Figure 7.
Top panel: module representation of different tree priors with Ψ as a pivot node (note that Ψ denotes a time tree with edge lengths here, not simply a topology): a) Yule process (Yule 1925), b) constant rate birth–death process (Nee et al. 1994), c) decreasing speciation rate birth–death process [speciation rate: λ*exp(− αt), e.g., in Höhna (2014)] and d) Coalescent process (Kingman 1982). Bottom panel: different rate matrix modules with Q as a pivot node: e) Jukes–Cantor rate matrix where all exchangeability rates and all base frequencies are equal (Jukes and Cantor 1969), f) F81 rate matrix where all exchangeability rates are equal but the base frequencies are drawn from a Dirichlet distribution (Felsenstein 1981), g) T92 rate matrix with a parameter for the frequency of the GC content πGC and a transition-transversion rate (Tamura 1992) and h) HKY85 rate matrix with the base frequencies drawn from a Dirichlet distribution and an estimated transition-transversion rate (Hasegawa et al. 1985).