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Table 4 The models used to analyze the data from the 22 pairs of taxa from the Philippines ( M ), and a subset of nine of those pairs from the Islands of Negros and Panay ( M )

From: An improved approximate-Bayesian model-choice method for estimating shared evolutionary history

Model

Priors

M m s B a y e s

t∼D U{1,…,Y} τ∼U(0,34.64 [ 17.3 M G A]) θ A ∼U(0,0.01) θD1,θD2∼B e t a(1,1)×2×U(0,0.01) ζD1∼U(0,1) ζD2∼U(0,1)

M U n i f o r m

t∼D U{a(Y)} τ∼E x p(m e a n=10 [ 5 M G A]) θ A ∼E x p(m e a n=0.005) θD1∼E x p(m e a n=0.005) θD2∼E x p(m e a n=0.005)

 

ζD1∼B e t a(5,1) ζD2∼B e t a(5,1)

M D P P

t∼D P(χ∼G a m m a(1.5,18.1)) τ∼E x p(m e a n=10 [ 5 M G A]) θ A ∼E x p(m e a n=0.005) θD1∼E x p(m e a n=0.005)

 

θD2∼E x p(m e a n=0.005) ζD1∼B e t a(5,1) ζD2∼B e t a(5,1)

M DPP inform

t∼D P(χ ∼G a m m a(1.5,18.1)) τ ∼E x p(m e a n=6 [ 3 M G A]) θ A ∼E x p(m e a n=0.005) θD1 ∼E x p(m e a n=0.005)

 

θD2 ∼E x p(m e a n=0.005) ζD1∼B e t a(5,1) ζD2∼B e t a(5,1)

M DPP simple

t∼D P(χ∼G a m m a(1.5,18.1)) τ∼E x p(m e a n=10 [ 5 M G A]) θ A =θD1=θD2∼E x p(m e a n=0.005) ζD1=ζD2=1.0

M DPP

t∼D P(χ∼G a m m a(1.5,5.0)) τ∼E x p(m e a n=10 [ 5 M G A]) θ A ∼E x p(m e a n=0.005) θD1=θD2∼E x p(m e a n=0.005)

 

ζD1=ζD2=1.0

  1. In addition to the n −1 coalescent times, the M DPP simple has only a single θ parameter for each taxon pair. The remaining M models have three θ, two ζ D , and one τ B parameter. The distributions of divergence times are given in units of 4N C generations followed in brackets by units of millions of generations ago (MGA), with the former converted to the latter assuming a per-site rate of 1 × 10−8 mutations per generation. The M DPP model (and its M DPP ∘ counterpart that samples over ordered divergence models) has only two θ parameters (the descendant populations of each pair share the same θ parameter, and there are no bottleneck parameters).