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1 Thanks to Paul Lewis and Joe Felsenstein for the use of slides

2 Review Hennigian logic reconstructs the tree if we know polarity of characters and there is no homoplasy UPGMA infers a tree from a distance matrix: groups based on similarity fails to give the correct tree if rates of character evolution vary much modern distance-based approaches: extend the ideas behind Buneman s (1971) approach try to find trees and branch lengths, such that the path lengths implied by the tree match the pairwise distances that are estimated from character data. are not sensitive to variation in rate. do not use all of the information in the data.

3 Imperfections of distance base approaches Summarizing the character data into a distance matrix loses information. We cannot tell which characters evolve quickly and which evolve slowly from pairwise comparisons.

4 Species 1 C G A C Species 2 C G A T Species 3 C G A C Species 4 C G A T Species 5 C G A C Species 6 C G A T Species 7 C G A C Species 8 C G A T Species 9 C G G C Species 10 C G G T Species 11 C G G C Species 12 C G G T Species 13 C G G C Species 14 C G G T Species 15 C G G C Species 16 C G G T

5 Imperfections of distance base approaches Summarizing the character data into a distance matrix loses information. We cannot tell which characters evolve quickly and which evolve slowly from pairwise comparisons. Reconstructing character histories on a tree can reveal homoplasy this means we can t condense the character data before we start looking for trees.

6 Species 1 C G A C C A G G T... Species 2 C G A C C A G G T... Species 3 C G G T C C G G T... Species 4 C G G C C T G G T... One of the 3 possible trees: Same tree with states at character 6 instead of species names Species 1 Species 3 A C Species 2 Species 4 A T

7 Standard Parsimony

8 Things to note about the last slide 2 steps was the minimum score attainable. Multiple ancestral character state reconstructions gave a score of 2. Enumeration of all possible ancestral character states is not the most efficient algorithm.

9 Each character (site) is assumed to be independene To calculate the parsimony score for a tree we simply sum the scores for every site Species 1 C G A C C A G G T Species 2 C G A C C A G G T Species 3 C G G T C C G G T Species 4 C G G C C T G G T Score Species 1 Species 3 Tree 1 has a score of 4 Species 2 Species 4

10 Considering a different tree We can repeat the scoring for each tree Species 1 C G A C C A G G T Species 2 C G A C C A G G T Species 3 C G G T C C G G T Species 4 C G G C C T G G T Score Species 1 Species 2 Tree 2 has a score of 5 Species 3 Species 4

11 One more tree Tree 3 has the same score as tree Species 1 C G A C C A G G T Species 2 C G A C C A G G T Species 3 C G G T C C G G T Species 4 C G G C C T G G T Score Species 1 Species 2 Tree 3 has a score of 5 Species 4 Species 3

12 Parsimony criterion prefers tree 1 Tree 1 required the fewest number of state changes (DNA substitutions) to explain the data. Some parsimony advocates equate the preference for the fewest number of changes to the general scientific principle of preferring the simplest explanation (Ockham s Razor), but this connection has not been made in a rigorous manner. The parsimony criterion is equivalent to minimizing homoplasy.

13 In the example matrix at the beginning of these slides, only character 3 is parsimony informative Species 1 C G A C C A G G T Species 2 C G A C C A G G T Species 3 C G G T C C G G T Species 4 C G G C C T G G T Max score Min score

14 Assumptions about the evolutionary process can be incorporated using different step costs Fitch Parsimony unordered

15 Stepmatrices Fitch Parsimony Stepmatrix To A C G T A From C G T

16 Stepmatrices Transversion-Transition 5:1 Stepmatrix To A C G T A From C G T

17 5:1 Transversion:Transition parsimony

18 Stepmatrix considerations Parsimony scores from different stepmatrices cannot be meaningfully compared (31 under Fitch is not better than 45 under a transversion:transition stepmatrix) Parsimony cannot be used to infer the stepmatrix weights

19 Other Parsimony variants Dollo derived state can only arise once, but reversals can be frequent (e.g. restriction enzyme sites). weighted - usually means that different characters are weighted differently (slower, more reliable characters usually given higher weights). implied weights?

20 Scoring trees under parsimony is fast A C C A A G

21 Scoring trees under parsimony is fast Fitch algorithm A C C A A G {A,C} +1 {A,G} +1 3 steps {A} {A, C} +1 {A}

22 Scoring a trees under parsimony Fitch and Sankoff algorithms are fast (# of calculations increases linearly with the # of leaves, despite the fact that the # of possible ancestral state reconstructions increases exponentially). Fitch and Sankoff algorithms are guaranteed to succeed (return the minimum # of changes). Elaborations of these algorithms allow us to reconstruct ancestral states.

23 Qualitative description of parsimony It can perform well even when changes are not rare. Does not prefer to put changes on one branch over another Hard to characterize statistically the set of conditions in which parsimony is guaranteed to work well is very restrictive (low probability of change and not too much branch length heterogeneity); Parsimony often performs well in simulation studies (even when outside the zones in which it is guaranteed to work); Estimates of the tree can be extremely biased.

24 Long branch attraction Felsenstein, J Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27:

25 Long branch attraction A G Felsenstein, J Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: The probability of a parsimony informative site due to inheritance is very low, (roughly ) A G

26 Long branch attraction A A Felsenstein, J Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: The probability of a parsimony informative site due to inheritance is very low, (roughly ) G G The probability of a misleading parsimony informative site due to parallelism is much higher (roughly 0.008).

27 Long branch attraction Parsimony is almost guaranteed to get this tree wrong True Inferred

28 Inconsistency Statistical Consistency (roughly speaking) is converging to the true answer as the amount of data goes to. Parsimony based tree inference is not consistent for some tree shapes. In fact it can be positively misleading : Felsenstein zone tree Many clocklike trees with short internal branch lengths and long terminal branches (Penny et al., 1989, Huelsenbeck and Lander, 2003). Methods for assessing confidence (e.g. bootstrapping) will indicate that you should be very confident in the wrong answer.

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Maximum Likelihood This presentation is based almost entirely on Peter G. Fosters - "The Idiot s Guide to the Zen of Likelihood in a Nutshell in Seven Days for Dummies, Unleashed. http://www.bioinf.org/molsys/data/idiots.pdf

What is Phylogenetics

What is Phylogenetics Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features)

Chapter 19 Organizing Information About Species: Taxonomy and Cladistics An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics