At first glance, the list of animals could suggest any zoo. There’s an elephant, an armadillo, an opossum, a dolphin, a sloth, a hedgehog, big and small bats, a couple of shrews, some fish, a macaque, an orangutan, a chimpanzee and a gorilla—to name a few of the more familiar creatures. But this menagerie is not at all like any zoo that has been constructed before. There are no cages, no concession stands and, in fact, no animals. It is a “virtual” zoo that contains only the DNA sequences of those animals—the hundreds of millions to billions of letters of DNA code that make up the genetic recipe for each species. The most excited visitors to this new molecular zoo are evolutionary biologists, because within it lies a massive and detailed record of evolution. For many decades, scientists have longed to understand how the great diversity of species has arisen. We have known for half a century that changes in physical traits, from body color to brain size, stem from changes in DNA. Determining precisely what changes to the vast expanse of DNA sequences are responsible for giving animals their unique appearance was out of reach until recently, however. Biologists are now deciphering the DNA record to locate the instructions that make assorted species of flies, fish or finches look different from one another and that make us humans different from chimpanzees. This quest has led to a profound change in our perspective. For most of the past 40 years or so, researchers have focused most of their attention on genes—the nucleotide sequences in DNA that encode the amino acid chains that form proteins. But to our surprise, it has turned out that differences in appearance are deceiving: very different animals have very similar sets of genes. By following the trail of evolution, devices are being found within DNA—genetic “switches”—that do not encode any proteins but that regulate when and where genes are used. Changes in these switches are crucial to the evolution of anatomy and provide new insights into how the seemingly endless forms of the animal kingdom have evolved. Anatomy Genes and the Coding Paradox For a long time, scientists certainly expected the anatomical differences among animals to be reflected in clear differences among the contents of their genomes. When we compare mammalian genomes such as those of the mouse, rat, dog, human and chimpanzee, however, we see that their respective gene catalogues are remarkably similar. The approximate number of genes in each animal’s genome (about 20,000 or so) and the relative positions of many genes have been fairly well maintained over 100 million years of evolution. That is not to say there are no differences in gene number and location. But at first glance, nothing in these gene inventories shouts out “mouse” or “dog” or “human.” When comparing mouse and human genomes, for example, biologists are able to identify a mouse counterpart for at least 99 percent of all our genes. In other words, we humans do not, as some once assumed, have more genes than our pets, pests, livestock or even a puffer fish. Disappointing, perhaps, but we’ll have to get over it. When biologists look at individual genes in detail, similarity among species is also the rule. The DNA sequences of any two versions of a gene, as well as the proteins they encode, are generally alike to a degree that simply reflects the relative amount of time that has elapsed since the two species diverged from a common ancestor. This preservation of coding sequences over evolutionary time is especially puzzling when one considers the genes involved in body building and body patterning. Only a small fraction of all genes—fewer than 10 percent—are devoted to the construction and patterning of animal bodies during their development from fertilized egg to adult. The rest are involved in the everyday tasks of cells within various organs and tissues. Anatomical differences among animals—differences in the number, size, shape or color of body parts—must somehow involve the genes for body building. Indeed, the study of the pivotal role played in evolution by genes and processes associated with the development of anatomy has even earned its own nickname: evo-devo. For specialists, like ourselves, in that area of research, the discovery that body-building proteins are even more alike on average than other proteins was especially intriguing because of the paradox it seemed to pose: animals as different as a mouse and an elephant are shaped by a common set of very similar, functionally indistinguishable body-building proteins. The same applies to humans and our closest living relatives—most of our proteins differ from those of the chimpanzee by only one or two of the several hundred amino acids that comprise each protein, and 29 percent of our proteins are exactly identical in sequence. How do we explain this disparity between evolution at the two levels of proteins and anatomy? Somewhere in all of that genomic DNA there must be meaningful differences that have evolved. The trick is to find them, and the trick to doing that has been deciding where to look. It turns out that those places are much harder to locate than are genes themselves. Genetic Switches In humans, the protein-coding stretches of DNA make up only about 1.5 percent of our genome, so genes are really like little islands of information in a vast sea of DNA sequence. Much of the remaining noncoding DNA does nothing that we know of, but some of those sequences participate in the very important task of regulating gene expression. And these regulatory sequences are key to evolution. The expression of a gene entails the transcription of the DNA sequence into a messenger RNA (mRNA) version and the translation of that mRNA into a protein sequence. The expression of most genes is regulated at the transcriptional level—cells do not waste energy making -mRNAs and proteins they do not need. Many genes are therefore expressed only in an organ-, tissue- or cell type–specific manner. Certain noncoding DNA sequences play a critical part in directing when and where that happens. They are components of “genetic switches” that turn genes on or off at the right time and place in the body. Sequence-specific DNA-binding proteins called transcription factors, which are the other components of the switch, recognize those DNA sequences, often called enhancers. The binding of the transcription factors to the enhancer within a cell nucleus determines whether the switch and the gene are on or off in that cell. Every gene has at least one enhancer. Unlike the genes themselves, whose coding regions are readily identified because of the genetic code’s fairly simple grammar, enhancers cannot be recognized solely on the basis of their DNA sequences and must be identified experimentally. Enhancers are usually hundreds of base pairs in length and may be located on either side of a gene or even within a noncoding stretch inside a gene. They can also be thousands of nucleotides away from the gene itself. Most important to our discussion here is the fact that some genes have many separate enhancers. This is particularly true for genes that encode proteins that shape anatomy. Each enhancer independently regulates the expression of the gene in different parts of the body and at different times in the animal’s life cycle, such that the complete expression of a gene is a patchwork of multiple, independently controlled sites of expression. These enhancers enable the same gene to be used many times in different contexts and thus greatly expand the functional versatility of individual genes. A gene involved in coloring the body parts of the fruit fly illustrates the modular logic of this gene regulation system. The somewhat confusingly named Yellow gene encodes a protein that promotes the formation of black pigmentation (mutant flies without this protein are Yellow). The Yellow gene has separate enhancers that activate it during the development of a variety of fly body parts, including the wings and abdomen. Because the Yellow gene plays a role during the development of so many tissues, mutations in the gene itself could be disastrous if they alter or disable the function of the protein; they would affect the function of the Yellow pigmentation protein throughout the organism. In contrast, changes in just one of the gene’s enhancers will affect only the function of that enhancer and only the Yellow gene expression governed by that enhancer, leaving the expression and function of the protein in other tissues unchanged. The evolutionary implications of the modular regulation of body-patterning genes are profound. In theory, mutations in enhancers would allow individual body traits to be selectively modified without changing genes or proteins themselves. And in the past few years, direct evidence has emerged that this is frequently how the evolution of various body parts and patterns has occurred. Evolving Switches One of the most important strategies in biology is to identify the simplest experimental models of the phenomenon one wishes to understand. With respect to the evolution of body pattern, coloration fits the bill. It is one of the most obvious features of animals and plays a major role in how animals interact with their environment and with one another. Body-color patterns in fruit flies have diversified rapidly among closely related species, and analyses of how fruit flies got their spots and stripes illustrate how and why the evolution of genetic switches shapes the evolution of anatomy. In some species, the males have intense black spots on the edges of their wings, whereas other species lack these spots. In some of these same species, males have a very dark abdomen (which is how the most famous fruit fly, Drosophila melanogaster, got its name: melanogaster means “black belly”), whereas males of other species lack this black band. In wing-spotted species, the male displays his spots to the female as he courts her with a dance. We have found that in spotted species, the Yellow protein is produced at very high levels in the cells that will make the spot and at low levels in the rest of the wing cells. In unspotted species, Yellow is made only at low levels throughout the wing, generating just a light dusting of black pigment. To figure out how Yellow is produced in a wing spot in some species and not others, we searched the DNA sequences around the Yellow gene for the enhancers that control its expression in various body parts. In unspotted species, there is an enhancer that drives Yellow expression in a low uniform pattern in the wing. This wing-enhancer activity generates the fly wings’ light-gray color. When the corresponding piece of DNA was analyzed from a spotted species, we found that it drives both this low-level pattern and the intense spot pattern of gene expression. What has happened in the course of evolution of spotted species is that new binding sites for transcription factors made in the wing evolved in the Yellow wing-enhancer DNA sequence. These changes created an expression pattern—wing spots—without altering where the Yellow protein is made or how it functions elsewhere in the body [see box]. A similar story applies to the evolution of the black band in the abdomen, but with a twist. Whereas we are naturally inclined to think that the presence of a feature in one species and its absence in another related species is the result of a gain by the first, that is often not the case. A flip side to evolution, the loss of features, is very common, though much less appreciated. The loss of body characters perhaps best illustrates why the evolution of enhancers is the more likely path for the evolution of anatomy. One enhancer of the Yellow gene governs its expression in the abdomen. In males of species with the black band, this enhancer drives the expression of the Yellow gene at high levels in cells at the rear of the abdomen. But some species, such as Drosophila kikkawai, lost this band of pigmentation in the course of evolution. In D. kikkawai, the enhancer can no longer drive high levels of Yellow expression in the rear of the abdomen because a few mutations have disrupted some of its transcription factor binding sites. It is important to emphasize that the Yellow gene remains active elsewhere in the body and that its biochemical function is intact. Although one path to losing the black band could have been through mutations that inactivate the Yellow gene and its protein, this path is not permitted by natural selection, because the loss of Yellow function elsewhere in the body would have additional, detrimental consequences. Losses of features may or may not be beneficial for survival or greater reproductive success, but some losses are adaptive because they facilitate some change in lifestyle. Hind limbs, for example, have been lost many times in vertebrates—by snakes, lizards, whales and manatees—and those losses are associated with adaptation to different habitats and means of locomotion. The evolutionary forerunners of the hind limbs of four-legged vertebrates are the pelvic fins of fish. Dramatic differences in pelvic fin anatomy have also evolved in closely related fish populations. The three-spined stickleback fish occurs in two forms in many lakes in North America—an open-water form that has a full spiny pelvis, and a shallow-water, bottom-dwelling form with a dramatically reduced pelvis and shrunken spines. In open water, the long spines help to protect the fish from being swallowed by larger predators. But on the lake bottom, those spines are a liability because dragonfly larvae that feed on the young fish can grasp them. The differences in pelvic morphology among these fish have evolved repeatedly in just 10,000 years since the last Ice Age. Long-spined oceanic sticklebacks colonized many separate lakes, and the reduced form evolved independently several times. Because the fish are so closely related and interbreed in the laboratory, geneticists can map the genes involved in the reduction of the stickleback pelvis. David M. Kingsley of Stanford University, along with Dolph Schluter of the University of British Columbia and colleagues, has shown that changes in the expression of a gene involved in the building of the pelvic skeleton are associated with the pelvic reduction. Like most other body-building genes, the Pitx1 gene has multiple jobs in the development of the fish. But its expression is selectively lost in the area of the fish that will give rise to the pelvic-fin bud and spines. Once again, evolutionary changes in an enhancer are responsible. There are no coding changes in the Pitx1 protein between different forms of the stickleback. Yellow, Pitx1 and most other body-building and body-patterning genes are said to be pleiotropic, in that they influence the formation or appearance of multiple traits. Mutations in the coding sequence of a pleiotropic gene have multiple effects on all the traits controlled by this gene, and that drastic amount of change is unlikely to be tolerated by natural selection. The key lesson from the evolution of spots, stripes and skeletons is that mutations in regulatory sequences circumvent the pleiotropic effects of mutations in coding sequences and allow for the selective modification of individual body parts. Mutations in regulatory sequences are not the exclusive mode of evolution—they are just the more likely path when a gene has multiple roles and one of those roles is selectively modified. Common Genes, Endless Variety The evolution of enhancers is not at all limited to genes affecting body form nor just to fruit flies and weird fish. Quite a few examples of evolutionary changes in regulatory sequences that alter gene expression have been demonstrated for human traits as well. One of the more striking cases in recent human evolution represents an adaptation, through selective loss of gene expression, to an environment where malaria is endemic. In addition to the familiar A, B and O blood types, other so-called minor blood types have been well studied. The status of a protein called Duffy, present on the surface of red blood cells, defines one of these types. The Duffy protein constitutes part of the receptor that is used by a malaria-causing parasite, Plasmodium vivax, to infect red cells, but in West Africa the protein is absent from the blood cells of almost 100 percent of the population, making individuals resistant to infection. The Duffy gene is also expressed in several other body tissues, including cells of the spleen, the kidneys and the brain. In the African population, Duffy expression in those other tissues is preserved. Not surprisingly, these Duffy-negative individuals carry a mutation in an enhancer of the Duffy gene that knocks out the binding site for a transcription factor that activates Duffy expression in red blood cell precursors but that has no effect on Duffy production elsewhere in the body. Gregory A. Wray of Duke University and his collaborators have identified other aspects of human biology that have evolved through mutations in enhancers in different human genes. One of the most intriguing associations revealed thus far involves divergence in the great ape and human regulatory sequences controlling the Prodynorphin gene, which encodes a set of small opioid proteins produced in the brain and involved in perception, behavior and memory. The human gene is more highly expressed in response to stimuli than is the chimpanzee version, and strong evidence suggests that the human regulatory sequence evolved under natural selection—that is, it was retained because it was advantageous. As these examples illustrate, mutations in regulatory DNA have undoubtedly played a role in human evolution and regulatory variation may be an important source of physical and health differences among individuals as well. Because scientists cannot tinker with the DNA of living humans the way we can with flies and fish, it is somewhat harder to study certain examples of regulatory DNA changes responsible for our divergence from other species, although some new methods for analyzing genomes are producing encouraging leads [see box]. These are still early days for research into the evolution of gene-regulating DNA sequences. And hundreds of thousands of genetic switches in the virtual zoo of genomes have yet to be discovered or investigated. Biologists are already learning new principles, however, that have predictive value for future studies: evolutionary changes to anatomy, particularly those involving pleiotropic genes, are more likely to happen via changes to gene enhancers than to the genes themselves. This phenomenon also reveals how very diverse groups of animals can share most, if not all, the genes involved in body building and body patterning—contrary to scientists’ early expectations, it is mostly a matter of how and when those genes are used that shapes the different forms of the animal kingdom. If we really want to understand what makes the human form different from that of other apes or what makes an elephant distinct from a mouse, for that matter, much of that information lies not in our respective genes and proteins but in an entirely different realm of our genomes that remains to be explored. Editor’s Note: This story was originally printed with the title “Regulating Evolution”
The most excited visitors to this new molecular zoo are evolutionary biologists, because within it lies a massive and detailed record of evolution. For many decades, scientists have longed to understand how the great diversity of species has arisen. We have known for half a century that changes in physical traits, from body color to brain size, stem from changes in DNA. Determining precisely what changes to the vast expanse of DNA sequences are responsible for giving animals their unique appearance was out of reach until recently, however.
Biologists are now deciphering the DNA record to locate the instructions that make assorted species of flies, fish or finches look different from one another and that make us humans different from chimpanzees. This quest has led to a profound change in our perspective. For most of the past 40 years or so, researchers have focused most of their attention on genes—the nucleotide sequences in DNA that encode the amino acid chains that form proteins. But to our surprise, it has turned out that differences in appearance are deceiving: very different animals have very similar sets of genes. By following the trail of evolution, devices are being found within DNA—genetic “switches”—that do not encode any proteins but that regulate when and where genes are used. Changes in these switches are crucial to the evolution of anatomy and provide new insights into how the seemingly endless forms of the animal kingdom have evolved.
Anatomy Genes and the Coding Paradox For a long time, scientists certainly expected the anatomical differences among animals to be reflected in clear differences among the contents of their genomes. When we compare mammalian genomes such as those of the mouse, rat, dog, human and chimpanzee, however, we see that their respective gene catalogues are remarkably similar. The approximate number of genes in each animal’s genome (about 20,000 or so) and the relative positions of many genes have been fairly well maintained over 100 million years of evolution. That is not to say there are no differences in gene number and location. But at first glance, nothing in these gene inventories shouts out “mouse” or “dog” or “human.” When comparing mouse and human genomes, for example, biologists are able to identify a mouse counterpart for at least 99 percent of all our genes.
In other words, we humans do not, as some once assumed, have more genes than our pets, pests, livestock or even a puffer fish. Disappointing, perhaps, but we’ll have to get over it.
When biologists look at individual genes in detail, similarity among species is also the rule. The DNA sequences of any two versions of a gene, as well as the proteins they encode, are generally alike to a degree that simply reflects the relative amount of time that has elapsed since the two species diverged from a common ancestor. This preservation of coding sequences over evolutionary time is especially puzzling when one considers the genes involved in body building and body patterning.
Only a small fraction of all genes—fewer than 10 percent—are devoted to the construction and patterning of animal bodies during their development from fertilized egg to adult. The rest are involved in the everyday tasks of cells within various organs and tissues. Anatomical differences among animals—differences in the number, size, shape or color of body parts—must somehow involve the genes for body building. Indeed, the study of the pivotal role played in evolution by genes and processes associated with the development of anatomy has even earned its own nickname: evo-devo. For specialists, like ourselves, in that area of research, the discovery that body-building proteins are even more alike on average than other proteins was especially intriguing because of the paradox it seemed to pose: animals as different as a mouse and an elephant are shaped by a common set of very similar, functionally indistinguishable body-building proteins. The same applies to humans and our closest living relatives—most of our proteins differ from those of the chimpanzee by only one or two of the several hundred amino acids that comprise each protein, and 29 percent of our proteins are exactly identical in sequence. How do we explain this disparity between evolution at the two levels of proteins and anatomy? Somewhere in all of that genomic DNA there must be meaningful differences that have evolved. The trick is to find them, and the trick to doing that has been deciding where to look. It turns out that those places are much harder to locate than are genes themselves.
Genetic Switches In humans, the protein-coding stretches of DNA make up only about 1.5 percent of our genome, so genes are really like little islands of information in a vast sea of DNA sequence. Much of the remaining noncoding DNA does nothing that we know of, but some of those sequences participate in the very important task of regulating gene expression. And these regulatory sequences are key to evolution.
The expression of a gene entails the transcription of the DNA sequence into a messenger RNA (mRNA) version and the translation of that mRNA into a protein sequence. The expression of most genes is regulated at the transcriptional level—cells do not waste energy making -mRNAs and proteins they do not need. Many genes are therefore expressed only in an organ-, tissue- or cell type–specific manner. Certain noncoding DNA sequences play a critical part in directing when and where that happens. They are components of “genetic switches” that turn genes on or off at the right time and place in the body. Sequence-specific DNA-binding proteins called transcription factors, which are the other components of the switch, recognize those DNA sequences, often called enhancers. The binding of the transcription factors to the enhancer within a cell nucleus determines whether the switch and the gene are on or off in that cell.
Every gene has at least one enhancer. Unlike the genes themselves, whose coding regions are readily identified because of the genetic code’s fairly simple grammar, enhancers cannot be recognized solely on the basis of their DNA sequences and must be identified experimentally. Enhancers are usually hundreds of base pairs in length and may be located on either side of a gene or even within a noncoding stretch inside a gene. They can also be thousands of nucleotides away from the gene itself.
Most important to our discussion here is the fact that some genes have many separate enhancers. This is particularly true for genes that encode proteins that shape anatomy. Each enhancer independently regulates the expression of the gene in different parts of the body and at different times in the animal’s life cycle, such that the complete expression of a gene is a patchwork of multiple, independently controlled sites of expression. These enhancers enable the same gene to be used many times in different contexts and thus greatly expand the functional versatility of individual genes.
A gene involved in coloring the body parts of the fruit fly illustrates the modular logic of this gene regulation system. The somewhat confusingly named Yellow gene encodes a protein that promotes the formation of black pigmentation (mutant flies without this protein are Yellow). The Yellow gene has separate enhancers that activate it during the development of a variety of fly body parts, including the wings and abdomen.
Because the Yellow gene plays a role during the development of so many tissues, mutations in the gene itself could be disastrous if they alter or disable the function of the protein; they would affect the function of the Yellow pigmentation protein throughout the organism. In contrast, changes in just one of the gene’s enhancers will affect only the function of that enhancer and only the Yellow gene expression governed by that enhancer, leaving the expression and function of the protein in other tissues unchanged.
The evolutionary implications of the modular regulation of body-patterning genes are profound. In theory, mutations in enhancers would allow individual body traits to be selectively modified without changing genes or proteins themselves. And in the past few years, direct evidence has emerged that this is frequently how the evolution of various body parts and patterns has occurred.
Evolving Switches One of the most important strategies in biology is to identify the simplest experimental models of the phenomenon one wishes to understand. With respect to the evolution of body pattern, coloration fits the bill. It is one of the most obvious features of animals and plays a major role in how animals interact with their environment and with one another. Body-color patterns in fruit flies have diversified rapidly among closely related species, and analyses of how fruit flies got their spots and stripes illustrate how and why the evolution of genetic switches shapes the evolution of anatomy.
In some species, the males have intense black spots on the edges of their wings, whereas other species lack these spots. In some of these same species, males have a very dark abdomen (which is how the most famous fruit fly, Drosophila melanogaster, got its name: melanogaster means “black belly”), whereas males of other species lack this black band. In wing-spotted species, the male displays his spots to the female as he courts her with a dance. We have found that in spotted species, the Yellow protein is produced at very high levels in the cells that will make the spot and at low levels in the rest of the wing cells. In unspotted species, Yellow is made only at low levels throughout the wing, generating just a light dusting of black pigment.
To figure out how Yellow is produced in a wing spot in some species and not others, we searched the DNA sequences around the Yellow gene for the enhancers that control its expression in various body parts. In unspotted species, there is an enhancer that drives Yellow expression in a low uniform pattern in the wing. This wing-enhancer activity generates the fly wings’ light-gray color. When the corresponding piece of DNA was analyzed from a spotted species, we found that it drives both this low-level pattern and the intense spot pattern of gene expression. What has happened in the course of evolution of spotted species is that new binding sites for transcription factors made in the wing evolved in the Yellow wing-enhancer DNA sequence. These changes created an expression pattern—wing spots—without altering where the Yellow protein is made or how it functions elsewhere in the body [see box].
A similar story applies to the evolution of the black band in the abdomen, but with a twist. Whereas we are naturally inclined to think that the presence of a feature in one species and its absence in another related species is the result of a gain by the first, that is often not the case. A flip side to evolution, the loss of features, is very common, though much less appreciated. The loss of body characters perhaps best illustrates why the evolution of enhancers is the more likely path for the evolution of anatomy.
One enhancer of the Yellow gene governs its expression in the abdomen. In males of species with the black band, this enhancer drives the expression of the Yellow gene at high levels in cells at the rear of the abdomen. But some species, such as Drosophila kikkawai, lost this band of pigmentation in the course of evolution. In D. kikkawai, the enhancer can no longer drive high levels of Yellow expression in the rear of the abdomen because a few mutations have disrupted some of its transcription factor binding sites.
It is important to emphasize that the Yellow gene remains active elsewhere in the body and that its biochemical function is intact. Although one path to losing the black band could have been through mutations that inactivate the Yellow gene and its protein, this path is not permitted by natural selection, because the loss of Yellow function elsewhere in the body would have additional, detrimental consequences.
Losses of features may or may not be beneficial for survival or greater reproductive success, but some losses are adaptive because they facilitate some change in lifestyle. Hind limbs, for example, have been lost many times in vertebrates—by snakes, lizards, whales and manatees—and those losses are associated with adaptation to different habitats and means of locomotion. The evolutionary forerunners of the hind limbs of four-legged vertebrates are the pelvic fins of fish. Dramatic differences in pelvic fin anatomy have also evolved in closely related fish populations. The three-spined stickleback fish occurs in two forms in many lakes in North America—an open-water form that has a full spiny pelvis, and a shallow-water, bottom-dwelling form with a dramatically reduced pelvis and shrunken spines. In open water, the long spines help to protect the fish from being swallowed by larger predators. But on the lake bottom, those spines are a liability because dragonfly larvae that feed on the young fish can grasp them.
The differences in pelvic morphology among these fish have evolved repeatedly in just 10,000 years since the last Ice Age. Long-spined oceanic sticklebacks colonized many separate lakes, and the reduced form evolved independently several times. Because the fish are so closely related and interbreed in the laboratory, geneticists can map the genes involved in the reduction of the stickleback pelvis. David M. Kingsley of Stanford University, along with Dolph Schluter of the University of British Columbia and colleagues, has shown that changes in the expression of a gene involved in the building of the pelvic skeleton are associated with the pelvic reduction. Like most other body-building genes, the Pitx1 gene has multiple jobs in the development of the fish. But its expression is selectively lost in the area of the fish that will give rise to the pelvic-fin bud and spines. Once again, evolutionary changes in an enhancer are responsible. There are no coding changes in the Pitx1 protein between different forms of the stickleback.
Yellow, Pitx1 and most other body-building and body-patterning genes are said to be pleiotropic, in that they influence the formation or appearance of multiple traits. Mutations in the coding sequence of a pleiotropic gene have multiple effects on all the traits controlled by this gene, and that drastic amount of change is unlikely to be tolerated by natural selection. The key lesson from the evolution of spots, stripes and skeletons is that mutations in regulatory sequences circumvent the pleiotropic effects of mutations in coding sequences and allow for the selective modification of individual body parts. Mutations in regulatory sequences are not the exclusive mode of evolution—they are just the more likely path when a gene has multiple roles and one of those roles is selectively modified.
Common Genes, Endless Variety The evolution of enhancers is not at all limited to genes affecting body form nor just to fruit flies and weird fish. Quite a few examples of evolutionary changes in regulatory sequences that alter gene expression have been demonstrated for human traits as well.
One of the more striking cases in recent human evolution represents an adaptation, through selective loss of gene expression, to an environment where malaria is endemic. In addition to the familiar A, B and O blood types, other so-called minor blood types have been well studied. The status of a protein called Duffy, present on the surface of red blood cells, defines one of these types. The Duffy protein constitutes part of the receptor that is used by a malaria-causing parasite, Plasmodium vivax, to infect red cells, but in West Africa the protein is absent from the blood cells of almost 100 percent of the population, making individuals resistant to infection. The Duffy gene is also expressed in several other body tissues, including cells of the spleen, the kidneys and the brain. In the African population, Duffy expression in those other tissues is preserved. Not surprisingly, these Duffy-negative individuals carry a mutation in an enhancer of the Duffy gene that knocks out the binding site for a transcription factor that activates Duffy expression in red blood cell precursors but that has no effect on Duffy production elsewhere in the body.
Gregory A. Wray of Duke University and his collaborators have identified other aspects of human biology that have evolved through mutations in enhancers in different human genes. One of the most intriguing associations revealed thus far involves divergence in the great ape and human regulatory sequences controlling the Prodynorphin gene, which encodes a set of small opioid proteins produced in the brain and involved in perception, behavior and memory. The human gene is more highly expressed in response to stimuli than is the chimpanzee version, and strong evidence suggests that the human regulatory sequence evolved under natural selection—that is, it was retained because it was advantageous.
As these examples illustrate, mutations in regulatory DNA have undoubtedly played a role in human evolution and regulatory variation may be an important source of physical and health differences among individuals as well. Because scientists cannot tinker with the DNA of living humans the way we can with flies and fish, it is somewhat harder to study certain examples of regulatory DNA changes responsible for our divergence from other species, although some new methods for analyzing genomes are producing encouraging leads [see box].
These are still early days for research into the evolution of gene-regulating DNA sequences. And hundreds of thousands of genetic switches in the virtual zoo of genomes have yet to be discovered or investigated. Biologists are already learning new principles, however, that have predictive value for future studies: evolutionary changes to anatomy, particularly those involving pleiotropic genes, are more likely to happen via changes to gene enhancers than to the genes themselves.
This phenomenon also reveals how very diverse groups of animals can share most, if not all, the genes involved in body building and body patterning—contrary to scientists’ early expectations, it is mostly a matter of how and when those genes are used that shapes the different forms of the animal kingdom. If we really want to understand what makes the human form different from that of other apes or what makes an elephant distinct from a mouse, for that matter, much of that information lies not in our respective genes and proteins but in an entirely different realm of our genomes that remains to be explored.
Editor’s Note: This story was originally printed with the title “Regulating Evolution”
