The vast store of sequence data now available in DNA databases has been a source of insight into evolutionary processes. Whole-genome sequences are also providing new information about how genomes evolve and the processes that shape the size, complexity, and organization of genomes.

GENE DUPLICATION New genes have evolved through the duplication of whole genes and their subsequent divergence. As we saw in Chapter 8, this process creates gene families: sets of genes that are similar in sequence but encode different products. For example, humans possess 13 different genes that encode globin molecules, which take part in oxygen transport (Figure 18.20). All of these genes have a similar structure, with three exons separated by two introns. They are assumed to have evolved through repeated duplication and divergence from a single globin gene in a distant ancestor. This ancestral gene is thought to have been most similar to the present-day myoglobin gene, and it was probably first duplicated to produce an α/β-globin precursor gene and the myoglobin gene. The α/β-globin gene then underwent another duplication to give rise to a primordial α-globin gene and a primordial β-globin gene. Subsequent duplications led to multiple α-globin and β-globin genes. Similarly, vertebrates contain four clusters of Hox genes, each cluster comprising from 9 to 11 genes. Hox genes play an important role in development.

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Some gene families include genes that are arrayed in tandem on the same chromosome; others are dispersed among different chromosomes. Gene duplication is a common occurrence in eukaryotic genomes; for example, about 5% of the human genome consists of duplicated segments.

Gene duplication provides a mechanism for the addition of new genes with novel functions. Once a gene has been duplicated, there are two copies of that gene, one of which is then free to change and potentially take on a new function. The extra copy of the gene may, for example, become active at a different time in development, or be expressed in a different tissue, or even diverge and encode a protein containing different amino acids. The most common fate of duplicate genes, however, is that one copy acquires a mutation that renders it nonfunctional and becomes a pseudogene. Pseudogenes are common in the genomes of complex eukaryotes; the human genome is estimated to contain as many as 20,000 pseudogenes.

WHOLE-GENOME DUPLICATION In addition to the duplication of individual genes, whole genomes of some organisms have been duplicated in the past. For example, a comparison of the genome of the yeast Saccharomyces cerevisiae with the genomes of other fungi reveals that S. cerevisiae, or one of its immediate ancestors, underwent a whole-genome duplication, which generated two copies of every gene. Many of the copies subsequently acquired new functions; others acquired mutations that destroyed their original function and then diverged into random DNA sequences.

Whole-genome duplication can take place through polyploidy. During their evolution, flowering plants have undergone a number of whole-genome duplications through polyploidy (see Section 6.4). While polyploidy is less common in animals, genetic evidence suggests that several whole-genome duplication events have occurred during animal evolution. In 1970, Susumu Ohno proposed that early vertebrates underwent two rounds of genome duplication. Called the 2R hypothesis, this idea has been controversial, but recent data from genome sequencing have provided support for it.

HORIZONTAL GENE TRANSFER Traditionally, scientists assumed that organisms acquire their genomes through vertical transmission—transfer through reproduction of genetic information from parents to offspring—and most phylogenetic trees assume vertical transmission of genetic information. Findings from DNA-sequence studies reveal that DNA sequences are sometimes transmitted by horizontal gene transfer, in which DNA is exchanged between individuals of different species (see Section 7.2). This process is especially common among bacteria, and there are a number of documented cases in which genes have been transferred from bacteria to eukaryotes. The extent of horizontal gene transfer among eukaryotic organisms is controversial, as there are few well-documented cases. Horizontal gene transfer can obscure phylogenetic relationships and make the reconstruction of phylogenetic trees difficult.