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Chapter 5 Character–Based Methods of Phylogenetics

Chapter 5 Character–Based Methods of Phylogenetics. 暨南大學資訊工程學系 黃光璿 (HUANG, Guan-Shieng) 2004/04/05. 5.1 Parsimony. Mutations are exceedingly rare events. The most unlikely events a model invokes, the less likely the model is to be correct.

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Chapter 5 Character–Based Methods of Phylogenetics

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  1. Chapter 5Character–Based Methods of Phylogenetics 暨南大學資訊工程學系 黃光璿 (HUANG, Guan-Shieng) 2004/04/05

  2. 5.1 Parsimony • Mutations are exceedingly rare events. • The most unlikely events a model invokes, the less likely the model is to be correct. •  The fewest number of mutations to explain a state is the most likely to be correct.

  3. Ockham's Razor • the philosophic rule states that entities should not be multiplied unnecessarily

  4. 5.1.1 Informative and Uninformative Sites

  5. 5.1.1 Informative and Uninformative Sites • informative sites • have information to construct a tree • uninformative sites • have no information in the sense of parsimony principle.

  6. uninformative

  7. uninformative

  8. informative

  9. informative

  10. A position to be informative must have • at least two different nucleotides • each of these nucleotides to present at least twice.

  11. informative sites • synapomorphy: support the internal branches (true) • homoplasy: acquired as a result of parallel evolution of convergence (false) • 眼睛：humans, flies, mollusks (軟體動物)

  12. 5.1.2 Unweighted Parsimony • Every possible tree is considered individually for each informative site. • The tree with the minimum overall costs are reported.

  13. There are several problems: • The number of alternative unrooted trees increases dramatically. • Calculating the number of substitutions invoked by each alternative tree is difficult.

  14. The second problem can be solved by • intersection: if the intersection of the two sets of its children is not empty • union: if it is empty. • The number of unions is the minimum number of substitutions. • For uninformative site, it is the number of different nucleotides minus one.

  15. /* the uth position in the kth sequence */

  16. 5.1.4 Weighted Parsimony • Not all mutations are equivalent • Some sequences (e.g., non-coding seq.) are more prone to indel than others. • Functional importance differs from gene to gene. • Subtle substitution biases usually vary between genes and between species.  Weights (scoring matrices) can be added to reflect these differences.

  17. Calculating the optimal costs

  18. Finding the internal nodes

  19. 5.2 Inferred Ancestral Sequences • Can be derived while constructing the tree. •  No missing link! • 如何取樣本? It may be bias.

  20. 5.3 Strategies for Faster Searches • The number of different phylogenetic tree grows enormously. • 10 sequences  2M for exhaustive search

  21. 參考資料及圖片出處 • Fundamental Concepts of BioinformaticsDan E. Krane and Michael L. Raymer, Benjamin/Cummings, 2003. • Biological Sequence Analysis– Probabilistic models of proteins and nucleic acidsR. Durbin, S. Eddy, A. Krogh, G. Mitchison, Cambridge University Press, 1998. • Biology, by Sylvia S. Mader, 8th edition, McGraw-Hill, 2003.

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