A complete DNA sequence reveals both the genes an organism possesses and the genes it lacks. When we compare the three domains of the living world, we can begin to see which genes are common to all of them and must therefore have been present in the cell that was ancestral to all present-day living things, and which genes are peculiar to a single branch in the tree of life. To explain the findings, however, we need to consider a little more closely how new genes arise and genomes evolve.
The raw material of evolution is the DNA sequence that already exists: there is no natural mechanism for making long stretches of new random sequence. In this sense, no gene is ever entirely new. Innovation can, however, occur in several ways (Figure 1–19): 1.
Intragenic mutation: an existing gene can be randomly modified by changes in its DNA sequence, through various types of error that occur mainly in the process of DNA replication.
2.
Gene duplication: an existing gene can be accidentally duplicated so as to create a pair of initially identical genes within a single cell; these two genes may then diverge in the course of evolution.
3.
DNA segment shuffling: two or more existing genes can break and rejoin to make a hybrid gene consisting of DNA segments that originally belonged to separate genes.
4.
Horizontal (intercellular) transfer: a piece of DNA can be transferred from the genome of one cell to that of another—even to that of another species. This process is in contrast with the usual vertical transfer of genetic information from parent to progeny.
Each of these types of change leaves a characteristic trace in the DNA sequence of the organism, and there is clear evidence that all four processes have frequently
Figure 1–18 Genetic information conserved since the days of the last common ancestor of all living things.
A part of the gene for the smaller of the two main rRnA components of the ribosome is shown. (The complete molecule is about 1500–1900 nucleotides long, depending on species.) corresponding segments of nucleotide sequence from an archaean (Methanococcus jannaschii), a bacterium (Escherichia coli), and a eukaryote (Homo sapiens) are aligned. sites where the nucleotides are identical between species are indicated by a vertical line; the human sequence is repeated at the bottom of the alignment so that all three two-way comparisons can be seen. A dot halfway along the E. coli sequence denotes a site where a nucleotide has been either deleted from the bacterial lineage in the course of evolution or inserted in the other two lineages. note that the sequences from these three organisms, representative of the three domains of the living world, still retain unmistakable similarities.
occurred. In later chapters, we discuss the underlying mechanisms, but for the present we focus on the consequences.
Gene duplications Give Rise to Families of Related Genes Within a single cell
A cell duplicates its entire genome each time it divides into two daughter cells. However, accidents occasionally result in the inappropriate duplication of just part of the genome, with retention of original and duplicate segments in a single cell. Once a gene has been duplicated in this way, one of the two gene copies is free to mutate and become specialized to perform a different function within the same cell. Repeated rounds of this process of duplication and divergence, over many millions of years, have enabled one gene to give rise to a family of genes that may all be found within a single genome. Analysis of the DNA sequence of prokaryotic genomes reveals many examples of such gene families: in the bacterium Bacillus subtilis, for example, 47% of the genes have one or more obvious relatives (Figure 1–20).