Molecular Evolution: Understanding the Process and Analyzing Phylogenetic Relationships

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. 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) TreesPresenting Evolutionary Relationships

11. Phylogenetic Trees

12. Phylogenetic Trees

13. The Four Stepsof 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 TreesVersusSpecies 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: 325-326 (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 (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. (李文雄院士)