Runt Gene Evolution Figure 1. Phylogenetic tree (Bayesian inference) of chordate Runt genes. Numbers refer to branch support (Bayesian posterior probability) for the internal branches adjacent to the nodes. Sea urchin Runt genes were used to root the tree. Branch length reflects the number of substitutions per alignment site (compare scale bar). doi:10.1371/journal.pgen.1000025.g001 common ancestor of jawed vertebrates harboured three Runt genes. In addition our results indicate that the dogfish ScRunx1–3 genes are orthologous to the Amniota Runx1–3 genes. In contrast to this, the two hagfish Runt genes did not cluster with any of the three paralogous Runt genes from higher vertebrates. As outlined in Figure 2 several lineage specific Runt gene duplications have occurred: (a) in the sea urchin lineage, (b) in the stem species of bony fish and (c) probably also in hagfish. But there is a need for further data e.g. from whole genome comparison, to determine if the two hagfish Runt genes are a result of a Runt gene duplication in the stem species of vertebrates or evolved by a separate gene duplication event in the hagfish lineage. PLoS Genetics | www.plosgenetics.org 3 March 2008 | Volume 4 | Issue 3 | e1000025