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

Abstract

Phylostratigraphy is a computational framework for dating the emergence of sequences (usually genes) 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. These simulations called into question some of our previously published work on patterns of gene emergence and evolution inferred from phylostratigraphy. Here, we re-assessed these simulations and found major problems including unrealistic parameter choices, irreproducibility, statistical flaws and partial representation of results. We found that, even with a possible overall BLAST false negative rate between 5-15%, the large majority (>74%) 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 our previous findings, we repeated our analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support our published 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.