The evolution of novel protein-coding genes from noncoding regions of the genome 
is one of the most compelling pieces of evidence for genetic innovations in 
nature. One popular approach to identify de novo genes is phylostratigraphy, 
which consists of determining the approximate time of origin (age) of a gene 
based on its distribution along a species phylogeny. Several studies have 
revealed significant flaws in determining the age of genes, including de novo 
genes, using phylostratigraphy alone. However, the rate of false positives in de 
novo gene surveys, based on phylostratigraphy, remains unknown. Here, I 
reanalyze the findings from three studies, two of which identified tens to 
hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered 
approach. Most putative de novo genes discovered in these investigations are no 
longer included in recently updated mouse gene sets. Using a combination of 
synteny information and sequence similarity searches, I show that ∼60% of the 
remaining 381 putative de novo genes share homology with genes from other 
vertebrates, originated through gene duplication, and/or share no synteny 
information with nonrodent mammals. These results led to an estimated rate of 
∼12 de novo genes per million years in mouse. Contrary to a previous study 
(Wilson BA, Foy SG, Neme R, Masel J. 2017. Young genes are highly disordered as 
predicted by the preadaptation hypothesis of de novo gene birth. Nat Ecol Evol. 
1:0146), I found no evidence supporting the preadaptation hypothesis of de novo 
gene formation. Nearly half of the de novo genes confirmed in this study are 
within older genes, indicating that co-option of preexisting regulatory regions 
and a higher GC content may facilitate the origin of novel genes.