Biology Chapters Summary - Phylogeny and Tree of Life PDF

Biology Chapters Summary and more Chapter 26 - Phylogeny and the Tree of Life Introduction To determine these relationships, scientists rely on two main approaches. First, they compare morphological characteristics, such as the size, shape, and presence or absence of different anatomical features...

Biology Chapters Summary and more Chapter 26 - Phylogeny and the Tree of Life Introduction To determine these relationships, scientists rely on two main approaches. First, they compare morphological characteristics, such as the size, shape, and presence or absence of different anatomical features. - Example: Dinosaurs share a number of anatomical features with birds such as fused clavicles (wishbone) and the shifting of the pubic bone toward the back. A second approach for determining evolutionary relationships is by comparing molecular characteristics. This is now the dominant way to compare organisms and it primarily relies on the comparison of spe- cific DNA or protein sequences. - Example: Computer programs are used to determine similarities among these molecular characteris- tics. While the morphological evidence linking dinosaurs and birds is strong, getting DNA or protein sequence information from extinct organisms is a particular challenge. Phylogenetic trees - Ultimately, these different characteristics are used to create a phylogenetic tree. These trees, or phy- logenies, are hypotheses of the evolutionary history between different organisms. - Example: For example, in an approach known as phylogenetic bracketing, we can pre- dict that features shared by two groups of closely related, extant organisms (birds and crocodilians) are present in their common ancestor and all of its descendants (which includes dinosaurs) unless independent data indicate otherwise. Vocab - phylogeny, the evolutionary history of a species or group of species. - systematics, a discipline focused on classifying organ- isms and determining their evolutionary relationships. 26.1 Organisms share many characteristics because of common ancestry (see Concept 22.3). As a result, we can learn a great deal about a species if we know its evolutionary history. - an organism is likely to share many of its genes, metabolic pathways, and structural proteins with its close relatives. Taxonomy - How organisms are named and classified. Binomial Nomenclature The two-part format of the scientific name, com- monly called a binomial, was instituted in the 18th century by Carolus Linnaeus - How to name: The first part of a binomial is the name of the genus (plural, genera) to which the species belongs. The second part, called the specific epithet, is unique for each species within the genus. - An example of a binomial is Castor canadensis Hierarchical Classification Beyond genera, taxonomists employ progressively more comprehensive categories of classifica- tion. The taxonomic system named after Linnaeus, the Linnaean system, places related genera in the same family, families into orders, orders into classes, classes into phyla (singular, phylum), phyla into kingdoms, and, more recently, kingdoms into domains Linking Classification and Phylogeny The evolutionary history of a group of organisms can be rep- resented in a branching diagram called a phylogenetic tree. - Sometimes, however, taxonomists have placed a species within a genus (or other group) to which it is not most closely related. - One reason for misclassification might be that over the course of evolution, a species has lost a key feature shared by its close relatives. If DNA or other new evidence indicates that such a mistake has occurred, the organism may be reclassified to accurately reflect its evolu- tionary history. Visualizing Phylogenetic Relationships Regardless of how groups are named, a phylogenetic tree represents a hypothesis about evolutionary relationships. The relationships are often depicted as a series of dichotomies, or two-way branch points. Each branch point (or internal node) represents common ances- tor of the two evolutionary lineages diverging from it. The pattern of branching is called the tree topology. Sister taxa, groups of organisms that share an immediate common ancestor that is not shared by any other group. - Example: Figure below, the evolutionary lineage leading to lizards shares an immediate common ancestor with the lineage leading to chimpanzees and humans. Thus, we can describe this portion of the tree by saying that of the groups shown here, lizards are the sister taxon to a group consisting of chimpanzees and humans. This tree, like all of the phylogenetic trees in this book, is rooted, which means that a branch point within the tree (often drawn farthest to the left) represents the most recent common ancestor of all taxa in the tree. Basal Taxon = Sister Taxa Best tree? - Most parsimonious - “simplest Cladogram - No scale Phylogram - Scale 26.2 Phylogenies are inferred from morphological and molecular data To infer phylogeny, systematists must gather as much information as possible about the morphology, genes, and bio- chemistry of the relevant organisms. It is important to focus on features that result from common ancestry, because only such features reflect evolutionary relationships. Morphological and Molecular Homologies Recall that phenotypic and genetic similarities due to shared ancestry are called homologies. - Examples: similarity in the number and arrangement of bones in the forelimbs of mammals is due to their descent from a common ancestor with the same bone structure In the same way, genes or other DNA sequences are homologous if they are descended from sequences carried by a common ancestor. Organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences. HOWEVER The morphological diver- gence between related species can be great and their genetic divergence small (or vice versa). Sorting Homology from Analogy Source of confusion in constructing a phylogeny is similarity between organisms that is due to convergent evolution—called analogy Convergent evolution - occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages. - Example: the two mole-like animals illustrated below are very similar in their external appearance. However, their internal anatomy, physiology, and reproductive systems are very dissimilar. Another clue to distinguishing between homology and analogy is the complexity of the characters being compared. The more elements that are similar in two complex structures, the more likely it is that the structures evolved from a common ancestor. - Example: For instance, the skulls of an adult human and an adult chimpanzee both consist of many bones fused together. The compositions of the skulls match almost per- fectly, bone for bone. It is highly improbable that such com- plex structures, matching in so many details, have separate origins. - Genetic Example: The same argument applies to comparisons at the gene level. Genes are sequences of thousands of nucleotides, each of which represents an inherited character in the form of one of the four DNA bases: A (adenine), G (guanine), C (cytosine), or T (thymine). If genes in two organisms share many portions of their nucleotide sequences, it is likely that the genes are homologous. Evaluating Molecular Homologies The first step after sequencing the molecules is to align comparable sequences from the species being studied. If the species are very closely related, the sequences probably differ at only one or a few sites. - Example: certain noncoding DNAsequences near a particular gene are very similar in two species, except that the first base of the sequence has been deleted in one of the species. The effect is that the remaining sequence shifts back one notch. - To address such problems, researchers have developed computer programs that estimate the best way to align compa- rable DNA segments of differing lengths Just as with morphological characters, it is necessary to distinguish homology from analogy in evaluating molecular similarities for evolutionary studies. Two sequences that resemble each other at many points along their length most likely are homologous Homoplasies - The bases that their otherwise very different sequences happen to share may simply be coincidental matches 26.3 In the approach to systematics called cladistics, common ancestry is the primary criterion used to classify organisms. Biologists attempt to place species into groups called clades, each of which includes an ancestral species and all of its descendants. Shared Ancestral and Shared Derived Characters Shared Derived - Synapomorphy Single Derived - Apomorphy Shared Ancestry - Symplesiomorphy Single Ancestry - Plesiomorphy Inferring Phylogenies using Derived Characters Shared derived (Synapomorphy) characters are unique to particular clades. Outgroup = Sister Taxa = Basal Taxon A suitable outgroup can be determined based on evidence from morphology, paleontology, embryonic devel- opment, and gene sequences. - Outgroups are very similar to the common ancestor By comparing members of the ingroup with each other and with the outgroup, we can determine which characters were derived at the various branch points of vertebrate evo- lution. Maximum Parsimony and Maximum Likelihood According to the principle of maximum parsimony, we should first investigate the simplest explanation that is consistent with the facts. - Trees based on morphology, the most parsimonious tree, require the fewest evolutionary events, as measured by the origin of shared derived morphological characters. - For phylogenies based on DNA, the most parsimonious tree requires the fewest base changes. Interpreting Phylogenetic Trees It’s important to recognize that phylogenetic trees are hypotheses about how the various organisms in the tree are related to one another. A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees. Phylogenetic trees are also intended to show patterns of descent, not phenotypic similarity. - Example: For example, even though crocodiles are more closely related to birds than to lizards, they - look more like lizards because morphology has changed dramatically in the bird lineage. Cladogram VS Phylogram 26.4 The analysis of molecular data helps us uncover evolutionary relationships between groups that have little common ground for morpho- logical comparison, such as animals and fungi. Different genes can evolve at different rates, even in the same evolutionary lineage. As a result, molecular trees can represent short or long periods of time, depending on which genes are used.  - Example: The DNA that codes for ribosomal RNA (rRNA) changes relatively slowly. Therefore, comparisons of DNA sequences in these genes are useful for investigating relationships between taxa that diverged hundreds of millions of years ago. - Example: Mitochondrial DNA (mtDNA) evolves relatively rapidly and can be used to explore recent evolutionary events. Gene duplication and Gene Families Molecular techniques now allow us to trace the phylogenies of gene duplications and the influence of these duplications on genome evolution. These molecular phylogenies must account for repeated duplications that have resulted in gene families, groups of related genes within an organism’s genome Orthologous genes, the homology is the result of a speciation event and hence occurs between genes found in dif- ferent species - Example: The genes that code for cytochrome c (a protein that functions in electron transport chains) in humans and dogs are orthologous. Paralogous genes, the homology results from gene duplication; hence, multiple copies of these genes have diverged from one another within a species Orthologous genes can only diverge after speciation has taken place, that is, after the genes are found in separate gene pools. - Example: the cytochrome c genes in humans and dogs serve the same function, the gene’s sequence in humans has diverged from that in dogs in the time since these species last shared a common ancestor. Paralogous genes, on the other hand, can diverge within a species because they are present in more than one copy in the genome. - Example: The paralogous genes that make up the olfactory receptor gene family in mice have diverged from each other during their long evolutionary history. They now specify proteins that confer sensitivity to a wide variety of molecules, ranging from food odours to sex pheromones. Genome Evolution First, lineages that diverged long ago often share many orthologous genes. Such commonalities explain why disparate organisms nevertheless share many biochemical and developmental pathways The number of genes a species has doesn’t seem to increase through duplication at the same rate as per- ceived phenotypic complexity. BUT there is carrying versatility: A single human gene can encode multiple proteins that perform different tasks in various body tissues. 26.5 Molecular Clocks Molecular clock, an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates. Assumptions when forming a Molecular Clock - Mutation Rate is constant - Mutation rates are comparable btw species - Mutation rates are constant across all genes Difference in Clock Speed Mutation rate in neutral genes -> Regular mutation rate Mutation rate in important genes -> relatively slow Potential Problems with Molecular Clocks Many irregularities are likely to be the result of natural selection, with certain DNA changes favored over others. But because the direction of natural selection may change repeatedly over long periods of time (and hence may average out), some genes experiencing selection can nevertheless serve as approximate markers of elapsed time. Another question arises when researchers attempt to extend molecular clocks beyond the time span documented by the fossil record. - These estimates assume that the clocks have been constant for all that time. Such estimates are highly uncertain. How to fix these issues? - Calibrating molecular clocks with data on the rates at which genes have evolved in different taxa. - Using many genes rather than the common approach of using just one or a few genes 26.6 From 2 Kingdoms to 3 Domains In most phylogenetic trees in this chapter, the internal branch points bifurcate, meaning they separate into two branches. Branch into 3 or more? - Polytomy To reduce polytomy - Scientists have to collect data from different species and/or try different approaches to compar- ing the species on the tree. The Important Role of Horizontal Gene Transfer This reconstruction of the tree of life is based in part on sequence comparisons of rRNA genes, which code for the RNA components of ribosomes. However, some other genes reveal a different set of relationships. What causes trees based on data from different genes to yield such different results? Horizontal gene transfer, a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and perhaps fusions of organisms (as when a host and its endosymbiont become a single organism). THERE ARE 3 METHODS OF HORIZONTAL GENE TRANSFER Overall, horizontal gene transfer has played a key role throughout the evolutionary history of life and it continues to occur today. Some biologists have argued that horizontal gene transfer was so common that the early history of life should be represented not as a dichotomously branching. Chapter 27 - Bacteria and Archaea Prokaryotes are indeed masters of adaptation and live in the most unexpected places. (Literally that's the intro so much of it is just examples) Cell-Surface Structures The cell walls of prokaryotes differ in structure from those of eukaryotes. In eukaryotes that have cell walls, such as plants and fungi, the walls are usually made of cellulose or chitin. In contrast, most bacterial cell walls contain peptidoglycan, a polymer composed of modified sugars cross-linked by short polypeptides. This molecular fabric encloses the entire bacterium and anchors other molecules that extend from its surface. Archaeal cell walls contain a vari- ety of polysaccharides and proteins but lack peptidoglycan. Gram Stain - Test to see if it is Gram Positive or Gram Negative Bacteria. Samples are first stained with crystal violet dye and iodine, then rinsed in alcohol, and finally stained with a red dye such as safranin that enters the cell and binds to its DNA. If the stain is purple - Gram Positive If the stain is pink or red - Gram negative Gram-positive bacteria have simpler walls with a relatively large amount of peptidoglycan. The walls of gram-negative bacteria have less peptidoglycan and are structurally more complex, with an outer membrane that contains lipopolysaccharides (carbohydrates bonded to lipids). - The lipid portions of the lipopolysaccharides in the walls of many gram-negative bacteria are toxic, causing fever or shock. Furthermore, the outer membrane of a gram-negative bacterium helps protect it from the body’s defenses. Gram -ve bacteria are usually more resistant than Gram +ve, why? -> The outer membrane impedes entry of the drugs. Drugs like penicillin target the peptidoglycan of bacteria, thus not targeting the body cells The cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein. This layer is called a capsule if it is dense and well-defined or a slime layer if it is less well organised. Some prokaryotes stick to their substrate or to one another by means of hairlike appendages called fimbriae (singular, fimbria) Endospores Certain bacteria develop resis- tant cells called endospores when they lack an essential nutrient. - The original cell produces a copy of its chromosome and surrounds it with a tough multilayered structure, forming the endospore. - Water is removed from the endospore, and its metabolism halts. The original cell then lyses, releasing the endospore. - Endospores are VERY DURABLE and can remain dormant for centuries. Will ‘wake up’ under optimal conditions. Motility About half of all prokaryotes are capable of taxis, a directed movement toward or away from a stimulus Many prokaryotes use flagella to move ALSO Prokaryotic flagella differ greatly from eukaryotic flagella: They are one-tenth the width and are not covered by an extension of the plasma membrane. They are also very different in molecular composition and their mechanism of propulsion. Among prokaryotes, bacterial and archaeal fla- gella are similar in size and rotation mechanism, but they are composed of different proteins. OVERALL, due to such differences, they both arose independently, (Analogous) Evolutionary Origins of Bacterial Flagella Bacterial Flagella has 3 main parts: the motor, hook, and filament and they themselves are composed of 42 diff proteins. Summary -> Remember the “less complex eye example” from BIO152 - Essentially its that These findings suggest that the bacterial flagellum evolved as other proteins were added to an ancestral secretory system. This is an example of exaptation, the process in which existing structures take on new functions through descent with modification. Internal Organization and DNA The cells of prokaryotes are simpler than those of eukaryotes in both their internal structure and the physical arrangement of their DNA. - Prokaryotic cells lack the complex compartmentalization found in eukaryotic cells. The genome of a prokaryote is structurally different from a eukaryotic genome and in most cases has considerably less DNA. - Prokaryotes generally have circular chromosomes, whereas eukaryotes have linear chromosomes. Prokaryotes the chromosome is associated with many fewer proteins than are the chromosomes of eukaryotes. Also unlike eukaryotes, prokaryotes lack a membrane-bounded nucleus; - their chromosome is located in the nucleoid, a region of cytoplasm that is not enclosed by a membrane. Although DNA replication, transcription, and translation are fundamentally similar processes in prokaryotes and eukaryotes, some of the details are different. - prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes and differ in their protein and RNA content. - These differences allow cer- tain antibiotics, such as erythromycin and tetracycline, to bind to ribosomes and block protein synthesis in prokaryotes but not in eukaryotes. HOWEVER - not without side-effects since mitochondria have a translational sys- tem similar to that of prokaryotes, from which they evolved Reproduction By binary fission, a single prokaryotic cell divides into 2 cells, which then divide into 4, 8, 16, and so on. Limiting Factors: - The cells eventually exhaust their nutrient supply - poison themselves with metabolic wastes - face competition from other microorganisms - consumed by other organisms. 27.2 Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes Evolution cannot occur without genetic variation Three factors that give rise to high levels of genetic diversity in prokaryotes: rapid reproduction, mutation, and genetic recombination. Rapid Reproduction and Mutation Prokaryotes do not reproduce sexually, so at first glance their extensive genetic vari- ation may seem puzzling. But in many species, this variation can result from a combination of rapid reproduction and mutation. The key point is that new mutations, though rare on a per gene basis, can increase genetic diversity quickly in species with short generation times and large populations. -> This leads to rapid evolution. IMPORTANT TO NOTE - Prokaryotes are not “primitive” or “inferior” in an evolutionary sense. They are, in fact, highly evolved: For 3.5 billion years, prokaryotic populations have responded successfully to many types of environmental challenges. Genetic Recombination Additional diversity arises from genetic recombination, the combining of DNA from two sources. In eukaryotes, the sexual processes of meiosis and fertilization combine DNA from two individuals in a single zygote. Three other mechanisms—transformation, transduction, and conjugation—can bring together prokaryotic DNA from different individuals: Also: Vertical Gene Transfer: Gene transfer from parent to offspring Transformation and Transduction Transformation - “uptake of for eign DNA from its surroundings.” - Once inside the cell, the foreign DNA can be incorporated into the genome by homologous DNA exchange. Transduction - phages (from “bacteriophages,”the viruses that infect bacteria) carry prokaryotic genes from one host cell to another. In most cases, transduction results from accidents that occur during the phage replicative cycle Conjugation and Plasmids Conjugation - DNA is transferred between two prokaryotic cells (usually of the same species) that are temporarily joined. In bacteria, the DNA transfer is always one way: One cell donates the DNA, and the other receives it. 1) First, a pilus of the donor cell attaches to the recipient 2) The pilus then retracts, pulling the two cells together, like a grappling hook. 3) Formation of a temporary structure between the two cells, a “mating bridge,” through which the donor may transfer DNA to the recipient. Ability to do this is due to a piece of DNA called the F Factor (contains 25 genes) F factor in its plasmid form - F plasmid - Cells containing the F plasmid, designated F+ cells, function as DNA donors during conjuga- tion. Cells lacking the F factor, designated F-, function as DNA recipients during conjugation. The F+ condition is transferable in the sense that an F+ cell converts an F- cell to F+ if a copy of the entire F plasmid is transferred. The F Factor in the Chromosome Chromosomal genes can be transferred during conjugation when the do- nor cell’s F factor is integrated into the chromosome. Hfr cell (high frequency of recombination) - F built into the chromosome Like an F+ cell, an Hfr cell functions as a donor during conjugation with an F- cell. When chromosomal DNA from an Hfr cell enters an F- cell, homologous regions of the Hfr and F- chromosomes may align, allowing segments of their DNA to be exchanged. This entire section is BS I pray for you all R Plasmids and Antibiotic Resistance Sometimes, mutation in a chromosomal gene of the pathogen can confer resistance. - In other cases, bacteria have “resistance genes,” which code for enzymes that specifically destroy or otherwise hinder the effectiveness of certain antibiot- ics, such as tetracycline or ampicillin. Such resistance genes are carried by plasmids known as R plasmids (R for resistance). Exposing a bacterial population to a specific antibiotic, whether in a laboratory culture or within a host organism, will kill antibiotic-sensitive bacteria but not those that happen to have R plasmids with genes that counter the antibiotic. - After -> Natural Selection-> etc etc more adapted will spread genes, etc etc 27.3 (THIS CHAPTER IS VERY IMPORTANT FOR NAMING CERTAIN BACTERIA PLEASE PLEASE PLEASE READ) Like all organisms, prokaryotes can be categorised by how they obtain energy and the carbon used in building the organic molecules that make up cells. Phototrophs - Obtain energy from light Chemotrophs - Obtain energy from chemicals Autotrophs - Organisms that only need CO2 as a carbon source. Heterotroph - A heterotroph is an organism that eats other plants or animals for energy and nutrients. These prefixes can be mixed and matched to form more specific classifications. - Photoautotroph - a photosynthetic organism (such as a green plant or a cyanobacterium) that utilises energy from light to synthesise organic molecules (it plant) - Chemoheterotroph - microbes that use organic chemical substances as sources of energy and organic compounds as the main source of carbon. (It eats things) - Mixotroph - deriving nourishment from both autotrophic and heterotrophic mechanisms - Chemoautotroph - an organism, typically a bacterium, which derives energy from the oxidation of inorganic compounds. - Photoheterotroph - they are organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source Role of Oxygen in Metabolism Obligate aerobes - use O2 for cellular respiration and cannot grow without it. Obligate anaerobes - are poisoned by O2. Facultative anaerobes - use O2 if it is present but can also carry out fermenta- tion or anaerobic respiration in an anaerobic environment. Nitrogen Metabolism For example, some cyanobacteria and some methanogens (a group of archaea) convert atmospheric nitrogen (N2) to ammonia (NH3), a process called nitrogen fixation. -> The nitrogen is then incorporated into amino acids and other organic molecules. Nitrogen fixation by prokaryotes has a large impact on other organisms. - nitrogen-fixing prokaryotes can increase the nitrogen available to plants, which cannot use atmospheric nitrogen but can use the nitrogen com- pounds that the prokaryotes produce from ammonia Metabolic Cooperation Cooperation between prokaryotic cells allows them to use environmental resources they could not use as individual cells Metabolic cooperation between different prokaryotic species often occurs in surface-coating colonies known as biofilms. Cells in a biofilm secrete signaling molecules that recruit nearby cells, causing the colonies to grow. (Think of them working together so well they act as a single organism) 27.4 Richter said this chapter we needed to skim, but due to him bamboozling us in the past, and my now developed trust issues, I would like to still summarize this chapter for our benefit. An overview of Prokaryotic Diversity One lesson from studying prokaryotic phylogeny is that the genetic diversity of prokaryotes is immense. “Theres is a lot” TACK - First letters of all the Taxa basically all of the TACK can survive different extreme environments and there is a lot of debate and overlap, pls dont hurt me for a better explanation its literally 1:50am my head is throbbing. Major groups of bacteria Another important lesson from molecular systematics is that horizontal gene transfer played a key role in the evolu- tion of prokaryotes. Bacteria Every major mode of nutrition and metabolism is represented among bacteria, and even a small taxonomic group of bacteria may contain species exhibiting many different nutritional modes. Archaea Extremophiles - meaning “lovers” of extreme conditions (from the Greek philos, lover), and include extreme halophiles and extreme thermophiles. - Extreme halophiles - live in highly saline environments (some tolerate the salinity, others need it to survive) - Extreme thermophiles - thrive in very hot environments - Methanogens - archaea that release methane as a by-product of their unique ways of obtaining energy  - Many methanogens use CO2 to oxidise H2, a process that produces both energy and methane waste. Among the strictest of anaerobes, methanogens are poisoned by O2. Many extreme halophiles and all known methanogens are archaea in the clade Euryarchaeota 27.5 Prokaryotes play crucial roles in the biosphere Chemical Recycling Ecosystems depend on the continual recycling of chemical elements between the living and nonliving com- ponents of the environment, and prokaryotes play a major role in this process. - Chemoheterotrophic prokaryotes function as decomposers, breaking down dead organisms as well as waste products and thereby unlocking supplies of carbon, nitrogen, and other elements. Cyanobacteria - Phototrophic Prokaryotes -> use CO2 to make sugars (like plants) Under some conditions, prokaryotes can increase the availability of nutrients that plants require for growth, such as nitrogen, phosphorus, and potassium Prokaryotes can also decrease the availability of key plant nutri- ents; this occurs when prokaryotes “immobilize” nutrients by using them to synthesize molecules that remain within their cells. Ecological Interactions Symbiosis - an ecological relationship in which two spe- cies live in close contact with each other Host - A larger organism that harbors a smaller organism Symbiote - “The smaller organism” Mutualism - an ecological interaction between two species in which both benefit Commensalism- ecological relationship in which one species benefits while the other is not harmed or helped in any significant way Parasitism - an ecological relationship in which a parasite eats the cell contents, tissues, or body fluids of its host; as a group, parasites harm but usually do not kill their host, at least not immediately Pathogens - Parasites that cause disease Mutualistic Bacteria Can form “microbiomes” like gut bacteria Pathogenic Bacteria All the pathogenic prokaryotes known to date are bacteria Pathogenic prokaryotes usually cause illness by producing poisons, which are classified as exotoxins or endotoxins. Exotoxins are proteins secreted by certain bacteria and other organisms. Endotoxins are lipopolysaccharide components of the outer membrane of gram-negative bacteria. In contrast to exotoxins, endotoxins are released only when the bacteria die and their cell walls break down. Horizontal gene transfer can also spread genes associated with virulence, turning normally harmless bacteria into potent pathogens. Chapter 28 - Protists 28.1 Protists, along with plants, animals, and fungi, are classified as eukaryotes; they are in domain Eukarya, one of the three domains of life. Eukaryotic cells also have a well-developed cytoskeleton that extends throughout the cell The cyto- skeleton provides the structural support that enables eukaryotic cells to have asymmetric (irregular) forms, as well as to change in shape as they feed, move, or grow. In contrast, prokaryotic cells lack a well-developed cytoskeleton, thus limit- ing the extent to which they can maintain asymmetric forms or change shape over time. Structural and Functional Diversity in Protists In fact, protists exhibit more structural and functional diversity than the eukaryotes with which we are most familiar—plants, animals, and fungi. - For example, most protists are unicellular, although there are some colonial and multicellular species. Protists are also very diverse in their nutrition. Some protists are photoautotrophs and contain chloroplasts. Some are heterotrophs, absorbing organic molecules or ingesting larger food particles. Still other protists, called mixotrophs, combine photosynthesis and heterotrophic nutrition Photoautotrophy, heterotrophy, and mixotrophy have all arisen independently in many different protist lineages. Can also reproduce sexaully and asexually Four Supergroups of Eukaryotes (The picture wouldnt resize, and I dont have a degree in graphic design, IM SORRY) Endosymbiosis in Eukaryotic Evolution What gave rise to the enormous diversity of protists that exist today? Endosymbiosis, a relationship between two species in which one organism lives inside the cell or cells of another organism (the host) Mitochondria and plastids are derived from prokaryotes that were engulfed by the ancestors of early eukaryotic cells - The evidence also suggests that mitochondria evolved before plastids. Endosymbiosis and the Spread of Photosynthesis Photosynthesis—a complex metabolic process involving hundreds of proteins—was passed around several times as eukaryotes evolved. The first occurrence of this was when oxygenic photosynthesis, which first appeared in cyanobac- teria, was transferred to a eukaryotic cell - endosymbiosis between cyanobacteria and a non-photosynthetic eukaryote and ended with the evolu- tion of a chloroplast - Biologists call this event a primary endosymbiosis because it was the first transfer of photosynthe- sis from a prokaryote to a eukaryote. Photosynthesis continued to be passed to diverse groups and across kingdoms in a process called secondary endosymbiosis. There is considerable evidence to suggest that on several occasions non-photosynthetic eukaryotes picked up photosynthesis by maintaining an endosymbiosis with another eukaryote, specifically a red or green alga. 28.2 Diplomonads and Parabasalids The protists in these two groups lack plastids and have modi- fied mitochondria (until recently, they were thought to lack mitochondria altogether). Most diplomonads and parabasa- lids are found in anaerobic environments. \ Diplomonads - - Have modified mitochondria called mitosomes - LAck electron transport chains - Get energy from anaerobic metabolic pathways - Many are parasites - Structurally -> have 2 nuclei and multiple flagella Parabasalids - - Have reduced mitochondria called hydrogenosomes -> releases some energy anaerobically, releasing hydrogen as a byprod Euglenozoans - - diverse clade that includes predatory heterotrophs, photosynthetic autotrophs, mixotrophs, and parasites. The main mor- phological feature that distinguishes protists in this clade is the presence of a rod with either a spiral or a crystalline structure inside each of their flagella - Kinetoplastids - Have a single, large mitochondrion. - Has organized mass of DNA with thousands of interlocking circles called a kinetoplast - Feed on prokaryotes in marine environments - Euglenid - Has pocket at one end with 1-2 flagella - Some are mixotrophs I WOULD LIKE TO TAKE THE TIME TO SAY THAT THERE ARE MORE CONCEPTS THAT WE NEED TO KNOW. IT DOESN'T CUT OFF AT THE FIRST 2 SECTIONS. Why must we suffer like this 29.3 Stramenopiles - Has “hairy” flagellum composition - 3 groups -> diatoms, brown algae, oomycetes Diatoms - Unicellular - Have glass-like wall made of silicon dioxide - Large proportion are phytoplankton - Very widespread and abundant - When they bloom large amounts formed - With this, they absorb a lot of CO2, die, then sink to the ocean floor. So they reintroduce CO2 to the earth Brown Algae - Largest and most complex - All are multicellular - “Seaweeds” - Root-like holdfast - Stem-like stripe - Leaf-like blades - All these independently arose **ALTERNATION OF GENERATIONS** The most complex life cycles include an alternation of generations, the alternation of multicellular haploid and diploid forms. Oomycetes - Include water moulds, white rusts, downy mildews - Previously classified as fungi Alveolates - Subgroup of SAR - Have membrane-bound sacs (alveoli) just under plasma membrane Dinoflagellates - CElls are reinforced by cellulose plates - Flagella spin to propel the organism forward - Ancestors were photosynthetic - Now mostly mixotrophic and heterotrophic There is a bit more but IDK if he’s gonna do smth with it. Chapter 29 - Plant Diversity 1: How plants Colonized Land Introduction Started out as thin coatings of cyanobacteria about 1.2 billion years ago, evolved into what we see today. 29.1 Plants evolved from green algae - Green algae called charophytes are the closest relatives of modern plants. Morphological and Molecular Evidence Many important traits of plants also appear in a variety of algae - Multicellularity - Similar photosynthetic pigments - Cellulose cell walls BUT, some traits arose independently The charophytes, however, are the only algae that share the following three distinctive traits with plants, strongly suggesting that they are the closest living relatives of plants: 1) Rings of cellulose-synthesising proteins 2) Structure of flagellated sperm 3) Formation of a phragmoplast Adaptations Enabling the Move to Land In charophytes, a layer of a durable polymer called sporopollenin prevents exposed zygotes from drying out. A similar chemical adaptation is found in the tough sporopollenin walls that encase the spores of plants. All the traits enabled the move to land. Many benefits but many challenges - Scarcity of water - Lack of structural support - New fertilisation methods needed. Derived traits of plants - Cuticle - Covering - Consists of wax and polymers - acts as waterproofing - prevents desiccation - prevents microbial attack - Stomata - Specialized pors - support exchange of CO2 and O2 - Minimize water loss Early plants didnt have roots, how did they conduct nutrients? - They formed symbiotic relationships with Fungi (mutualistic) -> Called mycorrhizae The Origin and Diversification of Plants The algae most closely related to plants include many uni- cellular species and small colonial species.  - One way to distinguish groups of plants is whether or not they have an extensive system of vascular tissue, plants that have such tissue are classified as vascular plants. - Those that dont? - Non-Vascular plants - Nonvascular plants are often informally called bryophytes - Vascular plants, which form a clade that comprises about 93% of all extant plant species, can be categorized further into smaller clades. - Two of these clades are the lycophytes (club mosses and their relatives) and the monilophytes (ferns and their relatives). The plants in each of these clades lack seeds, which is why collectively the two clades are often informally called seedless vascular plants. Seed - embryo packaged with a supply of nutrients inside a protective coat. Seed plants can be divided into two groups, gymnosperms and angiosperms, based on the absence or presence of enclosed chambers in which seeds mature. Gymnosperms - are grouped together as “naked seed” plants because their seeds are not enclosed in chambers. Angiosperms - are a huge clade consisting of all flowering plants. Angiosperm seeds develop inside cham- bers called ovaries, which originate within flowers and mature into fruits. 29.2 Mosses and other nonvascular plants have life cycles dominated by gametophytes - The nonvascular plants (bryophytes) are rep- resented today by three phyla of small herbaceous (nonwoody) plants: liverworts (phylum Hepatophyta), mosses (phylum Bryophyta), and horn- worts (phylum Anthocerophyta) - These 3 diverged early in plant evolution - All 3 acquired special adaptations Non-vascular plants - Haploid Gametophytes are the dominant stage in the life cycle. When bryophyte spores are dispersed to a favourable habitat, such as moist soil or tree bark, they may germinate and grow into gametophytes. Germinating moss spores, for example, characteristically produce a mass of green, branched, one-cell-thick filaments known as a protonema. The gametophytes are anchored by delicate rhizoids, which are long, tubular single cells (in liverworts and horn- worts) or filaments of cells (in mosses). - While structurally similar to root hairs (not roots!), rhizoids primary function is for attachment to the substrate (kinda like roots, but not really) Some bryophyte gametophytes are bisexual, but in mosses the archegonia and antheridia are typically carried on separate female and male gametophytes. - Flagellated sperm swim through a film of water toward eggs, entering the archegonia in response to chemical attractants. - The fact that sperm swim through water to reach the egg also means that in species with separate male and female gametophytes (most mosses), sexual reproduction is likely to be more successful when individuals are located close to one another. Bryophyte Sporophytes They cannot live indepen- dently. They remain attached to their parental gameto- phytes, from which they absorb sugars, amino acids, minerals, and water. A typical bryophyte sporophyte consists of a foot, a seta, and a sporangium. - Foot - Absorbs nutrients from gametophyte - Seta - (or stalk) conducts these materials to the sporangium (also called the capsule) - Typically, the upper part of the capsule features a ring of interlocking, tooth-like structures known as the peristome. These “teeth” open under dry conditions and close again when it is moist. This allows spores to be dis- charged gradually, via periodic gusts of wind that can carry them long distances. Both moss and hornwort sporophytes also have specialised pores called stomata, which are also found in all vascular plants. (controls water loss in the plant) 29.3 Ferns and seedless plants were the first plants to grow tall Just history, don't need to know this I think Origins and traits of Vascular plants Ancient relatives of vascular plants had branched sporophytes that were not dependent on gametophytes for nutrition, their branching allowed more complex bodies with multiple sporangia. As competition increased, plant complexity increased. And more competition, more vascular plants. Early vascular plants already had some derived traits of today’s vascular plants, but they lacked roots and some other adaptations that evolved later. Main traits that characterise vascular plants - Dominant sporophytes - Transport water in xylem and phloem - Well developed roots and leaves including spore bearing leaves -> Sporophylls - Life Cycles with Dominant Sporophyte Bryophytes (non-vascular plants) -> gametophyte dominant lifecycles - Reductions in gametophyte size occurred among extant vascular plants; in these groups, the sporophyte generation is the larger and more complex form in the alternation of generations Transport in Xylem and Phloem Xylem - conducts most of the water and minerals. - Contain tracheids - Tube shaped cells that carry water and minerals from roots - Water conducting cells are lignified (cell is strengthened by lignin) Phloem - Cells arranged into tubes that distribute organic products Lignified tissue allowed vascular plants to grow tall. Tall is good, plant like be tall Evolution of Roots Roots - Organs that absorb nutrients in the soil as well as anchor the vascular plant. - Evolved from the underground stem Evolution of leaves We’re in university biology, if you dont know photosynthesis I am worried for you Microphylls - leaves that are small, usually spine-shaped, and supported by a single strand of vascular tissue. Megaphylls - is larger leaves with a highly branched vascular system and is present in all vascular plants except lycophytes. - Higher photosynthetic productivity than microphylls due to the larger surface area served by the network of veins. Sporophylls and Spore Variations Sporophylls - modified leaves that bear sporangia. Most seedless vascular plants are: Homosporous: One type of sporangium, one type of spore -> usually develops into a bisexual gametophyte Heterosporous - two types of sporangia and produces two kinds of spores: megasporophylls and micro- sporophylls. Megasporophylls have megasporangia, which produce megaspores, spores that develop into female gametophytes. Microsporophylls have microsporangia, which produce microspores, smaller spores that develop into male gametophytes. Classification of Seedless Vascular Plants Two clades of living seedless vascular plants: the lycophytes (phylum Lycophyta) and the monilophytes (phylum Monilophyta) Lycophytes - Club moss, spike moss, quillworts. Monilophytes - Ferns, horsetails, whiskferns -> Form a clade -> Common ancestor and ALL the descendants The significance of seedless Vascular Plants The ancestors of living lycophytes, horsetails, and ferns, along with their extinct seedless vascular relatives, grew to great heights during the Devonian and early Carboniferous periods, forming the first forests. How did their dramatic growth affect Earth and its other life? - Large drop in CO2 Levels - Caused Global cooling and glacial formation - The actions of roots contributed to this - Roots broke down calcium and magnesium rocks in the soil - The rocks reacted with CO2 found in rain water - Then the sediment settles at the bottom of the ocean - Formed from coal formation Chapter 30 - Plant Diversity 2: Evolution of Seed Plants Seeds and pollen grains are key adaptations for like on land In addition to seeds, the following are common to all seed plants: reduced gametophytes, heterospory, ovules, and pollen Advantage of reduced Gametophyte Mosses and other bryophytes have life cycles dominated by gametophytes, whereas ferns and other seedless vascular plants have sporophyte-dominated life cycles. Gametophytes of seedless vascular plants are visible to the naked eye, the gametophytes of seed plants are mostly microscopic. This miniaturisation allowed for an important evolutionary innovation in seed plants: Their tiny gametophytes can develop from spores retained within the sporangia of the parental sporophyte Arrangement allows - Protection from environmental stress - Protection from UV radiation and drying out - Also allows dependent gametophytes to obtain nutrients from the sporophyte Heterospory: The Rule among Seed Plants Most seedless plants are homosporous—they produce one kind of spore, which usually gives rise to a bisexual gametophyte - Ferns and other close rela- tives of seed plants are homosporous Seed plants or their ancestors became heterosporous, producing two kinds of spores: - Megasporangia on modified leaves called megasporophylls produce megaspores that give rise to female gametophytes - Produces 1 megaspore - Microsporangia on modified leaves called microsporophylls produce microspores that give rise to male gametophytes. - Produces many microspore The miniaturisation of seed plant gametophytes likely contributed to the great success of this clade. Ovules and Production of Eggs A layer of sporophyte tissue called an integument envelops and protects the megasporangium. Gymnosperm Megasporangium - 1 integument Angiosperm Megasporangium - 2 integument The whole structure—megasporangium, megaspore, and their integument(s)—is called an ovule. Inside each ovule a female gameto- phyte develops from a megaspore and produces one or more eggs. Pollen and Production of Sperm A microspore develops into a pollen grain that consists of a male gametophyte enclosed within the pollen wall. The outer layer of the pollen cell wall -> is composed of molecules secreted by sporophyte cells - Male gametophyte is considered to be in the pollen grain The tough pollen wall contains sporopollenin, protects a pollen grain as it is transported If a pollen grain germinates (begins growing), it gives rise to a pollen tube that discharges sperm into the female gameto- phyte within the ovule. In nonvascular plants and seedless vascular plants such ferns, free-living gametophytes release flagellated sperm that swim through a film of water to reach eggs. Seed plants a sperm-producing male gametophyte inside a pollen grain can be carried long distances, eliminating the dependence on water for sperm transport. - contributed to the colonisation of land. The evolutionary advantage of seeds If a sperm fertilizes an egg of a seed plant, the zygote grows into a sporophyte embryo. Until the advent of seeds, the spore was the only protective stage in any plant life cycle Although mosses and other seedless plants continue to be very successful today, seeds represent a major evolutionary innovation that contributed to the opening of new ways of life for seed plants. What advantages do seeds provide over spores?  Seed Spore Multicellular, embryo protected by a layer of Usually single celled tissue, the seed coat. Can remain dormant for a very long amount Shorter lifespans of time Has stored food supply Does not have stored food When conditions are met, seed will germinate Evolution of the Seed Fossils from that time reveal that some plants acquired features that are also present in seed plants, such as megaspores and microspores 30.2 Gymnosperms bear “naked” seeds, typically on cones. Extant seed plants form two sister clades: gymno- sperms and angiosperms. - Gymnosperms - “naked” seeds exposed on sporophylls in cones -> “Cone-Bearing” (Conifers) - Angiosperms - seeds enclosed in chambers that form fruits The Life Cycle of a Pine Seed Plant Evolution has 3 reproductive adaptations (these are not all) - Increased sporophyte dominance - The advent of the seed as a resistant dispersible stage - appearance of pollen as an airborne agent that brings gametes together The pine tree is the sporophyte; its sporangia are located on scalelike structures packed densely in cones. All seed plants are heterosporous - Produce diff types of spores Pollen cones have a relatively simple structure: - Their scales are modified leaves (microsporophylls) that bear microsporangia. - Within each microsporangium, cells called microsporocytes undergo meiosis, producing haploid micro- spores. Each microspore develops into a pollen grain Ovulate cones are more complex: - Their scales are compound structures composed of both modified leaves (megasporophylls bearing megasporangia) and modified stem tissue.  - In each megasporangium, megasporocytes undergo meiosis and produce haploid megaspores inside the ovule. Surviving megaspores develop into female gametophytes, which are retained within the sporangia. For many While these seed structures are quite different from the berries of angiosperms, they ulti- mately have the same function; to attract animals for seed dispersal. Evolution of Gymnosperms They have the key terrestrial adaptations found in all seed plants, such as seeds and pollen. In addition, some gym- nosperms were particularly well suited to arid conditions because of the thick cuticles and relatively small surface areas of their needle-shaped leaves. Gymnosperm Diversity Of the 10 plant phyla (see Table 29.1), four are gym- nosperms: Cycadophyta, Ginkgophyta, Gnetophyta, and Coniferophyta. It is uncertain how the four phyla of gym- nosperms are related to each other. 30.3 The reproductive adaptations of angiosperms include flowers and fruits Angiosperms - “flowering plants” Characteristics of Angiosperms Flowers - a unique angiosperm structure specialized for sexual reproduction. - Insects or other animals transfer pollen from one flower to the sex organs on another flower - some angiosperms are wind-pollinated, particularly those species that occur in dense populations - Contain 4 specialized leaves  - Sepals - green and enclose the flower before it opens - Petals - brightly coloured in most flowers and aid in attracting pollinators. - Stamens and carpels are sporophylls, modified leaves that are spe- cialized for reproduction. - Stamens - are microsporophylls: They produce microspores that develop into pollen grains containing male gametophytes. - Contain - Filament - Terminal sac - Anter - Where the pollen is produced - Carpels - megasporophylls: They produce megaspores that give rise to female gametophytes. - Contain (the 3 structures make up the Pistil) - Stigma - Receives pollen - Style - Ovary - Contains 1 or more ovules -> will develop into a seed when fertilized Fruits As seeds develop from ovules after fertilization, the ovary wall thickens and the ovary matures into a fruit. Fruits protect seeds and aid in their dispersal Mature fruits - Fleshy - Dry - Aid in seed dispersal The angiosperm life cycle 1) The flower of the sporophyte produces microspores that form male gametophytes and megaspores that form female game- tophytes. - Each male gametophyte has two haploid cells: a generative cell that divides, forming two sperm, and a tube cell that produces a pollen tube. - Each ovule, which develops in the ovary, con- tains a female gametophyte, also known as an embryo sac 2) Pollen is carried to the sticky stigma at the tip of a carpel 3) The pollen grain adheres to the stigma of a carpel.  4) The tube cell produces a pollen tube that grows down within the style of the carpel. After reaching the ovary, the pollen tube penetrates through the micropyle, a pore in the integuments(tough protective outer layer) of the ovule, and discharges two sperm cells into the female gametophyte. 5) One sperm fertilises the egg, forming a diploid zygote. 6) The other sperm fuses with the two nuclei in the large central cell of the female gametophyte, producing a triploid cell. 7) This type of double fertilisation, in which one fertilisation event produces a zygote and the other produces a triploid cell, is unique to angiosperms. 8) The ovule matures into a seed. The zygote develops into a sporophyte embryo with a rudi- mentary root and one or two seed leaves called cotyledons (an embryonic leaf in seed-bearing plants, one or more of which are the first leaves to appear from a germinating seed) Function of double fertilisation - Synchronises the development of food storage in the seed with the development of the embryo. Summary The seed consists of the embryo, the endosperm, and a seed coat derived from the integuments. An ovary develops into a fruit as its ovules become seeds. After being dispersed, a seed may germinate if environ mental conditions are favourable. The coat ruptures and the embryo emerges as a seedling, using food stored in the endosperm and cotyledons until it can produce its own food by photosynthesis. Angiosperm evolution We don't know, literally the textbook says “we dont know” idk what else to tell you Angiosperm Phylogeny Living gymnosperms are a monophyletic group (most recent ancestor AND all descendants) Evolutionary Links Between Angiosperms and Animals Plants and animals have interacted for hundreds of millions of years, and those interactions have led to evolutionary change. Ex: pollinator-plant interactions Angiosperm Diversity Divided flowering plants into two groups, based partly on the number of cotyledons, or seed leaves, in the embryo. Species with one cotyledon were called monocots, and those with two were called dicots. Other features, such as flower and leaf structure, were also used to define the two groups. Recent DNA studies, however, indicate that the species traditionally called dicots are paraphyletic. Eudicots - “true dicots” 30.4 Plants are important for humans, thats it 30.5 Threats to Plant Diversity Although plants may be a renewable resource, plant diversity is not. The exploding human population and its demand for space and resources are extinguishing plant species at a high rate. The loss of plant species is often accompanied by the loss of insects and other rainforest animals. Chapter 31 - Fungi Fungi are a huge and important component of the biosphere. Fungi are not only diverse and widespread but also essen- tial for the well-being of most ecosystems. They break down or- ganic material and recycle nutrients, allowing other organisms to assimilate essential chemical elements. 31.1 Fungi are heterotrophs that feed by absorption Despite their vast diversity, all fungi share some key traits, most importantly the way they derive nutrition. In addition, many fungi grow by forming multicellular filaments, a body structure that plays an important role in how they obtain food. Nutrition and Ecology Like animals, fungi are heterotrophs: They cannot make their own food as plants and algae can. Fungi do not ingest (eat) their food. Instead, a fungus absorbs nutrients from the environment outside of its body. Accomplish this task by secreting powerful hydrolytic enzymes into their surroundings. These enzymes break down complex molecules to smaller organic compounds that the fungi can absorb into their bodies and use. Other fungi use enzymes to penetrate the walls of cells, enabling the fungi to absorb nutrients from the cells. - Fungi that are decomposers break down and absorb nutrients from nonliving organic material - Some parasitic fungi are pathogenic, including many species that cause diseases in plants. - Mutualistic fungi also absorb nutrients from a host organism, but they reciprocate with actions that benefit the host Body Structure The most common fungal body structures are multicellular filaments and single cells (yeasts). Many species can grow as both filaments and yeasts, but even more grow only as filaments; relatively few species grow only as single-celled yeasts. The morphology of multicellular fungi enhances their ability to grow into and absorb nutrients from their surroundings. The bodies of these fungi typically form a network of tiny filaments called hyphae. Hyphae consist of tubular cell walls surrounding the plasma membrane and cytoplasm of the cells H are divided into cells by cross-walls, or septa.  - Septa generally have pores large enough to allow ribosomes, mitochondria, and even nuclei to flow from cell to cell. Some fungi lack septa. Known as coenocytic fungi Specialised Hyphae in Mycorrhizal Fungi Some fungi have specialised hyphae that allow them to feed on living animals. Other fungal species have specialised hyphae called haustoria that enable them to extract nutrients from plants Some fungi that have specialised branch- ing hyphae such as arbuscules that they use to exchange nutrients with their plant hosts. Such mutually beneficial relationships between fungi and plant roots are called mycorrhizae (mutualism) - Mycorrhizal fungi (fungi that form mycorrhizae) can improve delivery of minerals to plants because the vast mycelial networks of the fungi are more efficient than the plants roots at acquiring these minerals. - The plants supply the fungi with organic nutrients such as carbohydrates. There are two main types of mycorrhizal fungi. - Ectomy­corrhizal fungi form sheaths of hyphae over the surface of a root and typically grow into the extracellular spaces of the root cortex - Arbuscular mycorrhizal fungi extend branching hyphae through the root cell wall and into tubes formed by invagination (pushing inward) of the root cell plasma membrane 31.2 Fungi produce spores through sexual or asexual life cycles Most fungi propagate themselves by producing vast numbers of spores, either sexually or asexually. Spores can be carried long distances by wind or water. If they land in a moist place where there is food, they germinate, producing new mycelia. Sexual Reproduction The nuclei of fungal hyphae and the spores of most fungal species are haploid. In fungi, sexual reproduction often begins when hyphae from two mycelia release sexual signalling molecules called pheromones. If the mycelia are of different mating types, the pheromones from each partner bind to receptors on the other, and the hyphae extend toward the source of the pheromones. When the hyphae meet, they fuse. The union of the cytoplasms of two parent mycelia is known as plasmogamy Parts of the fused mycelium contain coexisting, genetically different nuclei. Such a mycelium is said to be a heterokaryon In some species, the haploid nuclei pair off two to a cell, one from each parent. Such a mycelium is dikaryotic After a period of time During karyogamy, the haploid nuclei contributed by the two parents fuse, producing diploid cells. - Zygotes and other transient structures form Asexual Reproduction Many fungi reproduce asexually by growing as filamentous fungi that pro- duce (haploid) spores by mitosis; such species are informally called moulds if they form visible mycelia. - Other fungi reproduce asexually by growing as single-celled yeasts 31.3 The ancestor of fungi was an aquatic, single-celled, flagellated protist The Origin of Fungi Phylogenetic analyses suggest that fungi evolved from a flagellated ancestor. - DNA sequence data indicate that these three groups of eukaryotes—the fungi, the animals, and their protistan relatives—form a monophyletic group - Members of this clade are called opisthokonts, a name that refers to the posterior location of the flagellum in these organisms. DNA sequence data also indicate that fungi are more closely related to several groups of single-celled protists than they are to animals, suggesting that the ancestor of fungi was unicellular. Together, these results suggest that multicellularity evolved in animals and fungi indepen- dently, from different single-celled ancestors. (This was asked in Midterm 2) Basal Fungal Groups Insights into the nature of basal fungal groups have begun to emerge from recent genomic studies. The Move to Land Fungi may well have colonized land before plants did so. Life on land before the arrival of plants as a “green slime” that consisted of cyanobacteria, algae, and a variety of small, heterotrophic species, including fungi. With their capacity for extracellular digestion, fungi would have been well suited for feeding on other early terrestrial organisms Once on land, some fungi formed symbiotic associations with early land plants (mycorrhizal associations) 31.5 Fungi as Decomposers (Saprotrophs) Fungi are well adapted as decomposers of organic material, including the cellulose and lignin of plant cell walls. As a result, fungi and bacteria are primarily responsible for keeping ecosystems stocked with the inorganic nutrients essential for plant growth Fungi as Mutualists Fungi may form mutualistic relationships with plants, algae, cyanobacteria, and animals. Mutualistic fungi absorb nutri- ents from a host organism, but they reciprocate with actions that benefit the host (ex: mycorrhizal associations) - Fungus-Plant Mutualisms - All plants in their natural ecosystem seem to harbour fungal endophytes (but keep in mind that bacteria can be endo- phytes as well). These symbiotic fungi live entirely within the tissue (leaves, stems, flowers, and so on), often living in the space between the cells, without causing noticeable harm. - (see SA #2 of Midterm 2) - Fungus-Animal Mutualisms - As mentioned earlier, some fungi share their digestive services with animals, helping break down plant material in the guts of cattle and other grazing mammals. Many species of ants take advantage of the digestive power of fungi by raising them in “farms.” - Lichens - A lichen is a symbiotic association between a photosynthetic microorganism and a fungus in which millions of photo- synthetic cells are held in a mass of fungal hyphae. Lichens grow on the surfaces of rocks, rotting logs, trees, and roofs in various forms.  - Fungi as Parasites - Like mutualistic fungi, parasitic fungi absorb nutrients from the cells of liv- ing hosts, but they provide no benefit in - Although animals are less susceptible to parasitic fungi than are plants, about 500 fungi are known to parasitize ani- mals. - The general term for an infection caused by a fungal parasite is mycosis. In humans, skin mycoses include the disease ring- worm, so named because it appears as circular red areas on the skin. The ascomycetes that cause ringworm can infect almost any skin surface. Practical Uses of Fungi The dangers posed by fungi should not overshadow their immense benefits. We depend on their ecological services as decomposers and recyclers of organic matter. And without mycorrhizae, farming would be far less productive. - Consumable - Ripen cheese - Produce alcohol - Bread - Many fungi have great medical value as well. (penicillin) Chapter 32 - An overview of Animal Diversity 32.1 Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers - Listing features shared by all animals is challenging, as there are exceptions to nearly every criterion we might select. Nutritional Mode Animals differ from both plants and fungi in their mode of nutrition. - Plants are autotrophic eukaryotes capable of generating organic molecules through photosynthesis. - Fungi are heterotrophs that grow on or near their food and that feed by absorption. - Unlike plants, animals cannot construct all of their own organic molecules and so, in most cases, they ingest them—either by eating other living organisms or by eating nonliving organic material. Cell Structure and Specialization Animals are eukaryotes, and like plants and most fungi, animals are multicellular. - a variety of proteins external to the cell membrane provide structural support to animal cells and connect them to one another (collagen) - The cells of most animals are organized into tissues, groups of similar cells that act as a functional unit Reproduction and Development - Most animals reproduce sexually, and the diploid stage usually dominates the life cycle. - The haploid stage is composed of gametes (eggs and sperm) that are produced directly by meiotic division by the diploid stage. - The cells of the haploid stage do not undergo further cell division, unlike what occurs in plants and fungi. In most animal species, a small, flagellated sperm fertilizes a larger, nonmotile egg, forming a diploid zygote  - During the development of most animals, cleavage leads to the formation of a multicellular stage called a blastula, which in many animals takes the form of a hollow ball - After the blastula stage is the process of gastrulation, during which the layers of embryonic tissues that will develop into adult body parts are produced. The resulting developmental stage is called a gastrula. 32.3 A body plan is a particular set of morphological and developmental traits integrated into a functional whole—the living animal. Symmetry A basic feature of animal bodies is their type of symmetry—or absence of symmetry. - Radial - Bilateral - Has 2 axis of orientation: - Dorsal(top) - Ventral(bottom) - Left - Right - Anterior(front) - Posterior(back) - Cephalization - Central nervous system in the “head region” Tissues Animal body plans also vary with regard to tissue organiza- tion. Recall that tissues are collections of specialized cells that act as a functional unit. - Sponges lack true tissue - In all other animals, the embryo becomes layered through the process of gastrulation. As development progresses, these layers, called germ layers, form the various tissues and organs of the body - Ectoderm, the germ layer covering the surface of the embryo, gives rise to the outer covering of the animal and, in some phyla, to the central ner- vous system. - Endoderm, the innermost germ layer, lines the pouch that forms during gastrulation (the archenteron) and gives rise to the lining of the digestive tract (or cavity) and organs such as the liver and lungs of vertebrates. Two germ layers - Diploblastic, ex: cnidarians All bilateral animals have a third germ layer, called the mesoderm, which fills much of the space between the ecto- derm and endoderm. Bilateral symmetry -> triploblastic (having three germ layers). - The mesoderm forms the muscles and most other organs between the digestive tract and the outer covering of the animal. Body Cavities Nearly all animals have body cavities, which are fluid-filled spaces located between different tissue layers. Functions include - Structural Support - Formation of inner transport system - Allows efficient gas exchange - Removal of waste Larger animals have a coelom a body cavity between the digestive track (derived from the endoderm) and the outer body wall (derived from the outer body wall). - Coelom - derived from mesoderm - Functions vary from animal to animal Protostome and Deuterostome Development Based on certain aspects of early development, many animals can be described as having one of two developmental modes: protostome development or deuterostome development. Distinguished by differences in - Cleavage - coelom formation - fate of the blastopore. Cleavage Many animals with protostome development undergo spiral cleavage, in which the planes of cell division are diagonal to the vertical axis of the embryo; as seen in the eight-cell stage of the embryo, smaller cells are centered over the grooves between larger, underlying cells - Determinate cleavage of some animals with protostome development rigidly casts (“determines”) the devel- opmental fate of each embryonic cell very early. - EXAMPLE: A cell isolated from a snail at the four-cell stage, for example, cannot develop into a whole animal. Instead, after repeated divisions, such a cell will form an inviable embryo that lacks many parts. Deuterostome development is predominantly characterized by radial cleavage. - Most animals with deuterostome development also have indeterminate cleavage, meaning that each cell produced by early cleavage divisions retains the capacity to develop into a complete embryo. - For example, if the cells of a sea urchin embryo are separated at the four-cell stage, each can form a complete larva. Similarly, it is the indeterminate cleavage of the human zygote that makes identical twins possible. Fate of the blastopore - In deuterostome development, the mouth is derived from the secondary opening, and the blastopore usu- ally forms the anus. - In protostome development, the mouth gener- ally develops from the first opening, the blastopore 32.4 Views of animal phylogeny continue to be shaped by new molecular and morphological data As animals with diverse body plans radiated during the early Cambrian period, some lineages arose, thrived for a period of time, and then became extinct, leaving no descendants. The Diversification of Animals Zoologists currently recognize about three dozen phyla of extant animals. Researchers infer evolutionary relationships among these phyla by analyzing: - whole genomes - morphological traits - ribosomal RNA (rRNA) genes - Hox genes - protein-coding nuclear genes - mitochondrial genes. 1. All animals share a common ancestor. - Current evidence indicates that animals are monophyletic, in the clade Metazoa. 2. Sponges are basal animals. - Among the extant taxa, sponges (phylum Porifera) branch from the base of the animal tree. Recent morphological and molecular analyses indicate that sponges are monophyletic 3. Eumetazoa is a clade of animals with true tissues. - All animals except for sponges and a few others belong to a clade of eumetazoans (“true animals”). True tissues evolved in the common ancestor of living eumetazoans. 4. Most animal phyla belong to the clade Bilateria. - Bilateral symmetry and the presence of three germ layers are shared derived characters that help define the clade Bilateria. Hemichor- dates (acorn worms), echinoderms (sea stars and relatives), and chordates are members of the bilaterian clade Deuterostomia; thus, the term deuterostome refers not only to a mode of animal development, but also to the members of this clade. Bilaterians also diversified in two major clades that are composed entirely of invertebrates - Ecdysozoa refers to a characteristic shared by nematodes, arthropods, and some of the other ecdysozoan phyla - These animals secrete external skeletons (exoskeletons). - As the animal grows,it molts, squirming out of its old exoskeleton and secret- ing a larger one - Lophotrochozoa refers to two different features observed in some animals belonging to this clade. - Some such as ectoprocts, develop a lophophore (crown of ciliated tenta- cles that function in feeding) - Others go through the developmental stage called trochophore larva Chapter 33 - An Introduction to Vertebrates THERE ARE A LOT OF PICTURES I'M SO SORRY 33.1 Sponges are basal animals that lack true tissues - Animals in the phylum Porifera are known informally as sponges. - Sponges are suspension feeders: They capture food particles suspended in the water that passes through their body, which in some species resembles a sac perforated with pores. - Water is drawn through the pores into a central cavity, the spongocoel, and then flows out of the sponge through a larger opening called the osculum - lining the interior of the spongocoel are flagellated choanocytes, or collar cells. These cells engulf bacteria and other food particles by phagocytosis. - Gas exchange and waste removal done via diffusion in water - The body of a sponge consists of two layers of cells sepa- rated by a gelatinous region called the mesohyl. - Most sponges are hermaphrodites, meaning that each individual functions as both male and female in sexual reproduction by producing sperm and eggs. 33.2 Cnidarians are an ancient phylum of eumetazoans All animals except sponges and a few other groups belong to the clade Eumetazoa, animals with true tissues. - Yet most cnidarians still exhibit the relatively simple, diploblastic, radial body plan that existed in early members of the group. - The basic body plan of a cnidarian is a sac with a central digestive compartment, the gastrovascular cavity. A single opening to this cavity functions as both mouth and anus There are two variations on this body plan - The sessile polyp and the motile medusa - Polyps are cylindrical forms that adhere to the substrate by the aboral end of their body (the end opposite the mouth) and extend their tentacles, waiting for prey. - A medusa (plural, medusae) resem- bles a flattened, mouth-down version of the polyp. It moves freely in the water. Cnidarians are predators that often use tentacles arranged in a ring around their mouth to capture prey and push the food into their gastrovascular cavity, where digestion begins. Enzymes are secreted into the cavity, thus breaking down the prey. The tentacles are armed with batteries of cnidocytes, cells unique to cnidarians that function in defense and prey capture Contractile tissues and nerves occur in their simplest forms in cnidarians. Cnidarians have no brain, and the noncentralized nerve net is associated with sensory structures that are distributed around the body. (Think like a poisoned harpoon gun) Medusozoans All cnidarians that produce a medusa are members of clade Medusozoa Anthozoans Sea anemones and corals belong to the clade Anthozoa. These cnidarians occur only as polyps. 33.3 ( I speedran this section. Theres too much info, read the Labs, they do a much better job) Lophotrochozoans, a clade identified by molecular data, have the widest range of animal body forms The vast majority of animal species belong to the clade Bilateria, whose members exhibit bilateral symmetry and triploblastic development. Flatworms Parasitic species - Trematodes - Tapeworms - Rotifers Acanthocephalans Acanthocephalans (1100 species) are sexually reproducing parasites of vertebrates that lack a complete digestive tract and usually are less than 20 cm long. All are parasites Lophophorates: Ectoprocts and Brachiopods Bilaterians in the phyla Ectoprocta and Brachiopoda are among those known as lophophorates. Ectoprocts are colonial animals that superficially resemble clumps of moss. - In most species, the colony is encased in a hard exoskeleton (external skeleton) studded with pores. - Most ectoproct species live in the sea, where they are among the most widespread and numerous sessile animals. Several species are important reef builders. Brachiopods, or lamp shells, superficially resemble clams and other hinge-shelled molluscs, but the two halves of the brachiopod shell are dorsal and ventral rather than lateral, as in clams. - All brachiopods are marine. Most live attached to the seafloor by a stalk, opening their shell slightly to allow water to flow through the lophophore. Molluscs Snails and slugs, oysters and clams, and octopuses and squids are all molluscs (phylum Mollusca) Have 3 main bodyparts - Muscular foot - Visceral mass containing all the organs - Mantle - A fold of tissue that drapes over the visceral mass and makes a shell Chitons Chitons have an oval-shaped body and a shell composed of eight dorsal plates (Figure 33.17). The chiton’s body itself, however, is unsegmented. Gastropods About three-quarters of all living species of molluscs are gastropods. - Most gastropods are marine. - Still other gastropods have adapted to life on land, where snails and slugs thrive in habi tats ranging from deserts to rain forests. Bivalves - The molluscs of the clade Bivalvia are all aquatic and include many species of clams, oysters, mussels, and scallops. - Bivalves have a shell divided into two halves. - The halves are hinged, and powerful adductor muscles draw them tightly together to protect the animal’s soft body. - Bivalves have no distinct head, and the radula has been lost. Cephalopods - Cephalopods are active marine predators. They use their tentacles to grasp prey, which they then bite with beak-like jaws and immobilize with a toxin present in their saliva. - Cephalopods are the only molluscs with a closed circulatory system, in which the blood remains separate from fluid in the body cavity. - They also have well-developed sense organs and a complex brain. - The ability to learn and behave in a complex manner is probably more critical to fast-moving predators than to sedentary animals such as clams. Annelids - Annelida means “little rings,” referring to the annelid body’s resemblance to a series of fused rings. - Annelids are segmented worms that live in the sea, in most freshwater habitats, and in damp soil. - Annelids range in length from less than 1 mm to more than 3 m. Errantians - As their name suggests, many errantians are mobile - Many are predators, while others are grazers that feed on large, multicellular algae - In many errantians, each body segment has a pair of promi- nent paddle-like or ridge-like structures called parapodia (“beside feet”) that function in locomotion - Sedentarians Species in the other major clade of annelids, Sedentaria (from the Latin sedere, sit), tend to be less mobile than those in Errantia. (literally that's it, they made an entire taxon on lazy annelids) Leeches Some leeches are parasites that suck blood by attaching temporarily to other animals, including humans, but most are predators that feed on other invertebrates. Earthworms Earthworms eat their way through the soil, extracting nutrients as the soil passes through the alimentary canal. Undigested material, mixed with mucus secreted into the canal, is eliminated as fecal castings through the anus. Farmers value earthworms because the animals till and aerate the earth, and their castings improve the texture of the soil. 33.4 Ecdysozoans are the most species-rich animal group Nematodes Among the most ubiquitous of animals, nematodes, or roundworms, are found in most aquatic habitats, in the soil, in the moist tissues of plants, and in the body fluids and tissues of animals. In contrast to annelids, nematodes do not have segmented bodies. - A nematode’s body is covered by a tough cuticle - Lack a circulatory system - Nutrients carried via fluid in the hemocoel Arthropods - Arthropod Origins - General Characteristics (open circulatory) Chelicerates Myriapods Pancrustaceans Crustaceans Insects Chapter 34 - The Origin and Evolution of Vertebrates 34.1 Chordates have a notochord and a dorsal, hollow nerve cord - Vertebrates are members of the phylum Chordata, the chordates. Chordates are bilaterian (bilaterally symmetrical) animals, and within Bilateria, they belong to the clade of animals known as Deuterostomia - There are two groups of invertebrate deuterostomes that are more closely related to vertebrates than they are to other invertebrates - Cephalochprdates - Urochordates Derived Characters of Chordates All chordates share a set of derived characters, though many species possess some of these traits only during embryonic illustrates four key characters of chordates: a notochord; a dorsal, hollow nerve cord; pharyngeal slits or clefts; and a muscular, post-anal tail. Notochord Chordates are named for a skeletal structure, the notochord, present in all chordate embryos as well as in some adult chor- dates. The notochord is a longitudinal, flexible rod located between the digestive tube and the nerve cord. It is composed of large, fluid-filled cells encased in fairly stiff, fibrous tissue. The notochord provides skeletal support throughout most of the length of a chordate, and in larvae or adults that retain it, it also provides a firm but flexible structure against which mus- cles can work during swimming. Dorsal, Hollow Nerve Cord The nerve cord of a chordate embryo develops from a plate of ectoderm that rolls into a tube located dorsal to the notochord. The resulting dorsal, hollow nerve cord is unique to chordates. Pharyngeal Slits or Clefts The digestive tube of chordates extends from the mouth to the anus. The region just posterior to the mouth is the pharynx. In all chordate embryos, a series of arches separate by grooves forms along the sides of the pharynx. In most chordates, these grooves (known as pharyngeal clefts) develop into slits that open to the outside of the body. These pharyngeal slits allow water entering the mouth to exit the body without passing through the entire digestive tract. Muscular, Post-Anal Tail Chordates have a tail that extends posterior to the anus, although in many species it is greatly reduced during embrytFonic development. In contrast, most non chordates have a digestive tract. The chordate tail contains skeletal elements and mus- cles, and it helps propel many aquatic species in the water. Lancelets The most basal (earliest- diverging) group of living chordates are animals called lancelets (Cephalochordata), which get their name from their bladelike shape. As larvae, lancelets develop a notochord, a dorsal, hol- low nerve cord, numerous pharyngeal slits, and a post-anal tail. Tunicates Recent molecular studies in- dicate that the tunicates (Urochordata) are more closely related to other chordates than are lancelets. The chordate characters of tunicates are most apparent during their larval stage, which may be as brief as a few minutes. Once a tunicate has settled on a substrate, it undergoes a radical metamorphosis in which many of its chordate characters disappear. Its tail and notochord are resorbed; its nervous system degenerates; and its remaining organs rotate 90°. As an adult, a tunicate draws in water through an incurrent siphon; the water then passes through the pharyngeal slits into a chamber called the atrium and exits through an excurrent siphon Early Chordate Evolution Although lancelets and tunicates are relatively obscure animals, they occupy key positions in the history of life and can provide clues about the evolutionary origin of vertebrates Research on lancelets has also revealed important clues about the evolution of the chordate brain. Rather than a full- fledged brain, lancelets have only a slightly swollen tip on the anterior end of their dorsal nerve cord. As for tunicates, several of their genomes have been com- pletely sequenced and can be used to identify genes likely to have been present in early chordates. Researchers have suggested that ancestral chordates had genes associated with vertebrate organs such as the heart and thyroid gland. These genes are found in tunicates and vertebrates but are absent from nonchordate invertebrates. 34.2 Vertebrates are chordates that have a backbone During the Cambrian period, half a billion years ago, a lineage of chordates gave rise to vertebrates. With a skeletal system and a more complex nervous system than that of their ancestors, vertebrates became more efficient at two essential tasks: capturing food and avoiding being eaten. Derived Characters of Vertebrates Living vertebrates share a set of derived characters that distin- guish them from other chordates. In the majority of vertebrates, however, the vertebrae enclose the spinal cord and have taken over the mechanical roles of the notochord. Another feature unique to vertebrates is the neural crest, a collection of cells that appears along the edges of the clos- ing neural tube of an embryo Hagfishes and Lampreys The hagfishes (Myxini) and the lampreys (Petromyzontida) are the only lineages of living verte- brates whose members lack jaws. Unlike most verte- brates, lampreys and hag- fishes also do not have a backbone. Hagfishes The hagfishes are jawless vertebrates that have highly reduced vertebrae and a skull that is made of cartilage. Lampreys The second group of living jawless vertebrates, the lampreys, consists of about 38 species inhabiting various marine and freshwater environments. Most are parasites that feed by clamping their round, jawless mouth onto the flank of a live fish, their “host.” They then use their rasping tongue to penetrate the skin of the fish and ingest the fish’s blood and other tissues. 34.3 Gnathostomes are vertebrates that have jaws Hagfish and lampreys are survivors from the early Paleozoic era, when jawless vertebrates were common. Since then, jawless vertebrates have been far outnumbered by jawed vertebrates, known as gnathostomes. Derived Characters of Gnathostomes Gnathostomes (“jaw mouth”) are named for their jaws, hinged structures that, especially with the help of teeth, enable gnathostomes to grip food items firmly and slice them. According to one hypothesis, gnathostome jaws evolved by modification of the skeletal rods that had previously supported the anterior pharyngeal (gill) slits. The common ancestors of all gnathostomes underwent an additional duplication of Hox genes, such that the single set present in early chordates became four. The gnathostome forebrain is enlarged compared to that of other vertebrates, mainly in association with enhanced senses of smell and vision. Another characteristic of aquatic gnathostomes is the lateral line system, a row of organs along each side of the body that are sensitive to vibrations in the surrounding water. Chondrichthyans (Sharks, Rays, and Their Relatives) Sharks, rays, and their relatives include some of the biggest and most successful vertebrate pred- ators in the oceans. They belong to the clade Chondrichthyes, which means “cartilage fish.” As their name indicates, the chondrichthyans have a skeleton composed predominantly of cartilage. Ray-Finned Fishes and Lobe-Fins The vast majority of verte- brates belong to the clade of gnathostomes called Osteichthyes. Unlike chondrichthyans, nearly all living osteichthyans have an ossified (bony) endoskeleton with a hard matrix of calcium phosphate. Like many other taxonomic names, the name Osteichthyes (“bony fish”) was coined long before the advent of phylogenetic systematics. Include tetra- pods along with bony fishes in the clade Osteichthyes. (its just fish) Ray-Finned Fishes Nearly all the aquatic osteichthyans familiar to us are among the over 27 000 species of ray-finned fishes. Lobe-Fins Like the ray-finned fishes, the other major lineage of osteich- thyans, the lobe-fins (Sarcopterygii). The key derived character of lobe-fins is the presence of rod-shaped bones surrounded by a thick layer of muscle in their pectoral and pelvic fins. 34.4 Tetrapods are gnathostomes that have limbs One of the most significant events in vertebrate history was when the fins of some lobe-fins evolved into the limbs and feet of tetrapods. Until then, all vertebrates had shared the same basic fishlike anatomy. After tetrapods moved onto land, they took on many new forms, from leaping frogs to flying eagles to bipedal humans. Derived Characters of Tetrapods - 4 feet - In tetrapods, the head is separated from the body by a neck that originally had one vertebra on which the skull could move up and down. - Later, the head could also swing from side to side. - The bones of the pelvic girdle, to which the hind legs are attached, are fused to the backbone, permitting forces generated by the hind legs against the ground to be trans- ferred to the rest of the body. - Except for some fully aquatic species, the adults of living tetrapods do not have gills; during embryonic development, the pharyngeal clefts instead give rise to parts of the ears, certain glands, and other structures. The Origin of Tetrapods Those that entered particularly shallow, oxygen-poor water could use their lungs to breathe air. Some species probably used their stout fins to help them move across logs or the muddy bottom (moving their fins in an alternating gait, as do some living lobe-fins). Thus, the tetrapod body was simply a modification of a preexisting body plan. The discovery of a fossil called Tiktaalik in northern Canada has provided new details on how this process of modification occurred. Like a fish, this species had fins, gills, and lungs, and its body was covered in scales, but it had a full set of ribs that assisted it in breathing air. It also had neck, shoulders, and a limb structure reminiscent of modem mammals Amphibians For the love of god please tell me you know what an amphibian is Salamanders Some are entirely aquatic, but others live on land as adults or throughout life. Most salamanders that live on land walk with a side-to-side bending of the body, a trait also found in early terrestrial tetrapods. Paedomorphosis, the retention of juvenile characteristics after maturation, is common among aquatic salamanders; the axolotl, for instance, retains larval features even when it is sexually mature. Frogs Frogs are better suited than salamanders for moving on land. Adult frogs use their powerful hind legs to hop along the terrain. Although often distinctive in appearance, the animals known as “toads” are simply frogs that have leathery skin or other adaptations for life on land. A frog nabs insects and other prey by flicking out its long, sticky tongue, which is attached to the front of the mouth. Frogs display a great variety of adaptations that help them avoid being eaten by larger predators. Their skin glands secrete distasteful or even poisonous mucus. Many poisonous species have bright colouration, which predators apparently associate with danger. Lifestyle and Ecology of Amphibians The term amphibian refers to the life stages of many frog species that live first in water and then on land. The larval stage of a frog, called a tadpole, is usually an aquatic herbivore with gills, a lateral line system resembling that of aquatic vertebrates, and a long, finned tail. The tadpole initially lacks legs; it swims by undulating its tail. During the metamorphosis that leads to the “second life,” the tadpole develops legs, lungs, a pair of external eardrums, and a digestive system adapted to a carnivorous diet. At the same time, the gills disappear; the lateral line system also disappears in most species. The young frog crawls onto shore and becomes a terrestrial hunter. In spite of their name, however, many amphibians do not live a dual—aquatic and terrestrial—life. There are some strictly aquatic or strictly terrestrial frogs, salamanders, and caecilians. Moreover, salamander and caecilian larvae look much like the adults, and typically both the larvae and the adults are carnivorous. One reason amphibians require relatively wet habitats is that they rely heavily on their moist skin for gas exchange—if their skin dries out, they cannot get enough oxygen. In addition, amphibians typically lay their eggs in water or in moist environments on land; their eggs lack a shell and dehydrate quickly in dry air. Amniotes are tetrapods that have a terrestrially adapted egg The amniotes are a group of tetrapods whose extant members are the reptiles (including birds) and mammals. During their evolution, amniotes acquired a number of new adaptations to life on land. Derived Characters of Amniotes - Amniotes use their rib cage to ventilate their lungs. This method is more efficient than throat-based ventilation, which amphibians use as a supplement to breathing through their skin. - Amniotic egg - Contains 4 specialized membranes - Amnion - Chorion - Yolk sac - Allantois The amniotic egg is named for the amnion, which encloses a compartment of fluid that bathes the embryo and acts as a hydraulic shock absorber. Membranes are for - Gas Exchange - Transfer of stored nutrients to the embryo - Waste storage The amniotic egg was a key evolutionary innovation for terrestrial life: It allowed the embryo to develop on land in its own private “pond,” hence reducing the dependence of tetrapods on an aqueous environment for reproduction. Early Amniotes It is not yet possible to say when the amniotic egg evolved, although it must have existed in the last common ancestor of living amniotes, which all have amniotic eggs. Based on where their fossils have been found, the earliest amniotes lived in warm, moist environments, as did the first tetrapods. Over time, early amniotes expanded into a wide range of new environments. Reptiles The reptile clade includes tuataras, lizards, snakes, turtles, crocodilians, and birds, along with a number of extinct groups, such as plesiosaurs and ichthyosaurs. As a group, the reptiles share several derived char- acters that distinguish. Fertilization must occur internally, before the eggshell is secreted. Reptiles such as lizards and snakes are sometimes described as “cold-blooded” because they do not use their metabolism extensively to control their body temperature. A more accurate description of these reptiles is to say that they are ectothermic, which means that they absorb external heat as their main source of body heat. Turtles Turtles are one of the most distinctive groups of reptiles alive today. For example, turtles do not have any holes in their skull behind the eye sockets, whereas other reptiles have two holes behind each eye socket. Recall that such skull holes are a key derived trait of the diapsids. Thus, until recently it was not clear whether turt