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So Is Archaeopteryx a Real Bird After All?
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Peter Nyikos
Nov 29, 2022, 10:55:04 AM11/29/22
to
It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
This seemingly technical question has down to earth implications: did flight among birds
go through a four-winged phase, or did birds always rely on two-winged powered flight?
Here is a paper that discusses this question in the process of describing phylogenetic methods
that put *Archaeopteryx* it "robustly" back into Avialae.
Other phylogenetic methods support the other practice, and readers are invited to compare them
and to draw their own conclusions.
"Likelihood reinstates *Archaeopteryx* as a primitive bird"
Michael S. Y. Lee and Trevor H. Worthy
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297401/
Abstract:
The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs.
However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1.
These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx–deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx–bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.
I am unable to come to any decision about this due to lack of experience
with these phylogenetic methods.
I hope our s.b.p. expert, John Harshman, can give us some insight on what to make of this paper.
The article is free access, but you may need to click on "FREE Full text" at the upper right
of the webpage I linked to see it.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos
rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
This seemingly technical question has down to earth implications: did flight among birds
go through a four-winged phase, or did birds always rely on two-winged powered flight?
Here is a paper that discusses this question in the process of describing phylogenetic methods
that put *Archaeopteryx* it "robustly" back into Avialae.
Other phylogenetic methods support the other practice, and readers are invited to compare them
and to draw their own conclusions.
"Likelihood reinstates *Archaeopteryx* as a primitive bird"
Michael S. Y. Lee and Trevor H. Worthy
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297401/
Abstract:
The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs.
However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1.
These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx–deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx–bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.
I am unable to come to any decision about this due to lack of experience
with these phylogenetic methods.
I hope our s.b.p. expert, John Harshman, can give us some insight on what to make of this paper.
The article is free access, but you may need to click on "FREE Full text" at the upper right
of the webpage I linked to see it.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos
erik simpson
Nov 29, 2022, 11:36:40 AM11/29/22
to
"The results here do not demonstrate unequivocally that Archaeopteryx belongs with birds rather than with deinonychosaurs; bootstrap support is only approximately 73 per cent, while the posterior probability of 1 is tempered by arguments that Bayesian inference can greatly overestimate support if the models implemented are inadequate [8,23]. Resolution of the precise position of Archaeopteryx will likely require more empirical data such as new fossils or novel characters."
Despite your contempt for my recommendation of a fairly-easily read textbook on phylogenetic trees,
I still think your understanding would be augemented by it. (It goes beyond what you learned from Romer.)
John Harshman
Nov 29, 2022, 1:40:24 PM11/29/22
to
On 11/29/22 7:55 AM, Peter Nyikos wrote:
> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
>
> This seemingly technical question has down to earth implications: did flight among birds
> go through a four-winged phase, or did birds always rely on two-winged powered flight?
>
> Here is a paper that discusses this question in the process of describing phylogenetic methods
> that put *Archaeopteryx* it "robustly" back into Avialae.
> Other phylogenetic methods support the other practice, and readers are invited to compare them
> and to draw their own conclusions.
>
> "Likelihood reinstates *Archaeopteryx* as a primitive bird"
> Michael S. Y. Lee and Trevor H. Worthy
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297401/
>
> Abstract:
> The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs.
>
> However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1.
>
> These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx–deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx–bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.
>
>
> I am unable to come to any decision about this due to lack of experience
> with these phylogenetic methods.
> I hope our s.b.p. expert, John Harshman, can give us some insight on what to make of this paper.
Simple enough. That region of the tree is not very well supported, and
> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
>
> This seemingly technical question has down to earth implications: did flight among birds
> go through a four-winged phase, or did birds always rely on two-winged powered flight?
>
> Here is a paper that discusses this question in the process of describing phylogenetic methods
> that put *Archaeopteryx* it "robustly" back into Avialae.
> Other phylogenetic methods support the other practice, and readers are invited to compare them
> and to draw their own conclusions.
>
> "Likelihood reinstates *Archaeopteryx* as a primitive bird"
> Michael S. Y. Lee and Trevor H. Worthy
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297401/
>
> Abstract:
> The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs.
>
> However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1.
>
> These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx–deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx–bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.
>
>
> I am unable to come to any decision about this due to lack of experience
> with these phylogenetic methods.
> I hope our s.b.p. expert, John Harshman, can give us some insight on what to make of this paper.
small differences in analysis or character choice can change topology.
This has been true for as long as the matter has been examined. I will
note that at least some specimens of Archaeopteryx have what look like
flight feathers on the rear legs, though less prominently so than in
Microraptor.
As for whether Archaopteryx is a bird, isn't that a matter of personal
taste in definitions?
One more thing: "a posterior probability of 1" is not as strong a
measure as one might suppose and is a common artifact of Bayesian
analyses that aren't getting "good mixing". We are left with ambiguity.
John Harshman
Nov 29, 2022, 1:41:41 PM11/29/22
to
erik simpson
Nov 29, 2022, 4:00:13 PM11/29/22
to
you to read carefully, although they are an annoying reminder of undergrad days...
Peter Nyikos
Nov 30, 2022, 1:25:07 PM11/30/22
to
John, I'll think some more later about what you wrote about the technical aspects
of phylogenetic methods. For now I will focus on what I call the "down to earth"
implications in my second paragraph below.
On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> > It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> > rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> >
> > This seemingly technical question has down to earth implications: did flight among birds
> > go through a four-winged phase, or did birds always rely on two-winged powered flight?
<snip to get to your words on this, John>
> I will note that at least some specimens of Archaeopteryx have what look like
> flight feathers on the rear legs, though less prominently so than in
> Microraptor.
"flight feathers" indicates a very noticeable lack of symmetry, making these feathers
into miniature airfoils. AFAIK this need not indicate powered flight.
It would seem that they would be at least as good for gliding.
Would you agree, John?
I'd also like to hear from Daud Deden on this. We've talked a lot about
the difference between gliding and powered flight in the last two months or so.
As for Microraptor, which all analyses by the authors place among the deinonychosaurs,
the linked article says:
"Powered, forewing-only flight typical of modern birds has been generally inferred to be present only in *Archaeopteryx* and other birds [2,5,20].The flight capabilities of some deinonychosaurs remain contentious: the most proficient, *Microraptor gui,* used both the forelimbs and hindlimbs, and has been argued to be a glider [21] and asymmetric pennaceous feathers indicating aerodynamic ability are known only in dromaeosaurus outside of birds [22]."
Note the attribution of forewing-only flight to *Archaeopteryx* despite the feathers on the
legs that you mention, John. Those feathers might make substantial contributions to flight
just like the tail feathers (retrices) are known to do in present-day birds.
>
> As for whether Archaopteryx is a bird, isn't that a matter of personal
> taste in definitions?
To some extent, yes, but placing it in Avialae, as the Baysean and ML analyses do, would satisfy
a lot more personal tastes than relying on flight remiges to define it as one.
The rest of the paragraph I quoted takes us back to more technical aspects of
the analyses, but it also weaves it in with more talk about powered flight.
"The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina at Columbia
http://people.math.sc.edu/nyikos
of phylogenetic methods. For now I will focus on what I call the "down to earth"
implications in my second paragraph below.
On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> > It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> > rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> >
> > This seemingly technical question has down to earth implications: did flight among birds
> > go through a four-winged phase, or did birds always rely on two-winged powered flight?
> I will note that at least some specimens of Archaeopteryx have what look like
> flight feathers on the rear legs, though less prominently so than in
> Microraptor.
into miniature airfoils. AFAIK this need not indicate powered flight.
It would seem that they would be at least as good for gliding.
Would you agree, John?
I'd also like to hear from Daud Deden on this. We've talked a lot about
the difference between gliding and powered flight in the last two months or so.
As for Microraptor, which all analyses by the authors place among the deinonychosaurs,
the linked article says:
"Powered, forewing-only flight typical of modern birds has been generally inferred to be present only in *Archaeopteryx* and other birds [2,5,20].The flight capabilities of some deinonychosaurs remain contentious: the most proficient, *Microraptor gui,* used both the forelimbs and hindlimbs, and has been argued to be a glider [21] and asymmetric pennaceous feathers indicating aerodynamic ability are known only in dromaeosaurus outside of birds [22]."
Note the attribution of forewing-only flight to *Archaeopteryx* despite the feathers on the
legs that you mention, John. Those feathers might make substantial contributions to flight
just like the tail feathers (retrices) are known to do in present-day birds.
>
> As for whether Archaopteryx is a bird, isn't that a matter of personal
> taste in definitions?
a lot more personal tastes than relying on flight remiges to define it as one.
The rest of the paragraph I quoted takes us back to more technical aspects of
the analyses, but it also weaves it in with more talk about powered flight.
"The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
John Harshman
Nov 30, 2022, 3:14:30 PM11/30/22
to
On 11/30/22 10:25 AM, Peter Nyikos wrote:
> John, I'll think some more later about what you wrote about the technical aspects
> of phylogenetic methods. For now I will focus on what I call the "down to earth"
> implications in my second paragraph below.
>
> On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
>> On 11/29/22 7:55 AM, Peter Nyikos wrote:
>>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
>>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
>>>
>>> This seemingly technical question has down to earth implications: did flight among birds
>>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
>
>
> <snip to get to your words on this, John>
>
>
>> I will note that at least some specimens of Archaeopteryx have what look like
>> flight feathers on the rear legs, though less prominently so than in
>> Microraptor.
>
> "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> into miniature airfoils. AFAIK this need not indicate powered flight.
> It would seem that they would be at least as good for gliding.
> Would you agree, John?
Yes, though it seems clear that Archaeopteryx was flying, though I would
> John, I'll think some more later about what you wrote about the technical aspects
> of phylogenetic methods. For now I will focus on what I call the "down to earth"
> implications in my second paragraph below.
>
> On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
>> On 11/29/22 7:55 AM, Peter Nyikos wrote:
>>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
>>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
>>>
>>> This seemingly technical question has down to earth implications: did flight among birds
>>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
>
>
> <snip to get to your words on this, John>
>
>
>> I will note that at least some specimens of Archaeopteryx have what look like
>> flight feathers on the rear legs, though less prominently so than in
>> Microraptor.
>
> "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> into miniature airfoils. AFAIK this need not indicate powered flight.
> It would seem that they would be at least as good for gliding.
> Would you agree, John?
not suppose that he was flapping his legs.
> I'd also like to hear from Daud Deden on this. We've talked a lot about
> the difference between gliding and powered flight in the last two months or so.
>
> As for Microraptor, which all analyses by the authors place among the deinonychosaurs,
> the linked article says:
>
> "Powered, forewing-only flight typical of modern birds has been generally inferred to be present only in *Archaeopteryx* and other birds [2,5,20].The flight capabilities of some deinonychosaurs remain contentious: the most proficient, *Microraptor gui,* used both the forelimbs and hindlimbs, and has been argued to be a glider [21] and asymmetric pennaceous feathers indicating aerodynamic ability are known only in dromaeosaurus outside of birds [22]."
>
> Note the attribution of forewing-only flight to *Archaeopteryx* despite the feathers on the
> legs that you mention, John. Those feathers might make substantial contributions to flight
> just like the tail feathers (retrices) are known to do in present-day birds.
>> As for whether Archaopteryx is a bird, isn't that a matter of personal
>> taste in definitions?
>
> To some extent, yes, but placing it in Avialae, as the Baysean and ML analyses do, would satisfy
> a lot more personal tastes than relying on flight remiges to define it as one.
>
>
> The rest of the paragraph I quoted takes us back to more technical aspects of
> the analyses, but it also weaves it in with more talk about powered flight.
>
> "The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
Daud Deden
Nov 30, 2022, 9:56:12 PM11/30/22
to
On Wednesday, November 30, 2022 at 3:14:30 PM UTC-5, John Harshman wrote:
> On 11/30/22 10:25 AM, Peter Nyikos wrote:
> > John, I'll think some more later about what you wrote about the technical aspects
> > of phylogenetic methods. For now I will focus on what I call the "down to earth"
> > implications in my second paragraph below.
> >
> > On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> >> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> >>>
> >>> This seemingly technical question has down to earth implications: did flight among birds
> >>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
> >
> >
> > <snip to get to your words on this, John>
> >
> >
> >> I will note that at least some specimens of Archaeopteryx have what look like
> >> flight feathers on the rear legs, though less prominently so than in
> >> Microraptor.
> >
> > "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> > into miniature airfoils. AFAIK this need not indicate powered flight.
> > It would seem that they would be at least as good for gliding.
> > Would you agree, John?
> Yes, though it seems clear that Archaeopteryx was flying, though I would
> not suppose that he was flapping his legs.
> > I'd also like to hear from Daud Deden on this. We've talked a lot about
> > the difference between gliding and powered flight in the last two months or so.
https://www.bbc.com/news/science-environment-43386262
> On 11/30/22 10:25 AM, Peter Nyikos wrote:
> > John, I'll think some more later about what you wrote about the technical aspects
> > of phylogenetic methods. For now I will focus on what I call the "down to earth"
> > implications in my second paragraph below.
> >
> > On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> >> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> >>>
> >>> This seemingly technical question has down to earth implications: did flight among birds
> >>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
> >
> >
> > <snip to get to your words on this, John>
> >
> >
> >> I will note that at least some specimens of Archaeopteryx have what look like
> >> flight feathers on the rear legs, though less prominently so than in
> >> Microraptor.
> >
> > "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> > into miniature airfoils. AFAIK this need not indicate powered flight.
> > It would seem that they would be at least as good for gliding.
> > Would you agree, John?
> Yes, though it seems clear that Archaeopteryx was flying, though I would
> not suppose that he was flapping his legs.
> > I'd also like to hear from Daud Deden on this. We've talked a lot about
> > the difference between gliding and powered flight in the last two months or so.
Per picture, asymmetrical feathers on the rear legs would add both to (pheasant-like) gliding length and to uplift during whole body flapping, if broad bony tail and rear legs were united during forewing strokes.
I watched a duck with injured legs try to lift off, it couldn't push down against earth so it couldn't launch upwards.
The short widespread tailfan of modern birds differs from archaics with long bony tails, the liftoff must have been different. Archy had clawed wings so it could climb trees, had weak wings, had heavy jaws counterbalanced by bony tail, indicating flight from trees imo.
Peter Nyikos
Dec 5, 2022, 8:08:43 AM12/5/22
to
On Wednesday, November 30, 2022 at 9:56:12 PM UTC-5, daud....@gmail.com wrote:
> On Wednesday, November 30, 2022 at 3:14:30 PM UTC-5, John Harshman wrote:
> > On 11/30/22 10:25 AM, Peter Nyikos wrote:
> > > John, I'll think some more later about what you wrote about the technical aspects
> > > of phylogenetic methods. For now I will focus on what I call the "down to earth"
> > > implications in my second paragraph below.
> > >
> > > On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> > >> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> > >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> > >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> > >>>
> > >>> This seemingly technical question has down to earth implications: did flight among birds
> > >>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
> > >
> > >
> > > <snip to get to your words on this, John>
> > >
> > >
> > >> I will note that at least some specimens of Archaeopteryx have what look like
> > >> flight feathers on the rear legs, though less prominently so than in
> > >> Microraptor.
> > >
> > > "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> > > into miniature airfoils. AFAIK this need not indicate powered flight.
> > > It would seem that they would be at least as good for gliding.
> > > Would you agree, John?
> > Yes, though it seems clear that Archaeopteryx was flying, though I would
> > not suppose that he was flapping his legs.
> > > I'd also like to hear from Daud Deden on this. We've talked a lot about
> > > the difference between gliding and powered flight in the last two months or so.
Daud, it's amazing how you keep coming up with links that are right on-topic.
> On Wednesday, November 30, 2022 at 3:14:30 PM UTC-5, John Harshman wrote:
> > On 11/30/22 10:25 AM, Peter Nyikos wrote:
> > > John, I'll think some more later about what you wrote about the technical aspects
> > > of phylogenetic methods. For now I will focus on what I call the "down to earth"
> > > implications in my second paragraph below.
> > >
> > > On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> > >> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> > >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> > >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> > >>>
> > >>> This seemingly technical question has down to earth implications: did flight among birds
> > >>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
> > >
> > >
> > > <snip to get to your words on this, John>
> > >
> > >
> > >> I will note that at least some specimens of Archaeopteryx have what look like
> > >> flight feathers on the rear legs, though less prominently so than in
> > >> Microraptor.
> > >
> > > "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> > > into miniature airfoils. AFAIK this need not indicate powered flight.
> > > It would seem that they would be at least as good for gliding.
> > > Would you agree, John?
> > Yes, though it seems clear that Archaeopteryx was flying, though I would
> > not suppose that he was flapping his legs.
> > > I'd also like to hear from Daud Deden on this. We've talked a lot about
> > > the difference between gliding and powered flight in the last two months or so.
> https://www.bbc.com/news/science-environment-43386262
Here is one on-topic aspect that you may have overlooked:
"Despite once being thought of as the first bird, experts now view the animal as a flying dinosaur."
Notice how well it goes with my introductory words to this whole thread:
[repeated from top]
> > >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> > >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
A red flag goes up whenever I see the word "experts." We mathematicians hardly ever use the word
> > >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
when talking about fellow mathematicians. We use expressions like "world-class researcher"
or "great lecturer". We are experts in our little specialties, but we don't use the word even there.
The highest praise is, "If anyone knows the answer to this problem, the first person to ask is _______"
That said, the line I quoted does give a big indication of which way the wind
is blowing. I've asked Trevor Worthy, with whom I corresponded several years ago,
what kind of reception his joint paper has received in the years since the paper
appeared in 2011. No answer yet, but here is the information on that paper again:
"Likelihood reinstates *Archaeopteryx* as a primitive bird"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297401/
> Per picture, asymmetrical feathers on the rear legs would add both to (pheasant-like) gliding length and to uplift during whole body flapping, if broad bony tail and rear legs were united during forewing strokes.
> I watched a duck with injured legs try to lift off, it couldn't push down against earth so it couldn't launch upwards.
> The short widespread tailfan of modern birds differs from archaics with long bony tails, the liftoff must have been different. Archy had clawed wings so it could climb trees, had weak wings, had heavy jaws counterbalanced by bony tail, indicating flight from trees imo.
> > >
> > > As for Microraptor, which all analyses by the authors place among the deinonychosaurs,
> > > the linked article says:
> > >
> > > "Powered, forewing-only flight typical of modern birds has been generally inferred to be present only in *Archaeopteryx* and other birds [2,5,20].The flight capabilities of some deinonychosaurs remain contentious: the most proficient, *Microraptor gui,* used both the forelimbs and hindlimbs, and has been argued to be a glider [21] and asymmetric pennaceous feathers indicating aerodynamic ability are known only in dromaeosaurus outside of birds [22]."
was impractical, but now I am having second thoughts.
The fastest swimming stroke is the American crawl, AFAIK. It involves a flutter kick,
beating the legs almost stiff-legged in short alternate strokes that move up and down.
Might Microraptor have used a variation on it for getting fast through the air?
It's also used in the only backstroke I've ever seen in competitive swimming,
except for underwater starts, which use a dolphin kick. The dolphin kick
moves the legs simultaneously, and it is the only kick that is allowed
these days in the butterfly. [IIRC it's illegal to use the older frog kick.]
> > >
> > > Note the attribution of forewing-only flight to *Archaeopteryx* despite the feathers on the
> > > legs that you mention, John. Those feathers might make substantial contributions to flight
> > > just like the tail feathers (retrices) are known to do in present-day birds.
> > That seems most likely. Lift only, not thrust.
<snip for focus>
> > > The rest of the paragraph I quoted takes us back to more technical aspects of
> > > the analyses, but it also weaves it in with more talk about powered flight.
> > >
> > > "The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
Was it just a help to providing lift, or did he think about swimming
along the same lines that I did just now?
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
when I use only my legs to propel myself. Evidently there are fine points to it that
my body never picked up.
Popping Mad
Dec 6, 2022, 7:53:34 PM12/6/22
to
On 11/29/22 11:36, erik simpson wrote:
> Despite your contempt for my recommendation of a fairly-easily read textbook on phylogenetic trees,
> I still think your understanding would be augemented by it. (It goes beyond what you learned from Romer.)
what text is that?
> Despite your contempt for my recommendation of a fairly-easily read textbook on phylogenetic trees,
> I still think your understanding would be augemented by it. (It goes beyond what you learned from Romer.)
John Harshman
Dec 6, 2022, 8:15:19 PM12/6/22
to
Daud Deden
Dec 8, 2022, 3:14:49 PM12/8/22
to
Peter Nyikos
Dec 8, 2022, 7:15:03 PM12/8/22
to
On Wednesday, November 30, 2022 at 3:14:30 PM UTC-5, John Harshman wrote:
> On 11/30/22 10:25 AM, Peter Nyikos wrote:
> > John, I'll think some more later about what you wrote about the technical aspects
> > of phylogenetic methods. For now I will focus on what I call the "down to earth"
> > implications in my second paragraph below.
> >
> > On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> >> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> >>>
> >>> This seemingly technical question has down to earth implications: did flight among birds
> >>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
> >
> >
> > <snip to get to your words on this, John>
> >
> >
> >> I will note that at least some specimens of Archaeopteryx have what look like
> >> flight feathers on the rear legs, though less prominently so than in
> >> Microraptor.
> >
> > "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> > into miniature airfoils. AFAIK this need not indicate powered flight.
> > It would seem that they would be at least as good for gliding.
> > Would you agree, John?
> Yes, though it seems clear that Archaeopteryx was flying, though I would
> not suppose that he was flapping his legs.
That was and still is my impression, but I am having second thoughts about this
> On 11/30/22 10:25 AM, Peter Nyikos wrote:
> > John, I'll think some more later about what you wrote about the technical aspects
> > of phylogenetic methods. For now I will focus on what I call the "down to earth"
> > implications in my second paragraph below.
> >
> > On Tuesday, November 29, 2022 at 1:40:24 PM UTC-5, John Harshman wrote:
> >> On 11/29/22 7:55 AM, Peter Nyikos wrote:
> >>> It's become a widespread practice to look upon *Archaeopteryx* as a bird relative
> >>> rather than an actual bird (member of Avialae). This practice puts it among the deinonychosaurs.
> >>>
> >>> This seemingly technical question has down to earth implications: did flight among birds
> >>> go through a four-winged phase, or did birds always rely on two-winged powered flight?
> >
> >
> > <snip to get to your words on this, John>
> >
> >
> >> I will note that at least some specimens of Archaeopteryx have what look like
> >> flight feathers on the rear legs, though less prominently so than in
> >> Microraptor.
> >
> > "flight feathers" indicates a very noticeable lack of symmetry, making these feathers
> > into miniature airfoils. AFAIK this need not indicate powered flight.
> > It would seem that they would be at least as good for gliding.
> > Would you agree, John?
> Yes, though it seems clear that Archaeopteryx was flying, though I would
> not suppose that he was flapping his legs.
also being true of Microraptor.
The fastest swimming stroke is the American crawl, AFAIK, although the Australian crawl
may be better for some. Both involve a flutter kick,
beating the legs almost stiff-legged in short alternate strokes that move up and down.
Might *Microraptor* have used a variation on it for getting fast through the air?
It's also used in the only backstroke I've ever seen in competitive swimming,
except for underwater starts, which use a dolphin kick. The dolphin kick
moves the legs simultaneously, and it is the only kick that is allowed
[IIRC it's illegal to use the older frog kick in swimming competition.]
So this is another possible way *Microraptor* might have flapped its legs,
although "flapped" might not be the best word to use here.
What do you think of this idea, John? I don't know why what
works so well in water would not work in air, with the proper "equipment."
<snip for focus>
> > As for Microraptor, which all analyses by the authors place among the deinonychosaurs,
> > the linked article says:
> >
> > "Powered, forewing-only flight typical of modern birds has been generally inferred to be present only in *Archaeopteryx* and other birds [2,5,20].The flight capabilities of some deinonychosaurs remain contentious: the most proficient, *Microraptor gui,* used both the forelimbs and hindlimbs, and has been argued to be a glider [21] and asymmetric pennaceous feathers indicating aerodynamic ability are known only in dromaeosaurus outside of birds [22]."
> >
> > Note the attribution of forewing-only flight to *Archaeopteryx* despite the feathers on the
> > legs that you mention, John. Those feathers might make substantial contributions to flight
> > just like the tail feathers (retrices) are known to do in present-day birds.
> That seems most likely. Lift only, not thrust.
One would think that what works so well in water might also work in air, with the proper "equipment."
> >> As for whether Archaopteryx is a bird, isn't that a matter of personal
> >> taste in definitions?
> >
> > To some extent, yes, but placing it in Avialae, as the Baysean and ML analyses do, would satisfy
> > a lot more personal tastes than relying on flight remiges to define it as one.
> >
> >
> > The rest of the paragraph I quoted takes us back to more technical aspects of
> > the analyses, but it also weaves it in with more talk about powered flight.
> >
> > "The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
> I don't think we can reliably distinguish the difference with current data.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
John Harshman
Dec 9, 2022, 2:05:59 PM12/9/22
to
thrust, but it would be all wrong for lift and would make no use of the
flight feathers. The legs would have to be splayed in some way for that,
as in the various reconstructions.
And as for flapping the splayed, lift-producing legs, I don't think
Microraptor would have had the proper muscles for that sort of thing.
Theropod legs just aren't made for that.
>>> As for Microraptor, which all analyses by the authors place among the deinonychosaurs,
>>> the linked article says:
>>>
>>> "Powered, forewing-only flight typical of modern birds has been generally inferred to be present only in *Archaeopteryx* and other birds [2,5,20].The flight capabilities of some deinonychosaurs remain contentious: the most proficient, *Microraptor gui,* used both the forelimbs and hindlimbs, and has been argued to be a glider [21] and asymmetric pennaceous feathers indicating aerodynamic ability are known only in dromaeosaurus outside of birds [22]."
>>>
>>> Note the attribution of forewing-only flight to *Archaeopteryx* despite the feathers on the
>>> legs that you mention, John. Those feathers might make substantial contributions to flight
>>> just like the tail feathers (retrices) are known to do in present-day birds.
>
>> That seems most likely. Lift only, not thrust.
>
> I'm still inclined to think this, but I'd like to see your reaction to what I wrote about *Microraptor*.
>
> One would think that what works so well in water might also work in air, with the proper "equipment."
equipment.
>>>> As for whether Archaopteryx is a bird, isn't that a matter of personal
>>>> taste in definitions?
>>>
>>> To some extent, yes, but placing it in Avialae, as the Baysean and ML analyses do, would satisfy
>>> a lot more personal tastes than relying on flight remiges to define it as one.
>>>
>>>
>>> The rest of the paragraph I quoted takes us back to more technical aspects of
>>> the analyses, but it also weaves it in with more talk about powered flight.
>>>
>>> "The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
>
>> I don't think we can reliably distinguish the difference with current data.
>
> I suppose you are talking about phylogeny here, not the details of flight.
I'm talking about both the shape of the tree and the optimization of
>>>> As for whether Archaopteryx is a bird, isn't that a matter of personal
>>>> taste in definitions?
>>>
>>> To some extent, yes, but placing it in Avialae, as the Baysean and ML analyses do, would satisfy
>>> a lot more personal tastes than relying on flight remiges to define it as one.
>>>
>>>
>>> The rest of the paragraph I quoted takes us back to more technical aspects of
>>> the analyses, but it also weaves it in with more talk about powered flight.
>>>
>>> "The likelihood-based phylogenies are consistent with a single origin of typical forewing-driven flight with no losses in basal birds (i.e. the taxa here sampled); in contrast, the parsimony tree implies either minimally two origins (in Archaeopteryx/Wellnhoferia, and in ‘true’ birds), or an earlier origin at the base of Paraves (with subsequent reduced flying ability or modifications to four-winged locomotion in various deinonychosaurs; [17,21])."
>
>> I don't think we can reliably distinguish the difference with current data.
>
> I suppose you are talking about phylogeny here, not the details of flight.
character changes on that tree.
erik simpson
Dec 9, 2022, 2:18:24 PM12/9/22
to
You might check
https://en.wikipedia.org/wiki/Tradeoffs_for_locomotion_in_air_and_water
- Capt. Obvious
Peter Nyikos
Dec 14, 2022, 12:08:23 PM12/14/22
to
> Water and air have many differences; a similar remark holds for swimming and flight.
I looked, but the closest things l could find were tradeoffs for birds wanting to swim in water,
and nothing about flapping hind wings in air. As usual, paleontology was off the Wikipedia radar screen.
> - Capt. Obvious
It's Obvious that you didn't look at it, Capt.
Peter Nyikos
Professor, Dept. of Mathematics
http://people.math.sc.edu/nyikos
Peter Nyikos
Dec 16, 2022, 9:55:30 AM12/16/22
to
On Tuesday, December 6, 2022 at 7:53:34 PM UTC-5, Popping Mad wrote:
> On 11/29/22 11:36, erik simpson wrote:
> > Despite your contempt for my recommendation of a fairly-easily read textbook on phylogenetic trees,
> > I still think your understanding would be augemented by it.
> what text is that?
> On 11/29/22 11:36, erik simpson wrote:
> > Despite your contempt for my recommendation of a fairly-easily read textbook on phylogenetic trees,
> > I still think your understanding would be augemented by it.
Methinks Erik wants you to go on a wild-goose chase to divert you from the sophisticated ideas you
talked about back in 2016 that neither he nor Harshman could handle.
Methinks it is like the one he demonstrably sent me on with
his "Capt. Obvious" nonsense after he wrote the above.
https://groups.google.com/g/sci.bio.paleontology/c/4bG1D7uLcT0/m/fcb5xjSaBgAJ
The one review that he linked of the textbook Erik is peddling talked about excruciatingly elementary
problems that students have trouble with.
>> (It goes beyond what you learned from Romer.)
with an intelligent mind. I started to explain their advantages in a reply to a stereotypic post
by Harshman over in t.o.
https://groups.google.com/g/talk.origins/c/WATJ1V2lWcI/m/aoDvlVdwBgAJ
Re: Darwin of the Gaps
Dec 13, 2022, 9:55:20 PM
I continued in a subsequent post and will continue to explain them.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
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