Evolution__3rd_Edition

560 PART 5 / Macroevolution
Molecular clocks suggest
duplications occurred at certain
times in angiosperm evolution
Vertebrate origins may be
associated with genome
duplication
the population, the genome size of the species will have gone up or down. The genome
sequence of a modern species can be used to infer when duplications and deletions have
occurred in the past, and we can ask what evolutionary events are associated with
changes in the genome site.
For example, the genome sequence of the weed Arabidopsis thaliana was published
in December 2000. Arabidopsis is a common small weed, and is the main flowering
plant of genomic research. Vision et al. (2000) analyzed the Arabidopsis genome and
found a large number of blocks of genes that looked like duplicates: that is, one stretch
of DNA looked like a duplicate of another stretch of DNA in the same genome. The
duplications are not for single genes, or the whole genome, but for intermediate lengths
of DNA and contain several genes. Vision et al. concentrated on 103 blocks, each containing
seven or more genes. For each pair of duplicate blocks, they compared the
sequence of the two (paralogous) copies of each gene. They then used a molecular clock
inference to estimate the time when the duplication occurred.
Most of the duplications seem to date back to three periods, at 100, 140, and 170 million
years ago. Some of the duplications are older, perhaps 200 million years old. A few
of them are more recent, being about 50 million years old. The modern Arabidopsis
genome seems to reflect 3–5 major duplication periods in the past. These duplications
mainly occurred in the Mesozoic geological era, 100–200 million years ago, which was
a crucial time for the origin of the angiosperms. In Section 18.5 (p. 538), we saw that the
time of origin of the angiosperms is uncertain. However, the molecular clock suggests
that the dicotyledons split from monocotyledons about 180–210 million years ago. If
so, the earliest (200 million-year-old) duplications now visible in the Arabidopsis
genome may have originated at this time. In that case, one of the major breakthroughs
of angiosperm evolution a the origin of dicotyledons a would have been associated
with a round of increased gene numbers.
In summary, Vision et al. (2000) used the genome sequence of Arabidposis to identify
duplicated regions of DNA and the time when the duplications evolved. They suggested
some associations between these duplications and evolutionary events. The
association of the 200 million-year-old duplications and the origin of dicotyledons is
just one example. Their suggestions, however, are tentative and require more research.
The idea that duplications may be associated with the origin of a major group is an
example of the kind of hypothesis we can test, even if the test is at present rudimentary.
(Box 22.1, p. 624, will look at another association between gene duplication and an
evolutionary event a the origin of alcohol metabolism and the origin of fruit.)
We can now turn to another major evolutionary event that has been hypothesized to
be associated with gene duplications: the origin of the vertebrates. Ohno (1970) used
early measurements of the weight of DNA in several vertebrate and invertebrate species
to argue that the whole genome had duplicated twice near the origin of the vertebrates.
The vertebrate genomes were about four times the size of the invertebrate genomes in
Ohno’s sample. This is now sometimes called the “2R” hypothesis, named after the two
rounds of genome doubling. If gene numbers did increase fourfold at that time, the
extra genes might be part of the explanation for the origin of vertebrates. Ohno’s
hypothesis was relatively neglected until biologists noticed in the late 1980s that vertebrates
contain four sets of Hox genes, compared with a single set in the fruitfly. The
quadrupled Hox gene set seemed to fit Ohno’s hypothesis.
The total number of genes in vertebrates, however, is not four times the number
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