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Author
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Topic: How similar are phylogenetic trees?
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Kleinman
Member (Idle past 534 days) Posts: 2142 From: United States Joined: 10-06-2016
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Message 16 of 27 (877863)
06-22-2020 5:27 PM
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Reply to: Message 15 by Taq
06-22-2020 5:09 PM
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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 |
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Taq
Member Posts: 10255 Joined: 03-06-2009 Member Rating: 7.6
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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.
| This message is a reply to: | | | Message 1 by Jerry Johnson, posted 06-20-2020 6:32 AM | | Jerry Johnson has not replied |
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Taq
Member Posts: 10255 Joined: 03-06-2009 Member Rating: 7.6
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Message 18 of 27 (877865)
06-22-2020 5:31 PM
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Reply to: Message 16 by Kleinman
06-22-2020 5:27 PM
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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?
| This message is a reply to: | | | Message 16 by Kleinman, posted 06-22-2020 5:27 PM | | Kleinman has replied |
| Replies to this message: | | | Message 20 by Kleinman, posted 06-22-2020 6:07 PM | | Taq has replied |
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Jerry Johnson
Junior Member (Idle past 1573 days) Posts: 5 Joined: 06-20-2020
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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. If not, then you can't say that phylogenetic trees are evidence of evolution. So my question is still relevant, how close are the different trees to one another?
| 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 21 by AZPaul3, posted 06-22-2020 6:35 PM | | Jerry Johnson has replied | | | Message 26 by Taq, posted 06-23-2020 12:22 PM | | Jerry Johnson has not replied |
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Kleinman
Member (Idle past 534 days) Posts: 2142 From: United States Joined: 10-06-2016
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Message 20 of 27 (877870)
06-22-2020 6:07 PM
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Reply to: Message 18 by Taq
06-22-2020 5:31 PM
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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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AZPaul3
Member Posts: 8632 From: Phoenix Joined: 11-06-2006 Member Rating: 8.7
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you'll build several phylogenetic trees for them based on several different genes and proteins, then you should get very similar trees. Not only should they be very similar they *must* be very similar. They may not be exact in every detail but very similar is a no-brainer since we already know the chemistry of life is exceptionally consistent across related lineages. I was talking more phylogenetic trees based upon morphology in cases where we do not have chemistry/genetics to assess. Old fossils. Lineages among the dinoserians for example. There, professional honest disagreements still rage but, as I said, they are in the fine details, like, which bone shape is closest to this other bone shape. Making those kinds of trees takes a practiced eye with many years experience.
Factio Republicana delenda est.
I am antifa.
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Jerry Johnson
Junior Member (Idle past 1573 days) Posts: 5 Joined: 06-20-2020
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Message 22 of 27 (877901)
06-23-2020 8:54 AM
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Reply to: Message 21 by AZPaul3
06-22-2020 6:35 PM
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AZPaul3: "Not only should they be very similar they *must* be very similar". OK, so where can I see this? Where can I find a research that compared several phylogenetic trees (based on different genes and proteins) and showed how much they resemble each other? (BTW: How can I add a quote to my post? I can't find this option anywhere)
| This message is a reply to: | | | Message 21 by AZPaul3, posted 06-22-2020 6:35 PM | | AZPaul3 has replied |
| Replies to this message: | | | Message 23 by JonF, posted 06-23-2020 8:59 AM | | Jerry Johnson has not replied | | | Message 24 by Tangle, posted 06-23-2020 9:30 AM | | Jerry Johnson has not replied | | | Message 27 by AZPaul3, posted 06-23-2020 12:47 PM | | Jerry Johnson has not replied |
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JonF
Member (Idle past 366 days) Posts: 6174 Joined: 06-23-2003
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This board doesn't have buttons. Type. {quote} hjhgfffb9i{/quote} Replace curly braces with square brackets [ ].
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Tangle
Member Posts: 9568 From: UK Joined: 10-07-2011 Member Rating: 7.3
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Jerry Johnson writes: OK, so where can I see this? Where can I find a research that compared several phylogenetic trees (based on different genes and proteins) and showed how much they resemble each other? Do you have any background in biology at all? If not this stuff is going to get very hard to follow very quickly. What you're looking for is called molecular phylogenics. Here's a starter Molecular phylogenetics - Wikipedia Quotes Inorder to get
Jerry Johnson writes: OK, so where can I see this? Where can I find a research that compared several phylogenetic trees (based on different genes and proteins) and showed how much they resemble each other? I typed {qs=Jerry Johnson}OK, so where can I see this? Where can I find a research that compared several phylogenetic trees (based on different genes and proteins) and showed how much they resemble each other?{/qs} But used [ ] instead of { } If you look underneath to the right, you'll see 'peek' that lets you see how people have done what they done 
Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London.I am Finland. Soy Barcelona "Life, don't talk to me about life" - Marvin the Paranoid Android "Science adjusts it's views based on what's observed. Faith is the denial of observation so that Belief can be preserved." - Tim Minchin, in his beat poem, Storm.
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Taq
Member Posts: 10255 Joined: 03-06-2009 Member Rating: 7.6
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Message 25 of 27 (877918)
06-23-2020 12:18 PM
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Reply to: Message 20 by Kleinman
06-22-2020 6:07 PM
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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.
| This message is a reply to: | | | Message 20 by Kleinman, posted 06-22-2020 6:07 PM | | Kleinman has not replied |
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Taq
Member Posts: 10255 Joined: 03-06-2009 Member Rating: 7.6
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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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AZPaul3
Member Posts: 8632 From: Phoenix Joined: 11-06-2006 Member Rating: 8.7
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I don't think you are going to find the kind of comparison listings you seem to be looking for without doing a whole lot of work. I suggest, if you have Google Scholar or equivalent, searching molecular phylogenetics and evolution. The results will show you how wide and deep the field has become. Then, if you are so inclined, you can go through hundreds of those studies you find and compare the phylogenies they present. But, maybe just reading on the general topic would satisfy your need. Like, Straggler said above, go to Molecular phylogenetics - Wikipedia then google your way around the net to your hearts content.
Factio Republicana delenda est.
I am antifa.
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