#33 · Genomics

Rooting sensitivity, Potts-phylogeny coupling, and bounded coalescent inference

The common thread is the phylogenetic tree as the object of inference when gene histories, sequence states, or population lineages must be modelled jointly or compared. The triplet-based study evaluates how gene tree rooting, or its absence, affects species tree estimation with STELAR, benchmarked against ASTRAL on simulated and empirical data. PhyloPotts couples a Potts model of sequence dependence with phylogeny through a first-order approximation, reporting improved ancestral sequence reconstruction accuracy and an open-source BEAST 2 implementation. The bounded coalescent preprint instead treats effective population size trajectories as a point process, offering exact simulation and MCMC inference, and addresses population dynamics rather than tree comparison directly. What is new is explicit treatment of rooting sensitivity in triplet-based inference and the coupling of sequence-level Potts structure with phylogeny.