Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

Abstract

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

Fig. 1.

The figure illustrates the example presented in the text. In A, a gene tree, thin black, is shown as evolving inside a discretized species tree. The edges discussed in the text are marked by arrows. Vertices in S are marked by gray ellipses, while the vertices augmented to form S′ are marked by thin horizontal lines. Two gene tree vertices have been introduced in order to break gene tree edges that pass species tree vertex X. Each of these vertices are in the reconciliation placed on X and has a child placed on Y but not on Z. In both cases, this indicates a loss in the species lineage leading to Z. In B, the tree is cut into the sliced subtrees discussed in the text.