Download perspectives - Biology Learning Center

PERSPECTIVES
OPINION
Opening Darwin’s black box:
teaching evolution through
developmental genetics
Scott F. Gilbert
When biologists are asked to discuss the
evidence for evolution at public forums, they
usually use well-established microevolutionary
examples. Although these examples show
the efficacy of evolution within species, they
often leave audiences susceptable to the
arguments of creationists who deny that
evolution can create new structures and
species. Recent studies from evolutionary
developmental biology are beginning to
provide case studies that specifically address
these concerns. This perspective presents
some of this new evidence and provides a
framework in which to explain homology and
phylogeny to such audiences.
When asked to discuss evolution at public
forums, an hour or so is often given to outline
the main principles of evolution and to give
examples. I think that, until recently, our best
examples came from microevolutionary studies — looking at evolution within a species.
However, although they are useful for
explaining evolutionary processes, focusing
exclusively on microevolutionary studies left
openings for creationists to challenge whether
species can be generated by evolutionary
means. As well as providing new insights into
evolution, evolutionary developmental biology has recently produced evidence that
argues directly against the claims of creationists, by shedding light on macroevolutionary
(above the species-level) processes. Here, I
discuss some of this evidence and provide a
framework for how we might wish to teach
NATURE REVIEWS | GENETICS
evolution. I discuss one possible way — there
are certainly others.
Evolution has generated our planet’s biodiversity, and over the past century scientists
have become able to explain the mechanisms
by which changes in animal body structure can
be produced, inherited and selected. Genetics
is crucial to this understanding. The MODERN
SYNTHESIS initially explained evolution through
the mathematics of population genetics.
Although population genetics has remained
the core of the modern synthesis, it has also
come to include studies from ecology, biogeography, paleontology, and more recently cytogenetics and molecular genetics. Population
genetics, itself a marriage of Mendelian particulate inheritance and Darwin’s natural selection, is able to explain how different alleles
spread through the population, whereas cytogenetics and molecular genetics are able to
explain the origins of these alleles through
mutation and recombination.
Until recently, the best examples of evolution in action came from microevolutionary
studies. Such studies explained, for instance,
how natural selection could cause moth colouration to become darker and change the
beak shape in the Galapagos finches. For
the Galapagos finches, selection by drought
conditions allowed those individuals with certain beak shapes to survive, transmit their
beak shape to their offspring and change the
beak morphology that had been characteristic
of the species1. This illustrates the main tenets
of natural selection: variation within a species;
overabundance of individuals within a species;
differential survival of those most fit for the
environmental circumstances; and the inheritance of those traits by the progeny of the survivours. The molecular version of the modern
synthesis showed that evolution can even
work over small timescales and therefore
clearly showed how the principles of genetics
and natural selection can, for example, explain
the origins of pesticide-resistant insects and
antibiotic-resistant bacteria2–4.
The existence and efficacy of microevolution is widely accepted, even by most creationists5. But creationists are not concerned
about antibiotic-sensitive bacteria becoming
antibiotic-resistant or about the beak shape
changes of Galapagos finch species. They
have remained bacteria and finches, respectively, so nothing much has changed — no
new species has been created. To creationists,
the synthesis of evolution and genetics cannot explain how some fish became amphibians, how some reptiles became mammals, or
how some apes became human (see the online
links box for a link to material dealing specifically with arguments recently put forward
by creationists). Behe6 named this inability
to explain the creation of new taxa through
genetics “Darwin’s black box”. When the box
is opened, he expects evidence of the Deity to
be found. However, inside Darwin’s black box
resides merely another type of genetics —
developmental genetics.
If genetics is Darwin’s ‘missing evidence’7,
then developmental genetics is needed to
complete the picture given by molecular and
population genetics. Fifty years ago, British
biologist C. H. Waddington was trying to
bring developmental biology into the modern synthesis8–10, and he noted that evolution
had two principal components. There was
the traditional component (that is, natural
selection) that worked on adults that compete for reproductive success, and an embryological component, in which variation
was created and constrained. “The changes
that produced new body plans…”, wrote
Waddington11, “…were inheritable changes
VOLUME 4 | SEPTEMBER 2003 | 7 3 5
PERSPECTIVES
in the patterns of embryonic development.
Changes in genotypes only have ostensible
effects in evolution if they bring with them
alterations in the epigenetic processes by
which phenotypes come into being; and the
kinds of change possible in the adult form of
an animal are limited to the possible alterations in the epigenetic system by which it is
produced.” Both the selective and the developmental sides of evolution are important. In
1977, the two sides of evolution began to be
bridged. Nobel Laureate François Jacob proposed the idea that evolution was bricolage —
tinkering, not engineering12. Moreover, Jacob
claimed that evolutionary biologists should
look at evolution not only in adults, but also
during development, because evolution
works not only on adults but also on the
‘recipes’ for adults. Therefore, to study large
changes in evolution, biologists needed to
look for changes in the regulatory genes that
make the embryo, not just in the structural
genes that provide fitness within populations.
The last quarter of a century has borne out
this idea. It took a while for developmental
genetics to reach maturity, but it can now be
added to the mix of population genetics and
molecular genetics to explain evolution.
Moreover, when developmental genetics is
added, macroevolution can be explained
much more easily. The microevolutionary
processes of mutation and recombination can
be analysed to determine how specific genetic
changes have created new types of organisms
by altering their development. So, when confronted with the classic evolutionary question
of how the arthropod body plan arose, Hughes
and Kaufman began their study by stating,
“To answer the question by invoking natural
selection is correct but insufficient. The fangs
of a centipede … and the claws of a lobster
accord these organisms a fitness advantage.
However, the crux of this mystery is this:
From what developmental genetic changes did
these novelties arise in the first place?” (REF. 13).
Here, I propose a way of teaching evolution that highlights developmental genetics.
As such, it confronts the creationist challenges directly and shows how changes in
gene expression can cause a marked evolutionary change. Both population genetics
and developmental genetics, as well as contributions from other fields such as palaentology and biogeography, are required for any
theory of evolution, but I propose that students will learn the principles of evolution
most easily from examples of development. I
illustrate my argument with examples, most
of which come from vertebrates and insects,
and so I apologize in advance to the allies of
all other clades.
736
| SEPTEMBER 2003 | VOLUME 4
Teaching phylogeny and homology
In 1859, Darwin wrote “It is generally acknowledged that all organic beings have been formed
on two great laws — Unity of Type and
Conditions of Existence” (REF. 14).While natural
selection explained adaptation to the “offices of
existence”, embryonic homologies explained
“unity of type” (REF. 14). Together, they would
produce the idea of ‘descent with modification’.
Using this concept, Darwin could explain the
similarities of animal form through descent
from a common ancestor and the differences
by natural selection in different environments.
When introducing evolution to students, biologists usually concentrate on natural selection,
the main mechanism of Darwinian evolution.
This is important. It shows that there is variation within a species; that most animals die
before reproducing; that the mortality can be
selective; and that the progeny resulting from
such selection are more fit for their environment, having inherited the genes that made
their parents fit. But this is only half of the
story. The other half concerns the unity of type
and the question of homology, that is, the fact
that animals are joined together into groups
with similar features.
“…I propose that students
will learn the principles of
evolution most easily from
examples of development.”
To show this unity of type and how animals are variations on a relatively small set of
themes, Darwin followed von Baer’s principles and looked to embryonic and larval
stages, because the earlier stages of animal
development could show homologies that are
obscured in the adult. In On the Origin of
Species, Darwin celebrated the case of the barnacle, the larvae of which showed that it is a
shrimp-like arthropod14, and in Descent of
Man15, he gloried in Alexander Kowalevsky’s
discovery that the tunicate — previously classified as a shell-less mollusk — is actually a
chordate. It has a NOTOCHORD and pharyngeal
slits that come from the same cell layers as
those of fish and chickens. So, the two great
domains of the animal kingdom — invertebrates and vertebrates — were united through
larval homologies. “Thus, if we may rely on
embryology, ever the safest guide in classification, it seems that we have at last gained a clue
to the source whence the Vertebrata were
derived.” (REF. 15).
But homology can be a tricky concept. If
used alone (and some creationists imply that
it is), it risks forming a circular argument
wherein structures are considered homologous because of common origin, and these
animals are said to have a common origin
because they have homologous structures. An
independent assessment of ancestry and origins is needed. Although we have this independent assessment now, it was not avilable to
Darwin. Without this independent assessment, the study of macroevolution became
embroiled in disputes about whether similar
structures were the result of common ancestry or convergence. The frustration about
whether similarities came from common
ancestry (homology) or common environments (HOMOPLASY) caused biologists of the
first three decades of the twentieth century to
leave this area of research and begin the microevolutionary studies that related evolution to
genetic variation within species (for example,
see REFS 16,17).“The geneticist…”, said William
Bateson in 1922, “…is the successor of the
morphologist.” (REF. 18).
I find that I can teach the relationships of
homologies and evolution best by looking at
one of the other passengers on the HMS
Beagle. The Tierra del Fuegan, York Minster,
was a bit older than Darwin, but like Darwin,
he had been trained in theology (FIG. 1a). York
Minster had been abducted by Captain Fitzroy
on the first voyage of the HMS Beagle to the
southern tip of South America, and Fitzroy
had him educated in London as a missionary.
Both he and Darwin completed their theological training in 1830. Newly baptized, this Tierra
del Fuegan was now being repatriated to
spread the Gospel in his homeland19. Imagine
his education. He would have been told of different religions: Judaism, Catholicism, Russian
and Greek Orthodoxy, Lutheranism and, of
course, Anglicanism. There are differences
and similarities between these religions: they
share similar, but different Bibles; sing similar,
but different hymns; and worship similar, but
different Gods. How was he to make sense of
them? Do these similar religions have a common origin or are they separate acts of religious faith? No-one can go back in time. How
would he determine whether the religions
come from a common ancestor and if the
similarities are due to this common origin?
First, there would be material evidence.
The Tierra del Fuegan would have the evidence of archaeology. Biblical archeology had
uncovered artefacts showing shared histories
and transitions. He could be shown concrete
evidence of religious history (such as Herod’s
palace), linking Judaism and Christianity. Just
as archeology can reveal the history and
www.nature.com/reviews/genetics
PERSPECTIVES
a
b
West/East
Greek
Orthodox
Christian
Judaism
(Roman
empire
variants)
c
Papal authority
Greek
Orthodox
Christian
Russian
Orthodox
Lutheran
Judaism
(Roman
empire
variants)
Russian
Orthodox
Lutheran
Anglican
Anglican
Catholic
Catholic
Reform
Judaism
Reform
Judaism
Conservative
Judaism
Conservative
Judaism
Orthodox
Judaism
Orthodox
Judaism
Figure 1 | York Minster and two rival cladograms of western religion. a | York Minster, a Tierra del Fuegan, aboard the HMS Beagle. b,c | Cladograms that could
be constructed on the basis of the theological analogues of material evidence, homology and vestigial apparatus. In b, non-allegiance to the papacy is a derived
chatacter that evolved twice in the history of the Christian clade, once in Eastern Orthodoxy, and then independently in Protestantism. In c, papal authority is considered
a derived trait that evolved before the split between the East and West churches. For simplicity, Islam and many other religions have been omitted from the diagram.
genealogy between religions, so paleontology
reveals the history and transitions between
groups of animals.
Second, York Minster could use vestigial
apparatus and homologies to show the
genealogical connection between faiths. He
might argue that Christian Bibles have lists of
Semitic kings that would not be there were it
not for their inclusion in an earlier religion.
The fact that so many strange stories, such as
that of Onan, Samson, Ahab and Jezebel,
occur in the Hebrew Bible, the Protestant
Bibles and the Catholic Bible would indicate
that there is a common origin. His shipmate
Darwin would similarly argue that such
strange things as the aortic arches would not
be present in mammals and amphibians were
they not in the earlier ancestors from which
they arose. The aortic arches would not be
‘invented’ twice, especially when most of the
mammalian aortic arches degenerate.
On the basis of his knowledge of homologies, vestigial apparatus and material artefacts,
York Minster could draw a cladogram of religions. One such cladogram is shown in FIG. 1b.
It should be noted that the first separation is
between the Jewish and Christian ‘clades’. Then
there is a division in the Christian ‘clade’
between the Eastern and Western Churches.
Then there is a split in the Western Church
between Catholicism and the Protestant
denominations. This cladogram views the
liturgy and Bible translation as fundamental
characteristics. However, another cladogram
can be made. This alternative (FIG. 1c) views the
papacy as a derived trait (not seen in Jewish,
Orthodox or Protestant lineages). So, together,
Protestantism and Orthodoxy split from
NATURE REVIEWS | GENETICS
Catholicism, and only later do they branch
off into Eastern and Western derivatives.
Instead of the East/West distinction being
primary, the second cladogram is made on
the papacy/non-papacy distinction.
How could York Minster decide which model is
correct? How do we know that the model in FIG.1b
is correct and the model in FIG.1c is wrong? Here,
York Minster had a huge advantage over Charles
Darwin.There were textual records for the histories
of the churches.York Minster might say that the
best evidence is neither from material artefacts nor
from arguments about homologies and vestigial
apparatus (as the lack of allegiance to the papacy
could result either from common ancestry or from
two independent events), but from textual evidence.In religions,this would be the set of documents that show the splitting of one religion into
two or more new religions.Henry VIII’s 1534 Act of
Supremacy and Martin Luther’s 95 Theses (1517)
would be such documents,showing the separation
of Protestant Christianity from Catholicism and
not fromOrthodoxy.
Darwin and his colleagues could draw
branched-chain evolutionary trees of the
animal kingdom that were based on embryonic homologies, adult homologies, vestigial
apparatuses and the fossil record. But, until
recently, there were many versions of these
trees, because there was no independent
assessment of homology except for the fossil
record. And here is where macroevolution,
the study of phylogeny — of evolution above
the species-level — encountered a problem.
It did not have such documentation. Except
for the fossil record, which was much worse
for Darwin than it is for us today, there was
no independent assessment for common
origins. Not until the arrival of molecular
genetics would evolution have a powerful
way of getting around the homology question. It wasn’t until the late 1970s that we
could access the historical records of genes,
and they turned out to be a treasure trove
beyond measure. By finding rare and shared
molecular similarities, the genealogical relationships between higher taxa can be found.
Later phylogenetic reconstructions also
included LIKELIHOOD AND BAYESIAN ESTIMATION
TESTS for deciding which paths of evolution
were most probable. Evolutionary problems
that had been intractable to Darwin and
early evolutionary biologists have now been
solved. The phylogeny of insects, for example, was fraught with problems of homoplasy16. However, a rare gene rearrangement
shared between insects and crustaceans has
now shown the common ancestry of these
two groups20, refuting the alternative
hypothesis that insects were derived from a
myriapod-like ancestor. Similarities in 18S
ribosomal RNA sequences, coupled with the
same duplication of certain Hox genes in
particular phyla, linked a set of invertebrates
into the ecdysozoan clade and established a
particular set of genealogical relationships
among the invertebrates21,22. Similarly, we
have a record telling us that the whale and
hippopotamus are closely related and that
both arose from an ancestor that is in common with the cow and deer23. The phylogeny
of animals has become less a matter of interpreting visual evidence and more a matter of
reading the documentation.
By looking at the cladograms of religion,
and by showing how molecular evidence fills
VOLUME 4 | SEPTEMBER 2003 | 7 3 7
PERSPECTIVES
the gaps in our assessment of homology, we
can explain evolution to the public, and we can
also directly counter creationists’ claims that
evolutionary biology is based on circular
arguments about homology relationships.
Evolutionary developmental biology
The ability to find and sequence genes has
done more than provide evolutionary biologists with an independent assessment of
animal relationships. It has enabled developmental biologists to look at the causal
mechanisms wherein small changes in genes
can generate large morphological differences.
In 1977, three publications paved the way for
evolutionary developmental biology. These
publications were the aforementioned article
Evolution and tinkering12, Stephen J. Gould’s
book Ontogeny and Phylogeny 24 and Maxam
and Gilbert’s technique for DNA sequencing 25. In Ontogeny and Phylogeny, Gould
showed how the German biologist Ernst
Haeckel had misrepresented the field of evolutionary embryology and made it into an
unscientific and racist doctrine. Indeed, the
first half of this book exorcises Haeckel’s ghost
so that some other model of evolution and
development could be put in place of Haeckel’s
Biogenetic Law, wherein ‘ontogeny recapitulates phylogeny.’ Jacob’s paper proposed a new
model that could be tested, and the paper on
DNA sequencing established a method that
could test it.
The first discoveries in evolutionary developmental genetics showed the remarkable
homology of genetic instructions. Indeed, the
developmental instructions for forming several analogous organs were shown to be
homologous. For example, the fly eye and
mouse eye have very little in common as to
their origin or structure. However, Walter
Gehring’s group showed that the instructions
to form both the mouse and the fly eye are
based on a set of homologous genes, such as
Pax6 (REF. 26). The instructions are so similar
that fly IMAGINAL DISCS will form an eye (a
Drosophila eye) under the instruction of the
rodent Pax6 gene27. Not only is eye development dependent on the Pax6 gene throughout the animal kingdom, but the genes that
interact with Pax6 to form the photoreceptor cells also seem to be evolutionarily
conserved28,29. Therefore, whereas it was previously thought that eyes formed independently many different times30, we now find
that each type of eye is but a variation on a
theme. Moreover, many of the genes that
specify the formation of the heart, the nervous system and the anterioposterior body
axis also seem to be the same throughout
the animal kingdom, despite the enormous
diversity of these structures31,32.
So, whereas creationists are fond of saying
that Darwin admitted that he had no idea
how an organ as precise and as complicated
as an eye could evolve, we now have the basic
Chicken hindlimb
Duck hindlimb
BMP
Gremlin
Apoptosis
Newborn
Figure 2 | Regulation of chicken limb apoptosis by BMPs. Autopods of chicken feet (top) and duck feet
(bottom) at similar stages. The in situ hybridizations show that while bone morphogenetic proteins (BMPs)
are expressed in both the chicken and duck hindlimb webbing, the duck hindlimb also shows expression of
gremlin in the webbing (arrows). Gremlin is an inhibitor of BMPs. The pattern of cell death (shown by neutral
red dye accumulation) becomes distinctly different in the two types of webbing. Reproduced with
permission from REF. 33 © Sinauer Associates (2003) and REF. 41 © The Company of Biologists (1999).
738
| SEPTEMBER 2003 | VOLUME 4
scheme. First, the genes that generated the
photoreceptors of the primitive eyes of flatworms and other invertebrates are now used
in the formation of the complex eye types. The
entire optic system did not have to be invented
de novo. Rather, there was descent with modification. Second, the retina and lens are in their
respective positions because the lens helps
build the retina and the retina helps build the
lens26,33. This type of reciprocal induction is
found whenever complex organs are being
made. The blood vessels are able to get into the
RENAL GLOMERULI because the developing cells of
the renal glomeruli induce blood-vessel formation in the mesoderm next to them34,35.
Third, complex systems with new properties
can be generated by the interactions of simpler
systems. Using computer programs that show
the salient features of evolution — replication,
variation and differential fitness — Lenski and
colleagues36 showed that mutation and selection could evolve complex functions out of
simpler ones, and that, in some instances,
mutations that were originally deleterious
when they first emerged became steppingstones in the evolution of more complex
programmes. Importantly, there were several cases in which the amalgamation of
simpler programmes into a more complex
programme involved no intermediates.
Development is complicated and interconnected; it is not irreducibly complex.
However, although the first wave of evolutionary developmental biology uncovered the
remarkable similarities among very diverse
organisms, it was obvious that there had to be
profound differences in the ways these genes
were being used. For example, although we
specify our anterior-posterior axis using Hox
genes that are similar to those of fruit flies, we
do not activate them by the same paths, nor
do they have the same targets. Similarly, we
might use Pax6 to specify our eye-forming
regions, but our visual system does not
form from imaginal discs. So there must be
important differences as well as important
similarities. If we are talking about descent
with modification, we expect both underlying
similarities and secondary differences. Can
these differences in developmental genetics
explain morphological differences? During
the past five years, we have seen that there are
at least five ways in which changes in developmental regulatory genes can mediate evolutionarily important morphological changes.
Mutating the regulatory genes. One way to
produce evolutionary change is to mutate
regulatory genes. This seems to have been the
case with the Ultrabithorax (Ubx) gene, which
has undergone a mutation in the insect clade.
www.nature.com/reviews/genetics
PERSPECTIVES
As a result of this mutation, the Ubx protein
of insects (but not of other arthropod
groups) now represses Distal-less expression37,38. This means that insects will only
have thoracic legs. Whereas other arthropods
— millipedes, centipedes and crustaceans —
are known for their many legs, insects have
but six. As Jacob predicted, mutations in regulatory genes can give them new properties.
Altering the genetic targets of regulatory
proteins. In many instances, large changes in
evolution can be made by maintaining the
same patterns of regulatory protein expression but altering their downstream targets.
This can be seen in the difference between
four-winged butterflies and two-winged fruit
flies and houseflies. The butterfly hindwing
differs from the Drosophila HALTERE, but both
structures are generated through the action of
the Ubx protein on the larval imaginal discs
of the third thoracic segment. However, Ubx
regulates different genes in the butterfly imaginal discs from the ones in the Drosophila
imaginal discs. So the DIPTERANS have diverged
from other four-winged insects through
changes in the Ubx-responsive genes of the
thoracic imaginal discs39, 40.
Altering the spatial expression of regulatory
genes. A mutation in the actual protein or its
receptor is not needed to effect evolutionary
change. A change in the expression pattern of
a regulatory protein can also be vitally important. For example, changes in the spatial
expression of regulatory genes can explain
how the duck got its webbed feet41. Here, the
expression of bone morphogenetic protein 4
(BMP4) in the interdigital spaces signals these
‘webbing’ cells to undergo apoptosis. Duck
and chicken hindlimbs have the same pattern
of BMP4 gene expression, both embryos
expressing BMP4 in the interdigital cells of
the foot. Where they differ is in the expression
of a BMP inhibitor protein, Gremlin (FIG. 2).
Gremlin expression is seen in both the chicken
and duck hindlimbs, where it is found around
the digits. In the duck, however, and not in the
chicken, the Gremlin gene is also expressed in
the interdigital cells. The Gremlin protein
made there prevents BMP from signaling for
cell death in the webbing, and the result is a
webbed foot. This can be experimentally tested
by adding Gremlin-containing beads into the
interdigital regions of the embryonic chicken
hindlimb. When this is done, the chicken foot
resembles that of a duck (FIG. 3). This is bricolage. The protein hasn’t changed, it is just
being expressed at a different place.
Changing the pattern of regulatory gene
expression has also been shown to correlate
with the type of vertebra formed by the SOMITES
and the type of appendage formed by crustaceans42–44. It has also been correlated with the
formation of feathers from scales. Feathers
have long been proposed as an evolutionary
novelty, and creationists say that feathers cannot be generated from any other structure.
However, recent papers present evidence
that differences in the expression of Sonic
hedgehog (Shh) and BMP proteins separate
the feather from the scale45,46. Moreover, when
the expression of Shh or BMP2 is altered, the
feather pattern changes. The results corre-
a
b
Figure 3 | Inhibition of cell death by inhibiting
BMP. a| Control chicken hindlimbs have extensive
apoptosis in the space between the digits, leading
to the absence of webbing. b | When beads
soaked with Gremlin protein, an inhibitor of bone
morphogenetic protein (BMP), are placed into the
interdigital mesoderm, the webbing persists and
generates a duck-like foot. Reproduced with
permission from REF. 41 © The Company of
Biologists (1999).
spond exceptionally well to a proposed mechanism of feather production from archosaurian
scales. Changing the pattern of regulatory gene
expression has also been correlated with the
loss of limbs in snakes47.
Changes in the temporal expression of regulatory genes. In addition to getting evolutionary
change by altering the spatial expression of
genes, remarkable changes can be obtained by
altering the temporal expression of genes.
Heterochronic (temporal) changes in Wnt5
gene expression are responsible for the changes
between direct and indirect developing sea
urchins48. Heterochronic changes also seem to
Glossary
BAYESIAN
IMAGINAL DISCS
NOTOCHORD
A branch of statistics that focuses on the posterior
probability of hypotheses. The posterior probability is
proportional to the product of the prior probability and
the likelihood.
Thickenings of the epidermis in larval insects. These
structures produce the adult wings, legs, eyes, antennae,
mouth and genitalia during metamorphosis.
A rod of mesodermal cells in the dorsal midline
beneath the neural tube. It is the major characteristic
of chordates.
INSTAR
POLYPHENISM
The period between larval insect molts.
Phenotypic variation not attributable to genetic
differences: the product of environmental stimuli
on particular genotypes. One example is seasonal
polyphenism, whereby individuals with the same
genotype manifest different phenotypes owing to
temperature.
DIPTERANS
Insects with two wings, such as flies and mosquitos.
ECLOSION
The emergence of the adult insect from its pupal case.
HALTERE
Balancers. Club-like tissue arising from the imaginal disc
in the third segment of dipterans.
HOMOPLASY
Similarity whereby structures have similar form or
function but not the same ancestral origin. Homoplasies
often result from convergent evolution whereby different
organisms in the same environment produce similar
adaptions.
HYPOPHYSEAL
Pituitary.
NATURE REVIEWS | GENETICS
LIKELIHOOD ESTIMATION TEST
A statistical method that calculates the probability of the
observed data under varying hypotheses to estimate model
parameters that best explain the observed data and determine
the relative strengths of alternative hypotheses.
MODERN SYNTHESIS
Neo-Darwinism. The theory that natural selection, acting
on randomly generated variation, is the major cause of
evolution.
REACTION NORMS
A situation in a population in which the genotype
provides a graded response to environmental
conditions.
NEURAL CREST CELLS
RENAL GLOMERULI
A migratory cell population that arises at the lateral
edges of the neural plate, and which differentiates
into numerous cell types including skull and facial
bone, pigment cells, adrenal medullary cell, and
the neurons and glia of the sensory and
autonomic nervous systems.
A cluster of capillaries in the kidney cortex.
SOMITES
Blocks of mesoderm along the vertebrate body axis
that further differentiate into dermal skin, bone and
muscle.
VOLUME 4 | SEPTEMBER 2003 | 7 3 9
PERSPECTIVES
Population genetics
Developmental genetics
Variation within
populations
Variation between
populations
Genes in
adults competing for
reproductive success
Genes in embryonic
and larval organisms
building structures
Survival of the fittest
Arrival of the fittest
Natural selection
Phylogeny
A new evolutionary
synthesis explaining
biodiversity
Figure 4 | A newly emerging evolutionary
synthesis. The classic approach to evolution has
been that of population genetics. It emphasized
variations within a species that allowed certain adult
individuals to reproduce more frequently. In this
way, it could explain natural selection. The
developmental approach looks at variation between
populations, and it emphasizes the regulatory
genes that are responsible for organ formation. Its
explanations are more apt to explain evolutionary
novelty and constraint. Together, population
genetics and developmental genetics make a
more complete genetic approach to evolution.
be responsible for another evolutionary novelty, the vertebrate jaw — one of the problems
that puzzled evolutionary embryologists in the
early 1900s. In the lamprey, the naso-hypophyseal plate is retained and prevents the migration of NEURAL CREST CELLS rostrally. In jawed
vertebrates, this plate separates very early in
development into the nasal and HYPOPHYSEAL
neural tissues, thereby making a path for the
rostral migration of neural crest cells. This
allows the formation of a new structure, the
jaw. As Kuratani and colleagues conclude,
“The clue to solve this problem, therefore, will
not be obtained by comparative anatomy of
the adult structures, but rather by discrimination of conserved and newly acquired patterns
of gene expression… Molecular developmental biology has taken the initial steps into this
old question of comparative zoology, but it
has already suggested new directions in which
a solution may lie.” (REF. 49).
Selection of variants that are caused by
developmental plasticity. In many organisms,
the genotype does not directly predict the phenotype. Rather, the genotype provides a range
of potential phenotypes and the exact phenotype will be induced by the environment.
Usually, the environmental stimulus is sensed
by the neuroendocrine system and the hor-
740
| SEPTEMBER 2003 | VOLUME 4
mones control the expression of particular
genes9,50. This is known as developmental plasticity and it is the basis for REACTION NORMS and
POLYPHENISMS. At different points in their ranges
one extreme of this plasticity might become
genetically fixed51–54. This ability of a developmentally plastic trait to become genetically
fixed has been documented numerous times
in the laboratory and could provide a rapid
means for the origin of new species55,56.
A new evolutionary synthesis
The developmental genetic approach to evolution complements the traditional population genetic approach. They are both needed.
The mechanisms of genetic change in regulatory genes are the same as those of structural
genes, and once these evolutionary novelties
are generated they must still be selected. The
traditional differences between the population genetic and developmental genetic
approaches to evolution are summarized in
FIG. 4 . These differences are beginning to
blur as both population geneticists and
developmental geneticists start studying
allelic variations of developmental regulatory
genes within populations57.
I would emphasize the importance of
including examples from the developmental
genetics approach when discussing evolution
in public. In addition to being easier to understand than the population genetic approach
to teaching evolution, the developmental
approach might have other advantages. First,
the developmental genetic approach uses
examples that everyone can understand from
visual experience. Second, evolution at the
level of developmental regulatory genes might
be the main source of variation. In humans
(that animal for which variations have been
catalogued most carefully), genes are heterozygous at more functional cis-regulatory
sites (>16,000) than at exon sites (<13,000).
Ordinary small-scale mutations contribute to
large variations in transcription rates across
the genome and so to human variation57.
Third, these examples address the questions
of evolutionary novelty that creationists
say cannot be explained by evolution — how
insects have fewer legs than centipedes,
how snakes lost their legs, how birds got
feathers and ducks got their webbed feet. We
are therefore able to show where creationists
are wrong and how their ideas about homology and morphological novelties are out of
date. If the processes of evolution were
viewed solely from the population genetic
perspective, it would appear very difficult to
explain the origins of feathers, teeth and eyes.
They seem to be (in the words of the creationists) “irreducibly complex”6. However,
when the perspectives of embryonic induction and developmental genetics are added,
these novelties become explainable, at least in
outline, if not yet in detail. Such information
is crucial if we are to counter the distortions
of science by creationists58.
J. B. S. Haldane, the editor of the volume
in which Waddington published the abovementioned paper, commented on this idea
using a wonderfully apt developmental metaphor,“To sum up, then, a number of workers
are groping from their own different standpoints towards a new synthesis, while producing facts which do not fit too well into the
currently accepted synthesis. The current
instar of the evolution theory may be defined
by such books as those of Huxley, Simpson,
Dobzhansky, Mayr, and Stebbins. We are certainly not ready for a new moult, but signs of
new organs are perhaps visible.” (REF. 59).
Today, exactly half a century later, we can
report that the organs have formed and the
INSTAR has ECLOSED. Evolutionary developmental biology has become a normative part of
evolutionary biology and should provide
wonderful and informative new ways of teaching evolution to biology students and to the
general public.
Scott F. Gilbert is at Swarthmore College,
Swarthmore, Pennsylvania 19081, USA.
e-mail: [email protected]
doi:10.1038nrg1159
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
Grant, P. R. Ecology and Evolution of Darwin’s Finches
(Princeton Univ. Press, Princeton, New Jersey, 1986).
McKenzie, J. A. & Batterham, P. Predicting insecticide
resistance: mutagenesis, selection and response.
Philos. Trans. R. Soc. Lond. B 353, 1729–1734
(1998).
Raymond, M., Chevillon, C., Guillemaud, T., Lenormand, T.
& Pasteur, N. An overview of the evolution of
overproduced esterases in the mosquito Culex pipiens.
Philos. Trans. R. Soc. Lond. B 353, 1707–1711 (1998).
Normark, B. H., & Normark, S. Evolution and spread of
antibiotic resistance. J. Intern. Med. 252, 91–106
(2002).
Pigliucci, M. Phenotypic Plasticity: Beyond Nature
and Nurture (Johns Hopkins Univ. Press, Baltimore,
2001).
Behe, M. J. Darwin’s Black Box: the Biochemical
Challenge to Evolution (Free Press, New York, 1996).
Kettlewell, H. B. D. Darwin’s missing evidence. Sci.
Amer. 200, 48–53 (1959).
Hall, B. K. Waddington’s legacy in development and
evolution. Am. Zool. 32, 113–122 (1992).
Gilbert, S. F. Diachronic biology meets evo–devo:
C. H. Waddington’s approach to evolutionary
developmental biology. Am. Zool. 40, 729–737 (2002).
Slack, J. M. Conrad Hal Waddington: the last Renaissance
biologist? Nature Rev. Genet. 3, 889–895 (2002).
Waddington, C. H. Canalization of development and the
inheritance of acquired characteristics. Nature 150,
563–565 (1942).
Jacob, F. Evolution and tinkering. Science 196,
1161–1166 (1977).
Hughes, C. G. & Kaufman, T. Hox genes and the
evolution of the arthropod body plan. Evo. Dev. 4,
459–499 (2002).
Darwin, C. On the Origin of Species (John Murray,
London, 1859).
Darwin, C. The Descent of Man and Selection in Relation
to Sex 2 Vols, 2nd edn (John Murray, London, 1874).
Bowler, P. Life’s Splendid Drama (Univ. of Chicago Press,
Chicago, 1996).
www.nature.com/reviews/genetics
PERSPECTIVES
17. Gilbert, S. F. Bearing crosses: a historiography of
genetics and embryology. Am. J. Med. Genet. 76,
168–182 (1998).
18. Bateson, W. Evolutionary faith and modern doubts.
Science 40, 1412–1415 (1922).
19. Desmond, A. & Moore. J. Darwin: the Life of a
Tormented Evolutionist (Norton, New York, 1991).
20. Boore, J. L., Lavrov, D. V. & Brown, W. M. Gene
translocation links insects and crustaceans. Nature 392,
667–668 (1998).
21. Aguinaldo, A. M. et al. Evidence for a clade of
nematodes, arthropods and other moulting animals.
Nature 387, 489–493 (1997).
22. De Rosa, R. et al. Hox genes in brachiopods and
priapulids and protostome evolution. Nature 399,
772–776 (1999).
23. Shimamura, M. et al. Molecular evidence from
retroposons that whales form a clade within even-toed
ungulates. Nature 388, 666–670 (1997).
24. Gould, S. J. Ontogeny and Phylogeny (Harvard Univ.
Press, Cambridge, Massachusetts, 1977).
25. Maxam, A. & Gilbert, W. A new method for sequencing
DNA. Proc. Natl Acad. Sci. USA 74, 560–564 (1977).
26. Gehring, W. J. The genetic control of eye development
and its implications for the evolution of the various eyetypes. Int. J. Dev. Biol. 46, 65–73 (2002).
27. Halder, G., Callaerts, P., & Gehring, W. J. Induction of
ectopic eyes by targeted expression of the eyeless gene
in Drosophila. Science 267, 1788–1792 (1995)
28. Pineda, D. et al. Searching for the prototypic eye genetic
network: Sine oculis is essential for eye regeneration in
planarians. Proc. Natl Acad. Sci. USA 97, 4525–4529
(2000).
29. Wawersik, S. & Maas, R. L. Vertebrate eye development
as modeled in Drosophila. Hum. Mol. Genet. 9, 917–925
(2000).
30. Salvini-Plawin, L. V. & Mayr, E. Evolution of
photoreceptors and eyes. Evol. Biol. 10, 207–263 (1977).
31. Erwin, D. H. The origin of bodyplans. Am. Zool. 39,
617–629 (1999).
32. Pichaud, F. & Desplan, C. Pax genes and eye
organogenesis. Curr. Opin. Genet. Dev. 12, 430–434
(2002).
33. Gilbert, S. F. Developmental Biology 7th edn (Sinauer
Associates, Sunderland, Massachusetts, 2003).
34. Aitkenhead, M. et al. Paracrine and autocrine regulation
of vascular endothelial growth factor during tissue
differentiation in the quail. Dev. Dyn. 212, 1–13 (1998).
35. Eremina, V. et al. Glomerular-specific alterations of
VEGF-A expression lead to distinct congenital and
acquired renal diseases. J. Clin. Invest. 111, 707–716
(2003).
36. Lenski, R. E., Ofria, C., Pennock, R. T. & Adami, C.
The evolutionary origin of complex features. Nature 423,
139–144(2003).
37. Galant, R. & Carroll, S. B. Evolution of a transcriptional
repression domain in an insect Hox protein. Nature 415,
910–913 (2002).
38. Ronshaugen, M., McGinnis, N. & McGinnis, W.
Hox protein mutation and macroevolution of the
insect body plan. Nature 415, 914–917 (2002).
39. Carroll, S. B., Weatherbee, S. D. & Langeland, J. A.
Homeotic genes and the regulation and evolution of
insect wing number. Nature 375, 58–61 (1995).
40. Weatherbee, S. D. et al. Ultrabithorax function in butterfly
wings and the evolution of insect wing patterns. Curr.
Biol. 9, 109–115 (1999).
41. Merino, R. et al. The BMP antagonist Gremlin regulates
outgrowth, chondrogenesis and programmed cell death
in the developing limb. Development 126, 5515–5522
(1999).
42. Gaunt, S. J. Conservation in the Hox code during
morphological evolution. Int. J. Dev. Biol. 38, 549–552
(1994).
43. Burke, A. C., Nelson, A. C., Morgan, B. A. &
Tabin, C. Hox genes and the evolution of vertebrate
axial morphology. Development 121, 333–346
(1995).
44. Averof, M. & Patel, N. H. Crustacean appendage
evolution associated with changes in Hox gene
expression. Nature 388, 682–686 (1997).
45. Harris, M. P., Fallon, J. F. & Prum, R. O. Shh–BMP2
signaling module and the evolutionary origin and
diversification of feathers. J. Exp. Zool. Part B Mol. Dev.
Evol. 294, 160–176 (2002).
46. Yu, M., Wu, P., Widelitz, R. B. & Chuong. C. M. The
morphogenesis of feathers. Nature 420, 308–312 (2002).
47. Cohn, M. J. & Tickle, C. Developmental basis of
limblessness and axial patterning in snakes. Nature 399,
474–479 (1999).
NATURE REVIEWS | GENETICS
48. Ferkowicz, M. J. & Raff, R. A. Wnt gene expression in sea
urchin development: heterochronies associated with the
evolution of developmental mode. Evol. Dev. 3, 24–33
(2001).
49. Kuratani, S., Nobusada, Y., Horigome, N. & Shigetani, Y.
Embryology of the lamprey and evolution of the vertebrate
jaw: insights from molecular and developmental
perspectives. Philos. Trans. R. Soc. Lond. B 356,
1615–1632 (2001).
50. Nijhout, H. F. Development and evolution of adaptive
polyphenisms. Evol. Dev. 5, 9–18 (2003).
51. Waddington, C. H. in Evolution (Soc. Exp. Biol. Symp. VII)
(eds Brown, R. & Danielli, J. F.) 186–199 (Cambridge Univ.
Press. Cambridge, UK, 1953).
52. Schmalhausen, I. I. Factors of Evolution: the Theory of
Stabilizing Selection (Univ. of Chicago Press, Chicago,
1949).
53. Shapiro, A. M. Seasonal polyphenism. Evol. Biol. 9,
259–333 (1976).
54. Brakefield, P. M. et al. Development, plasticity, and
evolution of butterfly eyespot patterns. Nature 384,
236–242 (1996).
55. West-Eberhard, M. J. Phenotypic plasticity and the
origins of diversity. Annu. Rev. Ecol. Syst. 20, 249–278
(1989).
56. West–Eberhard, M. J. Developmental Plasticity and
Evolution. Oxford University Press (2003).
57. Rockman, M. V. & Wray, G. A. Abundant raw material for
cis-regulatory evolution in humans. Mol. Biol. Evol.
19,1991–2004 (2002).
58. Pigliucci, M. Denying Evolution: Creationism, Scientism,
and the Nature of Science (Sinauer Associates,
Sunderland, Massachusetts, 2002).
59. Haldane, J. B. S. Foreword. in Evolution (Soc. Exp. Biol.
Symp. VII) (eds Brown, R. & Danielli, J. F.) ix–xix
(Cambridge Univ. Press, Cambridge, UK, 1953).
Acknowledgements
This Perspective is based on a talk originally presented as a lecture to the Society for Developmental Biology (SDB) at its annual
meeting in 2002. I wish to thank the Education Committee of the
SDB for the opportunity to write it and to Kenneth Miller and Sean
Carroll for their helpful comments. Funding was from the National
Science Foundation and from Swarthmore College, Pennsylvania.
Online links
DATABASES
The following terms in this article are linked online to:
FlyBase: http://flybase.bio.indiana.edu
Distal-less | Ubx
LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink
Pax6
Swiss-Prot: http://www.expasy.ch
BMP2 | BMP4 | Gremlin | Sonic hedgehog
FURTHER INFORMATION
Evolution, development, and creationism — a supplement:
http://zygote.swarthmore.edu/Darwin
Access to this interactive links box is free online.
OPINION
Vertebrate gene predictions and
the problem of large genes
Jun Wang, ShengTing Li, Yong Zhang, HongKun Zheng, Zhao Xu, Jia Ye,
Jun Yu and Gane Ka-Shu Wong
To find unknown protein-coding genes,
annotation pipelines use a combination of
ab initio gene prediction and similarity to
experimentally confirmed genes or
proteins. Here, we show that although the
ab initio predictions have an intrinsically
high false-positive rate, they also have a
consistently low false-negative rate.
The incorporation of similarity information is
meant to reduce the false-positive rate, but
in doing so it increases the false-negative
rate. The crucial variable is gene size
(including introns) — genes of the most
extreme sizes, especially very large genes,
are most likely to be incorrectly predicted.
We live in the halcyon days of large-scale
DNA sequencing. Each release of a
sequenced genome is accompanied by a list
of genes, many of which are computer predictions. Experimental confirmation in the
form of sequenced transcripts of full-length
cDNAs is extensive for mice1,2, less so for
humans3 and non-existent for pufferfish4.
For invertebrate genomes, cDNAs are less
important because the genes are smaller and
easier to predict. Nevertheless, the many
fruitfly 5 and nematode6 cDNAs that were
produced after their genomes were sequenced
have been invaluable in finding residual
errors in the definition of exon boundaries.
As it is difficult to get cDNAs that are
expressed transiently, or at low levels, in specific tissues and at specific developmental
stages, predicting genes will remain an integral part of DNA sequence analysis for the
foreseeable future. Therefore, it is imperative
for the biologists who use gene-prediction
programs to understand what they can and
cannot do. Although some features of these
programs are better than is commonly
thought, others are worse. It is tempting to
dismiss the programs as being inherently
unreliable (see BOX 1 for a note on fluctuations in gene number in the human genome),
but, in fact, they fail for specific reasons that
can be understood with minimal jargon and
without delving into algorithmic minutiae.
ANNOTATION PIPELINES have been comprehensively reviewed7. Every pipeline incorporates
information from known genes. No pipeline
ever substitutes a predicted gene for a known
VOLUME 4 | SEPTEMBER 2003 | 7 4 1