Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

Gene duplication is an important process in the functional divergence of genes and genomes. Several processes have been described that lead to duplicate gene retention over different timescales after both smaller-scale events and whole-genome duplication, including neofunctionalization, subfunctiona...

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Main Authors:	Konrad, Anke, Teufel, Ashley I., Grahnen, Johan A., Liberles, David A.
Format:	Online
Language:	English
Published:	Oxford University Press 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205605/

id	pubmed-3205605
recordtype	oai_dc
spelling	pubmed-32056052011-11-01 Toward a General Model for the Evolutionary Dynamics of Gene Duplicates Konrad, Anke Teufel, Ashley I. Grahnen, Johan A. Liberles, David A. Research Articles Gene duplication is an important process in the functional divergence of genes and genomes. Several processes have been described that lead to duplicate gene retention over different timescales after both smaller-scale events and whole-genome duplication, including neofunctionalization, subfunctionalization, and dosage balance. Two common modes of duplicate gene loss include nonfunctionalization and loss due to population dynamics (failed fixation). Previous work has characterized expectations of duplicate gene retention under the neofunctionalization and subfunctionalization models. Here, that work is extended to dosage balance using simulations. A general model for duplicate gene loss/retention is then presented that is capable of fitting expectations under the different models, is defined at t = 0, and decays to an orthologous asymptotic rate rather than zero, based upon a modified Weibull hazard function. The model in a maximum likelihood framework shows the property of identifiability, recovering the evolutionary mechanism and parameters of simulation. This model is also capable of recovering the evolutionary mechanism of simulation from data generated using an unrelated network population genetic model. Lastly, the general model is applied as part of a mixture model to recent gene duplicates from the Oikopleura dioica genome, suggesting that neofunctionalization may be an important process leading to duplicate gene retention in that organism. Oxford University Press 2011-09-12 /pmc/articles/PMC3205605/ /pubmed/21920903 http://dx.doi.org/10.1093/gbe/evr093 Text en © The Author(s) 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Konrad, Anke Teufel, Ashley I. Grahnen, Johan A. Liberles, David A.
spellingShingle	Konrad, Anke Teufel, Ashley I. Grahnen, Johan A. Liberles, David A. Toward a General Model for the Evolutionary Dynamics of Gene Duplicates
author_facet	Konrad, Anke Teufel, Ashley I. Grahnen, Johan A. Liberles, David A.
author_sort	Konrad, Anke
title	Toward a General Model for the Evolutionary Dynamics of Gene Duplicates
title_short	Toward a General Model for the Evolutionary Dynamics of Gene Duplicates
title_full	Toward a General Model for the Evolutionary Dynamics of Gene Duplicates
title_fullStr	Toward a General Model for the Evolutionary Dynamics of Gene Duplicates
title_full_unstemmed	Toward a General Model for the Evolutionary Dynamics of Gene Duplicates
title_sort	toward a general model for the evolutionary dynamics of gene duplicates
description	Gene duplication is an important process in the functional divergence of genes and genomes. Several processes have been described that lead to duplicate gene retention over different timescales after both smaller-scale events and whole-genome duplication, including neofunctionalization, subfunctionalization, and dosage balance. Two common modes of duplicate gene loss include nonfunctionalization and loss due to population dynamics (failed fixation). Previous work has characterized expectations of duplicate gene retention under the neofunctionalization and subfunctionalization models. Here, that work is extended to dosage balance using simulations. A general model for duplicate gene loss/retention is then presented that is capable of fitting expectations under the different models, is defined at t = 0, and decays to an orthologous asymptotic rate rather than zero, based upon a modified Weibull hazard function. The model in a maximum likelihood framework shows the property of identifiability, recovering the evolutionary mechanism and parameters of simulation. This model is also capable of recovering the evolutionary mechanism of simulation from data generated using an unrelated network population genetic model. Lastly, the general model is applied as part of a mixture model to recent gene duplicates from the Oikopleura dioica genome, suggesting that neofunctionalization may be an important process leading to duplicate gene retention in that organism.
publisher	Oxford University Press
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205605/
_version_	1611484819254935552

Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

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