Errors in DNA replication, DNA recombination, or DNA repair can lead either to simple local changes in DNA sequence—so-called point mutations such as the substitution of one base pair for another—or to large-scale genome rearrangements such as deletions, duplications, inversions, and translocations of DNA from one chromosome to another. In addition to these failures of the genetic machinery, genomes contain mobile DNA elements that are an important source of genomic change (see Table 5–3, p. 267). These transposable DNA elements (transposons) are parasitic DNA sequences that can spread within the genomes they colonize. In the process, they often disrupt the function or alter the regulation of existing genes. On occasion, they have created altogether novel genes through fusions between transposon sequences and segments of existing genes. Over long periods of evolutionary time, DNA transposition events have profoundly affected genomes, so much so that nearly half of the DNA in the human genome consists of recognizable relics of past transposition events (Figure 4–62). Even more of our genome is thought to have been derived from transpositions that occurred so long ago (>108 years) that the sequences can no longer be traced to transposons.
The genome Sequences of Two Species Differ in Proportion to the length of Time Since They Have Separately Evolved
The differences between the genomes of species alive today have accumulated over more than 3 billion years. Although we lack a direct record of changes over time, scientists can reconstruct the process of genome evolution from detailed comparisons of the genomes of contemporary organisms.
The basic organizing framework for comparative genomics is the phylogenetic tree. A simple example is the tree describing the divergence of humans from the great apes (Figure 4–63). The primary support for this tree comes from comparisons of gene or protein sequences. For example, comparisons between the sequences of human genes or proteins and those of the great apes typically reveal the fewest differences between human and chimpanzee and the most between human and orangutan.
For closely related organisms such as humans and chimpanzees, it is relatively easy to reconstruct the gene sequences of the extinct, last common ancestor of the two species (Figure 4–64). The close similarity between human and chimpanzee genes is mainly due to the short time that has been available for the accumulation of mutations in the two diverging lineages, rather than to functional constraints
TRANSPOSONS nonrepetitive DNA that is