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Author Topic:   Discussion of Phylogenetic Methods
caffeine
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Message 76 of 288 (795924)
12-19-2016 4:20 PM
Reply to: Message 27 by jar
12-18-2016 12:21 PM


The purpose of phylogenetics
vaporwave writes:

Again, the whole phylogenetic practice boils down to: IF evolution is true, this is likely how it happened. But it doesn't reveal more than that.

Several of you have criticised vaporwave for this point, but it strikes me that on this point he is entirely correct. Phylogenetics is precisely what he says. Phylogenetic methods are means of calculating the most probable tree topologies given that a group of organisms share a common ancestor. These are not techniques to establish that evolution occured, but rather the means to figure how it did once we've taken that for granted.

I think we need to get away from the idea that the robustness of phylogenetic trees is a massive support for evolution, since a lot of phylogenies have turned out to be not very robust at all. The molecular revolution in phylogenetics has transformed our understanding of the tree of life. Consider the traditional classification of mammals as exemplified by Gaylord-Simpson's. He divided Eutherian mammals into four cohorts, only two of which are monophyletic based on our current understanding. At the order level he did better - only two of his 15 orders of extant eutherians were non-monophyletic; but this is not so impressive. Most of these are relationships which are obvious to the naked eye; and sometimes match with the idea of creationist kinds. His concepts of the interrelationships between these orders, however, bears very little relationship to modern systematics.

Phylogenetics does not make any sense as evidence for evolution. That's not what it's meant to be. Phylogenetics is what we do once we know evolution has occured. It's all about techniques to figure out how.


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caffeine
Member
Posts: 1699
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.9


Message 166 of 288 (796045)
12-21-2016 12:58 PM
Reply to: Message 115 by Taq
12-20-2016 10:38 AM


Re: The purpose of phylogenetics
So many posts, no wonder creationists feel overwhelmed!

From my understanding, that simply isn't true. Phylogenetics is a test for common ancestry and evolution through vertical inheritance. The various methods for detecting phylogenies return values that measure the phylogenetic signal. A result with low statistical significance indicates a lack of phylogenetic signal. This can be due to a lack of data or a lack of common ancestry and evolution.

This is precisely the kind of reasoning I was questioning; for the simple reason that it leads us to odd conclusions. Consider these chaps:



I think we can all safely agree that these are all frogs. And yet I chose these because they represent one of the branches of the tree of life where we lack any sort of consensus phylogeny. These are all natatanuran frogs (not a great name, but the other names proposed for this clade are worse); and the interrelationships between natatanuran families are something of a mystery. Different studies produce wildly different phylogenies; none of which habve significant statistical support.

The issue here is not issing data - we have a lot of genes to work with. The issue is that these do not carry much phylogenetic signal in this case. As with other similar cases, it is usually argued to be the result of a rapid radiation at the origin of the extant families.

I have never seen anyone argue that an absence of phylogenetic signal implies that the organisms being studied are unrelated; so this is not clearly never used as a test of common ancestry. We already know that ranoid frogs are all related - to suggest otherwise would be laughable - and so researchers seek other loci or other techniques that might be more informative instead. Common ancestry was a well-established fact before anyone started doing cladistics.


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caffeine
Member
Posts: 1699
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.9


Message 168 of 288 (796047)
12-21-2016 1:38 PM
Reply to: Message 167 by Dr Adequate
12-21-2016 1:23 PM


Re: The purpose of phylogenetics
I think you're over-interpreting what he meant by "lack of data".

I have no idea what point you're trying to make.


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caffeine
Member
Posts: 1699
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.9


Message 172 of 288 (796054)
12-21-2016 4:13 PM
Reply to: Message 169 by PaulK
12-21-2016 2:01 PM


Re: The purpose of phylogenetics
I think that your point is a little pedantic.

To set it in context before somebody tries to make it much more than it is:

First, confused phylogenetic information is hardly the worst case for evolution, even if it were general (and if it was general I think we would have a rather different version of evolutionary theory).

My point is not that the problems in phylogenetics are a problem for evolutionary theory. They can often be iluminating, since the most problematic and controversial parts of phylogeny are not arbitrarily distributed. If you look at vertebrate phylogeny, the bits that are most difficult to resolve make sense within our understanding of history (usually). They are often the results of explosive radiations - like that of Neoaves and percomorph fishes after the end-Cretaceous extinction.

I'm taking issue with the point I've seen Taq and others make more than once on these forums, that phylogenetics by itself is a test of common ancestry. Since we don't reject common ancestry when we cannot produce a well supported phylogeny, it seems dishonest to say we're testing evolution this way.

I think that your point is a little pedantic.

If you don't approve of pedantry, what are you doing on an internet forum?

Edited by caffeine, : Correct (my own) confusion over nomenclature


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caffeine
Member
Posts: 1699
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.9


Message 173 of 288 (796055)
12-21-2016 4:19 PM
Reply to: Message 170 by Dr Adequate
12-21-2016 2:03 PM


Re: The purpose of phylogenetics
Well he can speak for himself, but surely from context by "lack of data" he doesn't mean to imply that we have no genes to work with, he just means that there's a lot of noise and no signal.

His whole point (as I understood it) was that an absence of signal would imply a lack of common ancestry, but we know that there are parts of the phylogeny where signal is swamped by noise. In this case, we cannot claim that presence or absence of signal can be used as a test of common ancestry.


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caffeine
Member
Posts: 1699
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.9


Message 177 of 288 (796059)
12-21-2016 4:53 PM
Reply to: Message 174 by PaulK
12-21-2016 4:37 PM


Re: The purpose of phylogenetics
I think it is something of a parody of phylogeny to say that common ancestry is simply assumed. It is certainly possble in principle for the data to be inconsistent with any likely ancestry - indeed the only reason common ancestry is assumed now is because it has already been established beyond reasonable doubt - in large part by the evidence used to establish phylogeny.

I don't see it as a parody. It seems to me you have to assume common ancestry in order to research phylogeny. All the techniques we have for building a phylogeny assume there is actually one there to discover. I don't understand how a falsification of common ancestry is supposed to differ from an unresolvable polytomy like that amongst Natatanuran families.

I understand what you mean that people may misrepresent what I say as a challenge to evolution; but it's precisely the fear of misrepresentation that makes me wary of the idea of presenting phylogenetics as evidence for evolution. This is probably because I spend a lot more time reading about the difficult bits than the easy bits. If nothing else I think it's a tactical error in arguing with am honest creationist, since the difficult bits are of course those focused on by researchers. If a curious creationist heads over to the literature on phyogenetics; he's going to find lots of arguments about the complicated radiations we cannot resolve and the problematic taxa that jump around the tree from one analysis to another.


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caffeine
Member
Posts: 1699
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.9


Message 178 of 288 (796060)
12-21-2016 5:04 PM
Reply to: Message 175 by Dr Adequate
12-21-2016 4:38 PM


Re: The purpose of phylogenetics
No, no, he said "A result with low statistical significance indicates a lack of phylogenetic signal. This can be due to a lack of data or a lack of common ancestry and evolution." As concessions go, this is a fairly mild one. A lack of common ancestry could produce that, or indeed anything else so far as we know.

(It is, however, plain, I think, that a strong and "wrong" signal would be a major anomaly. Consider, for example, if in bits of the genome that don't affect anatomy (cytochrome of any flavor, ERVs, etc) there was a strong signal putting bats with birds or whales with fish ...)

Well, if you take individual bits of the genome you get all sorts of odd results - results which I have seen creationists get very excited about. Over on EvolutionFairyTale there was a thread about one regulatory gene which, taken in isolation, produced trees in which teleosts were sister to all other vertebrates.

A lack of common ancestry could produce that, or indeed anything else so far as we know.

If 'anything else' could produce that, then it's not evidence of anything.


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