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Chapter 27: Phylogenies and the History of Life Key Concepts o Phylogenies and the fossil record are the major tools that biologists use to study the history of life. o The Cambrian explosion was the rapid morphological and ecological diversification of animals that occurred during the Cambrian period. o 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. o 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.  Section 27.4 Outline: Adaptive Radiations  One broad pattern that can be observed in the tree of life is that dense groups of branches are scattered throughout the tree. These star phylogenies (Figure 27.14a) represent major diversification over a relatively short period of time, a process known as adaptive radiation. The Cambrian explosion can be considered an extremely large–scale adaptive radiation. Ecological Opportunity as a Trigger  One of the most consistent themes in adaptive radiations is ecological opportunity.  Biologists have documented adaptive radiations of the Anolis lizards of the Caribbean islands (Figure 27.15b).  On the two islands studied, the same four ecological types eventually evolved, because the islands had similar varieties of habitats. Morphological Innovation as a Trigger  Adaptive radiation is usually associated with a new ecological opportunity or morphological innovation.  After adaptive radiation, rapid speciation and morphological divergence are tightly linked.  Web animation – Adaptive radiation  Section 27.5 Outline: Mass Extinctions  How Do Background and Mass Extinctions Differ? What Killed the Dinosaurs? Selectivity Recovery A mass extinction is the rapid extinction of a large number of lineages scattered throughout the tree of life. A mass extinction occurs when at least 60% of the species present are wiped out within 1 million years. Mass extinctions are caused by catastrophic episodes. Paleontologists traditionally recognize five mass extinctions ("The Big Five") (Figure 27.17). Background extinction is the lower, average rate of extinction, representing the normal loss of some species that always occurs. How Do Background and Mass Extinctions Differ?  Background extinctions typically occur when normal environmental change, emerging diseases, or competition reduces certain populations to zero.  Mass extinctions result from extraordinary, sudden, and temporary changes in the environment.  During a mass extinction, species do not die out due to poor adaptation. Instead, species die out from exposure to exceptionally harsh, short–term conditions.  Natural selection causes most background extinctions, whereas mass extinctions function like genetic drift. What Killed the Dinosaurs?  The impact hypothesis for the extinction of dinosaurs proposed that an asteroid struck Earth and snuffed out an estimated 60–80% of the multicellular species alive.  Conclusive evidence—including iridium, shocked quartz, and microtektites found in rock layers dated to 65 million years ago, as well as a huge crater off the —has led researchers to accept the impact hypothesis. Selectivity  Some evolutionary lineages were better able than others to withstand the environmental change brought on by the asteroid impact.  Why certain groups survived while others perished is still a mystery. Recovery  Ferns appear to have replaced diverse woody and flowering plants in many habitats following the K–T extinction.  Mammals diversified to fill the niches left empty following the dinosaur extinctions. Chapter 28: Bacteria and Archaea Key Concepts o 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. o 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: 1. fertilizing contaminated sites to encourage the growth of existing bacteria and archaea that degrade toxic compounds 2. 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 o 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. o 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. o 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. o 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 understanding protist diversity by combining data on the morphology of key groups and phylogenetic analyses of DNA sequence data. Microscopy: Studying Cell Structure  Many protists have a characteristic overall form with synapomorphies—shared, derived traits that are used to distinguish major monophyletic groups.  Eight major groups of eukaryotes came to be identified on the basis of diagnostic morphological characteristics (Table 29.2). Evaluating Molecular Phylogenies  The current phylogenetic tree based on sequence data has identified eight major lineages of eukaryotes (Figure 29.8). Discovering New Lineages via Direct Sequencing  Direct sequencing is based on collecting organisms from a habitat and analyzing their DNA without growing larger populations of individuals in laboratory culture.  This has led to the discovery of several new lineages of eukaryotes, including protists.   Section 29.3 Outline: What Themes Occur in the Diversification of Protists?  What Morphological Innovations Evolved in Protists? The Nuclear Envelope The Mitochondrion Structures for Support and Protection Multicellularity How Do Protists Find Food? Ingestive Feeding Absorptive Feeding Photosynthesis Diversity in Lifestyles How Do Protists Move? How Do Protists Reproduce? Sexual versus Asexual Reproduction Variation in Life Cycles Because protists are a paraphyletic group, they do not share derived characteristics that set them apart from all other lineages on the tree of life. The key to understanding the protists is to recognize the important innovations that occurred as they evolved. What Morphological Innovations Evolved in Protists?  The earliest eukaryotes were probably single–celled organisms with a nucleus and endomembrane system, mitochondria, and a cytoskeleton, but no cell wall.  It is also likely that these cells swam using a novel type of flagellum. The Nuclear Envelope  The leading hypothesis for the origination of the nuclear envelope is that it is derived from the infoldings of the plasma membrane (Figure 29.10).  The endoplasmic reticulum may have also originated this way. The Mitochondrion  Mitochondria are organelles that generate ATP using pyruvate as an electron donor and oxygen as the ultimate electron acceptor.  The endosymbiosis theory proposes that mitochondria originated when a bacterial cell took up residence inside a eukaryote about 2 billion years ago.  Symbiosis occurs when individuals of two different species live in physical contact.  Endosymbiosis occurs when an organism of one species lives inside an organism of another species.  The endosymbiosis theory proposed that mitochondria evolved through a series of steps (Figure 29.11).  The process began when eukaryotic cells started to used their cytoskeletal elements to surround and engulf smaller prey, which then began to live symbiotically within its eukaryotic host.  The engulfed cell survived by absorbing carbon molecules with high potential energy from its host and oxidizing them, using oxygen as a final electron acceptor.  The host cell, in contrast, is proposed to be a predator capable only of anaerobic fermentation.  Observations consistent with the endosymbiosis theory include the following:  Mitochondria are about the size of an average bacterium and replicate by fission, as do bacteria.  Mitochondria have their own ribosomes to manufacture their own proteins.  Mitochondria have double membranes, consistent with the engulfing mechanism.  Mitochondria have their own genomes with genes that code for the enzymes needed to replicate and transcribe their own genomes.  Phylogenetic data support the endosymbiosis theory (Figure 29.12).  The mitochondrial gene sequences turned out to be much more closely related to the sequences from alpha proteobacteria that to sequences from the nuclear DNA of eukaryotes. Structures for Support and Protection  The basic structure of the cytoskeleton does not vary much among protists.  The presence and nature of other structures that provide support and protection forthe cell does vary significantly among protists.  Many protists have cell walls; others have hard external structures called a test or a shell; others have rigid structures inside the plasma membrane.  In many cases, these novel structures represent synapomorphies that identify monophyletic groups among protists.  In many cases, the diversification of protists has been associated with the evolution of innovative structures for support and protection. Multicellularity  In some lineages of protists, the key morphological innovation was multicellularity.  Multicellularity is a synapomorphy shared by all of the brown algae and all of the plamodial and cellular slime molds. It also arose in some lineages of red algae.  An array of novel morphological traits played a key role as protists diversified: the nucleus and endomembrane system, the mitochondrion, structures for protection and support, and multicellularity. How Do Protists Find Food?  One of the most important stories in the diversification of protists was the evolution of a novel method for finding food.  Many protists ingest their food – they eat bacteria, archaea, or even other protists whole.  Protists feed by (1) ingesting packets of food, (2) absorbing organic molecules directly from the environment, or (3) performing photosynthesis. Ingestive Feeding  Some protists are large enough to engulf bacteria and archaea.  Many protists are large enough to surround and ingest other protists or microscopic animals.  The engulfing process is possible in protists that lack a cell wall.  A flexible membrane and dynamic cytoskeleton give these species the ability to surround and swallow prey with long, fingerlike projections called pseudopodia (Figure 29.14a). Absorptive Feeding  Absorptive feeding occurs when nutrients are taken up directly from the environment, across the plasma membrane.  Absorptive feeding is common among protists.  Some protists are decomposers that feed on dead organic matter, or detritus.  Many other protists are parasites that live inside other organisms and absorb their nutrition directly from the environment inside their host, causing damage to the host. Photosynthesis  The endosymbiois theory contends that the chloroplast, the organelle where photosynthesis takes place in , originated when a protist engulfed a cyanobacterium.  The evidence for an endosymbiotic origin for the chloroplast is even more persuasive than for mitochondria.  Secondary endosymbiosis occurs when an organism engulfs a photosynthetic cell and retains its chloroplasts as intracellular symbionts (Figure 29.15).  The chloroplasts from secondary endosymbiosis are surrounded by four membranes, instead of two  Photosynthesis arose in protists by primary endosymbiosis, the spread among lineages vie secondary endosymbiosis (Figure 29.16).  The major photosynthetic groups of protists are distinguished by the pigments they contain (Table 29.3). Diversity in Lifestyles  Ingestive, absorptive, and photosynthetic lifestyles occur in protists and many other eukaryotic lineages, and all three can occur within a single clade. How Do Protists Move?  Amoeboid motion is a sliding movement observed in some protists that is accomplished by streaming of pseudopodia (Figure 29.19a).  The other major mode of locomotion involves flagella (Figure 29.19b) or cilia (Figure 29.19c).  Flagella and cilia have identical structures, but flagella are long and are usually found alone or in pairs, whereas cilia are short and numerous. How Do Protists Reproduce?  Sexual reproduction evolved in protists and produces offspring that are genetically different from their parents.  Asexual reproduction results in offspring are genetically identical to the parent.  Most protists undergo asexual reproduction routinely. Many protists undergo sexual reproduction only intermittently. Sexual versus Asexual Reproduction  Many parasites evolve very quickly, and sexual reproduction allows natural selection of host individuals that can withstand attack by new strains of parasites. Variation in Life Cycles  A life cycle describes the sequence of events that occur as individuals grow, mature,and reproduce.  Every aspect of a life cycle is variable among protists (Figure 29.20).  Alternation of generations (Figure 29.21) is a phenomenon in which the haploid and diploid phases of the life cycle are multicellular.  The multicellular haploid form is called a gametophyte, and the diploid form is a sporophyte.  A spore is a single cell that develops into an adult organism but is not a product of fusion by gametes.  When alternation of generation occurs, a spore divides by mitosis to form a haploid, multicellular gametophyte.  The haploid gametes produced by the gametophyte then fuse to form a diploid zygote that grows into the diploid, multicellular sporophyte.  Web animation: Alternation of Generations in a Protist   Section 29.4 Outline: Key Lineages of Protists  Excavata Excavata – Diplomonadida Excavata – Parabasalida Discicristata Discicristata – Euglenida Alveolata Alveolata – Ciliata Alveolata – Dinoflagellata Alveolata – Apicomplexa Stramenopila (Heterokonta) Stramenopila – Oomycota Stramenopila – Diatoms Stramenopila – Phaeophyta (Brown Algae) Rhizaria Rhizaria – Foraminifera Plantae Rhodophyta – Red Algae Amoebozoa Myxogastrida – Plasmodial Slime Molds Each of the eight major Eukarya lineages has at least one distinctive morphological characteristics. But once an ancestor evolved a set of distinctive characteristics, its descendents diversified into a wide array of lifestyles. Each of the eight lineages represents a similar radiation of species into a wide array of lifestyles. In each case, the readiation began with a morphological innovation. Excavata  The excavates are named for the excavated feeding groove found on one side of the cell.  The excavates lack mitochondria, but the ancestors were thought to have them. Excavata – Diplomonadida  Giardia intestinalis is the first diplomonad species described.  Each cell has two nuclei, each associated with four flagella.  Only asexual reproduction occurs. Excavata – Parabasalida  No free–living parabasalids are known – all species described to date live inside animals.  Parabasalids lack a cell wall and mitochondria, reproduce asexually (some also reproduce sexually), and feed by engulfing. Discicristata  The discicristates are all unicellular and were named for the distinctive disc shape of the cristae in their mitochondria. Discicristata – Euglenida  Euglenids lack an external wall and reproduce asexually.  Most ingest bacteria or other small cells, although some are photosynthetic. Alveolata  Alveolates are distinguished by small sacs, called alveoli, that are located just under their plasma membranes.  All members of this lineage are unicellular but are diverse in morphology and lifestyle. Alveolata – Ciliata  Ciliates have a micronucleus and a macronucleus, can reproduce asexually or by conjugation, and use cilia for locomotion. Alveolata – Dinoflagellata  Most dinoflagellates are unicellular.  Some species are capable of bioluminescence—they emit light via an enzyme–catalyzed reaction.  About half the dinoflagellate species are photosynthetic.  Both asexual and sexual reproduction occur. Cells from sexual reproduction may form tough cysts that allow them to remain dormant until environmental conditions improve. Alveolata – Apicomplexa  Apicomplexa are parasitic, have an apical complex at one end, and reproduce sexually or asexually. Stramenopila (Heterokonta)  At some stage of their life cycle, all stramenopiles have flagella that are covered with distinctive hollow hairs  This lineage includes a large number of unicellular forms, but some are multicellular. Stramenopila – Oomycota  Oomycetes resemble fungi, and many have long branching filaments called hyphae.  They are extremely important decomposers in aquatic ecosystems. Stramenopila – Diatoms  Diatoms are unicellular or form chains of cells.  Diatom cells are supported by external, silicon–rich, glassy shells and are photosynthetic.  They are the most important producer of carbon compounds in the water. Stramenopila – Phaeophyta (Brown Algae)  Phaeophyta (brown algae) are photosynthetic and sessile—permanently fixed to a substrate— although their reproductive cells may be motile—capable of locomotion.  They form forests that are important habitats. Rhizaria  Rhizarians are single–celled amoeba that lack cell walls.  They move by amoeboid motion and produce long, slender pseudopodia. Rhizaria – Foraminifera  Foraminifera have multiple nuclei and feed by engulfment with pseudopodia.  The tests of dead forams commonly form extensive sedimentary deposits when they settle out of the water, producing layers that eventually solidify into chalk, limestone, or marble. Plantae  Plantae refers to the monophyletic group that includes red algae, green algae, land plants, and glaucophyte algae.  All of these lineages are descended from a common ancestor that engulfed a cyanobacterium, beginning the endosymbiosis that led to the evolution of the chloroplast. Rhodophyta (Red Algae)  Rhodophyta (red algae) have cell walls composed of cellulose and other polymers and have no flagella.  Almost all red algae are photosynthetic.  Some species contribute to reef building. Amoebozoa  Species in the Amoebozoa lack cell walls and take in food by engulfing it.  They move via amoeboid motion and produce large, lobe–like pseudopodia.  Major subgroups in the lineage are lobose amoebae, cellular slime molds, and plasmodial slime molds.  Amoebae are abundant in freshwater habitats and in wet soils.  Some are parasites of humans and other animals. Myxogastrida (Plasmodial Slime Molds)  The plasmodial slime molds form a huge supercell with many nuclei.  They are important decomposers in forest ecosystems. Chapter 30: Green Plants Key Concepts o The green plants include both the green algae and the land plants. Green algae are an important source of oxygen and provide food for aquatic organisms; land plants hold soil and water in place, build soil, moderate extreme temperatures and winds, and provide food for other organisms. o Land plants were the first multicellular organisms that could live with most of their tissues exposed to the air. A series of key adaptations allowed them to survive on land. In terms of total mass, plants dominate today's terrestrial environments. o Once plants were able to grow on land, a sequence of important evolutionary changes made it possible for them to reproduce efficiently—even in extremely dry environments.  Section 30.1 Outline: Why Do Biologists Study the Green Plants?  Plants Provide Ecosystem Services Plants Provide Humans with Food, Fuel, Building Materials, and Medicines Agriculture, forestry, and horticulture are among the most important endeavors supported by biological science. Biologists study plants not only because they are captivating organisms but also because they keep us alive. Plants Provide Ecosystem Services  An ecosystem consists of all the organisms in a particular area, along with physical components of the environment, such as the atmosphere, precipitation, surface water, sunlight, soil, and nutrients.  Plants provide ecosystem services because they add to the quality of the atmosphere, surface water, soild, and other physical components of an ecosystem.  Plants alter the landscape in ways that benefit other organisms: –They produce oxygen via oxygenic photosynthesis –They build soil by providing food for decomposers –They hold soil and prevent nutrients from being lost by erosion by wind and water –They moderate the local climate by providing shade, reducing the impact of winds that dry out landscapes or make them colder.  Perhaps the most important ecosystem service provided by plants involves food.  They are the dominant primary producers in terrestrial ecosystems and provide the base of the food chain in the vast majority of terrestrial habitats (Figure 30.2).  Plants are eaten by herbivores, which are eaten by carnivores, which are eaten by omnivores—organisms that eat both plants and animals.  Omnivores feed at several different levels in the terrestrial food chain.  Green plants are the key to the carbon cycle on the continents. Plants Provide Humans with Food, Fuel, Building Materials, and Medicines  Plants provide most of our food supply as well as a significant percentage of the fuel, fibers, building materials, and medicines that we use.  Agricultural research began with the initial domestication of crop plants.  Artificial selection for plants with certain properties can lead to dramatic changes in plant characteristics (Figure 30.3b).  Humans have relied on plant–based fuels such as wood and coal (Figure 30.4).  Plants are a key source of drugs(Table 30.1).  Section 30.2 Outline: How Do Biologists Study Green Plants?  Analyzing Morphological Traits Using the Fossil Record Evaluating Molecular Phylogenies To understand how green plants originated and diversified, biologists use three tools: They compare the fundamental morphological features of various green algae and green plants They analyze the fossil record of the lineage They assess similarities and differences in DNA sequences from homologous genes to estimate phylogenetic trees Analyzing Morphological Traits  Green algae have long been hypothesized to be closely related to plants on the basis of several key morphological traits.  The green algae include species that are unicellular, colonial, or multicellular and that live in marine or freshwater habitats.  Based on morphology, the most important phyla of plants are grouped into three categories: nonvascular plants, seedless vascular plants, and seed plants.  Nonvascular plants lack vascular tissue—specialized groups of cells that conduct water or dissolved nutrients from one part of the plant body to another.  Seedless vascular plants have well–developed vascular tissue but do not make seeds.  A seed consists of an embryo and a store of nutritive tissue, surrounded by a tough protective layer.  Seed plants have vascular tissue and make seeds.  Within the seed plants, gymnosperms produce seeds that do not develop in an enclosed structure. In the flowering plants, or angiosperms, seeds develop inside a protective structure called a carpel. Using the Fossil Record  The fossil record for green algae began 700–725 million years ago.  The fossil record for land plants began 475 million years ago.  The fossil record for plants is massive and is broken up into five segments, each of which encompasses a major event in the diversification of land plants (Figure 30.7).  According to the fossil record, the green algae appear first, followed by the nonvascular plants, seedless vascular plants, and seed plants. Evaluating Molecular Phylogenies  The phylogenetic tree shown in Figure 30.8 has several important points: 1. Land plants probably evolved from green algae. 2. The green algal group called Charales is the sister group to land plants—meaning that Charales are their closest living relative. 3. The green plants are monophyletic, meaning that a single common ancestor gave rise to all of the green algae and land plants. 4. The green algae group is paraphyletic; the land plants are monophyletic. 5. The nonvascular plants are the most basal groups among land plants. 6. Morphological simplicity of the whisk ferns is probably a derived trait, meaning that complex structures have been lost in this lineage. 7. Seeds and flowers evolved only once.  Section 30.3 Outline: What Themes Occur in the Diversification of Green Plants?  The Transition to Land, I: How Did Plants Adapt to Dry Conditions? Preventing Water Loss: Cuticle and Stomata Transporting Water: Vascular Tissue and Upright Growth Mapping Evolutionary Changes on the Phylogenetic Tree The Transition to Land, II: How Do Plants Reproduce in Dry Conditions? Retaining and Nourishing Offspring: Land Plants as Embryophytes Alternation of Generations The Gametophyte–Dominant to Sporophyte–Dominant Trend in Life Cycles Heterospory Pollen Seeds Flowers Fruits The Angiosperm Radiation The story of land plants is the story of adaptations that allowed photosynthetic organisms to move from aquatic to terrestrial environments. The Transition to Land I: How Did Plants Adapt to Dry Conditions? Plants had to adapt to conditions in which only a portion of their tissues are wet. The adaptation to the water problem arose in two steps: (1) prevention of water loss from cells, and (2) transportation of water from tissues with access to water to tissues without access. Preventing Water Loss: Cuticle and Stomata Cuticle is a waxy, watertight sealant that gives plants the ability to survive in dry environments. Gas exchange is accomplished by stomata, which have a pore that opens and closes as the guard cells change shape (Figure 30.9). Transporting Water: Vascular Tissue and Upright Growth The first land plants probably lacked rigidity and were low and sprawling. The evolution of vascular tissue allowed early plants to support erect stems and transport water from roots to aboveground tissues. Vascular tissue evolved in a series of gradual steps that provided an increasing level of structural support, allowing plants to grow upright (Figure 30.10). Mapping Evolutionary Changes on the Phylogenetic Tree The major innovations that allowed plants to adapt to life on land are shown in Figure 30.11. Web animation: Plant Evolution and the Phylogenetic Tree The Transition to Land II: How Do Plants Reproduce in Dry Conditions? Innovations that were instrumental for efficient plant reproduction in a dry environment include: –development of spores that resist drying –gametes were produced in complex, multicellular structures –the embryo was retained on the parent plant and nourished by it Retaining and Nourishing Offspring: Land Plants as Embryophytes The gametophytes of early land plants contain specialized reproductive organs called gametangia that protected gametes from drying and mechanical damage. Individuals produce distinctive male and female gametangia. –The sperm–producing structure is the antheridium. –The egg–producing structure is the archegonium. In land plants, the zygote is retained on the gametophyte after fertilization and begins to develop on the parent plant to form a multicellular embryo that remains attached to the parent and is nourished by it. Alternation of Generations All land plants undergo alternation of generations. They have a multicellular haploid phase called the gametophyte and a multicellular diploid phase known as the sporophyte. The relationship between gametophyte and sporophyte is variable (Figure 30.14). Alternation of generations involves the same basic sequence of events (Figure 30.15): –Gametophytes produce gametes by mitosis. both the gametophyte and gametes are haploid. –Two gametes unite during fertilization to form a diploid zygote. –The zygote divides by mitosis and develops into a multicellular, diploid sporophyte. –The sporophyte produces spores by meiosis. Spores are haploid. –Spores divide by mitosis and develop into a haploid gametophyte. The Gametophyte–Dominant to Sporophyte–Dominant Trend in Life Cycles In land plants, the relationship between gametophyte and sporophyte is highly variable. Gametophyte–dominated life cycles evolved early; sporophyte–dominated life cycles evolved later (Figure 30.16). Heterospory Another important innovation found in seed plants is heterospory, the production of two distinct types of spore–producing structures and thus two distinct types of spores. Homosporous plants produce a single type of spore that develops into a bisexual gametophytes that produce both eggs and sperm. The two types of spore–producing structures in heterosporous species are microsporangia and macrosporangia (Figure 30.18). Microsporangia produce microspores that develop into male gametophytes that produce sperm. Macrosporangia produce megaspores that develop into female gametophytes that produce eggs. Thus, the gametophytes of seed plants are either male or female, but never both. Pollen When pollen evolved, heterosporous plants lost their dependence on water for fertilization. Seeds A seed is a structure that includes a developing embryo and a food supply surrounded by a tough coat. Seeds allow embryos to be dispersed to a new habitat, away from the parent plant. Seeds are often dispersed by wind, water, or animals. Flowers Flowering plants, or angiosperms, are the most diverse land plants living today. About 250,000 species have been described, and more are discovered each year. The success of angiosperms in terms of geographical distribution, number of individuals, and number of species revolves around a reproductive organ: the flower. Flowers contain two key reproductive structures: the stamens and carpels. The stamen contains the anther, where microsporangia develop. The carpel contains the ovary where the ovules are found. The evolution of the flower is an elaboration of heterospory, with the key innovation being the evolution of the ovary. Stamens and carpels are enclosed by modified leaves called cepals and petals. Flowers vary in size, structure, scent, and color in order to attract different pollinators. Heterospory in gymnosperms and angiosperms is shown in Figures 30.20 and 30.21, respectively, and show the key features of microspore and megaspore production. Fruits A fruit is a structure that is derived from the ovary and encloses one or more seed. The evolution of fruit made efficient seed dispersal possible. The adaptations that allow land plants to reproduce in dry environments are summarized in Figure 30.25. The Angiosperm Radiation Angiosperms represent one of the great adaptive radiations in the history of life. An adaptive radiation occurs when a single lineage produces a large number of descendant species that are adapted to a wide variety of habitats. The diversification of angiosperms is associated with three key adaptations: (1) vessels, (2) flowers, and (3) fruits. These adaptations allow angiosperms to transport water, pollen, and seeds efficiently. Monocots are monophyletic; dicots are paraphyletic. Because dicots are not a natural grouping, most biologists call them eudicots (Figure 30.27). Section 30.4 Outline: Key Lineages of Green Plants  Green Algae Ulvophyceae (Ulvophytes) Coleochaetophyceae (Coleochaetes) Charaphyceae (Stoneworts) Nonvascular Plants (―Bryophytes‖) Land Plants >Hepaticophyta (Liverworts) Land Plants >Anthocerophyta (Hornworts) Land Plants >Bryophyta (Mosses) Seedless Vascular Plants Vascular Plants >Lycophyta (Lycophytes, or Club Mosses) Vascular Plants >Psilotophyta (Whisk Ferns) Vascular Plants >Sphenophyta (Horsetails) Vascular Plants >Pteridophyta (Ferns) Seed Plants Gymnosperms >Cycadophyta (Cycads) Gymnosperms >Ginkgophyta (Ginkgos) Gymnosperms >Coniferophyta (Conifers) Gymnosperms > Gnetophyta (Gnetophytes) Gymnosperms >Pinophyta (Pines) Anthophyta (Angiosperms) The evolution of cuticle, pores, stomata, and water–conducting tissues allowed green plants to grow on land, where resources for photosynthesis are abundant. Once the green plants were on land, the evolution of gametangia, retained embryos, pollen, seeds, and flowers enabled them to reproduce efficiently even in very dry environments. Green Algae  The green algae are a paraphyletic group that totals about 7000 species.  Their chloroplasts have a double membrane and chlorophylls a and b, but relatively few accessory pigments.  Green algae live in close association with an array of other organisms. Ulvophyceae (Ulvophytes)  Ulvophytes are important primary producers in aquatic areas. Coleochaetophyceae (Coleochaetes)  Most grow as flat sheets of cells, and the multicellular individuals are haploid.  The coleochaetes are strictly freshwater algae that grow attached to aquatic plants or over submerged rocks) Charaphyceae (Stoneworts)  Stoneworts commonly accumulate crusts of calcium carbonate over their surfaces.  They are freshwater algae and are a good indicator that water is not polluted. Nonvascular Plants ("Bryophytes")  The nonvascular plants, or bryophytes, are the most basal lineages of land plants.  The evolutionary relationships amon the three lineages with living representatives (liverworts, hornworts, and mosses) are still unclear (Figure 30.33). Hepaticophyta (Liverworts)  Liverworts can grow on bare rock or tree bark and contribute to the initial stages of soil formation. Anthocerophyta (Hornworts)  The sporophytes look like horns and have stomata. Bryophyta (Mosses)  Mosses can be abundant in extreme environments and can become dormant.  Mosses cannot grow taller than a few centimeters because they lack a true vascular tissue. Seedless Vascular Plants  The seedless vascular plants are a paraphyletic group that forms a grade between the nonvascular plants and the seed plants (Figure 30.37).  All species of seedless vascular plants have conducting tissues with cells that are reinforced with lignin, forming vascular tissue. Lycophyta (Lycophytes, or Club Mosses)  Lycophytes are the most ancient plant lineage with roots, a belowground system of tissues and organs that anchors the plant and is responsible for absorbing water and mineral nutrients. Psilotophyta (Whisk Ferns)  Whisk ferns are restricted to tropical regions and have no fossil record. Sphenophyta (Horsetails)  Horsetails can flourish in waterlogged soils by allowing oxygen to diffuse down their hollow stems. Pteridophyta (Ferns)  Ferns are the only seedless vascular plants to have large, well–developed leaves.  These leaves give the plant a large surface area with which to capture sunlight for photosynthesis. Seed Plants  The seed plants are a monophyletic group that consists of the gymnosperms and the angiosperms (Figure 30.42).  Seed plants are defined by the production of seeds and pollen grains. Cycadophyta (Cycads)  Cycads harbor large numbers of symbiotic, nitrogen–fixing cyanobacteria, which are important sources of nutrients. Ginkgophyta (Ginkgos)  Only one species of ginkgos is alive today. It is deciduous, and individual trees are either male or female. Coniferophyta (Conifers)  This group is named for its reproductive structure, the cone, in which microsporangia and megasporangia are produced.  Conifers dominate all high–latitude and high–altitude forests. Gnetophyta (Gnetophytes)  Gnetophytes have vessel elements in addition to tracheids. Pinophyta (Pines)  Pines have a unique arrangement of needle–like leaves.  All living species make wood as a support structure Anthophyta (Angiosperms)  The defining adaptation of angiosperms is the flower.  Flowering plants supply the food that supports virtually every other species. ______________________________________________________________________ Chapter 31: Fungi Key Concepts o Fungi are important in part because many species live in close association with land plants. They supply plants with key nutrients and decompose dead wood. They are the master recyclers of nutrients in terrestrial environments. o All fungi make their living by absorbing nutrients from living or dead organisms. Fungi secrete enzymes so that digestion takes place outside their cells. Their morphology provides a large amount of surface area for efficient absorption. o Many fungi have unusual life cycles. It is common for species to have a long-lived heterokaryotic stage, in which cells contain haploid nuclei from two different individuals. Although most species reproduce sexually, very few species produce gametes.  Section 31.1 Outline: Why Do Biologists Study Fungi?  Fungi Provide Nutrients for Land Plants Fungi Are Key Model Organisms in Eukaryotic Genetics Fungi nourish the plants that nourish us. They affect global warming, because they are critical to the carbon cycle on land. A handful of species can cause debilitating diseases in humans and crop plants. Fungi Provide Nutrients for Land Plants  Mycorrhizal associations between fungi and plant roots allow faster plant growth (Figure 31.1). Fungi Provide Nutrients for Land Plants  Saprophytes are fungi that make their living by digesting dead plant material.  They play a key role in carbon cycling.  The carbon cycle has two basic components: (1) the fixation of carbon by land plants, and (2) the release of CO2 from plants, animals, and fungi as the result of cellular respiration (Figure 31.3).  For most carbon atoms, fungi connect the two components. Fungi Provide Nutrients for Land Plants  Although parasitic fungi cause athlete’s foot, vaginitis, diaper rash, ringworm, pneumonia, and thrush in humans, the incidence of fungal infections in humans is very low.  Their major destructive impact is on crops (Figure 31.4). Fungi Are Key Model Organisms in Eukaryotic Genetics  The yeast Saccharomyces cerevisiae is very important in basic research on cell biology and molecular genetics.  It is easy to culture and manipulate in the lab, grows rapidly, and mutants can easily be created and transferred among individuals.  Section 31.2 Outline: How Do Biologists Study Fungi?  Analyzing Morphological Traits The Nature of the Fungal Mycelium Reproductive Structures Evaluating Molecular Phylogenies Experimental Studies of Mutualism About 80,000 species of fungi have been described and named; about 1000 more are discovered each year. The fungi are so poorly studied that the known species are widely regarded as a tiny fraction of the real total, estimated at 1.65 million species or even higher. Analyzing Morphological Traits  Fungi have very simple bodies. Two growth forms exist: (1) single–celled forms (yeasts) and (2) multicellular filamentous forms (mycelia) (Figure 31.5).  Some fungi adopt both life–forms. The Nature of the Fungal Mycelium  Mycelia grow out in the direction of food sources and die back in areas where food is running out.  The filaments that make up a mycelium are called hyphae, and most are haploid or heterokaryotic, with two haploid nuclei (Figure 31.6).  Each filament is separated by cell–like compartments called septa.  Because mycelia are composed of branching hyphae, the body of a fungus has a high surface– area–to–volume ratio.  This makes absorption extremely efficient but also makes fungi prone to drying out.  Mycelia are an adaptation to the absorptive lifestyle of fungi. Thus, reproductive organs—not feeding structures—are the only thick, fleshy structures that fungi produce. Reproductive Structures  There are four major groups of fungi based on reproductive structures (Figure 31.7): the Chytridiomycota, the Zygomycota, the Basidiomycota, and the Ascomycota.  Chytridiomycota (chytrids) live primarily in water and have spores and gametes with flagella.  Zygomycota have haploid hyphae of different mating types. Hyphae of different mating types may become yoked together and the cells of the hyphae fuse to form a spore–producing structure called a zygosporangium.  Basidiomycota, or club fungi, have basidia that form at the ends of hyphae and produce spores. Mushrooms, bracket fungi, and puffballs are among the complex reproductive structures this group produces.  Ascomycota, or sac fungi, produce complex reproductive structures. The tips of hyphae inside these structures produce distinctive saclike cells, called asci, that generate spores. Evaluating Molecular Phylogenies  Fungi are more closely related to animals than land plants (Figure 31.8).  The Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota have traditionally been recognized as separate phyla (Figure 31.9).  Chytrids are the most basal group of fungi.  Chytridiomycota and Zygomycota are paraphyletic. A single common ancestor did not give rise to all species within each phylum.  Microsporidians are phylogenetically within the fungi.  The Basidiomycota and Ascomycota are monophyletic. Experimental Studies of Mutualism  Fungi and land plants often have a symbiotic relationship—one of close association.  Mutualism is a symbiotic relationship that provides benefits to both the host and the fungus.  In a parasitic symbiotic relationship, one species benefits at the expense of the other.  In a commensal relationship, one species benefits while the other is unaffected.  Experimental evidence indicates that mycorrhizal fungi and plants are mutualistic (Figure 31.10).  Section 31.3 Outline: What Themes Occur in the Diversification of Fungi?  Fungi Participate in Several Types of Mutualisms Extomycorrhizal Fungi Arbuscular Mycorrhizal Fungi (AMF) Are Endophytes Mutualists? What Adaptations Make Fungi Effective Decomposers? Extracellular Digestions Lignin Degradation Cellulose Digestion Variation in Life Cycles Unique Aspects of Fungal Life Cycles The evolution of novel methods for absorbing nutrients from a wide array of food sources drove the diversification of fungi. Fungi Participate in Several Types of Mutualisms  Fungi can be involved in both mycorrhizal associations and endophytic (aboveground) associations with plants. Extomycorrhizal Fungi  Ectomycorrhizal fungi (EMF) form a dense network of hyphae that cover a plant's roots but do not enter the root cells (Figure 30.11a). Hyphae also extend into the soil.  Most EMF are basidiomycetes.  EMF provide nitrogen and phosphate ions to the host plant and receive sugars and other complex carbon compounds in return. Arbuscular Mycorrhizal Fungi (AMF)  Arbuscular mycorrhizal fungi (AMF) grow into the cells of root tissue and directly contact the plasma membrane of the plant cell (Figure 31.11b).  AMF are from the lineage Glomeromycota.  AMF are extremely common and extremely ancient.  AMF provide phosphorus to the plants, but they do not provide nitrogen. Are Endophytes Mutualists?  Endophytes are not parasitic. Most are mutualistic and some are commensals—the fungi and the plants simply coexist with no observable effect, either deleterious or beneficial, on the host plant. What Adaptations Make Fungi Effective Decomposers?  Saprophytic fungi seek out large, complex molecules such as cellulose, lignin, proteins, and nucleic acids and break them down into hundreds or thousands of smaller compounds.  Although bacteria and archaea are also important decomposers in terrestrial environments, fungi and a few bacterial species are the only organisms that can digest wood completely (Figure 31.12). Extracellular Digestions  Fungi secrete enzymes for extracellular digestion—digestion that takes place outside the fungus.  Compounds resulting from enzymatic action are then absorbed by the hyphae.  Basidiomycetes can degrade both lignin and cellulose completely. Lignin Degradation  Lignin peroxidase is an enzyme that catalyzes the removal of a single electron from an atom in the aromatic rings of lignin.  This oxidation step creates a free radical and leads to a series of uncontrolled and unpredictable reactions that end up splitting the polymer into smaller units.  Fungi cannot oxidize lignin to produce ATP and cannot grow on lignin
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