Maximum parsimony
- 1. MAXIMUM PARSIMONY SHRUTHI K 18308019 II M.Sc MICROBIOLOGY
- 2. Phylogenetic trees, or evolutionary trees, are the basic structures necessary to examine the relationships among organisms. They model evolutionary events of vertical and horizontal descent. The parsimony method is one such approach where it minimises the number of steps to generate variations from common ancestral sequences. It prefers simplest explanation over more complex explanations. A multiple sequence alignment (msa) is required to predict which sequence positions are likely to correspond.
- 3. For each aligned position, phylogenetic trees that require the smallest number of evolutionary changes to produce the observed sequence changes from ancestral sequences are identified. Finally, those trees that produce the smallest number of changes overall for all sequence positions are identified. McLennan, D.A. Evo Edu Outreach (2010) 3: 506. https://doi.org/10.1007/s12052- 010-0273-6
- 4. A rooted tree is used to make inferences about the most common ancestor of the leaves or branches of the tree. Most commonly the root is referred to as ‘outgroup’. An unrooted tree is used to make an illustration about the leaves or branches, but not make assumption regarding a common ancestor. V.K., Singh & Singh, Anil & Kayastha, Arvind & Singh, Brahma. (2014). Legumes in the Omic Era. 10.1007/978-1- 4614-8370-0_12.
- 5. External nodes: things under comparison; operational taxonomic units (OTUs). Internal nodes: ancestral units; hypothetical; goal is to group current day units. Topology: branching pattern of a tree. Branch length: amount of difference that occurred along a branch. Monophyletic group, or clade, is a group of organisms that consists of all the descendants of a common ancestor.
- 6. Entrez: www.ncbi.nlm.nih.gov/Taxonomy Ribosomal database project: rdp.cme.msu.edu/html/ Tree of Life: phylogeny.arizona.edu/tree/phylogeny.html PHYLLIP PACKAGE: i. DNAPERS ii. DNAPENNY – For more sequences 1. DNACOMP – finds tree that supports largest number of sites. 2. DNAMOVE – interactive analysis of parsimony
- 7. Tree of life: Analyzing changes that have occurred in evolution of different organisms. Phylogenetic relationships among genes can help predict which ones might have similar functions (e.g., ortholog detection). Follow changes occuring in rapidly changing species (e.g., HIV virus)
- 8. This is an example of character based method. They are based on sequence character rather than pairwise distances. They count mutational events accumulated on the sequences and may therefore avoid loss of information when character is converted to distances. Thereby evolutionary dynamics can be studied and ancestral approaches can also be studied. Maximum parsimony is an example for this method.
- 9. The parsimony method chooses a tree that has fewest evolutionary changes or mutations or shortest overall branch length. Based on Occam’s razor philosophy. Reduces chances of inconsistencies, ambiguities and redundancies. By minimizing the changes, the method minimizes the phylogenetic noise owing to homoplasy and independent evolution.
- 10. •The four-way multiple sequence alignment contains positions that fall into two categories – informative and uninformative sites. • For the first position all four sequences have same character and no mutations- invariant • Position 2 and 4 have minimum two mutations which are derived from ancestors - informative
- 12. 1 2 3 4 5 6 7 8 9 10 A – A T G G A T T T C G B – A T G G C G T T C G C – G C G G A G T T C G D – G C G G C G T T T G Now, lets map one of these characters onto an unrooted tree Note that we must assign states to ancestral nodes A D B C T C T C T C 1 step T C T C C T 5 steps A B C D T T C C
- 13. 1 2 3 4 5 6 7 8 9 10 A – A T G G A T T T C G B – A T G G C G T T C G C – G C G G A G T T C G D – G C G G C G T T T G site 1 - 1 step A B C D A B C D A B C D A A G G A C A C T T C C site 5 - 2 steps on two equally parsimonious trees site 2 - 1 step
- 14. Mapping should also be done for all other sites Sites 3,4,7,8,10 – 0 steps Mapping should also be done for all possible trees site 6 – 1 step 1 2 3 4 5 6 7 8 9 10 A – A T G G A T T T C G B – A T G G C G T T C G C – G C G G A G T T C G D – G C G G C G T T T G G T G G G G C T C C C C site 9 - 1 step
- 15. There are three possible unrooted trees for four taxa. B C D A A B D C A D B C ((A,B),(C,D)) ((A,D),(C,B)) ((A,C),(B,D))
- 16. CTND… Evaluate each possible tree for all sites to determine the smallest total number of changes necessary to generate each one Note sites 3,4,6,7,8,9,10 are the same for every tree – parsimony uninformative Sites Tree 1 2 3 4 5 6 7 8 9 10 Total ((A,B),(C,D)) 1 1 0 0 2 1 0 0 1 0 6 ((A,D),(C,B)) 2 2 0 0 2 1 0 0 1 0 8 ((A,C),(B,D)) 2 2 0 0 1 1 0 0 1 0 7
- 17. WEIGHTED PARSIMONY Suppose we weight transversions with twice the value of transitions Site 5 is now weighted twice as much as sites 1 and 2 Sites Tree 1 2 3 4 5 6 7 8 9 10 Total ((A,B),(C,D)) 1 1 0 0 4 1 0 0 1 0 8 ((A,D),(C,B)) 2 2 0 0 4 1 0 0 1 0 10 ((A,C),(B,D)) 2 2 0 0 2 1 0 0 1 0 8
- 18. ADVANTAGES Easy to understand Makes relatively few assumptions. Well studied mathematically Many useful software packages More theoretical arguments: 1. Methodologically, parsimony forces us to maximize homologous similarity. This is not necessarily true for other methods 2. Parsimony is based on an evolutionary assumption – evolutionary change is rare. Not true at all for most distance methods
- 19. DISADVANTAGES Why not use parsimony? Not consistent, under some scenarios it is possible (even likely) to get the wrong tree Long-branch attraction – similar to rate heterogeneity problem encountered with distance methods When DNA substitution rates are high, the probability that two lineages will convergently evolve the same nucleotide at the same site increases. When this happens, parsimony erroneously interprets this similarity as a synapomorphy (i.e., evolving once in the common ancestor of the two lineages).
- 20. VERSIONS Versions of parsimony Fitch parsimony – no limitations on permissible character changes, reversible P(A->T) = P(T->A) Wagner parsimony – allows ordered transformations (to get from C to G, you must proceed through A), reversible Dollo parsimony – consider restriction site characters P(0->1) ≠ P(1->0) Limited non-reversibility – derived states cannot be lost and regained Works really well for mobile element insertion data Camin-Sokal parsimony – evolutionary changes are irreversible Transversion parsimony – ignores transitions or downweights them severely
- 21. Refers to phylogenetic artifact in which rapidly evolving taxa with long branches are placed together. It is regardless of their true positions. Due to assumption that all lineages evolve at the same rate and that all mutations contribute to branch length. A B D C Long branch
- 22. The edges leading to sequences/taxa A and C are long relative to other branches in the tree, reflecting the relatively greater number of substitutions that have occurred along those two edges. The long branch attraction occurs when rates of evolution show considerable variation among sequences, or where the sequences being analysed are quite divergent. How to overcome Long Branch Attraction? To reduce the effects of long edges is to add sequences/taxa that join onto those edges thus breaking them up.
- 23. Krane, Raymer.ML, Fundamental concepts of bioinformatics, 2003, Pearson education Xiong.J, Essential bioinformatics, 2006, Cambridge University press. Bioinformatics: Sequence and Genome Analysis by Mount D., 2004 Cold Spring Harbor Laboratory Press, New York.