Toward Reducing Phylostratigraphic Errors and Biases

Abstract

Phylostratigraphy is a method for estimating gene age, usually applied to large numbers of genes in order to detect nonrandom age-distributions of gene properties that could shed light on mechanisms of gene origination and evolution. However, phylostratigraphy underestimates gene age with a nonnegligible probability. The underestimation is severer for genes with certain properties, creating spurious age distributions of these properties and those correlated with these properties. Here we explore three strategies to reduce phylostratigraphic error/bias. First, we test several alternative homology detection methods (PSIBLAST, HMMER, PHMMER, OMA, and GLAM2Scan) in phylostratigraphy, but fail to find any that noticeably outperforms the commonly used BLASTP. Second, using machine learning, we look for predictors of error-prone genes to exclude from phylostratigraphy, but cannot identify reliable predictors. Finally, we remove from phylostratigraphic analysis genes exhibiting errors in simulation, which by definition minimizes error/bias if the simulation is sufficiently realistic. Using this last approach, we show that some previously reported phylostratigraphic trends (e.g., younger proteins tend to evolve more rapidly and be shorter) disappear or even reverse, reconfirming the necessity of controlling phylostratigraphic error/bias. Taken together, our analyses demonstrate that phylostratigraphic errors/biases are refractory to several potential solutions but can be controlled at least partially by the exclusion of error-prone genes identified via realistic simulations. These results are expected to stimulate the judicious use of error-aware phylostratigraphy and reevaluation of previous phylostratigraphic findings.