The phylogeny below shows the relationship between six species based on whole genome data. The sequence of a part of a particular gene from each species is provided at the tips of the tree. Based on the principle of parsimony, which one of the following is the expected sequence for the ancestor X?
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Work out each ancestral position separately using the fewest base changes needed to explain the tips in each half of the tree, then combine the four positions.
Step 1: Read the tree structure and the tip sequences.
The tree splits at X into two major branches. The upper branch groups three tips: ATGG and AAGG are sister species, and that pair is joined by AACG. The lower branch groups the other three tips: AACT sits apart, while ATGG and ATCG are sister species, and that pair joins AACT. So the topology is
\[
X = \big((\text{ATGG},\text{AAGG}),\text{AACG}\big) \ \text{and} \ \big(\text{AACT},(\text{ATGG},\text{ATCG})\big)
\]
Step 2: Apply parsimony one letter position at a time.
Parsimony reconstructs each ancestral node by taking, at every position, whichever base needs the fewest changes to explain the tips below it. For two tips, this means taking the shared base if they agree, or keeping both as a shared possibility if they disagree; when a node's options are then compared with a third source and they share a base, that shared base wins.
Step 3: Reconstruct position 1 (first letter).
All six tips start with A: ATGG, AAGG, AACG, AACT, ATGG, ATCG. Since every tip agrees, both major branches and X itself must have A at position 1.
Step 4: Reconstruct position 2 (second letter).
In the upper branch, ATGG has T and AAGG has A, so their common ancestor could be either T or A. Comparing this against AACG, which has A, the shared option is A, so the upper branch's ancestor is A. In the lower branch, AACT has A, while the ATGG and ATCG pair share T, so their combined ancestor could be A or T. Comparing the two major branches, the upper gives A and the lower gives A or T, and A is common to both, so X takes A at position 2.
Step 5: Reconstruct position 3 (third letter).
In the upper branch, ATGG and AAGG both have G, but AACG has C, giving a combined possibility of G or C for that branch. In the lower branch, AACT has C, and the ATGG and ATCG pair share G, giving a combined possibility of C or G. Comparing G-or-C from the upper branch with C-or-G from the lower branch, C is the value common to both, so X takes C at position 3.
Step 6: Reconstruct position 4 (fourth letter).
In the upper branch, ATGG, AAGG, and AACG all end in G, so the upper ancestor is G with no ambiguity. In the lower branch, AACT ends in T while the ATGG and ATCG pair both end in G, giving a combined possibility of T or G. Comparing G from the upper branch with T-or-G from the lower branch, G is common to both, so X takes G at position 4.
Step 7: Assemble the ancestral sequence.
Putting the four positions together, A, A, C, G, gives the sequence AACG for ancestor X, which requires the fewest total base changes across the whole tree compared to any other candidate sequence.
