Tweets by @slimsuite |
## UPGMA Worked ExampleThe tabs below include a walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI site for generating a UPGMA tree from a distance matrix can be found here. UPGMA is a distance method and therefore needs a distance matrix. UPGMA is "ultrametric", meaning that all the terminal nodes ( Each round of UPGMA follows the same pattern. The two sequences joined (B and F) are removed from the original matrix and replaced by the new clade (BF). Each distance between BF and the other sequences (A, C, D, E and G) is the mean distance between them and B and F from the original matrix. E.g. d(A,BF) = (d(A,B) + d(A,F))/2. Identify the shortest pairwise distance in the Each time the new matrix is made, distance are taken from the original matrix (top). All of the values to be replaced in the new matrix will come from the rows and columns corresponding to the sequences in the new clade (A and D), highlighted by the dashed orange boxes. As before, mean values are calculated using the individual pairwise values from the original matrix. Where the new cluster (AD) is being compared to the previous cluster (BF), Again, the shortest pairwise distance in the Again, when generating the new matrix, use the pairwise distances from the original matrix. UPGMA is The rest of the new BFG columns and rows are calculated as the mean distances of B, F and G with the remaining sequences C and E. Note that The cycle is repeated as before. This time, no new sequences are added but the two existing clades (AD and BFG) are joined at a depth of half the mean pairwise distance between AD and BFG. All possible tip-to-tip distances between A/D and B/F/G add up to the full distance. Again, the distance matrix shrinks by one and mean distances are calculated for the new clade, ADBFG. Make penultimate join using shortest pairwise distance in Once the final join has been made, the UPGMA tree is complete. UPGMA is inherently rooted and thus the root is placed at the deepest point of the tree, at a depth of half the final mean pairwise distance. All root to tip distances are the same, meaning that this method assumes a molecular clock for sequence data, Once the UPGMA method is finished, all the pairwise distances in the original matrix will have contributed to one E.g. the two green pairwise distances (d(B,G) and d(F,G)) generated the distance 12.50 used in the third cycle to join BF and G.For clarity, this data represents only a subset of the taxa included in the original Fitch & Margoliash paper. In this example, therefore, human (B) and monkey (F) are the closest pair, which next group with dog (G) (the other mammal), then the chicken (D)/turtle (A) (the other Amniota), then tuna (fish) (C) to form a vertebrate clade and finally moth (insect) (E). Based on this data, Cytochrome C supports the known phylogenetic relationship of these organisms. In the original paper, they get the same relationship for these organisms (and more!) using a different method. Animated PowerPoint version available upon request. If you have any questions, please contact Dr Richard Edwards. © 2016 RJ Edwards. Contact: richard.edwards@unsw.edu.au. |