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Department
Biology
Course
BIO152H5
Professor
Fiona Rawle
Semester
Fall

Description
Chapter 27: Phylogenies and the History of Life Key Concepts Phylogenies and the fossil record are the major tools that biologists use to study the history of life. The Cambrian explosion was the rapid morphological and ecological diversification of animals that occurred during the Cambrian period. Adaptive radiations are a major pattern in the history of life. They are instances of rapid diversification associated with new ecological opportunities and new morphological innovations. Mass extinctions have occurred repeatedly throughout the history of life. They rapidly eliminate most of the species alive in a more or less random manner. Section 27.1 Outline: Tools for Studying History: Phylogenetic Trees A Field Guide to Reading Phylogenetic Trees How Do Researchers Estimate Phylogenies? How Can Biologists Distinguish Homology from Homoplasy? Whale Evolution: A Case History The evolutionary history of a group of organisms is called a phylogeny. A phylogenetic tree shows ancestor–descendant relationships among populations or species. A Field Guide to Reading Phylogenetic Trees Figure 27.1 shows the parts of a phylogenetic tree. Branches represent populations through time. Adjacent branches are sister taxa (a taxon is any named group of organisms). Nodes occur where an ancestral group split into two or more descendant groups. A polytomy is a node where more than two descendant groups branch off. Tips are the tree's endpoints and represent living groups or a group’s end in extinction. In rooted phylogenies the most ancient node of the tree is shown at the bottom. The location of this node is determined using an outgroup, a taxonomic group that diverged before the rest of the taxa being studied. An ancestor and all its descendants form a monophyletic group (also called a clade or lineage). Figure 27.3 shows alternative phylogenetic trees for representing the same evolutionary relationships. How Do Researchers Estimate Phylogenies? Morphological and/or genetic characteristics are used to estimate phylogenetic relationships among species. The phenetic approach to estimating trees is based on the overall similarity among populations. A tree is built that clusters the most similar populations and places more divergent populations on more distant branches. The cladistic approach to inferring trees focuses on synapomorphies, the shared derived characters of the species under study. A synapomorphy is a trait that certain populations or species have that exists in no others. When many such traits have been measured, traits unique to each monophyletic group are identified and the groups are placed on a tree in the correct relationship to one another (Figure 27.4). How Can Biologists Distinguish Homology from Homoplasy? Problems can arise with both cladistic and phenetic analysis because similar traits can evolve independently in two distant species rather than from a trait present in a common ancestor. Homoplasy occurs when traits are similar for reasons other than common ancestry (Figure 27.5a). Homology occurs when traits are similar due to shared ancestry (Figure 27.5b). Convergent evolution occurs when natural selection favors similar solutions to the problems posed by a similar way of making a living. Convergent evolution is a common cause of homoplasy. If similar traits found in distantly related lineages are indeed similar due to common ancenstry, then similar traits should be found in many intervening lineages on the tree of life. Parsimony is a principle of logic stating that the most likely explanation or pattern is the one that implies the least amount of change. Convergent evolution and other causes of homoplasy should be rare compared with similarity due to share descent, so the tree that implies the fewest overall evolutionary changed should be the one that most accurately reflects what really happened during evolution. Whale Evolution: A Case History Traditionally, phylogenetic trees based on morphological data place whales outside of the artiodactyls— mammals that have hooves, an even number of toes, and an unusual pulley–shaped ankle bone (astralagus) (Figure 27.7a). DNA sequence data, however, suggest a close relationship between whales and hippos (Figure 27.7b). Recent data on short interspersed nuclear elements (SINEs) show that whales and hippos share several SINE genes that are absent in other artiodactyl groups (Figure 27.7c). These SINEs are shared derived traits (synapomorphies) and support the hypothesis that whales and hippos are indeed closely related. Section 27.2 Outline: Tools for Studying History: The Fossil Record How Do Fossils Form? Limitations of the Fossil Record Life's Timeline The fossil record provides the only direct evidence about what organisms that lived in the past looked like, where they lived, and when they existed. A fossil is the physical trace left by an organism that lived in the past. The fossil record is the total collection of fossils that have been found throughout the world. How Do Fossils Form? Most fossils form when an organism is buried in sediment before decomposition occurs. Four types of fossils are intact fossils, compression fossils, cast fossils, and premineralized fossils. Fossilization is an extremely rare event. Limitations of the Fossil Record There are several features and limitations of the fossil record that must be recognized: habitat bias, taxonomic bias, temporal bias, and abundance bias. Habitat bias occurs because organisms that live in areas where sediments are actively being deposited are more likely to form fossils than are organisms that live in other habitats. Taxonomic bias is due to the fact that some organisms (e.g., those with bones) are more likely to decay slowly and leave fossil evidence. Temporal bias occurs because more recent fossils are more common than ancient fossils. Abundance bias occurs because organisms that are abundant, widespread, and present on Earth for a long time leave evidence much more often than do species that are rare, local, or ephemeral. Paleontologists—scientists who study fossils—recognize that they are limited to asking questions about tiny and scattered segments on the tree of life. Yet analyzing fossils is the only way scientists have of examining the physical appearance of extinct forms and inferring how they lived. Life's Timeline Major events in the history of life are marked on the timeline shown in Figure 27.10, which has been broken into four segments (the Precambrian, the Paleozoic, the Mesozoic, and the Cenozoic). The Precambrian era encompasses the Hadean, Archaean, and Proterozoic eons. In the Precambrian era, almost all life was unicellular and hardly any oxygen was present. Many animal groups—including fungi, land plants, and land animals—appeared in the Paleozoic era. The Mesozoic era, also known as the Age of Reptiles, ended with the extinction of the dinosaurs. The Cenozoic era is known as the Age of Mammals. Section 27.3 Outline: The Cambrian Explosion Cambrian Fossils: An Overview The Doushantuo Microfossils The Edicaran Faunas The Burgess Shale Faunas Did Gene Duplication Trigger the Cambrian Explosion? Animals first originated around 565 million years ago (Mya). Soon after that, animals diversified into almost all the major groups extant today. This is known as the Cambrian explosion. Cambrian Fossils: An Overview The Cambrian explosion is documented by three major fossil assemblages (Figure 27.12a). The presence of these exceptionally rich deposits before, during, and after the Cambrian explosion makes the fossil record for this event extraordinarily complete. The Doushantuo Microfossils Researchers identified sponges, cyanobacteria, and multicellular algae in samples dated 570–580 Mya. They also found what they concluded were animal embryos in early stages. The Edicaran Faunas Sponges, jellyfish, comb jellies, and traces of other animals dated 544–565 Mya are found in fossils from the Ediacara Hills of Australia. The Burgess Shale Faunas Virtually every major animal group is represented in the Burgess Shale fossils, which date 525–515 Mya. These fossils indicated a tremendous increase in the size and morphological complexity of animals, accompanied by diversification in how they made a living. Did Gene Duplication Trigger the Cambrian Explosion? Many researchers predicted there would be a strong association between the order in which animal lineages appeared during evolutionary history, the number of Hox genes present in each lineage, and each lineage's morphological complexity and body size. A phylogenetic tree of Hox genes in animals in general support this hypothesis (Figure 27.13). The following conclusions can be made from this phylogeny: –the number of genes in the Hox cluster appears to have expanded during the course of evolution –Hox genes appear to have been created by gene duplication events because the genes within the cluster are similar in structure and base sequence –the entire Hox cluster was duplicated and then duplicated again in the lineage leading to vertebrates Duplication of Hox genes has been important in making the elaboration of animal body plans possible. However, changes in expression and function of existing genes have been equally or even more important. Chapter 28: Bacteria and Archaea Key Concepts Bacteria and archaea have a profound impact on humans and global ecosystems. A few bacteria cause important infectious diseases; some bacterial and archaeal species are effective at cleaning up pollution; photosynthetic bacteria were responsible for the evolution of the oxygen atmosphere; bacteria and archaea cycle nutrients through every terrestrial and aquatic environment. Bacteria and archaea have been evolving for billions of years and are extremely sophisticated organisms. Although they are small and relatively simple morphologically, they live in virtually every habitat known and use remarkably diverse types of compounds in cellular respiration and fermentation. Section 28.1 Outline: Why Do Biologists Study Bacteria and Archaea? Some Bacteria Cause Disease Bacteria Can Clean Up Pollution Extremophiles How Do Small Cells Affect Global Change? The Oxygen Revolution The Nitrogen Cycle Nitrate Pollution Biologists study bacteria and archaea for many reasons. The ubiquity and abundance of bacteria make them exceptionally important in both human and natural economies. Some Bacteria Cause Disease No archaea are known to cause disease in humans. Bacteria that cause disease are said to be pathogenic. An infectious disease is one spread by being passed from an infected individual to an uninfected individual. Koch’s experiments became the basis for the germ theory of disease, which holds that infectious diseases are caused by bacteria and viruses. Koch’s postulates are used to confirm a causative link between a specific infectious disease and an infectious microbe: –The microbe must be present in individuals suffering from the disease and absent from healthy individuals. –The organism must be isolated and grown in a pure culture away from the host organism. –If organisms from the pure culture are injected into organisms a healthy experimental animal, the disease symptoms should appear. –The organism should be isolated from the diseased experimental animal, again grown in pure culture, and demonstrated by its size, shape, and color to be the same as the original organism. Bacteria Can Clean Up Pollution Some of the most serious pollutants in soils, rivers, and ponds consist of organic compounds that were originally used as solvents or fuels but leaked or were spilled into the environment. These pollutants do not dissolve in water and accumulate in sediments. Bioremediation is the use of bacteria and archaea to degrade pollutants. This is often based on complementary strategies: fertilizing contaminated sites to encourage the growth of existing bacteria and archaea that degrade toxic compounds adding specific species of bacteria and archaea to contaminated sites. Extremophiles Bacteria or archaea that live in high–salt, high–temperature, low–temperature, or high–pressure habitats are called extremophiles. Archaea are abundant forms of life in environments such as hot springs at the bottom of the ocean, where water as hot as 300°C emerges and mixes with 4°C seawater. Understanding extremophiles may help explain how life on Earth began. Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life. How Do Small Cells Affect Global Change? Bacteria and archaea can live in extreme environments and use toxic compounds as food because they produce extremely sophisticated enzymes. The complex chemistry and abundance of bacteria and archaea make them potent forces for global change. The Oxygen Revolution No free molecular oxygen existed for the first 2.3 billion years of Earth's history. Cyanobacteria, a lineage of photosynthetic bacteria, were the first organisms to perform oxygenic (oxygen–producing) photosynthesis. Cyanobacteria were responsible for a fundamental change in Earth’s atmosphere to one with a high concentration oxygen. Once oxygen was common in the oceans, aerobic respiration became possible. Prior to this, only anaerobic respiration was possible and cells had to use compounds other than oxygen as the final electron acceptor. Oxygen is an efficient electron acceptor and much more energy is released with oxygen as the ultimate electron acceptor rather than other substances (Figure 28.5). The Nitrogen Cycle Although molecular nitrogen (N2) is extremely abundant in the atmosphere, most organisms cannot use it. All eukaryotes and many bacteria and archaea must obtain their N in a form such as ammonia (NH3) or nitrate (NO3). The only organisms capable of converting molecular nitrogen to ammonia are bacteria. The steps in nitrogen fixation are complex and highly endergonic redox reactions. Certain species of cyanobacteria in water can fix nitrogen. On land, nitrogen–fixing bacteria live in close association with plants—often taking up residence in nodules. Nitrate Pollution The widespread use of ammonia fertilizers is causing serious pollution problems. When ammonia is added to the soil, much of it is used by bacteria and nitrite (NO2–) or nitrate (NO3–) is released. Nitrates cause pollution in aquatic environments (Figure 28.7). In an aquatic ecosystem, nitrates can decrease the oxygen content, causing anaerobic “dead zones” to develop. Section 28.2 Outline: How Do Biologists Study Bacteria and Archaea? Using Enrichment Cultures Direct Sequencing Evaluating Molecular Phylogenies Our understanding of the Bacteria and Archaea domains is advancing more rapidly now than at any time during the past 100 years—and perhaps faster than our understanding of any other lineages on the tree of life. Using Enrichment Cultures Enrichment cultures are based on establishing a specific set of growing conditions – temperature, lighting, substrate, types of available food, etc. Cells that thrive under the specified conditions will increase in numbers enough to be isolated and studied in detail (Figure 28.9). Direct Sequencing Direct sequencing is a strategy for documenting the presence of bacteria and archaea that cannot be grown in pure culture. It is based on identifying phylogenetic species. Figure 28.10 outlines the steps in a direct sequencing study. Direct sequencing has been used to discover two new lineages of Archaea, the Korarchaeota and the Nanoarchaeota. Evaluating Molecular Phylogenies Some of the most useful phylogenetic trees for the Bacteria and Archaea have been based on studies of SSU RNA. Phylogenetic trees based on morphology were found to be incorrect (Figure 28.11). The tree of life based on ribosomal RNA sequences (Figure 28.1) shows three domains—Archaea, Bacteria, and Eukarya—and is now accepted as correct. Web animation – Tree of Life Bacteria were the first lineage to diverge from the common ancestor of all living organisms. The Archaea and Eukarya are more closely related to each other than to the Bacteria. Figure 28.12 shows how the major lineages within Bacteria and Archaea are related to one another. Section 28.3 Outline: What Themes Occur in the Diversification of Bacteria and Archaea? Morphological Diversity Metabolic Diversity Producing ATP via Photosynthesis: Variation in Electron Sources and Pigments Producing ATP via Cellular Respiration: Variation in Electron Donors and Acceptors Producing ATP via Fermentation: Variation in Substrates Obtaining Building–Block Compounds: Pathways for Fixing Carbon Bacteria and archaea are capable of living in a wide array of environments because they vary in cell structure and in how they make a living. Morphological Diversity Bacteria and archaea show extensive morphological diversity in terms of size, shape, and mobility. Gram staining distinguishes bacteria by the type of cell wall (Figure 28.14). Gram–positive cells retain Gram stain better than Gram–negative cells due to differences in peptidoglycan and an outer membrane. Metabolic Diversity All organisms must acquire chemical energy in the form of ATP and obtain carbon compounds that can serve as building blocks for synthesis of cellular components. Bacteria and archaea produce ATP in three ways: –photophosphorylation –cellular respiration with sugars serving as electron donors or fermentation –cellular respiration with inorganic compounds serving as the electron donor Phototrophs use light energy to promoter electrons to the top of electron transport chains. ATP is produced by photophorsphorylation. Chemoorganotrophs oxidize organic molecules with high potential energy. ATP may be produced by cellular respiration using sugars as electron donors or by fermentation pathways. Chemolithotrophs oxidize inorganic molecules with high potential energy. ATP is produced by cellular respiration with organic compounds serving as the electron donor. Bacteria and archaea obtain building block compounds by synthesizing them from simple starting materials or by absorbing them from their environment. Autotrophs manufacture their own carbon–containing compounds. Heterotrophs live by consuming them. Table 28.3a summarizes the six methods for obtaining energy and carbon and the names for organisms that use each. Of these six methods, only two are observed in eukaryotes, but bacteria and archaea can use all six. Producing ATP via Photosynthesis: Variation in Electron Sources and Pigments Photosynthetic species use the energy in light to raise electrons to high–energy states. As these electrons are stepped down in energy through electron transport chains, the energy released is used to generate ATP. Many phototrophic bacteria use molecules other than water as the electron donor for non–oxygenic photosynthesis. Producing ATP via Cellular Respiration: Variation in Electron Donors and Acceptors In cellular respiration, a molecule with high potential energy serves as an electron donor and is oxidized, and a molecule with low potential energy serves as a final electron acceptor and is reduced. The potential energy difference is converted into ATP (Figure 28.15). Bacteria and archaea can exploit a wide variety of electron donors and acceptors (Table 28.4). When electron donors other than sugars and electron acceptors other than oxygen are used, byproducts other than water and carbon dioxide are produced. The metabolic diversity of bacteria and archaea explains several things: – their ecological diversity – their key role in cleaning up some types of pollution – their role in global change, including nutrient cycling (Figure 28.16) Producing ATP via Fermentation: Variation in Substrates Fermentation is a strategy for making ATP without using electron transport chains. In fermentation, no outside electron acceptor is used; redox reactions are internally balanced. Fermentation is a much less efficient way to make ATP compared with cellular respiration. The diversity of enzymatic pathways in bacterial and archaeal fermentations extends the metabolic repertoire of these organisms. Bacteria and archaea can, as a group, use virtually any molecule with relatively high potential energy as a source of high–energy electrons for producing ATP. Obtaining Building–Block Compounds: Pathways for Fixing Carbon Some bacteria and archaea use the Calvin cycle to transform carbon dioxide to organic molecules. Other bacteria and archaea obtain carbon by absorbing organic compounds released in dead tissues. Several groups of bacteria fix CO2 using pathways other than the Calvin cycle. Compared to eukaryotes, the metabolic capabilities of bacteria and archaea are remarkably sophisticated and complex. Section 28.4 Outline: Key Lineages of Bacteria and Archaea Bacteria Archaea The relationships among the major lineages within Bacteria and Archaea are still uncertain in some cases. However, most of the lineages themselves are well studied. Bacteria There are at least 16 major lineages (phyla) of bacteria (Figure 28.17). Some were recognized by distinctive morphological characteristics, others by phylogenetic analyses of gene sequence data. Firmicutes have been called low–GC Gram positives and most are rod shaped or spherical. Spirochetes are distinguished by their corkscrew shape and unusual flagella. Actinobacteria are sometimes called the high–GC Gram positives. –Species from the genus Streptomyces produce over 500 distinct antibiotics. Chlamydiales are spherical and very tiny. –They live as parasites inside animal cells and get almost all of their nutrition from their hosts. Cyanobacteria were formerly known as blue–green algae. –They produce much of the oxygen and nitrogen and many organic compounds that feed other organisms in freshwater and marine environments. Proteobacteria form five major subgroups and are very diverse in morphology and metabolism. –Pathogenic proteobacteria cause Legionnaire’s disease, cholera, dysentery, and gonorrhea. Archaea Archaea live in virtually every habitat, including extreme environments. –However, there are no known parasitic archaea. The Archaea domain is composed of at least two major phyla (Figure 28.25). Crenarchaeota are the only life–forms present in certain extreme environments, such as high–pressure, very hot, very cold, or very acidic environments. The Euryarchaeota live in every conceivable habitat, including high–salt, high–pH, and low–pH environments. –The Euryarchaeota include the methanogens, which contribute about 2 billion tons of methane to the atmosphere each year. Chapter 29: Protists Key Concepts Protists are a paraphyletic grouping that includes all eukaryotes except the green plants, fungi, and animals. Biologists study protists to understand how eukaryotes evolved, because they are important in freshwater and marine ecosystems and global warming and because some species cause debilitating diseases in plants, humans, and other organisms. Protists are diverse morphologically. They vary in the types of organelles they contain; they may be unicellular or multicellular, and they may have a cell wall or other external covering, or no such covering. Protists vary widely in terms of how they find food. Many species are photosynthetic, while others obtain carbon compounds by ingesting food or parasitizing other organisms. Protists vary widely in terms of how they reproduce. Sexual reproductive evolved in protists, and many protist species can reproduce both sexually and asexually. Section 29.1 Outline: Why Do Biologists Study Protists? Impacts on Human Health and Welfare Malaria Harmful Algal Blooms Ecological Importance of Protists Protists Play a Key Role in Aquatic Food Chains Could Protists Help Reduce Global Warming? Biologists study protists because they are intrinsically interesting, because they are so important medically and ecologically, and because they are critical to understanding the evolution of plants, fungi, and animals. Impacts on Human Health and Welfare The most spectacular crop failure in history, the Irish potato famine, was caused by a protist: Phytophthora infestans. Malaria Malaria, the world's most chronic public health problem, is caused by Plasmodium (Figure 29.3). A number of other human health problems are also caused by protists (Table 29.1). Harmful Algal Blooms Harmful algal blooms occur when toxin–producing protists reach high densities in an aquatic environment. Algal blooms of dinoflagellates are known as red tides. Ecological Importance of Protists Protists represent just 10% of the total number of named eukaryotic species and have relatively low species diversity but are extraordinarily abundant. Species that produce chemical energy by photosynthesis are called primary producers. Diatoms, for example, are photosynthetic protists that rank among the leading primary producers in the oceans because they are so abundant. Production of organic molecules in the world’s oceans, in turn, is responsible for almost half of the total carbon that is fixed on Earth. Protists Play a Key Role in Aquatic Food Chains Small organisms that live near the surface of oceans or lakes and that drift along or swim only short distances are called plankton. The organic compounds produced by phytoplankton (photosynthetic plankton) are the basis of food chains in freshwater and marine environments (Figure 29.5). A food chain describes nutritional relationships among organisms. Could Protists Help Reduce Global Warming? The movement of carbon atoms from carbon dioxide molecules in the atmosphere to organisms in the soil or the ocean and then back to the atmosphere is called the global carbon cycle. Protists play a key role in the global carbon cycle and act as carbon sinks that could help reduce global warming (Figure 29.6). A carbon sink is a long–lived carbon reservoir. Section 29.2 Outline: How Do Biologists Study Protists? Microscopy: Studying Cell Structure Evaluating Molecular Phylogenies Discovering New Lineages via Direct Sequencing Although protists have been the focus of intense study, they are so diverse that it has been difficult to find any overall patterns in their evolution and diversification. Recently, researchers have made dramatic progress in underst
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