???? Molecular Evolution - PowerPoint PPT Presentation

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???? Molecular Evolution

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Title: ???? Molecular Evolution


1
???? Molecular Evolution
  • ???
  • ?????????

2
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

3
Prokaryotic cells
  • Single cell organisms
  • Two main types bacteria and archaea
  • Relatively simple structure

4
Eukaryotic cells
  • Single cell or multicellular organisms
  • Plants and animals
  • Structurally more complex organelles,
    cytoskeleton

5
Modification?
6
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Taxonomy and Systematics
7
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.

8
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

9
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

10
Phylogenetic (Evolutionary) Trees Presenting
Evolutionary Relationships
11
Phylogenetic Trees
12
Phylogenetic Trees
13
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

14
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

15
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

16
3 rooted trees that can be drawn from the
unrooted tree shown above, each representing the
different evolutionary pathways possible between
these four genes
17
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
18
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

19
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

20
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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25
Carl Woese, Univ. Illinois
26
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)

27
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28
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29
Lineage tree of life on earth
30
Common Ancestor ?
31
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32
Mitochondrial DNA and Human Evolution
Nature 325(1987)31-36
  • Allan Wilson, UC Berkeley

33
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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40
???? 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

41
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

42
(?????)
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