Identifying Single Copy Orthologs in Metazoa
Figure 2
Gene tree reconciliation process.
Reconciling a gene tree with a (guide) species tree. A) Given the species tree on the left, we need to estimate the most parsimonious number of duplications and losses that explain the topology and distribution of the gene tree (on the right). In order to assess correctly the number of duplications and losses, we need to find the best rooting of the gene tree. To this end, the gene tree is rooted at every possible position, and for each rooting, the most parsimonious number of duplications and losses is calculated. The rooting that requires the fewest number of steps (duplications and losses) is considered the most parsimonious rooting of the gene tree. For example: the reconciliations for two possible rootings are shown: positions X and Y in panes B) and C). The positions of duplication events are indicated with a diamond, losses are indicated with a dashed line. B) Rooting the gene tree at position X in B) requires duplication and two losses, while rooting at position Y in C) requires 1 duplication and 1 loss. Of the two rootings, position Y is the most parsimonious. The numbers on the internal branches indicate the internal branch of the species tree in A)that they are mapped to. If we were trying to identify single copy genes at the hierarchical level of internal branch 2 on the species tree, then the sub-tree marked with a * in C) would represent a gene family that has been in single copy since this hierarchical level.