Surveys of Phylogenetic Footprints in Large Gene Clusters

Gene regulatory regions in noncoding genomic sequences are subject to stabilizing selection and therefore evolve much slower than adjacent non-functional DNA. The resulting phylogenetic footprints can be detected by comparison of the sequences surrounding orthologous genes in different species [8]. Experimental evidence from a variety of sources shows that a major mode of developmental gene evolution is based on the modification of cis-regulatory elements. Therefore the loss and acquisition of conserved non-coding sequences in some lineages, but not others, provides evidence for the evolutionary modification of cis-regulatory elements.