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

View ORCID ProfileCaroline M. Weisman, View ORCID ProfileAndrew W. Murray, View ORCID ProfileSean R. Eddy
doi: https://doi.org/10.1101/2020.02.27.968420
Caroline M. Weisman
1Department of Molecular & Cellular Biology, Harvard University, Cambridge MA, USA
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Andrew W. Murray
1Department of Molecular & Cellular Biology, Harvard University, Cambridge MA, USA
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Sean R. Eddy
1Department of Molecular & Cellular Biology, Harvard University, Cambridge MA, USA
2Howard Hughes Medical Institute, Harvard University, Cambridge MA, USA
3John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge MA, USA
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  • For correspondence: seaneddy@fas.harvard.edu
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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.

Footnotes

  • http://github.com/caraweisman/abSENSE

  • http://eddylab.org/abSENSE

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 28, 2020.
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Many but not all lineage-specific genes can be explained by homology detection failure
Caroline M. Weisman, Andrew W. Murray, Sean R. Eddy
bioRxiv 2020.02.27.968420; doi: https://doi.org/10.1101/2020.02.27.968420
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Many but not all lineage-specific genes can be explained by homology detection failure
Caroline M. Weisman, Andrew W. Murray, Sean R. Eddy
bioRxiv 2020.02.27.968420; doi: https://doi.org/10.1101/2020.02.27.968420

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