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Topic: Nodes with support lower than 70% (Read 163 times) previous topic - next topic

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  • socrates1
Nodes with support lower than 70%
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.

Re: Nodes with support lower than 70%
Reply #1
No it isn't. Did you not notice the 94% confidence support value for the whole of Coelurosauria? Including Paraves?
Why do I bother?

Re: Nodes with support lower than 70%
Reply #2
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.
What is the pterosaur to bird theory based on?
Is it better?

Unless you can present something else, with some indication that it could be better, none of this matters.
Present it, and there will be something to discuss.

  • Faid
Re: Nodes with support lower than 70%
Reply #3
No it isn't. Did you not notice the 94% confidence support value for the whole of Coelurosauria? Including Paraves?

^^^^^^

(Not that "socrates" will respond)
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • VoxRat
  • wtactualf
Re: Nodes with support lower than 70%
Reply #4
From 17 years ago, but I don't think anything has emerged since to damage the case:
Dinosaurs and Birds - an Update
Quote
In a short paper in Nature, John Ostrom (1973) first laid out a case for the descent of birds from theropod dinosaurs. At the time, other ideas had recently been proposed, linking birds to crocodiles or to a more vaguely defined group of archosaurs (the group that includes birds, dinosaurs, crocodiles, pterosaurs, and many extinct relatives). Although all three hypotheses had early proponents. only the dinosaur-bird hypothesis survived the decade, mainly because (1) the evidence was convincing. (2) the hypothesis survived repeated tests using cladistic analysis, and (3) the afternatives were too vaguely phrased. there was no convincing evidence for them, and they failed repeated cladistic testing. The public tends to think that there is a substantial controversy among scientists about the ancestry of birds, partly because the public does not understand cladistics and partly because cladistics is rejected as a method by the opponents of the dinosaur-bird hypothesis.
...
Next time you encounter a newspaper or television story on this or any scientific issue, get to the bottom of it with two questions: (1) What exact hypothesis is being proposed here to supplant another one (and it cannot be simply that the first hypothesis is wrong: we assume that in all tests)? (2) What methods are being used, if not the standard methods in the field, and how do we know that these are better than the standard methods? If and when the opponents of the dinosaur-bird hypothesis manage to give satisfactory answers to these two questions, they will be taken seriously.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Nodes with support lower than 70%
Reply #5
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.


It is interesting that the dinosaur to bird theory is considered one of the premiere examples of an established phylogeny.
But we can clearly see the problem is the lack of a statistically supported link between tyrannoraptors and basal paraves. And of course the huge polytomy at the base. It really fails on all counts even using the accepted cladistic analyses.

  • Faid
Re: Nodes with support lower than 70%
Reply #6
As expected, "socrates" does not respond to others, even when his thread remains in the science forum. His previous excuses were just lies.

End of the line.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Nodes with support lower than 70%
Reply #7
"That is all I intend to say on this topic" in 3... 2... :rofl:
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Nodes with support lower than 70%
Reply #8
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.


It is interesting that the dinosaur to bird theory is considered one of the premiere examples of an established phylogeny.
But we can clearly see the problem is the lack of a statistically supported link between tyrannoraptors and basal paraves. And of course the huge polytomy at the base. It really fails on all counts even using the accepted cladistic analyses.
Does your refusal to deal with objections mean that you are choosing to get moved to ARSE?

Considering:
If you wanted to have me deal with objections, you would not have moved it to this section. That was your choice.
that seems likely.
  • Last Edit: June 15, 2017, 06:49:58 AM by Saunt Taunga

  • socrates1
Re: Nodes with support lower than 70%
Reply #9
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.


It is interesting that the dinosaur to bird theory is considered one of the premiere examples of an established phylogeny.
But we can clearly see the problem is the lack of a statistically supported link between tyrannoraptors and basal paraves. And of course the huge polytomy at the base. It really fails on all counts even using the accepted cladistic analyses.

It would really be interesting to see how the jackknife unresolved value of 65 is calculated. From my email correspondence with experts in the field, I understand that the statistical support values are based on characters and not on synapomorphies. So the jackknife value of 65 may well just represent the fact that ALL the taxa involved are members of Ornithodira.

  • Faid
Re: Nodes with support lower than 70%
Reply #10
Wherever his threads end up, he's toast. He agreed to criteria by which Paraves are resolved as part of the coelurosaur clade (94% bootstrap support). He totally screwed himself.

Anything else?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Nodes with support lower than 70%
Reply #11
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.


[Words]

[More wprds]
94% bootstrap support for Paraves within coelurosaurs, "socrates".

We accept your apology.

Anything else?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Nodes with support lower than 70%
Reply #12
I see this has been moved. This is obviously not something you want me to say anything more on. I understand.

  • socrates1
Re: Nodes with support lower than 70%
Reply #13
Well I am off to continue my research and correspondence with the experts. Please feel free to continue posting.

  • Faid
Re: Nodes with support lower than 70%
Reply #14
I see this has been moved. This is obviously not something you want me to say anything more on. I understand.
Too late for that excuse, "socrates". You did not respond to posts when the thread was in Science. You had your chance and you blew it.

94% bootstrap support for Paraves as coelurosaurs, champ. You can run away, or continue pretending. It makes no difference.

End of the line.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Nodes with support lower than 70%
Reply #15
Well I am off to continue my research and correspondence with the experts. Please feel free to continue posting.
I see you chose "run away". Wise choice.

:wave:
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • VoxRat
  • wtactualf
Re: Nodes with support lower than 70%
Reply #16
Well I am off to continue my research and correspondence with the experts. Please feel free to continue posting.
:rofl:
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Nodes with support lower than 70%
Reply #17
For shits and giggles I went and looked at Sterling Nesbitt's big archosaur paper from a few years back.

He doesn't have a bird in his phylogeny, but he does have Velociraptor which Sucky here thinks is a bird of some kind, and he does have Allosaurus. And he finds them to be each other's closest relatives. He doesn't use jacknife or boostrap values, but Bremer Support. Anything over 3 is considered "good". Anything over 5 is "highly supported". The Velociraptor/Allosaurus node has a value of 9. Dinosauria, which does not include pterosaurs, has a value of 7.

Care to "discuss" this Sucky?

I thought not.
Why do I bother?

  • VoxRat
  • wtactualf
Re: Nodes with support lower than 70%
Reply #18
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins