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Author Topic:   How similar are phylogenetic trees?
Jerry Johnson
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Posts: 5
Joined: 06-20-2020


Message 1 of 27 (877684)
06-20-2020 6:32 AM


Hi all,

I read that phylogenetic trees are one of the strongest evidence of evolution, because we get a very similar trees for different genes and proteins. But I can't find anywhere ANY concrete/specific numbers. How many phylogenetic trees where constructed so far? 1000? 50,000? a million? How similar are they to one another? 99%? 95%? 80%?

I would really like to see some numbers, where can I find them?

I'm asking this because I came across a video claiming that phylogenetic trees do NOT support evolution:

Is Homology Evidence for Evolution? | Long Story Short

So, if you have some numbers it will really help.

Thanks.

(I wanted to ask this in the "Biological Evolution" forum but I got a message telling me that I can post only here)

Edited by Jerry Johnson, : No reason given.


Replies to this message:
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AdminNosy
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Message 2 of 27 (877686)
06-20-2020 9:19 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the How similar are phylogenetic trees? thread in the Proposed New Topics forum.

  
AZPaul3
Member
Posts: 5118
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.1


Message 3 of 27 (877688)
06-20-2020 10:23 AM
Reply to: Message 1 by Jerry Johnson
06-20-2020 6:32 AM


Hello Jerry. Welcome to EvC.

I’m not sure you are understanding what phylogenetic trees are. They are graphics of the proposed evolutionary relationships among closely related species based on some specific criteria. Honest disagreements among the scientists making these trees often results in multiple different trees proposed for the same lineages. And the scope of the tree (how many different lineages or organisms are to be represented) depends on the purpose of the tree. There are tress limited to just a few hundred species of beetle and there are trees made to represent the entire class of mammalia.

It doesn’t matter “how many” trees there are presently since the criteria can differ from one graph to another and each needs to be updated as new information is assessed. There is also the issue that there are so many lineages of organisms on this planet that have yet to be found let alone charted. I don’t have numbers for you but I can imagine there are 10s of thousands of such graphs drawn past and present are already in the books with many millions more yet to be studied. The same goes for homologies in genetic studies

Each one is unique as to the lineage and the criteria for analysis. But the one great big overwhelming similarity among ALL such trees is the concept of the nested hierarchy. The concept that organisms appearing later in the tree are inclusive (on the same related branching structure) of all the species that came before.

Here is one such tree meant to represent all life:

Here is one dealing in hemoglobin:

Here is one for flys:

You can see the wide scope in subject as well as presentation.

Again, Jerry, welcome to the forum. Stick around. Tell us about yourself.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
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AZPaul3
Member
Posts: 5118
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.1


(1)
Message 4 of 27 (877689)
06-20-2020 10:42 AM
Reply to: Message 1 by Jerry Johnson
06-20-2020 6:32 AM


Just an aside, please, Jerry

If you are out to learn about reality I suggest you avoid the Discovery Institute (maker of that video). They lie.

Just like Kent Hovind and Ken Ham and their creation ministries, they lie. Even when their lies are exposed and even acknowledged by themselves they continue to use the same lies over again. They have ulterior motives and the truth is not among them.


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 1 by Jerry Johnson, posted 06-20-2020 6:32 AM Jerry Johnson has not yet responded

  
Jerry Johnson
Junior Member
Posts: 5
Joined: 06-20-2020


Message 5 of 27 (877711)
06-20-2020 4:32 PM
Reply to: Message 3 by AZPaul3
06-20-2020 10:23 AM


Hi AZPaul3,

I'm from the north and I'm very interested in evolution.

Your answer really confused me. Yes I understand what phylogenetic trees are, but if you can't compare between different trees and you can't say in how much percents they differ from one another, then how can you (I mean the science) say that they are strong evidence of evolution?

If each scientist can come up with another tree for the same animals, and you cannot compare this trees then what's the point? One will put bears on the same branch together with cats and dogs, and another researcher will put bears on the same branch with Giraffes and tigers.

So what's the point? How is it an evidence of evolution?

Edited by Jerry Johnson, : No reason given.

Edited by Jerry Johnson, : No reason given.


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Replies to this message:
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jar
Member
Posts: 32654
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.8


Message 6 of 27 (877714)
06-20-2020 4:41 PM
Reply to: Message 5 by Jerry Johnson
06-20-2020 4:32 PM


Stop and think.

If you were making a tree of mammals would bears on the same branch together with cats and dogs and Giraffes and tigers?

Now if you were making a tree of carnivorous mammals, which of those items would be left out?

Now if you were making a tree of herbivore mammals, which of those items would be left out?


My Sister's Website: Rose Hill Studios     My Website: My Website

This message is a reply to:
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Replies to this message:
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Jerry Johnson
Junior Member
Posts: 5
Joined: 06-20-2020


Message 7 of 27 (877715)
06-20-2020 4:51 PM
Reply to: Message 6 by jar
06-20-2020 4:41 PM


jar,

Maybe it wan't the best example, but still I'm talking about a situation where different scientists constructing a phylogenetic tree for the same animals, and each one of them came up with another tree.

If you can't compare these trees then how can you conclude something about them or about their accuracy?


This message is a reply to:
 Message 6 by jar, posted 06-20-2020 4:41 PM jar has responded

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jar
Member
Posts: 32654
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.8


Message 8 of 27 (877718)
06-20-2020 5:11 PM
Reply to: Message 7 by Jerry Johnson
06-20-2020 4:51 PM


JJ writes:

If you can't compare these trees then how can you conclude something about them or about their accuracy?

Why you examine the evidence used to create the tree as well as the reason it was created.

It really is that simple.

It is all truly simple and ALL of the evidence has led to the inescapable conclusion that life on the earth evolved over billions of years.

Any other position is at best simply uninformed but more often simply a con job.


My Sister's Website: Rose Hill Studios     My Website: My Website

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jar
Member
Posts: 32654
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.8


Message 9 of 27 (877719)
06-20-2020 5:26 PM


to show how simple it really is ...
I offer a few examples for you and hope you can use them.

Look at a tree that has cow, dog, seal, giraffe, lion, bat, bird.

Now that would be a valid tree of currently living species.

Look at a tree that has cow, dog, seal, giraffe, lion, bat. That would be a valid tree of mammals but the bird would lack features that allow it to be called a mammal.

Phylogenetic trees are not just random associations. They are based on the actual physical evidence that is found in each item in the list.

Even critters as different as a bat, a seal, a lion and a giraffe share common features that allow them to be classified under the broad tree called mammals.


My Sister's Website: Rose Hill Studios     My Website: My Website

  
AnswersInGenitals
Member
Posts: 564
Joined: 07-20-2006
Member Rating: 2.3


(1)
Message 10 of 27 (877721)
06-20-2020 5:43 PM
Reply to: Message 5 by Jerry Johnson
06-20-2020 4:32 PM


evidence vs. proof positive
The site you posted and the comments liked to use cars as an example. Is a blue ford four door sedan more similar to a blue chevy sedan or to a white ford pickup? The two sedans are more similar in outward appearance and function but the two fords will have far more parts in common, e. g., might have the exact same engines. This difference doesn’t mean that such comparisons are useless, just that it depends on what aspects are being considered. This difference will also be reflected in a discussion of the historical derivation of current designs (i. e., their evolution).

I will also point out a common error made in the video you reference and almost all the comments. That is to not recognize the difference between an observation being evidence for a theory and that observation being proof beyond any possible doubt for that theory. The pervasiveness of both morphological and genetic trees is evidence for the theory of evolution because if these trees did not exist, if life consisted of distinct species or kinds that had no morphological similarity and totally different genetic chemistries that would firmly disprove the theory of evolution. This is not circular logic. If Mr. A is found shot to death and Mr. B is found to be standing over Mr. A and holding a smoking gun than that is evidence that Mr. B is Mr. A’s killer, because if Mr. B was miles away at the time of the murder he could not be the killer. Also, Mr. B could have found Mr. A’s dead body and instinctively picked up the gun. But his holding the gun is still evidence that he might be the killer. Most of the commenters in you reference would misrepresent this as a circular argument: “If Mr.B is the killer, we might find him standing over the body holding a smoking gun. We find Mr. B standing over the body holding the smoking gun, therefore he must be the killer.” Evidence is just evidence, not proof positive.

Also note that neither of the two scenarios described above, 1) strong morphologic and genetic trees and 2) total lack of morphologic and genetic similarity are compatible with the ‘intelligent design’ and the ‘god-didit’ theories. In fact, any observation, positive or negative, is compatible with those two theories. This is why scientists don’t treat those theories scientifically.


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AnswersInGenitals
Member
Posts: 564
Joined: 07-20-2006
Member Rating: 2.3


Message 11 of 27 (877722)
06-20-2020 6:11 PM
Reply to: Message 8 by jar
06-20-2020 5:11 PM


Let's choose our words carefully
…has led to the inescapable conclusion…

I think we have to be very careful in using this phrase, particularly give the position JJ is coming from. ‘Intelligent Design’ and ‘god-didit’ both offer convenient escape hatches in this matter. It might be useful to delineate four possible categories of explanation for the diversity of life:

1) an intelligent, capricious entity created all the species individually,
2) an intelligent, capricious entity created a mechanism for all species to evolve as evidenced by the fossil record, phylogenetic trees, etc.,
3) natural processes guided only by the laws of physics, chemistry, and statistics led to the evolution of all species as evidenced by the fossil record, phylogenetic trees, etc.,

- 3A) Darwin’s proposed mechanism including later enhancements (the modern synthesis, genetic drift, etc.),

- 3B) Lamark’s proposed mechanism,

- 3C) for completeness, I’ll throw in Empedocles’ mechanism, which includes random variation but not descent with modification,

4) any other scenario one can think of (I can’t think of any, but panspermia maybe).


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AZPaul3
Member
Posts: 5118
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.1


Message 12 of 27 (877723)
06-20-2020 6:33 PM
Reply to: Message 7 by Jerry Johnson
06-20-2020 4:51 PM


I can understand your confusion. You are looking at phylogenetic trees as some absolute. They are not. They are hypothesis.

Scientists may disagree whether one species of beetle is more or less closely related to another but they all classify both of those beetles as sub-order Myxophaga instead of sub-order Polyphaga. It's sorta almost the same as some long lost relatives disagreeing on who was born first, you or your brother. Everyone knows you both are from the same family born of the same parents. Except instead of you and your brother we're dealing with species of bugs.

The importance in getting the right bug in its proper slot in relation to all the other bugs is one of accuracy and pride at being an entomologist and having all your colleagues agreeing with you.

And while there may still be some controversy over some placements in the tree they are in the deep fine details. The more robust pictures we have today, especially with the advent of genetic information to build from these last 20 years, have pretty much solidified the major relationships.

The importance to the field of evolution is in the nested hierarchies and the evolutionary relationships revealed. We can see with great confidence that these 1500 species of Polyphaga are quite far removed from the 280 species of Carnivora.

Probably a bad example.

The fact that relationships of organisms fall among species, genus, family, order and beyond, when accurately portrayed is one of the strongest evidences of the theory of evolution and the determination of common ancestry.

What did you think the phylogenetic tree would tell us? What were you looking for that might be missing?

Edited by AZPaul3, : No reason given.


Factio Republicana delenda est.
I am antifa.

This message is a reply to:
 Message 7 by Jerry Johnson, posted 06-20-2020 4:51 PM Jerry Johnson has not yet responded

  
jar
Member
Posts: 32654
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.8


Message 13 of 27 (877725)
06-20-2020 8:09 PM
Reply to: Message 11 by AnswersInGenitals
06-20-2020 6:11 PM


Re: Let's choose our words carefully
All of those were addressed in the part of my post you omitted.

My Sister's Website: Rose Hill Studios     My Website: My Website

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Kleinman
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Posts: 386
From: United States
Joined: 10-06-2016
Member Rating: 1.1


Message 14 of 27 (877785)
06-21-2020 8:42 PM
Reply to: Message 1 by Jerry Johnson
06-20-2020 6:32 AM


Jerry Johnson writes:

Hi all,
I read that phylogenetic trees are one of the strongest evidence of evolution, because we get a very similar trees for different genes and proteins. But I can't find anywhere ANY concrete/specific numbers. How many phylogenetic trees where constructed so far? 1000? 50,000? a million? How similar are they to one another? 99%? 95%? 80%?

I would really like to see some numbers, where can I find them?

I'm asking this because I came across a video claiming that phylogenetic trees do NOT support evolution:

Is Homology Evidence for Evolution? | Long Story Short

So, if you have some numbers it will really help.

Thanks.

(I wanted to ask this in the "Biological Evolution" forum but I got a message telling me that I can post only here)


There are a couple problems with using homology to determine relatedness. The first is if you only use the coding portion of the genome and ignore the non-coding portions (which control the coding portions), you can come to very incorrect conclusions. For example, crocodiles have a beta-keratin gene so some may jump to the conclusion that that crocodiles are somehow related to birds. The problem is that the non-coding regions determine the structure of the beta-keratin. Therefore the non-coding portion has to evolve as well to change the scale formation into feathers and they have to be the correct kind of feathers. The second problem is that the mathematics which is used to determine relatedness based on homologous portions of genomes in different species is incorrect. If you want to see how they do that calculation, you can read about it here. If you don't understand the mathematic of Markov chains, this link will not make sense but I assure, their math is incorrect.
Models of DNA evolution - Wikipedia

Don't expect any of the posters on this forum to correctly explain this math.


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Taq
Member
Posts: 8409
Joined: 03-06-2009
Member Rating: 1.9


Message 15 of 27 (877859)
06-22-2020 5:09 PM
Reply to: Message 14 by Kleinman
06-21-2020 8:42 PM


Kleinman writes:

There are a couple problems with using homology to determine relatedness. The first is if you only use the coding portion of the genome and ignore the non-coding portions (which control the coding portions), you can come to very incorrect conclusions. For example, crocodiles have a beta-keratin gene so some may jump to the conclusion that that crocodiles are somehow related to birds.

They are using phylogenetic signal to determine relatedness, not homology all by itself. You can use the coding regions of open reading frames, the promoters upstream of the reading frames, transposon sequences, ERVs, pseudogenes, or just any old random piece of DNA almost anywhere in the genome. For different sequences you would have to take saturation of mutations into account which is why functional DNA, both coding and non-coding, is often used. There is a certain point where neutrally evolving DNA can see two or more mutations at the same site, but this would only be counted as a single mutation when comparing those sequences. That's what we would call saturation.

The other point is that DNA sequences are independent of morphology. If you wanted to, you could completely change DNA sequences and still get nearly identical species. You could start by changing the anti-codons on tRNAs which would create very different DNA sequences for the same amino acid sequence. The vast majority of vertebrate genomes have no sequence specific function, and they could be drastically changed without impacting morphology. Many, many proteins have no impact on morphology, such as cytochrome c, which means they could differ drastically even in species that are nearly identical from a morphological standpoint.

So there is no reason other than common ancestry and evolution why phylogenies based on genetic sequences should match phylogenies based on morphology.


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