# Can somebody explain why mouse and cow are the least related based on this sequenece alignment?

Answer key says out of the choices, the mouse and cow and the least related. Is it because they have the most number of differences out of the four choices? (Hedgehog/Horse is 5, dog/horse is 3, mouse/cow is 7, and mouse/dog is 3). I know there are more complex ways to make the tree, as shown in this video: https://www.youtube.com/watch?v=09eD4A_HxVQ, but I just wanted to know if my logic is correct here. This is for AP biology and we did not learn anything about the technique used in the video. Thank you.

• Welcome to the site. The image is confusing as there is no reference sequence - normally you would have a sequence to compare them all to. As this is clearly homework - what do you know about genetic difference; how might we measure this? Do you think having a greater number of differences leads to more or less similarity?
– bob1
Commented Apr 19, 2023 at 2:23
• I would think having a greater number of differences would lead to less similarity. The video I referenced also didn't have a reference sequence, but I don't think we're supposed to do it that way. Commented Apr 19, 2023 at 2:37
• So, you have your answer, and you knew it all along. The reference sequence makes it easier for multiple comparisons, but as the answers in your question are binary, you take one as reference and calculate the numbers of differences between the two, then do the same for the next pair (as you obviously did).
– bob1
Commented Apr 19, 2023 at 2:41
• The problem there only exists in your mind - those weren't part of the options you were given, so you don't have to worry about that part. No need for a tree.
– bob1
Commented Apr 19, 2023 at 2:55
• The question says nothing about phylogenetic trees and nor should you as it would be absurd to try to construct one from these contrived data. I loath and detest MCQs in teaching, but the question is clearly testing one idea — that the longer evolutionary time there is between the organisms from which sequences have been derived, the greater chance there is of mutations occurring. You would do better to ponder the simplification in the scoring system — why is a transition scored the same as a transversion (not to mention the convenient absence of insertions and deletions). Commented Apr 20, 2023 at 15:01

Answer C (Mouse and Cow) is the correct answer to the question, because among the four answer choices, mouse and cow share the earliest common ancestor*.

OP developed this tree** by following the method in the YouTube tutorial.

Under this tree, mouse and cow are more distantly related than the other provided answers because the common ancestor of mouse and cow is deeper in the tree than the common ancestors of the other answer pairs.

However, mouse and cow are not the most distantly related pair across the entire tree. The tree OP constructed*** shows that cow is equally related to each of the four other species. This is because the common ancestor between cow and any other species is the same. Cow/horse are just as distantly-related as cow/mouse, cow/dog, or cow/hedgehog, because each of those pairs diverged at the same point in the tree (with the most recent common ancestor of all five species).

Finally, the algorithm used to construct the tree can make a difference, so it's a little unfair to provide a set of sequences and have someone think up the tree. In this case the question author probably just expected the student to count up the nucleotide differences and select the pair with the most (which most of the time will be the most phylogenetically distant).

*Edit: This originally stated that they were "farthest apart in the tree", but I thought this would lead to confusion with OP's drawing where Cow and Mouse are separated by the greatest horizontal distance in the diagram. To be clear, horizontal distance in the drawing is essentially uninformative to relatedness. One could draw a tree with the same topology as OP's where Cow and Mouse are right next to each other, and it would not change the interpretation.

**I didn't confirm if this is a correct application of that method, but we can assume it is.

***This tree is not accurate to reality. Our best understanding of relationships among these species would put cow sister to horse, who are both sister to dog, who are all sister to hedgehog, who are all sister to mouse. So, basically the exact opposite of this tree. (Although I believe OP correctly constructed their version based on the provided sequences.)

• Thank you for the answer. I have a question about how you said the cow is equally related to all four based on the cladogram I drew. I uploaded another one with some characters added on it. imgur.com/7Ffr5iK So based on what I understand, you said the cow is equally related to all four have the shared character "red" right? But you would say the hedgehog and the mouse are the most closely related to each other because they share the most number of characters. Thank you. Commented Apr 20, 2023 at 3:13
• Not exactly. To talk about relatedness, you need to have the tree, because the shape of the tree (called the topology) shows you which common ancestor is shared by certain species. Now in order to make the tree, we do use characters, but 1) hopefully we have a lot 2) they're usually not as well-behaved as yours 3) if we're asking how a character evolved it hopefully wasn't used to build the tree, and 4) there are many methods of constructing a tree from the characters. Methods like the video just use simple similarity, but really, some evolutionary model should be applied to the characters. Commented Apr 20, 2023 at 20:47
• But, yes, mouse and hedgehog are most closely related in that tree. We know that because they share a more recent common ancestor than other pairs; not because their "color" character is most similar. If you added another species, like zebra, you wouldn't be able to say if mouse/hedgehog or horse/zebra we more closely related (although some types of phylogenetic trees do use informative branch lengths, so that could maybe tell you). Commented Apr 20, 2023 at 20:52