The Diversity of Life (updated)

Editor's Notes

• #3: How did life on earth begin? What is life? Life is defined by the ability to replicate and by the presence of some sort of metabolic activity.
• #4: Earth formed about four and a half billion years ago from clouds of dust and gases left over after the formation of the sun. The earliest life forms that we have evidence of are fossilized bacteria-like cells found in rocks that are 3.4 billion years old. From that initial point at earth’s formation, there now is tremendous biodiversity, the variety and variability among all genes, species, and ecosystems, on the planet. In this chapter we explore in more detail how this biodiversity might have come to be, and how we name groups of organisms and determine the relatedness of those groups to one another.
• #5: We begin by returning to the question of the origin of life on earth 
• #6: Section 10.1 Opener Life on earth arose in a very different environment than we experience today. (Shown here: the formation of volcanic rock in Hawaii.) In the beginning, there was nothing. Now there is something. How did life on earth begin? Let’s define what we mean by “life.” Here we give just a basic definition: Life is defined by the ability to replicate and by the presence of some sort of metabolic activity.  
• #7: Earth formed 4.5 billion years ago. The oldest rocks, found in Greenland, are about 3.8 billion years old. The earliest life forms appeared not long after these rocks were formed: fossilized bacteria-like cells have been found in rocks that are 3.4 billion years old. How did these first organisms arise? Some have suggested that life may have originated elsewhere in the universe and traveled to earth, possibly carried on a meteor. There is little evidence for this idea, however, and it is hotly debated whether microbes could even survive the multi-million-year trip to earth in the cold vacuum of space with no protection from ultraviolet and other forms of radiation; experimental data have been unable to answer this question definitely. Most scientists believe, instead, that life originated on earth, probably in several distinct phases 
• #8: The conditions on earth around the time of the origin of life were very different than they are today. In particular, chemical analyses of old rocks reveals that there was no oxygen gas present. The atmosphere included large amounts of carbon dioxide, nitrogen, methane, ammonia, hydrogen, and hydrogen sulfide. Most of these molecules were produced by volcanic eruptions. It was in this environment that some locations on earth probably served as the cradle of life or what Darwin called the “warm little pond” (Figure 10-1 Darwin’s “warm little pond”).
• #9: Critical to the origin of life was the formation of small molecules containing carbon and hydrogen. Because of their chemical structures, these molecules bond very easily and in many ways, causing them to have a huge variety of functions that make them indispensable for the chemical processes of life. There are several plausible scenarios for how the creation of small organic molecules may have occurred at this time. The most likely comes from some simple, but revealing four-step experiments done in 1953 by a 23-year-old student named Stanley Miller and his advisor, Harold Urey (Figure 10-2 part 1 A promising first step). 
• #10: 1. They created a model of the “warm little pond” and their best estimate of earth’s early atmosphere: a flask of water with H2, CH4 (methane), and NH3 (ammonia). 2. They subjected their mini-world to sparks, to simulate lighting. 3. And they cooled the atmosphere so that any compounds in it would rain back down into the water. 4. Then they waited and examined the water to see what happened  Figure 10-2 part 2 A promising first step.
• #11: They didn’t have to wait long to get exciting results. Within a matter of days they discovered many organic molecules, including five different amino acids in their primordial sea. (Using more sensitive equipment, reanalyses in 2008 revealed that all 20 amino acids present in living organisms were present in the experimental residues.) The Urey-Miller experiments are still far from proof that a life arose from non-life, and questions remain, such as whether the environment they assumed was reasonable. Without oxygen gas, for example, earth’s atmosphere would not have had an ozone layer protecting the early environment from the harmful ultraviolet radiation that breaks down methane and ammonia. Still, the experiments are a promising first step, suggesting that complex organic compounds, including amino acids—the primary constituents of proteins and an essential component of living systems—could have been produced from inorganic chemicals and lightning energy in the primitive environment of earth.
• #12: After the generation of numerous organic molecules such as amino acids, the second phase in the generation of life from non-life was probably the assembly of these building block molecules into self-replicating, information-containing molecules. This is where things get a bit more speculative. It’s complicated enough to generate a complex organic molecule, but its a whole lot more complicated to generate an organic molecule that can replicate itself. To get to the replication phase/stage, researchers believed that enzymes were required.
• #13: Recently, researchers discovered a molecule that could unexpectedly function as an enzyme that links together nucleic acids (such as DNA or RNA). The molecule wasn’t a protein but was, instead, a molecule of the nucleic acid RNA, which stores information just as DNA does.
• #14: To learn that RNA can also do what proteins do—catalyze reactions necessary for replication—is notable because it means that this single, relatively simple molecule could have been a self-replicating system and a precursor to cellular life. These findings have given rise to the RNA World hypothesis, which proposes that the world may have been filled with RNA-based life before it became filled with the DNA-based life we see today.
• #15: These self-replicating molecules raise an important question: When exactly was the threshold between living and non-living crossed? In the RNA World, self-replicating nucleic acid molecules carried the information of how to replicate and served as the machinery to actually carry out the replication. Is that enough? At this point, it is reasonable to ask the question: What exactly is “life”? How do we define it? (Potential for engaging students with this question)
• #16: In rocks from South Africa, the fossils of 3.4 billion-year-old cells have been found. These cells appear to be prokaryotic cells, similar to living bacterial cells, with no nucleus, no organelles, and a circular strand of genetic information (Figure 10-3 Ancient prokaryotic cells). They even look like they are in the process of dividing. Were these the first living organisms on earth? And were they descendants of earlier, self-replicating molecules of RNA? Because no earlier fossils have been found, it is difficult to answer these questions.
• #17: Most scientists agree with the general definition we learned at the start of this chapter that life is defined by two characteristics: the ability to replicate and the ability to carry out some sort of metabolism. By this definition, following the first two phases described above, the self-replicating RNA molecules were right on the border, satisfying the first condition but not the second. We now explore the critical third phase in the generation of life from non-life, the development of a membrane that separated these small molecules from their surroundings, thus compartmentalizing them into cells and making metabolic activity possible 
• #18: One way that self-replicating molecules could acquire chemicals and use them in the controlled reactions of metabolism was by packaging the molecules within membranes. Membranes make numerous aspects of metabolism possible. In particular they make it possible for chemicals inside the cell to be at higher concentrations that they are outside the cell.
• #19: Some evidence suggests that the first cells may simply have come together spontaneously. Specifically, researchers have found that mixtures of phospholipids placed in water or salt solutions tend to spontaneously form small spherical units that resemble living cells. These units may even “sprout” new buds at their surface, appearing to divide. Because the cell-like units don’t pass on any genetic material, however, they cannot be considered to be alive. If at some point in the past these units incorporated some self-replicating molecules inside, however, maybe by forming around them, such microspheres may have been important in the third phase in the generation of life from non-life: the compartmentalization of self-replicating, information-containing molecules into cells. If this did occur, the final step in the creation of something from nothing would be complete (Fig. 10-4 Are microspheres a key stage in the origin of life?).
• #20: Section 10.2 Opener A world of beauty. There are more than 230,000 species of flowering plants.
• #21: A cat and a mouse are different things. Oprah Winfrey and Bill Gates, on the other hand, are different versions of the same thing. That is, although they are different individuals, they both are humans. We generally distinguish between different kinds of living organisms: a rose versus a daisy, a wasp versus a fly, a snake versus a frog. Similarly, we lump other organisms into the same group and recognize them as different versions of the same thing: red roses and yellow roses, Chihuahuas and Dalmatians. How do we know when to classify two individuals as members of different groups and when to classify them as two individuals who are members of the same group?   And how do we classify two individuals that are somewhat similar, but seem too different to classify as the same thing, such as a mouse and a rat or a goat and a sheep? Figure 10-5 The same but not the same. We recognize Bill Gates and Oprah Winfrey as members of the same species, but can you tell whether the rose and the tulip or the wood mouse and the common brown rat are from the same species? (Hint: They’re not.)
• #22: Biologists use the word species to label different kinds of organisms. According to the biological species concept: Species are natural populations of organisms that interbreed with each other or could possibly interbreed, and that cannot interbreed with organisms outside their own group.
• #23: Figure 10-6 An interbreeding population. This herd of Dall sheep lives in the remote regions of Denali National Park, Alaska.
• #24: Notice that the biological species concept completely ignores physical appearance when defining a species and instead emphasizes reproductive isolation, the inability of the individuals from two populations to produce fertile offspring with each other, thereby making it impossible for them to exchange genes. Let’s clarify two important features of the biological species concept. First, it says that members of a species are either actually interbreeding or could possibly interbreed. This emphasis means that just because two individuals are physically separated, they aren’t necessarily in different species. A person living in the United States and a person living in Iceland, for example, may not be able to mate because of the distance between them, but if they were brought to the same location, they could mate if they wanted to. So we do not consider them to be reproductively isolated. Second, our definition refers to “natural” populations. This distinction is important because in captivity occasionally individuals may interbreed that which would not interbreed in the wild, such as zebra and horse (Figure 10-7 Interbreeding is not enough).
• #25: There are two types of barriers that prevent individuals of different species from reproducing: prezygotic barriers and postzygotic barriers. (Remember, an egg that has been fertilized by a sperm cell is a zygote.) Figure 10-8 Barriers to reproduction. With postzygotic barriers to reproduction, even if fertilization does occur, the animal (such as the mule, on the right) is usually sterile.
• #27: These barriers include situations in which the members have different courtship rituals or have sufficient physical differences that they are unable to mate. In some cases, individuals from two different species can and do mate but physical or biochemical factors prevent the male gamete from fertilizing the female gamete.
• #28: Postzygotic barriers occur after fertilization and generally prevent the production of fertile offspring from individuals of two different species (such offspring are called hybrids). These barriers are responsible for the production of hybrid individuals that either do not survive long after fertilization or, if they do survive, are infertile or have reduced fertility. Mules, for example, are the hybrid offspring of horses and donkeys; although they can survive, they cannot breed with each other or produce offspring.
• #29: Keeping track of a large group of anything requires an organizational system. Many libraries, for example, catalog their books using the Dewey Decimal System, which organizes books into ten different classes, further subdivides each class into ten divisions, and each division into ten sections. On your computer, you store your electronic files within virtual folders and subfolders that can be organized by name, size, or type.
• #30: With the huge number of species on earth, such a classification system is particularly important. Biologists use the system developed by the Swedish biologist Carolus Linnaeus in the mid-1700s and published in his book called Systema Naturae (“System of Nature”).   Here’s how it works (Figure 10-9 Name that zebra. Equus quagga): Every species is given a scientific name that consists of two parts, a genus (plural = genera) and a specific epithet. Linnaeus gave humans the name Homo sapiens, meaning “wise man.” Homo is the genus and sapiens is the specific epithet. (The genus is capitalized and the genus and specific epithet are both italicized.) The redwood tree has the name Sequoia sempevirens.
• #31: The strength of Linnaeus’s system is that it is a hierarchical system; that is, each element of the system falls under just a single element in the level just above it. In Linnaeus’s system, the species is the most narrow classification for an organism. The specific epithet for every species within a genus is unique, but many different species may all be placed within the same genus. Similarly, many genera are grouped within a broader group, called a family. And many families are grouped within an order. Orders are grouped within a class. Classes are grouped within a phylum. And at the highest level of Linnaeus’s system, all phyla were classified under one of three kingdoms: the animal kingdom, the plant kingdom, or the “mineral kingdom.” Today, many of the species classifications that Linnaeus described have been revised and some of his designations, such as the “mineral kingdom,” have been left out. Also, all of the kingdoms are now classified under an even higher order of classification, the domain. But Linnaeus’s basic hierarchical structure remains and all life on earth is still named using this system, with all organisms belonging to one of the three domains.
• #32: Biologists, like all humans, can be biased. When investigating the natural world, for example, they often focus on plants and animals, to the exclusion of the rest of the earth’s rich biodiversity. This gets them into trouble when it comes to a concept such as the biological species concept. While the biological species concept is remarkably useful when describing most plants and animals, it falls short of representing a universal and definitive way of distinguishing many life forms (Figure 10-10: A useful concept that can’t always be easily applied).
• #33: The biological species concept defines species as groups of interbreeding individuals. But this is a useless distinction for the asexual species of the world. Recall from Chapter 6 that asexual reproduction—common among single-celled organisms (including all bacteria), many plants, and some animals—is a form of reproduction that doesn’t involve fertilization or even two individuals. Rather, the cell (or cells) of an individual simply divide, creating a new individual. Asexually reproducing organisms don’t have a partner or need a partner, they just divide. Because asexual reproduction does not involve any interbreeding, the concept of reproductive isolation is no longer meaningful and it would seem that every individual should be considered a separate species. But clearly that’s not a helpful rule to follow.
• #34: When it comes to classifying fossil species, differences in the sizes and shapes of fossil bones can never reveal definitively whether there was reproductive isolation between the individuals from whom the bones came. This makes it impossible to apply the biological species concept.
• #35: Based on fossils, it appears that modern-day humans, Homo sapiens, evolved from a related species called Homo erectus about 250,000 to 400,000 years ago. This seems reasonable until you consider that your parents—who are in the species Homo sapiens—were born to your Homo sapiens grandparent who were born to your Homo sapiens great grandparents, and so on. If humans evolved from Homo erectus, at what exact point did H. erectus turn into H. sapiens? It may not be possible to identify an exact point at which the change occurred.
• #37: In the center of Asia live some small, insect-eating songbirds called greenish warblers which are unable to live at the higher elevations of the Tibetan mountain range. Because of this limitation, the warblers live in a ring around the mountain range.
• #38: At the southern end of the ring, in northwest India, the warblers interbreed with each other. Then, as the warblers move north along either side of the mountain range, the population splits. On each side, the warblers interbreed, but warblers from each side do not interbreed because the mountain range separates them. When the two “side” populations of warblers meet up again at the northern end of the ring in the forests of Siberia, they can no longer interbreed.
• #39: What happened? Gradual changes in the warblers on each side of the mountain range accumulated so that the two populations that meet up in Siberia are sufficiently different physically and behaviorally that they have become reproductively incompatible. But because the two non-interbreeding populations are connected by gene flow through other populations, there is no exact point at which one species stops and the other begins. So where do you draw the line? The greenish warblers are just one example of more than 20 such ring species that have been described.
• #40: Increasingly, hybridization—the interbreeding of closely related species—has been observed, among plant species and among animal species. This phenomenon fits with the biological species concept as long as postzygotic barriers have evolved, so that the hybrids are weak and unable to reproduce. But in some cases, such as among butterflies in the genus Heliconius, the hybrids have high survival rates and are fertile, whether interbreeding with other hybrids or with individuals from either of the parents’ species, suggesting that the borders between the species are not so clear cut.
• #41: All of these shortcomings have prompted the development of several alternative approaches to defining what a species is. These alternatives tend to focus on aspects of organisms other than reproductive isolation as defining features. The most commonly used alternative is the morphological species concept, which characterizes species based on physical features such as body size and shape. Although the choice of which features to use is subjective, an important feature of the morphological species concept is that it can be used effectively to classify asexual species. And because it doesn’t require knowledge of whether individuals can actually interbreed, the morphological species concept is a bit easier to use than the biological species concept when observing organisms in the wild.
• #42: Biologists don’t really have a clue about how many species there are on earth. Estimates of the number vary tremendously, from low estimates of 5 million to high estimates of 100 million. Biologists do, however, know the process by which they all arose.
• #43: The process of speciation, in which one species splits into two distinct species, occurs in two distinct phases and requires more than just evolutionary change in a population. The first phase of speciation is reproductive isolation (which we’ve already discussed), through which two populations come to have independent evolutionary fates. The second phase of speciation is genetic divergence, in which two populations evolving as separate entities can accumulate physical and behavioral differences over time as they become adapted differently to features of their environments, including predators and types and abundances of food available.
• #44: Suppose one population of squirrels is split into two separate populations because the climate grows wetter in their habitat and a river forms and splits it in two. Because the squirrels cannot cross the river, the population on one side is reproductively isolated from the population on the other side. Over time, the populations on either side have different evolutionary paths as they adapt to particular features of their habitats, which may differ on either side of the river. Eventually, the two populations may genetically diverge enough such that if the river separating them disappeared, upon coming back into contact, squirrels from the two populations might no longer be able to interbreed. Two species of antelope ground squirrels formed on the north and south rims of the Grand Canyon as a result of allopatric speciation (Figure 10-11 Geographic isolation can result in genetic divergence).
• #45: An example of allopatric speciation can be seen in the various species of finches found in the Galapagos Islands. Individuals from the nearest mainland, South America, colonized one or more of the Galapagos islands. (And later, additional islands may have been colonized by birds from the mainland or from previously colonized islands.) But because the islands are far apart from one another, the finches tended not to travel between islands and these colonization events are rare, so the populations remained reproductively isolated from one another. Consequently, 14 different species of finches have evolved in the Galapagos Islands, each of which specializes in eating certain of the wide range of different insects, buds, and seeds that occur on the islands (Figure 10-12 Five of the 14 Galapagos Island finch species), while only one species of finches is found on the South American mainland nearest the island.
• #46: Speciation can also occur among populations that overlap geographically. This type of speciation is called sympatric speciation. Among animals it is rare for populations of the same animal to become reproductively isolated when they coexist in the same area, so this method of speciation is relatively uncommon. But among plants it is common, and it occurs in one of two ways (Figure 10-13 Speciation without geographic isolation).  
• #47: Section 10.3 Opener The diversity of life on earth can be thought of as branching like a tree.
• #48: Charles Darwin proposed and documented that species could in fact change and give rise to new species. With Darwin, the classification of species acquired a new goal and a more important function. In The Origin of Species Darwin wrote: “Our classifications will come to be, as far as they can be so made, genealogies.” That is, Darwin proposed that the classifications of organisms would resemble family trees that link parents and offspring over long periods of time. With these words, Darwin was the first to link classification with evolution.
• #49: Classification such as that used by Linnaeus just involved placing organisms within groups as a function of their apparent similarity with each other. The modern incarnation of Darwin’s vision of classification is called systematics and has the broader goal of reconstructing the phylogeny, or evolutionary history, of organisms. That is, through systematics all species, even extinct species, are named and arranged in a manner that indicates the common ancestors they share and the points at which they diverged from each other.
• #50: The common ancestor points at which species diverge are called nodes. A complete phylogeny of all organisms therefore, is like a family tree, for all species past and present.
• #51: Nodes illustrated. A phylogenetic tree shows not only the relationships among organisms but also presents a hypothesis about the evolutionary history of species. Figure 10-14 Mapping common ancestors. At the beginning of life on earth, there was the first living organism, one that could replicate itself and that had a metabolism. Then a speciation event occurred. After this event, the population of the first living organisms split into independent evolutionary lineages. The phylogenetic tree had its first branch, and there was not biodiversity. It is important to remember that phylogenies are hypotheses, and like any hypotheses they are subject to revision and modification. Over hundreds of millions of years since then, speciation events continued to occur and today the tree has branches with millions (or possibly tens of millions) of tips that represent all species on earth. And it doesn’t stop here—even today, speciation continues to add new branches all the time.
• #52: Most human cultures and religions have a sacred Tree of Life. The bodhi tree that the Buddha sat beneath for seven years to achieve the ultimate truth is the Tree of Enlightenment; the apple tree in the Garden of Eden is the Tree of Knowledge. The history of the relationship between all organisms that constitute life on earth is another Tree of Life. The trunk and branches of an evolutionary tree represent ancestor-descendant relationships that link living organisms with all life that has ever existed on earth. The evolutionary tree of life can be thought of as one giant tree, but as a practical matter, biologists often study only particular branches. These branches can be illustrated as big trees or little trees and can be expanded to include whatever organisms the biologist is studying: the tree might, for example, include all animals or just the rodents.
• #53: In evolutionary trees, it does not matter on which side of the tree you put a particular group of organisms. Any branches can be spun around the nodes at which they split (Fig. 10 -14).
• #54: This pinwheel effect means that you cannot assume that rats are more evolutionarily advanced than mice, or vice versa. They are equally advanced in the sense that both groups derived from the same speciation event. Phylogenetic trees only show which groups are most closely related to which other groups Figure 10-14 part 1 Mapping common ancestors.
• #55: Evolutionary trees tell us many things, but one thing they do not tell us is which groups are most “primitive” and which are most “advanced.” This property of phylogenetic trees can serve to undermine some of our most sacred beliefs, such as the one that humans are the pinnacle of evolution. Many trees can be drawn to support this idea, including Figure 10 -14. But notice that if you rotate this tree around any one of its nodes, you can get a number of different trees.
• #56: What trees do tell us is which groups are most closely related to which other groups. One of the most interesting revelations of “tree thinking” is that fungi, such as mushrooms, yeasts, and molds, are more closely related to animals than to plants. By analyzing the genetic composition of plants, fungi, and animals, biologists have been able to determine that the relationship between the three groups is that shown in Figure 10-15. We investigate this surprising fact in Chapter 11. Figure 10-15 A growing tree.
• #57: Biologists use the term monophyletic to describe a group in which all of the individuals are more closely related to each other than to any individuals outside of that group. Monophyletic groups are determined by looking at the nodes of the trees.
• #58: Animals and fungi, taken together, compose a monophyletic group because they all share a more recent common ancestor (designated by node “A” in Figure 10-16) than either of them shares with plants. Plants and fungi, taken together, do not compose a monophyletic group because their common ancestor (at the point of node “B”) is also shared by animals. But plants, fungi, and animals, all taken together, do compose a monophyletic group by virtue of all three sharing the common ancestor at node “B.” Figure 10-16 Members of a monophyletic group share a common ancestor and the group contains all of the descendants of that ancestor.
• #59: Reading an evolutionary tree reveals what groups are most closely related and can give us an approximation of how long it has been since they shared a common ancestor. But how are evolutionary trees—that might hypothesize historical events that happened, in the case of the cat–dog split, 60 million years ago—constructed in the first place?
• #60: Until recently, these trees were assembled by looking carefully at numerous physical features of species and generating tables that compared these features across the species. Figure 10-17 (Looking for clues in body structures) is a simple example of such a table. With only three features, this table shows a clear split between the characteristics of the lion and the hyena, on one hand, and the wolf and the bear on the other. For most of the 1900s, biologists classifying organisms would often use 50 or more characters to generate a tree.
• #61: Beginning in the 1980s, biologists began using molecular sequences rather than physical traits to generate evolutionary trees. The rationale for this approach is that organisms inherit DNA from their ancestors and so as species diverge, their DNA sequences also diverge, becoming increasingly different. As more time that passes following the splitting of one species into two, the differences in their DNA sequences becomes greater. By comparing how similar the DNA sequences are between two groups, it is possible to estimate how long it has been since they shared a common ancestor (Figure 10-18 DNA sequences reveal evolutionary relatedness).