Illustration of methods. A. A phylogeny of the species we used with internal branches labeled. B. An element (green) and repeats (blue) within a 750 kb window. C. Constrained and unconstrained models. For each branch of the phylogeny, the element and the repeats are constrained to be proportional to each other. S is a tree wide scaling factor which accounts for the fact that elements vary in their general level of conservation (i.e. throughout the tree). The unconstrained model is the same as the constrained model, except that for whatever branch we are interested in (here the human terminal branch) we have added another variable F, which allows the element branch to be longer. We calculate the likelihood of the data under these two models. D. The constant of proportionality for each branch is based on the whole genome ratio between element and repeats for a particular branch.
Bush and Lahn BMC Evolutionary Biology 2008 8:17 doi:10.1186/1471-2148-8-17