Figure 1. Overview of the Phylo-HMGP model.

(A) Example of the state space and state transition probabilities of the Phylo-HMGP model associated with the continuous genomic data in (C). S_i represents a hidden state. Each hidden state is determined by a phylogenetic model ψ_i, which is parameterized by the selection strengths α_i, Brownian motion intensities σ_i, and the optimal values θ_i of ancestor species and observed species on the corresponding phylogenetic tree. α_i, σ_i, and θ_i are all vectors. (B) Illustration of the Ornstein-Uhlenbeck (OU) processes along the species tree specified in (C). X(t) represents the continuous trait at time t. The trajectories of different colors along time correspond to the evolution of the continuous trait in different lineages specified by the corresponding colors in (C), respectively. The time points t₁, t₂, t₃, and t₄ represent the speciation time points, which correspond to the speciation events shown in (C). The observations of the five species also represent an example of state S₂ in (C). (C) Simplified representation of input and output of the Phylo-HMGP model. The five tracks of continuous signals represent the observations from five species. S_i represents the underlying hidden states. Specifically, the example is the replication timing data, where ‘early’ and ‘late’ represent the early and late stages of replication timing, respectively. The species tree alongside the continuous data tracks shows the evolutionary relationships among the five species in this study. See also Figure S2, Figure S8, and Figure S9.