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Author Topic:   How similar are phylogenetic trees?
Taq
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Posts: 9973
Joined: 03-06-2009
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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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 Message 14 by Kleinman, posted 06-21-2020 8:42 PM Kleinman has replied

Replies to this message:
 Message 16 by Kleinman, posted 06-22-2020 5:27 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 17 of 27 (877864)
06-22-2020 5:29 PM
Reply to: Message 1 by Jerry Johnson
06-20-2020 6:32 AM


Jerry writes:
How many phylogenetic trees where constructed so far? 1000? 50,000? a million?
You would have to search the mountains of peer reviewed papers to get that number. I don't think anyone is really searching. A search for "phylogeny" at Google Scholar returns over a million hits. Each paper can have more than one phylogeny.
As to matches between phyolgenies, it isn't a percentage. Rather, it is a p value which tells you the probability of a random distribution of characters giving you the same phylogenetic signal.
TalkOrigins has a primer on phylogenetics:
29+ Evidences for Macroevolution: Phylogenetics
They also have the statistics for incongruent trees:
29+ Evidences for Macroevolution: Statistics of Incongruent Phylogenetic Trees
I'm asking this because I came across a video claiming that phylogenetic trees do NOT support evolution:
YouTube science is about as reliable as getting medical advice at the pub. There are actually a few really good science channels on YouTube, and then there is the parade of anti-science channels and organizations like the Discovery Institute. It's a bit like going to an anti-vax channel to learn about immunology.
Edited by Taq, : No reason given.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 18 of 27 (877865)
06-22-2020 5:31 PM
Reply to: Message 16 by Kleinman
06-22-2020 5:27 PM


Kleinman writes:
What is even worse is that the transition matrix used to predict relatedness using Markov chain DNA evolution is incorrect.
Am I to assume that your hobby horse is going to make an appearance in every thread?

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 Message 16 by Kleinman, posted 06-22-2020 5:27 PM Kleinman has replied

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 Message 20 by Kleinman, posted 06-22-2020 6:07 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 25 of 27 (877918)
06-23-2020 12:18 PM
Reply to: Message 20 by Kleinman
06-22-2020 6:07 PM


Kleinman writes:
In fact, this particular video from Kishony mega-plate experiment shows the phylogenic trees for this particular experiment.
You are wearing out your hobby horse.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 26 of 27 (877920)
06-23-2020 12:22 PM
Reply to: Message 19 by Jerry Johnson
06-22-2020 5:37 PM


Jerry Johnson writes:
Thanks for your answers, but still, I expect that if you'll take several represent animals (monkeys, humans, dogs, cats, zebras, horses, birds, bats, squirrels, fish, whales, dolphins ...) and you'll build several phylogenetic trees for them based on several different genes and proteins, then you should get very similar trees.
It depends on sequence conservation and the location of the gene. Mitochondrial genes evolve faster so they can reach mutation saturation faster. For example, cytochrome b is found in the mitochondrial genome and it is usually only used for closely related species. Pseudogenes are going to change more quickly, so you have to again take mutation saturation into account.
It's a lot like a set of scales. Some scales can measure the weight of a semi-truck while another can measure the weight of a feather. You don't use the sensitive scale to measure the weight of a semi-truck.

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