Some parts of the genome will change more easily than others in the course of evolution. A segment of DNA that does not code for protein and has no significant regulatory role is free to change at a rate limited only by the frequency of random errors. In contrast, a gene that codes for a highly optimized essential protein or RNA molecule cannot alter so easily: when mistakes occur, the faulty cells are almost always eliminated. Genes of this latter sort are therefore highly conserved. Through 3.5 billion years or more of evolutionary history, many features of the genome have changed beyond all recognition, but the most highly conserved genes remain perfectly recognizable in all living species.
Figure 1–17 The three major divisions (domains) of the living world. note that the word bacteria was originally used to refer to prokaryotes in general, but more recently has been redefined to refer to eubacteria specifically. The tree shown here is based on comparisons of the nucleotide sequence of a ribosomal RnA (rRnA) subunit in the different species, and the distances in the diagram represent estimates of the numbers of evolutionary changes that have occurred in this molecule in each lineage (see Figure 1–18). The parts of the tree shrouded in gray cloud represent uncertainties about details of the true pattern of species divergence in the course of evolution: comparisons of nucleotide or amino acid sequences of molecules other than rRnA, as well as other arguments, can lead to somewhat different trees. As indicated, the nucleus of the eukaryotic cell is now thought to have emerged from a sub-branch within the archaea, so that in the beginning the tree  of life had only two branches—bacteria and archaea.
GTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCC human GCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTTAAAGGAATTGGCGGGGGAGCACTACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGCATCTTACCA Methanococcus ACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGC.ACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCT E. coli GTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCC human
These latter genes are the ones we must examine if we wish to trace family relationships between the most distantly related organisms in the tree of life. The initial studies that led to the classification of the living world into the three domains of bacteria, archaea, and eukaryotes were based chiefly on analysis of one of the rRNA components of the ribosome. Because the translation of RNA into protein is fundamental to all living cells, this component of the ribosome has been very well conserved since early in the history of life on Earth (Figure 1–18).
Natural selection has generally favored those prokaryotic cells that can reproduce the fastest by taking up raw materials from their environment and replicating themselves most efficiently, at the maximal rate permitted by the available food supplies. Small size implies a large ratio of surface area to volume, thereby helping to maximize the uptake of nutrients across the plasma membrane and boosting a cell’s reproductive rate.
Presumably for these reasons, most prokaryotic cells carry very little superfluous baggage; their genomes are small, with genes packed closely together and minimal quantities of regulatory DNA between them. The small genome size has made it easy to use modern DNA sequencing techniques to determine complete genome sequences. We now have this information for thousands of species of bacteria and archaea, as well as for hundreds of species of eukaryotes. Most bacterial and archaeal genomes contain between 106 and 107 nucleotide pairs, encoding 1000–6000 genes.