title: Integrating Sequence Evolution into Probabilistic Orthology Analysis.
abstract: Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and jointly takes into account the current gene tree, all possible reconciliations to the species tree, and the, typically strong, signal conveyed by the sequences. We compare our method with PrIME-GEM, a probabilistic orthology approach built on a probabilistic duplication-loss model, and MrBayesMPR, a probabilistic orthology approach that is based on conventional Bayesian inference coupled with MPR. We find that DLRSOrthology outperforms these competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts.
authors.affiliation: School of Computer Science and Communication, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden;
authors.forename: Ikram
authors.initials: I
authors.lastname: Ullah
authors.affiliation: Department of Numerical Analysis and Computer Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden;
authors.forename: Joel
authors.initials: J
authors.lastname: Sjöstrand
authors.affiliation: School of Computer Science and Communication, KTH Royal Institute of Technology, Stockholm, Sweden;
authors.forename: Peter
authors.initials: P
authors.lastname: Andersson
authors.affiliation: Atherosclerosis Research Unit, Dept. of Medicine, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden;
authors.forename: Bengt
authors.initials: B
authors.lastname: Sennblad
authors.affiliation: School of Computer Science and Communication, Science for Life Laboratory, Swedish e-Science Research Center (SeRC), KTH Royal Institute of Technology, Stockholm, Sweden; jensl@csc.kth.se.
authors.forename: Jens
authors.initials: J
authors.lastname: Lagergren
mesh_terms: D000465:Algorithms; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D010802:Phylogeny; D017385:Sequence Homology; D012984:Software
keywords: Comparative genomics; gene duplication; gene loss; orthology; paralogy; phylogenetics; probabilistic modeling; relaxed molecular clock; sequence evolution; tree realization; tree reconciliation