MOLECULAR EVOLUTION MB437 and ADVANCES IN MOLECULAR EVOLUTION MB537

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MOLECULAR EVOLUTION MB437 and ADVANCES IN
MOLECULAR EVOLUTION MB537 Marcie McClure, Ph.D.
,mars_at_parvati.msu.montana.edu, 994-7370
Fall, 2006, Tu/Th 1100-1215 Cooley-B2 Lectur
e 1 8/29/06 Organization Introduction
What is molecular evolution? Lecture 2 8/31/0
6 The BIG BANG and formation of the
elements necessary for life. Lecture 3 9/5/06
Biogenesis I The primitive earth and the
prebiotic soup. Lecture 4 9/7/06
Biogenesis II Self-assembly, Energetics
and Bioinformational Molecules.
Lecture 5 9/12/06
Biogenesis III Protein or Nucleic Acids first?
RNA or DNA? Lecture 6 9/14/06
The RNA world the three Domains of life and
LUCA. Lecture 7 9/19/06 Origin of the Ge
netic Code and more on LUCA Lecture 8 9/21/06
Genomes Content and
Architecture. Lecture 9 9/26/06
Mutation nucleotide substitutions and
amino acid replacements. Lecture 10 9/28/06
Methods Analyzing sequences rates/patterns.
Lecture 11 10/3/06 open
discussion Lecture 12 10/5/06 Molecular Ph
ylogeny I History, terms, definitions, and
limits. Lecture 13 10/10/06. Molecular Phylo
geny II How to determine a phylogenetic tree.
Lecture 14 10/12/06 Molecular Phylogeny
III Improvements and Extensions to Genome
Trees. Lecture 15 10/17/06 NEW? Bayesian and
HMM Approaches to plylogenetic reconstruction
Lecture 16 10/19/06 Deviation from
Tree-like behavior horizontal transmission of
information Lecture 17 10/24/06 open discu
ssion Lecture 18 10/26/06 Convergent Evolut
ion the antifreeze story. Lecture 19 10/31/06
Evolution of Viruses Lecture 20 11/2/06
Retroid Agents eukaryotic hosts and disease
states. Lecture 21 11/7/06 UNIVERSITY HOLIDAY
Lecture 22 11/9/06 Bioethics of the
Human Genome Project/ Introduction to
Bioinformatics. Lecture 23 11/14/06 Exam
ples of in silico research I the RNA polymerase
story. Lecture 24 11/16/06 Examples of in
silico research II the Genome Parsing Suite
finds Retroid Agents. Lecture 25 11/21/06 Pr
otein Disorder predictions Measles the elegance
of in silico and wet experiments
11/22-24/06 THANKSGIVING HOLIDAY
Lecture 26 11/28/06 Lecture 27 12/30/06 Le
cture 28 12/5/06 Lecture 29 12/7/06
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• What questions should be answered?
• How and When was RNA transferred to DNA?
• How and When did the genetic code evolve?
• How and When did translation evolve?
• How and When did real cell membranes evolve?
• Where did the nucleus come from?
• How did Eukaryotic compartmentalization occur?

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• Ideas we have covered
• RNA preceded DNA as genetic information.
• Accepted worldwide.
• 2) Prokaryotes lead to Eukaryotes.
• The classical notion of simple goes to complex.
• 3) Looking for LUCA by the minimal gene set
  approach.
  
• Not successful.
• 4) Prokaryotes are streamlined Eukaryotes.
• The realization that formally complexity can be
  streamlined.
  

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The LUCA American style LUCA as a community 20
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Carl Woese and Ford Doolittle
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How did the genetic code evolve?
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Theoretical model of the evolution of the the ge
netic code
Christen DuDuve
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Figure2-31 The chemical structures of the
principal bases in nucleic acids. In nucleic
acids and nucleotides, the 9 nitrogen atom of
purines and the 1 nitrogen atom of pyrimidines
are bonded to the 1 carbon of ribose or
deoxyribose.
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The LUCA Chinese/French style LUCA as an Archea
n
2003 Xue and colleagues
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The LUCA American style The Ring of Life 2004
Jim Lake and Maria Riveria
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FIG. 2. The evolution of genomes is represented
by genome bands containing multiple gene fibers.
Each fiber corresponds to a gene present in the
conditioning genome. Gene losses during the
course of evolution are indicated by a change of
color from gray (P) to white (A), and gene
additions are represented by a change from white
(A) to gray (P). Even though genomes X, Y, and Z
may contain genes not found in the conditioning
genome, only genes present in the conditioning
genome are shown, because genes absent in the
conditioning genomes are not analyzed. The order
of genes corresponds to that found in the
conditioning genome and not in the other genomes,
because extensive synteny is generally not
observed
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The LUCA English style LUCA as an Eubacteria 2
001-2002
Tom Cavaler-Smith
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The latest LUCA New Zealand style
The Irreducible Nature of the Eukaryotic Cell
2006 David Penny and crew
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The lastest LUCA French style Three RNA cells a
nd
Three DNA viruses 2006 Patrick Forterre