One of the greatest promises of modern genetics is the ability to identify loci responsible for, or at least highly correlated with, important physical traits and disease susceptibility. This will enable benefits ranging from improved disease risk assessment and crop design to ultimately a better understanding of how genotype variation effects variations in phenotypes. A key component in this t...

Accurate reconstruction of ancestral character states on a phylogeny is crucial in many genomics studies. We study how to select species to achieve the best reconstruction of ancestral character states on a phylogeny. We first show that the marginal maximum likelihood has the monotonicity property that more taxa give better reconstruction, but the Fitch method does not have it even on an ultram...

Optimal growth temperature is a complex trait involving many cellular components, and its physiology is not yet fully understood. Evolution of continuous characters, such as optimal growth temperature, is often modeled as a one-dimensional random walk, but such a model may be an oversimplification given the complex processes underlying the evolution of continuous characters. Recent articles hav...

Maximum-likelihood methods are used extensively in phylogenetic studies [3]. In particular, aminoacid sequences of ancestral species have been inferred using these methods [7]. Such ancestral reconstruction tasks aim at identifying either the most likely sequence in a specific ancestor species (marginal reconstruction), or the most likely set of ancestral states corresponding to all the ancestr...

Recent advances in the automation of metabolic model reconstruction have led to the availability of draft-quality metabolic models (predicted reaction complements) for multiple bacterial species. These reaction complements can be considered as trait representations and can be used for ancestral state reconstruction to infer the most likely metabolic complements of common ancestors of all bacter...