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 Lecture 1
8/29/06 Organization Introduction What is
molecular evolution? Lecture 2 8/31/06
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 Genetic 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 Phylogeny I History, terms,
definitions, and limits. Lecture 13 10/10/06.
Molecular Phylogeny 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 discussion Lecture 18
10/26/06 Convergent Evolution 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
Examples 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 Protein 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 Lecture 28 12/5/06 Lecture 29
12/7/06
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BASIC OUTLINE OF CLASS

• 1) Speculation and research on the origin of
  life.
• 2) The RNA world as an intermediary to the DNA
  world generalities, history and current
• A) What was the RNA world like
• B) Current three domain view
• C) LUCA
• 1) RNA to DNA, David Penny
• 2) Universal Proteins Woese/Olsen, Koonin
• 3) Phylogenetics Forterre
• What is missing in talking about RNA
  gtDNAgtprotein?
• 3) Genome Content and Architecture
• A) Size and the C paradox
• B) Types of DNA
• 4) Mutation
• A) types of changes
• B) rates and patterns
• 5) Phylogenetic Reconstruction
• Complex genome analysis. What are the mechanisms
  of molecular evolution.
• The Genome Projects content and distribution
• 8) Bioinformatics

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Basic Strategy
Search Databases
Annotate and Preparation of Sequences
Multiple Alignment of Sequences
Refined Multiple Alignment
Analysis of Multiple Alignment
McClure, 2000
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Neutral/positive/negative selection??????????

• NS sites have a higher probability of leading to
  a change, perhaps deleterious, in a protein. In
  classical term this is called purifying or
  negative selection.
• The converse is also true. NS changes have a
  chance of improving function. When this happens
  it is called positive selection.
• 3) S site changes do not change the protein.
  When there is no change in the protein it is
  called what neutral.

• Evolution under the neutral theory, predicts,
  using the null hypothesis dS dN or Ks Kn
• When dS gt dN or dS/dN gt 1, then purifying or
  negative Darwinian selection has occurred
• When dN lt dS or dS/dN lt 1, then positive
  Darwinian selection has occurred.

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Why did the molecular clock hypothesis stir such
controversy?

• 1) A constant rate of protein evolution did not
  fit with ideas of the erratic tempo of evolution
  observed at the higher levels of complexity, i.e.
  morphological and physiological.
• 2) As observed after gene duplication rates of
  change accelerate as they do during periods of
  adaptive radiation.
• 3) Many studies on viral evolution demonstrate
  that the rate of accumulated mutation is a
  function of environmental condition.

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Evaluation of the MC hypothesis

• From DNA sequence analyses from several orders of
  mammals evidence does not support a global clock
  for the order Mammalia. Significant variance in
  sub. Rates is found both within and between
  orders
• 2) Variation between species also exists. Flys
  evolve 5-10x the rate of vertebrates.
• Bottomline
• Basically there is no Molecular Clock, but there
  maybe local clocks given enough data

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Do rates of change vary among and between plastid
versus nuclear genes?

• 1) Mammalian mito. genome---structurally stable
  --little variation from mammal to mammal
• a) circular genome dsDNA, 15-17K BP, about
  1/10,000 of the smallest animal genome
• b) doesnt code for much only unique sequences
  13 protein-coding genes,
• two rRNA gene clusters, 22 tRNAs and control
  regions for RX and TX
• c) S sites 10X, NS sites vary among proteins
  but much greater than nuclear genes
• in contrast to
• 2) Plant mito. genome--structurally
  unstable--under goes freq. rearrangement,
  duplication and deletion of genes
• a) circular, linear or subgenomic circles--
  genome varies from 40K to 2,500K BP--
• b) coding content at a minimum--3 rRNA clusters,
  unknown number of tRNAs, 15-30 proteins
• c) lower rates N and NS then nuclear genes
• in contrast to
• 3) to chloroplasts in vascular plants,
  structurally stable
• a) circular genome, 120K-220K BP--both strands
  encode genes
• b) tobacco chloroplasts 37 tRNA genes, 8 of
  which have single introns,
• 8 rRNA clusters, 45 proteins (five of which have
  one intron and 2 of which have 2 introns)

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Is there any correlation between organellar
genome stability and rates of change ?

• In mammals mito DNA evolves very rapidly, but
  there is little spatial or size variation among
  species.
• In plants mito DNA evolves quite slowly, but
  there is significant rearrangement of the genome.
• 3) In chloroplasts the rates of both evolution
  and structural rearrangement is quite low.

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