Exercise 8: Another Bioinformatics Exercise: A Distance Method of Inferring Phylogeny

Names: ______________________________

In this activity, we will construct a phylogenetic tree using five homologous DNA sequences from primates. Because the sequences have been made up, we cannot deduce any real estimates of genetic distance; to create a meaningful phylogenetic tree from real data would require far longer sequences. Nonetheless, the fictional sequences (in Table 2 below) have been chosen to give a reasonably accurate picture of primate relationships based on genetic distance.

A tutorial similar to this exercise can be viewed at:

https://www.youtube.com/watch?v=09eD4A_HxVQ&ab_channel=OxfordAcademic%28OxfordUniversityPress%29

Table 1. DNA sequences of 6 species of primates

Primate Sequence

1 Neanderthal (n) TGGTCCTGCAGTCCTCTCCTGGCGCCCCGGGCGCGAGCGGTTGTCC

2 Human (h) TGGTCCTGCTGTCCTCTCCTGGCGCCCTGGGCGCGAGCGGATGTCC

3 Chimpanzee (c) TGATCCTGCAGTCCTCTTCTGGCGCCCTGGGCGCGTGCGGTTGTCC

4 Lowland Gorilla TGGACCTGCAGTCATCTTCTGCCCGCCCGAGCGCTTGCCGATGTCC

5 Mountain Gorilla (g) TGGACCTGCAGTCATCTTCTGCCCGCCCGAGCGCTTGCCGATGACC

6 Orangutan (o) ACAACCTGCACTCCTATTCTGCCGAGCCGGGCGCGTGGCAAAGTCC

Count or estimate the number of difference between and among different species of primates.

Table 2. Pairwise sequence differences between primates

Neanderthal

1 Human

2 Chimpanzee

3 Lowland Gorilla 4 Mountain Gorilla 5 Orangutan

6

1 Neanderthal

0 3 ? ? ? ?

2 Human 0 5 ? ? 15

3 Chimpanzee 0 11 ? ?

4 Lowland Gorilla 0 1 ?

5 Mountain Gorilla 0 ?

5 Orangutan 0

Based on the pairwise difference between two sequences, get the averages of the two most closely related taxa. This will give the proportional distance between the two sequences. These values will represent evolutionary distances. Based on the values you estimated in Table 1, construct a preliminary branches for the most closely related taxa

Table 2.

1/2 3 4/5

6

1/2 0

4 + 5/2 = 4.5 8 + 11/2 = 9.5 ?

3 0 ? ?

4/5 0 ?

6 0

Examine the new matrix (Table 2) and reconstruct a new matrix combing those pairs that are most closely related putative species. Estimate the average difference between each of the two closest sister taxa as given in the example. Draw a your phylogenetic tree below.