On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene RetentionReport as inadecuate




On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention - Download this document for free, or read online. Document in PDF available to download.

1

Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA

2

Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA

3

School of Mathematics and Physics, University of Tasmania, Hobart, TAS 7001, Australia





*

Authors to whom correspondence should be addressed.



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. View Full-Text

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





Author: Ashley I. Teufel 1, Jing Zhao 2, Malgorzata OReilly 3,* , Liang Liu 2,* and David A. Liberles 1,*

Source: http://mdpi.com/



DOWNLOAD PDF




Related documents