Biological Diversity 1010 Lecture Slides PDF

BIOL1010 Biology: Biological Diversity and Interactions Instructor: Dr. Elizabeth Hughes Location: 330 Allen Building Day and Time: Tuesday, Thursday 1:00 – 2:15 Introduction to Biology Textbook chapter: 1.1 – 1.10  What is Biology? Biology: Scientific study of...

BIOL1010 Biology: Biological Diversity and Interactions Instructor: Dr. Elizabeth Hughes Location: 330 Allen Building Day and Time: Tuesday, Thursday 1:00 – 2:15 Introduction to Biology Textbook chapter: 1.1 – 1.10  What is Biology? Biology: Scientific study of life What is life? Composed of cells Regulation of the internal environment Take in and use energy Respond to the environment Cells give rise to new cells Can be unicellular or multicellular  Nomenclature Nomenclature: The naming of organisms Binomial, italicized, scientific name Genus and specific epithet Example: Homo sapiens 1.8 million species named so far Estimate 10-100 million species exist Taxonomy Classify species based on evolutionary history and relationships Domain: Eukarya Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Carnivora Family: Ailuridae Genus: Ailurus Species: fulgens Domains of Life Prokaryotes Domain bacteria Domain archaea Small simple cells Eukaryotes Domain Eukarya Includes protists, plants, fungi, and animals Large complex cells  Hierarchy of Organization Emergent properties: Novel properties arise at each higher level What is Science? Science: An approach to understanding the natural world A search for information and explanations for natural phenomena Data: Recorded observations Qualitative and quantitative  The Scientific Method 1. Observation 2. Question 3. Hypothesis: Proposed explanation for a set of observations 4. Prediction: What can be done to test the hypothesis “If…then” comments 5. Experiment: Scientific test carried out under controlled conditions 6. Conclusions: Was the hypothesis supported or rejected? Scientific Theory Broad in scope and supported by a large body of evidence Example: The Theory of Evolution Explains many scientific observations Supported by an extremely large amount of evidence that uses the scientific method Has never been contradicted or disproven by any scientific data https://infograph.venngage.com/p/77697/new-report-title  Controlled Experiments Variables: Factors that vary Weight of a human infant in an experiment over their first 6 months of life Independent variable: The factor manipulated by the researchers Dependent variable Dependent variable: Weight (Kg) Measure used to judge the outcome of the experiment Is affected by the independent variable Controlled experiment: Age (months) Experimental group is Independent variable compared with a control group Controlled Experiment  Clinical Studies or Trials Tests done on humans Placebo: A treatment that does not contain the medication being tested Double-blind trial: Neither the subjects nor the scientists know who is in which group Observational Studies Retrospective study: Interviews, medical records, death certificates allow scientists to attempt to identify factors that led to a specific outcome Prospective study: Cohort of participants is enrolled and data is collected over a period of time The Process of Science  Science and Technology Science: Gain of knowledge to explain natural phenomenon Scientists make discoveries Technology: Application of scientific knowledge Engineers make inventions Science and technology are closely interwoven Drawbacks of Technology: Climate change, toxic wastes, deforestation, increasing rates of extinction Science is working to find answers Evolution as the Core Theme of Biology Diversity of Life: Differences between species Unity of life: Similarities between species Evolution: The process of change that has transformed life on Earth from its earliest forms to the vast array of organisms living today Darwin’s Theory of Evolution The history of life as documented by fossils and other evidence Mechanism of natural selection Descent with modification: species living today arose from a succession of ancestors that were different from them Darwin’s Observations and Inferences Observations: Individual variation: Individuals in a population vary in their traits, many of which are heritable Overproduction of offspring: All species can produce far more offspring than the environment can support resulting in competition for resources Inferences: Unequal reproductive success: Individuals with inherited traits best suited to the local environment are more likely to survive and reproduce than less well-suited individuals Accumulation of favourable traits over time: due to unequal reproductive success, a higher and higher proportion of individuals in the population will have the advantageous trait  Natural Selection Many small changes leads to major alterations of species and the evolution of new species Evidence from fossil record, experiments, observations of natural selection, and DNA comparisons The Tree of Life Each species represents a twig on a branch of the tree of life Extends back in time to ancestral species Artificial Selection Humans impact evolution through selective breeding of plants and animals Choose which organisms reproduce Advances in biotechnology Genetic engineering produces enhanced crops Drought tolerance, improved growth, increased nutrition  Unintentional Evolution Habitat loss and climate change causes the loss of species Use of antibiotics has caused the evolution of antibiotic-resistant bacteria Pesticide use has caused pesticide resistance in insects Understanding evolution lets us create vaccines and medical treatments, and develop strategies for conservation Topic 2: Evolution Textbook chapter 13.1 – 13.16 Science in the Age of Charles Darwin Aristotle: Species are fixed, permanent forms that do not evolve Judeo-Christian culture: each form of life was individually created in its present-day form Earth is 6000 years old Western world: All living species came into being relatively recently and are unchanging in form  Charles Darwin Five-year voyage on the HMS Beagle Survey ship charting the South American coast Collected fossils, and living plants and animals What makes an organism well suited to its environment? Observations of Geographic Proximity Geographic proximity is a better predictor of relationships among organisms than similarity of environment Galapagos Islands Most animals are found nowhere else in the world, but still resemble South American species Marine iguana resemble South American Land- dwelling iguanas Each island had its own distinct variety of giant tortoise Geological Changes Charles Lyell Principles of Geology Earth was sculpted over millions of years by gradual geologic processes that continue today Darwin witnessed an earthquake that raised the coastline of Chile almost a meter If the Earth is still changing, maybe organisms are too  Descent with Modification Present-day species are the descendants of ancient ancestors that they still resemble in some ways Differences accumulate over time Natural selection: Individuals with certain traits are more likely to survive and reproduce than are individuals who do not have those traits Adaptations: Modifications that fit species to specific ways of life in their environment Darwin’s Writings On the origin of species by means of natural selection Observations and experiments in biology, geology, and paleontology This is now a scientific theory Evolution: Genetic changes in a population from generation to generation  Fossils Imprints or remains of organisms that lived in the past Organic substances decay, hard parts remain Bones, teeth, shells Casts: Dead organism decays leaving an empty mold that fills with minerals dissolved in water Imprints: Footprints, burrows, coprolites Provide evidence of an organism’s behaviour Entire organisms: Encased in a medium that prevents decomposition Fossils Strata: Layers of rock Younger strata on top of older strata Paleontologist: Scientist who studies fossils Fossil record: The chronicle of evolution over millions of years of geologic time engraved in the order in which fossils appear in rock strata Incomplete Transitional Forms Fossils linking different groups of organisms Whales evolved from land- dwelling animals Cloven-hoofed mammal Amphibians evolved from fish Birds evolved from dinosaurs Mammals evolved from a reptilian ancestor  Homology Homology: Similarity resulting from common ancestry Characteristics are altered by natural selection as descendants face different environmental conditions Homologous structures: Variations on an anatomical structure that has been adapted to different functions Molecular Homology Molecular biology: Study of the molecular basis of genes and gene expression Homologous genes: Genes with closely matched sequences Must have been inherited from a relatively recent common ancestor  Darwin’s Boldest Hypothesis All life-forms are related Same genetic language (DNA, RNA) Genetic code Many homologous genes Similarities are seen early in development that are less evident in mature organisms Homology Vestigial structures: Remnants of features that served important functions in the organism’s ancestors Small pelvis and hind-leg bones of ancient whales Eye remnants in blind cave fish Pseudogenes: Genes that have lost their function even though homologous genes in related species are fully functional GLO enzyme for making vitamin C Evolutionary Trees and Homology  Artificial Selection Darwin studied natural selection by examining artificial selection Artificial selection: The selective breeding of domesticated plants and animals to promote the occurrence of desirable traits  Natural Selection Variation among individuals Heritability: The transmission of a trait from parent to offspring Production of more individuals than the limited resources can support leads to a struggle for existence Over time, many adaptations will accumulate Natural selection is adaptive evolution  Examples of Natural Selection Change in beak size of Galapagos finches Pesticide resistance in insects Antibiotic resistance in bacteria  Notes on Natural Selection Individuals do not evolve, populations evolve Only heritable traits can be amplified or diminished Evolution does not lead to perfectly adapted organisms Natural selection is an editing process, not a creative mechanism Natural selection is contingent on time and place  Genetic Variation Mutation produces new alleles Can be beneficial or detrimental Benefits are mostly seen when the environment is changing in a way that mutations that were once a disadvantage are now favourable Example: DDT resistance in houseflies A mutation makes houseflies resistant to DDT This mutation also reduces their growth rate Before DDT: A reduction in growth rate was detrimental to the flies Once DDT was introduced: the mutation was advantageous Natural selection increased the frequency of the mutation in the fly population Genetic Variation Chromosomal mutations (deletions, disruptions, rearrangements) are almost always harmful Duplications can be quite good Prokaryotes show effects of mutations much faster than eukaryotes Sexual reproduction produces high levels of genetic variation due to shuffling of alleles  Populations Population: A group of individuals of the same species that live in the same area and can potentially interbreed Members of a population are more closely related to each other than they are to members of a different population  Gene Pool Gene pool: All copies of every type of allele at every locus in all members of the population Microevolution: changes in allele frequency in a population Genotype frequency = Number of animals with the genotype/total number of animals Allele frequency = Number of alleles in a gene pool/total number of alleles  Hardy-Weinberg Equation Allows us to determine whether a population is evolving Hardy-Weinberg equilibrium: Allele frequencies in the gene pool remain constant Conditions for the Hardy-Weinberg Equilibrium Very large population No gene flow between populations No mutations Random mating No natural selection If evolution is occurring, allele and genotype frequencies will not match our calculations  Hardy-Weinberg Equation in Public Health Example: If 1 in 10,000 people suffer from the recessive disease phenylketonuria (PKU), how many people in the population are carriers for the allele? q2 = 1/10,000 = 0.0001 q = √(0.0001) = 0.01 p+q=1 p = 1 – q = 1 – 0.01 = 0.99 p2 + 2pq + q2 = 1 (Heterozygotes are carriers = 2pq) 2pq = 2 x 0.99 x 0.01 = 0.0198 1.98% of the population are carriers of the allele for phenylketonuria  Genetic Drift The frequency of alleles is more stable from one generation to the next when a population is large Genetic drift: Chance events cause allele frequencies to fluctuate unpredictably from one generation to the next Example: A small population of rabbits has brown fur (dominant allele) or white fur (recessive allele). By chance all the babies born in a litter have white fur. This means that pure chance has lowered the frequency of the brown allele and increased the frequency of the white allele. Genetic Drift - The Bottleneck Effect Catastrophes kill large numbers of individuals, leaving a small surviving population that is unlikely to have the same genetic makeup as the original population  Genetic Drift - The Founder Effect A few individuals colonize an island or other new habitat Unlikely that the genetic makeup of the colonists represents the gene pool of the larger population Example: The relatively high frequency of inherited disorders among some human populations established by small numbers of colonists 15 people colonized the islands of Tristan de Cunha One colonist carried the recessive allele for retinitis pigmentosa Now the frequency of this allele is 10 times higher in the population on those islands than in the British population they came from Gene Flow A population may gain or lose alleles when fertile individuals move into or out of a population or when gametes are transferred between populations Reduces differences between populations Relative Fitness Relative fitness: The contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals The fittest individuals are the ones that produce the largest number of viable fertile offspring “Survival of the fittest” Direct competition Indirect competition Natural Selection Directional selection: Acts against individuals at one phenotypic extreme Stabilizing selection: Favours intermediate phenotypes Disruptive selection: Favours individuals at both ends of a phenotypic range  Sexual Selection Sexual selection: Individuals with certain traits are more likely to obtain mates Sexual dimorphism: Differences in appearance between males and females of a species Size Colouration Adornments  Sexual Selection Intrasexual selection: Individuals compete directly with members of the same sex for mates Physical combat Ritualized displays Intersexual selection: Individuals of one sex are choosy in selecting their mates Most attractive are often the largest or the male with the most colourful adornments Topic 3: Speciation Textbook chapter 14.1 – 14.11 Speciation Speciation: The process by which one species splits into two or more species Explains the diversity and unity of life New species share many characteristics because they are descended from a common ancestor  Species How can we define a species? Sometimes it’s not obvious Similarity between two species Diversity within a species  The Biological Species Concept Species: A group of populations whose members have the potential to interbreed in nature and produce fertile offspring United by being reproductively compatible Drawbacks: Distinct species that are capable of interbreeding produces hybrids No way to know if ancient organisms were once able to interbreed Cannot use for classification of organisms that reproduce asexually Other Definitions of Species Morphological species concept: Classification based on physical traits such as shape, size, and other morphological features Advantage: Can be applied to asexual organisms and fossils and does not rely on breeding information Disadvantage: Very subjective, disagreements on which features are important enough to distinguish a species  Other Definitions of Species Ecological species concept: Identification based on ecological niches focusing on unique adaptations to particular roles in a biological community Phylogenetic species concept: The smallest group of individuals that share a common ancestor and form one branch on the tree of life Morphology, DNA sequences, biochemical pathways What amount of difference is required to establish separate species?  Reproductive Barriers Biological features of the organism that prevents individuals of different species from interbreeding successfully Prezygotic barriers: Prevent mating or fertilization between species Postzygotic barriers: Operate after hybrid zygotes have formed Prezygotic Barriers Postzygotic Barriers  Allopatric Speciation A population is divided into geographically isolated subpopulations Splinter populations follow their own evolutionary course Gene flow is blocked Some populations are more easily divided than others Geographic Isolation and Speciation Speciation occurs when reproductive barriers are established Different food sources Different pollinators Different predators Natural selection must work on pre-existing variations Example of Evolution of Reproductiv e Barriers Sympatric Speciation A new species arises withing the same geographic area as its parent species Polyploidy Habitat differentiation Sexual selection Polyploidy is particularly common in plants Animals are more likely to undergo habitat differentiation or sexual selection  Polyploidy Cells have more than two complete sets of chromosomes Sexual Selection Individuals with certain traits are more likely to obtain mates Example: African cichlids Habitat: rocky shores, muddy bottom, open water Feeding: algae-scrapers, snail- crushers, leaf-biters, insect-eaters, fish-hunters Sexual selection: divergent females prefer red or blue mates based on sensitivity of their vision Light becomes increasingly red with depth in the water column Red males are visible to red-sensitive vision but invisible to blue-sensitive vision Red breeds in deep water, blue breeds in shallow water (habitat differentiation) Adaptive Radiation Common in isolated island chains Far enough apart for isolated evolution but close enough for occasional dispersals Adaptive radiation: The evolution of many diverse species from a common ancestor A founder population evolves to its new environment, then a few individuals form a new founder population on a new island Eventual recolonization of the original island Coexistence with the original ancestral species Hybrid Zones Hybrid zones: Regions in which members of different species meet and mate, producing at least some hybrid offspring Outcomes of Hybrid Zones Reinforcement: Hybrid offspring are less fit than members of both parent species Barriers between species will be stronger where they overlap Example: Pied flycatchers and collared flycatchers have different colouration in sympatric areas compared to allopatric areas (affects sexual selection) Outcomes of Hybrid Zones Fusion: Speciation process reverses due to weak reproductive barriers Example: African cichlids Pollution has altered water clarity, changing how colours are perceived by females The behavioural barrier crumbles causing high amounts of interbreeding Outcomes of Hybrid Zones Stability: Hybrids continue to be produced and allow for some gene flow between populations Each species maintains its own integrity Example: An island inhabited by two finch species that occasionally interbreed Punctuated Equilibria Long periods of little apparent morphological change interrupted by relatively brief periods of sudden change Many fossils appear suddenly in a layer of rock and then persist unchanged through many strata, then disappear just as suddenly Other fossils diverge gradually over long periods of time Speed of speciation: 4000 years – 40 million years Average: 6.5 million years Evolutionary History Textbook sections 15.1 – 15.9 Conditions on Early Earth 4.6 bya: vast swirling cloud of dust Gasses, dust, rocks collided and stuck together Immense heat: Earth was a molten mass that sorted itself into layers based on density 4 bya: bombardment of Earth slowed Atmosphere thick with water vapor and compounds released by volcanic eruptions Nitrogen, nitrogen oxides, CO2, CH4, NH3, H2, H2S Earth cooled, water vapor condensed into oceans Intense lightning, volcanic activity, UV radiation Earliest Evidence for Life Fossils 3.5 billion years old Stromatolites Made by ancient photosynthetic prokaryotes Prokaryotes bound thin films of sediment together Still formed today in shallow salty bays such as Shark Bay, Australia Earliest life likely arose approximately 3.9 bya How Did Life Arise? Louis Pasteur: Life arises only by the reproduction of preexisting life How did life arise in the first place? Abiotic synthesis of small organic molecules The joining of these small molecules into polymers Packaging molecules into “protocells” Origin of self-replicating molecules that make inheritance possible  1. Abiotic Synthesis of Organic Molecules Oparin and Haldane: conditions on Early Earth could have spontaneously generated organic molecules Reducing atmosphere Energy from lightning and intense UV radiation Stanley Miller (1953) tested this hypothesis  Stanley Miller’s Results Identification of organic molecules Hydrocarbons Amino acids Experiment has been repeated many times using various hypothesized atmospheric conditions Reanalyzing samples using modern equipment 22 amino acids Other hypotheses: Life may have begun in submerged volcanoes or deep sea hydrothermal vents Meteorites were the source of Earth’s first organic molecules  2. Abiotic Synthesis of Polymers Present-day: Enzymes catalyze the joining of monomers Experiment: Drip dilute solutions of amino acids and other monomers onto hot sand, clay, or rock Heat vaporizes water, concentrating monomers Monomers spontaneously bond together in chains Simulates waves splashing organic monomers onto lava or hot rocks and then rinsed polymers back into the sea 3. Formation of Protocells Small membrane-enclosed vesicles form when lipids are mixed with water Clay thought to be common on early Earth Vesicles form at a faster rate Organic molecules become concentrated on the surface of the clay Vesicles grow and divide (reproduction) Vesicles can absorb clay particles  4. Self-Replicating RNA Short RNA molecules assemble spontaneously from nucleotide monomers New RNA molecules complementary to the starting molecule can assemble Ribozymes: RNA molecules that act as catalysts RNA world: hypothetical period in the evolution of life when RNA served as both rudimentary genes and catalytic molecules  Conclusions 2013: Researcher constructed a protocell enclosing self-replicating RNA Natural selection would have shaped the properties of these protocells and early “genes” Mutations would result in new variation DNA replaced RNA as the repository of genetic information More stable molecule  Macroevolution Macroevolution: evolutionary change above the species level Origin of new groups of organisms through speciation and mass extinctions 4 eons of geologic time: Hadean eon, Archaean eon, Proterozoic eon, Phanerozoic eon  Major events of Macroevolution Origin of Prokaryotes Prokaryotic photosynthesis saturated the seas with oxygen Oxygenation of the atmosphere Mass extinction of prokaryotes that could not survive in an oxygenated world Evolution of cellular respiration Major events of Macroevolution Origin of single-celled eukaryotes Small prokaryotic cells capable of aerobic respiration or photosynthesis took up life inside larger cells (endosymbiont theory)  Major events of Macroevolution Origin of Multicellular eukaryotes Descendants include algae, plants, fungi, animals Original multicellular eukaryotes were small algae Larger organisms evolved later Cambrian explosion: great increase in the diversity of animal forms Major events of Macroevolution Colonization of land Plants associated with fungi (symbiotic relationship) Animals followed the plants Radiometric Dating Calculate the age of rocks and fossils Radiometric dating: Based on the rate of decay of radioactive isotopes Half-life: the time required for 50% of the isotope in a sample to decay Example: Carbon- dating Organisms contain C-12 and C-14 Stable C-12 remains the same, radioactive C-14 decays Half-life = 5730 years Diversity of Life - Prokaryotes Textbook chapter 16.1 – 16.11  Prokaryotic Cells No membrane-bound nucleus No membrane-bound organelles Much smaller than eukaryotes Found anywhere there is life Biomass of prokaryotes is 10X that of eukaryotes Metagenomics: Isolation and sequencing of DNA in environmental samples Microbiome: collection of genomes of all species in the environment Domains Bacteria and Archaea Microbiota Microbiota: Community of microorganisms that live in and on our body Several hundred different species and genetic strains Carry out many positive functions for our health Example: intestinal microbiota supply us with vitamins and help with nutrient extraction from foods Microbiota guards against pathogenic intruders Pathogens: disease-causing agents Prokaryotes in the Environment Decompose dead organisms and organic waste material Return vital chemicals to the environment Chemical cycling Example: They make nitrogen available to plants and other organisms Cell Shape Important for identification of bacteria Cocci (coccus): spherical Streptococci: chains of spherical cells Staphylococcus: clusters of spherical cells Bacilli (bacillus): rod-shaped cells Spirilla: short, rigid spirals Spirochete: longer more flexible spirals Cell Wall Function: Physical protection Protection from osmotic lysis Made from peptidoglycan in bacteria, different substance in archaea Gram stain: staining technique that distinguishes between Gram- positive and Gram-negative cells Gram-positive cells: thick cell wall Stains purple Gram-negative cells: thin cell wall sandwiched between the cell membrane and an outer membrane Stains pink  Capsule Sticky layer of polysaccharides and sometimes protein Allows adherence to a surface or to other individuals in a colony Shields pathogenic prokaryotes from attacks by their host’s immune system Example: capsule of Streptococcus allows it to attach to respiratory tract cells  Projections Flagella Allow movement in response to chemical or physical signals in their environments Naked protein structures Can be concentrated at poles of the cell or be scattered over the full cell Fimbriae Allow attachment to surfaces or each other Example: Neisseria gonorrhoeae attaches to cells of the reproductive tract and to sperm cells to travel through a woman’s reproductive tract  Adaptations to Environmental Changes Reproduce quickly in favourable environments Refrigeration slows growth Every time DNA is replicated a few spontaneous mutations occur Results in high amounts of genetic variation in a short period of time One cell possessing a beneficial allele takes advantage of the new conditions Example: exposure to antibiotics selects for individuals that are antibiotic resistant Prokaryotic DNA Chromosome 1/1000 the size of a eukaryotic genome One long circular chromosome All genes required for survival under typical conditions Plasmid Small circular DNA molecules Replicate independently of the chromosome Carry genes that enhance survival under certain conditions Can be transferred from one cell to another Endospores Formed under harsh or unfavourable conditions A cell encloses a copy of its DNA inside a thick protective coat Endospore dehydrates to stop its metabolic activity When conditions improve, the endospore rehydrates and resumes growth Survive all kinds of conditions and persist in a dormant state for decades Very difficult to destroy Nutritional Diversity Sources of energy Phototrophs: energy from sunlight Chemotrophs: energy stored in chemicals Organic: sugars, etc Inorganic: H2S, S, Fe-compounds, NH3 Sources of Carbon Autotrophs: acquire carbon from inorganic sources Heterotrophs: obtain carbon from organic compounds Modes of Nutrition  Biofilms Highly organized colonies attached to surfaces Rock, soil, organic material, living tissue, metal, plastic, stagnant water Can consist of one or several species or prokaryotes, protists, and fungi Formation: Prokaryotes secrete signaling molecules to attract nearby cells into a cluster Cells produce a substance that glues cells to each other and a surface Members of the community coordinate the division of labour, defense against invaders, and other activities Channels allow import of nutrients and export of wastes  Biofilms Common in disease-causing bacteria Example: ear infections, urinary tract infections, pneumonia Form on implanted medical devices Catheters, replacement joints, pacemakers Antibiotics can often not penetrate beyond the outer layer of cells Form in the environment Clog and corrode pipes, gum up filters and drains, coat hulls of ships Can even survive chlorination Bioremediation The use of organisms to remove pollutants from soil, air, or water Prokaryotes are capable of degrading pollutants Oil, solvents, pesticides Workers use methods to speed up the activity of microbes Example: chemical dispersants can be sprayed on oil spills to break it into small droplets that microbes can attack Wastewater Treatment Sewage is passed through screens and shredders Solid material (sludge) settles out from liquid waste Sludge is added to a culture of anaerobic prokaryotes Microbes decompose the organic matter Liquid wastes are sprayed onto rocks covered in biofilm bacteria which remove organic material Outflow from rock bed is sterilized and then released to rivers or oceans  Prokaryotic Evolution First major split in the history of life was the divergence of bacteria from other organisms Later divergence separated archaea and eukarya Archaea are more closely related to eukaryotes than to bacteria  Archaea Abundant in many habitats One of the most abundant cell types in the oceans Thrive in extreme environments Unusual proteins and other molecular adaptations that allow survival Extreme halophiles: live in extreme salty conditions (ex. Dead Sea, seawater evaporating ponds) 15-30% salt (ocean is 3% salt) Very little competition because other cells will shrivel Red, purple, yellow growth  Archaea Extreme thermophiles: live in very hot water Deep ocean vents Can also be acidophiles which thrive in acid such as acidic pools at Yellowstone National Park Methanogens: live in anaerobic environments and make methane as a waste product Anaerobic mud at the bottom of lakes and swamps Solid waste landfills Digestive tract of animals that rely on cellulose for nutrition Methane can be collected and used as a source of energy Methane is a greenhouse gas Groups of Bacteria 5 groups based on comparisons of genetic sequences Proteobacteria Gram-positive bacteria Cyanobacteria Chlamydias Spirochetes Proteobacteria Gram-negative All 4 modes of nutrition are included Chemoheterotrophs include Escherichia coli and pathogens such as Vibrio cholera Photoautotrophs include Thiomargarita namibiensis which uses H2S to generate organic molecules from CO2 Photoheterotrophs include Rhodopseudomonas which cannot fix carbon Chemoautotrophs include soil bacteria such as Nitrosomonas which fixes nitrogen  Proteobacteria Can live symbiotically with a eukaryotic host Symbiosis: close association between organisms of two or ore species where both benefit Endosymbiosis: one species (endosymbiont) lives inside the other Example: mitochondria evolved from aerobic proteobacteria Example: endosymbiotic proteobacteria live in root nodules of legumes Gram-Positive Bacteria High amount of diversity Actinomycetes Colonies of branched chains of cells Common in soil where they decompose organic matter Streptomyces Genus of soil bacteria Cultured by pharmaceutical companies as a source of antibiotics (ex. Streptomycin) Pathogens such as Staphylococcus and Streptococcus Bacillus anthracis Cyanobacteria Only group that have plant-like oxygen-generating photosynthesis Provide food for organisms in freshwater and marine ecosystems Some form specialized cells that fix nitrogen Many symbiotic relationships with other organisms Fungi, mosses, marine invertebrates Endosymbiotic cyanobacteria are the origin of chloroplasts Chlamydias Live inside eukaryotic host cells Chlamydia trachomatis Common cause of blindness in developing countries Causes nongonococcal urethritis which is the most common sexually transmitted infection in the US  Spirochetes Helical bacteria that spiral through their environments by means of rotating internal filaments Pathogens Treponema pallidum: syphilis Borrelia burgdorferi: Lyme disease Some Bacteria Cause Disease Exotoxin: proteins that bacterial cell secrete into their environment Ex. Staphylococcus aureus Commonly found on skin and in nasal passages Causes disease if it enters through a wound One exotoxin destroys white blood cells (MRSA) Food can be contaminated with exotoxins that cause vomiting and diarrhea  Some Bacteria Cause Disease Endotoxins: Lipid component of the outer membrane of Gram-negative bacteria Released when the cell dies or is digested by a defensive cell Symptoms: fever, aches, septic shock (drop in blood pressure) Ex. Neisseria meningitidis causes meningitis Can kill a healthy person in a matter of days or hours Ex. Salmonella causes food poisoning  Bacteria as Biological Weapons Due to their disease-causing potential Antibiotics can kill the bacteria but cannot eliminate the toxins already present in the body Highest priority threats Bacillus anthracis endospores Endospores can be inhaled and then germinate in the lungs Cells produce an exotoxin that accumulates in blood Clostridium botulinum exotoxin Botulinum toxin is the deadliest poison known to man Blocks transmission of nerve signals causing paralysis of muscles used for breathing Botox: relaxing facial muscles that cause wrinkles Koch’s Postulates 1. Find the same bacterium in every case of the disease 2. Isolate the bacterium and grow in pure culture 3. Show that the bacterium causes disease when inoculated into a healthy subject 4. Re-isolate the bacterium Example: Barry Marshall Hypothesis: Helicobacter pylori causes inflammation of the stomach lining that causes ulcers Swallowed the bacterium himself, developed gastritis, cured the infection with antibiotics  Stomach Microbiota Most strains of Helicobacter pylori do not cause ulcers, they are instead important members of our microbiota Low levels of H. pylori causes continuous output of the hormone ghrelin Ghrelin sends hunger signals to the brain Should decrease after meals Leads to overeating Absence of H. pylori is correlated to increased body mass index Dating Fossils C-14 is useful for relatively young fossils Up to about 75,000 years old Potassium-40 is used to date volcanic rock hundreds of millions of years old Half-life: 1.3 billion years Date rock above and below the fossil The Fossil Record Fossil record: the sequence in which fossils appear in rock strata Archive of evolutionary history Geologic Record: Earth’s history  Hadean, Archaean, and Proterozoic Eons 1. Hadean Eon: The Origin of the Earth 2. Archaean Eon: The first evidence of life on our planet 3 Prokaryotes Oxygenation of the atmosphere 3. Proterozoic Eon: The 2 first eukaryotes appeared in the fossil record First unicellular 1 eukaryotes First multicellular eukaryotes Phanerozoic Eon The Phanerozoic eon is divided into 3 eras Paleozoic, Mesozoic, Cenozoic Each is then divided into periods Boundaries between eras marked by mass extinctions The boundaries between periods are often marked by lesser extinctions  Cambrian explosion Early on, virtually all life was aquatic Colonization of land Fossils of many lineages that gave rise to present day organisms Fossils of many lineages that have gone extinct  The age of reptiles Many reptilian fossils, including those of dinosaurs Evolution of the first mammals and flowering plants (angiosperms) By the end of the era, dinosaurs had become extinct except for the lineage that evolved into birds  Very fast evolution of a wide range mammals, birds, insects, and angiosperms The era is divided into epochs The modern genus of humans (Homo) emerged in the Pleistocene epoch Continental Drift Plate tectonics: Crust consists of irregularly-shaped plates floating on the mantle Continental drift: movements in the mantle cause the plates to move Example: North America and Europe are drifting apart 2cm per year Plates slide past each other forming regions where earthquakes are common Plates may collide, forming mountains Supercontinent: all land masses come together  Pangaea Supercontinent at the end of the Paleozoic era Ocean basins deepened, draining shallow coastal seas Destroyed the habitats of most marine species Interior of the continent was cold and dry Pangaea broke apart Geographic isolation Organisms evolved in isolation from other members of their species Biogeography: the study of past and present distribution of organisms Example: Island countries have many species that exist nowhere else in the world  Example: Marsupials Mammals whose young complete their embryonic development in a pouch Most found in Australia More than 100 species live in Central and South America Some in North America Marsupials must have originated when continents were joined Fossils: Originated in Asia, dispersed to South America when Antarctica was still attached, moved to Australia before the separated  Mass Extinctions Majority of species have gone extinct Habitat was destroyed Unfavourable climatic change Changes to the biological community Mass extinction: 50% or more of Earth’s species are swept away in a relatively short amount of time 5 mass extinction in the history of the planet Are we currently going through a 6th mass extinction? Consequences Collapse of ecological communities Once an evolution lineage disappears it cannot reappear, the course of evolution is changed forever 5 – 10 million years for diversity of life to recover to previous levels Sometimes up to 100 million years  Permian Extinction Boundary between the Paleozoic and Mesozoic eras 96% of marine life, 70% of terrestrial life Extinction lasted 500,000 years Widespread volcanic eruptions Lava, ash, noxious gases Production of enough carbon dioxide to warm the global climate by 6°C Warming caused the poles to be closer in temperature to the equator causing slower mixing of ocean water, causing a drop in oxygen in the water Marine organisms perished, anaerobic bacteria thrived Bacteria produced poisonous hydrogen sulfide causing high amount of acid rain that killed terrestrial organisms  Cretaceous Extinction 66 million years ago More than 50% of marine species and many terrestrial species including dinosaurs Asteroid or large comet hit the Earth Impact crater in the Caribbean Sea near Mexico 10km diameter Huge cloud of dust high in iridium Blocked light and disturbed global climate for months  Adaptive Radiations Periods of evolutionary change in which many new species evolve from a common ancestor Mass extinctions Evolutionary innovation that allow a group of organisms to exploit an unused resource Ex. Colonization of land Evolution of a new group of organisms can cause adaptive evolution of another new group of organisms Ex. Proliferation of land plants stimulated adaptive radiation of pollinators and herbivores  Adaptive Radiation After Mass Extinctions Large scale adaptive radiations followed each mass extinction Survivors became adapted to vacant ecological roles or niches Example: Mammals Small creatures with limited diversity in the age of dinosaurs Dramatic adaptive radiation after the extinction of dinosaurs Genes That Control Development Evo-devo: interface of evolutionary biology and developmental biology Slight genetic changes become magnified into major morphological differences between species Genes that program development control the rate, timing, spatial pattern of change in an organism’s form as it goes from a zygote to an adult Changes in Rate and Timing of Developmental Events Paedomorphosis: retention in the adult body of structures that were juvenile features in ancestral species Example: Salamanders have aquatic larvae with gills Larvae undergo metamorphosis to become adults with lungs Axolotl is a salamander that retains gills and other larval features as a mature adult Example: Humans and Chimpanzees Very similar as fetuses Chimpanzee: accelerated growth of the jaw Elongated skull Sloping forehead Massive jaws Humans: slowed growth of the jaw, continued growth of the brain Head proportions resemble that of a child or baby chimpanzee Large more complex brain  Changes in Spatial Patterns Homeotic genes: The master control genes Determine where basic features will develop Changes in the expression of homeotic genes affect development Example: tetrapods vs snakes One pattern of expression of two homeotic genes results in forelimb and rib formation Other pattern of expression results in rib formation without limbs Snakes evolved from a four-limbed ancestor  New Genes and Changes in Genes and Gene Regulation Gene duplications give the possibility for mutations and the evolution of new genes Example: Evolution of vertebrates from invertebrates Mutations affecting regulation of developmental genes Example: Changes in homeotic gene regulation allowed evolution of snakes Example: Three-spined stickleback fish Ocean and lakes in western Canada Ocean: gene turned on - bony plates and spines to deter predatory fish Lake: gene turned off - armor is absent due to lack of predators and low calcium  Novel Structures Process of refinement Complex structures evolve in increments from simple structures with the same basic function Example: Evolution of eyes from simple ancestral patches of photoreceptor cells One evolutionary origin of light-sensitive cells All animals with eyes have the same master genes for regulation of eye development  Novel Structures Exaptations: Structures that evolve with one function are co-opted for another function Natural selection improves existing structures in the context of current use Each intermediate stage has a function in the organism’s current situation Example: Evolution of feathers A lineage of dinosaurs had feathers but could not fly Functions: insulation (thermoregulation), camouflage, mating displays Long forelimbs with feathers could have evolved flight starting with gliding or flapping  Evolution is not Goal Directed Trends are not goals Example: Evolution of horses Hyracotherium: size of a large dog, four toes on the front feet and 3 toes on the back feet, browse on shrubs and trees Modern horses (Equus): larger, one toe on each foot, grazes on grass Trend: larger, grazing, one toe Reality: many lineages with variation, this is just the only one that survived Example: strong selection pressure for fast grazers as they lived in grasslands and had many predators  Studying Evolutionary Trends Speciation: birth of a species Extinction: death of a species New species diverge as the offspring of their ancestral species There is unequal survival of species and unequal generation of new species The species that generates the greatest number of new species determines the direction of major evolutionary trends  Taxonomy Why do we need a scientific method for naming species? Common names are ambiguous Many species of squirrels, daisies, tomatoes, etc. Different regions may use the same common name for different species Bluebells is a different type of flower depending on if you are in Scotland, England, Texas, or eastern US Common names can be misleading Fish that are not actually fish…. Jellyfish – A cnidarian Crayfish – A crustacean Silverfish – An insect  Phylogeny: The Phylogeny evolutionary history of a species or group of species Systematics: classifying organisms and determining their evolutionary relationships Phylogenetic trees: branching diagrams that reflect the hierarchical classification of groups Indicates the pattern of descent from the last common ancestor  Constructing a Phylogenetic Tree Morphological and molecular data Evidence from the fossil record Important features are the ones that result from common ancestry  Convergent Evolution Convergent evolution: Similar adaptations arise in unrelated organisms due to the need to adapt to similar environments Analogy: Similarity due to convergent evolution Example: analogy between the Australian ‘mole’ and the American mole Australian mole is a marsupial American mole is a eutherian Similarities arose as they both became adapted to burrowing lifestyles  Cladistics Method for constructing phylogenetic trees Cladistics: organisms are grouped by common ancestry Clade: ancestral species and all its evolutionary descendants Monophyletic: inclusive group of ancestor and descendants Shared ancestral character: common to members of a clade but originated in an ancestor that is not a member of the clade Example: Mammals all have a backbone but that does not differentiate mammals from other vertebrates Shared derived character: common to members of a clade but is not found in its ancestors Inferring Phylogeny Compares organisms according to the presence or absence of a set of characters Outgroup: Species from a lineage that is closely related but not part of the group of species we are studying Ingroup: The group of species we are studying  Parsimony: The adoption of Parsimony the simplest explanation for observed phenomena Phylogenetic trees should be constructed to have the smallest number of evolutionary branching points as possible Example: unlikely that gestation evolved twice so beavers are more related to kangaroos than to a platypus Tree construction involves very complex data Uses computers to build Trees are Hypotheses to be Tested Example: Birds and Crocodiles Birds are most closely related to crocodiles 4-chambered hearts, ‘sing’ to defend territories and attract mates, build nests Prediction: if our phylogeny is correct, their common ancestor (dinosaurs) should have these same features Fossil evidence shows dinosaurs built nests and cared for eggs Molecular Molecular systematics: Using DNA or other molecules to infer Systematics relatedness Early impact of DNA analysis: Creation of the domain level of classification Previously there were 5 kingdoms Monera, protista, plantae, fungi, animalia Genes that evolve slowly (ex. rRNA) used for broad classifications Fungi more closely related to animals than plants Genes that evolve quickly (ex. mtDNA) used for narrow classifications Classification on different species of bear  Genome Evolution Homologous genes can extend over huge evolutionary distances 99% of genes in humans and mice are homologous 50% of human genes are homologous with yeast genes Commonality demonstrates that all living organisms share many biochemical and developmental pathways Gene duplication Increases number of genes Provides opportunities for evolutionary change Molecular techniques can be used to trace when and where genes have diverged  Molecular Clocks Molecular changes keep better track of time than changes in morphology Example: sharks and tuna diverged 420 million years ago Example: dolphins and bats diverged 60 million years ago Molecular clock: method that estimates the time required for a given amount of evolutionary change Some genes or regions of genomes accumulate changes at a constant rate Graph the number of nucleotide differences against dates of evolutionary branch points known from the fossil record  Example: When did Humans Start Wearing Clothes? We link this to evolution of body lice Blood-sucking insect that live in the fur or hair of most mammal species Loss of body hair restricted lice to human heads Clothing then offered a new habitat Divergence into two species of lice – Head lice and body lice Based on the divergence of head lice and body lice, we can estimate that humans started wearing clothes 83,000 – 170,000 years ago  Constructing the Tree of Life is a Work in Progress Hypotheses are constantly being revised or even rejected as new evidence comes to light Example: Lots of questions still surrounding protist classifications Not monophyletic, should maybe not be considered a single kingdom  Horizontal Gene Transfer Horizontal gene transfer: Genes are transferred from one genome to another through mechanisms such as plasmid exchange and viral infection or the fusion of different organisms Two major events Gene transfer between a mitochondrial ancestor and the ancestor of eukaryotes Gene transfer between a chloroplast ancestor and the ancestor of green plants Diversity of Life - Prokaryotes Textbook chapter 16.1 – 16.11  Prokaryotic Cells No membrane-bound nucleus No membrane-bound organelles Much smaller than eukaryotes Found anywhere there is life Biomass of prokaryotes is 10X that of eukaryotes Metagenomics: Isolation and sequencing of DNA in environmental samples Microbiome: collection of genomes of all species in the environment Domains Bacteria and Archaea Microbiota Microbiota: Community of microorganisms that live in and on our body Several hundred different species and genetic strains Carry out many positive functions for our health Example: intestinal microbiota supply us with vitamins and help with nutrient extraction from foods Microbiota guards against pathogenic intruders Pathogens: disease-causing agents Prokaryotes in the Environment Decompose dead organisms and organic waste material Return vital chemicals to the environment Chemical cycling Example: They make nitrogen available to plants and other organisms Cell Shape Important for identification of bacteria Cocci (coccus): spherical Streptococci: chains of spherical cells Staphylococcus: clusters of spherical cells Bacilli (bacillus): rod-shaped cells Spirilla: short, rigid spirals Spirochete: longer more flexible spirals Cell Wall Function: Physical protection Protection from osmotic lysis Made from peptidoglycan in bacteria, different substance in archaea Gram stain: staining technique that distinguishes between Gram- positive and Gram-negative cells Gram-positive cells: thick cell wall Stains purple Gram-negative cells: thin cell wall sandwiched between the cell membrane and an outer membrane Stains pink  Capsule Sticky layer of polysaccharides and sometimes protein Allows adherence to a surface or to other individuals in a colony Shields pathogenic prokaryotes from attacks by their host’s immune system Example: capsule of Streptococcus allows it to attach to respiratory tract cells  Projections Flagella Allow movement in response to chemical or physical signals in their environments Naked protein structures Can be concentrated at poles of the cell or be scattered over the full cell Fimbriae Allow attachment to surfaces or each other Example: Neisseria gonorrhoeae attaches to cells of the reproductive tract and to sperm cells to travel through a woman’s reproductive tract  Adaptations to Environmental Changes Reproduce quickly in favourable environments Refrigeration slows growth Every time DNA is replicated a few spontaneous mutations occur Results in high amounts of genetic variation in a short period of time One cell possessing a beneficial allele takes advantage of the new conditions Example: exposure to antibiotics selects for individuals that are antibiotic resistant Prokaryotic DNA Chromosome 1/1000 the size of a eukaryotic genome One long circular chromosome All genes required for survival under typical conditions Plasmid Small circular DNA molecules Replicate independently of the chromosome Carry genes that enhance survival under certain conditions Can be transferred from one cell to another Endospores Formed under harsh or unfavourable conditions A cell encloses a copy of its DNA inside a thick protective coat Endospore dehydrates to stop its metabolic activity When conditions improve, the endospore rehydrates and resumes growth Survive all kinds of conditions and persist in a dormant state for decades Very difficult to destroy Nutritional Diversity Sources of energy Phototrophs: energy from sunlight Chemotrophs: energy stored in chemicals Organic: sugars, etc Inorganic: H2S, S, Fe-compounds, NH3 Sources of Carbon Autotrophs: acquire carbon from inorganic sources Heterotrophs: obtain carbon from organic compounds Modes of Nutrition  Biofilms Highly organized colonies attached to surfaces Rock, soil, organic material, living tissue, metal, plastic, stagnant water Can consist of one or several species or prokaryotes, protists, and fungi Formation: Prokaryotes secrete signaling molecules to attract nearby cells into a cluster Cells produce a substance that glues cells to each other and a surface Members of the community coordinate the division of labour, defense against invaders, and other activities Channels allow import of nutrients and export of wastes  Biofilms Common in disease-causing bacteria Example: ear infections, urinary tract infections, pneumonia Form on implanted medical devices Catheters, replacement joints, pacemakers Antibiotics can often not penetrate beyond the outer layer of cells Form in the environment Clog and corrode pipes, gum up filters and drains, coat hulls of ships Can even survive chlorination Bioremediation The use of organisms to remove pollutants from soil, air, or water Prokaryotes are capable of degrading pollutants Oil, solvents, pesticides Workers use methods to speed up the activity of microbes Example: chemical dispersants can be sprayed on oil spills to break it into small droplets that microbes can attack Wastewater Treatment Sewage is passed through screens and shredders Solid material (sludge) settles out from liquid waste Sludge is added to a culture of anaerobic prokaryotes Microbes decompose the organic matter Liquid wastes are sprayed onto rocks covered in biofilm bacteria which remove organic material Outflow from rock bed is sterilized and then released to rivers or oceans  Prokaryotic Evolution First major split in the history of life was the divergence of bacteria from other organisms Later divergence separated archaea and eukarya Archaea are more closely related to eukaryotes than to bacteria  Archaea Abundant in many habitats One of the most abundant cell types in the oceans Thrive in extreme environments Unusual proteins and other molecular adaptations that allow survival Extreme halophiles: live in extreme salty conditions (ex. Dead Sea, seawater evaporating ponds) 15-30% salt (ocean is 3% salt) Very little competition because other cells will shrivel Red, purple, yellow growth  Archaea Extreme thermophiles: live in very hot water Deep ocean vents Can also be acidophiles which thrive in acid such as acidic pools at Yellowstone National Park Methanogens: live in anaerobic environments and make methane as a waste product Anaerobic mud at the bottom of lakes and swamps Solid waste landfills Digestive tract of animals that rely on cellulose for nutrition Methane can be collected and used as a source of energy Methane is a greenhouse gas Groups of Bacteria 5 groups based on comparisons of genetic sequences Proteobacteria Gram-positive bacteria Cyanobacteria Chlamydias Spirochetes Proteobacteria Gram-negative All 4 modes of nutrition are included Chemoheterotrophs include Escherichia coli and pathogens such as Vibrio cholera Photoautotrophs include Thiomargarita namibiensis which uses H2S to generate organic molecules from CO2 Photoheterotrophs include Rhodopseudomonas which cannot fix carbon Chemoautotrophs include soil bacteria such as Nitrosomonas which fixes nitrogen  Proteobacteria Can live symbiotically with a eukaryotic host Symbiosis: close association between organisms of two or ore species where both benefit Endosymbiosis: one species (endosymbiont) lives inside the other Example: mitochondria evolved from aerobic proteobacteria Example: endosymbiotic proteobacteria live in root nodules of legumes Gram-Positive Bacteria High amount of diversity Actinomycetes Colonies of branched chains of cells Common in soil where they decompose organic matter Streptomyces Genus of soil bacteria Cultured by pharmaceutical companies as a source of antibiotics (ex. Streptomycin) Pathogens such as Staphylococcus and Streptococcus Bacillus anthracis Cyanobacteria Only group that have plant-like oxygen-generating photosynthesis Provide food for organisms in freshwater and marine ecosystems Some form specialized cells that fix nitrogen Many symbiotic relationships with other organisms Fungi, mosses, marine invertebrates Endosymbiotic cyanobacteria are the origin of chloroplasts Chlamydias Live inside eukaryotic host cells Chlamydia trachomatis Common cause of blindness in developing countries Causes nongonococcal urethritis which is the most common sexually transmitted infection in the US  Spirochetes Helical bacteria that spiral through their environments by means of rotating internal filaments Pathogens Treponema pallidum: syphilis Borrelia burgdorferi: Lyme disease Some Bacteria Cause Disease Exotoxin: proteins that bacterial cell secrete into their environment Ex. Staphylococcus aureus Commonly found on skin and in nasal passages Causes disease if it enters through a wound One exotoxin destroys white blood cells (MRSA) Food can be contaminated with exotoxins that cause vomiting and diarrhea  Some Bacteria Cause Disease Endotoxins: Lipid component of the outer membrane of Gram-negative bacteria Released when the cell dies or is digested by a defensive cell Symptoms: fever, aches, septic shock (drop in blood pressure) Ex. Neisseria meningitidis causes meningitis Can kill a healthy person in a matter of days or hours Ex. Salmonella causes food poisoning  Bacteria as Biological Weapons Due to their disease-causing potential Antibiotics can kill the bacteria but cannot eliminate the toxins already present in the body Highest priority threats Bacillus anthracis endospores Endospores can be inhaled and then germinate in the lungs Cells produce an exotoxin that accumulates in blood Clostridium botulinum exotoxin Botulinum toxin is the deadliest poison known to man Blocks transmission of nerve signals causing paralysis of muscles used for breathing Botox: relaxing facial muscles that cause wrinkles Koch’s Postulates 1. Find the same bacterium in every case of the disease 2. Isolate the bacterium and grow in pure culture 3. Show that the bacterium causes disease when inoculated into a healthy subject 4. Re-isolate the bacterium Example: Barry Marshall Hypothesis: Helicobacter pylori causes inflammation of the stomach lining that causes ulcers Swallowed the bacterium himself, developed gastritis, cured the infection with antibiotics  Stomach Microbiota Most strains of Helicobacter pylori do not cause ulcers, they are instead important members of our microbiota Low levels of H. pylori causes continuous output of the hormone ghrelin Ghrelin sends hunger signals to the brain Should decrease after meals Leads to overeating Absence of H. pylori is correlated to increased body mass index Diversity of Life - Protists Textbook chapter 16.12 – 16.19 Protists Eukaryotes that are not plants, animals, or fungi Mostly unicellular Algae: autotrophs, producing food by photosynthesis Protozoans: heterotrophs, eating bacteria and other protists Some heterotrophic protists obtain nutrients by absorption Parasites: derive nutrients from a living host which is harmed in the process Mixotrophs: capable of both photosynthesis and heterotrophy  Protists Diverse habitats Found anywhere there is moisture including damp soil and leaf litter Bodies of various host organisms Endosymbionts in termite guts to help digest cellulose The simplest eukaryotes But cells can be some of the most elaborate in the world Eukaryotes Membrane-enclosed nucleus with multiple chromosomes Membrane-bound organelles Flagella and cilia with 9+2 microtubule arrangement  Protist Supergroups Multiple clades Some lineages more closely related to plants, fungi, animals, other protists Four monophyletic supergroups SAR Excavata Unikonta Archaeplastida  SAR Supergroup Three clades Stramenopila Alveolata Rhizaria Stramenopiles Diatoms: unicellular algae Some of the most important photosynthetic organisms on Earth Glassy cell wall containing silica Freshwater and marine environments Store food reserves as droplets of lipids or carbohydrates Lipids keep the cells buoyant Make up diatomaceous earth Filtering, polishing  Stramenopiles Brown algae Multicellular, marine Seaweeds: marine algae that have large multicellular bodies but lack roots, stems, and leaves Example: Kelp forests used as feeding grounds by many organisms Water molds Heterotrophic unicellular organisms Decompose dead plants and animals Freshwater habitats Resemble fungi Parasitize skin and gills of fish, and plants such as potatoes, tomatoes, cacao, squash  Alveolates Dinoflagellates Unicellular autotrophs, heterotrophs, and mixotrophs Marine and freshwater plankton Blooms cause “red tides” Warm coastal waters turn pinkish-orange Can produce neurotoxins killing marine animals Reside inside cells of corals to provide energy  Alveolates Ciliates Cilia used for motility and to sweep food into their oral groove (cell mouth) Heterotrophs and mixotrophs Example: Paramecium Parasites Plasmodium causes malaria  Rhizaria Heterotrophs Amoebas: move and feed by means of pseudopodia (temporary extensions of the cell) Have thread-like pseudopodia Foraminiferans (forams) Ocean and freshwater Porous shells of calcium carbonate Pseudopodia extend through pores in the shell Fossilized shells are used as markers for rock age Rhizaria Radiolarians Internal skeleton of silica Shell of organic material Most are marine Skeleton and shell become part of the sediments after cells die Radiolarian ooze: sediments thick with radiolarians, hundreds of meters thick Algae as a Renewable Energy Source Fossil fuels: organic remains of organisms that lived hundreds or millions of years ago Diatoms: main source of oil Plants: main source of coal Can we use lipid droplets in diatoms and other algae as a renewable source of energy? Grow algae, harvest oil, process into biodiesel Bioreactors Hurdles to overcome What algae are most productive? Genetically engineer better species? Cost-effective methods of harvesting the oil? Excavata Supergroup Feeding groove on some cells Some have modified mitochondria Lack functional electron transport chains Must use anaerobic pathways for energy production Heterotrophs Example: termite endosymbiont Autotrophs and mixotrophs Example: Euglena  Excavata Supergroup Parasites Example: Trichomonas vaginalis Sexually transmitted parasite Feed on white blood cells and bacteria that line the vagina Also infects male reproductive tract but can only form smaller populations Treated with metronidazole Drug resistance is evolving  Excavata Supergroup Example: Giardia intestinalis Waterborne parasite that causes severe diarrhea Ingestion of water contaminated with feces Example: Trypanosoma Transmitted to humans by insects Causes sleeping sickness  Unikont Supergroup Protists that are closely related to fungi and animals 2 clades Amoebozoans Animals and fungi Amoebozoans Free-living amoebas: creep over rocks, stick, mud at the bottom of water bodies Parasitic amoebas: live inside a host Example: amoeboid dysentery (potentially fatal diarrhea) slime molds All use tube or lobe-shaped pseudopodia to engulf food particles Plasmodial Slime Molds Grow on moist, decaying organic matter Brightly pigmented Plasmodium: single multinucleate mass of cytoplasm undivided by plasma membranes Extends pseudopodia through soil and rotting logs to engulf food by phagocytosis Cytoplasm streams distribute nutrients and oxygen Reproductive structures: formed when food and water are in short supply When conditions are favourable spores release haploid gametes to form zygotes Cellular Slime Molds Common on rotting logs and decaying organic matter Free living unicells When food is scarce, amoeboid cells swarm together Forms a slug-like aggregate that moves together Some cells dry up and form a stalk Other cells differentiate into a reproductive structure containing spores  Archaeplastids Supergroup Almost all are autotrophic Red algae and green algae, and land plants Red Algae Accessory pigments mask chlorophyll Most are multicellular Cells can be encrusted with hard chalky deposits Example: important in building and maintaining coral reefs Produce carrageenan Gel used to stabilize products such as ice cream, chocolate milk, pudding, etc. Nori is used to wrap sushi Agar is collected from red algae  Green Algae Grass green chloroplasts Unicellular, colonial, or multicellular seaweeds Example: Chlamydomonas Unicellular biflagellate Common in freshwater lakes and ponds Example: Volvox Colonial, each ball is a colony of hundreds or thousands of biflagellate cells  Green Algae Example: Ulva Multicellular Alternation of generations Sporophytes: multicellular diploid form which produces spores by meiosis Gametophytes: multicellular haploid form which produces gametes by mitosis Evolution of Multicellularity Seaweeds, plants, animals, most fungi Various specialized cells that perform different functions and are dependent on each other We have seen multicellularity in three different supergroups Stramenophiles: brown algae Unikonts: fungi and animals Archaeplastids: red algae, green algae, land plants Hypothesis on Phylogeny Two unikont lineages led to animals and fungi Choanoflagellates are the closest relatives of animals and resemble the collar cells of sponges Nucleariids are the closest relatives of fungi Green algae led to plants Charophytes are the closest living relatives of land plants Diversity of Life - Protists Textbook chapter 16.12 – 16.19 Protists Eukaryotes that are not plants, animals, or fungi Mostly unicellular Algae: autotrophs, producing food by photosynthesis Protozoans: heterotrophs, eating bacteria and other protists Some heterotrophic protists obtain nutrients by absorption Parasites: derive nutrients from a living host which is harmed in the process Mixotrophs: capable of both photosynthesis and heterotrophy  Protists Diverse habitats Found anywhere there is moisture including damp soil and leaf litter Bodies of various host organisms Endosymbionts in termite guts to help digest cellulose The simplest eukaryotes But cells can be some of the most elaborate in the world Eukaryotes Membrane-enclosed nucleus with multiple chromosomes Membrane-bound organelles Flagella and cilia with 9+2 microtubule arrangement  Protist Supergroups Multiple clades Some lineages more closely related to plants, fungi, animals, other protists Four monophyletic supergroups SAR Excavata Unikonta Archaeplastida  SAR Supergroup Three clades Stramenopila Alveolata Rhizaria Stramenopiles Diatoms: unicellular algae Some of the most important photosynthetic organisms on Earth Glassy cell wall containing silica Freshwater and marine environments Store food reserves as droplets of lipids or carbohydrates Lipids keep the cells buoyant Make up diatomaceous earth Filtering, polishing  Stramenopiles Brown algae Multicellular, marine Seaweeds: marine algae that have large multicellular bodies but lack roots, stems, and leaves Example: Kelp forests used as feeding grounds by many organisms Water molds Heterotrophic unicellular organisms Decompose dead plants and animals Freshwater habitats Resemble fungi Parasitize skin and gills of fish, and plants such as potatoes, tomatoes, cacao, squash  Alveolates Dinoflagellates Unicellular autotrophs, heterotrophs, and mixotrophs Marine and freshwater plankton Blooms cause “red tides” Warm coastal waters turn pinkish-orange Can produce neurotoxins killing marine animals Reside inside cells of corals to provide energy  Alveolates Ciliates Cilia used for motility and to sweep food into their oral groove (cell mouth) Heterotrophs and mixotrophs Example: Paramecium Parasites Plasmodium causes malaria  Rhizaria Heterotrophs Amoebas: move and feed by means of pseudopodia (temporary extensions of the cell) Have thread-like pseudopodia Foraminiferans (forams) Ocean and freshwater Porous shells of calcium carbonate Pseudopodia extend through pores in the shell Fossilized shells are used as markers for rock age Rhizaria Radiolarians Internal skeleton of silica Shell of organic material Most are marine Skeleton and shell become part of the sediments after cells die Radiolarian ooze: sediments thick with radiolarians, hundreds of meters thick Algae as a Renewable Energy Source Fossil fuels: organic remains of organisms that lived hundreds or millions of years ago Diatoms: main source of oil Plants: main source of coal Can we use lipid droplets in diatoms and other algae as a renewable source of energy? Grow algae, harvest oil, process into biodiesel Bioreactors Hurdles to overcome What algae are most productive? Genetically engineer better species? Cost-effective methods of harvesting the oil? Excavata Supergroup Feeding groove on some cells Some have modified mitochondria Lack functional electron transport chains Must use anaerobic pathways for energy production Heterotrophs Example: termite endosymbiont Autotrophs and mixotrophs Example: Euglena  Excavata Supergroup Parasites Example: Trichomonas vaginalis Sexually transmitted parasite Feed on white blood cells and bacteria that line the vagina Also infects male reproductive tract but can only form smaller populations Treated with metronidazole Drug resistance is evolving  Excavata Supergroup Example: Giardia intestinalis Waterborne parasite that causes severe diarrhea Ingestion of water contaminated with feces Example: Trypanosoma Transmitted to humans by insects Causes sleeping sickness  Unikont Supergroup Protists that are closely related to fungi and animals 2 clades Amoebozoans Animals and fungi Amoebozoans Free-living amoebas: creep over rocks, stick, mud at the bottom of water bodies Parasitic amoebas: live inside a host Example: amoeboid dysentery (potentially fatal diarrhea) slime molds All use tube or lobe-shaped pseudopodia to engulf food particles Plasmodial Slime Molds Grow on moist, decaying organic matter Brightly pigmented Plasmodium: single multinucleate mass of cytoplasm undivided by plasma membranes Extends pseudopodia through soil and rotting logs to engulf food by phagocytosis Cytoplasm streams distribute nutrients and oxygen Reproductive structures: formed when food and water are in short supply When conditions are favourable spores release haploid gametes to form zygotes Cellular Slime Molds Common on rotting logs and decaying organic matter Free living unicells When food is scarce, amoeboid cells swarm together Forms a slug-like aggregate that moves together Some cells dry up and form a stalk Other cells differentiate into a reproductive structure containing spores  Archaeplastids Supergroup Almost all are autotrophic Red algae and green algae, and land plants Red Algae Accessory pigments mask chlorophyll Most are multicellular Cells can be encrusted with hard chalky deposits Example: important in building and maintaining coral reefs Produce carrageenan Gel used to stabilize products such as ice cream, chocolate milk, pudding, etc. Nori is used to wrap sushi Agar is collected from red algae  Green Algae Grass green chloroplasts Unicellular, colonial, or multicellular seaweeds Example: Chlamydomonas Unicellular biflagellate Common in freshwater lakes and ponds Example: Volvox Colonial, each ball is a colony of hundreds or thousands of biflagellate cells  Green Algae Example: Ulva Multicellular Alternation of generations Sporophytes: multicellular diploid form which produces spores by meiosis Gametophytes: multicellular haploid form which produces gametes by mitosis Evolution of Multicellularity Seaweeds, plants, animals, most fungi Various specialized cells that perform different functions and are dependent on each other We have seen multicellularity in three different supergroups Stramenophiles: brown algae Unikonts: fungi and animals Archaeplastids: red algae, green algae, land plants Hypothesis on Phylogeny Two unikont lineages led to animals and fungi Choanoflagellates are the closest relatives of animals and resemble the collar cells of sponges Nucleariids are the closest relatives of fungi Green algae led to plants Charophytes are the closest living relatives of land plants