1. 分子演化 Molecular Evolution
宣大衛
東華大學生命科學系

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. Taxonomy and Systematics
分類學
系統生物學 g
Taxonomy and Systematics

7. Phylogenetic Systematics
種系遺傳
系統生物學
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 漂移
- 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

23. Acipenser milkadoi – largest number of chromosomes of all vertebrate (about 500 mini and macrochromosomes) .

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: (1986)
Unrooted phylogenetic tree based on
16 s-like rRNA sequences. Aligned with 21 rRNA sequences (about 950 nt)

28. 細菌
古生菌
真核生物

29. Lineage tree of life on earth

30. Common Ancestor ?

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

36. 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 (20萬年前)
The common ancestor of all human may be
from Africa (非洲夏娃)

40. 如何做好 Phylogenic Analysis?
Choose informatic regions
Make an optimal ( 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. (李文雄院士)