Evolutionary diversification of ancestral genes across vertebrates and insects

Mantica, Federica; Irimia Martínez, Manuel

doi:http://dx.doi.org/10.1186/s13059-025-03699-z

Evolutionary diversification of ancestral genes across vertebrates and insects

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Mantica F, Irimia M. Evolutionary diversification of ancestral genes across vertebrates and insects. Genome Biol. 2025 Sep 4;26(1):268. DOI: 10.1186/s13059-025-03699-z

Abstract

Background: Vertebrates and insects diverged approximately 700 million years ago, and yet they retain a large core of conserved genes from their last common ancestor. These ancient genes present strong evolutionary constraints, which limit their overall sequence and expression divergence. However, these constraints can greatly vary across ancestral gene families and, in at least some cases, sequence and expression changes can have functional consequences. Importantly, overall patterns of sequence and expression divergence and their potential functional outcomes have never been explored in a genome-wide manner across large animal evolutionary distances. Results: We focus on approximately 7000 highly conserved genes shared between vertebrates and insects, and we investigate global patterns of molecular diversification driven by changes in sequence and gene expression. We identify molecular features generally linked to higher or lower diversification rates, together with gene groups with similar diversification profiles in both clades. Moreover, we discover that specific sets of genes underwent differential diversification during vertebrate and insect evolution, potentially contributing to the emergence of unique phenotypes in each clade. Conclusions: We generate a comprehensive dataset of measures of sequence and expression divergence across vertebrates and insects, which reveals a continuous spectrum of evolutionary constraints among highly conserved genes. These constraints are normally consistent between these two clades and are associated with specific molecular features, but in some cases we also identify instances of lineage-specific diversification likely linked to functional evolution.