Many, but not all, lineage-specific genes can be explained by homology detection failure

Genes for which homologs can be detected only in a limited group of evolutionarily

related species, called “lineage-specific genes,” are pervasive: essentially every

lineage has them, and they often comprise a sizable fraction of the group’s total genes.

Lineage-specific genes are often interpreted as “novel” genes, representing genetic

novelty born anew within that lineage. Here, we develop a simple method to test an

alternative null hypothesis: that lineage-specific genes do have homologs outside of

the lineage that, even while evolving at a constant rate in a novelty-free manner, have

merely become undetectable by search algorithms used to infer homology. We show

that this null hypothesis is sufficient to explain the lack of detected homologs of a large

number of lineage-specific genes in fungi and insects. However, we also find that a

minority of lineage-specific genes in both clades are not well-explained by this noveltyfree

model. The method provides a simple way of identifying which lineage-specific

genes call for special explanations beyond homology detection failure, highlighting

them as interesting candidates for further study.