Re: For Sean Pitman: Some real nested hierarchies

Seanpit wrote:
On Mar 12, 1:19 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
Seanpit wrote:
On Mar 11, 6:26 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
Have you read the paper? The figure 2 that you've copied onto your web
doesn't support your claim, but figure 3 blows it out of the water.
This is one ofSean'sfavorite techniques. If you show that he's wrong
about something, rather than reply directly to your point (or admit his
error, which would be correct), he posts a mass of irrelevant quoted
material -- as below:
Do you think Figure 3 "blows" the notion that some of the trees
produced place some groups of modern humans closer to chimps than
Neanderthals "out of the water"?
Yes.

Take a look at Fig. 3:
http://mbe.oxfordjournals.org/content/vol19/issue8/images/large/mbev-...
Notice, in particular, the middle tree. Notice that humans are placed
closer to chimps than are Neanderthals and that "Human A" is placed
the closest.
No they aren't. Now there are multiple definitions of "closest". That
tree shows that all three are equally closely related to chimps. If you
are talking about evolutionary distance, not relationships, the
neanderthal branch is a bit longer than the others, so that the two
humans have a bit less distance to the chimp; but even in this respect
both the humans are equally far from the chimp; human A is no closer
than human B.

Oh please . . . I'm not talking about evolutionary distance (as in the
absolute length of the lines drawn), but in the proposed
"relationship" distances (i.e., where the lines are supposed to have
diverged from the MRCA).

That particular confusion lies in supposing that there are such things as "basal lineages". Don't be too embarrassed. It's been shown that students have a very difficult time learning to interpret evolutionary trees properly, and even evolutionary biologists sometimes make this mistake. But in fact it's not possible for a single lineage to diverge. Two lineages diverge from each other. In that particular figure, the MCRA of Human A/HumanB/Neanderthal splits into two lineages, one of which later splits again. The three trees disagree about which two species are involved in the second split. However, they all agree that all three species are equally related to chimps. In the middle figure, the one you like, Human B and the Human A/Neanderthal common ancestor split apart first, and then Human A and Neanderthal split. This means that in some sense (though not a sense we ever actually use) the Human A/Human B/Neanderthal common ancestor is closer to chimps than the Human A/Neanderthal common ancestor. But that is by no means the same as claiming that Human B is closer to chimps than Human A.

One could easily excuse your ignorance here; after all, you aren't
supposed to be an expert in phylogenetic analysis. But it's hard to
excuse your arrogance, especially when directed at those who are experts.

What is hard to excuse here is your strawman building as well as your
arrogance. You even claim that it is quite a condescension on your
part to even discuss my ideas in this forum. Who is being arrogant
here?

Arrogant, perhaps. But justifiably so at least in this case. You are interpreting the tree you have brought up wrongly. Nobody who understands how to read an evolutionary tree would agree with your interpretation. And still you cling to your misconception. Why?

Gutierrez comments: "In the trees drawn in figure 3 , the best score
is for the tree that joins Neandertal and chimpanzee sequences.
However, the log-likelihoods are very similar between the alternative
topologies. The Kishino-Hasegawa test (Kishino and Hasegawa 1989 )
yielded no significant differences between them at the 5% level. This
example illustrates that likelihood mapping can select as the best
topology one that is not significantly better than the other two. A
third argument against the use of likelihood mapping in this study has
to do with the database population bias mentioned earlier. It is not
advisable to perform likelihood mapping with a database where most
human sequences are very similar among themselves."
What is also interesting about these trees is that originally the
suggested range of sequence differences for modern human mtDNA went
from 1 to 24 with an average of 8 substitutions. The mtDNA sequence
differences between modern humans and the single Neanderthal fossil
range from 22 to 36 substitutions, with the average being 27. In
other words, the two most different humans analyzed in this study, as
far as mtDNA substitutions are concerned, are different by 24
substitutions. The closest that any human in this study was to the
single specimen of Neanderthal mtDNA was 22 substitutions. This means
that there are some people living today that are closer to
Neanderthals in their mtDNA sequencing than they are to some other
modern human beings.
As has been pointed out to you before, this is not necessarily true. The
human who is 24 differences from some other human doesn't have to be the
same human who is 22 differences from a neanderthal. And I suspect he
isn't. You could easily have these data ranges and also have every human
be closer to every other human than he was to a neanderthal.

If you took the person that was 22 substitutions different from a
Neanderthal and compared that person to every other human being, are
you really suggesting that you would be unlikely to find any other
human being with more than 22 differences to this person? I find this
notion of yours to be statistically unlikely given a Poisson
distribution of a few billion people.

Feel free to find anything you like, but your impression is not based on anything real.

Someone might be found to be only 22
substitutions away from our Neanderthal, but 24 substitutions away
from his own next-door neighbor. Interesting isn't it?
Not particularly. I'm going to ignore your ridiculous and uninformed
speculations about species, if that's all right with you.

How kind . . .

De nada.

http://mbe.oxfordjournals.org/cgi/content/full/19/8/1359?ck=nck
Note that none of this has anything to do with some Africans being
closer to chimps than neanderthals are.
Please explain the middle tree in Figure 3 to me again . . .
Gladly. It shows two humans and a neanderthal, all three of them equally
distantly related to the chimp.

Not as far as the proposed origins of the various branches are
concerned. Those points of divergence are not "equally distance".

If by that you mean that the Human A/Human B/Neanderthal common ancestor is older than the Human A/Neanderthal common ancestor, you are right. But your original claim was that Human B was more closely related to the chimp than Human A was. And this is false.

This demonstrates quite nicely, by the
way, that a raw count of genetic distance has nothing to do with
relationships. The two humans are closer by distance to each other than
either is to the neanderthal, yet human B is (in the tree) more closely
related to the neanderthal than to human A.

That's my whole point.

No, that's not your point at all. If you think that what I just said and what you say below are the same thing, you are very, very confused.

Some groups of humans, depending upon the type
of tree you build with the data, are "more closely related" to chimps
than to other groups of humans. You just have to choose the "right"
tree is all.

No, you have to *misinterpret* the tree too. The tree doesn't show that at all. Everyone has been telling you this for some time now. I'll admit it's difficult to learn how to read a tree. But it's even more difficult when you refuse to even try to learn. The existence of a Human A/Human B/Neanderthal common ancestor on the tree means that each of them is equally closely related to anything outside that group.

.

Relevant Pages

  • Re: Neanderthal DNA
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  • Re: Neanderthal DNA
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  • Re: For Sean Pitman: Some real nested hierarchies
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