T HE EvoluTion of GEnEs And GEnomEs 365
Supercompact genomes have evolved in the world’s most abundant organisms
by yet another route [3]. Every milliliter of seawater near the surface of temperate
and tropical oceans around the world has some 10^6 cells of a planktonic bacterium
called Pelagibacter ubique. With only 1 Mb of DNA and fewer than 1500 genes, it
has the smallest genome of any free-living bacterium known [21]. Nothing about
it is superfluous: it has no introns, no transposons, no pseudogenes. Pelagibacter’s
population size worldwide is some 10^28 cells (more than 1 million times the num-
ber of stars in the universe!), so drift in this species is weak. In contrast to Buch-
nera, the streamlined genome of Pelagibacter appears to be the product of adap-
tation, likely to the very low nutrient levels in its environment. By paring down
its genome, the bacterium has reduced its need for the nitrogen and phosphorus
needed to replicate the DNA. The tiny genome also allows the cell size to be min-
iaturized, which may be a further advantage to Pelagibacter.
Animals and plants live at the other end of the genomic spectrum, with large
numbers of genes and vast amounts of DNA. Much of the variation in gene num-
ber in eukaryotes results from whole genome duplication. You saw earlier in this
chapter that bread wheat has nearly 100,000 genes, or about five times more than
we do. The ancestor of wheat had some 25,000 genes. During domestication, its
genome then doubled in size, not once but twice, by allopolyploidy [10]. If the
wheat follows the evolutionary path taken by many other plants, we can anticipate
that most of the duplicate genes will eventually be lost by deletion or become
pseudogenes, and ultimately the wheat’s gene number will decline to a level more
typical of flowering plants. The total size of the genome can also shrink by dele-
tion. This outcome has occurred many times independently in the crucifers (Bras-
sicaceae) [46].
What explains the large scatter in the DNA content of eukaryotes? As in the
prokaryotes, there is a trend for species with more genes to have larger genomes,
but the correlation is much weaker (see Figure 14.18). Whole genome duplication is
one factor at work. A second is the evolution of noncoding DNA driven by the pro-
liferation of transposable elements. A third major player in the evolution of genome
size may be random genetic drift. Animals and plants are much bigger than free-
living microbes, and as a result have much smaller population sizes. Their reduced
population size makes natural selection less efficient (see Chapter 7). If the dele-
tion of a segment of noncoding DNA produces a fitness benefit but the effect is
small relative to the strength of drift, selection will be largely powerless to slim
down the genomes of animals and plants [44].
Does that mean the 98 percent of our own genome that is noncoding is actu-
ally junk? We are still far from having a clear answer to this fundamental ques-
tion. Although much of our DNA originated as transposable elements, some of the
resulting “junk” now plays key roles in regulating gene expression, and the cell’s
metabolism has coevolved with the total quantity of DNA in the nucleus. Those
factors may diminish the selective benefit of deletions that eliminate noncod-
ing DNA. Like an addict and his drug, eukaryotes may not be able to break their
dependence on a bloated genome. But there is also good news in this story. When
ancient eukaryotes acquired large amounts of noncoding DNA, it opened up new
options for the evolution of gene regulation. That, in turn, may have enabled the
origin of complex life forms, including ourselves.
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