Function divergence after gene duplication has been considered to be an important mechanism for the evolution of new functions. Although gene expression profiles have been treated as an important indicator of gene function, large scale gene expression analysis has mostly focused on current relationships among genes, instead of their evolutionary relationships. By putting expression analysis int...

The problem of ancestral sequence reconstruction is the statistical inference of sequences that correspond to internal nodes in a phylgenetic tree [1]. Joint reconstruction is the task of seeking the most likely set of ancestral states corresponding to all the ancestral taxa, while marginal reconstruction aims at inferring the sequence in a specific internal node. In simple probabilistic models...

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rates become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the recons...

Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-microbe symbioses individually. Yet new phylogenetic predictive methods can use the wealth of accumulated data on diverse model organisms to ma...