How to Draw a Phylogenetic Tree
(Using differences in molecular sequence)

A phylogenetic tree uses data to indicate relatedness of different species. This webpage explains how to construct a phylogenetic tree using differences in molecular sequences (such as differences in amino acids, or differences in nucleotides).

Numbers in the table below represent mutational differences in a particular gene. Higher numbers indicate more genetic differences between two species. The longer two species (or subspecies) are isolated, the more likely there will be an accumulation of mutational differences.

Table: Cytochrome b DNA sequence differences between different species
	Species A	Species B	Species C	Species D	Species E	Species F
Species A	-	27	37	38	35	40
Species B	27	-	13	19	20	21
Species C	37	13	-	3	8	11
Species D	38	19	3	-	12	14
Species E	35	20	8	12	-	1
Species F	40	21	11	14	1	-

 

1. Identify the most different, or ancestral, species . This is the one that has the most mutational differences from the other species. In the chart above, the species with the most mutational differences (highest numbers) is Species A.

2. Select the next most different, or ancestral species, the one that shares a common ancestor with the previous species (Species A). To do this, look at the Species A column and look for the species that has the fewest mutational differences, which is Species B with 27.

3. Begin drawing the phylogenetic tree. This is commonly done by drawing a line with branches indicating a possible shared common ancestor. The break (or node) of a branch indicates a common ancestor, and the branch itself indicates speciation. In a phylogenetic tree, line length does not necessarily indicate the age of a species, just relatedness and ancestry.

4. Add the next organism . To do this, look at the second organism's data (Species B), and look for the most genetically similar organism (for that particular gene). From the table, Species B may share a common ancestor with Species C (13 differences).

5. Add the next organism. Looking at the Species C row and column, find the most genetically similar organism, which is Species D (3 differences).

6. Add the remaining organisms. Looking at Species D, the lowest number is still the "3" from the mutation differences with Species C. What this may indicate is that Species D shares a common ancestor with Species C, but not with the remaining species (Species E and Species F). Looking at Species E and Species F data, Species E is very similar to Species F , and Species E is similar to Species C . This suggests that Species E shared a common ancestor with Species C, not Species D. Species F then shares a common ancestor with Species E.

7. Check to confirm that your phylogenetic tree matches the data in the table.