Integrating sequence evolution into probabilistic orthology analysis

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...

直系同源分析（Orthology analysis）旨在甄别一对同源基因究竟是源自物种形成事件的直系同源基因（ortholog），还是源自基因重复事件的旁系同源基因（paralog），该分析在计算生物学、基因组注释以及系统发育推断领域均具有核心重要性。尤为关键的是，直系同源关系可高度预示两个基因具备功能等价性。当前主流的直系同源分析策略多通过将基因树与对应物种树进行调和来实现，其中最常用的便是最简约调和法（most parsimonious reconciliation, MPR）。然而，绝大多数此类系统发育直系同源分析方法在推断基因树时，并未考虑物种树所蕴含的约束条件；且更为重要的是，此类方法仅能通过预先重建的基因树，让基因序列对直系同源分析产生影响。我们提出了一种严谨全面的基于贝叶斯马尔可夫链蒙特卡罗（Bayesian Markov chain Monte Carlo）的方法DLRSOrthology，用于计算直系同源概率，其可高效枚举所有可能的……