title: Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.
abstract: BACKGROUND
  The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.
  
  
  RESULTS
  We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.
  
  
  CONCLUSIONS
  In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.
authors.affiliation: Institute of Informatics, Warsaw University, Warsaw 02-097, Poland. gorecki@mimuw.edu.pl
authors.forename: Pawel
authors.initials: P
authors.lastname: Górecki
authors.forename: Gordon J
authors.initials: GJ
authors.lastname: Burleigh
authors.forename: Oliver
authors.initials: O
authors.lastname: Eulenstein
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D019143:Evolution, Molecular; D020440:Gene Duplication; D049810:Genetic Speciation; D016678:Genome; D023281:Genomics / Q000379:methods; D016013:Likelihood Functions; D010802:Phylogeny; D012984:Software