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overabundance of individuals within a species; OPINION differential survival of those most fit for the environmental circumstances; and the inheri- tance of those traits by the progeny of the sur- Opening Darwin’s black box: vivours. The molecular version of the modern synthesis showed that evolution can even teaching evolution through work over small timescales and therefore clearly showed how the principles of genetics developmental genetics and natural selection can, for example, explain the origins of pesticide-resistant and antibiotic-resistant bacteria2–4. Scott F. Gilbert The existence and efficacy of microevolu- tion is widely accepted, even by most cre- When biologists are asked to discuss the evolution. I discuss one possible way — there ationists5.But creationists are not concerned evidence for evolution at public forums, they are certainly others. about antibiotic-sensitive bacteria becoming usually use well-established microevolutionary Evolution has generated our planet’s biodi- antibiotic-resistant or about the beak shape examples. Although these examples show versity, and over the past century scientists changes of Galapagos finch species. They the efficacy of evolution within species, they have become able to explain the mechanisms have remained bacteria and finches, respec- often leave audiences susceptable to the by which changes in animal body structure can tively, so nothing much has changed — no arguments of creationists who deny that be produced, inherited and selected. Genetics new species has been created. To creationists, evolution can create new structures and is crucial to this understanding. The MODERN the synthesis of evolution and genetics can- species. Recent studies from evolutionary SYNTHESIS initially explained evolution through not explain how some fish became amphib- developmental biology are beginning to the mathematics of population genetics. ians, how some reptiles became mammals, or provide case studies that specifically address Although population genetics has remained how some apes became human (see the online these concerns. This perspective presents the core of the modern synthesis, it has also links box for a link to material dealing specifi- some of this new evidence and provides a come to include studies from ecology, biogeog- cally with arguments recently put forward framework in which to explain homology and raphy, paleontology, and more recently cytoge- by creationists). Behe6 named this inability phylogeny to such audiences. netics and molecular genetics. Population to explain the creation of new taxa through genetics, itself a marriage of Mendelian partic- genetics “Darwin’s black box”.When the box When asked to discuss evolution at public ulate inheritance and Darwin’s natural selec- is opened, he expects evidence of the Deity to forums, an hour or so is often given to outline tion, is able to explain how different alleles be found. However, inside Darwin’s black box the main principles of evolution and to give spread through the population, whereas cyto- resides merely another type of genetics — examples. I think that, until recently, our best genetics and molecular genetics are able to developmental genetics. examples came from microevolutionary stud- explain the origins of these alleles through If genetics is Darwin’s ‘missing evidence’7, ies — looking at evolution within a species. mutation and recombination. then developmental genetics is needed to However, although they are useful for Until recently, the best examples of evolu- complete the picture given by molecular and explaining evolutionary processes, focusing tion in action came from microevolutionary population genetics. Fifty years ago, British exclusively on microevolutionary studies left studies. Such studies explained, for instance, biologist C. H. Waddington was trying to openings for creationists to challenge whether how natural selection could cause moth col- bring developmental biology into the mod- species can be generated by evolutionary ouration to become darker and change the ern synthesis8–10, and he noted that evolution means. As well as providing new insights into beak shape in the Galapagos finches. For had two principal components. There was evolution, evolutionary developmental biol- the Galapagos finches, selection by drought the traditional component (that is, natural ogy has recently produced evidence that conditions allowed those individuals with cer- selection) that worked on adults that com- argues directly against the claims of creation- tain beak shapes to survive, transmit their pete for reproductive success, and an embry- ists, by shedding light on macroevolutionary beak shape to their offspring and change the ological component, in which variation (above the species-level) processes. Here, I beak morphology that had been characteristic was created and constrained.“The changes discuss some of this evidence and provide a of the species1.This illustrates the main tenets that produced new body plans…”, wrote framework for how we might wish to teach of natural selection: variation within a species; Waddington11,“…were inheritable changes

NATURE REVIEWS | GENETICS VOLUME 4 | SEPTEMBER 2003 | 735 PERSPECTIVES in the patterns of . Teaching phylogeny and homology But homology can be a tricky concept. If Changes in genotypes only have ostensible In 1859, Darwin wrote “It is generally acknowl- used alone (and some creationists imply that effects in evolution if they bring with them edged that all organic beings have been formed it is), it risks forming a circular argument alterations in the epigenetic processes by on two great laws — Unity of Type and wherein structures are considered homolo- which phenotypes come into being; and the Conditions of Existence” (REF.14).While natural gous because of common origin, and these kinds of change possible in the adult form of selection explained adaptation to the “offices of animals are said to have a common origin an animal are limited to the possible alter- existence”,embryonic homologies explained because they have homologous structures. An ations in the epigenetic system by which it is “unity of type” (REF.14).Together, they would independent assessment of ancestry and ori- produced.”Both the selective and the devel- produce the idea of ‘descent with modification’. gins is needed. Although we have this inde- opmental sides of evolution are important. In Using this concept, Darwin could explain the pendent assessment now, it was not avilable to 1977, the two sides of evolution began to be similarities of animal form through descent Darwin. Without this independent assess- bridged. Nobel Laureate François Jacob pro- from a common ancestor and the differences ment, the study of macroevolution became posed the idea that evolution was bricolage — by natural selection in different environments. embroiled in disputes about whether similar tinkering, not engineering12.Moreover,Jacob When introducing evolution to students, biol- structures were the result of common ances- claimed that evolutionary biologists should ogists usually concentrate on natural selection, try or convergence. The frustration about look at evolution not only in adults, but also the main mechanism of Darwinian evolution. whether similarities came from common during development, because evolution This is important. It shows that there is varia- ancestry (homology) or common environ- works not only on adults but also on the tion within a species; that most animals die ments (HOMOPLASY) caused biologists of the ‘recipes’ for adults. Therefore, to study large before reproducing; that the mortality can be first three decades of the twentieth century to changes in evolution, biologists needed to selective; and that the progeny resulting from leave this area of research and begin the micro- look for changes in the regulatory genes that such selection are more fit for their environ- evolutionary studies that related evolution to make the embryo, not just in the structural ment, having inherited the genes that made genetic variation within species (for example, genes that provide fitness within populations. their parents fit. But this is only half of the see REFS 16,17).“The geneticist…”,said William The last quarter of a century has borne out story. The other half concerns the unity of type Bateson in 1922, “…is the successor of the this idea. It took a while for developmental and the question of homology, that is, the fact morphologist.” (REF.18). genetics to reach maturity, but it can now be that animals are joined together into groups I find that I can teach the relationships of added to the mix of population genetics and with similar features. homologies and evolution best by looking at molecular genetics to explain evolution. one of the other passengers on the HMS Moreover, when developmental genetics is Beagle. The Tierra del Fuegan,York Minster, added, macroevolution can be explained was a bit older than Darwin, but like Darwin, much more easily. The microevolutionary “…I propose that students he had been trained in theology (FIG. 1a).York processes of mutation and recombination can will learn the principles of Minster had been abducted by Captain Fitzroy be analysed to determine how specific genetic on the first voyage of the HMS Beagle to the changes have created new types of organisms evolution most easily from southern tip of South America, and Fitzroy by altering their development. So, when con- examples of development.” had him educated in London as a missionary. fronted with the classic evolutionary question Both he and Darwin completed their theologi- of how the arthropod body plan arose, Hughes cal training in 1830. Newly baptized, this Tierra and Kaufman began their study by stating, del Fuegan was now being repatriated to “To answer the question by invoking natural To show this unity of type and how ani- spread the Gospel in his homeland19.Imagine selection is correct but insufficient. The fangs mals are variations on a relatively small set of his education. He would have been told of dif- of a centipede … and the claws of a lobster themes, Darwin followed von Baer’s princi- ferent religions:Judaism, Catholicism, Russian accord these organisms a fitness advantage. ples and looked to embryonic and larval and Greek Orthodoxy, Lutheranism and, of However, the crux of this mystery is this: stages, because the earlier stages of animal course, Anglicanism. There are differences From what developmental genetic changes did development could show homologies that are and similarities between these religions: they these novelties arise in the first place?” (REF.13). obscured in the adult. In On the Origin of share similar, but different Bibles; sing similar, Here,I propose a way of teaching evolu- Species,Darwin celebrated the case of the bar- but different hymns; and worship similar, but tion that highlights developmental genetics. nacle, the larvae of which showed that it is a different Gods. How was he to make sense of As such, it confronts the creationist chal- shrimp-like arthropod14, and in Descent of them? Do these similar religions have a com- lenges directly and shows how changes in Man15,he gloried in Alexander Kowalevsky’s mon origin or are they separate acts of reli- gene expression can cause a marked evolu- discovery that the tunicate — previously clas- gious faith? No-one can go back in time. How tionary change. Both population genetics sified as a shell-less mollusk — is actually a would he determine whether the religions and developmental genetics, as well as contri- chordate. It has a NOTOCHORD and pharyngeal come from a common ancestor and if the butions from other fields such as palaentol- slits that come from the same cell layers as similarities are due to this common origin? ogy and biogeography, are required for any those of fish and chickens. So, the two great First, there would be material evidence. theory of evolution, but I propose that stu- domains of the animal kingdom — inverte- The Tierra del Fuegan would have the evi- dents will learn the principles of evolution brates and vertebrates — were united through dence of archaeology. Biblical archeology had most easily from examples of development. I larval homologies.“Thus, if we may rely on uncovered artefacts showing shared histories illustrate my argument with examples, most embryology, ever the safest guide in classifica- and transitions. He could be shown concrete of which come from vertebrates and insects, tion, it seems that we have at last gained a clue evidence of religious history (such as Herod’s and so I apologize in advance to the allies of to the source whence the Vertebrata were palace), linking Judaism and Christianity. Just all other clades. derived.” (REF.15). as archeology can reveal the history and

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a b c West/East Greek Papal authority Greek Orthodox Orthodox Christian Christian Russian Russian Orthodox Orthodox Judaism Judaism (Roman Lutheran (Roman Lutheran empire empire variants) variants) Anglican Anglican

Catholic Catholic

Reform Reform Judaism Judaism Conservative Conservative Judaism Judaism Orthodox Orthodox Judaism 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 Catholicism, and only later do they branch origins. Not until the arrival of molecular reveals the history and transitions between off into Eastern and Western derivatives. genetics would evolution have a powerful groups of animals. Instead of the East/West distinction being way of getting around the homology ques- Second,York Minster could use vestigial primary, the second cladogram is made on tion. It wasn’t until the late 1970s that we apparatus and homologies to show the the papacy/non-papacy distinction. could access the historical records of genes, genealogical connection between faiths. He How could York Minster decide which model is and they turned out to be a treasure trove might argue that Christian Bibles have lists of correct? How do we know that the model in FIG.1b beyond measure. By finding rare and shared Semitic kings that would not be there were it is correct and the model in FIG.1c is wrong? Here, molecular similarities, the genealogical rela- not for their inclusion in an earlier religion. York Minster had a huge advantage over Charles tionships between higher taxa can be found. The fact that so many strange stories, such as Darwin.There were textual records for the histories Later phylogenetic reconstructions also that of Onan, Samson, Ahab and Jezebel, of the churches.York Minster might say that the included LIKELIHOOD AND BAYESIAN ESTIMATION occur in the Hebrew Bible, the Protestant best evidence is neither from material artefacts nor TESTS for deciding which paths of evolution Bibles and the Catholic Bible would indicate from arguments about homologies and vestigial were most probable. Evolutionary problems that there is a common origin. His shipmate apparatus (as the lack of allegiance to the papacy that had been intractable to Darwin and Darwin would similarly argue that such could result either from common ancestry or from early evolutionary biologists have now been strange things as the aortic arches would not two independent events), but from textual evi- solved. The phylogeny of insects, for exam- be present in mammals and amphibians were dence.In religions,this would be the set of docu- ple, was fraught with problems of homo- they not in the earlier ancestors from which ments that show the splitting of one religion into plasy16.However,a rare gene rearrangement they arose. The aortic arches would not be two or more new religions.Henry VIII’s 1534 Act of shared between insects and crustaceans has ‘invented’ twice, especially when most of the Supremacy and Martin Luther’s 95 Theses (1517) now shown the common ancestry of these mammalian aortic arches degenerate. would be such documents,showing the separation two groups20,refuting the alternative On the basis of his knowledge of homolo- of Protestant Christianity from Catholicism and hypothesis that insects were derived from a gies, vestigial apparatus and material artefacts, not fromOrthodoxy. myriapod-like ancestor. Similarities in 18S York Minster could draw a cladogram of reli- Darwin and his colleagues could draw ribosomal RNA sequences, coupled with the gions. One such cladogram is shown in FIG. 1b. branched-chain evolutionary trees of the same duplication of certain Hox genes in It should be noted that the first separation is animal kingdom that were based on embry- particular phyla, linked a set of invertebrates between the Jewish and Christian ‘clades’.Then onic homologies, adult homologies, vestigial into the ecdysozoan clade and established a there is a division in the Christian ‘clade’ apparatuses and the fossil record. But, until particular set of genealogical relationships between the Eastern and Western Churches. recently, there were many versions of these among the invertebrates21,22.Similarly, we Then there is a split in the Western Church trees, because there was no independent have a record telling us that the whale and between Catholicism and the Protestant assessment of homology except for the fossil hippopotamus are closely related and that denominations. This cladogram views the record. And here is where macroevolution, both arose from an ancestor that is in com- liturgy and Bible translation as fundamental the study of phylogeny — of evolution above mon with the cow and deer23.The phylogeny characteristics. However, another cladogram the species-level — encountered a problem. of animals has become less a matter of inter- can be made. This alternative (FIG. 1c) views the It did not have such documentation. Except preting visual evidence and more a matter of papacy as a derived trait (not seen in Jewish, for the fossil record, which was much worse reading the documentation. Orthodox or Protestant lineages). So, together, for Darwin than it is for us today, there was By looking at the cladograms of religion, Protestantism and Orthodoxy split from no independent assessment for common and by showing how molecular evidence fills

NATURE REVIEWS | GENETICS VOLUME 4 | SEPTEMBER 2003 | 737 PERSPECTIVES the gaps in our assessment of homology, we The first discoveries in evolutionary devel- scheme. First, the genes that generated the can explain evolution to the public, and we can opmental genetics showed the remarkable photoreceptors of the primitive eyes of flat- also directly counter creationists’ claims that homology of genetic instructions. Indeed, the worms and other invertebrates are now used evolutionary biology is based on circular developmental instructions for forming sev- in the formation of the complex eye types. The arguments about homology relationships. eral analogous organs were shown to be entire optic system did not have to be invented homologous. For example, the fly eye and de novo.Rather, there was descent with modi- Evolutionary developmental biology mouse eye have very little in common as to fication. Second, the retina and lens are in their The ability to find and sequence genes has their origin or structure. However, Walter respective positions because the lens helps done more than provide evolutionary biolo- Gehring’s group showed that the instructions build the retina and the retina helps build the gists with an independent assessment of to form both the mouse and the fly eye are lens26,33.This type of reciprocal induction is animal relationships. It has enabled devel- based on a set of homologous genes, such as found whenever complex organs are being opmental biologists to look at the causal Pax6 (REF.26).The instructions are so similar made. The blood vessels are able to get into the mechanisms wherein small changes in genes that fly IMAGINAL DISCS will form an eye (a RENAL GLOMERULI because the developing cells of can generate large morphological differences. Drosophila eye) under the instruction of the the renal glomeruli induce blood-vessel for- In 1977, three publications paved the way for rodent Pax6 gene27.Not only is eye develop- mation in the mesoderm next to them34,35. evolutionary developmental biology. These ment dependent on the Pax6 gene through- Third, complex systems with new properties publications were the aforementioned article out the animal kingdom, but the genes that can be generated by the interactions of simpler Evolution and tinkering12,Stephen J. Gould’s interact with Pax6 to form the photo- systems. Using computer programs that show book Ontogeny and Phylogeny 24 and Maxam receptor cells also seem to be evolutionarily the salient features of evolution — replication, and Gilbert’s technique for DNA sequenc- conserved28,29.Therefore, whereas it was pre- variation and differential fitness — Lenski and ing 25.In Ontogeny and Phylogeny, Gould viously thought that eyes formed indepen- colleagues36 showed that mutation and selec- showed how the German biologist Ernst dently many different times30,we now find tion could evolve complex functions out of Haeckel had misrepresented the field of evo- that each type of eye is but a variation on a simpler ones, and that, in some instances, lutionary embryology and made it into an theme. Moreover, many of the genes that mutations that were originally deleterious unscientific and racist doctrine. Indeed, the specify the formation of the heart, the ner- when they first emerged became stepping- first half of this book exorcises Haeckel’s ghost vous system and the anterioposterior body stones in the evolution of more complex so that some other model of evolution and axis also seem to be the same throughout programmes. Importantly, there were sev- development could be put in place of Haeckel’s the animal kingdom, despite the enormous eral cases in which the amalgamation of Biogenetic Law, wherein ‘ontogeny recapitu- diversity of these structures31,32. simpler programmes into a more complex lates phylogeny.’Jacob’s paper proposed a new So, whereas creationists are fond of saying programme involved no intermediates. model that could be tested, and the paper on that Darwin admitted that he had no idea Development is complicated and intercon- DNA sequencing established a method that how an organ as precise and as complicated nected; it is not irreducibly complex. could test it. as an eye could evolve, we now have the basic However, although the first wave of evolu- tionary developmental biology uncovered the remarkable similarities among very diverse Chicken hindlimb 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 Duck hindlimb 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 develop- mental regulatory genes can mediate evolu- tionarily important morphological changes. BMP Gremlin Apoptosis Newborn Figure 2 | Regulation of chicken limb apoptosis by BMPs. Autopods of chicken feet (top) and duck feet Mutating the regulatory genes. One way to (bottom) at similar stages. The in situ hybridizations show that while bone morphogenetic proteins (BMPs) produce evolutionary change is to mutate 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 regulatory genes. This seems to have been the red dye accumulation) becomes distinctly different in the two types of webbing. Reproduced with case with the Ultrabithorax (Ubx) gene, which permission from REF. 33 © Sinauer Associates (2003) and REF. 41 © The Company of Biologists (1999). has undergone a mutation in the clade.

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As a result of this mutation, the Ubx protein expression of bone morphogenetic protein 4 ab of insects (but not of other arthropod (BMP4) in the interdigital spaces signals these groups) now represses Distal-less expres- ‘webbing’ cells to undergo apoptosis. Duck sion37,38.This means that insects will only and chicken hindlimbs have the same pattern have thoracic legs. Whereas other arthropods of BMP4 gene expression, both embryos — millipedes, centipedes and crustaceans — expressing BMP4 in the interdigital cells of are known for their many legs, insects have the foot. Where they differ is in the expression but six. As Jacob predicted, mutations in reg- of a BMP inhibitor protein, Gremlin (FIG. 2). ulatory genes can give them new properties. Gremlin expression is seen in both the chicken and duck hindlimbs, where it is found around Altering the genetic targets of regulatory the digits. In the duck, however, and not in the proteins. In many instances, large changes in chicken, the Gremlin gene is also expressed in Figure 3 | Inhibition of cell death by inhibiting evolution can be made by maintaining the the interdigital cells. The Gremlin protein BMP. a| Control chicken hindlimbs have extensive same patterns of regulatory protein expres- made there prevents BMP from signaling for apoptosis in the space between the digits, leading sion but altering their downstream targets. cell death in the webbing, and the result is a to the absence of webbing. b | When beads This can be seen in the difference between webbed foot. This can be experimentally tested soaked with Gremlin protein, an inhibitor of bone four-winged butterflies and two-winged fruit by adding Gremlin-containing beads into the morphogenetic protein (BMP), are placed into the interdigital mesoderm, the webbing persists and flies and houseflies. The butterfly hindwing interdigital regions of the embryonic chicken generates a duck-like foot. Reproduced with differs from the Drosophila HALTERE,but both hindlimb. When this is done, the chicken foot permission from REF. 41 © The Company of structures are generated through the action of resembles that of a duck (FIG. 3).This is brico- Biologists (1999). the Ubx protein on the larval imaginal discs lage. The protein hasn’t changed, it is just of the third thoracic segment. However, Ubx being expressed at a different place. regulates different genes in the butterfly imag- Changing the pattern of regulatory gene spond exceptionally well to a proposed mecha- inal discs from the ones in the Drosophila expression has also been shown to correlate nism of feather production from archosaurian imaginal discs. So the DIPTERANS have diverged with the type of vertebra formed by the SOMITES scales. Changing the pattern of regulatory gene from other four-winged insects through and the type of appendage formed by crus- expression has also been correlated with the changes in the Ubx-responsive genes of the taceans42–44.It has also been correlated with the loss of limbs in snakes47. thoracic imaginal discs39, 40. formation of feathers from scales. Feathers have long been proposed as an evolutionary Changes in the temporal expression of regula- Altering the spatial expression of regulatory novelty, and creationists say that feathers can- tory genes. In addition to getting evolutionary genes. A mutation in the actual protein or its not be generated from any other structure. change by altering the spatial expression of receptor is not needed to effect evolutionary However, recent papers present evidence genes, remarkable changes can be obtained by change. A change in the expression pattern of that differences in the expression of Sonic altering the temporal expression of genes. a regulatory protein can also be vitally impor- hedgehog (Shh) and BMP proteins separate Heterochronic (temporal) changes in Wnt5 tant. For example, changes in the spatial the feather from the scale45,46.Moreover,when gene expression are responsible for the changes expression of regulatory genes can explain the expression of Shh or BMP2 is altered, the between direct and indirect developing sea how the duck got its webbed feet41.Here,the feather pattern changes. The results corre- urchins48.Heterochronic changes also seem to

Glossary

BAYESIAN IMAGINAL DISCS NOTOCHORD A branch of statistics that focuses on the posterior Thickenings of the epidermis in larval insects. These A rod of mesodermal cells in the dorsal midline probability of hypotheses. The posterior probability is structures produce the adult wings, legs, eyes, antennae, beneath the neural tube. It is the major characteristic proportional to the product of the prior probability and mouth and genitalia during metamorphosis. of chordates. the likelihood. POLYPHENISM DIPTERANS The period between larval insect molts. Phenotypic variation not attributable to genetic Insects with two wings, such as flies and mosquitos. differences: the product of environmental stimuli LIKELIHOOD ESTIMATION TEST on particular genotypes. One example is seasonal A statistical method that calculates the probability of the ECLOSION polyphenism, whereby individuals with the same observed data under varying hypotheses to estimate model The emergence of the adult insect from its pupal case. genotype manifest different phenotypes owing to parameters that best explain the observed data and determine temperature. the relative strengths of alternative hypotheses. HALTERE Balancers. Club-like tissue arising from the imaginal disc REACTION NORMS MODERN SYNTHESIS in the third segment of dipterans. A situation in a population in which the genotype Neo-Darwinism. The theory that natural selection, acting on randomly generated variation, is the major cause of provides a graded response to environmental HOMOPLASY evolution. conditions. Similarity whereby structures have similar form or function but not the same ancestral origin. Homoplasies NEURAL CREST CELLS RENAL GLOMERULI often result from convergent evolution whereby different A migratory cell population that arises at the lateral A cluster of capillaries in the kidney cortex. organisms in the same environment produce similar edges of the neural plate, and which differentiates adaptions. into numerous cell types including skull and facial SOMITES bone, pigment cells, adrenal medullary cell, and Blocks of mesoderm along the vertebrate body axis HYPOPHYSEAL the neurons and glia of the sensory and that further differentiate into dermal skin, bone and Pituitary. autonomic nervous systems. muscle.

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Population genetics Developmental genetics mones control the expression of particular when the perspectives of embryonic induc- genes9,50.This is known as developmental plas- tion and developmental genetics are added, Variation within Variation between populations populations ticity and it is the basis for REACTION NORMS and these novelties become explainable, at least in POLYPHENISMS.At different points in their ranges outline, if not yet in detail. Such information one extreme of this plasticity might become is crucial if we are to counter the distortions Genes in Genes in embryonic genetically fixed51–54.This ability of a develop- of science by creationists58. adults competing for and larval organisms reproductive success building structures mentally plastic trait to become genetically J. B. S. Haldane, the editor of the volume fixed has been documented numerous times in which Waddington published the above- in the laboratory and could provide a rapid mentioned paper, commented on this idea Survival of the fittest Arrival of the fittest means for the origin of new species55,56. using a wonderfully apt developmental meta- phor,“To sum up, then, a number of workers A new evolutionary synthesis are groping from their own different stand- Natural selection Phylogeny The developmental genetic approach to evo- points towards a new synthesis, while produc- lution complements the traditional popula- ing facts which do not fit too well into the A new evolutionary tion genetic approach. They are both needed. currently accepted synthesis. The current synthesis explaining biodiversity The mechanisms of genetic change in regula- instar of the evolution theory may be defined tory genes are the same as those of structural by such books as those of Huxley, Simpson, genes, and once these evolutionary novelties Dobzhansky, Mayr, and Stebbins. We are cer- Figure 4 | A newly emerging evolutionary are generated they must still be selected. The tainly not ready for a new moult, but signs of synthesis. The classic approach to evolution has been that of population genetics. It emphasized traditional differences between the popula- new organs are perhaps visible.” (REF.59). variations within a species that allowed certain adult tion genetic and developmental genetic Today, exactly half a century later, we can individuals to reproduce more frequently. In this approaches to evolution are summarized in report that the organs have formed and the way, it could explain natural selection. The FIG. 4.These differences are beginning to INSTAR has ECLOSED.Evolutionary developmen- developmental approach looks at variation between blur as both population geneticists and tal biology has become a normative part of populations, and it emphasizes the regulatory developmental geneticists start studying evolutionary biology and should provide genes that are responsible for organ formation. Its explanations are more apt to explain evolutionary allelic variations of developmental regulatory wonderful and informative new ways of teach- 57 novelty and constraint. Together, population genes within populations . ing evolution to biology students and to the genetics and developmental genetics make a I would emphasize the importance of general public. more complete genetic approach to evolution. including examples from the developmental Scott F. Gilbert is at Swarthmore College, genetics approach when discussing evolution Swarthmore, Pennsylvania 19081, USA. in public. In addition to being easier to under- e-mail: [email protected] be responsible for another evolutionary nov- stand than the population genetic approach doi:10.1038nrg1159 elty, the vertebrate jaw — one of the problems to teaching evolution, the developmental 1. Grant, P. R. Ecology and Evolution of Darwin’s Finches that puzzled evolutionary embryologists in the approach might have other advantages. First, (Princeton Univ. Press, Princeton, New Jersey, 1986). early 1900s. In the lamprey, the naso-hypophy- the developmental genetic approach uses 2. McKenzie, J. A. & Batterham, P. Predicting insecticide resistance: mutagenesis, selection and response. seal plate is retained and prevents the migra- examples that everyone can understand from Philos. Trans. R. Soc. Lond. B 353, 1729–1734 tion of NEURAL CREST CELLS rostrally. In jawed visual experience. Second, evolution at the (1998). 3. Raymond, M., Chevillon, C., Guillemaud, T., Lenormand, T. vertebrates, this plate separates very early in level of developmental regulatory genes might & Pasteur, N. An overview of the evolution of development into the nasal and HYPOPHYSEAL be the main source of variation. In humans overproduced esterases in the mosquito Culex pipiens. Philos. Trans. R. Soc. Lond. B 353, 1707–1711 (1998). neural tissues, thereby making a path for the (that animal for which variations have been 4. Normark, B. H., & Normark, S. Evolution and spread of rostral migration of neural crest cells. This catalogued most carefully), genes are het- antibiotic resistance. J. Intern. Med. 252, 91–106 allows the formation of a new structure, the erozygous at more functional cis-regulatory (2002). 5. Pigliucci, M. Phenotypic Plasticity: Beyond Nature jaw. As Kuratani and colleagues conclude, sites (>16,000) than at exon sites (<13,000). and Nurture (Johns Hopkins Univ. Press, Baltimore, “The clue to solve this problem, therefore, will Ordinary small-scale mutations contribute to 2001). 6. Behe, M. J. Darwin’s Black Box: the Biochemical not be obtained by comparative anatomy of large variations in transcription rates across Challenge to Evolution (Free Press, New York, 1996). the adult structures, but rather by discrimina- the genome and so to human variation57. 7. Kettlewell, H. B. D. Darwin’s missing evidence. Sci. Amer. 200, 48–53 (1959). tion of conserved and newly acquired patterns Third, these examples address the questions 8. Hall, B. K. Waddington’s legacy in development and of gene expression… Molecular developmen- of evolutionary novelty that creationists evolution. Am. Zool. 32, 113–122 (1992). 9. Gilbert, S. F. Diachronic biology meets evo–devo: tal biology has taken the initial steps into this say cannot be explained by evolution — how C. H. Waddington’s approach to evolutionary old question of comparative zoology, but it insects have fewer legs than centipedes, developmental biology. Am. Zool. 40, 729–737 (2002). 10. Slack, J. M. Conrad Hal Waddington: the last Renaissance has already suggested new directions in which how snakes lost their legs, how birds got biologist? Nature Rev. Genet. 3, 889–895 (2002). a solution may lie.” (REF.49). feathers and ducks got their webbed feet. We 11. Waddington, C. H. Canalization of development and the are therefore able to show where creationists inheritance of acquired characteristics. Nature 150, 563–565 (1942). Selection of variants that are caused by are wrong and how their ideas about homol- 12. Jacob, F. Evolution and tinkering. Science 196, developmental plasticity. In many organisms, ogy and morphological novelties are out of 1161–1166 (1977). 13. Hughes, C. G. & Kaufman, T. Hox genes and the the genotype does not directly predict the phe- date. If the processes of evolution were evolution of the arthropod body plan. Evo. Dev. 4, notype. Rather, the genotype provides a range viewed solely from the population genetic 459–499 (2002). 14. Darwin, C. On the Origin of Species (John Murray, of potential phenotypes and the exact pheno- perspective, it would appear very difficult to London, 1859). type will be induced by the environment. explain the origins of feathers, teeth and eyes. 15. Darwin, C. The Descent of Man and Selection in Relation to Sex 2 Vols, 2nd edn (John Murray, London, 1874). Usually, the environmental stimulus is sensed They seem to be (in the words of the cre- 16. Bowler, P. Life’s Splendid Drama (Univ. of Chicago Press, by the neuroendocrine system and the hor- ationists) “irreducibly complex”6.However, Chicago, 1996).

740 | SEPTEMBER 2003 | VOLUME 4 www.nature.com/reviews/genetics PERSPECTIVES

17. Gilbert, S. F. Bearing crosses: a historiography of 48. Ferkowicz, M. J. & Raff, R. A. Wnt gene expression in sea 58. Pigliucci, M. Denying Evolution: Creationism, Scientism, genetics and embryology. Am. J. Med. Genet. 76, urchin development: heterochronies associated with the and the Nature of Science (Sinauer Associates, 168–182 (1998). evolution of developmental mode. Evol. Dev. 3, 24–33 Sunderland, Massachusetts, 2002). 18. Bateson, W. Evolutionary faith and modern doubts. (2001). 59. Haldane, J. B. S. Foreword. in Evolution (Soc. Exp. Biol. Science 40, 1412–1415 (1922). 49. Kuratani, S., Nobusada, Y., Horigome, N. & Shigetani, Y. Symp. VII) (eds Brown, R. & Danielli, J. F.) ix–xix 19. Desmond, A. & Moore. J. Darwin: the Life of a Embryology of the lamprey and evolution of the vertebrate (Cambridge Univ. Press, Cambridge, UK, 1953). Tormented Evolutionist (Norton, New York, 1991). jaw: insights from molecular and developmental 20. Boore, J. L., Lavrov, D. V. & Brown, W. M. Gene perspectives. Philos. Trans. R. Soc. Lond. B 356, Acknowledgements translocation links insects and crustaceans. Nature 392, 1615–1632 (2001). This Perspective is based on a talk originally presented as a lec- ture to the Society for Developmental Biology (SDB) at its annual 667–668 (1998). 50. Nijhout, H. F. Development and evolution of adaptive meeting in 2002. I wish to thank the Education Committee of the 21. Aguinaldo, A. M. et al. Evidence for a clade of polyphenisms. Evol. Dev. 5, 9–18 (2003). SDB for the opportunity to write it and to Kenneth Miller and Sean nematodes, arthropods and other moulting animals. 51. Waddington, C. H. in Evolution (Soc. Exp. Biol. Symp. VII) Nature 387, 489–493 (1997). Carroll for their helpful comments. Funding was from the National (eds Brown, R. & Danielli, J. F.) 186–199 (Cambridge Univ. 22. De Rosa, R. et al. Hox genes in brachiopods and Science Foundation and from Swarthmore College, Pennsylvania. Press. Cambridge, UK, 1953). priapulids and protostome evolution. Nature 399, 52. Schmalhausen, I. I. Factors of Evolution: the Theory of 772–776 (1999). Stabilizing Selection (Univ. of Chicago Press, Chicago, 23. Shimamura, M. et al. Molecular evidence from Online links 1949). retroposons that whales form a clade within even-toed 53. Shapiro, A. M. Seasonal polyphenism. Evol. Biol. 9, ungulates. Nature 388, 666–670 (1997). DATABASES 259–333 (1976). 24. Gould, S. J. Ontogeny and Phylogeny (Harvard Univ. The following terms in this article are linked online to: Press, Cambridge, Massachusetts, 1977). 54. Brakefield, P. M. et al. Development, plasticity, and FlyBase: http://flybase.bio.indiana.edu 25. Maxam, A. & Gilbert, W. A new method for sequencing evolution of butterfly eyespot patterns. Nature 384, Distal-less | Ubx DNA. Proc. Natl Acad. Sci. USA 74, 560–564 (1977). 236–242 (1996). LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink 26. Gehring, W. J. The genetic control of eye development 55. West-Eberhard, M. J. Phenotypic plasticity and the Pax6 and its implications for the evolution of the various eye- origins of diversity. Annu. Rev. Ecol. Syst. 20, 249–278 Swiss-Prot: http://www.expasy.ch types. Int. J. Dev. Biol. 46, 65–73 (2002). (1989). BMP2 | BMP4 | Gremlin | Sonic hedgehog 27. Halder, G., Callaerts, P., & Gehring, W. J. Induction of 56. West–Eberhard, M. J. Developmental Plasticity and ectopic eyes by targeted expression of the eyeless gene Evolution. Oxford University Press (2003). FURTHER INFORMATION in Drosophila. Science 267, 1788–1792 (1995) 57. Rockman, M. V. & Wray, G. A. Abundant raw material for Evolution, development, and creationism — a supplement: 28. Pineda, D. et al. Searching for the prototypic eye genetic cis-regulatory evolution in humans. Mol. Biol. Evol. http://zygote.swarthmore.edu/Darwin network: Sine oculis is essential for eye regeneration in 19,1991–2004 (2002). Access to this interactive links box is free online. 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 OPINION 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 Vertebrate gene predictions and (2002). 33. Gilbert, S. F. Developmental Biology 7th edn (Sinauer Associates, Sunderland, Massachusetts, 2003). 34. Aitkenhead, M. et al. Paracrine and autocrine regulation the problem of large genes 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 Jun Wang, ShengTing Li, Yong Zhang, HongKun Zheng, Zhao Xu, Jia Ye, VEGF-A expression lead to distinct congenital and acquired renal diseases. J. Clin. Invest. 111, 707–716 Jun Yu and Gane Ka-Shu Wong (2003). 36. Lenski, R. E., Ofria, C., Pennock, R. T. & Adami, C. To find unknown protein-coding genes, easier to predict. Nevertheless, the many The evolutionary origin of complex features. Nature 423, 5 6 139–144(2003). annotation pipelines use a combination of fruitfly and nematode cDNAs that were 37. Galant, R. & Carroll, S. B. Evolution of a transcriptional ab initio gene prediction and similarity to produced after their genomes were sequenced repression domain in an insect Hox protein. Nature 415, experimentally confirmed genes or 910–913 (2002). have been invaluable in finding residual 38. Ronshaugen, M., McGinnis, N. & McGinnis, W. proteins. Here, we show that although the errors in the definition of exon boundaries. Hox protein mutation and macroevolution of the ab initio predictions have an intrinsically As it is difficult to get cDNAs that are insect body plan. Nature 415, 914–917 (2002). 39. Carroll, S. B., Weatherbee, S. D. & Langeland, J. A. high false-positive rate, they also have a expressed transiently, or at low levels, in spe- Homeotic genes and the regulation and evolution of consistently low false-negative rate. cific tissues and at specific developmental number. Nature 375, 58–61 (1995). 40. Weatherbee, S. D. et al. Ultrabithorax function in butterfly The incorporation of similarity information is stages, predicting genes will remain an inte- wings and the evolution of insect wing patterns. Curr. meant to reduce the false-positive rate, but gral part of DNA sequence analysis for the Biol. 9, 109–115 (1999). 41. Merino, R. et al. The BMP antagonist Gremlin regulates in doing so it increases the false-negative foreseeable future. Therefore, it is imperative outgrowth, chondrogenesis and programmed cell death rate. The crucial variable is gene size for the biologists who use gene-prediction in the developing limb. Development 126, 5515–5522 (1999). (including introns) — genes of the most programs to understand what they can and 42. Gaunt, S. J. Conservation in the Hox code during extreme sizes, especially very large genes, cannot do. Although some features of these morphological evolution. Int. J. Dev. Biol. 38, 549–552 (1994). are most likely to be incorrectly predicted. programs are better than is commonly 43. Burke, A. C., Nelson, A. C., Morgan, B. A. & thought, others are worse. It is tempting to Tabin, C. Hox genes and the evolution of vertebrate axial morphology. Development 121, 333–346 We live in the halcyon days of large-scale dismiss the programs as being inherently (1995). DNA sequencing. Each release of a unreliable (see BOX 1 for a note on fluctua- 44. Averof, M. & Patel, N. H. Crustacean appendage evolution associated with changes in Hox gene sequenced genome is accompanied by a list tions in gene number in the human genome), expression. Nature 388, 682–686 (1997). of genes, many of which are computer pre- but, in fact, they fail for specific reasons that 45. Harris, M. P., Fallon, J. F. & Prum, R. O. Shh–BMP2 signaling module and the evolutionary origin and dictions. Experimental confirmation in the can be understood with minimal jargon and diversification of feathers. J. Exp. Zool. Part B Mol. Dev. form of sequenced transcripts of full-length without delving into algorithmic minutiae. Evol. 294, 160–176 (2002). 1,2 46. Yu, M., Wu, P., Widelitz, R. B. & Chuong. C. M. The cDNAs is extensive for mice , less so for ANNOTATION PIPELINES have been comprehen- morphogenesis of feathers. Nature 420, 308–312 (2002). humans3 and non-existent for pufferfish4. sively reviewed7.Every pipeline incorporates 47. Cohn, M. J. & Tickle, C. Developmental basis of limblessness and axial patterning in snakes. Nature 399, For invertebrate genomes, cDNAs are less information from known genes. No pipeline 474–479 (1999). important because the genes are smaller and ever substitutes a predicted gene for a known

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