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
FROM THE BIG BANG THROUGH THE CHEMICAL FACTS OF
LIFE TO LUCA FROM BASIC MOLECULAR EVOLUTION
ANALYSIS TO BIOINFORMATICS
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What is Molecular Evolution?
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How did the chemical evolution of life occur?
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SIMPLE DEFINITION OF LIFE
A living system demonstrates 1)
metabolism 2) organization 3)
reproduction 4) evolution
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Six Basic Areas of the Study of Molecular
Evolution

• The origin of life, biogenesis.
• The RNA world as intermediary to the DNA world.
• Population genetics.
• Phylogenetic reconstruction of genes and genomes.
• Molecular pattern recognition.
• Mechanisms of evolution.

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BASIC OUTLINE OF CLASS

• 1) Speculation and research on the origin of
  life.
• Structure of the arguments
• There are two approaches to the study of the
  origin of life
• From small to large
• From complex to simple
• We will cover six stages
• The Big Bang and formation of the elements
• The early earth environment
• Prebiotic chemistry
• Self-assembly processes
• Energetics
• Bioinformational molecules
• 2) The RNA world as an intermediary to the DNA
  world.
• 3) Genome organization
• 4) Mutation and Phylogenetic Reconstruction
• A) The systematists who study DNA sequence
  relationships with lt20 change.
• B) Molecular pattern recognitionists who
  study protein relationships with lt25
  conservation.
• 5) What are the mechanisms of molecular
  evolution? Special Topics
• 6) Bioethics and Intro to Bioinformatics

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WORKING DEFINITION OF COMPLEX GENOME
ANALYSIS

• The study of parameters involved in the evolution
  of genes and genomes
• Types of change divergence, duplication, and
  insertion/deletion
• Units of acquisition individual motifs, an
  ordered series of motifs (OSM) or subset thereof
  (modular evolution), and an entire gene or sets
  of genes (segmental evolution)
• Modes of acquisition splicing, transposition,
  translocation, inversion, and various types of
  recombination.
• Obviously any delineation of evolutionary
  interactions will change as our understanding and
  observation of evolutionary events progresses.

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McClure, 2000
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Which information should be used?

• Nucleic Acid Sequences?
• In general, for cellular sequences this is fine,
  especially if distant relationships are not of
  interest.
• NO CLUES as to the function of your sequence, but
  suspect it to code for a protein? Then DO NOT
  USE n.a. sequences to search for relationships.

• Protein Sequences?
• Any sequences suspected to encode proteins should
  be initially analyzed as amino acid residues,
  especially if you are interested in trying to
  deduce the residues involved in catalytic
  activity.
• REMEMBER viral rates of mutation are much greater
  than cellular ones, THEREFORE IT IS ALWAYS SAFEST
  to search viral sequences at the protein level!

Caution should be exercised in declaring a
sequence to be unrelated to anything in the
database one must define by what criteria such
a claim is made most of the commercial packages
available today will not find distant protein
relationships if you truly believe that you
have a novel sequence let the EXPERTS take a look
before you publish!!!
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Levels of Genomic Analysis

• INTRAGENIC (Sub-local relationship)
• Have all regions of a protein descended for a
  single common ancestor?
• 2) Has recombination occurred between
  homologous regions within the protein?
• Are all regions of the protein changing at the
  same rate?
• INDIVIDUAL GENES (Local relationships)- Analysis
  of each homologous gene-set provides information
  on
• Congruency of tree topology (if genes are all on
  the same genome then each gene-set should have
  the same topology).
• Recombination among homologues.
• Acquisition of new genes.
• Relative rates of change.
• COMPLETE GENOME (Global relationship)

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DEFINITION OF LIFE
BIO 100 Definition of a living system 1)
metabolism 2) organization 3)
reproduction 4) evolution A more
sophisticated version of these requirements Life
is a self-sustained chemical system capable of
undergoing Darwinian evolution. The Darwinian
evolutionary process includes
self-reproduction, material continuity over an
historical lineage, genetic variation and
natural selection. Or more abstractly The
attribute of the living state is defined as the
maintenance of a particular energy relationship
of the bounded system (i.e., the cell) to its
environment.
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