Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

• DOI: 10.1073/pnas.0806251106
• Publication Date: 2009-03-20T00:53:07Z
• Authors: Örjan Åkerborg; Bengt Sennblad; Lars Arvestad; Jens Lagergren
• Keywords: Tree (set theory)

We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and relaxed molecular clock for substitution rates, that enables genomewide analysis of families. The duplication loss process is major cause incongruence between species tree, deterministic methods have been developed to explain such differences through tree reconciliations. Although phylogenetic inference around decades, reconciliation are far less established. Based on our model, we implemented Bayesian tool, PrIME-GSR, takes known into account. Our implementation sound demonstrate its utility gene-family by applying it recently presented yeast data. validate PrIME-GSR comparing with previous analyses these data take advantage order information. In case study apply method the ADH family able draw biologically relevant conclusions concerning duplications creating key phenotypes. On higher level this shows biological relevance method. obtained results value clock. good performance will extend where conservation insufficient.