Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each b...

The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete morphological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (II) optimized by ML onto each of a Bayesian sample of trees; and (II...

The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for e...

For parsimony analysis of the edge length represent the observed number of changes. Reconstructiong ancestral states therefore defines also the edge lengths of a tree. However there can exist several equally parsimonious reconstructions or states can be ambiguous and therefore edge length can differ. ”MPR” reconstructs the ancestral states for each (internal) node as if the tree would be rooted...

Most of the eukaryotic protein-coding genes are interrupted by multiple introns. A substantial fraction of introns occupy the same position in orthologous genes from distant eukaryotes, such as plants and animals, and consequently are inferred to have been inherited from the common ancestor of these organisms. In contrast to these conserved introns, many other introns appear to have been gained...

Evolution is a historical process that has left its signature on the molecules and morphology of living organisms. Attempts to better understand the specific and general features of evolution involve making inferences about the past from these tell-tale signs (Felsenstein, 1985; Brooks and McLennan, 1991; Harvey and Pagel, 1991; Pagel, 1999). Ancestral state reconstruction is a powerful tool in...

The ancestral sequence reconstruction problem asks to predict the DNA or protein sequence of an ancestral species, given the sequences of extant species. Such reconstructions are fundamental to comparative genomics, as they provide information about extant genomes and the process of evolution that gave rise to them. Arguably the best method for ancestral reconstruction is maximum likelihood est...

Reconstruction of ancestral genomic features can be considered on multiple evolutionary scopes and at different levels of biological sequence information. For instance, one could anticipate the reconstruction of genomic features for the last common ancestor of all species on Earth, last universal common ancestor or LUCA, whereas others would focus on reconstructing these features in the last co...

Despite progresses in ancestral protein sequence reconstruction, much needs to be unraveled about the nature of the putative last common ancestral proteome that served as the prototype of all extant lifeforms. Here, we present data that indicate a steady decline (oil escape) in proteome hydrophobicity over species evolvedness (node number) evident in 272 diverse proteomes, which indicates a hig...

Contemporary inferences about evolution occasionally involve analyzing infinitely large feature spaces, requiring specific algorithmic techniques. We consider parsimony analysis over numerical characters, where knowing the feature values at terminal taxa allows one to infer ancestral features, namely, by minimizing the total number of changes on the edges using continuous-valued distance measur...