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Title: 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 novelty-free 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.  more » « less
Award ID(s):
1764269
PAR ID:
10328953
Author(s) / Creator(s):
; ;
Editor(s):
Malik, Harmit S.
Date Published:
Journal Name:
PLOS Biology
Volume:
18
Issue:
11
ISSN:
1545-7885
Page Range / eLocation ID:
e3000862
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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