https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/

Excerpts:
"The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.

"Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
[...]
"Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."

The article has two exquisitely detailed photographs of the cast of
what looks like a complete skeleton:
https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg

and a close-up of the skull cast:
Each in turn is further magnifiable about x2.

It very closely resembles the iconic Hesperornis, including the teeth
in the upper jaw being only in the proximal half.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina at Columbia
http://people.math.sc.edu/nyikos

PS The reason for the "ATTN: Popping mad" will become clear in my next
post to this thread, to follow soon after I see that this OP has posted.

On 10/14/22 4:12 PM, Peter Nyikos wrote:
> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>
> Excerpts:
> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>
> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
> [...]
> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>
> The article has two exquisitely detailed photographs of the cast of
> what looks like a complete skeleton:
> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>
> and a close-up of the skull cast:
> Each in turn is further magnifiable about x2.
>
> It very closely resembles the iconic Hesperornis, including the teeth
> in the upper jaw being only in the proximal half.

I believe that no bird has teeth on its premaxilla, not just
hesperornithids.

> PS The reason for the "ATTN: Popping mad" will become clear in my next
> post to this thread, to follow soon after I see that this OP has posted.
>
>

On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>
> Excerpts:
> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>
> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
> [...]
> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>
> The article has two exquisitely detailed photographs of the cast of
> what looks like a complete skeleton:
> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>
> and a close-up of the skull cast:
> Each in turn is further magnifiable about x2.
>
> It very closely resembles the iconic Hesperornis, including the teeth
> in the upper jaw being only in the proximal half.

Immediately after this came the following words:

"Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."

This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."

But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
where the following post by Ruben Safir, a.k.a. Popping mad, appeared:

_________________ repost___________________
On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
>On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:

>> I thought almost all birds are related to ducks.
>>
> All birds are related to ducks. All birds are related to elephants too.
> All life is related to all life.

right but I thought ducks were the stem group that survived the KP impact
================ end of repost of
https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
Re: Flamingo Origins
Sep 11, 2016, 2:11:37 AM

The thread ended with John Harshman replying, "That is not correct."

That still does not answer what, if any, the stem group that survived the KP impact *was*.
One would think that there were surviving members of Avialae outside the crown group Neornithes
that later went extinct. But if there were any, they are not to be found in the
phylogenetic tree at the bottom of the following page:

https://en.wikipedia.org/wiki/Euornithes

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

On Friday, October 14, 2022 at 7:18:54 PM UTC-4, John Harshman wrote:
> On 10/14/22 4:12 PM, Peter Nyikos wrote:
> > https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
> >
> > Excerpts:
> > "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
> >
> > "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
> > [...]
> > "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
> >
> > The article has two exquisitely detailed photographs of the cast of
> > what looks like a complete skeleton:
> > https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
> >
> > and a close-up of the skull cast:
> > Each in turn is further magnifiable about x2.
> >
> > It very closely resembles the iconic Hesperornis, including the teeth
> > in the upper jaw being only in the proximal half.

> I believe that no bird has teeth on its premaxilla, not just
> hesperornithids.

That may depend on your definition of "bird," but I suppose
you mean any member of Avialae, otherwise you might disqualify
the hesperornids themselves.

It may also depend on whether the following guess at the skeleton
of *Rahonavis* is correct, or whether its teeth are flights of fancy:

https://en.wikipedia.org/wiki/Rahonavis#/media/File:Maniraptoran_ROM.jpg

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina in Columbia
http://people.math.sc.edu/nyikos

> > PS The reason for the "ATTN: Popping mad" will become clear in my next
> > post to this thread, to follow soon after I see that this OP has posted..
> >
> >

On 10/14/22 5:07 PM, Peter Nyikos wrote:
> On Friday, October 14, 2022 at 7:18:54 PM UTC-4, John Harshman wrote:
>> On 10/14/22 4:12 PM, Peter Nyikos wrote:
>>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>>>
>>> Excerpts:
>>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>>>
>>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
>>> [...]
>>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>>>
>>> The article has two exquisitely detailed photographs of the cast of
>>> what looks like a complete skeleton:
>>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>>>
>>> and a close-up of the skull cast:
>>> Each in turn is further magnifiable about x2.
>>>
>>> It very closely resembles the iconic Hesperornis, including the teeth
>>> in the upper jaw being only in the proximal half.
>
>> I believe that no bird has teeth on its premaxilla, not just
>> hesperornithids.
>
> That may depend on your definition of "bird," but I suppose
> you mean any member of Avialae, otherwise you might disqualify
> the hesperornids themselves.
>
> It may also depend on whether the following guess at the skeleton
> of *Rahonavis* is correct, or whether its teeth are flights of fancy:
>
> https://en.wikipedia.org/wiki/Rahonavis#/media/File:Maniraptoran_ROM.jpg

Two points:

1. It appears to me that there are no teeth on the premaxilla in that
reconstruction.

2. As far as I can tell, the skull of Rahonavis is unknown.

https://palaeo-electronica.org/content/2020/3060-osteology-of-rahonavis

> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> Univ. of South Carolina in Columbia
> http://people.math.sc.edu/nyikos
>
>
>>> PS The reason for the "ATTN: Popping mad" will become clear in my next
>>> post to this thread, to follow soon after I see that this OP has posted.
>>>
>>>

On 10/14/22 4:54 PM, Peter Nyikos wrote:
> On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>>
>> Excerpts:
>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>>
>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
>> [...]
>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>>
>> The article has two exquisitely detailed photographs of the cast of
>> what looks like a complete skeleton:
>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>>
>> and a close-up of the skull cast:
>> Each in turn is further magnifiable about x2.
>>
>> It very closely resembles the iconic Hesperornis, including the teeth
>> in the upper jaw being only in the proximal half.
>
> Immediately after this came the following words:
>
> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>
> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."

Makes no sense to me either.

> But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
> where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
>
> _________________ repost___________________
> On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
>> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
>
>>> I thought almost all birds are related to ducks.
>>>
>> All birds are related to ducks. All birds are related to elephants too.
>> All life is related to all life.
>
> right but I thought ducks were the stem group that survived the KP impact
> ================ end of repost of
> https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
> Re: Flamingo Origins
> Sep 11, 2016, 2:11:37 AM
>
> The thread ended with John Harshman replying, "That is not correct."
>
> That still does not answer what, if any, the stem group that survived the KP impact *was*.

As far as I know, the stem group did not survive the K/T impact, if you
refer to the stem group of Aves/Neornithes. The stem group of
Galloanserae apparently did survive, as did apparent stem group members
of Anseriformes. But there's no need for any stem group Neornithes to
survive, since the crown group already existed in the Cretaceous.

> One would think that there were surviving members of Avialae outside the crown group Neornithes
> that later went extinct. But if there were any, they are not to be found in the
> phylogenetic tree at the bottom of the following page:

One might think so, but no such have been found.

> https://en.wikipedia.org/wiki/Euornithes
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos
>
>

Sorry to be a week late with this, John. I've been deeply involved
in discussions and debates in talk.origins on threads where you
seem to have been absent. What little time I had for s.b.p. was
taken up in answering questions of Daud and addressing
some of his conjectures regarding pterosaur origins.

On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
> On 10/14/22 4:54 PM, Peter Nyikos wrote:
> > On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
> >> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
> >>
> >> Excerpts:
> >> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
> >>
> >> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
> >> [...]
> >> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
> >>
> >> The article has two exquisitely detailed photographs of the cast of
> >> what looks like a complete skeleton:
> >> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
> >>
> >> and a close-up of the skull cast:
> >> Each in turn is further magnifiable about x2.
> >>
> >> It very closely resembles the iconic Hesperornis, including the teeth
> >> in the upper jaw being only in the proximal half.
> >
> > Immediately after this came the following words:
> >
> > "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >
> > This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> > is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."

> Makes no sense to me either.

My fragmentary reading on this makes me suspect that this is another "rotation of tree"
misconception. Because the first split seems to be between Galloanserae and
all other birds, the smaller of the two clades is given star billing for closeness of relationship.

This in turn seems to be based on the theory that palaeognaths are the result
of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
within that "all other birds" clade.

This theory has other ramifications; see below.

> > But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
> > where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
> >
> > _________________ repost___________________
> > On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
> >> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
> >
> >>> I thought almost all birds are related to ducks.
> >>>
> >> All birds are related to ducks. All birds are related to elephants too..
> >> All life is related to all life.
> >
> > right but I thought ducks were the stem group that survived the KP impact
> > ================ end of repost of
> > https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
> > Re: Flamingo Origins
> > Sep 11, 2016, 2:11:37 AM
> >
> > The thread ended with John Harshman replying, "That is not correct."
> >
> > That still does not answer what, if any, the stem group that survived the KP impact *was*.

> As far as I know, the stem group did not survive the K/T impact, if you
> refer to the stem group of Aves/Neornithes. The stem group of
> Galloanserae apparently did survive, as did apparent stem group members
> of Anseriformes.

So at least two bird lineages survived the K/P extinction? That makes the
bottleneck for birds look a little less vulnerable. It was getting to look like
birds could easily have suffered the fate of the pterosaurs -- complete extinction.

That's a really big What-If. What flying mammals besides the bats we know
might have occupied the missing niches? One can only speculate.

But if that neoteny theory is wrong, there are at least three bird lineages
surviving the K/P extinction.

> But there's no need for any stem group Neornithes to
> survive, since the crown group already existed in the Cretaceous.

But no fossils of palaeognaths are found from the Mesozoic?
How long might the "ghost taxa" have gone on?

> > One would think that there were surviving members of Avialae outside the crown group Neornithes
> > that later went extinct. But if there were any, they are not to be found in the
> > phylogenetic tree at the bottom of the following page:

> > https://en.wikipedia.org/wiki/Euornithes

> One might think so, but no such have been found.

However, if the neoteny theory is wrong, and paleognaths have some undiscovered
Cretaceous fossils, then "absence of evidence does not mean evidence of absence"
might easily hold for the stem Neornithes not being completely wiped out by the K/P disaster.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina at Columbia
http://people.math.sc.edu/nyikos

On 10/21/22 11:58 AM, Peter Nyikos wrote:
> Sorry to be a week late with this, John. I've been deeply involved
> in discussions and debates in talk.origins on threads where you
> seem to have been absent. What little time I had for s.b.p. was
> taken up in answering questions of Daud and addressing
> some of his conjectures regarding pterosaur origins.
>
>
> On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
>> On 10/14/22 4:54 PM, Peter Nyikos wrote:
>>> On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
>>>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>>>>
>>>> Excerpts:
>>>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>>>>
>>>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
>>>> [...]
>>>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>>>>
>>>> The article has two exquisitely detailed photographs of the cast of
>>>> what looks like a complete skeleton:
>>>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>>>>
>>>> and a close-up of the skull cast:
>>>> Each in turn is further magnifiable about x2.
>>>>
>>>> It very closely resembles the iconic Hesperornis, including the teeth
>>>> in the upper jaw being only in the proximal half.
>>>
>>> Immediately after this came the following words:
>>>
>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>
>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>
>> Makes no sense to me either.
>
> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> misconception. Because the first split seems to be between Galloanserae and
> all other birds, the smaller of the two clades is given star billing for closeness of relationship.

The first split is between Palaeognathae and all other birds. What you
have is the second split.

> This in turn seems to be based on the theory that palaeognaths are the result
> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
> within that "all other birds" clade.

Even if neoteny were correct, it wouldn't change the tree. Are you sure
that article is making such a claim?

> This theory has other ramifications; see below.
>
>
>>> But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
>>> where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
>>>
>>> _________________ repost___________________
>>> On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
>>>> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
>>>
>>>>> I thought almost all birds are related to ducks.
>>>>>
>>>> All birds are related to ducks. All birds are related to elephants too.
>>>> All life is related to all life.
>>>
>>> right but I thought ducks were the stem group that survived the KP impact
>>> ================ end of repost of
>>> https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
>>> Re: Flamingo Origins
>>> Sep 11, 2016, 2:11:37 AM
>>>
>>> The thread ended with John Harshman replying, "That is not correct."
>>>
>>> That still does not answer what, if any, the stem group that survived the KP impact *was*.
>
>> As far as I know, the stem group did not survive the K/T impact, if you
>> refer to the stem group of Aves/Neornithes. The stem group of
>> Galloanserae apparently did survive, as did apparent stem group members
>> of Anseriformes.
>
> So at least two bird lineages survived the K/P extinction? That makes the
> bottleneck for birds look a little less vulnerable. It was getting to look like
> birds could easily have suffered the fate of the pterosaurs -- complete extinction.

At least 7, actually, implied by the existence of Cretaceous
presbyornithids. And that's a minimum.

> That's a really big What-If. What flying mammals besides the bats we know
> might have occupied the missing niches? One can only speculate.
>
> But if that neoteny theory is wrong, there are at least three bird lineages
> surviving the K/P extinction.

Again, at least 7: paleognaths, neoaves, galliforms, anhimids,
presbyornithids, anseranatidae, anatidae.

>> But there's no need for any stem group Neornithes to
>> survive, since the crown group already existed in the Cretaceous.
>
> But no fossils of palaeognaths are found from the Mesozoic?
> How long might the "ghost taxa" have gone on?

Who knows? It's true that no such fossils are known, but they could have
been restricted to Antarctica, they could have been small and thus
unlikely to be preserved, all sorts of things.

>>> One would think that there were surviving members of Avialae outside the crown group Neornithes
>>> that later went extinct. But if there were any, they are not to be found in the
>>> phylogenetic tree at the bottom of the following page:
>
>>> https://en.wikipedia.org/wiki/Euornithes
>
>> One might think so, but no such have been found.
>
> However, if the neoteny theory is wrong, and paleognaths have some undiscovered
> Cretaceous fossils, then "absence of evidence does not mean evidence of absence"
> might easily hold for the stem Neornithes not being completely wiped out by the K/P disaster.

The neoteny theory is irrelevant, given the clear phylogeny of birds.
Given that phylogeny, there are definitely undiscovered Cretaceous
paleognaths and several other neornithine groups. True, we can't clearly
say that non stem-neornithin survived the K/T.

On Friday, October 21, 2022 at 3:24:55 PM UTC-4, John Harshman wrote:

That was a quick reply. My post was at 2:58 PM UTC-4. The time
your software gives below is PDT, UTC-7.

> On 10/21/22 11:58 AM, Peter Nyikos wrote:
> > Sorry to be a week late with this, John. I've been deeply involved
> > in discussions and debates in talk.origins on threads where you
> > seem to have been absent. What little time I had for s.b.p. was
> > taken up in answering questions of Daud and addressing
> > some of his conjectures regarding pterosaur origins.
> >
> >
> > On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
> >> On 10/14/22 4:54 PM, Peter Nyikos wrote:
> >>> On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
> >>>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
> >>>>
> >>>> Excerpts:
> >>>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
> >>>>
> >>>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
> >>>> [...]
> >>>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
> >>>>
> >>>> The article has two exquisitely detailed photographs of the cast of
> >>>> what looks like a complete skeleton:
> >>>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
> >>>>
> >>>> and a close-up of the skull cast:
> >>>> Each in turn is further magnifiable about x2.
> >>>>
> >>>> It very closely resembles the iconic Hesperornis, including the teeth
> >>>> in the upper jaw being only in the proximal half.
> >>>
> >>> Immediately after this came the following words:
> >>>
> >>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >>>
> >>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> >>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
> >
> >> Makes no sense to me either.
> >
> > My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> > misconception. Because the first split seems to be between Galloanserae and
> > all other birds, the smaller of the two clades is given star billing for closeness of relationship.

> The first split is between Palaeognathae and all other birds. What you have is the second split.

Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
But there is plenty of room for convergence when splits go that far back in time,
and plenty of loss of information when we do not have molecular information
for lithornithids.

Tinamous only go back to the Miocene, and they are weak fliers,
unlike some of the lithornithids.

> > This in turn seems to be based on the theory that palaeognaths are the result
> > of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
> > within that "all other birds" clade.

> Even if neoteny were correct, it wouldn't change the tree. Are you sure
> that article is making such a claim?

The one sentence is all it ever says in that direction.
The only person from the museum whom I have contacted
so far is a volunteer who only comes in on Fridays to
work on the fossil collection. He doesn't know who is
responsible for that sentence, or what's behind it.

But if he doesn't find out today, I can contact another
person there who is a full-time employee.

> > This theory has other ramifications; see below.
> >
> >
> >>> But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
> >>> where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
> >>>
> >>> _________________ repost___________________
> >>> On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
> >>>> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
> >>>
> >>>>> I thought almost all birds are related to ducks.
> >>>>>
> >>>> All birds are related to ducks. All birds are related to elephants too.
> >>>> All life is related to all life.
> >>>
> >>> right but I thought ducks were the stem group that survived the KP impact
> >>> ================ end of repost of
> >>> https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
> >>> Re: Flamingo Origins
> >>> Sep 11, 2016, 2:11:37 AM
> >>>
> >>> The thread ended with John Harshman replying, "That is not correct."
> >>>
> >>> That still does not answer what, if any, the stem group that survived the KP impact *was*.
> >
> >> As far as I know, the stem group did not survive the K/T impact, if you
> >> refer to the stem group of Aves/Neornithes. The stem group of
> >> Galloanserae apparently did survive, as did apparent stem group members
> >> of Anseriformes.
> >
> > So at least two bird lineages survived the K/P extinction? That makes the
> > bottleneck for birds look a little less vulnerable. It was getting to look like
> > birds could easily have suffered the fate of the pterosaurs -- complete extinction.

> At least 7, actually, implied by the existence of Cretaceous
> presbyornithids. And that's a minimum.

Known from actual fossils? Teviornis has considerable doubt cast on its being
a presbyornithid, what with the fragmentary evidence, and it did not
survive the K/P disaster. https://en.wikipedia.org/wiki/Teviornis

Zhylgaia's remains are even more tenuous, and the "or" in the following
sentence is striking:

"Its remains have been recovered from a Late Cretaceous or Paleogene deposit in Central Asia."
https://en.wikipedia.org/wiki/Zhylgaia

Presbyornis, Bumbalavis, and Wilaru are known only from the Cenozoic.

That exhausts the list of presbyornithids about which useful information
can be found in the following page and its links:

https://en.wikipedia.org/wiki/Presbyornithidae

There are other genera in red, meaning there is no wiki page for them.
Perhaps one of them is the one you have in mind.

> > That's a really big What-If. What flying mammals besides the bats we know
> > might have occupied the missing niches? One can only speculate.
> >
> > But if that neoteny theory is wrong, there are at least three bird lineages
> > surviving the K/P extinction.

> Again, at least 7: paleognaths, neoaves, galliforms, anhimids,
> presbyornithids, anseranatidae, anatidae.

Which bird did you have in mind from neoaves?

> >> But there's no need for any stem group Neornithes to
> >> survive, since the crown group already existed in the Cretaceous.
> >
> > But no fossils of palaeognaths are found from the Mesozoic?
> > How long might the "ghost taxa" have gone on?
> Who knows? It's true that no such fossils are known, but they could have
> been restricted to Antarctica, they could have been small and thus
> unlikely to be preserved, all sorts of things.
> >>> One would think that there were surviving members of Avialae outside the crown group Neornithes
> >>> that later went extinct. But if there were any, they are not to be found in the
> >>> phylogenetic tree at the bottom of the following page:
> >
> >>> https://en.wikipedia.org/wiki/Euornithes
> >
> >> One might think so, but no such have been found.
> >
> > However, if the neoteny theory is wrong, and paleognaths have some undiscovered
> > Cretaceous fossils, then "absence of evidence does not mean evidence of absence"
> > might easily hold for the stem Neornithes not being completely wiped out by the K/P disaster.

> The neoteny theory is irrelevant, given the clear phylogeny of birds.

"clear" depends on how seriously you take the doubts I documented above.

On 10/21/22 1:36 PM, Peter Nyikos wrote:
> On Friday, October 21, 2022 at 3:24:55 PM UTC-4, John Harshman wrote:
>
> That was a quick reply. My post was at 2:58 PM UTC-4. The time
> your software gives below is PDT, UTC-7.
>
>> On 10/21/22 11:58 AM, Peter Nyikos wrote:
>>> Sorry to be a week late with this, John. I've been deeply involved
>>> in discussions and debates in talk.origins on threads where you
>>> seem to have been absent. What little time I had for s.b.p. was
>>> taken up in answering questions of Daud and addressing
>>> some of his conjectures regarding pterosaur origins.
>>>
>>>
>>> On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
>>>> On 10/14/22 4:54 PM, Peter Nyikos wrote:
>>>>> On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
>>>>>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>>>>>>
>>>>>> Excerpts:
>>>>>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>>>>>>
>>>>>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
>>>>>> [...]
>>>>>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>>>>>>
>>>>>> The article has two exquisitely detailed photographs of the cast of
>>>>>> what looks like a complete skeleton:
>>>>>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>>>>>>
>>>>>> and a close-up of the skull cast:
>>>>>> Each in turn is further magnifiable about x2.
>>>>>>
>>>>>> It very closely resembles the iconic Hesperornis, including the teeth
>>>>>> in the upper jaw being only in the proximal half.
>>>>>
>>>>> Immediately after this came the following words:
>>>>>
>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>>>
>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>>>
>>>> Makes no sense to me either.
>>>
>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
>>> misconception. Because the first split seems to be between Galloanserae and
>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
>
>> The first split is between Palaeognathae and all other birds. What you have is the second split.
>
> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
> But there is plenty of room for convergence when splits go that far back in time,
> and plenty of loss of information when we do not have molecular information
> for lithornithids.

It's based on both molecular and morphological evidence, and your
complaints about molecular phylogenetics are not well-informed. I assure
you that this particular split is exceedingly well supported and can't
be accounted for by convergence.

> Tinamous only go back to the Miocene, and they are weak fliers,
> unlike some of the lithornithids.

I suspect that they go back farther than that. Are you assuming that the
fossil record preserves actual first appearances?

>>> This in turn seems to be based on the theory that palaeognaths are the result
>>> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
>>> within that "all other birds" clade.
>
>> Even if neoteny were correct, it wouldn't change the tree. Are you sure
>> that article is making such a claim?
>
> The one sentence is all it ever says in that direction.
> The only person from the museum whom I have contacted
> so far is a volunteer who only comes in on Fridays to
> work on the fossil collection. He doesn't know who is
> responsible for that sentence, or what's behind it.
>
> But if he doesn't find out today, I can contact another
> person there who is a full-time employee.
>
>
>>> This theory has other ramifications; see below.
>>>
>>>
>>>>> But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
>>>>> where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
>>>>>
>>>>> _________________ repost___________________
>>>>> On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
>>>>>> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
>>>>>
>>>>>>> I thought almost all birds are related to ducks.
>>>>>>>
>>>>>> All birds are related to ducks. All birds are related to elephants too.
>>>>>> All life is related to all life.
>>>>>
>>>>> right but I thought ducks were the stem group that survived the KP impact
>>>>> ================ end of repost of
>>>>> https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
>>>>> Re: Flamingo Origins
>>>>> Sep 11, 2016, 2:11:37 AM
>>>>>
>>>>> The thread ended with John Harshman replying, "That is not correct."
>>>>>
>>>>> That still does not answer what, if any, the stem group that survived the KP impact *was*.
>>>
>>>> As far as I know, the stem group did not survive the K/T impact, if you
>>>> refer to the stem group of Aves/Neornithes. The stem group of
>>>> Galloanserae apparently did survive, as did apparent stem group members
>>>> of Anseriformes.
>>>
>>> So at least two bird lineages survived the K/P extinction? That makes the
>>> bottleneck for birds look a little less vulnerable. It was getting to look like
>>> birds could easily have suffered the fate of the pterosaurs -- complete extinction.
>
>> At least 7, actually, implied by the existence of Cretaceous
>> presbyornithids. And that's a minimum.
>
> Known from actual fossils? Teviornis has considerable doubt cast on its being
> a presbyornithid, what with the fragmentary evidence, and it did not
> survive the K/P disaster. https://en.wikipedia.org/wiki/Teviornis

> Zhylgaia's remains are even more tenuous, and the "or" in the following
> sentence is striking:
>
> "Its remains have been recovered from a Late Cretaceous or Paleogene deposit in Central Asia."
> https://en.wikipedia.org/wiki/Zhylgaia
>
> Presbyornis, Bumbalavis, and Wilaru are known only from the Cenozoic.
>
> That exhausts the list of presbyornithids about which useful information
> can be found in the following page and its links:
>
> https://en.wikipedia.org/wiki/Presbyornithidae
>
> There are other genera in red, meaning there is no wiki page for them.
> Perhaps one of them is the one you have in mind.

I refer to fragmentary fossils found in New Jersey, which I don't recall
having been given a name. Vegavis is anothere possibility, though like
the other fossils you mention its identification as a presbyornithid has
been questioned.

However, time-calibrated phylogenetic analyses using various fossil taxa
give similar results, with 7 or more bird lineages crossing the K/T
boundary.

>>> That's a really big What-If. What flying mammals besides the bats we know
>>> might have occupied the missing niches? One can only speculate.
>>>
>>> But if that neoteny theory is wrong, there are at least three bird lineages
>>> surviving the K/P extinction.
>
>> Again, at least 7: paleognaths, neoaves, galliforms, anhimids,
>> presbyornithids, anseranatidae, anatidae.
>
> Which bird did you have in mind from neoaves?

It's all implied by the tree if we suppose there are Cretaceous
presbyornithids and that presbyornithids are the sister group of
anatids. I wasn't referring to any other fossils.

On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
> On 10/21/22 1:36 PM, Peter Nyikos wrote:
> > On Friday, October 21, 2022 at 3:24:55 PM UTC-4, John Harshman wrote:
> >>> On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
> >>>> On 10/14/22 4:54 PM, Peter Nyikos wrote:
> >>>>> On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
> >>>>>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
> >>>>>>
> >>>>>> Excerpts:
> >>>>>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
> >>>>>>
> >>>>>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
> >>>>>> [...]
> >>>>>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
> >>>>>>
> >>>>>> The article has two exquisitely detailed photographs of the cast of
> >>>>>> what looks like a complete skeleton:
> >>>>>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
> >>>>>>
> >>>>>> and a close-up of the skull cast:
> >>>>>> Each in turn is further magnifiable about x2.
> >>>>>>
> >>>>>> It very closely resembles the iconic Hesperornis, including the teeth
> >>>>>> in the upper jaw being only in the proximal half.
> >>>>>
> >>>>> Immediately after this came the following words:
> >>>>>
> >>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >>>>>
> >>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> >>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
> >>>
> >>>> Makes no sense to me either.
> >>>
> >>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> >>> misconception. Because the first split seems to be between Galloanserae and
> >>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
> >
> >> The first split is between Palaeognathae and all other birds. What you have is the second split.
> >
> > Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
> > But there is plenty of room for convergence when splits go that far back in time,
> > and plenty of loss of information when we do not have molecular information
> > for lithornithids.

> It's based on both molecular and morphological evidence,

Combined? or separate? Could you provide a reference where only the morphological is used?

> and your complaints about molecular phylogenetics are not well-informed.

You are trying to read my mind as to how well informed I am. I am not
giving all my information by any means.

> I assure you that this particular split is exceedingly well supported and can't
> be accounted for by convergence.

That last clause needs support. For one thing, it depends on what kind of neognaths
were included in the analysis, and the ratio of ratites to tinamous. We'd need a
non-volant large neognath to balance against each large ratite, and a small
non-volant neognath to balance against each kiwi. Also to be fair, all extant
volant neognaths need to be as weak fliers as tinamous used.

As for lithornis used, a fossil neognath that is used needs to have approximately
the same number of characters preserved.

And it's cheating to list penguins as non-volant: they "fly" thru the water with
their wings as almost their only source of propulsion.

> > Tinamous only go back to the Miocene, and they are weak fliers,
> > unlike some of the lithornithids.

> I suspect that they go back farther than that.

I assume that the tinamous you are basing this on
are widely disparate bunch morphologically. Am I right?

> Are you assuming that the
> fossil record preserves actual first appearances?

Of course not! That would be as bad as thinking that the Miocene *Obdurodon*
preserves the actual first appearance of platypuses.

I admit, I was sloppy in my formulation. I was mentally comparing known fossils with known fossils,
and NOT assuming that the tinamou contemporaries (if they went back that far) of the lithornids
were as weak fliers as the ones known to us now.

> >>> This in turn seems to be based on the theory that palaeognaths are the result
> >>> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
> >>> within that "all other birds" clade.
> >
> >> Even if neoteny were correct, it wouldn't change the tree.

Did the the analysis you are depending on compare the palaeognaths with immature neognaths,
or simply leave the palates out of the analysis altogether?

> >> Are you sure that article is making such a claim?
> >
> > The one sentence is all it ever says in that direction.
> > The only person from the museum whom I have contacted
> > so far is a volunteer who only comes in on Fridays to
> > work on the fossil collection. He doesn't know who is
> > responsible for that sentence, or what's behind it.
> >
> > But if he doesn't find out today, I can contact another
> > person there who is a full-time employee.
> >
> >
> >>> This theory has other ramifications; see below.
> >>>
> >>>
> >>>>> But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
> >>>>> where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
> >>>>>
> >>>>> _________________ repost___________________
> >>>>> On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
> >>>>>> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
> >>>>>
> >>>>>>> I thought almost all birds are related to ducks.
> >>>>>>>
> >>>>>> All birds are related to ducks. All birds are related to elephants too.
> >>>>>> All life is related to all life.
> >>>>>
> >>>>> right but I thought ducks were the stem group that survived the KP impact
> >>>>> ================ end of repost of
> >>>>> https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
> >>>>> Re: Flamingo Origins
> >>>>> Sep 11, 2016, 2:11:37 AM
> >>>>>
> >>>>> The thread ended with John Harshman replying, "That is not correct."
> >>>>>
> >>>>> That still does not answer what, if any, the stem group that survived the KP impact *was*.
> >>>
> >>>> As far as I know, the stem group did not survive the K/T impact, if you
> >>>> refer to the stem group of Aves/Neornithes. The stem group of
> >>>> Galloanserae apparently did survive, as did apparent stem group members
> >>>> of Anseriformes.
> >>>
> >>> So at least two bird lineages survived the K/P extinction? That makes the
> >>> bottleneck for birds look a little less vulnerable. It was getting to look like
> >>> birds could easily have suffered the fate of the pterosaurs -- complete extinction.
> >
> >> At least 7, actually, implied by the existence of Cretaceous
> >> presbyornithids. And that's a minimum.
> >
> > Known from actual fossils? Teviornis has considerable doubt cast on its being
> > a presbyornithid, what with the fragmentary evidence, and it did not
> > survive the K/P disaster. https://en.wikipedia.org/wiki/Teviornis
>
> > Zhylgaia's remains are even more tenuous, and the "or" in the following
> > sentence is striking:
> >
> > "Its remains have been recovered from a Late Cretaceous or Paleogene deposit in Central Asia."
> > https://en.wikipedia.org/wiki/Zhylgaia
> >
> > Presbyornis, Bumbalavis, and Wilaru are known only from the Cenozoic.
> >
> > That exhausts the list of presbyornithids about which useful information
> > can be found in the following page and its links:
> >
> > https://en.wikipedia.org/wiki/Presbyornithidae
> >
> > There are other genera in red, meaning there is no wiki page for them.
> > Perhaps one of them is the one you have in mind.

On 10/26/22 12:57 PM, Peter Nyikos wrote:
> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
>>> On Friday, October 21, 2022 at 3:24:55 PM UTC-4, John Harshman wrote:
>>>>> On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
>>>>>> On 10/14/22 4:54 PM, Peter Nyikos wrote:
>>>>>>> On Friday, October 14, 2022 at 7:12:45 PM UTC-4, Peter Nyikos wrote:
>>>>>>>> https://www.scmuseum.org/2022/09/13/state-museum-adds-new-fossil-to-collection/
>>>>>>>>
>>>>>>>> Excerpts:
>>>>>>>> "The South Carolina State Museum recently acquired the cast skeleton of an extinct bird called Parahesperornis (“alongside western bird”). This animal lived around 83 million years ago in what is now central Kansas, USA. At the time, the area was covered by the Western Interior Seaway, which stretched from Texas to Canada.
>>>>>>>>
>>>>>>>> "Parahesperornis was about three feet long and, although it couldn’t fly, it used strong legs and large feet to dive after fish, which it caught in its toothed jaws.
>>>>>>>> [...]
>>>>>>>> "Parahesperornis was described in 1984 and is one of about 30 species of related diving birds that are primarily from North America (USA and Canada), and less commonly from Europe and Asia."
>>>>>>>>
>>>>>>>> The article has two exquisitely detailed photographs of the cast of
>>>>>>>> what looks like a complete skeleton:
>>>>>>>> https://www.scmuseum1.org/wp-content/uploads/2022/09/Parahesperornis-Fossil-SC-State-Museum.jpg
>>>>>>>>
>>>>>>>> and a close-up of the skull cast:
>>>>>>>> Each in turn is further magnifiable about x2.
>>>>>>>>
>>>>>>>> It very closely resembles the iconic Hesperornis, including the teeth
>>>>>>>> in the upper jaw being only in the proximal half.
>>>>>>>
>>>>>>> Immediately after this came the following words:
>>>>>>>
>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>>>>>
>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>>>>>
>>>>>> Makes no sense to me either.
>>>>>
>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
>>>>> misconception. Because the first split seems to be between Galloanserae and
>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
>>>
>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
>>>
>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
>>> But there is plenty of room for convergence when splits go that far back in time,
>>> and plenty of loss of information when we do not have molecular information
>>> for lithornithids.
>
>> It's based on both molecular and morphological evidence,
>
> Combined? or separate? Could you provide a reference where only the morphological is used?

Separately, as a rule. Here's one:
https://repository.si.edu/handle/10088/21644

>> and your complaints about molecular phylogenetics are not well-informed.
>
> You are trying to read my mind as to how well informed I am. I am not
> giving all my information by any means.

Can we agree that I am likely to be better informed on this subject than
you are? After all, I've published on this very subject:

Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
flight in ratite birds. Proceedings of the National Academy of Sciences
2008; 105:13462-12467.

>> I assure you that this particular split is exceedingly well supported and can't
>> be accounted for by convergence.
>
> That last clause needs support. For one thing, it depends on what kind of neognaths
> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
> non-volant large neognath to balance against each large ratite, and a small
> non-volant neognath to balance against each kiwi. Also to be fair, all extant
> volant neognaths need to be as weak fliers as tinamous used.

Why is "non-volant" relevant to molecular data? Why is size relevant to
molecular data?

> As for lithornis used, a fossil neognath that is used needs to have approximately
> the same number of characters preserved.
>
> And it's cheating to list penguins as non-volant: they "fly" thru the water with
> their wings as almost their only source of propulsion.

It seems a pointless exercise regardless of whether penguins are excluded.

>>> Tinamous only go back to the Miocene, and they are weak fliers,
>>> unlike some of the lithornithids.
>
>> I suspect that they go back farther than that.
>
> I assume that the tinamous you are basing this on
> are widely disparate bunch morphologically. Am I right?

Not really. All tinamous look more or less alike.

>> Are you assuming that the
>> fossil record preserves actual first appearances?
>
> Of course not! That would be as bad as thinking that the Miocene *Obdurodon*
> preserves the actual first appearance of platypuses.
>
> I admit, I was sloppy in my formulation. I was mentally comparing known fossils with known fossils,
> and NOT assuming that the tinamou contemporaries (if they went back that far) of the lithornids
> were as weak fliers as the ones known to us now.

>>>>> This in turn seems to be based on the theory that palaeognaths are the result
>>>>> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
>>>>> within that "all other birds" clade.
>>>
>>>> Even if neoteny were correct, it wouldn't change the tree.
>
> Did the the analysis you are depending on compare the palaeognaths with immature neognaths,
> or simply leave the palates out of the analysis altogether?

The analyses I'm depending on are of DNA sequences. Whether palate
structure is convergent or not is not relevant to the tree.

>>>> Are you sure that article is making such a claim?
>>>
>>> The one sentence is all it ever says in that direction.
>>> The only person from the museum whom I have contacted
>>> so far is a volunteer who only comes in on Fridays to
>>> work on the fossil collection. He doesn't know who is
>>> responsible for that sentence, or what's behind it.
>>>
>>> But if he doesn't find out today, I can contact another
>>> person there who is a full-time employee.
>>>
>>>
>>>>> This theory has other ramifications; see below.
>>>>>
>>>>>
>>>>>>> But here comes the reason the "ATTN: Popping mad": I happened to catch an old thread
>>>>>>> where the following post by Ruben Safir, a.k.a. Popping mad, appeared:
>>>>>>>
>>>>>>> _________________ repost___________________
>>>>>>> On Thu, 01 Sep 2016 06:57:58 -0700, John Harshman wrote:
>>>>>>>> On Thursday, September 1, 2016 at 7:20:04 AM UTC-4, Popping mad wrote:
>>>>>>>
>>>>>>>>> I thought almost all birds are related to ducks.
>>>>>>>>>
>>>>>>>> All birds are related to ducks. All birds are related to elephants too.
>>>>>>>> All life is related to all life.
>>>>>>>
>>>>>>> right but I thought ducks were the stem group that survived the KP impact
>>>>>>> ================ end of repost of
>>>>>>> https://groups.google.com/g/sci.bio.paleontology/c/_ptAeRAPlT0/m/x4ZYemvgAAAJ
>>>>>>> Re: Flamingo Origins
>>>>>>> Sep 11, 2016, 2:11:37 AM
>>>>>>>
>>>>>>> The thread ended with John Harshman replying, "That is not correct."
>>>>>>>
>>>>>>> That still does not answer what, if any, the stem group that survived the KP impact *was*.
>>>>>
>>>>>> As far as I know, the stem group did not survive the K/T impact, if you
>>>>>> refer to the stem group of Aves/Neornithes. The stem group of
>>>>>> Galloanserae apparently did survive, as did apparent stem group members
>>>>>> of Anseriformes.
>>>>>
>>>>> So at least two bird lineages survived the K/P extinction? That makes the
>>>>> bottleneck for birds look a little less vulnerable. It was getting to look like
>>>>> birds could easily have suffered the fate of the pterosaurs -- complete extinction.
>>>
>>>> At least 7, actually, implied by the existence of Cretaceous
>>>> presbyornithids. And that's a minimum.
>>>
>>> Known from actual fossils? Teviornis has considerable doubt cast on its being
>>> a presbyornithid, what with the fragmentary evidence, and it did not
>>> survive the K/P disaster. https://en.wikipedia.org/wiki/Teviornis
>>
>>> Zhylgaia's remains are even more tenuous, and the "or" in the following
>>> sentence is striking:
>>>
>>> "Its remains have been recovered from a Late Cretaceous or Paleogene deposit in Central Asia."
>>> https://en.wikipedia.org/wiki/Zhylgaia
>>>
>>> Presbyornis, Bumbalavis, and Wilaru are known only from the Cenozoic.
>>>
>>> That exhausts the list of presbyornithids about which useful information
>>> can be found in the following page and its links:
>>>
>>> https://en.wikipedia.org/wiki/Presbyornithidae
>>>
>>> There are other genera in red, meaning there is no wiki page for them.
>>> Perhaps one of them is the one you have in mind.
>
>> I refer to fragmentary fossils found in New Jersey, which I don't recall
>> having been given a name. Vegavis is anothere possibility, though like
>> the other fossils you mention its identification as a presbyornithid has
>> been questioned.
>
> Yes, for example:
> Mayr, G., 2013. Perspective: The age of the crown group of passerine birds and its
> evolutionary significance -- molecular calibrations versus the fossil record.
> Systematics and Biodiversity 11 (1), 7--13.
>
>
>> However, time-calibrated phylogenetic analyses using various fossil taxa
>> give similar results, with 7 or more bird lineages crossing the K/T
>> boundary.
>
> With one possibility in doubt, what have you to replace it?

On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
> On 10/26/22 12:57 PM, Peter Nyikos wrote:
> > On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
> >> On 10/21/22 1:36 PM, Peter Nyikos wrote:

> >>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >>>>>>>
> >>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> >>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
> >>>>>
> >>>>>> Makes no sense to me either.
> >>>>>
> >>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> >>>>> misconception. Because the first split seems to be between Galloanserae and
> >>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
> >>>
> >>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
> >>>
> >>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
> >>> But there is plenty of room for convergence when splits go that far back in time,
> >>> and plenty of loss of information when we do not have molecular information
> >>> for lithornithids.
> >
> >> It's based on both molecular and morphological evidence,
> >
> > Combined? or separate? Could you provide a reference where only the morphological is used?

> Separately, as a rule. Here's one:
> https://repository.si.edu/handle/10088/21644

Thanks, I'll look into it on the weekend.

> >> and your complaints about molecular phylogenetics are not well-informed.
> >
> > You are trying to read my mind as to how well informed I am. I am not
> > giving all my information by any means.

> Can we agree that I am likely to be better informed on this subject than
> you are? After all, I've published on this very subject:
>
> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
> flight in ratite birds. Proceedings of the National Academy of Sciences
> 2008; 105:13462-12467.

Research and scholarship are utterly different talents. Isn't that obvious to you?

> >> I assure you that this particular split is exceedingly well supported and can't
> >> be accounted for by convergence.
> >
> > That last clause needs support. For one thing, it depends on what kind of neognaths
> > were included in the analysis, and the ratio of ratites to tinamous. We'd need a
> > non-volant large neognath to balance against each large ratite, and a small
> > non-volant neognath to balance against each kiwi. Also to be fair, all extant
> > volant neognaths need to be as weak fliers as tinamous used.

> Why is "non-volant" relevant to molecular data? Why is size relevant to
> molecular data?

Why switch to molecular studies? You cannot reasonably evaluate convergence
vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?

> > As for lithornis used, a fossil neognath that is used needs to have approximately
> > the same number of characters preserved.
> >
> > And it's cheating to list penguins as non-volant: they "fly" thru the water with
> > their wings as almost their only source of propulsion.

> It seems a pointless exercise regardless of whether penguins are excluded.

Unless it is done, we will never know whether one or more neognaths
would be transferred to the palaeognath clade by it, with convergence
overruling synapomorphy in those cases.

> >>> Tinamous only go back to the Miocene, and they are weak fliers,
> >>> unlike some of the lithornithids.
> >
> >> I suspect that they go back farther than that.
> >
> > I assume that the tinamous you are basing this on
> > are widely disparate bunch morphologically. Am I right?

> Not really. All tinamous look more or less alike.

Let's not bring primitive phenetics (external appearance) into the picture.

I'll assume you are talking about complete morphology.
But then, where's the basis for your suspicions if you stick with the crown group?

> >> Are you assuming that the
> >> fossil record preserves actual first appearances?
> >
> > Of course not! That would be as bad as thinking that the Miocene *Obdurodon*
> > preserves the actual first appearance of platypuses.
> >
> > I admit, I was sloppy in my formulation. I was mentally comparing known fossils with known fossils,
> > and NOT assuming that the tinamou contemporaries (if they went back that far) of the lithornids
> > were as weak fliers as the ones known to us now.
>
> >>>>> This in turn seems to be based on the theory that palaeognaths are the result
> >>>>> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
> >>>>> within that "all other birds" clade.
> >>>
> >>>> Even if neoteny were correct, it wouldn't change the tree.
> >
> > Did the the analysis you are depending on compare the palaeognaths with immature neognaths,
> > or simply leave the palates out of the analysis altogether?

> The analyses I'm depending on are of DNA sequences. Whether palate
> structure is convergent or not is not relevant to the tree.

Please, let's stick to morphological studies for now. You made the claim
that they also confirm that palaeognaths form a clade at the base
of the split in neornithes. Let's see how the issues I raise above play out
before going on to molecular studies.

Remainder deleted, to be replied to later.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of So. Carolina in Columbia
http://people.math.sc.edu/nyikos

On 10/27/22 5:55 AM, Peter Nyikos wrote:
> On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
>> On 10/26/22 12:57 PM, Peter Nyikos wrote:
>>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
>>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
>
>>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>>>>>>>
>>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>>>>>>>
>>>>>>>> Makes no sense to me either.
>>>>>>>
>>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
>>>>>>> misconception. Because the first split seems to be between Galloanserae and
>>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
>>>>>
>>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
>>>>>
>>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
>>>>> But there is plenty of room for convergence when splits go that far back in time,
>>>>> and plenty of loss of information when we do not have molecular information
>>>>> for lithornithids.
>>>
>>>> It's based on both molecular and morphological evidence,
>>>
>>> Combined? or separate? Could you provide a reference where only the morphological is used?
>
>> Separately, as a rule. Here's one:
>> https://repository.si.edu/handle/10088/21644
>
> Thanks, I'll look into it on the weekend.
>
>
>>>> and your complaints about molecular phylogenetics are not well-informed.
>>>
>>> You are trying to read my mind as to how well informed I am. I am not
>>> giving all my information by any means.
>
>> Can we agree that I am likely to be better informed on this subject than
>> you are? After all, I've published on this very subject:
>>
>> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
>> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
>> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
>> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
>> flight in ratite birds. Proceedings of the National Academy of Sciences
>> 2008; 105:13462-12467.
>
> Research and scholarship are utterly different talents. Isn't that obvious to you?

It isn't. I think they're both necessary components of any scientific
paper. And I think that paper is very good evidence that paleognaths are
monophyletic.

>>>> I assure you that this particular split is exceedingly well supported and can't
>>>> be accounted for by convergence.
>>>
>>> That last clause needs support. For one thing, it depends on what kind of neognaths
>>> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
>>> non-volant large neognath to balance against each large ratite, and a small
>>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
>>> volant neognaths need to be as weak fliers as tinamous used.
>
>> Why is "non-volant" relevant to molecular data? Why is size relevant to
>> molecular data?
>
> Why switch to molecular studies? You cannot reasonably evaluate convergence
> vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?

We are discussing whether paleognaths are a monophyletic sister group to
neognaths or are a polyphyletic assemblage united by convergence only.
That's not a question of character evolution but of tree shape. In the
latter case, however, convergence is an inevitable consequence, while in
the former, it's still possible but less likely.

And analysis of living taxa only is not useless, though fossils can
certainly help. Still, if the claim is that the paleognathous palate is
convergently derived as a consequence of flightlessness, it's difficult
to explain why tinamous have it, even without consideration of Lithornis.

>>> As for lithornis used, a fossil neognath that is used needs to have approximately
>>> the same number of characters preserved.
>>>
>>> And it's cheating to list penguins as non-volant: they "fly" thru the water with
>>> their wings as almost their only source of propulsion.
>
>> It seems a pointless exercise regardless of whether penguins are excluded.
>
> Unless it is done, we will never know whether one or more neognaths
> would be transferred to the palaeognath clade by it, with convergence
> overruling synapomorphy in those cases.

This assumes that molecular analyses are a victim of convergence, for
which you have no evidence. Further, that convergence would have to be
massive, affecting the entire genome, for which there is no evidence and
no mechanism. Finally, given such convergence, there's no reason to
expect that any similarities in size or morphology would be relevant to it.

>>>>> Tinamous only go back to the Miocene, and they are weak fliers,
>>>>> unlike some of the lithornithids.
>>>
>>>> I suspect that they go back farther than that.
>>>
>>> I assume that the tinamous you are basing this on
>>> are widely disparate bunch morphologically. Am I right?
>
>> Not really. All tinamous look more or less alike.
>
> Let's not bring primitive phenetics (external appearance) into the picture.

Why not? That's what "disparate bunch morphologically" is about.

> I'll assume you are talking about complete morphology.
> But then, where's the basis for your suspicions if you stick with the crown group?

Their positions on the paleognath tree, on which they're the sister
group of moas, and the lengths of the branches on that tree.

>>>> Are you assuming that the
>>>> fossil record preserves actual first appearances?
>>>
>>> Of course not! That would be as bad as thinking that the Miocene *Obdurodon*
>>> preserves the actual first appearance of platypuses.
>>>
>>> I admit, I was sloppy in my formulation. I was mentally comparing known fossils with known fossils,
>>> and NOT assuming that the tinamou contemporaries (if they went back that far) of the lithornids
>>> were as weak fliers as the ones known to us now.
>>
>>>>>>> This in turn seems to be based on the theory that palaeognaths are the result
>>>>>>> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
>>>>>>> within that "all other birds" clade.
>>>>>
>>>>>> Even if neoteny were correct, it wouldn't change the tree.
>>>
>>> Did the the analysis you are depending on compare the palaeognaths with immature neognaths,
>>> or simply leave the palates out of the analysis altogether?
>
>> The analyses I'm depending on are of DNA sequences. Whether palate
>> structure is convergent or not is not relevant to the tree.
>
> Please, let's stick to morphological studies for now. You made the claim
> that they also confirm that palaeognaths form a clade at the base
> of the split in neornithes. Let's see how the issues I raise above play out
> before going on to molecular studies.

The molecular studies show that the morphological studies were not in
fact confused by convergence in this matter. Why are they not relevant?

> Remainder deleted, to be replied to later.
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of So. Carolina in Columbia
> http://people.math.sc.edu/nyikos

On 10/27/22 5:55 AM, Peter Nyikos wrote:
> On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
>> On 10/26/22 12:57 PM, Peter Nyikos wrote:
>>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
>>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
>
>>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>>>>>>>
>>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>>>>>>>
>>>>>>>> Makes no sense to me either.
>>>>>>>
>>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
>>>>>>> misconception. Because the first split seems to be between Galloanserae and
>>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
>>>>>
>>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
>>>>>
>>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
>>>>> But there is plenty of room for convergence when splits go that far back in time,
>>>>> and plenty of loss of information when we do not have molecular information
>>>>> for lithornithids.
>>>
>>>> It's based on both molecular and morphological evidence,
>>>
>>> Combined? or separate? Could you provide a reference where only the morphological is used?
>
>> Separately, as a rule. Here's one:
>> https://repository.si.edu/handle/10088/21644
>
> Thanks, I'll look into it on the weekend.
>
>
>>>> and your complaints about molecular phylogenetics are not well-informed.
>>>
>>> You are trying to read my mind as to how well informed I am. I am not
>>> giving all my information by any means.
>
>> Can we agree that I am likely to be better informed on this subject than
>> you are? After all, I've published on this very subject:
>>
>> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
>> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
>> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
>> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
>> flight in ratite birds. Proceedings of the National Academy of Sciences
>> 2008; 105:13462-12467.
>
> Research and scholarship are utterly different talents. Isn't that obvious to you?
>
>
>>>> I assure you that this particular split is exceedingly well supported and can't
>>>> be accounted for by convergence.
>>>
>>> That last clause needs support. For one thing, it depends on what kind of neognaths
>>> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
>>> non-volant large neognath to balance against each large ratite, and a small
>>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
>>> volant neognaths need to be as weak fliers as tinamous used.
>
>> Why is "non-volant" relevant to molecular data? Why is size relevant to
>> molecular data?
>
> Why switch to molecular studies? You cannot reasonably evaluate convergence
> vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?
>
>
>>> As for lithornis used, a fossil neognath that is used needs to have approximately
>>> the same number of characters preserved.
>>>
>>> And it's cheating to list penguins as non-volant: they "fly" thru the water with
>>> their wings as almost their only source of propulsion.
>
>> It seems a pointless exercise regardless of whether penguins are excluded.
>
> Unless it is done, we will never know whether one or more neognaths
> would be transferred to the palaeognath clade by it, with convergence
> overruling synapomorphy in those cases.
>
>
>>>>> Tinamous only go back to the Miocene, and they are weak fliers,
>>>>> unlike some of the lithornithids.
>>>
>>>> I suspect that they go back farther than that.
>>>
>>> I assume that the tinamous you are basing this on
>>> are widely disparate bunch morphologically. Am I right?
>
>> Not really. All tinamous look more or less alike.
>
> Let's not bring primitive phenetics (external appearance) into the picture.
>
> I'll assume you are talking about complete morphology.
> But then, where's the basis for your suspicions if you stick with the crown group?
>
>
>>>> Are you assuming that the
>>>> fossil record preserves actual first appearances?
>>>
>>> Of course not! That would be as bad as thinking that the Miocene *Obdurodon*
>>> preserves the actual first appearance of platypuses.
>>>
>>> I admit, I was sloppy in my formulation. I was mentally comparing known fossils with known fossils,
>>> and NOT assuming that the tinamou contemporaries (if they went back that far) of the lithornids
>>> were as weak fliers as the ones known to us now.
>>
>>>>>>> This in turn seems to be based on the theory that palaeognaths are the result
>>>>>>> of neoteny, which makes their palate look like a plesimorphy but is actually an apomorphy
>>>>>>> within that "all other birds" clade.
>>>>>
>>>>>> Even if neoteny were correct, it wouldn't change the tree.
>>>
>>> Did the the analysis you are depending on compare the palaeognaths with immature neognaths,
>>> or simply leave the palates out of the analysis altogether?
>
>> The analyses I'm depending on are of DNA sequences. Whether palate
>> structure is convergent or not is not relevant to the tree.
>
> Please, let's stick to morphological studies for now. You made the claim
> that they also confirm that palaeognaths form a clade at the base
> of the split in neornithes. Let's see how the issues I raise above play out
> before going on to molecular studies.
>
>
> Remainder deleted, to be replied to later.

Here are a couple more morphological studies:

Cracraft, J. and Clarke, J. 2001. The basal clades of modern birds. Pp.
143-156 In J. Gauthier and L. F. Gall (eds), New Perspectives on the
Origin and Early Evolution of Birds: Proceedings of the International
Symposium In Honor of John H. Ostrom. Yale University Press, New Haven.

Mayr, G. and Clarke, J. 2003. The deep divergences of neornithine birds:
A phylogenetic analysis of morphological characters. Cladistics 19: 527-553.

On Thursday, October 27, 2022 at 9:21:21 AM UTC-4, John Harshman wrote:
> On 10/27/22 5:55 AM, Peter Nyikos wrote:
> > On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
> >> On 10/26/22 12:57 PM, Peter Nyikos wrote:
> >>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
> >>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
> >
> >>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >>>>>>>>>
> >>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> >>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
> >>>>>>>
> >>>>>>>> Makes no sense to me either.
> >>>>>>>
> >>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> >>>>>>> misconception. Because the first split seems to be between Galloanserae and
> >>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
> >>>>>
> >>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
> >>>>>
> >>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
> >>>>> But there is plenty of room for convergence when splits go that far back in time,
> >>>>> and plenty of loss of information when we do not have molecular information
> >>>>> for lithornithids.
> >>>
> >>>> It's based on both molecular and morphological evidence,
> >>>
> >>> Combined? or separate? Could you provide a reference where only the morphological is used?
> >
> >> Separately, as a rule. Here's one:
> >> https://repository.si.edu/handle/10088/21644
> >
> > Thanks, I'll look into it on the weekend.

I got a huge surprise: the authors' research supported the claim
that lithornids are outside the crown group! This would not only
give you an eighth group of birds that survived the K-P disaster,
but it would upend the generally accepted belief that only Neornithine
birds survived it.

> >
> >>>> and your complaints about molecular phylogenetics are not well-informed.
> >>>
> >>> You are trying to read my mind as to how well informed I am. I am not
> >>> giving all my information by any means.
> >
> >> Can we agree that I am likely to be better informed on this subject than
> >> you are? After all, I've published on this very subject:
> >>
> >> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
> >> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
> >> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
> >> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
> >> flight in ratite birds. Proceedings of the National Academy of Sciences
> >> 2008; 105:13462-12467.
> >
> > Research and scholarship are utterly different talents. Isn't that obvious to you?

> It isn't. I think they're both necessary components of any scientific
> paper.

You were comparing yourself to me, so talk about papers misses the point.

Isaak Asimov was the scientific scholar *par excellence*; IMHO his prodigious
output of expository papers [later anthologized] ranging over all the sciences
was more impressive than the science fiction for which he is better known.

On the other hand, his research record was below par even for a place
like Boston University School of Medicine:

"In December 1957, Asimov was dismissed from his teaching post, with effect from June 30, 1958, because he had stopped doing research. After a struggle which lasted for two years, he kept his title,[57] he gave the opening lecture each year for a biochemistry class,[58] and on October 18, 1979, the university honored his writing by promoting him to full professor of biochemistry.[59]"

In contrast, although Stephen Jay Gould was also an excellent scholar and expositor,
he wrote on less diverse areas of science, but he also had some major research accomplishments.

> And I think that paper is very good evidence that paleognaths are
> monophyletic.

I forget--does it make tinamous basal?

> >>>> I assure you that this particular split is exceedingly well supported and can't
> >>>> be accounted for by convergence.
> >>>
> >>> That last clause needs support. For one thing, it depends on what kind of neognaths
> >>> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
> >>> non-volant large neognath to balance against each large ratite, and a small
> >>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
> >>> volant neognaths need to be as weak fliers as tinamous used.
> >
> >> Why is "non-volant" relevant to molecular data? Why is size relevant to
> >> molecular data?

I let this slide at first, but your skepticism here is highly counter-intuitive.
Being active flyers promotes many alleles at the expense of others no matter
how near or far two groups of birds are from each other phylogenetically.
The same is true of size: remember Haldane's classic, "On Being the Right Size"?

> > Why switch to molecular studies? You cannot reasonably evaluate convergence
> > vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?

> We are discussing whether paleognaths are a monophyletic sister group to
> neognaths or are a polyphyletic assemblage united by convergence only.
> That's not a question of character evolution but of tree shape.

Aren't you confusing cause and effect? Whether two characters are
considered to be "the same" or only convergent is an integral part
of setting up the matrix, which in turn determines the tree, no?

A related phenomenon: the frame shift hypothesis causes cladists
to score the 2-3-4 arrangement of birds to be "the same"
as the 1-2-3 arrangement of theropods, in setting up the matrix.

> In the latter case, however, convergence is an inevitable consequence, while in
> the former, it's still possible but less likely.

Again putting the cart before the horse, ISTM.

>
> And analysis of living taxa only is not useless, though fossils can
> certainly help. Still, if the claim is that the paleognathous palate is
> convergently derived as a consequence of flightlessness,

Who would make such a claim, with tinamous in the background?
Only someone ignorant of them, it seems from what you say next:

> > it's difficult to explain why tinamous have it, even without consideration of Lithornis.

The only claim I made was that some researchers believe the paleognathous
palate of extant birds to be the result of neoteny, to which flightlessnes is
of questionable relevance.

> >>> As for lithornis used, a fossil neognath that is used needs to have approximately
> >>> the same number of characters preserved.
> >>>
> >>> And it's cheating to list penguins as non-volant: they "fly" thru the water with
> >>> their wings as almost their only source of propulsion.
> >
> >> It seems a pointless exercise regardless of whether penguins are excluded.
> >
> > Unless it is done, we will never know whether one or more neognaths
> > would be transferred to the palaeognath clade by it, with convergence
> > overruling synapomorphy in those cases.

Or vice versa, a paleognath being transferred to the neognath clade.

The talk in your reply shifted to molecular analyses, so I'd like to postpone
replying to that part until Friday.

Peter Nyikos
Professor, Dept. of Mathematics
University of So. Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos

On 11/1/22 12:34 PM, Peter Nyikos wrote:
> On Thursday, October 27, 2022 at 9:21:21 AM UTC-4, John Harshman wrote:
>> On 10/27/22 5:55 AM, Peter Nyikos wrote:
>>> On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
>>>> On 10/26/22 12:57 PM, Peter Nyikos wrote:
>>>>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
>>>>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
>>>
>>>>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>>>>>>>>>
>>>>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>>>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>>>>>>>>>
>>>>>>>>>> Makes no sense to me either.
>>>>>>>>>
>>>>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
>>>>>>>>> misconception. Because the first split seems to be between Galloanserae and
>>>>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
>>>>>>>
>>>>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
>>>>>>>
>>>>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
>>>>>>> But there is plenty of room for convergence when splits go that far back in time,
>>>>>>> and plenty of loss of information when we do not have molecular information
>>>>>>> for lithornithids.
>>>>>
>>>>>> It's based on both molecular and morphological evidence,
>>>>>
>>>>> Combined? or separate? Could you provide a reference where only the morphological is used?
>>>
>>>> Separately, as a rule. Here's one:
>>>> https://repository.si.edu/handle/10088/21644
>>>
>>> Thanks, I'll look into it on the weekend.
>
> I got a huge surprise: the authors' research supported the claim
> that lithornids are outside the crown group! This would not only
> give you an eighth group of birds that survived the K-P disaster,
> but it would upend the generally accepted belief that only Neornithine
> birds survived it.

I had forgotten that.

>>>>>> and your complaints about molecular phylogenetics are not well-informed.
>>>>>
>>>>> You are trying to read my mind as to how well informed I am. I am not
>>>>> giving all my information by any means.
>>>
>>>> Can we agree that I am likely to be better informed on this subject than
>>>> you are? After all, I've published on this very subject:
>>>>
>>>> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
>>>> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
>>>> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
>>>> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
>>>> flight in ratite birds. Proceedings of the National Academy of Sciences
>>>> 2008; 105:13462-12467.
>>>
>>> Research and scholarship are utterly different talents. Isn't that obvious to you?
>
>> It isn't. I think they're both necessary components of any scientific
>> paper.
>
> You were comparing yourself to me, so talk about papers misses the point.
>
> Isaak Asimov was the scientific scholar *par excellence*; IMHO his prodigious
> output of expository papers [later anthologized] ranging over all the sciences
> was more impressive than the science fiction for which he is better known.
>
> On the other hand, his research record was below par even for a place
> like Boston University School of Medicine:
>
> "In December 1957, Asimov was dismissed from his teaching post, with effect from June 30, 1958, because he had stopped doing research. After a struggle which lasted for two years, he kept his title,[57] he gave the opening lecture each year for a biochemistry class,[58] and on October 18, 1979, the university honored his writing by promoting him to full professor of biochemistry.[59]"
>
> In contrast, although Stephen Jay Gould was also an excellent scholar and expositor,
> he wrote on less diverse areas of science, but he also had some major research accomplishments.
>
>
>> And I think that paper is very good evidence that paleognaths are
>> monophyletic.
>
> I forget--does it make tinamous basal?

It does not. And in fact that's the main topic of the paper.

>>>>>> I assure you that this particular split is exceedingly well supported and can't
>>>>>> be accounted for by convergence.
>>>>>
>>>>> That last clause needs support. For one thing, it depends on what kind of neognaths
>>>>> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
>>>>> non-volant large neognath to balance against each large ratite, and a small
>>>>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
>>>>> volant neognaths need to be as weak fliers as tinamous used.
>>>
>>>> Why is "non-volant" relevant to molecular data? Why is size relevant to
>>>> molecular data?
>
> I let this slide at first, but your skepticism here is highly counter-intuitive.
> Being active flyers promotes many alleles at the expense of others no matter
> how near or far two groups of birds are from each other phylogenetically.
> The same is true of size: remember Haldane's classic, "On Being the Right Size"?

I'm afraid that shows a naive view of the nature of the data. Relatively
few loci have anything to do with flight or size, and in those loci
relatively few sites in the exons, and none in the introns. Further,
distantly related birds don't have the same selection of alleles to
choose from. If you're proposing extensive molecular convergence, that's
exceedingly unlikely to happen, and cases even within a single locus are
nearly unknown.

>>> Why switch to molecular studies? You cannot reasonably evaluate convergence
>>> vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?
>
>> We are discussing whether paleognaths are a monophyletic sister group to
>> neognaths or are a polyphyletic assemblage united by convergence only.
>> That's not a question of character evolution but of tree shape.
>
> Aren't you confusing cause and effect? Whether two characters are
> considered to be "the same" or only convergent is an integral part
> of setting up the matrix, which in turn determines the tree, no?

No. That would be an unwarranted bias in coding, requiring one to take
into account the tree being sought. Characters should be coded purely on
the basis of their observed states, and this is so in any legitimate
analysis. Convergence is inferred from the resulting tree, not a priori.

> A related phenomenon: the frame shift hypothesis causes cladists
> to score the 2-3-4 arrangement of birds to be "the same"
> as the 1-2-3 arrangement of theropods, in setting up the matrix.

That's because they are morphologically indistinguishable. 1-2-3 can be
distinguished from 2-3-4 only given an assumed tree.

>> In the latter case, however, convergence is an inevitable consequence, while in
>> the former, it's still possible but less likely.
>
> Again putting the cart before the horse, ISTM.

That's because you have an unfortunate view of how character coding
ought to be done. The way you suggest would serve only to confirm
whatever prior bias the coder had rather than to test that bias.

>> And analysis of living taxa only is not useless, though fossils can
>> certainly help. Still, if the claim is that the paleognathous palate is
>> convergently derived as a consequence of flightlessness,
>
> Who would make such a claim, with tinamous in the background?
> Only someone ignorant of them, it seems from what you say next:

But isn't that the claim you were referencing?

>>> it's difficult to explain why tinamous have it, even without consideration of Lithornis.
>
> The only claim I made was that some researchers believe the paleognathous
> palate of extant birds to be the result of neoteny, to which flightlessnes is
> of questionable relevance.

On Tuesday, November 1, 2022 at 9:00:11 PM UTC-4, John Harshman wrote:
> On 11/1/22 12:34 PM, Peter Nyikos wrote:
> > On Thursday, October 27, 2022 at 9:21:21 AM UTC-4, John Harshman wrote:
> >> On 10/27/22 5:55 AM, Peter Nyikos wrote:
> >>> On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
> >>>> On 10/26/22 12:57 PM, Peter Nyikos wrote:
> >>>>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
> >>>>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
> >>>
> >>>>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >>>>>>>>>>>
> >>>>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> >>>>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
> >>>>>>>>>
> >>>>>>>>>> Makes no sense to me either.
> >>>>>>>>>
> >>>>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> >>>>>>>>> misconception. Because the first split seems to be between Galloanserae and
> >>>>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
> >>>>>>>
> >>>>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
> >>>>>>>
> >>>>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
> >>>>>>> But there is plenty of room for convergence when splits go that far back in time,
> >>>>>>> and plenty of loss of information when we do not have molecular information
> >>>>>>> for lithornithids.
> >>>>>
> >>>>>> It's based on both molecular and morphological evidence,
> >>>>>
> >>>>> Combined? or separate? Could you provide a reference where only the morphological is used?
> >>>
> >>>> Separately, as a rule. Here's one:
> >>>> https://repository.si.edu/handle/10088/21644
> >>>
> >>> Thanks, I'll look into it on the weekend.
> >
> > I got a huge surprise: the authors' research supported the claim
> > that lithornids are outside the crown group! This would not only
> > give you an eighth group of birds that survived the K-P disaster,
> > but it would upend the generally accepted belief that only Neornithine
> > birds survived it.

> I had forgotten that.

Is't possible that the belief is NOT generally accepted after all,
and you just hadn't kept up with the discussion on which birds survived
the disaster since the paper was disseminated in 2007?

> >>>>>> and your complaints about molecular phylogenetics are not well-informed.
> >>>>>
> >>>>> You are trying to read my mind as to how well informed I am. I am not
> >>>>> giving all my information by any means.
> >>>
> >>>> Can we agree that I am likely to be better informed on this subject than
> >>>> you are? After all, I've published on this very subject:
> >>>>
> >>>> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
> >>>> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
> >>>> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
> >>>> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
> >>>> flight in ratite birds. Proceedings of the National Academy of Sciences
> >>>> 2008; 105:13462-12467.
> >>>
> >>> Research and scholarship are utterly different talents. Isn't that obvious to you?
> >
> >> It isn't. I think they're both necessary components of any scientific
> >> paper.
> >
> > You were comparing yourself to me, so talk about papers misses the point.
> >
> > Isaak Asimov was the scientific scholar *par excellence*; IMHO his prodigious
> > output of expository papers [later anthologized] ranging over all the sciences
> > was more impressive than the science fiction for which he is better known.
> >
> > On the other hand, his research record was below par even for a place
> > like Boston University School of Medicine:
> >
> > "In December 1957, Asimov was dismissed from his teaching post, with effect from June 30, 1958, because he had stopped doing research. After a struggle which lasted for two years, he kept his title,[57] he gave the opening lecture each year for a biochemistry class,[58] and on October 18, 1979, the university honored his writing by promoting him to full professor of biochemistry.[59]"
> >
> > In contrast, although Stephen Jay Gould was also an excellent scholar and expositor,
> > he wrote on less diverse areas of science, but he also had some major research accomplishments.
> >
> >
> >> And I think that paper is very good evidence that paleognaths are
> >> monophyletic.
> >
> > I forget--does it make tinamous basal?

> It does not. And in fact that's the main topic of the paper.

That leaves the question wide open as to what the LCA of ratites
(and tinamous, just to be on the safe side) was like. If it wasn't like *Lithornis*,
in what characters did it differ?

> >>>>>> I assure you that this particular split is exceedingly well supported and can't
> >>>>>> be accounted for by convergence.
> >>>>>
> >>>>> That last clause needs support. For one thing, it depends on what kind of neognaths
> >>>>> were included in the analysis, and the ratio of ratites to tinamous.. We'd need a
> >>>>> non-volant large neognath to balance against each large ratite, and a small
> >>>>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
> >>>>> volant neognaths need to be as weak fliers as tinamous used.
> >>>
> >>>> Why is "non-volant" relevant to molecular data? Why is size relevant to
> >>>> molecular data?
> >
> > I let this slide at first, but your skepticism here is highly counter-intuitive.
> > Being active flyers promotes many alleles at the expense of others no matter
> > how near or far two groups of birds are from each other phylogenetically.
> > The same is true of size: remember Haldane's classic, "On Being the Right Size"?

> I'm afraid that shows a naive view of the nature of the data. Relatively
> few loci have anything to do with flight or size, and in those loci
> relatively few sites in the exons, and none in the introns.

I'm not sure you got my point about flight or size. Are you including the
inevitable strengthening and thickening of legs as a result of loss of flight, well attested to
in just about every example of flight loss? In the other direction, are you
keeping in mind changes in musculature and nervous system needed for
coordinated flight? or the loss of bone mass to a bare minimum?

Also, there is the inevitable thickening of legs as a result of greater size,
and the loss of abilities that smaller animals have; for instance, elephants
can't jump worth a damn. No jumping ability, no need to have finely tuned
balance on landing after a jump.

> Further, distantly related birds don't have the same selection of alleles to
> choose from.

"the same" is knocking down a straw man. And any reasonable modification
seems counterintuitive, given the way Hox genes are preserved
all over the animal kingdom. Also it ignores lateral transfer via viruses.

> If you're proposing extensive molecular convergence, that's
> exceedingly unlikely to happen, and cases even within a single locus are
> nearly unknown.

Are you knocking down that strawman in that last clause?

Since you are so big on molecular methods, I think it's about time
you provided some reference for these confident comments of yours.
You're no geneticist, so you can't claim even as much expertise as
with the earlier claim that only crown group birds survived the K-P disaster.

> >>> Why switch to molecular studies? You cannot reasonably evaluate convergence
> >>> vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?
> >
> >> We are discussing whether paleognaths are a monophyletic sister group to
> >> neognaths or are a polyphyletic assemblage united by convergence only.
> >> That's not a question of character evolution but of tree shape.
> >
> > Aren't you confusing cause and effect? Whether two characters are
> > considered to be "the same" or only convergent is an integral part
> > of setting up the matrix, which in turn determines the tree, no?

On 11/4/22 6:06 PM, Peter Nyikos wrote:
> On Tuesday, November 1, 2022 at 9:00:11 PM UTC-4, John Harshman wrote:
>> On 11/1/22 12:34 PM, Peter Nyikos wrote:
>>> On Thursday, October 27, 2022 at 9:21:21 AM UTC-4, John Harshman wrote:
>>>> On 10/27/22 5:55 AM, Peter Nyikos wrote:
>>>>> On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
>>>>>> On 10/26/22 12:57 PM, Peter Nyikos wrote:
>>>>>>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
>>>>>>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
>>>>>
>>>>>>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
>>>>>>>>>>>>>
>>>>>>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
>>>>>>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
>>>>>>>>>>>
>>>>>>>>>>>> Makes no sense to me either.
>>>>>>>>>>>
>>>>>>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
>>>>>>>>>>> misconception. Because the first split seems to be between Galloanserae and
>>>>>>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
>>>>>>>>>
>>>>>>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
>>>>>>>>>
>>>>>>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
>>>>>>>>> But there is plenty of room for convergence when splits go that far back in time,
>>>>>>>>> and plenty of loss of information when we do not have molecular information
>>>>>>>>> for lithornithids.
>>>>>>>
>>>>>>>> It's based on both molecular and morphological evidence,
>>>>>>>
>>>>>>> Combined? or separate? Could you provide a reference where only the morphological is used?
>>>>>
>>>>>> Separately, as a rule. Here's one:
>>>>>> https://repository.si.edu/handle/10088/21644
>>>>>
>>>>> Thanks, I'll look into it on the weekend.
>>>
>>> I got a huge surprise: the authors' research supported the claim
>>> that lithornids are outside the crown group! This would not only
>>> give you an eighth group of birds that survived the K-P disaster,
>>> but it would upend the generally accepted belief that only Neornithine
>>> birds survived it.
>
>> I had forgotten that.
>
> Is't possible that the belief is NOT generally accepted after all,
> and you just hadn't kept up with the discussion on which birds survived
> the disaster since the paper was disseminated in 2007?

Sorry, you've lost me. What is this belief you wonder about?

>>>>>>>> and your complaints about molecular phylogenetics are not well-informed.
>>>>>>>
>>>>>>> You are trying to read my mind as to how well informed I am. I am not
>>>>>>> giving all my information by any means.
>>>>>
>>>>>> Can we agree that I am likely to be better informed on this subject than
>>>>>> you are? After all, I've published on this very subject:
>>>>>>
>>>>>> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
>>>>>> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
>>>>>> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
>>>>>> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
>>>>>> flight in ratite birds. Proceedings of the National Academy of Sciences
>>>>>> 2008; 105:13462-12467.
>>>>>
>>>>> Research and scholarship are utterly different talents. Isn't that obvious to you?
>>>
>>>> It isn't. I think they're both necessary components of any scientific
>>>> paper.
>>>
>>> You were comparing yourself to me, so talk about papers misses the point.
>>>
>>> Isaak Asimov was the scientific scholar *par excellence*; IMHO his prodigious
>>> output of expository papers [later anthologized] ranging over all the sciences
>>> was more impressive than the science fiction for which he is better known.
>>>
>>> On the other hand, his research record was below par even for a place
>>> like Boston University School of Medicine:
>>>
>>> "In December 1957, Asimov was dismissed from his teaching post, with effect from June 30, 1958, because he had stopped doing research. After a struggle which lasted for two years, he kept his title,[57] he gave the opening lecture each year for a biochemistry class,[58] and on October 18, 1979, the university honored his writing by promoting him to full professor of biochemistry.[59]"
>>>
>>> In contrast, although Stephen Jay Gould was also an excellent scholar and expositor,
>>> he wrote on less diverse areas of science, but he also had some major research accomplishments.
>>>
>>>
>>>> And I think that paper is very good evidence that paleognaths are
>>>> monophyletic.
>>>
>>> I forget--does it make tinamous basal?
>
>> It does not. And in fact that's the main topic of the paper.
>
> That leaves the question wide open as to what the LCA of ratites
> (and tinamous, just to be on the safe side) was like. If it wasn't like *Lithornis*,
> in what characters did it differ?

I don't believe it does, unless you think it's as easy to gain flight as
to lose it. And it seems that the central question here is whether that
ancestor could fly. This is all in the paper, incidentally, which it
might profit you to read.

>>>>>>>> I assure you that this particular split is exceedingly well supported and can't
>>>>>>>> be accounted for by convergence.
>>>>>>>
>>>>>>> That last clause needs support. For one thing, it depends on what kind of neognaths
>>>>>>> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
>>>>>>> non-volant large neognath to balance against each large ratite, and a small
>>>>>>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
>>>>>>> volant neognaths need to be as weak fliers as tinamous used.
>>>>>
>>>>>> Why is "non-volant" relevant to molecular data? Why is size relevant to
>>>>>> molecular data?
>>>
>>> I let this slide at first, but your skepticism here is highly counter-intuitive.
>>> Being active flyers promotes many alleles at the expense of others no matter
>>> how near or far two groups of birds are from each other phylogenetically.
>>> The same is true of size: remember Haldane's classic, "On Being the Right Size"?
>
>> I'm afraid that shows a naive view of the nature of the data. Relatively
>> few loci have anything to do with flight or size, and in those loci
>> relatively few sites in the exons, and none in the introns.
>
> I'm not sure you got my point about flight or size. Are you including the
> inevitable strengthening and thickening of legs as a result of loss of flight, well attested to
> in just about every example of flight loss? In the other direction, are you
> keeping in mind changes in musculature and nervous system needed for
> coordinated flight? or the loss of bone mass to a bare minimum?

Yes. I don't think you realize how small a percentage of the genome
you're talking about there.

> Also, there is the inevitable thickening of legs as a result of greater size,
> and the loss of abilities that smaller animals have; for instance, elephants
> can't jump worth a damn. No jumping ability, no need to have finely tuned
> balance on landing after a jump.

Now that's grasping at straws. It takes finely tuned balance to be a
cursorial biped, which most of the big ratites are. I'll admit it takes
less fine tuning to manage a slow walk, but of living ratites only kiwis
are like that.

On Tuesday, November 1, 2022 at 9:00:11 PM UTC-4, John Harshman wrote:
> On 11/1/22 12:34 PM, Peter Nyikos wrote:
> > On Thursday, October 27, 2022 at 9:21:21 AM UTC-4, John Harshman wrote:

Picking up where I left off last week, we begin with:

> >> And analysis of living taxa only is not useless, though fossils can
> >> certainly help. Still, if the claim is that the paleognathous palate is
> >> convergently derived as a consequence of flightlessness,
> >
> > Who would make such a claim, with tinamous in the background?
> > Only someone ignorant of them, it seems from what you say next:

> But isn't that the claim you were referencing?

Of course not! Where did you get such a wild idea?

> >>> it's difficult to explain why tinamous have it, even without consideration of Lithornis.
> >
> > The only claim I made was that some researchers believe the paleognathous
> > palate of extant birds to be the result of neoteny, to which flightlessnes is
> > of questionable relevance.

Note that last clause: it spoke directly to your "...as a consequence of flightlessness."

I don't know whether a reversion to an ancestral condition qualifies as
"convergence", but it may depend on how finely you code the condition.

The neoteny hypothesis has it that there is an early developmental palaeognathal state
which all immature neognaths go through, and neoteny causing some immature
neognaths to keep a palaeognathal character there, but growing and changing into an
adult paleognathal structure.

However, convergence, if that's the right word, might be partial: the adult stage of the neoteny-derived
birds might differ from the plesimorphic adult stage in some small respects, while still
being coded as "palaeognath".

> No also made (or perhaps merely repeated) the claim that paleognaths
> were independently derived from separate groups of neognaths.

Wrong again! Where did you get the wild idea that I was referring to separate groups
undergoing neoteny independently?

> >>>>> As for lithornis used, a fossil neognath that is used needs to have approximately
> >>>>> the same number of characters preserved.
> >>>>>
> >>>>> And it's cheating to list penguins as non-volant: they "fly" thru the water with
> >>>>> their wings as almost their only source of propulsion.
> >>>
> >>>> It seems a pointless exercise regardless of whether penguins are excluded.
> >>>
> >>> Unless it is done, we will never know whether one or more neognaths
> >>> would be transferred to the palaeognath clade by it, with convergence
> >>> overruling synapomorphy in those cases.

This is what might have confused you: I didn't claim that any such thing
would happen, only that we need to test the hypothesis that no such
overruling could take place no matter how the taxa in the analysis are chosen.

Choosing a good taxon for rooting the tree is important, by the way. I'd go all the way
back to Deinonychus, which someone once used to root the whole tree of Avialae, IIRC.
Much too close for Avialae IMO, but just right for Neornithes, I suggest.

> > Or vice versa, a paleognath being transferred to the neognath clade.

> How would what you suggest be relevant to such an analysis.

I'm not sure what "such an analysis" is supposed to refer to.

If you are referring to matching birds as close to each other in morphology as is feasible,
paleognath to neognath, it's because this is where we ordinarily think of the word "convergence".

Think of a cladogram with "convergent" marsupials included with their
placental counterparts: golden mole included along with marsupial mole,
marsupial "mice" along with shrews, bandicoots with elephant shrews,
"flying" phalangers" with "flying" squirrels and also with scale-tailed "flying" "squirrels,"
thylacine with wolf, etc. The matrix shouldn't give away what's matched with what,
but they are all there in one hotchpot.

For instance, might the huge morphological difference between the marsupial mole
and the other marsupials in the analysis be enough to pull it towards the golden mole
in the phylogenetic tree? maybe even to where a clade where the golden mole
sits is the marsupial mole's sister taxon?

> > The talk in your reply shifted to molecular analyses, so I'd like to postpone
> > replying to that part until Friday.

This got postponed, but we have talked some about molecular
analyses despite that, and I'll look to see this week whether the rest of
what you wrote has been indirectly dealt with, or not.

Peter Nyikos
Professor, Dept. of Mathematics
University. of So. Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos

Sorry to be gone from this thread for so long, John.
I decided to go way back to almost a month ago, because there were
some loose ends hanging, and (ironically!) they have to do
with a thread where they are very much timely, on which lineages of birds
and mammals survived the great K-P extinction.

On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
> On 10/26/22 12:57 PM, Peter Nyikos wrote:
> > On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
> >> On 10/21/22 1:36 PM, Peter Nyikos wrote:
> >>> On Friday, October 21, 2022 at 3:24:55 PM UTC-4, John Harshman wrote:
> >>>>> On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:

> >>>>>> As far as I know, the stem group did not survive the K/T impact, if you
> >>>>>> refer to the stem group of Aves/Neornithes.

As we saw, that could depend on whether lithornids were part of Neornithes,
or their sister group. I say "could" because AFAIK there are no known Cretaceous
lithornid fossils.

> >>>>>>The stem group of
> >>>>>> Galloanserae apparently did survive, as did apparent stem group members
> >>>>>> of Anseriformes.

Besides *Vegavis*, whose Galloanser status is debated, do you have
any others? ISTM you need two Cretaceous fossil birds to make
good on this matter; correct?

> >>>>>
> >>>>> So at least two bird lineages survived the K/P extinction? That makes the
> >>>>> bottleneck for birds look a little less vulnerable. It was getting to look like
> >>>>> birds could easily have suffered the fate of the pterosaurs -- complete extinction.
> >>>
> >>>> At least 7, actually, implied by the existence of Cretaceous
> >>>> presbyornithids. And that's a minimum.
> >>>
> >>> Known from actual fossils? Teviornis has considerable doubt cast on its being
> >>> a presbyornithid, what with the fragmentary evidence, and it did not
> >>> survive the K/P disaster. https://en.wikipedia.org/wiki/Teviornis
> >>
> >>> Zhylgaia's remains are even more tenuous, and the "or" in the following
> >>> sentence is striking:
> >>>
> >>> "Its remains have been recovered from a Late Cretaceous or Paleogene deposit in Central Asia."
> >>> https://en.wikipedia.org/wiki/Zhylgaia
> >>>
> >>> Presbyornis, Bumbalavis, and Wilaru are known only from the Cenozoic.
> >>>
> >>> That exhausts the list of presbyornithids about which useful information
> >>> can be found in the following page and its links:
> >>>
> >>> https://en.wikipedia.org/wiki/Presbyornithidae
> >>>
> >>> There are other genera in red, meaning there is no wiki page for them.
> >>> Perhaps one of them is the one you have in mind.
> >
> >> I refer to fragmentary fossils found in New Jersey, which I don't recall
> >> having been given a name. Vegavis is anothere possibility, though like
> >> the other fossils you mention its identification as a presbyornithid has
> >> been questioned.

Somewhat further down [snipped at end] you said presbyornithids
were crown anseriforms, so that would disqualify them from
either of the two you mentioned up there (stem groups
of Galloanserae and of Anseriformes).
> > Yes, for example:
> > Mayr, G., 2013. Perspective: The age of the crown group of passerine birds and its
> > evolutionary significance -- molecular calibrations versus the fossil record.
> > Systematics and Biodiversity 11 (1), 7--13.
> >
> >
> >> However, time-calibrated phylogenetic analyses using various fossil taxa
> >> give similar results, with 7 or more bird lineages crossing the K/T
> >> boundary.
> >
> > With one possibility in doubt, what have you to replace it?

Did you come across something along the following lines in the
intervening month?

> You would have to consult the various analyses. Generally they use
> Cenozoic fossils to calibrate a molecular tree.

That seems to cast doubt on the accuracy of the calibrations for
the upper Cretaceous.

I will continue my reply to this post in the ongoing thread,

Re: Which Mammals and Birds Survived the Great K-T Extinction, and Why?

Not only is the title more appropriate, but we seem to get down to
brass tacks further down in the post.

Hope to see you there [and here, for that matter].

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of So. Carolina at Columbia
http://people.math.sc.edu/nyikos

On 11/25/22 6:29 PM, Peter Nyikos wrote:
> Sorry to be gone from this thread for so long, John.
> I decided to go way back to almost a month ago, because there were
> some loose ends hanging, and (ironically!) they have to do
> with a thread where they are very much timely, on which lineages of birds
> and mammals survived the great K-P extinction.
>
> On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
>> On 10/26/22 12:57 PM, Peter Nyikos wrote:
>>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
>>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
>>>>> On Friday, October 21, 2022 at 3:24:55 PM UTC-4, John Harshman wrote:
>>>>>>> On Friday, October 14, 2022 at 9:34:10 PM UTC-4, John Harshman wrote:
>
>>>>>>>> As far as I know, the stem group did not survive the K/T impact, if you
>>>>>>>> refer to the stem group of Aves/Neornithes.
>
> As we saw, that could depend on whether lithornids were part of Neornithes,
> or their sister group. I say "could" because AFAIK there are no known Cretaceous
> lithornid fossils.

The proper term here is "lithornithid". What analysis was that again
that found them to be stem-neornithes?

>>>>>>>> The stem group of
>>>>>>>> Galloanserae apparently did survive, as did apparent stem group members
>>>>>>>> of Anseriformes.
>
> Besides *Vegavis*, whose Galloanser status is debated, do you have
> any others? ISTM you need two Cretaceous fossil birds to make
> good on this matter; correct?

I'm not sure Vegavis is debated in that way. But no, only one Cretaceous
fossil is needed, as long as it's the right one.

>>>>>>>
>>>>>>> So at least two bird lineages survived the K/P extinction? That makes the
>>>>>>> bottleneck for birds look a little less vulnerable. It was getting to look like
>>>>>>> birds could easily have suffered the fate of the pterosaurs -- complete extinction.
>>>>>
>>>>>> At least 7, actually, implied by the existence of Cretaceous
>>>>>> presbyornithids. And that's a minimum.
>>>>>
>>>>> Known from actual fossils? Teviornis has considerable doubt cast on its being
>>>>> a presbyornithid, what with the fragmentary evidence, and it did not
>>>>> survive the K/P disaster. https://en.wikipedia.org/wiki/Teviornis
>>>>
>>>>> Zhylgaia's remains are even more tenuous, and the "or" in the following
>>>>> sentence is striking:
>>>>>
>>>>> "Its remains have been recovered from a Late Cretaceous or Paleogene deposit in Central Asia."
>>>>> https://en.wikipedia.org/wiki/Zhylgaia
>>>>>
>>>>> Presbyornis, Bumbalavis, and Wilaru are known only from the Cenozoic.
>>>>>
>>>>> That exhausts the list of presbyornithids about which useful information
>>>>> can be found in the following page and its links:
>>>>>
>>>>> https://en.wikipedia.org/wiki/Presbyornithidae
>>>>>
>>>>> There are other genera in red, meaning there is no wiki page for them.
>>>>> Perhaps one of them is the one you have in mind.
>>>
>>>> I refer to fragmentary fossils found in New Jersey, which I don't recall
>>>> having been given a name. Vegavis is anothere possibility, though like
>>>> the other fossils you mention its identification as a presbyornithid has
>>>> been questioned.
>
> Somewhat further down [snipped at end] you said presbyornithids
> were crown anseriforms, so that would disqualify them from
> either of the two you mentioned up there (stem groups
> of Galloanserae and of Anseriformes).

That's right. The stem members are not presbyornithids.

>>> Yes, for example:
>>> Mayr, G., 2013. Perspective: The age of the crown group of passerine birds and its
>>> evolutionary significance -- molecular calibrations versus the fossil record.
>>> Systematics and Biodiversity 11 (1), 7--13.
>>>
>>>
>>>> However, time-calibrated phylogenetic analyses using various fossil taxa
>>>> give similar results, with 7 or more bird lineages crossing the K/T
>>>> boundary.
>>>
>>> With one possibility in doubt, what have you to replace it?
>
> Did you come across something along the following lines in the
> intervening month?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785986/

>> You would have to consult the various analyses. Generally they use
>> Cenozoic fossils to calibrate a molecular tree.
>
> That seems to cast doubt on the accuracy of the calibrations for
> the upper Cretaceous.

Why?

> I will continue my reply to this post in the ongoing thread,
>
> Re: Which Mammals and Birds Survived the Great K-T Extinction, and Why?
>
> Not only is the title more appropriate, but we seem to get down to
> brass tacks further down in the post.
>
> Hope to see you there [and here, for that matter].
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> Univ. of So. Carolina at Columbia
> http://people.math.sc.edu/nyikos