Biology Reference
In-Depth Information
This study focused on differences between paralogs, due to dupli-
cation. However, it is worth noting that we also found differences
between orthologs. For example, both zebrafish and Xenopus RAR
γ
transactivate with both the
-specific retinoids (as established
in mammals), and indeed have one amino acid in helix H3 that is iden-
tical to mammalian RAR
α
- and
γ
51
A more general con-
sideration of nuclear receptors shows that functional differences
between orthologs are not rare when distant organisms are compared.
For example, vertebrate Rev-erbs are orphan receptors involved in
circadian cycle regulation;
52
but E75, their insect ortholog (Fig. 1), is
a heme receptor involved in ecdysone regulation.
53
Thus, function
may change not only after duplication, but also between species
(see also Markov
et al
.
54
).
α
, but not to RAR
γ.
2.2.3. Biased gene loss after whole-genome duplication
After whole-genome duplication, duplicate copies of genes may evolve in
different manners, gaining or losing functions (reviewed in Semon and
Wolfe
55
). But the most common fate is certainly loss of one of the copies.
Although this may not seem very exciting in itself, the contrast between
which genes are lost and which ones are kept as duplicates has emerged
as one of the most important features of whole-genome duplication. The
rate of gene loss has been estimated at 88% in about 80 million years
since genome duplication in yeasts,
20
86 million years in
Arabidopsis
,
56
and 79% in about 61-67 million years in cereals.
23
By com-
paring only genes that were mapped to chromosomes in the fish
Tetraodon
and in humans, and whose evolutionary fate could be deter-
mined by phylogenetic analysis, we obtained a figure of 85% of gene loss
after whole-genome duplication in teleost fishes,
57
despite the greater age
of the event. These similar figures are best explained if most losses occur
rapidly after duplication,
58
so that subsequent evolution does not change
the figure significantly.
In an important study, Davis and Petrov
59
showed that slowly evolv-
ing genes are more likely to be found duplicated. The bias is similar in
yeast and in nematodes, and is maintained over evolutionary time, indicat-
ing that gene retention was also biased after the whole-genome duplication
70% in
≤
