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

Tomislav Domazet-Lošo, Anne Ruxandra Carvunis, M. Mar Albà, Martin Sebastijan Šestak, Robert Bakarić, Rafik Neme, Diethard Tautz, Yuseob Kim

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)843-856
Number of pages14
JournalMolecular Biology and Evolution
Volume34
Issue number4
DOIs
StatePublished - 1 Apr 2017

Keywords

  • BLAST
  • Gene age estimation
  • Genome analysis
  • Phylostratigraphy

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