Comments on Jeanson Accuses Duff Again

Where is the root?

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Sure. My comment was largely unrelated to Jeanson. I just wanted an excuse to bring up some cool new(ish) methods.

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There are actually 15 different bifrucated rooted trees for 4 leaves (taxa). Each rooted tree has a different history.

If you are designating one root then this means there will always be a number of possible rooted trees equivalent to that associated with n-1 leaves where n is the number of leaves on the unrooted tree.

I see that RootDigger works by using a non-reversible model of molecular evolution. But what non-reversible model is it? I can’t find where they specify the model.

Rooting by paralogs is an old idea; I recall seeing a tree rooted using W and Z versions of one gene (CHD) 20 years ago. This.

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According to the preprint it’s the Unrestricted Model (UNREST) from Yang 1994:

Or the better question for Joshua would be what are the nested clades on this unrooted tree?

So let me get this straight. It’s a general model in which each possible substitution A-T, T-A, A-G, G-A, etc. has a separately estimated rate parameter?

The STRIDE program implements an approach first used by Iwabe et al. and by Gogarten (both 1989) to root the great tree of life. Incidentally, the STRIDE paper cites the wrong paper of mine for long-branch attraction.

For a bif[ur]cating unrooted tree with n tip species, there are 2n-3 branches. The root can connect to any one of them, so there are 2n-3 times as many rooted as unrooted bifurcating trees. The result is that there are as many rooted birfurcating trees with n tips as there are unrooted trees with n+1 tips. An unrooted bifurcating tree does not indicate so much a set of clusters as it does a set of bipartitions of the set of species. A bipartition is a division of the tips into two nonintersecting sets. If the unrooted tree is correct, one or both of these sets will then be a clade.

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I believe that’s right, but I hadn’t even heard of it until an hour ago, so don’t take my word for it.

I think the relevant question in relation to how Nathaniel Jeanson is interpreting his trees is do unrooted trees have any inherent temporal polarity. They of course do not.

Are the legs drawn to scale? If so there is one unambiguous answer if there is constant mutation rate across the tree. It is at the midpoint of e5.

If they aren’t drawn to scale, or there is not a constant mutation rate, we can’t say where the root is, can we?

Joshua. Like Joe explained. There are in fact 15 possible rooted trees possible for these 4 taxa (leaves).

If you want to say you are adopting a midpoint rooting approach then you are in fact making a decision to root the tree and are giving it polarity. Without some decision about a root an unrooted tree has in fact no temporal information in it.

Jeanson makes no decision to root his trees either using an outgroup or a midpoint or any other approach and thus has no basis in assigning a relative time to any of the nodes.

Also Joshua you say you would root this tree at the midpoint but what if it were revealed that the tips are sequences derived from a fish, amphibian, croc and bird. Would your decision to root at the midpoint still be the correct one?

Not under the assumptions I explained. If it was drawn to scale and we assume constant mutation rate, then only one of those trees is correct.

Yes that would be correct and in this case it is not a ridiculous move to make. So I’m not at all clear what your objection is.

Can you show us the tree he is using? And what he claimed? I’d like to see the graphic and his claims. A midpoint method is likely what he was implicitly using.

Associating each lineage with Noah’s daughter in laws? Well that’s a different problem. I’m mainly pointing out that hammering for implicitly using a midpoint root on the tree (which is likely what he did) is not a strong criticism.

No Joshua. There are 15 possible rooted trees for any tree with four leaves. You are simply using a particular approach to choose one of them.

Sure. If it makes you feel better, go ahead and believe you have a point there. :slight_smile:

I cite the video in my recent blog post. On Jeanson’s Facebook page and in the video he explicitly says he doesn’t root his trees using an outgroup or midpoint or any other approach to rooting. He just “eyeballs” it. This isn’t a valid approach to rooting any tree.

It doesn’t make me feel one way or the other. It’s how this works Joshua.

Maybe you will have better luck explaining this to Joshua. I don’t seem to be having much luck.

Well that is quite absurd of him. Citation an quote please?

My guess still is that his root is quite close to the midpoint root.