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Author Topic:   Discussion of Phylogenetic Methods
Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


(3)
Message 6 of 288 (775614)
01-03-2016 7:59 AM
Reply to: Message 2 by herebedragons
01-01-2016 1:15 PM


Re: Introduction to Phylogenetic Methods
Thanks, herebedragons! Will be commenting on this in a bit in more depth. You've broken this down in an easier-to-understand manner than what you'd find in a lot of bioinformatics textbooks.
I'd definitely encourage the broader EvC community to weigh in on this topic with their own questions or comments of relevance to phylogenetics.

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Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


(2)
Message 14 of 288 (776172)
01-09-2016 5:55 PM
Reply to: Message 8 by Tanypteryx
01-05-2016 3:31 PM


Re: Introduction to Phylogenetic Methods
How many regions to try and construct a genetic clock?
Generally speaking, the more proteins used in a molecular clock analysis, the better. For your example -- a family that contains 11 species in 8 genera -- you'd want to avoid highly conserved proteins (e.g., serum albumin, cytochrome c), as there probably wouldn't be enough substitutions in these proteins across these closely related taxa to create a reliable molecular clock.
For more accurate results, you would also want divergence times of at least a couple of these species as determined by paleontology. In this way, you can calibrate the molecular clock for this family of organisms.
Edited by Genomicus, : No reason given.

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Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


Message 93 of 288 (795949)
12-20-2016 6:19 AM
Reply to: Message 76 by caffeine
12-19-2016 4:20 PM


Re: The purpose of phylogenetics
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.
Eh, I mean that's kind of a sweeping statement. There are a number of ways phylogenetics makes sense as a confirmation of the broad theory of common descent.
E.g., I conducted molecular phylogenetics research on a set of prokaryotic transporters. The phylogenies weren't congruent with the species phylogeny as established by dozens of well-conserved proteins. This suggested horizontal gene transfer, and when I hunted for signs of HGT (based on GC content analyses), they showed up exactly where one would expect if the species phylogeny was correct (p = .04, based on independent samples t-test).
These results really only make sense under a model of common ancestry -- and it is, in fact, what one would predict under that model.
There's plenty of other examples that could be cited, too. Mol phylogenetics is widely used by evolutionary biologists as a tool within the theory of evolution, but it has also stridently confirmed the theory of common descent.

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Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


Message 94 of 288 (795950)
12-20-2016 6:27 AM
Reply to: Message 87 by vaporwave
12-19-2016 7:15 PM


Re: The purpose of phylogenetics
As I said, there is a pattern. Animals that share similar anatomical systems tend to share similar genetic organization of that anatomy.
Your problem is you cannot see the distinction between this observation and your assumption of common ancestry.
I can see that distinction, but that distinction has little merit. It doesn't explain the general concordance of various types of molecular phylogenies: protein sequence data, ERVs, phylogenies constructed from synonymous sites, etc. These sorts of molecular phylogenies all point to a conclusion as inescapable-as-a-spaceship-in-a-black-hole: that the theory of common descent is the most robust explanation for life's diversity.

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 Message 96 by vaporwave, posted 12-20-2016 7:41 AM Genomicus has replied

  
Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


Message 97 of 288 (795954)
12-20-2016 7:48 AM
Reply to: Message 96 by vaporwave
12-20-2016 7:41 AM


Re: The purpose of phylogenetics
You are selecting a group of shared traits (e.g. mammals: endothermy, hair, neocortex, mammary glands, etc.) and bringing them into deeper focus on a molecular level, and finding the pattern of similarity to persist.
It's not the similarity that matters here. It is the concordant nested hierarchies of similarities that exist between disparate sequence data. Why would primate phylogenies created from synonymous sites match protein phylogenies if not for common descent? It's exactly what we'd expect from the thesis of shared ancestry among primates.

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 Message 99 by vaporwave, posted 12-20-2016 8:08 AM Genomicus has replied

  
Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


Message 100 of 288 (795958)
12-20-2016 8:30 AM
Reply to: Message 99 by vaporwave
12-20-2016 8:08 AM


Re: The purpose of phylogenetics
It's the concordant nested hierarchy of similarities that matters, because randomly distributed similarities would be rather contrary to the evolutionary synthesis. Of course, convergences will emerge throughout the evolutionary bush, but a clear pattern of nested hierarchies exists.
So why do primate phylogenies created from synonymous sites match phylogenies generated from amino acid sequence data?

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 Message 105 by vaporwave, posted 12-20-2016 9:08 AM Genomicus has replied

  
Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


Message 146 of 288 (796019)
12-21-2016 3:36 AM
Reply to: Message 105 by vaporwave
12-20-2016 9:08 AM


Re: The purpose of phylogenetics
Hi vaporwave,
Why do primate phylogenies constructed from protein sequences match phylogenies created from synonymous sites? Thx.

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Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 187 of 288 (796069)
12-21-2016 5:40 PM
Reply to: Message 186 by vaporwave
12-21-2016 5:36 PM


Re: The purpose of science
Hi vaporwave,
Any idea why primate phylogenies constructed from protein sequences match phylogenies created from synonymous sites?
You spend a lot of time responding to peeps who you also complain are overtly fixated on designers.
I am not.

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Replies to this message:
 Message 189 by vaporwave, posted 12-21-2016 6:57 PM Genomicus has replied

  
Genomicus
Member (Idle past 1932 days)
Posts: 852
Joined: 02-15-2012


Message 199 of 288 (796087)
12-22-2016 12:48 AM
Reply to: Message 189 by vaporwave
12-21-2016 6:57 PM


Re: The purpose of science
I assume whatever you're driving at is universal to all phylogenies, right?
It is significantly widespread among phylogenies constructed from well-conserved, non-saturated nucleic acid sequence sites -- and this is the data set that's relevant.
Why might this be the case? My explanation is evolutionary descent. And that's a robust explanation, too.
What's your explanation?

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Replies to this message:
 Message 200 by AZPaul3, posted 12-22-2016 1:50 AM Genomicus has not replied
 Message 201 by vaporwave, posted 12-22-2016 6:58 AM Genomicus has not replied

  
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