Journal
PLOS BIOLOGY
Volume 18, Issue 11, Pages -Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pbio.3000862
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Funding
- Howard Hughes Medical Institute investigator award
- NIH [RO1-GM43987]
- NSF-Simons Center for the Mathematical and Statistical Analysis of Biology (NSF) [1764269, 594596]
- FAS Division of Science, Research Computing Group at Harvard University
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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.
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