Download Gene duplication and divergence in the early evolution of

393
Gene duplication and divergence in the early evolution of vertebrates
Francoise Mazet* and Sebastian M Shimeld†
The duplication–degeneration–complementation model of
duplicate gene preservation by subfunctionalisation is currently
the best explanation for the high level of retention of duplicate
genes in early vertebrate evolution. But a direct test of the
applicability of this model to such ancient evolutionary events
may be difficult. More likely, recent duplications in other
lineages will allow us to establish general principles concerning
the fate of genes of different types that are duplicated in
different ways. These principles may be then extrapolated to
understanding the early evolution of the vertebrates.
Addresses
School of Animal and Microbial Sciences, University of Reading,
Whiteknights, Reading RG6 6AJ, UK
*e-mail: [email protected]
† e-mail: [email protected]
Current Opinion in Genetics & Development 2002, 12:393–396
0959-437X/02/$ — see front matter
© 2002 Elsevier Science Ltd. All rights reserved.
Abbreviation
DDC
duplication–degeneration–complementation
Introduction
Few authors doubt the prevalence of gene duplication in
the evolutionary history of the genomes of organisms of all
levels of biological organisation; the evidence, in the form of
multigene families in the genomes of individual organisms,
is overwhelming. But the importance of gene duplication
in evolutionary innovation, the degree and method of
duplicate gene preservation, and even the method of gene
duplication are all the subject of hotly contentious theories.
In this review we summarise some of these theories. In particular, we focus on the evolution of the vertebrates and on the
expansion during early vertebrate evolution of many of the
gene families that were involved in vertebrate development.
Maintenance of duplicated genes: why and how?
In some special cases it is easy to identify an adaptive advantage for organisms that possess multiple copies of a gene, for
example, the increased dosage of a protein that multiple
copies provide can protect individuals against pesticides (e.g.
see [1]). The importance of such short-term selective advantage should not be underestimated; however, a fundamental
assumption in most instances has been that for both daughter
genes of a duplication to be maintained by selection they
must in some way diverge. In particular it has been proposed
that duplication frees one copy from a requirement to maintain key functions, allowing it to evolve new functions [2];
such ‘neofunctionalisation’ could provide the genetic material for the evolution of new morphology — a process that could
be summarised as gene duplication → increased genetic complexity → increased morphological complexity (Figure 1a).
But as gene duplications take place within individuals within
populations, first we must assume that the duplicated allele
is neutral or immediately advantageous or it will be purged
from the population; second, for the above model of neofunctionalisation to occur, a gene duplication must evolve
new (i.e. divergent) functions and move to fixation in a population before one gene becomes a pseudogene. Selection
does not recognise ‘future potential’, and consequently the
classical model predicts a race between neofunctionalisation and pseudogene formation that should result in the
elimination of most duplicated genes.
Empirical evidence, however, does not support this
scheme but suggests that there is a much higher retention
of duplicate copies [3]. This seems to be a major paradox
that was turned upside-down by the duplication–degeneration–complementation (DDC) model, which takes into
account the multiple regulatory regions and the protein
structure domains of multiple genes [4••,5,6••]. This
model, in which functions are partitioned between daughter
genes (a process known as subfunctionalisation), has the
advantage of a firm foundation in population genetics, and
predicts in such cases that selection will act to maintain
both copies (Figure 1b). Consequently, the need for a
mutation to occur in the gene and confer a selectively
advantageous new phenotype is negated. At its extreme, the
DCC model suggests that a multifunctional state, and therefore
presumably some degree of complexity, must precede
duplication rather than follow it. It should be noted, however,
that although subfunctionalisation might be required for
initial duplicate maintenance, it is not incompatible with
subsequent neofunctionalisation (Figure 1c).
Gene duplication during early vertebrate
evolution
Do vertebrates have more genes than other animal taxa? The
number of predicted genes in the human genome, when
compared to the number in the sequenced genomes of
Drosophila and Caenorhabditis elegans, suggests that they do
[7,8]. But such comparisons should be treated with caution as
they assume that humans and Drosophila/C. elegans are representative of all vertebrates and invertebrates, respectively.
More informative are comparisons made with lineages that
diverged closer to the origin of vertebrates, such as ascidians,
which do support this interpretation as do surveys of
numerous individual gene families from amphioxus — the
closest living invertebrate to the vertebrates [9•,10]. Genes
that are involved in regulating development have been
especially well studied in this context, and most show
evidence of duplication that is specific to vertebrates
(Table 1). This degree of duplication has been proposed to
reflect genome duplication on the vertebrate stem — a
theory that is supported by the widespread occurrence
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Pattern formation and developmental mechanisms
Figure 1
A
(a) Degeneration
A
A
A
(b) Neofunctionalisation
(c) Subfunctionalisation
A
AC
A
AB
AB
A
AC
AB
B
BD
A
AB
Fates of duplicated genes. (a) The classical
model of degeneration of one copy after
duplication. (b) Neofunctionalisation, in which
initially identical duplicates with function A
diverge by acquiring new functions B and C.
(c) Subfunctionalisation, in which duplicate
genes with multiple functions A and B diverge
by reciprocal loss. The extension indicates the
possibility of subsequent neofunctionalisation
by acquisition of further functions C and D. It
is important to recognise that these models
are not mutually exclusive. It is likely that all
are correct to some degree and all occur to
some extent, but there may be variations
according to taxon, type of gene and type of
duplication. The important question is does
one model account for most of the preserved
duplications seen generally in nature or in
specific taxa?
Current Opinion in Genetics & Development
of paralogy in the human genome, but which has its
detractors [11,12].
Gene duplication, divergence and vertebrate evolution
Irrespective of the debate on the mode of duplication, it is
clear that vertebrates have more members of most ‘developmental’ gene families than do their closest relatives. It is
also clear that there is a correlation between the expansion
Table 1
Expansion during early vertebrate evolution for a selection
of gene families, and evidence for sub- or
neofunctionalisation.
Gene
family
Number of Number of Neofunctionalisation
amphioxus vertebrate and/or
genes
genes
subfunctionalisation References
Wnt8
1
2
Sub
[13]
Wnt1
1
1
NA
[26]
Wnt5
1
1
NA
[27]
Wnt3
1
2
?
[27]
Wnt7
1
2
?
[27]
Otx
1
2/3
Neo
[28]
Hh
1
3
Neo
[29]
HNF-3
1
3
?
[30]
Snail
1
3
Neo
[31]
Pax1/9 1
2
Neo
[32]
Hox
1
4
Neo
[33,34]
Pax3/7 1
2
Neo
[35]
Pitx
1
3
Sub + Neo
[36]
Dll
1 or 2
6
Neo
[37]
Sox1/2/3 1
3
Neo
[14]
Mnx
1
2
?
[38]
En
1
2
Neo
[39]
Islet
1
2
Neo
[40]
A question mark indicates that the evidence for either is
ambiguous. Please note this is our interpretation of the data and
does not necessarily reflect the views of the authors of each
publication. NA, not applicable.
of gene families and the complexity of the central nervous
system and other organ systems in vertebrates, at least with
respect to early vertebrate evolution. Development of the
vertebrate body plan requires the combinatorial action
of many genes and, notably, many vertebrate-specific
structures are marked by the expression of gene duplicates
(Table 1). Is there evidence here for the direct linking of
gene duplication with increasingly complex morphology?
If so, does it support one of the above theories in preference to the others?
Evidence for sub- and neofunctionalisation
To establish sub- and neofunctionalisation that is specific
to vertebrates, comparisons must be made between
vertebrate genes and those in their closest relatives, most
informatively in amphioxus. Many such studies have been
carried out in recent years on several gene families. Some
of these are listed in Table 1, together with our interpretation
of the pattern of evolution that they display.
Such comparisons reveal some indication of subfunctionalisation. A good example is the Wnt8 family, in which a
single gene in amphioxus possesses several domains of
expression that seem to have been subdivided between
the two vertebrate Wnt8 paralogues [13•]. But clear-cut
examples of subfunctionalisation are rare, with most gene
families instead showing evidence of neofunctionalisation.
A good example of this is the Sox1/Sox2/Sox3 family,
which in amphioxus is expressed only in the nervous
system — a site that we can deduce to be primitive by
comparison with expression in Drosophila [14]. In vertebrates, all three Sox genes are expressed in the central
nervous system and in some tissues that are presumed to
be vertebrate-specific, such as the epibranchial placodes
[15]. Other examples of such divergent multigene families
Gene duplication and divergence in the early evolution of vertebrates Mazet and Shimeld
in vertebrates are the Hedgehog, Engrailed, Pax1/Pax9
and Distalless families (Table 1).
Can we take the predominance of new functions in these
amphioxus/vertebrate gene family comparisons as evidence
in favour of neofunctionalisation over subfunctionalisation
in the early evolution of vertebrates, and consequently as
falsification of the DDC model? Our answer is we cannot.
First, with the available data we can only detect divergence
on the basis of expression, and not on the basis of evolutionary change of protein function. The latter is hard to test
experimentally, because it requires the ability to manipulate gene function in several taxa, although it may be
predicted perhaps by comparing rates of evolution in
different parts of the proteins of paralagous genes [16,17].
We also cannot rule out the possibility that neofunctionalisation followed subfunctionalisation. The evolutionary
separation between extant vertebrate and invertebrate
lineages is such that subtle subfunctionalisation may have
become obscured by subsequent change. Although examining the relative rates of evolution of paralogues has been
informative in the analysis of more recent duplications
[6••,18•,19•], it is unlikely that we will be able to use this
and more sophisticated molecular evolutionary analysis,
such as tests for adaptive evolution, to examine informatively early vertebrate evolution, principally owing to the
length of time of divergence. With this in mind, it may be
impossible to test definitively which process was most
significant in early vertebrate evolution.
An alternative approach is to examine similar, more recent
evolutionary events and extrapolate these findings to the
origin of vertebrates. For example, some lineages of teleost
fish have been found to possess duplicate copies of genes
that are present in single copy in other vertebrate lineages
and mapping data from zebrafish imply that this may have
resulted from a genome duplication, thereby presenting an
analogous situation to what occurred at the origin of vertebrates (though note this theory has its detractors) [20–22].
Comparison on a wide scale of the fates of these more
recently created paralagous genes will help to establish
general principles that can then be applied to vertebrate
origins. It is notable that some recent studies provide
strong evidence for subfunctionalisation of duplicate genes
in fish [23,24], whereas others suggest the evolution of new
functions [25]. It will be important to see which predominates but this will have to wait until many paralagous
genes with a variety of functions have been studied in
detail — a considerable undertaking.
Conclusions
Although many genes show evidence of duplication in
early vertebrate evolution, experimental analyses of
individual families suggests that there is a predominance
of neofunctionalisation, with little evidence of subfunctionalisation. This may, however, be an artefact of the
considerable length of time that vertebrates and their
nearest relatives have been separated. Direct tests of
395
hypotheses concerning the action of selection on such
ancient evolutionary events may never be possible, and
consequently we must look to more recent duplications,
such as those in teleost fish and amphibia, to establish
general principles that can be extrapolated to the base of
vertebrate evolution.
Acknowledgements
The authors would like to acknowledge the support of the BBSRC.
References and recommended reading
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