Figure 4–62 A representation of the nucleotide sequence content of the sequenced human genome. The lINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), retroviral-like elements, and DNA-only transposons are mobile genetic elements that have multiplied in our genome by replicating themselves and inserting the new copies in different positions. These mobile genetic elements are discussed in Chapter 5 (see Table 5–3, p. 267). Simple sequence repeats are short nucleotide sequences (less than 14 nucleotide pairs) that are repeated again and again for long stretches. Segmental duplications are large blocks of DNA sequence (1000–200,000 nucleotide pairs) that are present at two or more locations in the genome. The most highly repeated blocks of DNA in heterochromatin have not yet been completely sequenced; therefore about 10% of human DNA sequences are not represented in this diagram. (Data courtesy of E. margulies.) showing the relationship between 1.5 humans and the great apes based on nucleotide sequence data. As indicated, the sequences of the genomes of all four millions of years before present species are estimated to differ from the sequence of the genome of their last common ancestor by a little over 1.5%. because changes occur independently on both diverging lineages, pairwise comparisons reveal twice the sequence divergence from the last common ancestor. For example, human–orangutan comparisons typically show sequence 1.0 0.5 0.0 divergences of a little over 3%, while that have kept the sequences the same. Evidence for this view comes from the observation that the human and chimpanzee genomes are nearly identical even where there is no functional constraint on the nucleotide sequence—such as in the third position of “synonymous” codons (codons specifying the same amino acid but differing in their third nucleotide).
For much less closely related organisms, such as humans and chickens (which have evolved separately for about 300 million years), the sequence conservation found in genes is almost entirely due to purifying selection (that is, selection that eliminates individuals carrying mutations that interfere with important genetic functions), rather than to an inadequate time for mutations to occur.
Phylogenetic Trees Constructed from a Comparison of DNA Sequences Trace the Relationships of All Organisms
Phylogenetic trees based on molecular sequence data can be compared with the fossil record, and we get our best view of evolution by integrating the two approaches. The fossil record remains essential as a source of absolute dates, human–chimpanzee comparisons show divergences of approximately 1.2%. (modified from F.C. Chen and w.H. li,  Am. J. Hum. Genet. 68:444–456, 2001.)
Figure 4–64 Tracing the ancestral sequence from a sequence comparison of the coding regions of human and chimpanzee leptin genes. Reading left to right and top to bottom, a continuous gene is illustrated. leptin is a hormone that regulates food intake and energy utilization in response to the adequacy of 300-nucleotide segment of a leptin-coding fat reserves. As indicated by the codons boxed in green, only 5 nucleotides (of 120 441 total) differ between the two species.
moreover, in only one of the five positions does the difference in nucleotide lead to a difference in the encoded amino acid. For each of the five variant nucleotide positions, the corresponding sequence in the gorilla is also indicated. In two cases, sequence, while in three cases it agrees with the chimpanzee sequence.