Detecting gene innovations for phenotypic diversity across multiple genomes

TL;DR

This paper introduces Comparative-Phylostratigraphy, a software tool that analyzes gene emergence across genomes to understand their role in phenotypic diversity, demonstrated through ant genome studies.

Contribution

It presents a novel comparative method and open-source software for timing gene emergence and linking it to phenotypic traits across multiple species.

Findings

Identified significant gene evolution events in ant lineages.

Linked gene emergence with shifts in life-history traits.

Enabled integration of new genomic data for evolutionary analysis.

Abstract

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.