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

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  • Caroline M Weisman
  • Andrew W Murray
  • Sean R Eddy

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.

Suggested Citation

  • Caroline M Weisman & Andrew W Murray & Sean R Eddy, 2020. "Many, but not all, lineage-specific genes can be explained by homology detection failure," PLOS Biology, Public Library of Science, vol. 18(11), pages 1-24, November.
  • Handle: RePEc:plo:pbio00:3000862
    DOI: 10.1371/journal.pbio.3000862
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    Cited by:

    1. Erik Wright, 2024. "Accurately clustering biological sequences in linear time by relatedness sorting," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Pedro Patraquim & Emile G. Magny & José I. Pueyo & Ana Isabel Platero & Juan Pablo Couso, 2022. "Translation and natural selection of micropeptides from long non-canonical RNAs," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Junhui Peng & Li Zhao, 2024. "The origin and structural evolution of de novo genes in Drosophila," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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