Evolution, Natural Selection and Population Genetics

Bacteria that shrug off antibiotics, insects that survive pesticides and viruses that slip past last year's vaccine are all evolution happening in front of us. Evolution is the unifying idea of biology: it explains why living things share a genetic code, why they are so well suited to their environments, and why they are also full of odd compromises. This chapter traces how Darwin arrived at natural selection, lays out the evidence for evolution, and then gives you the tools of population genetics to measure evolutionary change and identify its causes.

Section 1Darwin and descent with modification

What evolution means

In the broadest sense, evolution is change over time in the heritable characteristics of populations. Darwin called it descent with modification: living species descend from ancestral species that were different from them, and all life is connected by common ancestry, like twigs on a single great tree. Population geneticists use a narrower, measurable definition: evolution is a change in allele frequencies in a population over generations. These definitions describe the same process at different scales. Small allele frequency changes within populations (microevolution) accumulate into the origin of new species and larger groups (macroevolution), the subject of the next chapter.

Evolution is both a pattern and a process. The pattern is what the evidence shows: species have changed and share ancestors. The process is the set of mechanisms that cause those changes, such as natural selection and genetic drift. Scientists are confident about the pattern, and actively research the relative importance of different processes.

Ideas that came before

Darwin did not work in a vacuum. Several earlier thinkers built pieces of the puzzle, often without accepting evolution themselves.

• Carl Linnaeus (1700s) developed binomial nomenclature (two part names such as Homo sapiens) and a nested hierarchy of groups. He saw the pattern as evidence of a divine plan, but Darwin later explained the nested pattern as the natural result of branching descent.
• Georges Cuvier founded paleontology, the study of fossils. He showed that fossils in deeper rock layers differ more from living species and that many species had gone extinct. He opposed evolution and explained the changes by catastrophism, a series of local catastrophes followed by repopulation from elsewhere.
• James Hutton argued that Earth's features formed by slow, continuous processes such as erosion and deposition, an idea called gradualism.
• Charles Lyell extended Hutton's thinking into uniformitarianism: the processes that shape Earth today worked at the same rates in the past. Two conclusions followed that deeply affected Darwin: Earth must be very old, and very slow processes acting over immense time can produce enormous change.
• Jean-Baptiste de Lamarck (1809) proposed the first comprehensive mechanism of evolution. He suggested that body parts used extensively become stronger (use and disuse) and that such acquired changes are passed to offspring (inheritance of acquired characteristics). The giraffe stretching its neck is the standard example. The mechanism is wrong (a bodybuilder's children are not born muscular), but Lamarck deserves credit for proposing that species change, that life is well fitted to its environment because of that change, and that the cause is natural.
• Thomas Malthus, an economist, argued that human populations tend to grow faster than their food supply, so much suffering results from the struggle for limited resources. Darwin realized the same logic applies to every species.

The voyage and the Galápagos

From 1831 to 1836 Charles Darwin sailed around the world as a naturalist aboard HMS Beagle, which was mapping the coast of South America. He collected thousands of specimens and noticed that species in South America resembled one another more than they resembled species in similar climates in Europe. Temperate South American plants and animals were more like tropical South American species than like temperate European ones. On the young volcanic Galápagos Islands, about 900 kilometers west of Ecuador, he found species found nowhere else that nevertheless resembled species on the mainland. Mockingbirds differed from island to island, and the local governor said he could tell which island a tortoise came from by its shell. The islands' finches, later studied in detail, varied in beak shape according to diet: thick crushing beaks for seeds, slender probing beaks for insects, and even a species that uses cactus spines as tools.

Darwin reasoned that a few colonists from the mainland had reached the islands, and their descendants had changed over generations as they adapted to different conditions on different islands. Back in England, he spent more than twenty years gathering evidence, breeding pigeons, corresponding with naturalists and refining his argument. In 1858 he received a manuscript from Alfred Russel Wallace, a naturalist working in Southeast Asia who had independently arrived at the same mechanism. Their ideas were presented together that year, and in 1859 Darwin published On the Origin of Species by Means of Natural Selection.

Natural selection: observations and inferences

Darwin's argument can be laid out as a short chain of observations and the conclusions they force.

• Observation 1. Members of a population vary in their traits.
• Observation 2. Many traits are inherited from parents by offspring.
• Observation 3. Every species can produce more offspring than the environment can support.
• Observation 4. Owing to limited resources, many offspring do not survive or reproduce.
• Inference 1. Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals.
• Inference 2. This unequal ability to survive and reproduce leads to the accumulation of favorable traits in the population over generations.

This is natural selection: the differential survival and reproduction of individuals because of differences in heritable traits. Over long periods, natural selection produces adaptations, inherited characteristics that enhance survival and reproduction in a particular environment. Darwin added that the process, acting over vast spans of time, could account for the diversity of life, because populations in different environments would accumulate different adaptations and eventually become different species.

Artificial selection as a model

Darwin opened On the Origin of Species with domesticated animals and plants because breeders had already shown what selection could do. By choosing which individuals breed, humans have produced the enormous variety of dog breeds from wolves and, from a single wild mustard species (Brassica oleracea), cabbage (selected for terminal buds), kale (leaves), broccoli (flower clusters and stems), cauliflower (flower clusters), kohlrabi (stems) and Brussels sprouts (lateral buds). If humans can change a species this much in a few thousand years, Darwin argued, nature selecting over millions of years could do far more. In artificial selection humans set the criterion; in natural selection the environment does.

Clearing up common misunderstandings

Three points about natural selection are easy to state and easy to forget:

1. Individuals do not evolve; populations do. Selection acts on individuals, because each one survives and reproduces or does not, but the evolutionary result is a change in the makeup of the population over generations. A single giraffe's neck never lengthens because of selection.
2. Only heritable traits matter. A muscle built in the gym, or a scar, is not passed on, so it cannot be selected in the evolutionary sense.
3. Selection is local and has no goal. A trait favored in one place or time may be useless or harmful in another. Natural selection does not plan ahead and does not aim at "higher" or more complex organisms; it favors whatever variants happen to reproduce best in current conditions.

Section 2Evidence for evolution

Darwin's case rested on many independent lines of evidence, and every one has grown stronger since. The power of the argument lies in agreement: anatomy, embryos, molecules, fossils, geography and direct observation all point to the same branching history.

Direct observation of evolutionary change

Evolution is often fast enough to watch. Soapberry bugs in Florida feed by piercing the fruit of plants with their beaks to reach the seeds. Their native host has large fruit, but in the last century they colonized an introduced plant with much smaller fruit. Within a few decades, bugs living on the introduced plant had evolved significantly shorter beaks, while bugs on the native plant kept long ones. Bugs from the two populations raised on the same food kept their beak differences, showing the change was genetic.

On the Galápagos island of Daphne Major, a severe drought in 1977 left mostly large, hard seeds. Medium ground finches with deeper beaks cracked them more easily and survived at higher rates, and the next generation had measurably deeper beaks on average. When wet years later favored small seeds, the trend partly reversed. Selection was measured directly in the wild, and its direction changed with the environment.

The most consequential example is drug resistance. Staphylococcus aureus resistant to methicillin (MRSA) appeared within a few years of the drug's introduction in 1959. Resistance arises when a bacterium acquires a gene (in this case one encoding an altered penicillin binding protein that the drug cannot inactivate). Exposure to the antibiotic does not create the resistance; it kills susceptible cells and leaves resistant ones to multiply. The same process drives resistance in HIV, malaria parasites, cancer cells under chemotherapy, insects exposed to pesticides and weeds exposed to herbicides.

Homology

Homology is similarity resulting from common ancestry. Homologous structures may now serve very different functions, but they share an underlying plan because they were inherited from a common ancestor.

• Anatomical homology. The forelimbs of humans, cats, whales and bats are used for grasping, walking, swimming and flying, yet all contain the same sequence of bones: one upper bone (humerus), two lower bones (radius and ulna), a cluster of wrist bones (carpals), and hand bones (metacarpals and phalanges). An engineer designing each limb from scratch would never choose the same parts list for a wing and a flipper. The shared pattern makes sense only as modification of an ancestral tetrapod limb.
• Embryological homology. At comparable stages, vertebrate embryos all have a post-anal tail and pharyngeal arches (with pouches between them). In fishes the arches become gill supports; in humans they become parts of the ear, jaw and throat. Shared embryonic structures reveal shared ancestry even when adults differ greatly.
• Molecular homology. All living things use DNA and essentially the same genetic code, the same 20 amino acids and the same basic machinery of transcription and translation. Proteins such as cytochrome c, found in organisms from yeast to humans, differ in amino acid sequence in proportion to how long ago the lineages split. Humans and chimpanzees have identical cytochrome c; humans and rhesus monkeys differ at one position; humans and yeast at roughly 40 percent of positions.

Vestigial structures and molecular leftovers

Vestigial structures are remnants of features that served important functions in an organism's ancestors but are reduced or have lost that function. Examples include the small pelvic and leg bones embedded in the bodies of whales and some snakes (pythons have tiny external spurs), the human tailbone (coccyx), the muscles that move the ear in humans, and the eyes of blind cave fishes, which form in the embryo and then degenerate. Each makes sense as an inheritance from an ancestor that used the structure.

Genomes contain the molecular equivalent. Pseudogenes are copies of genes that have accumulated disabling mutations. Most mammals make their own vitamin C, but humans and other primates carry a broken copy of the final enzyme gene in the pathway (GULO), with the same disabling mutation shared across species. That is why we must get vitamin C from food. The shared defect is hard to explain except by inheritance from a common ancestor in which it first arose.

Convergent evolution and analogy

Not every similarity reflects common ancestry. Convergent evolution is the independent evolution of similar features in different lineages that face similar environmental challenges. The resulting similar features are called analogous: they share function but not ancestry. The wings of insects, birds and bats are analogous as wings (insect wings are not built from limb bones at all). The streamlined bodies of sharks, dolphins and extinct ichthyosaurs, the eyes of octopuses and vertebrates, and the gliding membranes of Australian sugar gliders (marsupials) and North American flying squirrels (placental mammals) are other examples. Convergence is itself evidence of natural selection, because similar environments repeatedly favor similar solutions.

The fossil record

Fossils are preserved remains or traces of past organisms, usually found in sedimentary rock laid down in layers (strata), with younger layers on top of older ones. Their absolute ages are measured by radiometric dating of volcanic layers above and below, using the steady decay of radioactive isotopes with known half-lives. The fossil record shows that past organisms differed from present ones, that many species have gone extinct, and that groups appear in a consistent order: prokaryotes long before eukaryotes, fishes before amphibians, reptiles before mammals and birds.

Fossils also document transitional forms that link groups. Tiktaalik, about 375 million years old, had fish features (scales, fins, gills) together with tetrapod features (a flexible neck, sturdy fin bones homologous to the arm bones, and lungs). A series of fossils from about 50 to 40 million years ago traces whales from four legged land mammals: Pakicetus had legs but an ear region like a whale's, Ambulocetus was amphibious, Rodhocetus had shortened hind limbs, and Dorudon was fully aquatic with tiny vestigial hind limbs. Molecular data independently place whales within the even-toed hoofed mammals, closest to hippopotamuses, and the ankle bones of early fossil whales share a distinctive shape with that group. Archaeopteryx and many feathered dinosaurs similarly link birds to theropod dinosaurs.

Biogeography

Biogeography, the geographic distribution of species, reflects both evolution and the movement of continents. About 250 million years ago the continents were joined in the supercontinent Pangaea; as it broke apart, lineages on separate landmasses evolved independently. Australia's rich diversity of marsupials, which fill niches occupied elsewhere by placental mammals, reflects its long isolation. Islands are especially telling. They often have many endemic species (found nowhere else) that are closely related to species on the nearest mainland or neighboring island, rather than to species living in similar habitats far away. Oceanic islands also tend to lack groups that disperse poorly over sea, such as amphibians and land mammals, while having many birds, insects and plants that cross water easily. These patterns are expected if species arise from colonists and diverge in place; they are puzzling otherwise.

Section 3Hardy-Weinberg equilibrium and its assumptions

Populations, gene pools and allele frequencies

A population is a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring. All copies of every allele at every locus in all members of the population make up its gene pool. For a gene with two alleles, A and a, we describe the gene pool by the allele frequencies: by convention p is the frequency of one allele (often the dominant one) and q the frequency of the other. Because these are the only two alleles, p + q = 1. If only one allele exists at a locus in a population, that allele is said to be fixed (its frequency is 1).

Calculating allele frequencies from genotype counts is straightforward because each diploid individual carries two copies of the gene. Consider a population of 500 wildflowers in which flower color shows incomplete dominance: 320 plants are red (C^RC^R), 160 are pink (C^RC^W) and 20 are white (C^WC^W). The population holds 1,000 copies of the gene. Red plants contribute 640 copies of C^R and pink plants 160 more, for 800, so p = 800 / 1,000 = 0.8. White plants contribute 40 copies of C^W and pink plants 160, for 200, so q = 0.2. Check: p + q = 1.

The Hardy-Weinberg principle

In 1908 the mathematician G. H. Hardy and the physician Wilhelm Weinberg independently showed that Mendelian inheritance by itself does not change allele frequencies. The Hardy-Weinberg principle states that the frequencies of alleles and genotypes in a population will remain constant from generation to generation unless something acts to change them. Such a population is in Hardy-Weinberg equilibrium. Dominant alleles do not automatically become more common, and recessive alleles do not disappear just because they are recessive.

The reasoning treats reproduction as drawing gametes at random from the gene pool. If the frequency of allele A is p, then the chance that a random sperm carries A is p, and the chance that a random egg carries A is also p. The chance that both carry A is p × p = p². Likewise, the chance of aa is q². Heterozygotes can form two ways (A sperm with a egg, or a sperm with A egg), so their frequency is 2pq. Since these three genotypes are the only possibilities:

p² + 2pq + q² = 1

where p² is the frequency of AA, 2pq the frequency of Aa and q² the frequency of aa. In the wildflower example, the expected frequencies are 0.8² = 0.64 red, 2(0.8)(0.2) = 0.32 pink and 0.2² = 0.04 white. Multiplying by 500 gives 320, 160 and 20, exactly what was observed, so this population appears to be in equilibrium for this gene. A key consequence: under random mating, genotype frequencies reach Hardy-Weinberg proportions after a single generation, and the allele frequencies in the next generation equal those in the parents.

The five conditions

Hardy-Weinberg equilibrium holds only if five conditions are met. Each one, when violated, corresponds to a way a population can evolve.

Real populations rarely meet all five conditions perfectly, yet many loci are close to equilibrium, because the forces acting on them are weak. The value of the principle is that it provides a null model: a precise prediction of what would happen if evolution were not occurring at a locus. When observed genotype frequencies differ significantly from p², 2pq and q² (tested statistically, often with a chi-square test), something is acting on that locus, and the pattern of the deviation hints at what. A shortage of heterozygotes, for example, suggests inbreeding or a hidden subdivision of the population.

Using the equation in human genetics

The equation is often used to estimate how many people carry a recessive allele, because carriers cannot be counted by appearance. Suppose that about 1 in 2,500 babies of northern European ancestry is born with cystic fibrosis, an autosomal recessive disorder. Assuming equilibrium:

1. Affected individuals are aa, so q² = 1 / 2,500 = 0.0004.
2. q = √0.0004 = 0.02.
3. p = 1 − 0.02 = 0.98.
4. Carriers are Aa: 2pq = 2(0.98)(0.02) ≈ 0.039, or about 1 in 25 people.

The striking result is that carriers outnumber affected people about a hundredfold. Most copies of a rare recessive allele are hidden in heterozygotes, where selection cannot "see" them, which is one reason harmful recessive alleles persist. The same calculation for phenylketonuria (about 1 in 10,000 births) gives q = 0.01 and a carrier frequency of about 1 in 50. Such estimates guide genetic counseling and the design of carrier screening programs.

Section 4Natural selection, genetic drift and gene flow

Where variation comes from

Evolution needs heritable variation, and individuals in nearly every population differ genetically. Ultimately, new alleles arise by mutation, changes in DNA sequence caused by replication errors, radiation or chemicals. Most mutations that change a protein are harmful or neutral; a few are beneficial in a particular environment. Mutation also creates new genes, when gene duplication leaves an extra copy free to acquire a new function (the many olfactory receptor genes of mammals arose this way). Because the mutation rate per gene per generation is low in animals and plants, mutation alone changes allele frequencies very slowly. Prokaryotes and viruses, with huge populations and short generation times, generate new variants rapidly.

In sexually reproducing organisms, most of the variation seen in any one generation comes not from new mutation but from sexual reproduction reshuffling existing alleles: crossing over, independent assortment of chromosomes and random fertilization produce new combinations every generation. Diploidy also hides recessive alleles from selection in heterozygotes, preserving variation that may later prove useful.

Three main mechanisms of allele frequency change

Of the five ways a population can depart from Hardy-Weinberg equilibrium, three most directly change allele frequencies: natural selection, genetic drift and gene flow. Mutation contributes slowly, and nonrandom mating changes genotype frequencies but not allele frequencies on its own.

Genetic drift

Flip a fair coin 1,000 times and you will get close to 500 heads; flip it 10 times and 7 or 8 heads would not be surprising. The gametes that happen to form the next generation are a sample of the parents' gene pool, and like any sample, small ones deviate more from the source. Genetic drift is the change in allele frequencies from one generation to the next caused by such chance events. Imagine a population of wildflowers in which, purely by chance, a few plants carrying the white allele are trampled before they set seed. The white allele becomes rarer, not because it was worse but because of luck. Two situations make drift especially strong:

• The founder effect occurs when a few individuals become isolated from a larger population and establish a new one. The founders' gene pool may differ from the source by chance. Founder effects explain why some rare inherited disorders are common in isolated communities. An Amish community in Pennsylvania descended from a small group of founders has a high frequency of Ellis-van Creveld syndrome, a form of dwarfism with extra fingers that is rare elsewhere.
• The bottleneck effect occurs when a sudden change in the environment, such as a fire, flood or overhunting, drastically reduces population size. The survivors' gene pool may no longer reflect the original. Even if the population later recovers in number, its genetic variation stays low until mutation slowly restores it. Northern elephant seals were hunted down to perhaps 20 individuals in the 1890s; today there are well over 100,000, yet they show remarkably little genetic variation.

Drift has four key properties. It is significant in small populations. It can change allele frequencies at random, so an allele may increase even if it is slightly harmful. It leads to a loss of genetic variation within populations as alleles are lost or fixed. And it can fix harmful alleles. The greater prairie chicken of Illinois illustrates the danger. As prairie was converted to farmland, the population fell from millions to fewer than 50 birds in the 1990s, and fewer than half of their eggs hatched. When biologists brought in birds from larger populations in other states, adding new alleles by gene flow, egg hatching rates rose above 90 percent.

Gene flow

Gene flow is the transfer of alleles into or out of a population by the movement of fertile individuals or their gametes, such as pollen carried by wind or insects. It tends to reduce genetic differences between populations; if extensive enough, it can merge neighboring populations into one with a common gene pool. Gene flow can work against local adaptation: on islands where a bird population is adapted to local conditions, steady arrival of birds from a different environment can bring in alleles poorly suited to the island. It can also spread beneficial alleles, such as insecticide resistance alleles that have moved among mosquito populations. Human gene flow has increased greatly with modern travel and migration.

Relative fitness

Phrases such as "survival of the fittest" are misleading if taken to mean strength or aggression. In evolutionary terms, fitness is reproductive success. Relative fitness is the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals. A tough, long lived animal that leaves no offspring has a relative fitness of zero. Selection acts on whole organisms, so the relative fitness of an allele depends on the whole genetic and environmental context in which it is expressed.

Modes of selection

Natural selection can change the distribution of a heritable trait that varies continuously, such as size or beak depth, in three ways, depending on which phenotypes have the highest fitness.

• Directional selection favors individuals at one end of the range of phenotypes, shifting the population's frequency curve in that direction. It is common when the environment changes or a population moves to a new habitat: deeper finch beaks after drought, and larger black bears in cold glacial periods.
• Stabilizing selection favors intermediate variants and acts against both extremes, reducing variation and keeping the population stable for that trait. Human birth weight is a classic example: babies much lighter or much heavier than average historically had higher mortality.
• Disruptive selection favors individuals at both extremes over intermediates. In a population of black-bellied seedcracker finches in Cameroon, birds with small bills eat soft seeds efficiently and birds with large bills crack hard seeds, while birds with intermediate bills handle both poorly. Disruptive selection can be a step toward the formation of two species.

Sexual selection

Sexual selection is natural selection for mating success. It can produce sexual dimorphism, marked differences between the sexes in secondary sexual characteristics such as size, color, ornamentation and behavior. In intrasexual selection ("within the same sex"), individuals of one sex compete directly for mates, as when male elk clash antlers or male elephant seals fight for control of a beach. In intersexual selection ("between the sexes"), also called mate choice, individuals of one sex (usually females) are choosy in selecting mates. Showy traits such as the peacock's tail may increase predation risk but persist because they raise mating success. The good genes hypothesis proposes that ornaments signal overall genetic quality. Supporting this idea, female gray tree frogs prefer males with longer calls, and offspring sired by long calling males grew faster and survived better than offspring of short calling males in experiments.

Balancing selection

Why does so much genetic variation persist if selection tends to favor the best allele? Neutral variation (differences that do not affect fitness, such as many changes in noncoding DNA) drifts freely. In addition, balancing selection actively maintains two or more forms in a population. Two main mechanisms are recognized:

• Heterozygote advantage: heterozygotes have higher fitness than either homozygote. The best known case is the sickle cell allele (HbS). Homozygotes have sickle cell disease, but heterozygotes are protected against the most severe form of malaria, because infected red cells sickle and are removed. Where malaria is common, selection favors heterozygotes and keeps the HbS allele at a frequency far higher than its harm in homozygotes alone would allow; in parts of Africa about one in five people are carriers.
• Frequency-dependent selection: the fitness of a phenotype depends on how common it is. In a scale eating cichlid fish of Lake Tanganyika, individuals have mouths twisted either to the left or the right and attack prey fish from one side. Prey learn to guard against the more common attack, so whichever mouth type is rarer has the advantage; over years the frequencies of the two types oscillate around one half.

Section 5Adaptation and the limits of selection

What counts as an adaptation

An adaptation is a heritable trait that increased in frequency because it improved survival or reproduction in a particular environment. The camouflage of a stick insect, the water conserving kidneys of a desert kangaroo rat, the antifreeze proteins in the blood of Antarctic fishes and the echolocation of bats are all adaptations. Not every feature of an organism is an adaptation, however. A trait may be a side effect of something else that was selected, a leftover from ancestors, or the result of drift. Biologists test adaptive hypotheses the way they test any hypothesis: by predicting what should be true if the trait was favored by selection, then checking with comparisons among species, measurements of fitness in the wild or experiments.

A classic field study shows how. Guppies in Trinidad streams live either with dangerous predators or with only weak ones. Males in high predation streams are drab; males in low predation streams are colorful, because females prefer bright males. When researchers moved guppies from a high predation site to a stream with only weak predators, the males in the transplanted population became measurably more colorful within about 15 generations, as predicted.

Exaptation: new uses for old structures

Selection cannot plan ahead, so complex structures do not evolve "in order to" serve a future role. Instead, structures that evolved in one context are often co-opted for another. Such a feature is called an exaptation. Feathers first appeared in dinosaurs that could not fly; they probably served for insulation or display and were later co-opted for flight. The small bones of the mammalian middle ear evolved from bones that formed part of the jaw joint in ancestral synapsids. Exaptation explains how a structure that seems useless in an early, partial form can still have been favored: it was useful for something else.

Why natural selection cannot fashion perfect organisms

Organisms are well suited to their environments, but they are not perfectly designed. Four constraints explain why.

1. Selection can act only on existing variation. Natural selection favors the best of the phenotypes actually present in a population, which may not be the best imaginable. New advantageous alleles do not arise on demand. A population of bacteria exposed to a new drug survives only if some resistant variant already exists or arises in time.
2. Evolution is limited by historical constraints. Each species has a legacy of descent with modification from ancestral forms. Evolution modifies existing structures and adapts them to new situations rather than scrapping them and building from scratch. Birds did not grow a new pair of limbs for wings; their forelimbs were modified, which costs them the use of those limbs as hands. The human back and knee, inherited from four legged ancestors and modified for upright walking, are prone to injury for the same reason.
3. Adaptations are often compromises. Each organism must do many different things. A seal spends part of its time on rocks; it would probably walk better with legs, but its flippers serve swimming. Human limbs are flexible and allow versatile movement, but at the cost of dislocations, torn ligaments and sprains. Larger body size can bring dominance but also higher energy needs. Bacteria carrying resistance genes often grow more slowly than susceptible strains when no drug is present, a fitness cost that helps explain why resistance sometimes declines after antibiotic use is reduced.
4. Chance, natural selection and the environment interact. Chance events such as storms or founder events affect which alleles survive, regardless of their adaptive value, and the environment can change faster than a population adapts. A trait shaped by past conditions may become a poor fit; the human taste for sugar and fat was useful when such foods were scarce but contributes to obesity and diabetes in an environment where they are abundant, a situation called evolutionary mismatch.

A case study in historical constraint: the recurrent laryngeal nerve

In fishes, branches of the vagus nerve run to the gills, passing behind the blood vessels of the gill arches, and the heart sits just behind the head. As tetrapods evolved, the gill arch arteries were remodeled: one of them became part of the aortic arch, and the heart moved down into the chest as the neck lengthened. The nerve branch to the larynx, which develops from the old gill region, was still hooked behind that artery. It now runs from the brain down the neck into the chest, loops under the aortic arch on the left side, and climbs back up to the larynx. In humans the detour adds several centimeters; in a giraffe, it adds several meters. No engineer would design such a route, but it is exactly what descent with modification predicts.

Coevolution and arms races

Many of the most impressive adaptations arise because the environment includes other evolving species. When two species exert reciprocal selection on each other, they coevolve. Predators and prey, parasites and hosts, and flowers and their pollinators all show this pattern. Rough skinned newts in parts of western North America carry a potent nerve toxin, and the garter snakes that eat them have evolved resistance through changes in their sodium channels; where newts are most toxic, snakes are most resistant. Pathogens and the human immune system are locked in a similar arms race, which is why influenza vaccines must be updated and why bacteria keep evolving around new antibiotics. Because the "target" keeps moving, selection never reaches a final perfect state.

Putting it together

Evolution is not a ladder of progress toward a goal, and natural selection is not the only cause of evolutionary change. Variation arises by chance through mutation and recombination; which variants spread depends on selection, drift and gene flow acting together in a particular environment at a particular time. The result is organisms that are often exquisitely adapted but always bear the marks of their history and the compromises of their many tasks. The same principles explain the origin of new species, the subject of the next chapter.

Words worth knowing