phylogenetic tree analyse

Question

[elisheva]

Can anybody explain me which taxons are closer?

Whale ans Seal or Whale and frog?

thanks!!!

[GenoMax]

This has to be a homework question :)

[elisheva]

No' it's not. It's for general knowledge.

[Juke34]

The answer is Human - gorilla

Humain and gorilla ancestor diverged from orangoutan, then later the humain and gorilla ancestor diverges to give birth to those two distinct species. Actually the human lineage has given birth to 2 species from then: chimp and human...

[elisheva]

Can you please look again at the question. I'v update the question.

[Asaf]

The tree you attached assumes a molecular clock meaning evolution has the same pace in every branch, that's why all the nodes are aligned. In practice this assumption is not true and some nodes have longer branches, i.e. faster evolution. So, according to the tree you attached the answer is that Human and Gorilla and Gorilla and Orangutan have similar distances between them. In practice thought, the tree is different and the answer is different.

[elisheva]

Thank for the answer, Can you please have a look on the second question that I'v asked?

[Asaf]

You should measure the total branch lengths leading from A to B. Beware that the bootstrap value in the ancestor of frog is 0 meaning this split is with low confidence.

[elisheva]

Isn't the bootstraps values represent in percentage? What do you mean to measure the total branch length? So what is the final answer?

[Asaf]

Here it's fraction. (I assume the values represent bootstrap). Walk from A to B and measure the branches you pass. Do you have a ruler? :)

I took another look at the tree and it doesn't make any sense. You can't account on it.

Answer 1

[Juke34]

Let's apply a simple approach for the first tree: Right side is the current time, so hide the rest with a sheet (or your hand) and keep only the species names displayed. Then let's reverse the time and go back in the past by slowly sliding the sheet to the left. When you discover a whole path connecting different species it means you are at a common ancestor that gave as offspring all the connected species under this point. So, you must discover first the Human - Chimp ancestor, then keep going back to the past you will find the Human - Chimp - Gorilla ancestor , then the Human - Chimp - Gorilla - Orangutan ancestor, etc...

So, the last common ancestor of the Human and Orangutan (which is the first connecting point between Human and Orangutan when going back in the time), is older than the last common ancestor to Human and Gorilla ( which is the first connecting point of Human and Gorilla when going back in the time). Consequently the diverging time since the Human and Orangutan speciation is superior to the diverging time since the Human and Gorilla speciation.

You can apply the same rule for the second tree, but it make it a bit more difficult because all the species are not displayed at the same place on the right side even if they are representing the current time. Anyway, you can apply the same way to understand the relationship between the different species. So your answer is Whale ans Seal. It is a comparaison relative, you cannot in any way use this method to compare non-connected species like Mouse and Rat divergence time against Carp and Loach divergence time...

I was talking about relationship between the species, if you want to know the most similar sequences underlying that gave you the tree in this second tree, it seems that the gene under investigation from the whale is more similar to the one from the Frog than the one form the Seal. The lineage going to the Frog seems to have fixed more mutations... but this is another story... or rephrase your question if it was the thing you were interested in.

I hope my explanation is clear enough. I tried to stay as simple as possible.