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ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 0.0 UPGMA: Unweighted Pair-Group.

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Presentation on theme: "ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 0.0 UPGMA: Unweighted Pair-Group."— Presentation transcript:

1 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 0.0 UPGMA: Unweighted Pair-Group Method with Arithmetic mean Unweighted – all pairwise distances contribute equally. Pair-Group – groups are combined in pairs (dichotomies only). Arithmetic mean – pairwise distances to each group (clade) are mean distances to all members of that group. (Ultrametric – assumes molecular clock) Dr Richard Edwards ● University of Southampton ● r.edwards@southampton.ac.uk

2 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 0.5 + 0.5 = 1.0 1.0 / 2 1. Find the shortest pairwise distance. 2. Join two sequences/groups with shortest distance. 3. Depth of new branch = ½ shortest distance. 4. Tip-to-tip path length = shortest distance.

3 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ABFCDEG A 18.50 C 27.0031.50 D 8.0017.5026.00 E 33.0035.5041.0031.00 G 13.0012.5029.0014.0028.00 B F A C D E G (19 + 18) / 2 = 18.5 (31 + 32) / 2 = 31.5 (18 + 17) / 2 = 17.5 (36 + 35) / 2 = 35.5 (13 + 12) / 2 = 12.5 5. Calculate mean pairwise distances with other sequences in new matrix.

4 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ABFCDEG A 18.50 C 27.0031.50 D 8.0017.5026.00 E 33.0035.5041.0031.00 G 13.0012.5029.0014.0028.00 4.0 + 4.0 = 8.0 AD 4.0 8.0 / 2 6. Repeat cycle with new shortest distance.

5 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ABFCDEG A 18.50 C 27.0031.50 D 8.0017.5026.00 E 33.0035.5041.0031.00 G 13.0012.5029.0014.0028.00 AD 4.0

6 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFCEG AD BF 18.00 C 26.5031.50 E 32.0035.5041.00 G 13.5012.5029.0028.00 AD 4.0 A D B F C E G (19 + 18 + 18 + 17) / 4 = 18.0 (27 + 26) / 2 = 26.5 (33 + 31) / 2 = 32.0 (13 + 14) / 2 = 13.5

7 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFCEG AD BF 18.00 C 26.5031.50 E 32.0035.5041.00 G 13.5012.5029.0028.00 AD 4.0 G 6.25 0.5 + 5.75 + 6.25 = 12.5 5.75 6.25 12.5 / 2

8 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE AD BFG 16.50 C 26.5030.67 E 32.0033.0041.00 AD 4.0 G 6.25 5.75 6.25 A D CE B F G (19 + 18 + 13 + 18 + 17 + 14) / 6 = 16.5 New distances are mean values for all possible pairwise distances between groups.

9 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE AD BFG 16.50 C 26.5030.67 E 32.0033.0041.00 AD 4.0 G 6.25 5.75 6.25 A D CE B F G (31 + 32 + 29) / 3 = 30.67 (36 + 35 + 28) / 3 = 33.0 (19 + 18 + 13 + 18 + 17 + 14) / 6 = 16.5

10 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE AD BFG 16.50 C 26.5030.67 E 32.0033.0041.00 AD 4.0 G 6.25 5.75 6.25 8.25 16.5 / 2 4.25 2.0 4.0 + 4.25 + 0.5 + 5.75 + 4.25 = 16.5 6.25 + 2.0 = 16.5

11 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE C 29.00 E 32.6041.00 AD 4.0 G 6.25 5.75 6.25 8.25 4.25 2.0 (27 + 31 + 26 + 32 + 29) / 5 = 29.00 (33 + 36 + 31 + 35 + 28) / 5 = 32.60

12 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE C 29.00 E 32.6041.00 AD 4.0 G 6.25 5.75 6.25 4.25 2.0 C 8.25 14.5 29.0 / 2 5.25 14.5

13 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE E 34.00 AD 4.0 G 6.25 5.75 6.25 4.25 2.0 C 8.25 14.5 5.25 14.5 (33 + 36 + 41 +31 + 35 + 28) / 6 = 34.00

14 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 ADBFGCE E 34.00 AD 4.0 G 6.25 5.75 6.25 4.25 2.0 C 8.25 14.5 5.25 14.5 E 17.0 2.5 17.0 UPGMA assumes a molecular clock. The tree is rooted with the final joining of clades. All tip-to-tip distances via the root will have the same total distance, equal to the final mean distance.

15 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 AD 4.0 G 6.25 5.75 6.25 4.25 2.0 C 8.25 14.5 5.25 14.5 E 17.0 2.5 17.0 ADBFGC E 34.00 ADBFGC C 29.00 E 32.6041.00 ADBFGC 16.50 C 26.5030.67 E 32.0033.0041.00 ADBFCE 18.00 C 26.5031.50 E 32.0035.5041.00 G 13.5012.5029.0028.00 ABFCDE 18.50 C 27.0031.50 D 8.0017.5026.00 E 33.0035.5041.0031.00 G 13.0012.5029.0014.0028.00

16 ABCDEFG A B 19.00 C 27.0031.00 D 8.0018.0026.00 E 33.0036.0041.0031.00 F 18.001.0032.0017.0035.00 G 13.00 29.0014.0028.0012.00 BF 0.5 0.0 0.5 AD 4.0 G 6.25 5.75 6.25 4.25 2.0 C 8.25 14.5 5.25 14.5 E 17.0 2.5 17.0 The source data for this worked example is a selection of Cytochrome C distances from Table 3 of one of the seminal phylogenetic papers: Fitch WM & Margoliash E (1967). Construction of phylogenetic trees. Science 155:279-84. http://www.ncbi.nlm.nih.gov/pubmed/5334057 Turtle A Man B Tuna C Chicken D Moth E Monkey F Dog G Turtle Man 19 Tuna 2731 Chicken 81826 Moth 33364131 Monkey 181321735 Dog 13 29142812

17 Turtle A Man B Tuna C Chicken D Moth E Monkey F Dog G Turtle Man 19 Tuna 2731 Chicken 81826 Moth 33364131 Monkey 181321735 Dog 13 29142812 0.5 0.0 4.0 6.25 8.25 14.5 17.0 ManMonkeyTurtleChickenDogTunaMoth Primates MammalsReptilia Vertebrates Amniota The UPGMA tree based on this Cytochrome C data supports the known evolutionary relationships of these organisms.

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