Question

Consider the following matrix that shows the similarities between species are for a particular gene. A small number (e.g., 3) indicates the genes are very similar, in that only 3 amino acids are different. A larger number (e.g., 17) indicates the species are more different. Using this matrix, calculate and draw a similarity tree using UPGMA. Label the branch lengths. Take a photo of your labeled tree and upload it. Cow Mouse Gibbon Orangutan Gorilla Chimp 16 Cow Mouse Gibbon Orangutan Gorilla Chimp 16 15 16 15 14 14 14 7 5 6 4 5 3

Answer 1

	Cow	Mouse	Gibbon	Orangutan	Gorilla	Chimp
Cow
Mouse	16
Gibbon	17	15
Orangutan	16	14	7
Gorilla	15	14	5	4
Chimp	16	14	6	5	3

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1. Find the shortest pair distance.
2. Join the groups with shortest distances.
3. Length of the new branch is half of the shortest distance = 1/2 × distance.
4. Calculation of new mean pairwise distances with other sequence in the matrix.

Lenght of the branch = 3/2 = 1.5

In the first chimp and the Gorilla has the shortest distance.

	Cow	Mouse	Gibbon	Orangatan	Gorilla/Chimp
Cow
Mouse	16
Gibbon	7	15
Orangatan	16	14	7
Gorilla/Chimp	15.5	14	5.5	4.5

Pairwise calculation:-

Cow = (15+16)/2 = 15.5

Mouse = (14+14)/2 = 14

Gibbon = (5+6)/2 = 5.5

Orangatan = (4+5)/2 = 4.5

Length of the branch = 4.5/2 = 2.25

In these way repeat and calculate.

⬇️

	Cow	Mouse	Gibbon	Gorilla/Chimp/Orangatan
Cow
Mouse	16
Golibbon	17	15
Gorilla/Chimp/Orangatan	15.5	14	6

Calculating the new matrix same way.

Lenght of new branch = 6/2 = 3

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	Cow	Mouse	Gorilla/Chimp/Orangatan/Gibbon
Cow
Mouse	16
Gorilla/Chimp/Orangatan/Gibbon	16	14.25

Lenght of new branch = 14.25/2 = 7.125

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	Gorilla/Chimp/Orangatan/Gibbon/Mouse
Cow	16

Lenght of new branch = 16/2 = 8

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Tree using UPGMA :-