???? Molecular Evolution

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???? Molecular Evolution

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• ?????????

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Molecular Evolution

• An historical process that depends on alterations
  in the structure and organization of genes and
  gene products
• Fundamental aspects of cellular life are shared
  by different organisms and dependent on related
  genes
• Small changes in certain genes allow organisms to
  adapt to new niches

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Prokaryotic cells

• Single cell organisms
• Two main types bacteria and archaea
• Relatively simple structure

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Eukaryotic cells

• Single cell or multicellular organisms
• Plants and animals
• Structurally more complex organelles,
  cytoskeleton

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Modification?
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Taxonomy and Systematics
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Phylogenetic Systematics
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• The field of biology that deals with identifying
  and understanding the evolutionary relationships
  among the different kinds of life on earth, both
  living (extant) and dead (extinct).
• Evolutionary theory states that similarity among
  individuals or species is attributable to common
  descent, or inheritance from a common ancestor.
• Thus, the relationships established by
  phylogenetic systematics often describe a
  species' evolutionary history and, hence, its
  phylogeny (lineages or organisms or their genes.

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Understanding the Evolutionary Process

• Genetic Variation Changes in a gene pool,
• the genetic make-up of a specific population
• How Does Genetic Variation Occur?
• - DNA replication
• - Mutations

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The Driving Force of Evolution

• Selection genotype, fitness
• Genetic Drift ??
• - Fluctuations in the rate of evolutionary
  processes
• such as selection, migration, and
  mutation
• - Founder Effects - the difference between
  the gene
• pool of a population as a whole and that
  of a
• newly isolated population of the same
  species

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Phylogenetic (Evolutionary) Trees Presenting
Evolutionary Relationships
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Phylogenetic Trees
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Phylogenetic Trees
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The Four Steps of Phylogenetic Analysis

• Alignment - building the data model and
  extracting a dataset
• Determining the substitution model - consider
  sequence variation
• Tree building
• Tree evaluation

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Tree Building Key Features of DNA-based
Phylogenetic Trees

• Comparison of homologs, sequences that have
  common origins but may or may not have common
  activity
• Orthologs - homologs produced by speciation
• Paralogs - homologs produced by gene duplication
  within an organism (may have different functions)
  
• Xenologs - homologs resulting from the horizontal
  transfer of a gene between two organisms

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A typical gene-based phylogenetic tree

• The tree 4 external nodes (A, B, C, D) 4 genes
  
• 2 internal nodes (e, f)
  ancestral genes
• The branch lengths indicate the degree of
  evolutionary differences between the genes
• This particular tree is unrooted

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3 rooted trees that can be drawn from the
unrooted tree shown above, each representing the
different evolutionary pathways possible between
these four genes
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Outgroup
Outgroup, a gene that is less closely related to
A, B, C, and D than these genes are to each
other. Outgroups enable the root of the tree to
be located and the correct evolutionary pathway
to be identified
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Gene Trees Versus Species Trees - Why Are They
Different?

• It is assumed that a gene tree (molecular data),
  will be a more accurate than that obtainable by
  morphological comparisons
• The two events, mutation and speciation, do not
  always occur at the same time
• Molecular clocks require calibration with fossils
  to determine timing of origin of clades

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Molecular Clock Hypothesis

• Nucleotide (or amino acid) substitutions occur at
  a constant rate
• The degree of difference between two sequences
  can be used to assign a date to the time at which
  their ancestral sequence diverged
• The rate of molecular change differs among groups
  of organisms, among genes, and even among
  different parts of the same gene

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Sequence Identity Implies Structural Similarity
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Acipenser milkadoi largest number of
chromosomes of all vertebrate (about 500 mini
and macrochromosomes)

• .

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Carl Woese, Univ. Illinois
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Ribosomal RNA Phylogeny and the Primary Lines of
Evolutionary Descent

• Norman Pace, Gary Olson and Carl Woese
• Cell 45 325-326 (1986)
• Unrooted phylogenetic tree based on
• 16 s-like rRNA sequences. Aligned with 21
  rRNA sequences (about 950 nt)

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Lineage tree of life on earth
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Common Ancestor ?
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Mitochondrial DNA and Human Evolution
Nature 325(1987)31-36

• Allan Wilson, UC Berkeley

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Why Mitochondrial DNA?

• Mutation rate 10 x faster than nuclear genes
• Inherited maternally and does not recombine
• Approx 1016 identical Mt DNA molecules within a
  typical human

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Conclusions

• Assuming that mtDNA mutation rate is constant in
  humans, the sequence divergence of the mtDNAs can
  be calculated to give all the mtDNA a common
  ancestor that lived approx. 200,000 years ago
  (20???)
• The common ancestor of all human may be
• from Africa (????)

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???? Phylogenic Analysis?

• Choose informatic regions
• Make an optimal (500-700 bp) sequence alignment
• Use different methods to construct the trees
• Statistical test for phylogenetic trees

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Methods for Phylogenic Analysis

• Distance Matrix Method
• 1. UPGMA (Unweighted Pair Group Method with
• Arithmetic Average)
• 2. Neighborhood Joining Method
• Discrete Characteristic Methods
• 1. Parsimony Method
• 2. Maximum Likelihood Method

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