Data from: Pleiotropy increases with gene age in six model multicellular eukaryotes

Fundamental traits of genes, including function, length, and GC content,
all vary with gene age. Pleiotropy, where a single gene affects multiple
traits, arises through selection for novel traits and is expected to be
removed from the genome through subfunctionalization following duplication
events. It is unclear, however, how these opposing forces shape the
prevalence of pleiotropy through time. We hypothesized that the prevalence
of pleiotropy would be lowest in young genes, peak in middle-aged genes,
and then either decrease to a middling level in ancient genes or stay near
the middle-aged peak, depending on the balance between exaptation and
subfunctionalization. To address this question, we have calculated gene
age and pleiotropic status for several model multicellular eukaryotes,
including Homo sapiens, Mus musculus, Danio rerio, Drosophila
melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana. Gene age
was determined by finding the most distantly related species that shared
an ortholog using the Open Tree of Life and the Orthologous Matrix
Database (OMAdb). Pleiotropic status was determined using both
protein-protein interactions (STRINGdb) and associated biological
processes (Gene Ontology). We found that middle-aged and ancient genes
tend to be more pleiotropic than young genes, and that this relationship
holds across all species evaluated and across both modalities of measuring
pleiotropy. We also found absolute differences in the degree of pleiotropy
based on gene functional class, but only when looking at the biological
process count. From these results, we propose that there is a fundamental
relationship between pleiotropy and gene age, and further study of this
relationship may shed light on the mechanism behind the functional changes
genes undergo as they age.