Fig. 1.

Overview of the methodological improvements to robustly estimate gene-family founder events. A Relative gene ages are inferred based on the principles of genomic phylostratigraphy, where each gene of the focal species is compared against a sequence database to find the most distantly related homolog. However, gene age inferences should also take into account the presence or absence of homologs throughout all the intermediate nodes between the focal species and the most distant homolog to distinguish putative gene losses from putative genome contaminations and horizontal gene transfer events. B Gene age inferences based on homology alone are expected to reflect the same founder event for other related genes. Thus, the age inferences of all loci in a gene family should not be regarded as independent values, but as a single evolutionary event. This compensates for the limited traceability of some paralogs within a gene family, whose ages are corrected as the oldest reliable age assignment in the family. C The estimated bitscore decay of genes as a function of evolutionary distance can be used to predict the expected bitscore of homologs in distantly related taxa where the gene has not been found. This prediction enables the calculation of homology detection failure (HDF) probabilities, which acts as a test to determine if a gene's absense beyond its most distantly related homolog can be attributed to HDF (the expected bitscore falls below the detectability threshold) or a gene-family founder event