TuTh

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Fall 2009 MB437/537 3credits Molecular
EvolutionADVANCES IN Molecular Evolution
What ARE THE latest theories on the Origins of
life? What are genome Sequencing
projects Teaching us about evolutionary
Complexity? What are the Bioethical implications
of Your Future Research?
LUCA
From the Big Bang to Bioinformatics and Beyond

• Tu/Th
• 1100 AM - 1215 PM
• LEWIS HALL 110

Teach Evolution! Learn Science!
Professor Marcie McClure marsmcclure_at_gmail.com
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MOLECULAR EVOLUTION MB437
ADVANCES IN MOLECULAR EVOLUTION
MB537   SYLLABUS   Lecture 1 9/1/09
Comments. Organization Introduction Lecture 2
9/3/09 Evolution the Big Picture Lecture
3 9/8/09 The BIG BANG and formation of the
elements necessary for life. Lecture 4
9/10/09 Biogenesis I The primitive earth and
the prebiotic soup. Lecture 5 9/15/09
Biogenesis II Self-assembly, Energetics and the
Protocell. Lecture 6 917/09 Biogenesis III
More on protocelluar formation. Lecture 7
9/22/09 Biogenesis IV Protein or Nucleic Acids
first? RNA or DNA? Lecture 8 9/24/09
The RNA world the three Domains of life and
LUCA or LUCC. Lecture 9
9/29/09 Origin of the Genetic Code and more on
LUCC Lecture 10 10/01/09 Last Day of LUCA begin
Genomes Content and Architecture Chap
8 Lecture 11 10/6/09 open discussion Lecture 12
10/8/09 Mutation nucleotide substitutions and
amino acid replacements. Chap 1
3 Lecture 13 10/13/09 Methods Analyzing
sequences rates/patterns.
Chap 1, 3-4 Lecture 14 10/15/09 Molecular
Phylogeny I History, terms, definitions, and
limits. Chap 5 Lecture 15
10/20/09 Molecular Phylogeny II How to determine
a phylogenetic tree. Lecture 16 10/22/09
Molecular Phylogeny III Improvements and
Extensions to Genome Trees. Lecture 17 10/27/09
WHATS NEW? Bayesian and HMM Approaches to
phylogenetic reconstruction. Lecture 18
10/29/09 Deviation from Tree-like behavior
horizontal transmission of information. Lecture
19 11/3/09 EXAM Lecture 20
11/5/09 Convergent Evolution the antifreeze
story. Lecture 21 11/10/09 Evolution of
Viruses. Lecture 22 11/12/09 Retroid
Agents eukaryotic hosts and disease
states. Lecture 23 11/17/09 Do viral RNA
polymerases share ancestry? Lecture 24 11/19/09
Bioethics of the Human Genome Project/
Introduction to Bioinformatics. Lecture 25
11/24/09 open discussion 11/25-27/09 THANKSGIV
ING HOLIDAY Lecture 26 12/1/09 Lecture 27
12/3/09 Lecture 28 12/8/09 Lecture 29
12/9/09
BIG BANG PRIMORDIAL SOUP LUCA BASIC
MOLECULAR EVOLUTION ANALYSIS SPECIAL
TOPICS BIOETHICS
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Trees Networks
LUCA
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Last Lecture
No real data to support how the genetic code
arose-- but we all agree it cannot change--it is
frozen
LUCA
Penny RNA-----gtDNA early reverse
transcriptase LUCA as a eukaryote or early
ribonuclease reductase
Koonin looking for LUCA by minimal gene set ---
problem HRT
French view could have been a Eukaryotic
ancestor
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The LUCA American style LUCA as a
community 2002 Carl Woese and Ford Doolittle
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The LUCA Chinese/French style LUCA as an
Archean 2003 Xue and colleagues
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The model tRNAs and AAs co-evolved

• BY
• the mechanism of recruiting new amino acids was
  via isoacceptor tRNAs being charged with
  precursor amino acids that are subsequently
  converted to the final amino acid

AND 2) the code was fundamentally mutable
This model accounts for

• allocation of many neighboring codons to
  biosynthetically related amino acids

2) the lack of the ability to synthesized many
AAs under prebiotic conditions
3) current day pre-translational modification for
incorporate of GLN, Asn, Seleo-Cys and Fmet in
some organisms today.
Current evidence offered to support theory

• sequence similarity among tRNAs for amino acids
  from the same biosynthetic family.

2) by forced genetic encoding of 4-fluro-Trp
and other novel AAs.
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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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What is Hidden Markov Multiple Alignment?
A Bayesian inference of the shortest path a
sequence must take to have been generated by the
HMM.
What is Bayesian Inference?
Bayesian inference dates back to 1790.
Bayesian inference has always been controversial.
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Bayesian Inference is a different way of thinking
about probability. Bayesian inference is a
subjective interpretation of probability. When
the probability of an occurrence is unknown, an
opinion can be expressed about what is unknown as
a prior probability. What is a prior
probability? It is the probability distribution
of the proportions of value on the believe that
an observer has without knowledge of data. After
observing data, then one can alter an opinion
about the values assigned in the prior
probability. This new probability distribution,
called the the posterior distribution, is
calculated by Bayes' rule. All of the
observer's knowledge about the prior distribution
is contained in the posterior distribution, and
statistical inferences are made by summarizing
this distribution. Bayes rule turns prior
probabilities into posterior probabilities.
Posterior probabilities have some observation
about the data in them.
So what is so controversial about Bayesian
inference?
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There is no agreement on what proportion of value
should be placed on believes and opinions about
unknown events.
Furthermore, there is the issue of whether or not
a prior probability on an unknown event can even
exist.
This is a philosophical question not a scientific
one.
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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 2001-2002 Tom Cavaler-Smith
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The LUCA New Zealand style The Irreducible
Nature of the Eukaryotic Cell 2006 David
Penny and crew
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The Ribocentric view of Evolution
Comparison of genomic and proteomic data
strongly suggest that the three domains of life
evolved from a community of RNA-based cells. The
world of RNAs thrived, but complexity was limited
due to physical/chemical constrains of RNA.
Only by arguing that simple evolves to complex
can a case be made that Eukaryotes evolved
directly from Prokaryotes. The
Bacteria-Archaea fusion model of Eukaryotic
evolution does not account for genes and
complexes unique to Eukaryotes.
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Why are Eukaryotes Primordially Unique ?

• The Primal Eukaryotic Community (PECs) had many
  introns and possessed many of the proteins unique
  to the spliceosomes. About 1/2 of these proteins
  are unique to Eukaryotes

2) They contain various types of plastids
mitochondria, hydrogenosomes, chloroplasts etc.
3) Cellular Signature Structures are
spliceosomes, nuclei, the Golgi, nucleolar
proteomes, etc. only found in Eukaryotes.
4) Eukaryotic Signature Proteins are those with
no Prokaryotic homologues, they number in the
hundreds.
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Was the Primal Eukaryotic Community of predatory
raptor cells that engulfed other cells and
structures to give rise to modern day Eukaryotes
independent of a direct Prokaryotic descent?
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