Phylogenetic Analysis: Building Evolutionary Trees from Nucleic Acid and Protein Sequences, Slides of Genetics

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Phylogenetic Prediction docsity.com Phylogenetic trees Phylogenetic analysis of a family of related nucleic acid or protein sequences is a determination of how the family members might have been derived during evolution. The evolutionary relationships among the sequences are depicted by using a graph called a tree. Sequences are placed as the outer branches of the tree, and the branching relationship of the inner part of the tree then reflect the degree to which different sequences are related. docsity.com Rooted Trees  Two types of trees are usually found Rooted Un rooted  In a rooted tree, a root or basal is placed at the base of the tree representing a common ancestor of all of the other sequences.  A unique path leads from the root node to any other node, eventually reaching the outer most nodes and the sequences, and the direction of the path indicates the passage of evolutionary time. docsity.com Un Rooted Trees Sometimes the position of the root is difficult to locate resulting in an un rooted tree. An un rooted tree also depicts the relationship among taxa or sequences but does not provide information on a common ancestor to the group. Un rooted tree depicts the evolutionary relation ships among the sequences but it does not reveal the location of the oldest ancestry. docsity.com Challenge of phylogenetic analysis  The challenge of phylogenetic analysis is to determine the tree that best accounts for the observed variation in the sequences. A useful concept in this regard is the tree length. The sum of all the branch lengths in a tree is the tree length. docsity.com Fitch- Margoliash Method Fitch- Margoliash method uses a distance table obtained after pair wise alignment programs. The sequences are first combined into groups of three and the combined data are used to calculate the branch lengths in the tree. Additional sequences are then progressively added to the analysis.  This method of averaging distances is most accurate for trees with short branches.  The presence of long branches tends to decrease the reliability of the predictions. docsity.com Example 1:- For Three Sequences Suppose we have three A B C sequences A, B and C A - 22 39 The distance among the B - - 41sequences is shown in the C - - -distance table. Draw an un rooted tree with three branches emanating from a common node and label ends of the branches as shown in figure. docsity.com As the distance between A and B is shorter, the branch lengths between these sequences are expected to be shorter as shown in the figure.  Calculate lengths of the tree branches algebraically. The branch lengths may be calculated algebraically using the branch labels which are shown in figure as a, b and c. docsity.com Example 2:- More Than Three Sequences  Suppose we have five sequences A, B, C, D A B C D E and E A - 22 39 39 41 The distance table for B - - 41 41 43them is shown as follows: C - - - 18 20 D - - - - 10 E - - - - - docsity.com  The most closely related sequences given in the D E Avg ABCdistance table are D and E. A new table is made D - 10 32.7 with the remaining E - - 34.7 sequences combined. Avg - - - The average distances ABC from D to ABC and E to ABC are calculated. docsity.com Average ABC to D = (39+41+18)/3 =32.7 Average ABC to E = (41+43+20)/3 =34.7 Distance between D and E = d+e docsity.com D and E are now treated as a single composite sequence(DE) and a new distance table is updated. The distance from A to (DE) is the average of the distance of A to D and of A to E. The other distances to(DE) are calculated accordingly. docsity.com 2nd Step Now the smallest distance is between C and (DE) Now combine the remaining sequences which are A and B and repeat the same process docsity.com By repeating the process the tree which is formed is as: docsity.com How Reliable Are Phylogenetic Predictions??  For sequences that have diverged considerably, a phylogenetic analysis is more challenging.  A determination of the sequence changes that have occurred is more difficult because the msa may not be optimal and because multiple changes may have occurred in the aligned sequence positions.  Once a suitable alignment is found, then the predicted phylogenetic relationships become reliable docsity.com How Reliable Are Phylogenetic Predictions?? The most suitable way is to predict the phylogenetic evolution using two different approaches. If both the methods provide with the same prediction, then confidence in prediction is much higher. Another recommendation is to pay careful attention to the evolutionary assumptions and models that are used for both sequence alignment and tree construction. docsity.com ASSIGNMENT GROUP A:- (Study Maximum Parsimony method and present on 13th March, 2012 with examples. Submit a detailed report also with proper examples) Note:- The work of each individual of a group must be visible docsity.com