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

Caroline M Weisman, Andrew W Murray and Sean R Eddy

PLOS Biology, 2020, vol. 18, issue 11, 1-24

Abstract: 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.Lineage-specific gene families may arise from evolutionary innovations such as de novo gene origination, or may simply mean that a similarity search program failed to identify more distant homologs. A new computational method for modeling the expected decay of similarity search scores with evolutionary distance allows distinction between the two explanations.

Date: 2020
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Citations: View citations in EconPapers (3)

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Persistent link: https://EconPapers.repec.org/RePEc:plo:pbio00:3000862

DOI: 10.1371/journal.pbio.3000862

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