T HE EvoluTion of GEnEs And GEnomEs 363
genome, which is called Alu, is about 300 bp long (see Figure 12.12). Each of us has
more than a million copies of Alu that together make up more than 10 percent of
our genome [4]. Alu proliferates by making copies of itself: the DNA sequence is
transcribed into RNA, which is then reverse-transcribed into DNA and inserted
elsewhere in the genome.
Thus Alu and other TEs are parasites that work at the molecular level. They
reproduce not to improve the fitness of their host, but simply because they can.
By the nature of natural selection, any sequences that copy themselves more pro-
lifically than others will come to make up more of the genome. For this reason,
TEs are sometimes referred to as “selfish DNA” (see Chapter 12). The evolution-
ary origin of TEs is uncertain. One plausible hypothesis is that they are modified
viruses that evolved the ability to reproduce without leaving the cell. There are
two classes of TEs that differ in how they replicate (perhaps pointing to more than
one evolutionary origin). The Alu element is an example of a retrotransposon. Its
DNA is transcribed into RNA, but that molecule is then retrotranscribed into DNA
and reintegrated into the host’s genome. Like RNA viruses such as HIV, some
retrotransposons code for the reverse transcriptase that they need to retrotran-
scribe the RNA intermediate into DNA. But TEs such as Alu take parasitism to
the next level: they don’t make reverse transcriptase themselves, but instead use
the transcriptase made by other TEs and viruses. The second class of TE is DNA
transposons, which do not use an RNA intermediate in their life cycle. They are
much rarer in humans, in which they make up about 3 percent of the genome (see
Fig u re 14.14).
TEs can spread through a genome in an evolutionary epidemic, multiplying to
vast numbers over short periods of evolutionary time. Among species of Drosophila,
the fraction of the genome composed of TEs ranges by almost a factor of 10, from
3 percent to 25 percent [16]. The origin of a TE can be dated in two ways. The first
approach uses the divergence among different copies as a molecular clock (FIGURE
14.19). The second approach uses the age of the most recent common ancestor of
the species in which the TE is found. This phylogenetic approach suggests that
the Alu element infected primates about 65 Mya because it occurs only in primate
species that last shared a common ancestor at that time [4]. The molecular clock, in
contrast, suggests a much earlier origin (see Figure 14.19).
Like viruses, transposable elements are usually bad news for their host. The
insertion of a TE into the host’s genome causes a mutation that can disrupt aFutuyma Kirkpatrick Evolution, 4e
Sinauer Associates
Troutt Visual Services
Evolution4e_14.19.ai Date 02-02-2017Percent of genome200 150 100 50
Age (My)0.51.01.52.02.5L2 LTRMIRL1AluDNAFIGURE 14.19 Age distributions of transposable elements in the hu-
man genome. The graph shows the fraction of the current genome
that consists of TEs that inserted at a given time in the past. When a new
copy of a TE inserts, its sequence begins to diverge from that of other
copies. Copies that are more greatly diverged are therefore older, and
their ages can be estimated using a molecular clock (see Chapter 7). Age
distributions are shown for six different TEs: Alu elements, L1 and L2 long
interspersed nuclear elements (LINEs), mammalian interspersed repeats
(MIRs), long terminal repeats (LTRs), and DNA transposons (DNA). Alu
first infected the remote ancestors of humans about 175 Mya. They had
a burst of activity about 45 Mya, and about 2 percent of our genome is
now made up of Alu elements that inserted at that time. Lower activity
after then inserted additional copies. Taken together, the 1 million copies
of Alu now make up about 10 percent of our genome. By contrast, L1
elements had a protracted phase of proliferation much earlier, with a
second spike roughly 25 Mya. The total insertion rate of all TEs is indicat-
ed by the overall height of the plot: it reached a peak about 45 Mya and
is now much lower. (After [13].)14_EVOL4E_CH14.indd 363 3/22/17 2:44 PM