BIO1130-8-12 Slide Deck PDF

Topic 8 The tree of life Learning Outcomes Describe the 7 properties of life using an organism as an example Justify the importance of the C, H, N, and O in organic molecules Explain how specific properties of life emerged during the formation of protocells List some advantages of...

Topic 8 The tree of life Learning Outcomes Describe the 7 properties of life using an organism as an example Justify the importance of the C, H, N, and O in organic molecules Explain how specific properties of life emerged during the formation of protocells List some advantages of ribonucleic acid molecules for the emergence of life Explain how the fossil record can provide evidence for the evolution of organisms Compare two methods used to date fossils Describe how the Burgess Shale has contributed to our understanding of the evolution of animals Define mass extinction, and provide an example Define adaptive radiations, and provide an example Analyse graphical data to infer major changes in taxonomic diversity List different characteristics of L.U.C.A. Name characteristics that differ between the 3 domains Give examples of organisms for each of the 3 domains Explain the evolution of eukaryotes from endosymbiosis Explain the evolution of multicellularity 2  Topic 8 The tree of life 8.1 – Life and its origin 7 properties of life Heredity and evolution All living organisms share these properties Reproduction Growth and development Regulation Energy and and metabolism homeostasis Cellular Response to Living organism organization stimuli Virus are not considered organisms: No cellular organization No internal metabolism No growth or development 4 First evidence of life on Earth Age of the universe 13.8 billion years Age of the earth 4.6 billion years First direct evidence of life: 3.5 billion years James Webb Telescope (deep field) Fossil: preserved remnant or impression of an organism that lived in the past Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of sediment together Stromatolites – 3,500Ma (Shark Bay, AUS) 5 First evidence of life on Earth Age of the universe 13.8 billion years Age of the earth 4.6 billion years First direct evidence of life: 3.5 billion years James Webb Telescope (deep field) Fossil: preserved remnant or impression of an organism that lived in the past Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of sediment together Stromatolites Stromatolites – 450Ma(Shark – 3,500Ma (Ottawa, ON) Bay, AUS) 6 First evidence of life on Earth Age of the universe 13.8 billion years Age of the earth 4.6 billion years First direct evidence of life: 3.5 billion years James Webb Telescope (deep field) Fossil: preserved remnant or impression of an organism that lived in the past Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of sediment together Cyanobacteria Stromatolite (side view) Stromatolite (top view) Stromatolites Stromatolites – 450Ma(Shark – 3,500Ma (Ottawa, ON) Bay, AUS) 7 First evidence of life on Earth Age of the universe 13.8 billion years Age of the earth 4.6 billion years First direct evidence of life: 3.5 billion years James Webb Telescope (deep field) Fossil: preserved remnant or impression of an organism that lived in the past Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of sediment together Photosynthetic activity Sediments trapped Cyanobacteria Stromatolite (side view) Stromatolite (top view) 8 Life on Earth uses carbon (C) Highly abundant on earth and in the atmosphere CO2 on WASP-39 b (exoplanet) Human body composition Carbon (C), oxygen (O), hydrogen (H) and nitrogen (N) constitute the majority of biological molecules: Carbohydrates Proteins Fatty acids Nucleic acids, etc. 9 How did life originate on earth? From organic molecules to protocells Four necessary steps: 1. The abiotic synthesis of small organic molecules (monomers: amino acids, nitrogenous bases…) 2. The polymerization of small molecules into macromolecules (polymers: proteins, nucleic acids…) 3. The packaging of these molecules into protocells (precursors of cells, with only some components) 4. The origin of inheritance through the transmission of self-replicating molecules “Primordial soup” or “prebiotic soup”: Hypothetical set of conditions that led to the transition from the abiotic world to the biotic world (water, monomers, energy) 11 Stanley Miller’s experiment (1953) Artificial and spontaneous synthesis of organic matter under conditions mimicking the early earth’s atmosphere (methane, ammonia, hydrogen) and lightning (energy). → Synthesis of formaldehyde, hydrogen cyanide, amino acids and hydrocarbons… from abiotic molecules. Similar experiments simulating volcanoes led to the synthesis of more amino acids Murchison meteorite Re-analysis of Miller’s data Deep-sea vents (18 amino acids) 12 Formation of macromolecules From monomers (1 molecule) to oligomers (2-10 repeated molecules) or polymers (>10) Polymers of amino acids and nitrogenous bases can form spontaneously without enzymes or ribosomes. Precursor molecules (simple amino acids or nitrogen bases) Thermal energy (heat) Catalyst (chemical agent that selectively increases the rate of a reaction): Fe 2+, Pb2+, Mg2+, etc. Clay has been found to be a mineral catalyst for the polymerization of RNA. 13 Formation of protocells Protocell: droplet with membranes (ex: bilayer of fatty acids) that maintained an internal chemistry different from that of the environment Protocells were not living organisms… (lack genetic material). Experiments have shown… Vesicles can divide spontaneously (reproduction) Replication reactions inside vesicles (internal metabolism) Vesicles can increase in size (growth) Membranes can be selectively permeable (regulation) Membranes can perform metabolic reactions using external molecules (response to the environment) → Properties of life can emerge from the abiotic world. 14 Self-replication Proteins (e.g. enzymes) are synthesized from DNA and RNA. DNA and RNA are synthesized through enzymatic reactions. → So which came first? Enzymes or nucleic acids? RNA molecules can also be catalysts and function as enzymes: ribozymes Ribozymes can copy other RNA molecules: self-replication → “RNA world” Natural selection can favor RNA molecules that can self-replicate faster The passing of RNA of a splitting vesicle to daughter vesicles constitute inheritance Given this inheritance, some error in RNA replication, some variation in replication rate... … evolution through natural selection can proceed! 15  Topic 8 The tree of life 8.2 – Using fossil records What can fossils tell us? The Tree of Life The tree of life describes the evolutionary relationship between all organisms (living or extinct) Similarities in morphology, anatomy or genetic sequences can be used to group species together The tree topology is constantly changing as it is being refined with the accumulation of new data 18 Geological and fossils records Relative and absolute age of fossils can inform us on the evolutionary history of organisms: Many fossils belong to species that no longer exist and that went extinct Some fossils resemble organisms that still exist nowadays Organisms can undergo very rapid morphological changes Mary Anning (1799-1847) Plesiosaurus dolichodeirus Duria Antiquior Red Dead Redemption 2 Henry De la Beche (1830) 19 20 Geological and fossils records Biostratigraphy: determination of relative age (imprecise and/or inaccurate) → sedimentary rocks Radiometric dating: determination of absolute age (precise and accurate) → magmatic rocks Faunal succession: Specific vertical sequence of fossilized flora and fauna that can be identified reliably over wide horizontal distances. Grand Canyon, AZ Specific fossil composition help define biozones (intervals of geological strata). Cornwall, UK 21 Geological and fossils records Biostratigraphy: determination of relative age (imprecise and/or inaccurate) → sedimentary rocks Radiometric dating: determination of absolute age (precise and accurate) → magmatic rocks Faunal succession: Specific vertical sequence of fossilized flora and fauna that can be identified reliably over wide horizontal distances. Grand Canyon, AZ Specific fossil composition help define biozones (intervals of geological strata). Cornwall, UK 22 Geological and fossils records Biostratigraphy: determination of relative age (imprecise and/or inaccurate) → sedimentary rocks Radiometric dating: determination of absolute age (precise and accurate) → magmatic rocks Faunal succession: Specific vertical sequence of fossilized flora and fauna that can be identified reliably over wide horizontal distances. Grand Canyon, AZ Specific fossil composition help define biozones (intervals of geological strata). Cornwall, UK 23 Biostratigraphy Species that have very specific ecological requirements, that lived for a very short geological period are excellent biomarkers (or diagnostic species) for the chronological dating of sedimentary rocks. Ex: Foraminifera (unicellular aquatic eukaryotes) - Cambrian 540Mya very wide geographical distribution very specific habitats large morphological diversity often well preserved (CaCO3: calcium carbonate shell) 24 Radiometric dating Steve Leonard Radiometric dating uses changes in the isotope composition of: organisms during their transition into fossils magmatic rocks… but not sedimentary rocks Isotopes: elements with the same # of protons different # of neutrons At time of death, the organism no longer takes up any carbon from the environment. Then... → The unstable (parent) isotope 14C decays into a daughter isotope (14N) at a constant known rate. → The stable isotope 12C in the fossil remains constant until the fossil is discovered. Half-life: amount of time it takes for 50% of the parent isotope (14C) to decay into a daughter isotope (14N). Parent Daughter Half-life Dating range isotope isotope (years) (years) Carbon-14 Nitrogen-14 5,730 100 - 60,000 Potassium-40 Argon-40 1.25 Gy 10 My – 4.5 Gy 25 But the fossil record is often incomplete Many fossils were destroyed over time or not yet discovered Bias towards species that existed for long evolutionary times and those with hard shells/skeletons. Discontinuity in the fossil record can reflect important geological, ecological and evolutionary events: Plate tectonics, erosion, decrease in the rate (or halt) of sedimentation Changes in climate/habitat, retreat of seas and glaciers Species colonization, phenotypic evolution, speciation, extinction, etc. Spinophorosaurus nigerensis (~170Ma) 26 Biostratigraphy 27  Topic 8 The tree of life 8.3 – Mass extinctions, adaptive radiations and key innovations A changing world 29 The Cambrian explosion 30 The Cambrian explosion 31 The Burgess Shale (506Mya) Paleontological site in British Colombia (1909) → sediments with large diversity of fossilized animals Very different lifestyles: Benthic (living on the sediments) Endobenthic (living in the sediments) Nektonic (swimming freely) Burgess Shale Burgess Shale (Charles Walcott) Oryctocephalus Ottoia Marrella 32 The Cambrian explosion Many animal phyla we know today appeared around the same time: ~535-525 My (↑ morphological diversity) From soft-bodied to hard shells organisms: defensive adaptations transition from grazers/suspension feeders to predators → new body-plans, prey/predator relationships Evolutionary success of bilateral symmetry which already existed: Anterior sensing organs (development of a nervous system) Anterior predation appendages (prey capturing and feeding) Posterior appendages for movement (swimming, crawling, flying, etc.) Many adaptive radiations: Radial symmetry Bilateral symmetry → Period of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles in their communities. 33 Mass extinctions Geological/paleontological eras are defined by the massive changes in the abundance/composition of the fossil record such as mass extinctions (when large number of species become extinct). Mass extinctions can be caused by changes in temperature, massive volcanic eruptions, meteorites, etc. → All leading to a cascade of dramatic ecological events → Mass extinctions are always followed by new adaptive radiations and many new families and genera 34 Mass extinctions Geological/paleontological eras are defined by the massive changes in the abundance/composition of the fossil record such as mass extinctions (when large number of species become extinct). Mass extinctions can be caused by changes in temperature, massive volcanic eruptions, meteorites, etc. → All leading to a cascade of dramatic ecological events → Mass extinctions are always followed by new adaptive 3 radiations and many new families and genera 1 5 5 mass extinctions. 2 4 Permian extinction (3 in the figure): 96% species lost (81% marine, 70% terrestrial vertebrates) ↓ T°C (-250m sea level) followed by large ↑ T°C, ↓O2, ↑CO2, → ocean acidification, volcanic eruptions (Siberian Traps). 35 Mass extinctions Geological/paleontological eras are defined by the massive changes in the abundance/composition of the fossil record such as mass extinctions (when large number of species become extinct). Mass extinctions can be caused by changes in temperature, massive volcanic eruptions, meteorites, etc. → All leading to a cascade of dramatic ecological events → Mass extinctions are always followed by new adaptive 3 radiations and many new families and genera 1 5 5 mass extinctions. 2 4 Cretaceous - Paleogene (5 in the figure): - 75% species 36 Key innovations in the fossil record 6.5 Mya First cells (prokaryotes) 485 Mya Increase in atmospheric O2 concentration 635 Mya Endosymbiosis (eukaryotes) 3,500 Mya Sexual reproduction Multicellularity 1,200 Mya Colonization of land 1,800 Mya 2,700 Mya 37 Key innovations in the fossil record First cells (prokaryotes) Increase in atmospheric O2 concentration Endosymbiosis (eukaryotes) Sexual reproduction Multicellularity Colonization of land 38  Topic 8 The tree of life 8.4 – Three domains and millions of species Number of species in the tree Many species are still being discovered and many went extinct! → The number of species or members of a taxonomic level reaches an asymptote (an apparent maximum) The number of prokaryotes species remains highly unknown! Mora et al. 2011 40 Number of species in the tree Many species are still being discovered and many went extinct! → The number of species or members of a taxonomic level reaches an asymptote (an apparent maximum) The number of prokaryotes species remains highly unknown! Mora et al. 2011 Number of species predicted: >11,750,000… Predicted …but only ~1,410,500 are described! Described Land Of those, only ~200,000 oceanic species were described! Ocean 41 Last Universal Common Ancestor (L.U.C.A) All living organisms synthesize and use only L optical isomers of amino acids The genetic code, is almost universal LUCA was not necessarily the first living organism!! …but rather the latest organism that is ancestral to all existing living organisms we know today. In 2006, researchers analyzed 286,514 known proteins: → 355 genes were likely present in LUCA’s small circular DNA genome LUCA was likely living near deep-sea vents, deprived of oxygen (anaerobic) but rich CO2 and H2. 42 The Tree of Life – a 3 domains system Saccharomyces cerevisiae Pyrococcus furiosus Escherichia coli 43 The Tree of Life – a 3 domains system 44 Domain of Bacteria ~700,000 species estimated (10,000 are described) Very diverse metabolism Photosynthetic, aerobe, and anaerobe Can also use O2, SO42-, NO3-, NH3, H2S… Highly resistant to harsh conditions 45 Domain of Bacteria ~700,000 species estimated (10,000 are described) Very diverse metabolism Photosynthetic, aerobe, and anaerobe Can also use O2, SO42-, NO3-, NH3, H2S… Highly resistant to harsh conditions The most studied organism (cloning) Easily grown in the lab on petri dish Cell division every 20min at 37°C Escherichia coli 46 Domain of Archaea ~50,000 species estimated (500 are described) Are considered prokaryotes but different from bacteria Extremophiles: lives in extreme environmental conditions: acidic, hot, high salinity… Many are methanogens: use CO2 and H2 and produce CH4 (methane) 47 Domain of Archaea ~50,000 species estimated (500 are described) Are considered prokaryotes but different from bacteria Extremophiles: lives in extreme environmental conditions: acidic, hot, high salinity… Many are methanogens: use CO2 and H2 and produce CH4 (methane) 70-103°C and pH~5 to 9 Source of DNA polymerase: used in molecular biology labs for its heat-resistance → Polymerisation Chain Reaction: PCR (COVID19 testing, cloning, sequencing) Pyrococcus furiosus 48 Domain of Eukarya ~11,000,000 species estimated (1,400,000 are described) Evolved from prokaryotes within the Archaea branch Cytoskeleton, endomembrane system, nucleus Serial endosymbiosis: prokaryotic cells engulfed by an ancestral archaea cell (1,800Mya). → Mitochondrion, plastid: organelles possessing a circular DNA, their own transcription/translation proteins, ribosomes/membrane proteins similar to those of bacteria. → Benefits: the cell gains a new metabolic system (ex: aerobic respiration with increasing O2 concentrations). 49 Multicellularity (1,200 Mya) Some multicellular All multicellular Colonial hypothesis: colonies form through the cooperation of unicellular organisms of the same species → cells fail to separate (or separate and rejoin) → specialization can occur Ex: colonies of cyanobacteria Photosynthetic cells Nitrogen fixing cells (heterocyst) Anabaena circinalis Symbiosis hypothesis: cells from different species establish a mutually beneficial and long-term association… … not likely (requires both genomes to merge into a unique one). 50  Topic 9 Prokaryotes Learning Outcomes Differentiate bacteria and archaea based on morphological and anatomical characteristics Classify specific structures into Gram (+) and Gram (-) bacteria Defend the importance of bacteria using quantitative or qualitative examples Classify organisms based on nutritional requirements Provide arguments for the importance of prokaryotes in the ecosystem Explain how cellular mechanisms in bacteria can influence populations dynamic and evolution Describe mechanisms that can lead to the evolution of antibiotic resistance Explain three processes that can lead to the formation of a recombinant bacteria 52  Topic 9 Bacteria and archaea 9.1 – Characteristics of prokaryotes Prokaryotes Pro- (before in Greek) and karyon- (nucleus in Greek). The group of prokaryotes is considered a paraphyletic group → group of taxa that includes the common ancestor (L.U.C.A, likely a procaryote) and some of its descendants. 750,000 species Archaea are not bacteria! 54 Prokaryotes 0.5-5µm in size. Plasma membrane which constitutes a selective barrier with the environment. Cytoplasm (content of the cell within the plasma membrane) is only made of the cytosol: internal fluid containing organic molecules, proteins, metabolic waste, etc. Absence of nucleus: circular chromosome located in the nucleoid (region not enclosed by a membrane). Fimbriae: short appendages helping bacteria to adhere to the substrate or to other cells. Capsule: dense layer of polysaccharide or protein surrounding the cell wall. → protects the cell and allows the bacteria to adhere to substrates or cells Absence of organelles (membrane-enclosed structures with specialized functions) 55 Prokaryotes Bacteria lack histones (proteins that bind to the DNA and play a key role in the packaging of the genome in eukaryotic cells) but are present in some archaea. Protective cell wall made of peptidoglycan in bacteria (very different in archaea, made of pseudomurein). Flagellum: long cellular appendage specialized for locomotion → Taxis: directed movement towards or away from a stimulus 56 Gram classification Bacteria can be classed according to the structure of their cell wall into Gram (+) and Gram (-) Gram negative bacteria tend to be more resistant to antibiotic (the outer membrane blocks water soluble antibiotics) Clostridium tetani Escherichia coli (tetanus) (gastroenteritis) Staphylococcus aureus Yersinia pestis (infections and food intoxications) (plague) 57  Topic 9 Bacteria and archaea 9.2 – Nutrition and growth Are bacteria good or bad? Bacteria 60 Nutritional requirements Abundance and diversity in the microbiome can vary between/within a host. Bacteria can be responsible for many infectious diseases 1012 human cells for 1013 bacteria! → Digestion, vitamins, immunity, protection against infections… Microbiome: community of microorganisms that live on and in the human body (up to 400 species in the gut). Commensalism: symbiotic relationship where an organism benefits but the other is not helped or harmed. 61 Nutritional requirements Organism Chemical compound Energy source Light Glucose, H2S, NH3 Phototroph Chemotroph Inorganic compound Organic compound Inorganic compound Organic compound Carbon source (ex: CO2, HCO3-) (Glucose) (ex: CO2, HCO3-) (ex: Glucose, lipids) Photoautotroph Photoheterotroph Chemoautotroph Chemoheterotroph Anabaena sp. Rhodobacter sp. Sulfolobus sp. Clostridium sp. 62 Nutritional requirements Organism Chemical compound Energy source Light Glucose, H2S, NH3 Phototroph Chemotroph Inorganic compound Organic compound Inorganic compound Organic compound Carbon source (ex: CO2, HCO3-) (Glucose) (ex: CO2, HCO3-) (ex: Glucose, lipids) Photoautotroph Photoheterotroph Chemoautotroph Chemoheterotroph Anabaena sp. Rhodobacter sp. Sulfolobus sp. Clostridium sp. 63 Role of prokaryotes in the ecosystem Food webs depend on primary producers (ex: photoautotrophs) for two things: 1. Absorbing energy from outside the ecosystem (ex: sunlight): → Photoautotroph (ex: cyanobacteria) can… convert CO2 into sugars that enter the food chain produce O2 used by chemoheterotroph during respiration fix atmospheric N2 and produce proteins/nucleic acids Cyanobacteria 2. Assimilating minerals into biomass that is passed on upper trophic levels. → Decomposers: absorb and convert nutrients from nonliving organic material (corpses, fallen plant material…) into inorganic forms. = recycling of C, H, O, N, P between the biotic and the abiotic world. 64 Asexual reproduction Reproduction by binary fission: doubling in size and simple division in half (≠ mitosis) Binary fission requires the replication of the genome, initiated at the “Origin of Replication” The two daughter cells are clones of the mother cell. Escherichia coli 65 Prokaryotes can evolve rapidly Dr. Richard Lenski started a Long-Term Evolutionary Experiment (LTEE) in 1988 12 populations of E. coli are grown in parallel in low-glucose medium All populations adapted over time and grew faster compared to the ancestral population (= the control population) New mutations allowed populations to use glucose more efficiently (adaptation) At generation ~33,000 one population started to use citrate as a carbon source → A mutation in the citT gene allowed the transport citrate inside the cell in the presence of O2 → Even rare mutations during DNA replication (rate ~1 per 10 million divisions) can lead to rapid adaptation (large populations and short generation time ~20min) → Despite their small size and small genome, bacteria can evolve rapidly to harsh conditions. They have evolved for 3.5 billion years and are still evolving! 66 Asexual reproduction Reproduction by binary fission: doubling in size and simple division in half (≠ mitosis) Binary fission requires the replication of the genome, initiated at the “Origin of Replication” The two daughter cells are clones of the mother cell. The population doubles every generation → exponential growth curve (linear on a log scale) 1. Lag phase: synthesis of components required for growth 2. Log phase: rapid growth through cell divisions by a factor of 2 n (n = number of generations) 3. Stationary phase: population stops to grow (lack of nutrients, oxygen, metabolic waste accumulation, etc.), activation of stress response 4. Death phase: exponential loss of viability due to lack of nutrients, oxygen or prolonged exposure to waste 67  Topic 9 Bacteria and archaea 9.3 – Antibiotic resistance and genetic recombination Resistance to antibiotics Antibiotic: molecule that kills or inhibits the growth of bacteria Bacteria can evolve resistance to antibiotics! Normal bacteria colony Mutations can alter genes coding for proteins that are the target of antibiotic Growth inhibition → genetic variation between bacterial strains zone Penicillium colony (fungus) Resistance can be transmitted vertically through inheritance Penicillium inhibiting bacterial growth (Fleming 1929) → heritability of the acquired resistance Metabolism Only the resistant strains can grow DNA → selection for resistance Cell wall polymerase RNA polymerase Cell membrane But… more and more resistant strains → Many new antibiotics are synthesized to inhibit new cellular targets Protein synthesis 69 Conjugation Strains of bacteria from the same species can donate DNA through conjugation: 1. Two cells are temporarily joined through a pilus (hair-like structure) that draws the receiver cell closer 2. Establishment of a mating bridge (direct contact) 3. A plasmid (small circular chromosome) can be transferred from the donor to the receiver. F factor (Fertility factor) contains genes required to make the pilus (= selfish DNA: DNA that enhances its own transmission… relative to other DNA inside the cell). Genes carried by the R plasmid confer antibiotic resistance and can also spread through conjugation. R plasmid: resistance plasmid which contains both the antibiotic resistance genes… and the genes coding for the sex pilus (just like the F-factor does). 70 Conjugation Horizontal gene transfer Vertical gene transfer 71 Transduction Infection from a phage Bacteria can also exchange DNA through a virus called bacteriophage (a virus that infects bacteria). Replication of the phage genome and protein synthesis Assembly of the phage some bacterial DNA can be packaged in the new virus Infection of a new bacteria and recombination allows the integration of the donor’s allele in the recipient’s genome New bacterial genotype with → The phage therefore represents an a new allele combination intermediate between a donor cell and a recipient cell. 72 Transformation Bacteria can release their DNA (ex: after the cell death) which can be taken up by another bacteria directly from the extracellular environment. Occurs naturally when a bacteria recognizes a foreign DNA and transports it inside the cell Used in molecular biology laboratories to create new bacterial strains and clone a gene The new recombinant strain carries a plasmid with one or more genes of interest. Used for example in the production of the COVID19 vaccine! → copy the SARS-Cov2 spike protein gene into millions of copies 73 So… are bacteria good or bad?  Topic 10 Eukaryotes Learning Outcomes Compare prokaryotes and eukaryotes based on cellular characteristics Associate cellular structures of eukaryotes with their functions Justify why the evolution of multicellularity and sexual reproduction were key innovations Explain the benefits of both sexual reproduction and asexual reproduction Place on a life cycle the ploidy level (n or 2n), mitosis, spores, meiosis, gametes, fertilization, zygote Differentiate between the three types of life cycles Name examples of protists Explain the heterozygote advantage against malaria for individuals that have sickle cell anemia Draw mutualistic beneficial relationships between a fungus and a plant, or between a fungus and an algae 76 https://www.wooclap.com/BIO1130 77  Topic 10 Eukaryotes 10.1 – Characteristics of eukaryotes Eukaryotes Eu- (true in Greek) and karyon- (nucleus in Greek). The group of eukaryotes is considered a monophyletic group → it contains the common ancestor and all of the descendants Sea water Grypania spiralis Sediment (photosynthetic algae) 79 Eukaryotes Eu- (true in Greek) and karyon- (nucleus in Greek). The group of eukaryotes is considered a monophyletic group → it contains the common ancestor and all of the descendants First eukaryotic cells ~1,800My from endosymbiosis 80 Eukaryotes 10-100µm in size typically Plasma membrane which constitutes a selective barrier with the environment. Cytoplasm: total content of the cell bounded by the plasma membrane (and excluding the nucleus): - Cytosol (internal fluid containing organic molecules, proteins, metabolic waste, etc.) - Organelles (membrane-enclosed structures with specialized functions) - Inclusions (particles of insoluble substances) Nucleus: contains the genetic material in the form of chromosomes, made of chromatin (DNA + proteins) 81 Eukaryotes Endoplasmic Reticulum (ER): membranous network, continuous with the outer nuclear membrane. → Rough ER (ribosome-studded): synthesis of proteins → Smooth ER: (ribosome-free): synthesis of lipids, carbohydrate metabolism, steroids, detoxification, calcium storage. Golgi apparatus: protein and phospholipid modifications/trafficking Mitochondrion: double membrane-bound organelle performing cellular respiration. Uses oxygen to break down organic molecules and synthesize ATP. Possess its own DNA (endosymbiosis). Cytoskeleton: network of microtubules, microfilaments, and intermediate filaments (mechanical, structural, transport, motility and signalling functions). 82 Eukaryotes Peroxisome: oxidative organelle containing enzymes transferring hydrogen atoms from various substrates to oxygen (O2), producing and then degrading hydrogen peroxide (H 2O2) which is toxic for the cell. Lysosome: digestive organelle (hydrolysis of macromolecules) 83 Eukaryotes Peroxisome: oxidative organelle containing enzymes transferring hydrogen atoms from various substrates to oxygen (O2), producing and then degrading hydrogen peroxide (H 2O2) which is toxic for the cell. Lysosome: digestive organelle (hydrolysis of macromolecules) Flagellum: long cellular appendage specialized for locomotion. Projects from the cytoskeleton and covered by the plasma membrane. Prokaryotic flagella have a very different structure! 84 Photosynthetic Eukaryotes Photosynthetic eukaryotes have both mitochondria and plastids (origin: endosymbiosis) Plastids: family of closely related organelles: - Chloroplasts (photosynthesis) - Chromoplasts (fruit and flower pigmentation) - Amyloplasts (storage of starch = amylose) Chloroplasts: organelle that absorbs sunlight and uses it for the synthesis of organic compounds from carbon dioxide (CO2) and water (H2O). Possess its own DNA. 85 Great variety among eukaryotes Many eukaryotes show structural variation and also the presence or absence of organelles! Animal cells lack cell walls and lack chloroplasts. Plant cells have a central vacuole, a cell wall (cellulose), plastids, often lack flagella Fungi cells lack flagella, have a cell wall (chitin) and have less compartmentation between cells → passage of cytoplasm, organelles, nuclei… (syncytium: multinucleate cell deriving from cell fusion) Some eukaryotes show pseudopodia → cellular extension used in moving and feeding 86  Topic 10 Eukaryotes 10.2 – Sexual reproduction, life cycles and multicellularity Protists 88 Protists Paraphyletic group: includes the ancestor and only some of its descendants. → not a clade). Many branches are still phylogenetically unresolved and the classification still changes. 89 Protists Protists: Any eukaryote that is not a plant, animal, or fungus. Most of the eukaryotic lineages are protists! Most are unicellular but some are colonial or even multicellular. Large diversity in nutrition: Photoautotrophs Heterotrophs Mixotrophs (combine photo- and heterotrophy). Large diversity in reproduction… Asexual (division of the organism in two identical offspring) Sexual (fusion of gametes) …and life cycles: Haplontic/diplontic/haplo-diplontic 90 Sexual reproduction Diploid (2n) individuals of the same species can produce haploid (n) reproductive cells through meiosis These haploid reproductive cells often differ in size (anisogamy) The union of these haploid gametes (n) produce a diploid zygote (2n): fertilization 91 Sexual reproduction Disadvantages of reproducing sexually: It takes time and energy to look for a sexual partner (time spent not feeding) An individual “dilutes” its own genes every generation (only half of its genes are passed on). Reproductive output is decreased by half for a given sex (one sex does not contribute, often the males). → two-fold cost of sex. Advantages of reproducing sexually: New genetic combinations can be beneficial in changing environments. Elimination of deleterious alleles from the population. → can speed adaptation 92 Sexual reproduction Many genes together contribute to an individual’s fitness in a specific environment. → The combinations between all the different alleles are like “poker hands” Winning hands have combinations of cards that work well together → Winning hands have “survived” previous rounds (of selection) Sexual reproduction breaks apart favorable gene combinations built by past selection → Shuffling your cards can produce new combinations that may or may not work well … if the rules change frequently, winners might be better off shuffling their cards!! … if the environment changes over time, genetic associations built up by past selection can become detrimental Consequence: sexual reproduction can…. …speed up adaptation in a changing environment …eliminate deleterious alleles (“bad poker hands”) 93 Life Cycles Life cycle: generation-to-generation sequence of stages in the reproductive history of an organism. 2 phases: haploid (n) and diploid (2n) 3 types of cycles: Diplontic life cycle: Haplodiplontic life cycle: Haplontic life cycle: → multicellular diploid → multicellular diploid → unicellular diploid → multicellular haploid 94 Diplontic Haplo-diplontic Haplontic 95  Unicellular Multicellular Multicellular eukaryotes appeared 25 times independently! First direct evidence: 1,200My Increase in the surface area for diffusion Longer lifespan Specialization of cells into cell types, tissues and organs Protection, feeding, locomotion, reproduction Ex: spherical colonies up to 50,000 cells: Many flagellates somatic (outer layer) Few germ cells (gonidia, inner layer) Grosberg et al 2007 Volvox sp. (green algae) 96  Topic 10 Eukaryotes 10.3 – A few examples 98 Protists Trichomonas vaginalis infects Diatoms: unicellular algae with reproductive/urinary tracts. hard walls made of silica (SiO2) Paramecium caudatum Volvox sp. (predators) Foraminifera (biomarkers of sedimentary rocks) 99 Protists Ex: Plasmodium, parasite transmitted by mosquitos that causes malaria (200M infected and 600,000 death/year). Anopheles gambiae → Haplontic life cycle Inside mosquito Sporozoites (n) MEIOSIS Oocyst MEIOSIS FERTILIZATION Life cycle of Plasmodium falciparum 100 Protists β-globin In regions where malaria is endemic, individuals with sickle cells anemia (mutation in the β-globin, “S” allele) have a survival advantage against malaria fatality over people with normal hemoglobin, “A” alleles. Malaria relative survival Genotype Red blood cells from AS individual Sickle cells anemia inhibits the parasite infection of the host. → Infected cells of S-carrier are destroyed before the parasite can reproduce and infect other cells → Heterozygote advantage and higher frequency of the “S” allele in those regions 101 Protists Dinoflagellates: possess two flagella Can bloom (explosive population growth): “Red tide” Lingulodinium polyedra → coastal upwelling of nutrients (Nitrates, phosphates), → changes in temperatures, water pollutions, etc. Bioluminescence: production and emission of light. Mechanical stress (predator avoidance) → converts chemical energy into light inside a (scintillon) 102 Myxomycetes (slime molds) E.g., Blob Unicellular Physarum polycephalum Can be cut in many pieces Almost immortal Can move Synthesizes pigments Produces spores Can learn 720 sexes 103 Fungi Reproduce sexually and/or asexually. Heterotrophs and decomposers. Saccharomyces cerevisiae Normal bacteria colony Growth inhibition zone Penicillium colony (fungus) Penicillium inhibiting bacterial growth (Fleming 1929) 104 Lichen (a symbiotic association, not an organism) Lichen = symbiosis between a green algae and a fungus) 105 Choanoflagellates Choanoflagellate Single posterior flagellum (propulsion) and chitin in their cell walls (as in exoskeleton, skin, of many animals). 106  Topic 11 The evolution of plants Learning Outcomes Identify the main plant groups based on key characteristics Place the main plant groups on a phylogenetic tree List physical, chemical and biological problems faced by plants during land colonization; and their solutions Explain the causes and consequences of indeterminate growth Explain the expression “reduction of the gametophyte” Associate a plant structure with its ploidy level Provide arguments for the importance of vascularization in plants Explain the advantages of heterospory in plants Justify the evolutionary importance of five key innovations in plants Contrast key characteristics of gymnosperms and angiosperms Explain the process of double fertilization and its biological importance 108  Topic 11 The evolution of plants 11.1 – Key innovations of plants Plants Plants (= embryophytes): 470Mya Eukaryotes Multicellular Embryo Photoautotrophs Cell walls made of cellulose Chloroplasts with chlorophylls, beta-carotenes, xantophylls Sexual reproduction but asexual reproduction is common Development of an embryo that is dependent on its parent 1st photosynthetic organisms that lived permanently on land 110 Plants ~320,000 species of plants were described Reminder: fungi are not plants! Are responsible for a large amount of atmospheric O2 First direct evidence of plant (fossil): Cooksonia → no leaves, no roots, no flowers → had vascular tissues to conduct water → was liberating spores → had cell specialized in gas exchanges 111 Colonization on land Problems of living above the water line: Dry environment Strong effect of gravity No nutrients in the atmosphere Rapid changes in temperatures Advantages of living above the water line: Brighter sunlight, unfiltered by water and phytoplankton More CO2 in the atmosphere than in the water Abundance of nutrients on the shoreline Many adaptations allowed plants to colonize land: … the protection of the spores, the gametes, the zygote and the embryo … maximizing photosynthesis … growth to compensate the lack of movement towards resources 112 Key innovations Alternation of generations (haplodiplontic life cycle): multicellular 2n individual (sporophyte) multicellular n individual (gametophyte) (2n) (n) Embryo retained in the maternal gametophyte tissues → protection and nutrition (sugars, amino acids, etc.) (n) The spores are protected by a wall made of a highly resistant polymer (sporopollenin) (2n) Spore dispersion occurs in the air (independently from water) (n) 113 Key innovations (n) The egg is non-motile but the sperm cell can often swim in water (n) Presence of waxy cuticle: protects against desiccation Presence of stomata: pore surrounded by guard cells in the epidermis of leaves and stems allows gas exchange (CO2 and O2) and water loss regulation. 114 Key innovations Plants don’t move and show indeterminate growth: growth that is not terminated, giving rise to a structure not entirely predetermined genetically. → can respond to the environment (i.e., plasticity of the architecture) → maximizes exposure to resources: Nutrients and water (roots) Sunlight and CO2 (shoot: stems, branches, leaves, flowers) Apical meristem: region of undifferentiated stem cell that divide at the tip of roots and shoots. Stem cell proliferation with differentiation (and indeterminacy) is coordinated by the CLV3-WUS signaling pathway. Growth and cell identity doesn’t depend on cell line of origin but depends on: the cells relative positioning Somssich et al. (2016) the effects of the environment (light, water, nutrients, hormones, etc.) 115 Key innovations Mutations in the CLV3 gene increases cell proliferation, stem size, flower number, and fruit size in Arabidopsis. Plants don’t move and show indeterminate growth: growth that is not terminated, giving rise to a structure not entirely predetermined genetically. → can respond to the environment (i.e., plasticity of the architecture) Negative feedback loop between: CLV3 (differentiation-promoting peptide) → maximizes exposure to resources: WUS (stem cell-promoting transcription factor). Nutrients and water (roots) Sunlight and CO2 (shoot: stems, branches, leaves, flowers) Mutations Apical meristem: in theof region WUS gene decreases undifferentiated cell cell that divide at the stem proliferation, tip ofproduces irregular roots and shoots and shoots. just a few (defective) flowers in Arabidopsis. Stem cell proliferation with differentiation (and indeterminacy) is coordinated by the CLV3-WUS signaling pathway. Growth and cell identity doesn’t depend on cell line of origin but depends on: the cells relative positioning Somssich et al. (2016) the effects of the environment (light, water, nutrients, hormones, etc.) 116 Key innovations 117  Topic 11 The evolution of plants 11.2 – Non-vascular plants Bryophytes: paraphyletic group of all non-vascular plants. They do not produce seeds or flowers. Absence of specialized tissues that conduct water and nutrients 119 Plants Marchantia polymorpha Cups contain gemmae (cell buds) that can propagate and (asexual reproduction) and grow into a new individual. 120 Life cycle of a moss (bryophyte) Bryophytes have life cycles that are dominated by gametophytes. Spore germination and sperm cell swimming depend on water. No vascular system (stem/roots) Bryum argenteum Rhizoids: filament that attaches to the substrate. → no absorption of water/minerals Bryum argenteum 121  Topic 11 The evolution of plants 11.3 – Vascularization Tracheophytes: monophyletic group of all vascular plants → life-cycle dominated by the sporophyte (larger and more complex). → The gametophyte is reduced in size! 123 Vascularization Vascularization: presence of lignified tissues that transport water, nutrients andsugars through the plant. On land, sunlight, CO2, nutrients and H2O are not in the same location. → need a transport system to complete photosynthesis Two specialized transport tissues: Xylem: water and minerals to the leaves Phloem: sugars, the products of photosynthesis Lignin: polymer in cell walls (impermeable to water and structural support for gravity) → Plants now have the support to grow tall, disperse farther and compete for light First forests (Devonian ~380Mya) 124 Production of spores Leaves can be specialized to produce spores… … only 1 type (homosporous) producing a bisexual gametophyte: → most seedless vascular plants Fern Microsporangium … or 2 types (heterosporous) producing either a gametophyte or a gametophyte: → all seed plants Megasporangium Advantages of heterospory: for each spore: specific selection with specific functions a separate gametophyte can better nourish the embryo (no energy spent producing gametes) and gametophytes can mature at different times (no self-fertilization = higher genetic diversity) 125  Topic 11 The evolution of plants 11.4 – Seed and flower plants Spermatophytes: seed plants Seed: embryo surrounded by nutritive substances and a protective coat 127 Five key innovations of seed plants 1. An extremely reduced gametophyte (often microscopic) is protected from environmental stresses, from UV and from desiccation and is directly nourished from the sporophyte. = Pollen grain 128 Five key innovations of seed plants 2. Ovule: structure containing the megaspore → Fertilization without requiring water from the environment 3. Seed plants are heterosporous: Microspore → gametophyte (n) which can disperse farther. Megaspore → gametophyte (n) and nourishes of the developing embryo. 4. Pollen grain: gametophyte (n) enclosed within a pollen wall. → Can disperse very far (wind, animals, etc.). 129 Five key innovations of seed plants 5. Production of a seed: ↑ survival of plants during reproduction. embryo is nourished and can resist drought or low temperatures → Seed germination during favourable conditions. → Adaptations to many new environments. E.g., Jack pine: germination only after periodic fires Pinus banksiana (Jack pine) 130 Svalbard global seed vault (Norway) Long-term storage of duplicates of seeds collected around the world. → Loss of seeds due to mismanagement, accident, equipment failures, funding cuts, and natural disasters. -18°C, low oxygen Indigenous communities have deposited seeds duplicates: Parque de la Papa in Peru deposited 750 samples of potatoes (2015) The Cherokee Nation became the first US tribe to deposit 9 samples of heirloom food crops which predate European colonization. Cherokee Nation Principal Chief Chuck Hoskin Jr. and Secretary of Natural Resources Chad Harsha As of 2021… 1,081,026 distinct crop samples (>13,000 years of agricultural history) 131 Angiosperms Gymnosperms produce seeds (not enclosed in chambers) but no flowers 132 Gymnosperms Gymnosperms (gymno: naked, sperm: seed) → the seed is exposed on sporophylls and can survive years before germination. Seed after fertilization Pollen and seeds = key terrestrial adaptations. by pollen Evolved as the climate became much dryer (outcompeted many vascular seedless plants) Most sperm cells from gymnosperms are not flagellated (exception: Ginkgo) Sequoia sempervirens Pinus halepensis Sequoia Aleppo pine 133 Angiosperms Angiosperms flowering plants, produce seeds (enclosed in chambers: ovaries) → 90% of all living plant species 134 Flower plants Angiosperms (angio: receptacle, sperm: seed) ~250,000 species → seed enclosed in a chamber (carpel) that matures into a fruit Flower: modified leaves (sporophylls) specialized in reproduction → carpel (megasporophyll) produces the gametophyte Flower Seed after fertilization by pollen → stamen (microsporophyll) produces the gametophyte Coevolution with animal species who participate in pollination Fruit: mature ovary of a flower, that helps seed dispersal Wind (anemochory) Animals (zoochory) 135 Flower plants The transfer of pollen (pollination) to the female egg is independent of water (non-motile sperm). Cross-pollination (between individual plants) Double fertilization: one sperm cell fertilizes the egg → zygote the other sperm cell fuses with two nuclei of the central cell → endosperm (tissue that nourishes the developing embryo) The ovary matures into a fruit The ovules mature into seeds 136  Topic 12 The evolution of animals I Learning Outcomes List and define characteristics that are shared by all animals Demonstrate how genetic data can help determine the position of animals within the phylogeny Identify various modes of asexual reproduction in animals Justify the benefits of bilateral symmetry Explain how homeotic genes can affect the resemblance between different animal body plans Define key words in animal embryogenesis and development Associate each embryonic tissues with the organs they form Illustrate differences between the development of protostomes and deuterostomes Calculate, compare and explain the consequences of different surface-to-volume ratios Define the different modes of thermoregulations Determine the modes of thermoregulation based on graphical data Explain and provide examples of adaptations in response to physical/physiological problems that animals face on land 138  Topic 12 The evolution of animals I 12.1 – Characteristics of animals Animals First direct evidence. (560 Mya). Multicellular soft- bodied eukaryote. Molecules of cholesterol (only produced by animals). 140 What is an animal? Eukaryotes Multicellular Heterotroph (organic source of carbon to produce its own organic molecules) … with a few exceptions: Elysia chlorotica (sap sucking slug) → steal chloroplasts (kleptoplast) from algae but these are not transmitted to the next generation. Some photosynthesis proteins genes have been transferred to the slug’s genome! ~ 1.5M species 141 What is an animal? Eukaryotes Multicellular Heterotroph (organic source of carbon to produce its own organic molecules) … with a few exceptions: Elysia chlorotica (sap sucking slug) → steal chloroplasts (kleptoplast) from algae but these are not transmitted to the next generation. Some photosynthesis proteins genes have been transferred to the slug’s genome! Breathe oxygen (aerobic/oxidative respiration) ~ 1.5M species 142 What is an animal? Able to move Able to reproduce sexually (or both sexually and asexually) Cells organized into tissues (integrated group of cells with a common structure, function, or both.) Development goes through the blastula stage Absence of cell wall → extracellular matrix with interconnected proteins (e.g. collagen) to maintain cohesion and structural support. 143 Multicellularity: a key step Multicellularity requires the evolution cell adherence (attachment) and cell signaling (communication). Similarities between unicellular choanoflagellates and multicellular animals → Comparative analyses of genome sequences. Zebrafish Cadherins: proteins involved in cell-to-cell attachment Sponge (Oscarella carmela) …but animal cadherins also contain a highly conserved region not found in the choanoflagellates… → the cytoplasmic cadherin domain (CCD) Nichols et al 2012 → Transition to multicellularity in animals involved new ways of using proteins or parts of pre-existing proteins 144 Tissues and cell specialization Sponges have… …choanocytes that resemble choanoflagellates (feeding by filtration) …amoebocytes that transport nutrients to other cells and can differentiate into any other cell. 145 Tissues and cell specialization Sponges (porifera) do not have true tissues → cells are not connected together and are not separated from other tissues by membranous layers Sponges have… …choanocytes that resemble choanoflagellates (feeding by filtration) Sponges also do not have neurons …amoebocytes that transport nutrients to other cells and can differentiate into any This isother cell. in contrast with Eumetazoa Protostomia 146 Reproduction Life cycle is dominated by the diploid phase (multicellular, more complex individual): diplontic life cycle. The two haploid gametes (non-motile egg and flagellated sperm) are produced by meiosis and do not undergo mitosis: unicellular haploid phase. Sperm cell (Drosophila bifurca) 147 Reproduction All animals reproduce sexually, but some can also reproduce asexually: Budding in jellyfish 148 Reproduction All animals reproduce sexually, but some can also reproduce asexually: Fragmentation in sponges and flatworms (planaria) → Presence of neoblasts: undifferentiated stem cells that can regenerate an entire organism 149 Reproduction All animals reproduce sexually, but some can also reproduce asexually: Parthenogenesis: asexual reproduction in which females produce offspring from unfertilized eggs. Zebra shark New Mexico whiptail Stegostoma fasciatum Aspidoscelis neomexicanus 150  Topic 12 The evolution of animals I 12.2 – Body plans, embryogenesis and development Body plans Radial symmetry: Central axis No anterior or posterior region Bilateral symmetry: Dorsal and ventral sides Anterior region (mouth and sensory organs) Posterior region (tail, anus, feeding, locomotion) 152 Body plans Genes that control animal development are similar across a broad range of taxa. Hox genes play important roles in the development of animal embryos → control the expression of >100 other genes determining the morphology Hox genes are homeotic genes: regulatory genes that control the placement/spatial organization of body parts by controlling the developmental fate of groups of cells. → identity of tissues, orientation, segmentation, repetitions… The colour code indicates the parts of the embryos in which these genes are expressed and the adult body regions that result. 153 Body plans Some animals do not develop directly into adults → at least one larval stage with a very different morphology. Larva: sexually immature form of an animal that is morphologically distinct from the adult → usually eats different food, and lives in a different habitat than the adult (less competition) Metamorphosis: developmental transformation that turns the animal into a juvenile that resembles an adult but is not yet sexually mature. 154 Embryogenesis and development Diploid zygote undergoes mitosis (without cell growth) → blastula 8-cells stage, cell divisions can undergo either… Spiral cleavage: oblique to the axis of the body. Radial cleavage: parallel to the axis of the body. Determinate cleavage: each cell defines a specific part of the embryo. Indeterminate cleavage: each cell has the potential to produce a complete embryo. Gastrulation (formation of a gastrula through infolding) → Formation of embryonic tissues that will develop into adult body parts 155 Embryogenesis and development The archenteron represents the primitive gut (= external environment) Blastopore develops into: The blastopore corresponds to the opening of the archenteron the mouth (protostomes = “mouth 1st”) or… the anus in (deuterostomes = “mouth 2nd”) 156 Embryogenesis and development The archenteron represents the primitive gut (= external environment) Blastopore develops into: The blastopore corresponds to the opening of the archenteron the mouth (protostomes = “mouth 1st”) or… the anus in (deuterostomes = “mouth 2nd”) 157 Embryogenesis and development Animals with radial symmetry show two embryonic tissues only: Ectoderm Diploblastic (coral, jellyfish, cnidaria…) Endoderm Animals with bilateral symmetry show three embryonic tissues: Ectoderm Mesoderm Triploblastic (worms, insects, vertebrates…) Endoderm These embryonic tissues (germ layers) form the specific tissues and organs of the body. 158 Coelom and organs in the mesoderm The coelom corresponds to the cavity lined by tissues derived from the mesoderm between the digestive track (derived from the endoderm) and the outer body layer (derived from the ectoderm) Functions of body cavities: Structural support of the body (skeleton and hydrostatic skeleton) Transport and diffusion system (nutrients, gas exchanges, waste elimination…) Allow the growth of organs and their independent movements Some triploblastic animals lost the coelom (acoelomates) Organs are suspended in the coelom and become more specialized: More efficient digestion (digestive track) Increased production and storage of gametes (gonads) 159 Embryogenesis and development The infolding of the neural plate (from the ectoderm) forms the neural tube and many structures of the nervous and sensory system The notochord is a dorsal, longitudinal and flexible rod (from the mesoderm) along the anterior-posterior axis of a chordates → Gives structural support (the spine in vertebrates) 160