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dc.contributor.authorJames, J.E.
dc.contributor.authorNelson, P.G.
dc.contributor.authorMasel, J.
dc.date.accessioned2024-08-12T01:34:56Z
dc.date.available2024-08-12T01:34:56Z
dc.date.issued2023-03-22
dc.identifier.citationJennifer E James, Paul G Nelson, Joanna Masel, Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends, Molecular Biology and Evolution, Volume 40, Issue 4, April 2023, msad073, https://doi.org/10.1093/molbev/msad073
dc.identifier.issn0737-4038
dc.identifier.pmid36947137
dc.identifier.doi10.1093/molbev/msad073
dc.identifier.urihttp://hdl.handle.net/10150/674067
dc.description.abstractProtein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition. © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
dc.language.isoen
dc.publisherOxford University Press
dc.rights© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
dc.rights.urihttps://creativecommons.org/ licenses/by/4.0/
dc.subjectclade selection
dc.subjectCope's rule
dc.subjectgene families
dc.subjectintrinsic structural disorder
dc.subjectphylostratigraphy
dc.subjectprotein evolution
dc.subjectprotein folding
dc.titleDifferential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends
dc.typeArticle
dc.typetext
dc.contributor.departmentDepartment of Ecology & Evolutionary Biology, University of Arizona
dc.identifier.journalMolecular Biology and Evolution
dc.description.noteOpen access article
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
dc.eprint.versionFinal Published Version
dc.source.journaltitleMolecular Biology and Evolution
refterms.dateFOA2024-08-12T01:34:56Z


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© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
Except where otherwise noted, this item's license is described as © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).