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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ABCDEFG A B C D E F G 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 ●

ABCDEFG A B C D E F G BF = / 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.

ABCDEFG A B C D E F G BF ABFCDEG A C D E G B F A C D E G ( ) / 2 = 18.5 ( ) / 2 = 31.5 ( ) / 2 = 17.5 ( ) / 2 = 35.5 ( ) / 2 = Calculate mean pairwise distances with other sequences in new matrix.

ABCDEFG A B C D E F G BF ABFCDEG A C D E G = 8.0 AD / 2 6. Repeat cycle with new shortest distance.

ABCDEFG A B C D E F G BF ABFCDEG A C D E G AD 4.0

ABCDEFG A B C D E F G BF ADBFCEG AD BF C E G AD 4.0 A D B F C E G ( ) / 4 = 18.0 ( ) / 2 = 26.5 ( ) / 2 = 32.0 ( ) / 2 = 13.5

ABCDEFG A B C D E F G BF ADBFCEG AD BF C E G AD 4.0 G = / 2

ABCDEFG A B C D E F G BF ADBFGCE AD BFG C E AD 4.0 G A D CE B F G ( ) / 6 = 16.5 New distances are mean values for all possible pairwise distances between groups.

ABCDEFG A B C D E F G BF ADBFGCE AD BFG C E AD 4.0 G A D CE B F G ( ) / 3 = ( ) / 3 = 33.0 ( ) / 6 = 16.5

ABCDEFG A B C D E F G BF ADBFGCE AD BFG C E AD 4.0 G / = = 16.5

ABCDEFG A B C D E F G BF ADBFGCE C E AD 4.0 G ( ) / 5 = ( ) / 5 = 32.60

ABCDEFG A B C D E F G BF ADBFGCE C E AD 4.0 G C /

ABCDEFG A B C D E F G BF ADBFGCE E AD 4.0 G C ( ) / 6 = 34.00

ABCDEFG A B C D E F G BF ADBFGCE E AD 4.0 G C E 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.

ABCDEFG A B C D E F G BF AD 4.0 G C E ADBFGC E ADBFGC C E ADBFGC C E ADBFCE C E G ABFCDE C D E G

ABCDEFG A B C D E F G BF AD 4.0 G C E 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: Turtle A Man B Tuna C Chicken D Moth E Monkey F Dog G Turtle Man 19 Tuna 2731 Chicken Moth Monkey Dog

Turtle A Man B Tuna C Chicken D Moth E Monkey F Dog G Turtle Man 19 Tuna 2731 Chicken Moth Monkey Dog ManMonkeyTurtleChickenDogTunaMoth Primates MammalsReptilia Vertebrates Amniota The UPGMA tree based on this Cytochrome C data supports the known evolutionary relationships of these organisms.