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Consensus Trees

Consensus Trees. Loni Beaty. Review. Phylogenetic Trees -> Figure depicting evolutionary descent, communicating the evolutionary relationship among entities Important to know: Phylogenetic trees may not represent the true evolutionary history. Why is this?. Problems with Phylogenies.

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Consensus Trees

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  1. Consensus Trees Loni Beaty

  2. Review • Phylogenetic Trees -> Figure depicting evolutionary descent, communicating the evolutionary relationship among entities • Important to know: • Phylogenetic trees may not represent the true evolutionary history. • Why is this?

  3. Problems with Phylogenies • Why may a phylogenetic tree not actually be correct? • Horizontal gene transfer • Transfer of genetic material between organisms • Hybridization • A process to measure the degree of genetic similarity • Convergent Evolution • Acquiring the same or similar biological traits in unrelated lineages • Conserved sequences • Similar sequences occurring in RNA, DNA, protein sequences, etc. across species. • More genes needed to be taken into account from difference genomic sources

  4. So, What do we use then? • Consensus Trees: • A consensus tree is single evolutionary tree created from a group of phylogenetic trees. • Why do we use these? • Life scientists can study this single consensus tree, with the most robust branching patterns of the phylogenetic tree of how the taxa evolved.

  5. Tree Support • There are ways to express how good each phylogenetic tree is. • Statistical Resampling • Resulting trees are pooled and presented on a majority rule consensus tree. • Nodes labeled with percentage of trees in which they appear. • Bootstrapping • Resampling with replacement • More common • Jackknifing • Resampling without replacement • Bremer Support (aka Decay Index)

  6. Bremer Support • Difference in number of steps between the score of trees and the score of the most parsimonious tree not containing a particular clade. • A step is a change from one character state to another, or evolutionary transition. • The number of steps you have to add to lose a clade. • Therefore, the larger the number, the stronger the support for that node. • Decay indexes appear to be proportional to bootstrap percentages.

  7. Graph depicts relationship of 8 teleost fishes and an outgroup. Optimal tree is 82 steps long. If run at 83 steps, one step longer that the optimal, one ingroup collapses to form a trichotomy. If run at 83 steps, multiple ingroups have collapsed. This is continued until the whole tree is collapsed, and each node has a value. The overall result is the Decay Index. Bremer Support in PAUP

  8. Use of Data • Dispute among cladists which is best: • Character Congruence • Combine all data into a large data set and analyze together • Taxonomic Congruence • Combine trees produced from different data

  9. Types of Consensus Trees • There are quite a few types of consensus trees, but the more prominent are: • Strict • evolutionary relationships that appear in all of the trees • purists believe this is the only consensus method that should be considered • Semi-strict • Combine all possible solutions that are not contradicted • Sometimes called combinable component consensus • Majority Rule • branching patterns that exist in a majority of the trees

  10. If the relationship doesn’t appear on ALL of the phylogenetic trees, it doesn’t appear on the consensus tree. Another way of looking at it is a clade cannot be confirmed unless we’re sure of it. Strict consensus trees

  11. So long as no trees are contradicted by other trees, it can appear on the consesus tree. Another was to look at it is, a clade shouldn’t be refused unless there is a clear contridiction. SemiStrict Consensus Trees

  12. The grouping only has to be present in the majority of trees to be represented in the consensus tree. Majority is typically 50%. When only comparing two trees, Strict Consensus is used. Majority Rule Consensus Trees

  13. Useful programs • PAUP – Phylogenetic Analysis Using Parsimony • Program for inferring evolutionary trees and consensus trees • Parsimony is character-based tree estimation method. • TreeRot – program used to calculate the decay index

  14. References • http://www.geol.umd.edu/~tholtz/G331/lectures/cladistics5.pdf • DEGNAN J, DEGIORGIO M, BRYANT D, ROSENBERG N. Properties of Consensus Methods for Inferring Species Trees from Gene Trees. Systematic Biology [serial online]. February 2009;58(1):35-54. Available from: Academic Search Complete, Ipswich, MA. Accessed May 16, 2012. • http://www.sciencedirect.com.ezproxy.library.wwu.edu/science/article/pii/S0025556410001227 • Bioinformatics for Biologists text

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