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Bio160 Class Notes - Week 2

by: Aenea Mead

Bio160 Class Notes - Week 2 BIO 160

Aenea Mead
Cal Poly

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These note extensively cover everything related to phylogenetic trees. Included is a long vocabulary list, examples diagrams, explanations on how to read and draw phylogenetic trees. There is an ex...
Diversity and History of Life
Jennifer Yost
Class Notes
biological-evolution, phylogenetic trees, convergent-evolution, polyphyletic group, monophyletic group, paraphyletic group, prebiotic-soup-model, surface-metabolism-model, RNA-world-hypothesis, Organic-Compounds, three-domains-of-life
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This 6 page Class Notes was uploaded by Aenea Mead on Monday October 10, 2016. The Class Notes belongs to BIO 160 at California Polytechnic State University San Luis Obispo taught by Jennifer Yost in Fall 2016. Since its upload, it has received 2 views. For similar materials see Diversity and History of Life in Biology at California Polytechnic State University San Luis Obispo.


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Date Created: 10/10/16
FIRST FORMATION OF LIFE Two models exist for how complex molecules might have formed: 1) Prebiotic Soup Model:​ The thought behind this model is that when simple molecules from the atmosphere precipitated into the ocean and were given energy (sunlight), they reacted with each other to form more complex molecules. The molecules continued to become more complex until they were amino acids, which led directly to life. Stanley Miller tested this model by trying to simulate early Earth conditions in a lab. By adding heat and electric charges into the equation, he successfully produced amino acids using only simple molecules believed to have existed on early Earth. Unfortunately his findings are criticized by others scientists. One criticism of his work is that he used the incorrect basic molecules. Another criticism was that he had to introduce heat and electric current into the situation, rather than use only sunlight. The third criticism (that actually led to the second model) was that while all the simple molecules he used in his experiments were believed to have existed in the oceans of early Earth, the oceans are so vast that the likelihood of those molecules coming close enough to react with each other was too small. 2) Surface Metabolism Model​: As with the Prebiotic Soup Model, the theory is that simple molecules will react with one another when given an energy source to form more complex molecules. This theory was driven by the need to find a catalyst, which is missing from the Prebiotic Soup Model. The catalyst for the reaction comes from the high concentration of minerals in hydrothermal vents at the bottom of the ocean. A hydrothermal vent is where materials have leaked into cracks on the Earth’s crust, and then are pushed back out again full of minerals. The mineral rich material from the Earth forms a miniature volcano of sorts. When the simple molecules from the ocean come into contact with the mineral rich and heated hydrothermal vents, they react to form complex molecules and eventually amino acids. Carbon​: Carbon is an incredibly important element in regard to the development of life on Earth. It is very versatile because it only has four valence electrons, and therefore countless bonding potential. Carbon bonding to itself was an important step in life’s development. Chemical Evolution → Biological Evolution: 1) Production of simple molecules 2) Simple molecules → complex molecules (amino acids) 3) Amino acids link together 4) Self replicating cells are born = biological evolution! RNA World Hypothesis​: ​Chains of RNA, by being the first things that could replicate and evolve, were what began life. 1) A, C, U & G are the nucleotides 2) Nucleotides pair up to form base pairs (C+G, A+U) 3) Base pairs form strands 4) Two strands come together to replicate themselves 5) Ribosime is a strand of DNA capable of catalyzing chemical reactions ______________________________________________________________________________ PHYLOGENETIC TREES Vocab of the Structure of Phylogenetic Trees: ​ Phylogenetic Trees: graphical representation of hypothesis of evolutionary relationships among species ​ Sister groups: all the descendent following a specific node on a tree ​ Monophyletic group: a group of organisms which includes the most recent common ancestor and all of its descendants ​ Paraphyletic group: a group of organisms that includes that most recent common ancestor, but NOT​ all of its descendants ​ Polyphyletic group: species which have evolved certain traits convergently and therefore are not suitable to be placed in the same taxa ​ Out group: A distant common relative outside the clade being studied (often used as a reference point) ​ Sister trait: all the descendants following a specific node on a tree ​ Root: the place on a phylogenetic tree where the very first common ancestor would go ​ Tip: the places on a phylogenetic tree where the most current species are placed ​ Node: the place on a phylogenetic tree where speciation occurs - the node them becomes those two species most recent common ancestor ​ Branch: represent evolutionary lineages changing over time ​ Cladistics: method scientists currently use to build phylogenetic trees ​ Polytomy: not enough information to distinguish between two species or genus (this results in parts of a tree having more than two branches spring from one branching point / node) ​ Principle of Parsimony: most likely the simplest answer is the correct answer Vocab of Phylogenies: ​ Phylogeny: evolutionary history of a group of organisms ​ Character / trait: any attribute of an organism that can be defined or quantified (ie, color, number presence of a particular part, etc) ​ Character state: The specificity or a character of trait (ie. Trait would be having legs, but the state would be 3 or 4) ​ Taxon: any taxonomic group of rank (ie. group, order, class, species, genus, etc) ​ Clade: a group of organisms which evolved from a common ancestor ​ Common ancestor: a species from which two or more species evolved from ​ Speciation: when something prevents two halves of a population from mating with each other, and thus two separate species evolve ​ Homologous: things are similar due to a common ancestor ​ Derived: trait existing in more recent common ancestor ​ Synapomorphies: derived (new) trait; found in most common ancestor and all descendants ​ Ancestral: older “basal” trait existing in less recent common ancestor ​ Plesiomorphy: ancestral (old) trait; shared by multiple taxa because it is ancestral ​ Convergent evolution: A trait which appears in two unrelated lineages ​ Homoplasy: similar because of convergent evolution, ​NOT​ due to a common ancestor ​ Mass extinction: when a major cause or event results in an entire branch (or more) of the tree to go extinct ​ Background extinction: the natural rate at which species go extinct ​ Topology: the particular branching pattern of a tree (see example below) Phylogenetic Trees: ● These are a graphical representation of hypothesis of evolutionary relationships among species. ● Biologists primarily use synapomorphies to build a phylogenetic tree. ● When creating a phylogenetic tree the ​Principle of Parsimony​ is utilised (ie. the ​simplest ​ answer is most likely the c Ex: Homoplasy is rare and is not assumed unless there is not a simpler option ● As detailed and extensive as the tree is, it is important to keep in mind that is is all guesswork and that there are pieces missing. Over the centuries many scientists have expanded upon the tree, and while it much of it is likely correct, no one can go back in time to experience the life of certain species and how they evolved and therefore nothing is certain. How to read a phylogenetic tree: ​ ​ ​ Three Domains of Life: Bacteria, archaea, eukarya Archaea and eukarya are more closely related to each other than to bacteria, which came first


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