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Computation 2014, 2(3), 112-130; doi:10.3390/computation2030112
Article

On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention

1
, 2
, 3,* , 2,*  and 1,*
Received: 6 May 2014; in revised form: 29 July 2014 / Accepted: 14 August 2014 / Published: 28 August 2014
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)
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Abstract: Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models leads to a complex modeling problem. A discussion of the relationship between biological processes, existing models for duplicate gene retention and data is presented. Existing models are then extended in deriving two new birth/death models for phylogenetic application in a gene tree/species tree reconciliation framework to enable probabilistic inference of the mechanisms from model parameterization. The goal of this work is to synthesize a detailed discussion of modeling duplicate genes to address biological questions, moving from previous work to future trajectories with the aim of generating better models and better inference.
Keywords: gene duplication; gene loss; phylogeny; gene tree/species tree reconciliation; stochastic models; birth/death processes gene duplication; gene loss; phylogeny; gene tree/species tree reconciliation; stochastic models; birth/death processes
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Teufel, A.I.; Zhao, J.; O'Reilly, M.; Liu, L.; Liberles, D.A. On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention. Computation 2014, 2, 112-130.

AMA Style

Teufel AI, Zhao J, O'Reilly M, Liu L, Liberles DA. On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention. Computation. 2014; 2(3):112-130.

Chicago/Turabian Style

Teufel, Ashley I.; Zhao, Jing; O'Reilly, Malgorzata; Liu, Liang; Liberles, David A. 2014. "On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention." Computation 2, no. 3: 112-130.

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