0687, United States.
  • 4Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Barcelona, Spain.
  • 5Catalan Institution for Research and Advanced Studies, Barcelona, Spain.
  • 6Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, 10002 Zagreb, Croatia.
  • 7Max-Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Plön, Germany.


Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11-15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.

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