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Character-Based Phylogenetics: Parsimony and Ancestral Sequences

Explore character-based phylogenetic methods such as parsimony, informative vs. uninformative sites, weighted parsimony, and ancestral sequence inference. Understand the principles of Ockham's Razor and strategies for faster searches in tree construction. Learn about mutations, synapomorphy, and homoplasy in evolutionary analysis.

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Character-Based Phylogenetics: Parsimony and Ancestral Sequences

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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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