title: A generalized birth and death process for modeling the fates of gene duplication.
abstract: BACKGROUND
  Accurately estimating the timing and mode of gene duplications along the evolutionary history of species can provide invaluable information about underlying mechanisms by which the genomes of organisms evolved and the genes with novel functions arose. Mechanistic models have previously been introduced that allow for probabilistic inference of the evolutionary mechanism for duplicate gene retention based upon the average rate of loss over time of the duplicate. However, there is currently no probabilistic model embedded in a birth-death modeling framework that can take into account the effects of different evolutionary mechanisms of gene retention when analyzing gene family data.
  
  
  RESULTS
  In this study, we describe a generalized birth-death process for modeling the fates of gene duplication. Use of mechanistic models in a phylogenetic framework requires an age-dependent birth-death process. Starting with a single population corresponding to the lineage of a phylogenetic tree and with an assumption of a clock that starts ticking for each duplicate at its birth, an age-dependent birth-death process is developed by extending the results from the time-dependent birth-death process. The implementation of such models in a full phylogenetic framework is expected to enable large scale probabilistic analysis of duplicates in comparative genomic studies.
  
  
  CONCLUSIONS
  We develop an age-dependent birth-death model for understanding the mechanisms of gene retention, which allows a gene loss rate dependent on each duplication event. Simulation results indicate that different mechanisms of gene retentions produce distinct likelihood functions, which can be used with genomic data to quantitatively distinguish those mechanisms.
authors.affiliation: Department of Statistics, University of Georgia, 101 Cedar Street, Athens, GA, 30602, USA. jingzhao@uga.edu.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA. ateufel@uwyo.edu.|Center for Computational Genetics and Genomics and Department of Biology, Temple University, Philadelphia, PA, 19122, USA. ateufel@uwyo.edu.
authors.forename: Ashley I
authors.initials: AI
authors.lastname: Teufel
authors.affiliation: Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA. daliberles@temple.edu.|Center for Computational Genetics and Genomics and Department of Biology, Temple University, Philadelphia, PA, 19122, USA. daliberles@temple.edu.
authors.forename: David A
authors.initials: DA
authors.lastname: Liberles
authors.affiliation: Department of Statistics, University of Georgia, 101 Cedar Street, Athens, GA, 30602, USA. lliu@uga.edu.|Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA. lliu@uga.edu.
authors.forename: Liang
authors.initials: L
authors.lastname: Liu
mesh_terms: D003198:Computer Simulation; D019143:Evolution, Molecular; D020440:Gene Duplication; D023281:Genomics / Q000379:methods; D016013:Likelihood Functions; D015233:Models, Statistical; D010802:Phylogeny