Figure 3

Reconstruction of vertebrate posterior HoxD cluster evolution. A Dollo parsimony reconstruction of the evolution of HoxD cluster elements shows the ancestral presence of 16 conserved elements in jawed vertebrates. Divergence times of the species are taken from Alfaro et al. [73]. A schematic representation of the posterior HoxD cluster with correct relative distances is shown on the right. The human cluster is representative for placental mammals, except for the loss of footprint 14, which did not occur in other mammals. Potential ncRNAs are symbolized by orange ovals, putative cis-regulatory elements by blue ovals. Gain of elements is shown as full ovals, with the respective footprint number underneath, open ovals and bars represent the loss of a footprint and Hoxd gene, respectively. Ovals with dotted lines denote equivocal reconstruction of footprint 11, which is due to missing data in the chicken sequence. Gains and losses of footprints were not dated.