Life on Earth began about 3.5 billion years ago. At that point in the development of the Earth, the atmosphere was very different from what it is today. As opposed to the current atmosphere, which is mostly nitrogen and oxygen, the early Earth atmosphere contained mostly hydrogen, water, ammonia, and methane.

In experiments, scientists have showed that the electrical discharges of lightning, radioactivity, and ultraviolet light caused the elements in the early Earth atmosphere to form the basic molecules of biological chemistry, such as nucleotides, simple proteins, and ATP. It seems likely, then, that the Earth was covered in a hot, thin soup of water and organic materials. Over time, the molecules became more complex and began to collaborate to run metabolic processes. Eventually, the first cells came into being. These cells were heterotrophs, which could not produce their own food and instead fed on the organic material from the primordial soup. (These heterotrophs give this theory its name.)

The anaerobic metabolic processes of the heterotrophs released carbon dioxide into the atmosphere, which allowed for the evolution of photosynthetic autotrophs, which could use light and CO₂ to produce their own food. The autotrophs released oxygen into the atmosphere. For most of the original anaerobic heterotrophs, oxygen proved poisonous. The few heterotrophs that survived the change in environment generally evolved the capacity to carry out aerobic respiration. Over the subsequent billions of years, the aerobic autotrophs and heterotrophs became the dominant life-forms on the planet and evolved into all of the diversity of life now visible on Earth.

Humankind has always wondered about its origins and the origins of the life around it. Many cultures have ancient creation myths that explain the origin of the Earth and its life. In Western cultures, ideas about evolution were originally based on the Bible. The book of Genesis relates how God created all life on Earth about 6,000 years ago in a mass creation event. Proponents of creationism support the Genesis account and state that species were created exactly as they are currently found in nature. This oldest formal conception of the origin of life still has proponents today.

However, about 200 years ago, scientific evidence began to cast doubt on creationism. This evidence comes in a variety of forms.

Fossils provide the only direct evidence of the history of evolution. Fossil formation occurs when sediment covers some material or fills an impression. Very gradually, heat and pressure harden the sediment and surrounding minerals replace it, creating fossils. Fossils of prehistoric life can be bones, shells, or teeth that are buried in rock, and they can also be traces of leaves or footprints left behind by organisms.

Together, fossils can be used to construct a fossil record that offers a timeline of fossils reaching back through history. To puzzle together the fossil record, scientists have to be able to date the fossils to a certain time period. The strata of rock in which fossils are found give clues about their relative ages. If two fossils are found in the same geographic location, but one is found in a layer of sediment that is beneath the other layer, it is likely that the fossil in the lower layer is from an earlier era. After all, the first layer of sediment had to already be on the ground in order for the second layer to begin to build up on top of it. In addition to sediment layers, new techniques such as radioactive decay or carbon dating can also help determine a fossil’s age.

There are, however, limitations to the information fossils can supply. First of all, fossilization is an improbable event. Most often, remains and other traces of organisms are crushed or consumed before they can be fossilized. Additionally, fossils can only form in areas with sedimentary rock, such as ocean floors. Organisms that live in these environments are therefore more likely to become fossils. Finally, erosion of exposed surfaces or geological movements such as earthquakes can destroy already formed fossils. All of these conditions lead to large and numerous gaps in the fossil record.

Scientists often try to determine the relatedness of two organisms by comparing external and internal structures. The study of comparative anatomy is an extension of the logical reasoning that organisms with similar structures must have acquired these traits from a common ancestor. For example, the flipper of a whale and a human arm seem to be quite different when looked at on the outside. But the bone structure of each is surprisingly similar, suggesting that whales and humans have a common ancestor way back in prehistory. Anatomical features in different species that point to a common ancestor are called homologous structures.

However, comparative anatomists cannot just assume that every similar structure points to a common evolutionary origin. A hasty and reckless comparative anatomist might assume that bats and insects share a common ancestor, since both have wings. But a closer look at the structure of the wings shows that there is very little in common between them besides their function. In fact, the bat wing is much closer in structure to the arm of a man and the fin of a whale than it is to the wings of an insect. In other words, bats and insects evolved their ability to fly along two very separate evolutionary paths. These sorts of structures, which have superficial similarities because of similarity of function but do not result from a common ancestor, are called analogous structures.

In addition to homologous and analogous structures, vestigial structures, which serve no apparent modern function, can help determine how an organism may have evolved over time. In humans the appendix is useless, but in cows and other mammalian herbivores a similar structure is used to digest cellulose. The existence of the appendix suggests that humans share a common evolutionary ancestry with other mammalian herbivores. The fact that the appendix now serves no purpose in humans demonstrates that humans and mammalian herbivores long ago diverged in their evolutionary paths.

Homologous structures not present in adult organisms often do appear in some form during embryonic development. Species that bear little resemblance to each other in their adult forms may have strikingly similar embryonic stages. In some ways, it is almost as if the embryo passes through many evolutionary stages to produce the mature organism. For example, for a large portion of its development, the human embryo possesses a tail, much like those of our close primate relatives. This tail is usually reabsorbed before birth, but occasionally children are born with the ancestral structure intact. Even though they are not generally present in the adult organism, tails could be considered homologous traits between humans and primates.

In general, the more closely related two species are, the more their embryological processes of development resemble each other.

Just as comparative anatomy is used to determine the anatomical relatedness of species, molecular biology can be used to determine evolutionary relationships at the molecular level. Two species that are closely related will have fewer genetic or protein differences between them than two species that are distantly related and split in evolutionary development long in the past.

Certain genes or proteins in organisms change at a constant rate over time. These genes and proteins, called molecular clocks because they are so constant in their rate of change, are especially useful in comparing the molecular evolution of different species. Scientists can use the rate of change in the gene or protein to calculate the point at which two species last shared a common ancestor. For example, ribosomal RNA has a very slow rate of change, so it is commonly used as a molecular clock to determine relationships between extremely ancient species. Cytochrome c, a protein that plays an important role in aerobic respiration, is an example of a protein commonly used as a molecular clock.

In the nineteenth century, as increasing evidence suggested that species changed over time, scientists began to develop theories to explain how these changes arise. During this time, there were two notable theories of evolution. The first, proposed by Lamarck, turned out to be incorrect. The second, developed by Darwin, is the basis of all evolutionary theory.

The first notable theory of evolution was proposed by Jean-Baptiste Lamarck (1744–1829). He described a two-part mechanism by which evolutionary change was gradually introduced into the species and passed down through generations. His theory is referred to as the theory of transformation or Lamarckism.

The classic example used to explain Lamarckism is the elongated neck of the giraffe. According to Lamarck’s theory, a given giraffe could, over a lifetime of straining to reach high branches, develop an elongated neck. This vividly illustrates Lamarck’s belief that use could amplify or enhance a trait. Similarly, he believed that disuse would cause a trait to become reduced. According to Lamarck’s theory, the wings of penguins, for example, were understandably smaller than the wings of other birds because penguins did not use their wings to fly.

The second part of Lamarck’s mechanism for evolution involved the inheritance of acquired traits. He believed that if an organism’s traits changed over the course of its lifetime, the organism would pass these traits along to its offspring.

Lamarck’s theory has been proven wrong in both of its basic premises. First, an organism cannot fundamentally change its structure through use or disuse. A giraffe’s neck will not become longer or shorter by stretching for leaves. Second, modern genetics shows that it is impossible to pass on acquired traits; the traits that an organism can pass on are determined by the genotype of its sex cells, which does not change according to changes in phenotype.

While sailing aboard the HMS Beagle, the Englishman Charles Darwin had the opportunity to study the wildlife of the Galápagos Islands. On the islands, he was amazed by the great diversity of life. Most particularly, he took interest in the islands’ various finches, whose beaks were all highly adapted to their particular lifestyles. He hypothesized that there must be some process that created such diversity and adaptation, and he spent much of his time trying to puzzle out just what the process might be. In 1859, he published his theory of natural selection and the evolution it produced. Darwin explained his theory through four basic points:

Natural selection creates change within a species through competition, or the struggle for life. Members of a species compete with each other and with other species for resources. In this competition, the individuals that are the most fit—the individuals that have certain variations that make them better adapted to their environments—are the most able to survive, reproduce, and pass their traits on to their offspring. The competition that Darwin’s theory describes is sometimes called the survival of the fittest.

One of the best examples of natural selection is a true story that took place in England around the turn of the century. Near an agricultural town lived a species of moth. The moth spent much of its time perched on the lichen-covered bark of trees of the area. Most of the moths were of a pepper color, though a few were black. When the pepper-color moths were attached to the lichen-covered bark of the trees in the region, it was quite difficult for predators to see them. The black moths were easy to spot against the black-and-white speckled trunks.

The nearby city, however, slowly became industrialized. Smokestacks and foundries in the town puffed out soot and smoke into the air. In a fairly short time, the soot settled on everything, including the trees, and killed much of the lichen. As a result, the appearance of the trees became nearly black in color. Suddenly the pepper-color moths were obvious against the dark tree trunks, while the black moths that had been easy to spot now blended in against the trees. Over the course of years, residents of the town noticed that the population of the moths changed. Whereas about 90 percent of the moths used to be light, after the trees became black, the moth population became increasingly black.

When the trees were lighter in color, natural selection favored the pepper-color moths because those moths were more difficult for predators to spot. As a result, the pepper-color moths lived to reproduce and had pepper-color offspring, while far fewer of the black moths lived to produce black offspring. When the industry in the town killed off the lichen and covered the trees in soot, however, the selection pressure switched. Suddenly the black moths were more likely to survive and have offspring. In each generation, more black moths survived and had offspring, while fewer lighter moths survived to have offspring. Over time, the population as a whole evolved from mostly white in color to mostly black in color.

In a normal population without selection pressure, individual traits, such as height, vary in the population. Most individuals are of an average height, while fewer are extremely short or extremely tall. The distribution of height falls into a bell curve.

Natural selection can operate on this population in three basic ways. Stabilizing selection eliminates extreme individuals. A plant that is too short may not be able to compete with other plants for sunlight. However, extremely tall plants may be more susceptible to wind damage. Combined, these two selection pressures act to favor plants of medium height.

Directional selection selects against one extreme. In the familiar example of giraffe necks, there was a selection pressure against short necks, since individuals with short necks could not reach as many leaves on which to feed. As a result, the distribution of neck length shifted to favor individuals with long necks.

Disruptive selection eliminates intermediate individuals. For example, imagine a plant of extremely variable height that is pollinated by three different pollinator insects: one that was attracted to short plants, another that preferred plants of medium height, and a third that visited only the tallest plants. If the pollinator that preferred plants of medium height disappeared from an area, medium height plants would be selected against, and the population would tend toward both short and tall plants, but not plants of medium height.

Darwin’s theory of natural selection and evolution rests on two crucial ideas:

But Darwin had no idea how those variations came to be or how they were passed down from one generation to the next. Mendel’s experiments and the development of the science of genetics provided answers. Genetics explains that the phenotype—the physical attributes of an organism—is produced by an organism’s genotype. Through the mechanism of mutations, genetics explains how variations arose among individuals in the form of different alleles of genes. Meiosis, sexual reproduction, and the inheritance of alleles explain how the variations between organisms are passed down from parent to offspring.

With the modern understanding of genes and inheritance, it is possible to redefine natural selection and evolution in genetic terms. The particular alleles that an organism inherits from its parents determine that organism’s physical attributes and therefore its fitness for survival. When the forces of natural selection result in the survival of the fittest, what those forces are really doing is selecting which alleles will be passed on from one generation to the next.

Once you see that natural selection is actually a selection of the passage of alleles from generation to generation, you can further see that the forces of natural selection can change the frequency of each particular allele within a population’s gene pool, which is the sum total of all the alleles within a particular population. Using genetics, one can create a new definition of evolution as the change in the allele frequencies in the gene pool of a population over time. For example, in the population of moths we discussed earlier, after the trees darkened, the frequency of the alleles for black coloration increased in the gene pool, while the frequency of alleles for light coloration decreased.

The Hardy-Weinberg principle states that a sexually reproducing population will have stable allelic frequencies and therefore will not undergo evolution, given the following five conditions:

The Hardy-Weinberg principle proves that variability and inheritance alone are not enough to cause evolution; natural selection must drive evolution. A population that meets all of these conditions is said to be in Hardy-Weinberg equilibrium. Few natural populations ever experience Hardy-Weinberg equilibrium, though, since large populations are rarely found in isolation, all populations experience some level of mutation, and natural selection simply cannot be avoided.

The scientific definition of a species is a discrete group of organisms that can only breed within its own confines. In other words, the members of one species cannot interbreed with the members of another species. Each species is said to experience reproductive isolation. If you think about evolution in terms of genetics, this definition of species makes a great deal of sense: if species could interbreed, they could share gene flow, and their evolution would not be separate. But since species cannot interbreed, each species exists on its own individual path.

As populations change, new species evolve. This process is known as speciation. Through speciation, the earliest simple organisms were able to branch out and populate the world with millions of different species. Speciation is also called divergent evolution, since when a new species develops, it diverges from a previous form. All homologous traits are produced by divergent evolution. Whales and humans share a distant common ancestor. Through speciation, that ancestor underwent divergent evolution and gave rise to new species, which in turn gave rise to new species, which over the course of millions of years resulted in whales and humans. The original ancestor had a limb structure that, over millions of years and successive occurrences of divergent evolution, evolved into the fin of the whale and the arm of the human.

Speciation occurs when two populations become reproductively isolated. Once reproductive isolation occurs for a new species, it will begin to evolve independently. There are two main ways in which speciation might occur. Allopatric speciation occurs when populations of a species become geographically isolated so that they cannot interbreed. Over time, the populations may become genetically different in response to the unique selection pressures operating in their different environments. Eventually the genetic differences between the two populations will become so extreme that the two populations would be unable to interbreed even if the geographic barrier disappeared.

A second, more common form of speciation is adaptive radiation, which is the creation of several new species from a single parent species. Think of a population of a given species, which we’ll imaginatively name population 1. The population moves into a new habitat and establishes itself in a niche, or role, in the habitat (we discuss niches in more detail in the chapter on Ecology). In so doing, it adapts to its new environment and becomes different from the parent species. If a new population of the parent species, population 2, moves into the area, it too will try to occupy the same niche as population 1. Competition between population 1 and population 2 ensues, placing pressure on both groups to adapt to separate niches, further distinguishing them from each other and the parent species. As this happens many times in a given habitat, several new species may be formed from a single parent species in a relatively short time. The immense diversity of finches that Darwin observed on the Galápagos Islands is an excellent example of the products of adaptive radiation.

When different species inhabit similar environments, they face similar selection pressures, or use parts of their bodies to perform similar functions. These similarities can cause the species to evolve similar traits, in a process called convergent evolution. From living in the cold, watery, arctic regions, where most of the food exists underwater, penguins and killer whales have evolved some similar characteristics: both are streamlined to help them swim more quickly underwater, both have layers of fat to keep them warm, both have similar white-and-black coloration that helps them to avoid detection, and both have developed fins (or flippers) to propel them through the water. All of these similar traits are examples of analogous traits, which are the product of convergent evolution.

Convergent evolution sounds as if it is the opposite of divergent evolution, but that isn’t actually true. Convergent evolution is only superficial. From the outside, the fin of a whale may look like the flipper of a penguin, but the bone structure of a whale fin is still more similar to the limbs of other mammals than it is to the structure of penguin flippers. More importantly, convergent evolution never results in two species gaining the ability to interbreed; convergent evolution can’t take two species and turn them into one.