  Gene innovation is a key mechanism on the evolution and phenotypic diversity
of life forms. There is a need for tools able to study gene innovation across
an increasingly large number of genomic sequences to maximally capitalise our
understanding of biological systems. Here we present
Comparative-Phylostratigraphy, an open-source software suite that enables to
time the emergence of new genes across evolutionary time and to correlate
patterns of gene emergence with species traits simultaneously across whole
genomes from multiple species. Such a comparative strategy is a new powerful
tool for starting to dissect the relationship between gene innovation and
phenotypic diversity. We describe and showcase our method by analysing recently
published ant genomes. This new methodology identified significant bouts of new
gene evolution in ant clades, that are associated with shifts in life-history
traits. Our method allows easy integration of new genomic data as it becomes
available, and thus will be a valuable analytical tool for evolutionary
biologists interested in explaining the evolution of diversity of life at the
level of the genes.
