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Author Topic:   How similar are phylogenetic trees?
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


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.

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

Replies to this message:
 Message 15 by Taq, posted 06-22-2020 5:09 PM Kleinman has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 16 of 27 (877863)
06-22-2020 5:27 PM
Reply to: Message 15 by Taq
06-22-2020 5:09 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.
Taq writes:
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.
You can't use gross anatomy (morphology) to describe what is happening on the molecular level (genetic sequences). This is like trying to use classical physics to describe a quantum mechanical process. What is even worse is that the transition matrix used to predict relatedness using Markov chain DNA evolution is incorrect. But if you think it is correct, show how to use that math to describe the Kishony experiment.

This message is a reply to:
 Message 15 by Taq, posted 06-22-2020 5:09 PM Taq has replied

Replies to this message:
 Message 18 by Taq, posted 06-22-2020 5:31 PM Kleinman has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 20 of 27 (877870)
06-22-2020 6:07 PM
Reply to: Message 18 by Taq
06-22-2020 5:31 PM


Kleinman writes:
What is even worse is that the transition matrix used to predict relatedness using Markov chain DNA evolution is incorrect.
Taq writes:
Am I to assume that your hobby horse is going to make an appearance in every thread?
Don't blame me if you don't have a horse in this race. And DNA evolution is central to phylogenetics. And what do you have against common descent? In fact, this particular video from Kishony mega-plate experiment shows the phylogenic trees for this particular experiment. The phylogenetic trees are drawn at about 1:44 into the video.
https://www.youtube.com/watch?v=plVk4NVIUh8&t=6s

This message is a reply to:
 Message 18 by Taq, posted 06-22-2020 5:31 PM Taq has replied

Replies to this message:
 Message 25 by Taq, posted 06-23-2020 12:18 PM Kleinman has not replied

  
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