Evolution__3rd_Edition

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(a)
A
(b)
2
1
B
C
Vertebrate
1
2
D
Insect
The hypothesis can be tested by the
shape of gene trees
3
A
B
C
D
Insect
Vertebrate
in invertebrates. Humans are thought to have about 30,000 genes, against 13,000 in
fruitflies and 19,000 in the worm Caenorhabditis elegans. These gene numbers alone,
however, do not refute Ohno’s hypothesis, because some genes could have been lost
after the two rounds of duplications. Gene numbers might have initially increased from
15,000 to 60,000, and then almost half the new genes may have been lost between then
and modern humans. A stronger test of Ohno’s 2R hypothesis can be made using the
shape of gene trees (Hughes 1999; Martin 1999; Section 15.11.5, p. 457, defines gene
trees) (Figure 19.2).
The test uses any gene that appears to contain four paralogs in vertebrate genomes,
but only a single copy in invertebrate genomes. If Ohno’s hypothesis is correct, these
genes will all have originated in the same two rounds of duplication at the origin of the
vertebrates and the resulting gene tree of the four will be symmetric (Figure 19.2a). In
fact, in the majority of four-paralog sets analyzed by Hughes and Martin, the gene trees
were not symmetric (Figure 19.2b). The evidence does not support the 2R hypothesis,
which is one of the main reasons why many biologists currently doubt whether the origin
of vertebrates was also the occasion of two great rounds of gene doubling.
Vertebrates do contain more genes than invertebrates, but the extra genes probably
evolved in a series of separate events in different gene families rather than in one or two
big polyploidizations. Supporters of the 2R hypothesis still exist, however. They note
that the tests performed so far are preliminary, and use only a small number of genes.
They think there may be life in the old hypothesis yet, and it will certainly continue to
be tested, as new evidence or methods become available.
The research program that we have looked at in this section is concerned to test
whether new taxonomic groups evolve by means of gene duplications. In general, it is
interesting to test what genomic events underlie events in morphological evolution. A
new group might evolve by gene duplication, or sequence evolution within a fixed
number of genes, or a mix of the two factors. Genome sequences can be used to find out.
19.4 Genome size can shrink by gene loss
CHAPTER 19 / Evolutionary Genomics 561
Figure 19.2
Testing the 2R hypothesis by gene tree shape. The 2R hypothesis
suggests that two rounds of whole genome duplication occurred
near the origin of the vertebrates. A, B, C, and D are four related
copies of a gene, and they originated at gene duplications
(numbered 1, 2, and 3). (a) If the 2R hypothesis is right, genes
that have four related copies in a vertebrate genome should have
a symmetric gene tree (1 and 2 correspond to the two wholegenome
duplications). (b) In principle, these four genes could
have many other gene tree shapes. For instance, if a gene initially
duplicates and then only one of the copies duplicates again, and in
turn only one of the new copies duplicates again. The result is four
related genes, but not by two whole-genome duplication events.
Some bacteria live inside the cells of other species, either as parasites or intracellular
symbionts. All such bacteria that have been appropriately studied share a common