A Generalized Birth and Death Process for Modeling the Fates of Gene Duplication

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Presented at 2015 ICSA symposium


Several biological models have been proposed to depict the mechanisms that lead to different evolutionary fates of a gene duplicate. In this paper, we develop a probabilistic model for understanding the duplication/loss process under 4 different mechanisms of gene retention (nonfunctionalization, neofunctionalization, subfunctionalization, and dosage balance), which can produce distinct patterns for the loss rate of a duplicate over time. The probabilistic model for duplication times is based on the reconstruction process with a timedependent death rate that varies across 4 different mechanisms. We have derived the conditional density function of duplication times, given the first duplication time and the number of gene copies at the present time. The conditional density function can be used to simulate duplication times under different mechanisms for a fixed number of gene copies at the present time. The likelihood function for duplication times can be used to find the maximum likelihood estimates of model parameters. Duplication times simulated from different mechanisms exhibit distinct patterns, indicating that the proposed probabilistic model can be used to reveal the underlying mechanism that drives the process of gene duplication and loss during the history of a gene family.


2015 ICSA symposium


Fort Collins, CO

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