Title: ???? Molecular Evolution
1 ???? Molecular Evolution
2Molecular 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
3Prokaryotic cells
- Single cell organisms
- Two main types bacteria and archaea
- Relatively simple structure
4Eukaryotic cells
- Single cell or multicellular organisms
- Plants and animals
- Structurally more complex organelles,
cytoskeleton
5Modification?
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Taxonomy and Systematics
7Phylogenetic 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.
8Understanding 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
9The 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
10Phylogenetic (Evolutionary) Trees Presenting
Evolutionary Relationships
11Phylogenetic Trees
12Phylogenetic Trees
13The 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
14Tree 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
15A 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
163 rooted trees that can be drawn from the
unrooted tree shown above, each representing the
different evolutionary pathways possible between
these four genes
17Outgroup
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
18Gene 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
19Molecular 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
20Sequence Identity Implies Structural Similarity
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23Acipenser milkadoi largest number of
chromosomes of all vertebrate (about 500 mini
and macrochromosomes)
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25Carl Woese, Univ. Illinois
26Ribosomal 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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29 Lineage tree of life on earth
30Common Ancestor ?
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32Mitochondrial DNA and Human Evolution
Nature 325(1987)31-36
- Allan Wilson, UC Berkeley
33Why 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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36Conclusions
- 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
41Methods 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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