Topic 8 - The Tree of Life BIO1130 PDF

Welcome to the 2nd part of BIO1130! A few words on the 2nd part of the course • All lectures are in-person • No lecture videos to watch prior to class • Learning activities during class • Lectures are recorded and will be posted on BrightSpace • Material (including a few problems with their soluti...

Welcome to the 2nd part of BIO1130! A few words on the 2nd part of the course • All lectures are in-person • No lecture videos to watch prior to class • Learning activities during class • Lectures are recorded and will be posted on BrightSpace • Material (including a few problems with their solutions will be posted ahead of the lectures) • Additional Wooclap practice quizzes are available for Topic 8-16. They are not graded! • Midterm 2 will cover Topic 8-12 (from Pr. Delcourt) Pr. Delcourt's office hours will be in person - BSC 108 on... • Monday 1pm-2pm • Tuesday 10am-11am • Wednesday 3-4pm 2 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 4 https://www.wooclap.com/BIO1130 5 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 Growth and development Reproduction Regulation and homeostasis Energy and metabolism Cellular organization Living organism Response to stimuli Virus are not considered organisms: • No cellular organization • No internal metabolism • No growth or development 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 Stromatolites – 3,500Ma (Shark Bay, AUS) 8 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 – 3,500Ma – 450Ma(Shark (Ottawa, Bay, ON) AUS) 9 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 – 3,500Ma – 450Ma(Shark (Ottawa, Bay, ON) AUS) 10 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) 11 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. 12 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) 14 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). à Synthesis of formaldehyde, hydrogen cyanide, amino acids and hydrocarbons… from abiotic molecules. Similar experiments simulating volcanoes led to the synthesis of more amino acids Re-analysis of Miller’s data Deep-sea vents Murchison meteorite (18 amino acids) 15 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): Fe2+, Pb2+, Mg2+, etc. Clay has been found to be a mineral catalyst for the polymerization of RNA. 16 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) à Properties of life can emerge from the abiotic world. 17 Self-replication Proteins (e.g. enzymes) are synthesized from DNA and RNA. DNA and RNA are synthesized through enzymatic reactions. à 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 à “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! 18 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 21 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 Henry De la Beche (1830) Red Dead Redemption 2 22 23 Geological and fossils records • Biostratigraphy: determination of relative age (imprecise and/or inaccurate) à sedimentary rocks • Radiometric dating: determination of absolute age (precise and accurate) à 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 24 Geological and fossils records • Biostratigraphy: determination of relative age (imprecise and/or inaccurate) à sedimentary rocks • Radiometric dating: determination of absolute age (precise and accurate) à 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 25 Geological and fossils records • Biostratigraphy: determination of relative age (imprecise and/or inaccurate) à sedimentary rocks • Radiometric dating: determination of absolute age (precise and accurate) à 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 26 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) 27 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 à unstable (parent) isotope 14C decays into a daughter isotope (14N) at a constant known rate à stable isotope 12C in the fossil remains constant until the fossil is discovered. 2 14 C/1 C o i t Ra Half-life: amount of time it takes for 50% of the parent isotope (14C) to decay into a daughter isotope (14N). Parent isotope Daughter isotope Half-life (years) Dating range (years) Carbon-14 Nitrogen-14 5,730 100 - 60,000 Potassium-40 Argon-40 1.25 Gy 10 My – 4.5 Gy 28 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) 29 Biostratigraphy 30 Topic 8 The tree of life 8.3 – Mass extinctions, adaptive radiations and key innovations A changing world 32 The Cambrian explosion 33 The Cambrian explosion 34 The Burgess Shale (506Mya) Paleontological site in British Colombia (1909) à 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 35 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 à 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.) Radial symmetry Bilateral symmetry Many adaptive radiations: à 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. 36 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. à All leading to a cascade of dramatic ecological events à Mass extinctions are always followed by new adaptive radiations and many new families and genera 37 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. à All leading to a cascade of dramatic ecological events 3 à Mass extinctions are always followed by new adaptive 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, à ocean acidification, volcanic eruptions (Siberian Traps). 38 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. à All leading to a cascade of dramatic ecological events 3 à Mass extinctions are always followed by new adaptive radiations and many new families and genera 1 5 5 mass extinctions. 2 4 Cretaceous - Paleogene (5 in the figure): - 75% species 39 Key innovations in the fossil record 6.5 Mya • First cells (prokaryotes) • Increase in atmospheric O2 concentration 485 Mya 635 Mya • Endosymbiosis (eukaryotes) 3,500 Mya • Sexual reproduction • Multicellularity 1,200 Mya • Colonization of land 1,800 Mya 2,700 Mya 40 Key innovations in the fossil record • First cells (prokaryotes) • Increase in atmospheric O2 concentration • Endosymbiosis (eukaryotes) • Sexual reproduction • Multicellularity • Colonization of land 41 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! à 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 43 Number of species in the tree Many species are still being discovered and many went extinct! à The number of species or members of a taxonomic level reaches an asymptote (an apparent maximum) The number of prokaryotes species remains highly unknown! Number of species predicted: >11,750,000… …but only ~1,410,500 are described! Of those, only ~200,000 oceanic species were described! Mora et al. 2011 Predicted Described Land Ocean 44 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: à 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. 45 The Tree of Life – a 3 domains system Saccharomyces cerevisiae Pyrococcus furiosus Escherichia coli 46 The Tree of Life – a 3 domains system 47 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 48 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 49 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) 50 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 à Polymerisation Chain Reaction: PCR (COVID19 testing, cloning, sequencing) Pyrococcus furiosus 51 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). à Mitochondrion, plastid: organelles possessing a circular DNA, their own transcription/translation proteins, ribosomes/membrane proteins similar to those of bacteria. à Benefits: the cell gains a new metabolic system (ex: aerobic respiration with increasing O2 concentrations). 52 Multicellularity (1,200 Mya) Some multicellular All multicellular times 5 2 d e v l Evo dently! n e p e d n i • Colonial hypothesis: colonies form through the cooperation of unicellular organisms of the same species à cells fail to separate (or separate and rejoin) à 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). 53