Reconstructing Evolutionary Relationships PDF

# BSCC 1011: General Biology 2 Lecture Outline - Week 2: History of Life ## Reconstructing Evolutionary Relationships How do we learn about the history of life? What evidence indicates organisms share ancestors? - **Descent with Modification** (phrase coined by Charles Darwin) - Evidence for...

# BSCC 1011: General Biology 2 Lecture Outline - Week 2: History of Life ## Reconstructing Evolutionary Relationships How do we learn about the history of life? What evidence indicates organisms share ancestors? - **Descent with Modification** (phrase coined by Charles Darwin) - Evidence for shared ancestry (similarities) & for divergence (differences/alterations). - Used to: - Determine how organisms are related to one another & construct phylogenies. - Understand how & why evolution occurs. - **Biochemical Techniques** - Sequencing of DNA, RNA, and Proteins & comparing similarities & differences (due to mutation). - More closely related species tend to have more similar sequences. - Conserved genes do not change much across lineages and are usually very critical to survival and reproduction. Often used to establish a degree of relatedness. - *Example:* - Species A: 5'-ATCGTAGCGT-3' - Species B: 5'-ATCGGAGCTT-3' - Species C: 5'-A-CGTAGCGT-3' - Biochemical pathway comparison: Most organisms use similar pathways to capture and release energy and use the same amino acids to make proteins. - **Fossil Discovery and Analysis:** linking the present to the past. - Fossils may be: - **Hard body parts:** bones, teeth, shells, seeds, etc. - **Impressions** left by organisms in the sediment. - **Traces of existence:** tracks, nests, feces. - From fossils, we can learn: - **Estimated Age** (radiometric dating). - **Environmental conditions** at the time of fossil formation. - **Diet, lifestyle, habitats, method of movement.** - And more! - **Fossil Record:** vertical sequence of fossil layers (newest at top). - Biased & incomplete. - Fossilization is rare! (need right conditions and hard parts). - We have to find the fossils (more likely for wide-spread or long-lived lineages). ## A Brief History of Life on Earth ### Hypotheses vs. Theories | Category | Description | | ---------------- | ---------------------------------------------------------------------------------- | | **Scientific Hypothesis** | Explains why or how. Can be disproven if wrong. Cannot be proven. | | **Scientific Theory** | Explains broad phenomena. Well-supported after rigorous testing. Can be altered. Has predictive value. | ### Some Major Events 1. **Origin of Life:** How did the first cell(s) form? 2. **O2 revolution:** How did our atmosphere get oxygen? 3. **Eukaryotic cells:** How did eukaryotic cells evolve from prokaryotic cells? 4. **Multicellularity:** How did multicellular organisms evolve from unicellular ones? 5. **Colonization of land (terrestrial habitats):** How did eukaryotic organisms colonize land? ### Geologic Time: 4 Eons - **3 Precambrian Eons:** Hadean, Archaean, and Proterozoic. - **Precambrian** = prior to the Cambrian period of the Paleozoic Era (below). - **Phanerozoic:** Current Eon. - **3 Eras of the Phanerozoic:** Paleozoic, Mesozoic, and Cenozoic (current). - Each era contains periods, which contain epochs. | Eon | Era | Some Major Events | | -------- | -------- | -------------------------------------------------------------------------------------------------------------------------------------- | | Hadean | N/A | Formation of Earth ~4.5 BYA | | Archaean | N/A | 1st Life (unicellular prokaryotes) ~ 3.5-3.7 BYA; O2 Revolution (oxygenic photosynthetic bacteria): ~ 2.7 BYA | | Proterozoic | N/A | 1st eukaryotes (unicellular)~1.8 BYA; 1st multicellular organisms ~1.3 BYA; 1st animals~ 700 MYA (0.7 BYA) | | Phanerozoic | Paleozoic | Cambrian Explosion: Major animal diversification ~535-525 MYA (0.5BYA); Colonization of land by multicellular eukaryotes (plants/animals) 375-400 MYA (0.4 BYA) | | Phanerozoic | Mesozoic | Age of the Reptiles (includes Triassic, Jurassic, and Cretaceous periods); 1st Mammals ~220 MYA (0.2 BYA), 1st Flowering Plants (Angiosperms) ~ 140 MYA (0.14BYA) | | Phanerozoic | Cenozoic | Extinction of Dinosaurs & Rise of the Mammals ~ 65 MYA | - *3YA = Billion years ago, MYA = Million years ago* ## Origin of Life: How did life form? Likely steps in origin of life: 1. **Simple Organic Molecules**: 2. **Macromolecules (& Metabolism?)** 3. **Compartmentalization into a membrane (Protocell) (then metabolism?)** 4. **Inheritance & cell reproduction** - From here, cells could form populations of single-celled organisms, and these populations could evolve. Oldest bacterial fossils are about 3.7-3.5 billion years old. ### 1. **Formation of Simple Organic Molecules** - **Pre-Biotic Earth (before life):** - Atmosphere: H₂O vapor (condensed & cooled into oceans), N2, CO2, CH4, & others. - IMPT: NO O2 - Hydrothermal vents & deep ocean volcanoes ACTIVE. - Earth experienced HEAVY bombardment by meteorites. - **Formation of simple organics from inorganic molecules:** - Need a chemically reducing environment & **electron donors**. - *Proposed Hypotheses:* Prebiotic Soup, Extraterrestrial, Hydrothermal Vent. - These are not mutually exclusive. - **H1: Prebiotic soup (Oparin-Haldane Hypothesis): Ocean's surface** - Early Atmosphere = mainly reducing (but some oxidants were present). - Energy from UV light & lightning - Formation at atmosphere/ocean interface ("Top-Down"/"Heaven" hypothesis). - **Miller-Urey Expt (1953):** some amino acids formed. - Flaws with gas mixture used. - Follow up experiments by other labs with different gas mixtures yield similar results. - **Conclusion:** possible, although atmospheric composition may not have allowed for this. - **H2: Extraterrestrial Hypotheses:** (panspermia & related hypotheses): came from space. - **Organic molecules** arrived from space on meteorites. - Meteorites found on Earth have amino acids (AAs) & some other small organics, formed in space. - AAs = mixture of L & D isomer forms (note that cells use L forms only, D forms cannot be from Earth contamination). - **H3: Hydrothermal vents (Deep Ocean) Hypotheses ("Bottom Up"/"Hell" hypothesis) Deep sea** - First suggested when **chemoautotroph-based ecosystems** discovered on present day vents - Reducing Environment - Chemical reactions can provide energy for synthesis. - Some **iron sulfide (FeS2) chimneys** are moderate in temperature (40-90°C) & have catalytic activity. - **Macromolecules (& Metabolism?):** Which first? ### 2. Macromolecules (& Metabolism?): Which first? - **Two major hypotheses competing with each other:** RNA world & Metabolism 1st - **RNA World Hypothesis** (AKA Information 1st Hypothesis) - RNA was the 1st molecule for info storage & catalysis. - Evidence for catalysis: - Catalytic RNA still exists (ribozymes). - Ex: rRNA catalyzes peptide bond formation during translation). - Has special folding patterns including binding pockets for catalysis. - Many metabolic cofactors (ex: NADH/NADPH) have nucleotide components. - Remnants of RNA binding? - Part of Hypothesis: RNA was once template & catalyst for its own synthesis. - This ability hasn't been demonstrated to date. - Was protein synthesis before ribosomes possible? - In lab: ribozymes can catalyze peptide bond formation on own (& can join amino acids to tRNAs). - **Protein takeover of Catalysis?:** Once present took over most catalytic roles b/c - Proteins = More diverse/versatile (20 AA v. 4 bases). - Proteins More stable. - Hydrophobic portions (in core) possible. - Many bond types fold chain (see 4 levels of protein structure). - **DNA takeover of information storage?** - RNA prob. existed first. Evidence: - Ribose forms spontaneously from formaldehyde & is needed to make deoxyribose. - RNA primer needed in DNA synthesis. - dsDNA = more stable (better for long term & large content info storage). - 2 strands = stable configuration. - Base stacking stabilizes the molecule. - No 2'-OH group on deoxyribose (less reactive). - **Metabolism 1st Hypothesis:** Mineral catalysts near deep sea vents (FeS2 for ex) catalyzed metabolic reactions before nucleic acids & proteins formed. - RNA did not need to pre-date protein functions. - Evidence? - Reverse Kreb cycle Reactions (1), (2) and (4) can be driven by a metal catalyst and UV light. - Many enzymes use metal clusters in active sites. - **OR Maybe both Info. & Metab. co-occurred:** Recent article shows that chemical environments including HCN & H₂S allow for synthesis of lipid, nucleic acid, & protein precursors (simultaneously). ### 3. Compartmentalization into a membrane (Protocell) (then metabolism?) ### & 4. Inheritance & cell reproduction - **Protocell:** Droplets with lipid membranes & maintained internal chemistry. - Simple lipid membranes around a few macromolecules. - Protocells form on mineral substrates. - Vesicle self assembly = facilitated in presence of montmorillonite clay (from volcanic ash). - Formed around macromolecules? - In lab experiments, protocell-like oil droplets can form/fuse/divide. - How would protocells divide without a cytoskeleton? - Mechanical force (ex: pore-extrusion) → note fairly equal division of contents. - Once 1st full cells formed & reproduced could evolve. - **Evolution of life= genetic change in a population of organisms over time.** - Requires population of cells (at minimum) AND genetic change: originally arises through mutation. - Other mechanisms of evolution can act on genetic variants once they exist through mutation - **Microevolution v. Macroevolution:** Why do people still use these? - **Microevolution:** refers to smaller scale genetic change in a population. - Selection, drift, migration, mutations often considered part of this but can lead to "macroevolution". - **Macroevolution:** Large-scale evolutionary trends (result from microevolutionary processes). - Speciation & Emergence of larger groups (new Phyla, etc.) - **Extant:** A species or group of organisms that is still alive today - **Extinction:** complete loss of a species (99% of all species are extinct) - **Background Extinction:** species lost at a gradual rate, usually due to natural selection. - **Mass Extinction:** many lineages are lost due to extraordinary/sudden changes to environment. - 5 major mass extinctions have occurred (last = 65 MYA). All have been followed by major adaptive radiation events. - **Adaptive radiations:** explosions in diversification with multiple lineages/species emerging in a short time due to availability of many ecosystem roles (niches). - Can be triggered by: - **Mass extinction:** many species die, making their niches available. - **Colonization:** a new habitat is colonized by one or a few species that rapidly diversify and fill available niches. - **Innovation:** a new trait emerges in a population that allows it to take over a niche or group of niches. - **Nutrient explosion:** Large amount of nutrients become available/released from an abiotic reservoir. - **Are these gradual changes or sudden changes?** - **Gradualism:** small changes accumulate to give rise to large ones. - **Punctuated equilibrium:** long periods of no change, then sudden bursts of change. - **Fossil discovery and analysis:** can be used to track & date extinct species. - **Fossil Record:** vertical sequence of fossil layers (newest at top). - Biased & incomplete. - Fossilization is rare! (need right conditions and hard parts). - We have to find the fossils (more likely for wide-spread or long-lived lineages) - **Radiometric Dating:** - Radioactive isotopes: decay at steady rate. - Ex: 14C decays to 14N v. 12C and 13C (both stable). - **Radiocarbon dating:** Ratio of 14C to 12C useful for dating fossils up to 70,000 years old. - Other radioactive isotopes (30K, 234U, etc.) used for older materials. ### The Oxygen Revolution: How did our atmosphere get oxygen? - Earliest cells = prokaryotic producers (likely chemosynthesizers, aka chemoautotrophs). - Earliest photosynthetic producers (aka photoautotrophs) = prokaryotes that used cyclic version of light dependent reactions. - **Innovation: Noncyclic Light Dependent Reactions ~2.7 BYA in bacteria similar to cyanobacteria.** - **Photosystem II (PSII):** allows for more efficient conversion of light energy to chemical energy. - Oxidizes water to replace its electrons. O2 gas formed as a byproduct. - Electrons not recycled back to photosystems, NADPH electron carrier transfers more energy to sugar production in Calvin Cycle - O2 accumulation in water transferred into mineral deposits first, then dissolved O2 in water, then off-gassing into atmosphere. - **Major selective pressure:** O2 is highly reactive/can be damaging. - MANY prokaryotes at the time likely went extinct. - Survivors → adaptive radiation ### The First Eukaryotes: How did eukaryotic cells evolve from prokaryotic cells? - **1st Eukaryotes 1.8 Billion Years Ago - membrane bound.** - **Lokiarchaeum** (& other Asgaard archaea) Ancient archaea discovered in sediment of arctic ocean - Not eukaryotic, BUT: - Have eukaryotic cytoskeletal genes & lysosome genes. - Don't have genes for nucleus or mitochondria. - Were Archaea direct ancestors of Euks, rather that just sharing an ancestor with us? - How did organelles form in cells to give rise to Eukaryotes? - **Mitochondria:** acquired ~ 1.6 Billion Years Ago maybe before nucleus formed ### Endosymbiotic Theory: - Prokaryotic cell was ingested (phagocytized) by archaean cell but not destroyed. - A symbiotic relationship was formed and eventually led to complete interdependence between ingested and host cells. - The ingested prokaryote became the organelle (as it lost some life functions). - Likely explains formation of mitochondria (from a type of proteobacterium) and chloroplast (from a type of cyanobacterium) **INDEPENDENTLY**. - Mitochondrial acquisition likely occurred 1X in history of eukaryotes. - Plastid (including chloroplast) acquisition likely occurred LATER in multiple protist lineages **INDEPENDENTLY**. ### Evidence for formation of Mitochondria & Chloroplasts by Endosymbiosis - **Structurally similar to bacteria (membranes, ribosomes, size, shape).** - **Their ribosomes:** diverged a bit from bacteria but distinct from cytosolic ribosomes - Have own circular DNA separate from DNA in nucleus (replication confirms) - Own tRNAs & rRNAs - Self-replicate themselves in the cell (binary fission) - Sensitive to certain antibiotics. ### Invagination Theory - in folding - Cell membrane folds in itself and pinched off to form some organelles. - Perhaps to protect host DNA from mtDNA? - Believed to explain: Formation of nucleus, cytomembrane system organelles (ER, Golgi, lysosomes, peroxisomes), & vacuoles. - Membranes of these organelles have similar structure to cell membrane but flipped inside out. - Likely order of events probably: Mitochondrial Endosymbiosis → Invagination forming nucleus, etc. to form ancestor of all euks → Plastid endosymbiosis (in some euks only) ### Multicellularity: How did multicellular organisms evolve from unicellular ones? - Oldest known multicellular fossils ~ 1.3 BY old (red algae) - Evolved MANY (at least 46) times independently in: - Various protist lineages. - Various fungal lineages. - Once for the plant lineage. - Once for animal lineage. - Likely starts with unicellular organisms that begin to live in colonies. ### General Requirements: - Adhesion of some kind (ex: cadherin proteins in animal cell membranes or cellulose cell walls /plasmodesmata between plant cells) - Differentiation: Cells begin expressing different sets of genes (from same genome) to take on specialized tasks. - Communication: Cells use chemical messengers (ex: ions, neurotransmitters, hormones) to signal information to target cells (have receptor proteins for the messengers) ### Colonization of land (terrestrial habitats): How did eukaryotic organisms colonize land? - Prokaryotes likely moved onto land as early as 3.2 BYA. - Terrestrial multicellular eukaryotes: - Plants and Fungi likely moved to land together ~400-500 MYA. - Animals moved to land multiple times, notably: - Arthropods (esp. insects/spiders) ~450 MYA. - Tetrapods (ancestors of amphibians, reptiles/birds, and mammals) ~ 365 MYA - Challenges to life on land include: - Supporting the body/counteracting gravity (no water pressure around you). - Reproducing: getting gametes together in a dry environment. - Waterproofing/avoiding desiccation: keeping water in the body. - Acquiring and transporting nutrients (can't diffuse in from surrounding water). - Different groups handle these challenges in different ways: To be covered later....