 
Summary: 1
2008 by The University of Chicago. All rights reserved.DOI: 10.1086/527498
Appendix from P. A. Hohenlohe and S. J. Arnold, "MIPoD: A
HypothesisTesting Framework for Microevolutionary Inference from
Patterns of Divergence"
(Am. Nat., vol. 171, no. 3, p. 366)
Construction of the Phylogenetic Divergence Matrix
To further illustrate the construction of the phylogenetic divergence matrix A, we combine the G matrix shown
in figure 1A and the phylogeny shown in figure 2A. We thus have traits and taxa, so A will be am p 2 n p 3
6by6 matrix. First, the G matrix shown in figure 1A is parameterized by
S 5
p 0.6 , (A1)
J 0.8
so the 2by2 G matrix is
2.49 0.50
G p . (A2)
0.50 2.51
The matrix of shared ancestry T for the taxa x, y, and z is
t t t 1,000 200 200xx xy xz
T p t t t p 200 1,000 800 , (A3)yx yy yz
