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Lecture 1: Tree of Life

by: Jason Karlen

Lecture 1: Tree of Life Biol UA11

Marketplace > New York University > Biology > Biol UA11 > Lecture 1 Tree of Life
Jason Karlen

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Lecture Notes.
Principles of Biology II
Professor Eichenberger
Class Notes
25 ?




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This 6 page Class Notes was uploaded by Jason Karlen on Sunday September 4, 2016. The Class Notes belongs to Biol UA11 at New York University taught by Professor Eichenberger in Fall 2016. Since its upload, it has received 3 views. For similar materials see Principles of Biology II in Biology at New York University.


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Date Created: 09/04/16
1 The Tree of Life Eichenberger ­ Microbiology & Introduction to Animal Biology Chapter 26 Terms: The Tree of Life Ideas: ● Biogenesis: every living organism comes from a pre­existing living organism → tree of life w/ only 1 root ● Heterogenesis: some life forms arise spontaneously from non-living matter (i.e. decaying matter, broth) → spontaneous generation (many roots) Generation of Animals Aristotle: there are four elements earth, air water and fire (5th = quintessence or ether) Louis Pasteur: challenged the belief of spontaneous generation  Jan Baptist van Helmont ● experiment: place a soiled shirt in a vessel containing grains of wheat and after  appox 21 days you will create mice ○ the part it suggested thought was real: if you take water from a  spring and put it in a flask you will give rise to maggots, frog eggs, et. Francesco Redi (Redi’s Key Observation) ­ First Modern Experiment in Biology (1668) ● theory: all worms that are found in meat were derived directly through the  dropping of flies but not from the putrefaction (rotting) of the meat ● experiment: ○ positive control: take meat, wait, let maggots create ○ negative control: take meat, cover with paper, no maggots ○ EXPERIMENT: put cloth on the meet so flies are still attracted to  the meat and touch the cloth facing out, however as long as the cloth stays in  place there won’t be any maggots. When you flip the cloth, the eggs will be in  contact with the meat and then maggots will be made. ■ Conclusion: The flesh of dead animals can cannot  engender worms unless the eggs of the living are deposited in them Carolus Linnaeus: 1. Hierarchical organization 2. Use of binomial nomenclature Linnaeus is the father of taxonomy and systematics Terms ● Systematics: branch of biology that classifies organisms and  determines their evolutionary relationship (ie relatedness) 2 ● Taxonomy: ordered division and naming of animals ● Taxon: taxonomic unit at any level ○ can refer to species, genera, orders,  1) Hierarchical Organization: a) Species, Genus, Family, Order, Class, Phylum, Kingdom,  Domain 2) Binomial Nomenclature: a) genus + specific epithetic i) always italicized ii) genus is capitalized Linnaeus classified all species as either plants or animals (based on macroscopic morphological characteristics) ● invention of microscopic caused revisions in this categorization to accommodate  microscopic species ● 20th Century: Prokaryotes, Protists, Plants, Fungi, and Animals ● 1970s Carl Woese ○ an organism's genome is the evolutionary record of its evolutionary history ○ THREE DOMAIN SYSTEMS:  ■ Bacteria, Archaea and Eukaryotes Phylogeny = evolutionary history of a species or group of related species represented in a  phylogenetic tree ● Using morphologies to determine phylogenies ○ Organisms with similar morphologies are more likely to be more  closely related than organisms with different structures ● Homology vs. Analogy ○ Homology = similarity due to shared ancestry ○ Analogy = similarity due to convergent evolution ■ Convergent Evolution = when similar  environmental pressures and natural selection produce analogous  adaptations in organisms from different evolutionary lineages ● Homoplasies: analogous structures  that evolved independently ● Example ○ Microbes (both found  in soil, both make spores) = Streptomyces and Penicillium:  streptomyces are bacteria while penicillium is a eukaryote  but similar environmental conditions and look very similar. Carl Woese Paper: 3 Using Ribosomal RNA Sequence (small subunit) to determine evolutionary relationships ­  Archaea represent a new domain of life STEPS: 1. Align corresponding sequences to account for insertions and deletions 2. Count the number of mutations 3. Calculate the evolutionary distance with the ratio a. # of Mutations / # of Nucleotides in Sequence i. the higher the number of mutation the older the  divergence time* 4. Build Tree: a. the lower the ratio, the smaller the length of branch b. the higher the ratio, the longer the length of branch 16S rRNA as an evolutionary chronometer 1) Isolate DNA 2) Heat to separate strands; and specific primers 3) Primer extension w/ DNA polymerase 4) Repeat above steps to obtain many copies of 16S rRNA gene 5) Run agarose gel and check for correct sized product 6) Purify and sequence PCR product Reading Phylogenetic Tree: ­ trees show patterns of descent ­ do not indicate when species evolved or how much genetic change occurred in a  lineage ­ shouldn’t be assumed that taxon evolved from the taxon next to it. 4 Branch Point: represents divergence of two species Sister taxa: groups that share immediate common ancestor Rooted Tree: includes a branch to represent the last common ancestor of all taxa in the tree Polytomy: branch from which two or more groups emerge Orthologs/Paralogs: Orthologous genes: different species w/ common functionality and ancestry Paralogous: same species w/ gene duplication a Tree of Life is a record of life on Earth 5 Where did life come from? ­ Primordial (or prebiotic soup) ● Darwin ○ a pond with a mixture of ammonia, phosphoric salts, light, heat,  electricity, etc. present so a protein compound was chemically formed and ready  to undergo more complex changes. ● Oparin­Haldane Hypothesis ○ spontaneous generation of life occurred once when atmospheric  conditions found on earth were largely different from today ○ primitive atmosphere: CH4, CO2, NH3, H2 and H2O + solar  radiation (UV) ● Miller­Urey experiment (tested the Oparin­Haldane hypothesis) ○ chemical experiment that tested which simulated conditions of  early Earth 6 Set­Up: Water, heat source, have the ability to  produce lightning in a closed system  where everything is circulating. You  allow it to all go around. Take final  solution, and put it on paper  chromatography Results: Seven amino acids are producing,  including three (glycine, alanine and  aspartic acid) found in modern  organisms


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