A generalized phylogenetic tree is shown, leading to four different organisms, with A and D the most distantly related pairs. Examples of the types of questions that can be addressed by comparisons between genomes at the different distances are given in the boxes.

The unc-52 gene in C. elegans (A) and part of its homolog HSPG2 in human (B) are shown, with rectangles for exons and lines for introns; arrows along the introns show the direction of transcription. Both genes encode a chondroitin sulfate proteoglycan. The gene in C. elegans is much smaller (about 29 kb) than the gene in humans (about 180 kb; only the 5′ portion is shown in [B]). The positions of alignments between C. elegans and C. briggsae are shown by the purple rectangles in (A). The probability that alignments between human and mouse result from purifying selection are plotted along the Human Cons track in (B). Note that in both comparisons, substantial amounts of intronic and flanking regions align, and several peaks of likely-selected DNA are seen for the human-mouse alignments in the noncoding regions. Among these are candidates for regulatory elements.