Some ideas are discovered late in the history of a scientific discipline because they are subtle, complex or otherwise difficult. Natural selection was not one of these. Although compared with other revolutionary scientific ideas it was discovered fairly recently—Charles Darwin and Alfred Russel Wallace wrote on the subject in 1858, and Darwin’s On the Origin of Species appeared in 1859—the idea of natural selection is simplicity itself. Some kinds of organisms survive better in certain conditions than others do; such organisms leave more progeny and so become more common with time. The environment thus “selects” those organisms best adapted to present conditions. If environmental conditions change, organisms that happen to possess the most adaptive characteristics for those new conditions will come to predominate. Darwinism was revolutionary not because it made arcane claims about biology but because it suggested that nature’s underlying logic might be surprisingly simple.

In spite of this simplicity, the theory of natural selection has suffered a long and tortuous history. Darwin’s claim that species evolve was rapidly accepted by biologists, but his separate claim that natural selection drives most of the change was not. Indeed, natural selection was not accepted as a key evolutionary force until well into the 20th century.

The status of natural selection is now secure, reflecting decades of detailed empirical work. But the study of natural selection is by no means complete. Rather—partly because new experimental techniques have been developed and partly because the genetic mechanisms underlying natural selection are now the subject of meticulous empirical analysis—the study of natural selection is a more active area of biology than it was even two decades ago. Much of the recent experimental work on natural selection has focused on three goals: determining how common it is, identifying the precise genetic changes that give rise to the adaptations produced by natural selection, and assessing just how big a role natural selection plays in a key problem of evolutionary biology—the origin of new species.

Natural Selection: The Idea
The best way to appreciate evolution by natural selection is to consider organisms whose life cycle is short enough that many generations can be observed. Some bacteria can reproduce themselves every half an hour, so imagine a population of bacteria made up of two genetic types that are initially present in equal numbers. Assume, moreover, that both types breed true: type 1 bacteria produce only type 1 offspring, and type 2 bacteria produce only type 2s. Now suppose the environment suddenly changes: an antibiotic is introduced to which type 1s are resistant but to which type 2s are not. In the new environment, type 1s are fitter—that is, better adapted—than type 2s: they survive and so reproduce more often than type 2s do. The result is that type 1s produce more offspring than type 2s do.

“Fitness,” as used in evolutionary biology, is a technical term for this idea: it is the probability of surviving or reproducing in a given environment. The outcome of this selection process, repeated numberless times in different contexts, is what we all see in nature: plants and animals (and bacteria) that fit their environments in intricate ways.

Evolutionary geneticists can flesh out the preceding argument in much richer biological detail. We know, for instance, that genetic types originate in mutations of DNA—random changes in the sequence of nucleotides (or string made up of the letters A, G, C and T) that constitutes the “language” of the genome. We also know a good deal about the rate at which a common kind of mutation—the change of one letter of DNA to another—appears: each nucleotide in each gamete in each generation has about one chance in a billion of mutating to another nucleotide. Most important, we know something about the effects of mutations on fitness. The overwhelming majority of random mutations are harmful—that is, they reduce fitness; only a tiny minority are beneficial, increasing fitness. Most mutations are bad for the same reason that most typos in computer code are bad: in finely tuned systems, random tweaks are far more likely to disrupt function than to improve it.

Adaptive evolution is therefore a two-step process, with a strict division of labor between mutation and selection. In each generation, mutation brings new genetic variants into populations. Natural selection then screens them: the rigors of the environment reduce the frequency of “bad” (relatively unfit) variants and increase the frequency of “good” (relatively fit) ones. (It is worth noting that a population can store many genetic variants at once, and those variants can help it to meet changing conditions as they arise. The gene that protected the type 1 bacteria from the antibiotic may have been useless or even slightly harmful in the earlier, antibiotic-free environment, but its presence enabled the type 1s to survive when conditions changed.)

Population geneticists have also provided insight into natural selection by describing it mathematically. For example, geneticists have shown that the fitter a given type is within a population, the more rapidly it will increase in frequency; indeed, one can calculate just how quickly the increase will occur. Population geneticists have also discovered the surprising fact that natural selection has unimaginably keen “eyes,” which can detect astonishingly small differences in fitness among genetic types. In a population of a million individuals, natural selection can operate on fitness differences as small as one part in a million.

One remarkable feature of the argument for natural selection is that its logic seems valid for any level of biological entity—from gene to species. Biologists since Darwin, of course, have considered differences in fitness between individual organisms, but in principle natural selection could act on differences in survival or reproduction between other entities. For example, one might reason that species with broad geographic ranges will survive—as species—longer than species whose geographic ranges are narrow. After all, broad-ranging species can tolerate the extinctions of a few local populations more readily than species with restricted ranges can. The logic of natural selection might predict, then, that the proportion of broad-ranging species should increase with time.

Yet though this argument is formally sound—and evolutionists do suspect higher-level selection does take place now and then [see “What’s Good for the Group,” on page 51] (need to link)—most biologists agree that natural selection typically occurs at the level of individual organisms or genetic types. One reason is that the lifetimes of organisms are much shorter than the lifetimes of species. Thus, the natural selection of organisms typically overwhelms the natural selection of species.

How Common Is Natural Selection?
One of the simplest questions biologists can ask about natural selection has, surprisingly, been one of the hardest to answer: To what degree is it responsible for changes in the overall genetic makeup of a population? No one seriously doubts that natural selection drives the evolution of most physical traits in living creatures—there is no other plausible way to explain such large-scale features as beaks, biceps and brains. But there has been serious doubt about the extent of the role of natural selection in guiding change at the molecular level. Just what proportion of all evolutionary change in DNA is driven, over millions of years, by natural selection—as opposed to some other process?

Until the 1960s biologists had assumed that the answer was “almost all,” but a group of population geneticists led by Japanese investigator Motoo Kimura sharply challenged that view. Kimura argued that molecular evolution is not usually driven by “positive” natural selection—in which the environment increases the frequency of a beneficial type that is initially rare. Rather, he said, nearly all the genetic mutations that persist or reach high frequencies in populations are selectively neutral—they have no appreciable effect on fitness one way or the other. (Of course, harmful mutations continue to appear at a high rate, but they can never reach high frequencies in a population and thus are evolutionary dead ends.) Since neutral mutations are essentially invisible in the present environment, such changes can slip silently through a population, substantially altering its genetic composition over time. The process is called random genetic drift; it is the heart of the neutral theory of molecular evolution.

By the 1980s many evolutionary geneticists had accepted the neutral theory. But the data bearing on it were mostly indirect; more direct, critical tests were lacking. Two developments have helped fix that problem. First, population geneticists have devised simple statistical tests for distinguishing neutral changes in the genome from adaptive ones. Second, new technology has enabled entire genomes from many species to be sequenced, providing voluminous data on which these statistical tests can be applied. The new data suggest that the neutral theory underestimated the importance of natural selection.

In one study a team led by David J. Begun and Charles H. Langley, both at the University of California, Davis, compared the DNA sequences of two species of fruit fly in the genus Drosophila. They analyzed roughly 6,000 genes in each species, noting which genes had diverged since the two species had split off from a common ancestor. By applying a statistical test, they estimated that they could rule out neutral evolution in at least 19 percent of the 6,000 genes; in other words, natural selection drove the evolutionary divergence of a fifth of all genes studied. (Because the statistical test they employed was conservative, the actual proportion could be much larger.) The result does not suggest that neutral evolution is unimportant—after all, some of the remaining 81 percent of genes may have diverged by genetic drift. But it does prove that natural selection plays a bigger role in the divergence of species than most neutral theorists would have guessed. Similar studies have led most evolutionary geneticists to conclude that natural selection is a common driver of evolutionary change even in the sequences of nucleotides in DNA.

The Genetics of Natural Selection
Even when biologists turn to ordinary physical traits (“beaks, biceps and brains”) and are confident that natural selection drove evolutionary change, they are often in the dark about just how it happened. Until recently, for instance, little was known about the genetic changes that un­­derlie adaptive evolution. But with the new developments in genetics, biologists have been able to attack this problem head-on, and they are now attempting to answer several fundamen­tal questions about selection. When organisms adapt by natural selection to a new environment, do they do so because of changes in a few genes or many? Can those genes be identified? And are the same genes involved in independent cases of adaptation to the same environment?

Answering those questions is not easy. The main difficulty is that the increase in fitness arising from a beneficial mutation can be very small, making evolutionary change quite slow. One way evolutionary biologists have coped with this problem is to place populations of rapidly reproducing organisms in artificial environments where fitness differences are larger and evolution is, therefore, faster. It also helps if the populations of the organisms are large enough to provide a steady stream of mutations. In microbial experimental evolution, a population of genetically identical microorganisms is typically placed in a novel environment to which they must adapt. Since all the individuals begin by sharing the same DNA sequence, natural selection must operate only on new mutations that arise during the experiment. The experimenter can then plot how the fitness of the population changes with time by measuring the rate of reproduction in the new environment.

Some of the most intriguing research in experimental evolution has been performed with bacteriophages, viruses so small that they infect bacteria. Bacteriophages have commensurately tiny genomes, and so it is practical for biologists to sequence their entire genomes at the beginning and end of experiments as well as at any time in between. That makes it possible to track every genetic change that natural selection “grabs” and then perpetuates over time.

K. Kichler Holder and James J. Bull, both at the University of Texas at Austin, performed such an experiment with two closely related species of bacteriophages: ΦX174 and G4. Both viruses infect the common gut bacterium Escherichia coli. The experimenters subjected the bacteriophages to an unusually high temperature and allowed them to adapt to the new, warm environment. In both species, fitness in the new environment increased dramatically during the experiment. Moreover, in both cases the experimenters saw the same pattern: fitness improved rapidly near the start of the experiment and then leveled off with time. Remarkably, Holder and Bull were able to identify the exact DNA mutations underlying the increased fitness.

Natural Selection “in the Wild”
Although research in experimental evolution provides an unprecedented view of natural selection in action, the approach remains limited to simple organisms for which repeated sequencing of entire genomes is feasible. Some workers have also cautioned that experimental evolution might involve unnaturally harsh selective pressures—perhaps much harsher than the ones encountered in the wild. We would like, then, to study selection in higher organisms under more natural conditions—and so we must find another way to investigate the glacial pace of much evolutionary change.

To do so, evolutionists typically turn to populations or species that have been separated long enough that the adaptive differences between them that were crafted by natural selection are readily found. Biologists can then study those differences genetically. For example, Douglas W. Schemske of Michigan State University and H. D. Bradshaw, Jr., of the University of Washington analyzed natural selection in two species of monkeyflower. Though closely related, Mimulus lewisii is pollinated primarily by bumblebees, whereas M. cardinalis is pollinated primarily by hummingbirds. Data from other species show that bird pollination in the genus Mimulus evolved from bee pollination.

Flower color alone—M. lewisii has pink flowers, and M. cardinalis has red [see box at right]—explains much of these differences in pollinator preference. When Schemske and Bradshaw crossed the two species, they showed that this color difference is controlled to a considerable extent by what appears to be a single gene called Yellow Upper, or YUP. On the basis of that finding, they created two kinds of hybrids. In the first kind, the YUP gene came from M. cardinalis, but the rest of the hybrid’s genome derived from M. lewisii. The resulting flowers were orange. The second kind of hybrid was a “mirror image” of the first: the YUP gene came from M. lewisii, but the rest of the genome derived from M. cardinalis. The resulting flowers were pink.

When the hybrids were transplanted into the wild, the investigators noted that YUP had an enormous effect on pollinator visitation: M. lewisii plants, for instance, that carried YUP from M. cardinalis were visited by hummingbirds about 68 times more often than were pure M. lewisii plants; in the reciprocal experiment (M. cardinalis plants with YUP from M. lewisii), the effect was a 74-fold increase in bumblebee visits. There can be no doubt, then, that YUP played a major role in the evolution of bird pollination in M. cardinalis. Schemske and Bradshaw’s work shows that natural selection sometimes builds adaptations from what appear to be fairly simple genetic changes.

The Origin of Species
One of Darwin’s boldest claims for natural selection was that it explains how new species arise. (After all, the title of his masterpiece is On the Origin of Species.) But does it? What role does natural selection play in speciation, the splitting of a single lineage into two? To this day, these questions represent an important topic of re­­search in evolutionary biology.

To understand the answers to those questions, one must be clear about what evolutionists mean by “species.” Unlike Darwin, modern biologists generally adhere to the so-called biological species concept. The key idea is that species are reproductively isolated from one another—that is, they have genetically based traits preventing them from exchanging genes. Different species, in other words, have separate gene pools.

It is thought that two populations must be geographically isolated before reproductive isolation can evolve. The finches that inhabit various islands in the Galápagos Archipelago, which Darwin famously describes in Origin of Species, obviously diverged into the distinct species observed today after they became geographically isolated.

Once reproductive isolation does evolve, it can take several forms. For example, during courtship females of one species might refuse to mate with males of another (if the two species ever do come into geographic contact). Females of the butterfly species Pieris occidentalis, for instance, will not mate with males of the related species P. protodice, probably because the males of the two species have different wing patterns. And even if two species do court and mate, the inviability or sterility of any resulting hybrids can represent another form of reproductive isolation: genes cannot move from one species to another if all hybrids between them are dead or sterile. To contemporary biologists, then, the question of whether natural selection drives the origin of species reduces to the question of whether natural selection drives the origin of reproductive isolation.

For much of the 20th century, many evolutionists thought the answer was no. Instead they believed that genetic drift was the critical factor in speciation. One of the most intriguing findings from recent research on the origin of species is that the genetic drift hypothesis about the origin of species is probably wrong. Rather natural selection plays a major role in speciation.

A good example is the evolutionary history of the two monkeyflower species mentioned earlier. Because their pollinators seldom visit the “wrong” species of monkeyflower, the two species are almost completely isolated reproductively. Even though both species sometimes occur in the same locations in North America, a bumblebee that visits M. lewisii almost never visits M. cardinalis, and a hummingbird that visits M. cardinalis almost never visits M. lewisii. Thus, pollen is rarely transferred between the two species. In fact, Schemske and his colleagues showed that pollinator differences alone account for 98 percent of the total blockage in gene flow between the two species. In this case, then, there can be no doubt that natural selection shaped the plants’ adaptations to distinct pollinators and gave rise to strong reproductive isolation.

Other evidence for the role of natural selection in speciation has come from an unexpected quarter. In the past decade or so several evolutionary geneticists (including me) have identified half a dozen genes that cause hybrid sterility or inviability. The genes in question—studied mostly in species of Drosophila fruit flies—play various normal roles within the species: some encode enzymes, others encode structural proteins, and yet others encode proteins that bind to DNA.

These genes exhibit two striking patterns. First, among the genes that cause problems in hybrid offspring, it turns out that many have diverged extremely rapidly. Second, population genetics tests show that their rapid evolution was driven by natural selection.

The studies of the monkeyflower and of hybrid sterility in fruit flies only begin to scratch the surface of a large and growing literature that reveals the hand of natural selection in speciation. Indeed, most biologists now agree that natural selection is the key evolutionary force that drives not only evolutionary change within species but also the origin of new species. Although some laypeople continue to question the cogency or adequacy of natural selection, its status among evolutionary biologists in the past few decades has, perhaps ironically, only grown more secure.

Note: This article was originally printed with the title, "Testing Natural Selection".