Evolution__3rd_Edition

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Figure 19.1
The history of the human gene
set. The analysis is based on
protein-coding genes only. The
figure shows the percentage of
human genes that are shared
with other taxa. The fraction
of human genes that originated
on each branch is shown in
the tree, and the total percent
similarity of genes is shown
across the top. Thus, 32%
of modern human genes
originated after eukaryotes
diverged from prokaryotes (but
before animals diverged from
the rest of the eukaryotes), and
53% of human genes are shared
with all other eukaryotes. The
total at the top is approximately
equal to the sum of the
percentages in the tree up to
that branch (for example, 53%
at the top equals 21 + 32% in
the tree). Many modern human
genes originated by duplication
of ancestral genes. Thus, two
genes in humans may be similar
to one gene in yeast. If that gene
is absent from bacteria, both
the human genes are shown
as “originating” in the branch
between prokaryotes and
eukaryotes even though one of
the copies arose by duplication
later. Alternative splicing is
ignored. Non-protein-coding
genes and non-coding DNA
are excluded. From data in
International Human Genome
Sequencing Consortium
(2001).
Time (approx) (Myr)
500
1,500
2,000–2,500
3,500
1%
22%
CHAPTER 19 / Evolutionary Genomics 559
99% 75% 53% 21% % genes
Humans Vertebrates
Animals Eukaryotes
(non-vertebrates) (non-animals) Prokaryotes
shared with
humans
The history of our gene set, as described here, is very incomplete and uncertain. It is
incomplete because it is mainly based on comparisons with a small number of other
species, such as the mouse, fruitfly, worm, yeast, and Escherichia coli. The history will
become better known as the genomes of more species are sequenced, and we can compare
human DNA with DNA from a greater range of relatives. The history is also uncertain
for several reasons. The methods used to recognize genes in raw DNA sequence
data are subject to error. Genes may have been overlooked or wrongly compared. Also,
the analysis in Figure 19.1 takes no account of “alternative splicing” (Section 2.2, p. 24).
More than one protein can be read from a single gene, but the analysis considered only
one protein per gene.
Thirdly, homology was inferred from relative sequence similarity. A human protein
was taken to be a homolog of a protein in another species, if the human protein was
much more similar to that other protein than to randomly picked proteins. For conserved,
slowly evolving genes this criterion should give accurate, if approximate,
results. But for genes that have evolved steadily over time, the results may be misleading.
For instance, humans share a more recent common ancestor with all eukaryotes
then with all prokaryotes. A gene in a prokaryote has been evolving away from us
for longer, and may be less likely to be recognized as a homolog of a human gene, than a
gene in a eukaryote. For this reason, the fraction of genes shown as homologous in
Figure 19.1 could be biased by the technique used to recognize homologies. However,
improved criteria of homology can be developed, together with other improvements
in methods and data. We should then be able to flesh out the currently skeletal history
of human DNA.
19.3 The history of duplications can be inferred in a genomic
sequence
24%
Genomes, as a whole or in part, change size during evolution by means of duplications
and deletions (Section 2.5, p. 30). A duplication or deletion will initially be rare in
the population; it may arise as a unique mutation. Its frequency may then increase by
natural selection or random drift. Once a duplication or deletion has spread through
32%
21%