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

Computation

Ashley I. Teufel²  Jing Zhao³  Malgorzata O’Reilly¹  Liang Liu³ 

[1] School of Mathematics and Physics, University of Tasmania, Hobart, TAS 7001, Australia;Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA; E-Mail:;Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; E-Mail:

关键词: gene duplication;    gene loss;    phylogeny;    gene tree/species tree reconciliation;    stochastic models;    birth/death processes;   

DOI  :  10.3390/computation2030112

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland.