Evolutionary Trees and The Diversity of Life
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This document summarizes key points from a class on evolutionary biology and the tree of life. It discusses how organisms are classified into domains and monophyletic groups based on their evolutionary relationships and genetic similarities. The three domains are bacteria, archaea, and eukarya. Bacteria are single-celled organisms with circular DNA, while archaea include many species that live in extreme environments. The eukarya domain contains plants, animals, fungi and protists.
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Evolutionary Trees and The Diversity of Life
- 1. Day 18 November 6th The Tree of Life Dr. Amy B Hollingsworth The University of Akron Fall 2014
- 4. Are humans more advanced, evolutionarily, than cockroaches? Can bacteria be considered “lower” organisms?
- 6. Monophyletic Groups A group in which all of the individuals are more closely related to each other than to any individuals outside of that group Determined by looking at the nodes of the trees
- 8. Constructing evolutionary trees requires comparing similarities and differences between organisms.
- 11. 10.9 Similar structures don’t always reveal common ancestry.
- 13. The mapping of species’ characteristics onto phylogenetic trees Physical features – pre-1980 just looking at characteristics DNA sequences – post 1980, made it easier to track organisms and similarities
- 15. Convergent Evolution - which occurs when populations of organisms live in similar environments and so experience similar selective forces. • Analogous traits - are characteristics (such as bat wings and insect wings) that are the same because they were produced by convergent evolution and not because they descended from a common structure in an ancestor they shared.
- 16. How do you know whether traits are homologous or analogous? DNA Analysis Analogous traits: Features that are produced by convergent evolution Homologous traits: Features that are inherited from a common ancestor
- 17. 10.10–10.13 Macroevolution gives rise to great diversity.
- 18. 10.10 Macroevolution is evolution above the species level.
- 20. Short-term and Long-term Results Microevolution Macroevolution
- 21. 10.11 The pace of evolution is not constant.
- 23. 10.12 Adaptive radiations are times of extreme diversification. When a small number of species diversifies into a much larger number of species
- 24. Three Phenomena May Trigger Adaptive Radiations All result in access to plentiful new resources.
- 26. Colonizers find a large number of opportunities for adaptation and diversification. Galapagos finches Hawaiian fruit flies
- 27. Innovations such as the wings and rigid skeleton that appeared in insects… …helped them to diversify into the most successful group of animals. There are more than 800,000 species today!
- 28. 10.13 There have been several mass extinctions on earth.
- 30. Background Extinction Extinctions that occur at lower rates during periods other than periods of mass extinctions Occur mostly as the result of natural selection
- 32. Background and Mass Extinctions Have Different Causes Mass extinctions are due to extraordinary and sudden changes to the environment. Background extinctions occur mostly as the result of natural selection.
- 34. 10.14−10.17 An overview of the diversity of life on earth: organisms are divided into three domains.
- 35. 10.14 All living organisms are divided into one of three groups.
- 36. Classification Systems The two-kingdom system • Animal and plant The five-kingdom system • Monera, plant, animal, fungi, and protists
- 37. Classification Takes a Leap Forward Carl Woese, an American biologist, and his colleagues Examined nucleotide sequences Tracking changes
- 39. Woese’s approach is not perfect. Are viruses alive?
- 41. 10.15 The bacteria domain has tremendous biological diversity.
- 42. Why is morning breath so stinky?
- 44. Bacteria Are a Monophyletic Group All bacteria have a few features in common: Single-celled organisms with no nucleus or organelles One or more circular molecules of DNA Several methods of exchanging genetic information Asexual organisms
- 45. 10.16 The archaea domain includes many species living in extreme environments.
- 47. The archaea exhibit tremendous diversity and are often divided into five groups based on their physiological features. Thermophiles – live in hot places Halophiles – live in salty places High- and low-pH tolerant High-pressure tolerant – found 2.5 miles under the ocean’s surface Methanogens
- 48. 10.17 The eukarya domain consists of four kingdoms. Plants, Animals, Fungi, and Protists
Editor's Notes
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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?
- 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.
- 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).
- Whales and sharks have fins; bats and many insects have wings. Do bats have wings because they are most closely related to insects and inherited their wings from a common, winged ancestor, or did insects’ and bats’ wings evolve independently? As the evolutionary tree in Figure 10-19 makes clear, insects’ wings and bats’ wings evolved independently—an adaptation that arose separately on more than one occasion.
- The mapping of species’ characteristics onto phylogenetic trees provides us with the story of evolution. Prior to the 1980s, biologists had always tried to decode the process of evolution by comparing physical features of organisms such as the presence or absence of wings. With the advent of methods for comparing DNA sequences in the 1980s, however, tracing the history of life on earth has become a more rigorous science.
- Let’s look at a case that illuminates why the original methods were weaker (Figure 10-20 Looks can be deceiving). Initially, biologists thought that the African golden moles belonged in the order insectivores, which includes shrews, hedgehogs, and other moles. This belief seemed reasonable because these animals have many characteristics in common: They are small, they have long, narrow snouts, their eyes are tiny, and they live in underground burrows. Biologists thought that this group of characteristics evolved just once, and that every species in the insectivore order possessed these characteristics because they inherited them from a common ancestor. The DNA evidence revealed that the African golden moles are actually more closely related to elephants than they are to the insectivores, including all of the other mole species!
- Why do they look so similar to the insectivores? Because of a phenomenon called convergent evolution, which occurs when populations of organisms live in similar environments and so experience similar selective forces. Analogous traits are characteristics (such as bat wings and insect wings) that are the same because they were produced by convergent evolution and not because they descended from a common structure in an ancestor they shared. Figure 10-20 Looks can be deceiving.
- Features that are inherited from a common ancestor are called homologous features. All mammals have hair because they inherited that trait from a common ancestor. Similarly, among all reptiles, having a mouth is a homologous trait because all reptiles share a common ancestor who passed the trait to them. Analogous features are problematic when constructing evolutionary trees because they are the result of natural selection rather than common ancestry. As a consequence, these traits should not be considered a sign of relatedness between the organisms that have them and they should not be reflected as a sign of common ancestry when constructing an evolutionary tree.
- Section 10.4 Opener More than 400 Anolis lizard species exist.
- When water runs over rocks, it wears them away. The process is simple and slow, yet it is powerful enough to have created the Grand Canyon. To be sure, water running over rocks does not always make a Grand Canyon. Nonetheless, no additional physical processes are necessary. The process of evolution has a lot in common with a stream of water running over rocks: in the short term, it produces small changes in a population, yet the accumulation of these changes can be “canyon-esque” (Figure 10-21 From a trickle of water to the Grand Canyon). Let’s consider some examples.
- The production of 200-ton dinosaurs from rabbit-sized reptile ancestors. The diversification of flowering plants from a single species into more than 200,000 species. The emergence of animals that live on land. These large scale examples, which are the products of evolutionary change involving the origins of entirely new groups of organisms, are referred to as macroevolution. These examples can be contrasted with the increase in milk production in cows seen during the first half of the twentieth century, or the gradual change in the average beak size of birds depending on the patterns of rainfall—phenomena involving changes in allele frequencies in a population that are referred to as microevolution (Figure 10-22 The scale of evolution). They might seem like two very different processes, but they are not. Evolution, whether at the micro or macro level, is one thing only: a change in allele frequencies over time.
- The traditional model of how evolutionary change occurred was that used in the previous section to describe microevolution. Populations changed slowly but surely, gradually accumulating sufficient genetic differences for speciation—hence the phrase “evolution by creeps.” Spurred on by findings from the fossil record that do not always support this view, however, researchers have come to believe that evolution may commonly occur in brief periods of rapid evolutionary change right after speciation, followed by long periods with relatively little change—hence “evolution by jerks.” This newer view of the pace of evolution, in which rapid periods of evolutionary change are punctuated by longer periods with little change, is called punctuated equilibrium (Figure 10-23 The pace of evolution can be rapid or slow). In nature, there are examples of both gradual change and the irregular pattern of punctuated equilibrium. It’s not a situation in which one version is right and one is wrong.
- In a brief period of time, a small number of species diversified into a much larger number of species, able to live in a wide diversity of habitats. Called an adaptive radiation, such a large and rapid diversification has occurred many times throughout history.
- Three different phenomena tend to trigger adaptive radiations. After one of these phenomena occurs, surviving species find themselves in locations where they suddenly have access to plentiful new resources. Figure 10-24 A rapid diversification of species.
- With the disappearance of the dinosaurs, a world of “opportunities” opened up for the mammals. Where previously the dinosaurs had prevented mammals from utilizing resources, mammals suddenly had few competitors. Not surprisingly, the number of mammalian species on earth increased from a very small number—perhaps a few hundred—to about 130 genera, made up of more than 4,000 species overall, including primates, bats, horses, rodents, and the first completely aquatic mammals. This happened in about 10 million years, barely the blink of an eye by geological standards. Following other large-scale extinctions, numerous groups that suddenly had lost most of their competitors experienced adaptive radiations. Figure 10-24 part 1 A rapid diversification of species.
- In a rare event, one or a few birds or small insects will fly off from a mainland and end up on a distant island group, such as Hawaii or the Galapagos. But once they make it there, they tend to find a large number of opportunities for adaptation and diversification. In the Galapagos, for example, 14 species evolved from the single species of finch found on the nearest mainland, Ecuador, 600 miles away. In Hawaii, there are now several hundred species of fruit flies, all believed to have evolved from one species that colonized the islands and experienced an adaptive radiation. Perhaps a few flies were blown there by a storm or maybe they were carried there, stuck in the feathers of a bird. Figure 10-24 part 2 A rapid diversification of species.
- In the world of computers, software developers are always looking for the “killer app.” That is, the killer application, a new type of software that is so useful that it immediately leads to huge success, opening up a large new niche in the software market or expanding greatly an already-existing niche. The first spreadsheet, email program, and web browser were all killer apps. In nature, evolution sometimes produces killer apps., too. These are innovations such as the wings and rigid skeleton that appeared in insects and helped them to diversify into the most successful group of animals, with more than 800,000 species today (more than 100 times the number of mammalian species). The flower is an evolutionary innovation that propelled the flowering plants to an explosion of diversity and evolutionary success, relative to non-flowering plants, such as ferns and pine trees. Today, about nine out of ten plant species is a flowering plant. Figure 10-24 part 3 A rapid diversification of species.
- If the past is a guide to the future, we know this: no species lasts forever. Speciation is always producing new species, but extinction, the complete loss of all individuals in a species population, takes them away. Extinction, which is always occurring, is a risk faced by all species. For any given time in earth’s history, it is possible to estimate the rate of extinctions at that time, and the evidence reveals that these rates are far from constant (Figure 10-25 Extinction never sleeps). Although the particular details differ in most cases, extinctions generally fall into one of two categories: 1) “background” extinctions or 2) mass extinctions.
- Background extinction are the extinctions that occur at lower rates during periods other than periods of mass extinctions. Background extinctions occur mostly as the result of natural selection. Competition with other species, for example, may reduce a species’ size or the range over which it can grow. Or a species might be too slow to adapt to gradually changing environmental conditions and become extinct as its individuals die off.
- Mass extinctions are periods during which a large number of species on earth become extinct over a relatively short period of time. There have been at least five mass extinctions on earth, and during each of these extinctions 50% or more of the animal species living at the time became extinct (Figure 10-25 Extinction never sleeps).
- There is a fundamental difference between background and mass extinctions that goes beyond differences in rates. They have different causes. Mass extinctions are due to extraordinary and sudden changes to the environment (such as the asteroid that brought about the dinosaurs’ extinction). As a consequence, nothing more than bad luck is responsible for the extinction of species during mass extinctions; fit and unfit individuals alike perish.
- Of the five mass extinctions during the past 500 million years, the most recent is also the best understood. Sixty-five million years ago, a massive asteroid smashed into the Caribbean near the Yucatan Peninsula of Mexico (Figure 10-26 Catastrophic collision). The impact left a crater more than 100 miles wide and probably created an enormous fireball that caused fires worldwide, followed by a cloud of dust and debris that blocked all the sunlight from the earth and disturbed the climate worldwide for months.
- Section Opener Flower Hat jelly, Olindias formosa.
- In Linnaeus’s original classification, all organisms were put in either the animal kingdom or the plant kingdom. The two-kingdom system gave way in the 1960s to a five-kingdom system. At its core, the new system was a division based on the distinction between prokaryotic cells (those without nuclei) and eukaryotic cells (those with nuclei). The prokaryotes were put in one kingdom, the monera, and the only residents in this kingdom were the bacteria: single-celled organisms with no nucleus, no organelles, and genetic material that took the form of a circular strand of DNA. The eukaryotes—having a nucleus, compartmentalized organelles, and individual, linear pieces of DNA—were divided into four separate kingdoms: plants, animals, fungi, and protists, a group that includes all the single-celled eukaryotes, such as algae.
- The classification of organisms took a huge leap forward in the 1970s and 1980s and the five-kingdom system had to be discarded. Until that point, organisms had been classified primarily based on their appearance. But because the ultimate goal had changed to reconstruct phylogenetic trees that reflected the evolutionary history of earth’s diversity, Carl Woese, an American biologist, and his colleagues began classifying organisms by examining nucleotide sequences that they carried instead. Woese assumed the more similar the genetic sequences were between two species, the more closely related they were, and he built phylogenetic trees accordingly. The only way Woese could compare the evolutionary relatedness all of the organisms present on earth today was by examining one molecule that was found in all living organisms and looking at the degree to which it differed from species to species. He discovered a perfect candidate for this role: a molecule called ribosomal RNA. Ribosomal RNA has the same function in all organisms on earth, almost certainly because it comes from a common ancestor. Over time, however, its genetic sequence has changed a bit. Tracking these changes makes it possible to reconstruct the process of diversification and change that has taken place.
- The trees Woese’s genetic sequence data generated had some big surprises. First and foremost, the sequences revealed that the biggest division in the diversity of life on earth was not between plants and animals. It wasn’t even between prokaryotes and eukaryotes. The new trees revealed instead that the diversity among the microbes was dramatically greater than ever imagined—particularly because of the discovery of a completely new group of prokaryotes called archaea, which thrive in some of earth’s most extreme environments and differ greatly from bacteria. The tree of life was revised to show three primary branches called domains: the bacteria, the archaea, and the eukarya (Figure 10-27 All living organisms are classified into one of three groups).
- The three-domain, six-kingdom approach is not perfect and is still subject to revision. For example, it seems that single-celled protists are so diverse that they should be split into multiple distinct kingdoms. Also problematic is horizontal gene transfer in bacteria. Rather than passing genes simply from “parent” to “offspring,” they transfer genetic material directly into another species. This complicates phylogenies based on sequence data because it creates situations in which two organisms might have a genetic sequence that is similar not because they share a common ancestor, but as a result of a direct transfer. Additionally, a fourth group of incredibly diverse and important biological entities, the viruses, is not even included in the tree of life, because they are not considered to be living organisms. Viruses can replicate, but can only have metabolic activity by taking over the metabolic processes of another organism. Their lack of metabolic activity puts viruses just outside the definition of life we use in this book, but some scientists view viruses as living.
- As it stands currently, the most commonly accepted tree of life suggests that after the origin of life the following sequence of events occurred (Figure 10-28 From self-replicating metabolizing cells to complex organisms): 1. The bacteria arose from the first self-replicating, metabolizing cells. 2. There was a split between the bacteria and a line that gave rise to the archaea and eukarya. 3. The fusion of a bacterium and an archaean gave rise to the eukarya, which then split from the archaea line.
- Morning breath is stinky. When you wake up, your mouth contains huge amounts of bacterial waste products. Perhaps the only consolation for this situation is that it gives us a glimpse into just how diverse and resourceful bacteria are. At any given time, there are several hundred species of bacteria in your mouth—mostly residing on your tongue—all competing for the resources you put there (Figure 10-29). Some of the bacteria are aerobic, requiring oxygen for their metabolism, and others are anaerobic. At night, because the flow of saliva slows down and the oxygen content of your mouth decreases, the anaerobic bacteria start to get the upper hand in terms of growth and reproduction. These bacteria metabolize food bits in your mouth, plaque on your teeth and gums, and dead cells from the lining of your mouth, breaking down proteins in these molecules to use as their energy source. As they do so, waste products accumulate. Because proteins are made from amino acids, many of which contain the smelly chemical sulfur, their breakdown leads to the bad smell. In the morning, you breathe more and produce more saliva, both of which increase the oxygen level in your mouth. This tips the battle for space and food back in favor of the aerobic bacteria. Because aerobic bacteria prefer carbohydrates as their energy source and because carbohydrates don’t contain sulfur, as the aerobic bacteria start to outcompete the anaerobic bacteria the sulfur smell goes away. The aerobic bacteria are of course also filling your mouth with waste products, it’s just that their waste products don’t smell as bad.
- On a small scale, your mouth reveals some of the tremendous biological versatility of the bacteria: hundreds of species can live in a tiny area (in a teaspoon of soil, for example, there are more than a billion bacteria), they can thrive in a variety of unexpected habitats, they can utilize a variety of food sources, and they can survive and thrive with or without oxygen. Looking around the world, the diversity in the bacteria domain is even greater. A survey of the numbers shows the clear dominance of bacteria on our planet. By any measure, it is their planet: The biomass of bacteria (if they were all collected, dried out, and weighed) exceeds that of all the plants and animals on earth. Bacteria live in soil, air, water, arctic ice, and volcanic vents (Figure 10-30 We’re outnumbered). Many can even make their own food, either utilizing light from the sun or harnessing energy from chemicals such as ammonia.
- While they differ in many ways, the bacteria share a common ancestor, so all have a few features in common. All bacteria are single-celled organisms with no nucleus or organelles, one or more circular molecules of DNA as their genetic material, and several methods of exchanging genetic information. Because they are asexual, the biological species concept cannot be applied to them. Thus, bacteria are classified on the basis of physical appearance or, preferably, genetic sequences. While bacteria are responsible for many diseases (i.e., strep throat, cholera, syphilis, pneumonia, botulism, anthrax, leprosy, and tuberculosis), disease-causing bacteria are only a small fraction of the domain, and bacteria seem to get less credit for their many positive effects on our lives. Consider that bacteria (E. coli) that live in your gut help your body digest the food you eat and, in the process, make certain vitamins your body needs. Other bacteria (actinomycetes) produce antibiotics such as streptomycin. Other bacteria live symbiotically with plants as small fertilizer factories, converting nitrogen into a form that is useable to the plant. Bacteria also give taste to many foods, from sour cream to cheese, yogurt, and sourdough bread. Increasingly, bacteria are used in biotechnology from those that can metabolize crude oil and help in the cleanup of spills to transgenic bacteria used in the production of insulin and other medical products.
- Where once it was assumed that life could not survive, the archeans not only exist, but thrive and diversify (Figure 10-31 Archaea can thrive in the most inhospitable-seeming places). Analyses of genetic sequences indicate that the archaeans and the bacteria diverged about three billion years ago. Although it is likely that some genetic exchanges continued to occur between them, they have evolved in largely independent paths ever since. Approximately 2.5 billion years ago the eukarya split off from the archaea. The archaea are still grouped all in one kingdom within the domain archaea, but we have no idea how many species exist. Given that archaea are the dominant microbe in the deep seas, it may very well be that these organisms of which we were completely ignorant are the most common organisms on earth. It is still too early to tell.
- The archaea exhibit tremendous diversity and are often divided into five groups based on their physiological features: 1. Thermophiles (“heat lovers”), which live in very hot places 2. Halophiles (“salt lovers”), which live in very salty places 3. High- and low-pH-tolerant archaea 4. High-pressure-tolerant archaea, found as deep as 4,000 meters (about 2.5 miles) below the ocean surface, where the pressure is almost 6,000 pounds per square inch (compared with an air pressure of less than 15 pounds per square inch at sea level) 5. Methanogens, which are anaerobic and produce methane
- All are made up from eukaryotic cells—they have a membrane-enclosed nucleus—and each kingdom is almost entirely multicellular.
- The eukarya split from the archaea about 2.5 billion years ago (Figure 10-32 All shapes and sizes). At the time, the eukarya were single-celled and probably resembled modern protists more than any other modern eukarya. The split may have occurred when symbiotic bacteria became incorporated within an ancestor of the eukaryotes, in what would become the mitochondria. Later, approximately 1.5 billion years ago, a second important symbiosis between bacteria and eukarya resulted in what would become chloroplasts. Because they are so much easier to see than bacteria and archaea, a disproportionate number of the named species on earth are in the domain eukarya. In fact, of the 1.5 million named species on earth, the majority are eukarya, with about half being insects. This is more a result of the interests and biases of biologists than a reflection of the relative numbers of actual species in the world.