Molecular phylogeny - a problem instead of a solution

[lee_merrill]

Uhm, that quote demonstrates it. Relationships among phyla, not within phyla.

Well, that's still part of the state of molecular phylogeny, and a general statement about a major area at that.

They're not talking about the trees within major metazoan phyla - those all resolve just fine.

Source: Davalos et al.

In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

Source

© Copyright Original Source

Blessings,
Lee

[TheLurch]

Well, that's still part of the state of molecular phylogeny, and a general statement about a major area at that.

Source: Davalos et al.

In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

Source

© Copyright Original Source

Blessings,
Lee

Look, Lee, you're trying to dodge the big problem here: even when a paper clearly stated what it was looking about in the abstract, you couldn't understand it. You had to ask to have someone point out the how to interpret a phrase you yourself quoted.

Given that, why do you think you can understand anything to do with biology?

Multiple times in the past you've said "I'm happy to learn!" But the fact is that you're not. You're happy to ignore accurate information, and move on to the next argument without even recognizing any problems with the last. You are fully impervious to learning.

[rogue06]

Look, Lee, you're trying to dodge the big problem here: even when a paper clearly stated what it was looking about in the abstract, you couldn't understand it. You had to ask to have someone point out the how to interpret a phrase you yourself quoted.

Given that, why do you think you can understand anything to do with biology?

Multiple times in the past you've said "I'm happy to learn!" But the fact is that you're not. You're happy to ignore accurate information, and move on to the next argument without even recognizing any problems with the last. You are fully impervious to learning.

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[lee_merrill]

They're not talking about the trees within major metazoan phyla - those all resolve just fine.

Look Mr. Lurch, you're trying to dodge the big problem here, even when a paper clearly stated that there were problems within a metazoan phyla.

Given that, why do you think you can understand anything to do with biology?

Blessings,
Lee

[TheLurch]

Look Mr. Lurch, you're trying to dodge the big problem here, even when a paper clearly stated that there were problems within a metazoan phyla.

Given that, why do you think you can understand anything to do with biology?

And I explained exactly what those problems were - something that, I'll remind you, you couldn't figure out. You just knew that problems were convenient for your argument, so you hyped them without understanding them.

If you have any doubt I have a PhD in molecular and cell biology, I'm sure we can arrange for a mutually trusted source (maybe Cowpoke?) to confirm its existence.

[lee_merrill]

And I explained exactly what those problems were - something that, I'll remind you, you couldn't figure out.

Well, I couldn't read the paper, because it was behind a paywall, so I misunderstood what was meant by "among."

Dictionary.com on "among":

• in, into, or through the midst of; in association or connection with; surrounded by: He was among friends.
• in the midst of, so as to influence: missionary work among the local people.

If you have any doubt I have a PhD in molecular and cell biology, I'm sure we can arrange for a mutually trusted source (maybe Cowpoke?) to confirm its existence.

My concern is that you still do not acknowledge your error:

They're not talking about the trees within major metazoan phyla - those all resolve just fine.

But they don't...

Blessings,
Lee

[TheLurch]

Well, I couldn't read the paper, because it was behind a paywall, so I misunderstood what was meant by "among."

I got that from reading the abstract. If you understood biology, you could have too.

My concern is that you still do not acknowledge your error:
But they don't...

Ok, let me fully acknowledge all the issues I'm aware of here.

As I said, the paper argues that it's difficult to resolve rapid radiations. The ones it was focusing on are the ones early in the history of metazoan diversification at the phylum level. I did not acknowledge that rapid radiations also occur at some locations within metazoan phyla. There are definitely a number of examples of these that remain difficult to resolve; these are a minority of cases, but they definitely exist.

I'll also acknowledge another issue that hasn't come up in any of the papers under discussion, which is long branch attraction, where lineages that have a long time to accumulate change can appear to be more closely related than they are. This can typically be solved by adding more intermediate species to the phylogenetic tree, but can be a problem when we haven't sampled sufficient intermediate species, or most intermediate species have gone extinct.

Because we understand the circumstances in which these issues occur, we can recognize when they're issues, and when a phylogenetic tree is likely to be accurate - which it is in the vast majority of circumstances in which it is used. I acknowledge that, by not highlighting these subtleties, I may have given some people a mistaken impression that there were no subtleties at all.

You may contrast that with your continued attempts to make excuses for a blatant error, and continued attempts to start arguments over things you don't understand.

[rogue06]

My concern is that you still do not acknowledge your error:

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Alright buster. Do you have any idea the number of irony meters you are responsible for breaking with that remark?

[lee_merrill]

Because we understand the circumstances in which these issues occur, we can recognize when they're issues, and when a phylogenetic tree is likely to be accurate - which it is in the vast majority of circumstances in which it is used.

That's not the impression I get here:

Source: Davalos et al.

In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

© Copyright Original Source

Blessings,
Lee

[TheLurch]

That's not the impression I get here:

Source: Davalos et al.

In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

© Copyright Original Source

Blessings,
Lee

Given the history here, what would you think the odds of your impression being correct are?

[lee_merrill]

Given the history here, what would you think the odds of your impression being correct are?

The inability to make a molecular phylogeny work should therefore be interpreted as evidence of a rapid radiation.

That's false:

Source: Davalos et al.

The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats.

Source

© Copyright Original Source

They're not talking about the trees within major metazoan phyla - those all resolve just fine.

That's false:

Source: Davalos et al.

Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.

© Copyright Original Source

Because we understand the circumstances in which these issues occur, we can recognize when they're issues, and when a phylogenetic tree is likely to be accurate - which it is in the vast majority of circumstances in which it is used.

And that's false:

Source: Davalos et al.

In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

© Copyright Original Source

Does it not bother you to make false statements so often?

Blessings,
Lee

[TheLurch]

Does it not bother you to make false statements so often?

Before I go about explaining in detail why you're misinterpreting the paper you're quoting, a question: do you honestly think you understand this better than I do? Or are you just being petty?

[lee_merrill]

Before I go about explaining in detail why you're misinterpreting the paper you're quoting, a question: do you honestly think you understand this better than I do? Or are you just being petty?

Oh, I seriously believe you are misunderstanding. The statements in question seem pretty plain.

Blessings,
Lee

[TheLurch]

Oh, I seriously believe you are misunderstanding. The statements in question seem pretty plain.

So, your past errors, including the case here where you couldn't even interpret what you were quoting, don't give you any pause?

[rogue06]

So, your past errors, including the case here where you couldn't even interpret what you were quoting, don't give you any pause?

Yeah, but... Lee's read another article from Evolution News.