This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url: https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
are judged to be a clade due to the molecular evidence. But it is also "very new news"
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Yet, man is closer kin to skinny wings than to naked mole rats.
Primates + Dermoptera = Primatomorpha: https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five, the only difference is that the morphological tree puts Dermoptera as sister
to Scandentia rather than to Primates.

Nor so the molecular tree in the 2022 article. Its "very new news" is that Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.


There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.


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

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url: https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
are judged to be a clade due to the molecular evidence. But it is also "very new news"
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch. These are expected
to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.
Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five,
the only difference is that the morphological tree puts Dermoptera as sister to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An interesting question, but not a big thing.

Nor so the molecular tree in the 2022 article. Its "very new news" is that Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of
all sorts. It bears further investigation.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals


But the meat is in the supplemental information, if you want to get that
far. And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution
and KPg extinction on mammal diversification. Science 334, 521 (2011).

Haven't looked for it so far.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Yes, though it's not the amateur biologists but the science journalists
and university flacks that are the main representatives of that viewpoint.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 8/15/22 8:33 PM, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked
about below,
but they differ completely in who the closest relatives of primates
are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures
that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews
(Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very
old news" where these 5 orders
are judged to be a clade due to the molecular evidence. But it is also
"very new news"
about the placement of the orders within the clade. It is strongly at
odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch. These are expected
to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.
Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as
its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud
and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on
these five,
the only difference is that the morphological tree puts Dermoptera as
sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An interesting question, but not a big thing.

Nor so the molecular tree in the 2022 article. Its "very new news" is
that
Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of
all sorts. It bears further investigation.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

But the meat is in the supplemental information, if you want to get that
far. And even more, this seems to be the source of most of the molecular data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution
and KPg extinction on mammal diversification. Science 334, 521 (2011).

Haven't looked for it so far.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Yes, though it's not the amateur biologists but the science journalists
and university flacks that are the main representatives of that viewpoint.

So what is the general viewpoint on the KT boundary concerning
mammals and birds?

1. Only a small number of species or orders of both mammals and
birds survived the KT event. Perhaps one species of placental,
one species of marsupial, and one of monotreme, and all mammalian diversification happened afterward?

2. Vast numbers of orders of both mammals and birds predate the
KT event. Many species of both survived generally because they
were small.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 8/15/22 10:24 PM, Trolidan7 wrote:

On 8/15/22 8:33 PM, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked
about below,
but they differ completely in who the closest relatives of primates
are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures
that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews
(Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very
old news" where these 5 orders
are judged to be a clade due to the molecular evidence. But it is
also "very new news"
about the placement of the orders within the clade. It is strongly at
odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch. These are
expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.
Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires
as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that
Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on
these five,
the only difference is that the morphological tree puts Dermoptera as
sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An
interesting question, but not a big thing.

Nor so the molecular tree in the 2022 article. Its "very new news" is
that
Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses
of all sorts. It bears further investigation.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg
radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals



But the meat is in the supplemental information, if you want to get
that far. And even more, this seems to be the source of most of the
molecular data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial
Revolution and KPg extinction on mammal diversification. Science 334,
521 (2011).

Haven't looked for it so far.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Yes, though it's not the amateur biologists but the science
journalists and university flacks that are the main representatives of
that viewpoint.

So what is the general viewpoint on the KT boundary concerning
mammals and birds?

1. Only a small number of species or orders of both mammals and
birds survived the KT event.  Perhaps one species of placental,
one species of marsupial, and one of monotreme, and all mammalian diversification happened afterward?

2. Vast numbers of orders of both mammals and birds predate the
KT event.  Many species of both survived generally because they
were small.

Somewhere in between, and the evidence to work with isn't that great.
O'Leary et al. (cited above) conclude that placentals (the crown group)
can't be shown to pre-date the K/T boundary. Dated molecular trees
appear to show that at least 7 crown group birds passed the boundary,
but it could easily have been more. But the major radiations seem to
have been after the boundary. Presumably the survivors were those able
to hide under something non-flammable for an hour or so after the
impact. Being small and/or aquatic seems to have helped.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On Tuesday, August 16, 2022 at 1:24:12 AM UTC-4, Trolidan7 wrote:

On 8/15/22 8:33 PM, John Harshman wrote:

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

<snip for focus>

So what is the general viewpoint on the KT boundary concerning
mammals and birds?

1. Only a small number of species or orders of both mammals and
birds survived the KT event.

Yes, and it was devastating to sea life as well. Ammonites and many
other animals went extinct. The chalk cliffs of Dover
and other huge deposits of chalk are from the Cretaceous
[named after Crete, whose Greek name came to be attached to chalk],
and the organisms that made them may all have gone extinct.

Perhaps one species of placental,
one species of marsupial, and one of monotreme, and all mammalian diversification happened afterward?

Not sure about the others, but the article by O'Leary et.al. makes a case
for a single species of Placentalia. The case has been criticized, but it seems to be holding up well after nearly a decade has passed.

HOWEVER, do not confuse Placentalia with the bigger group Eutheria.
A good number in the bigger group survived the K-T disaster and became the extinct orders Pantodonta, Tillodonta, and Taeniodonta.

Also, if it is true that the extinct large South American metatherian carnivores,
such as the saber-toothed Thylacosmilus, are not in Marsupilia, then
we've got a similar case for marsupials.

These distinctions hinge on the difference between a crown group
and a total (crown + stem) group. A crown group is all descendants
of the last common ancestor of extant (living) representatives.
The stem "group" is all extinct animals that are closer to the
crown group than they are to all other crown groups.
The crown eutherians are the members of Placentalia;
the stem eutherians are all the others, including the survivors I mentioned above.
Similarly, Marsupilia is the crown group of the total group Metatheria.

Then, too, there were non-therian, non-monotreme mammals that survived for a while
before going extinct. The best known such group is Multituberculata.

2. Vast numbers of orders of both mammals and birds predate the
KT event. Many species of both survived generally because they
were small.

Correct; one rule of thumb is that no animal over 50 kilos survived.

The iconic giant turtle of the Cretaceous, Archelon, was way over 50 kg, and no turtle
known since then has been that large.


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

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url: https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

Towards the end, where I actually give the data on the 2022 molecular tree,
it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five,
the only difference is that the morphological tree puts Dermoptera as sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An interesting question, but not a big thing.

The big thing is that the 2022 morphological resolution is much closer to the 2017 molecular than the latter is to the 2022 molecular. Isn't morphological supposed to be so much less reliable than molecular that the latter always takes precedence
when available?

Also, I wonder where the 2022 morphological tree comes from. For many decades, Scandentia was believed to be closer to Primates than either is to Dermoptera. In fact, in _Evolution of the Vertebrates_ (1955), E.H. Colbert put them in Primates,
and even in the suborder Lemuroidea.

[Not] so the molecular tree in the 2022 article. Its "very new news" is that
Primates is all by its lonesome while the other four orders are in a separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of
all sorts. It bears further investigation.

So I guess you misread what I wrote earlier.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

Mills, the author of the popularization, is one of the co-authors.

It's a fascinating comparison of molecular and morphological
trees in the light of biogeography. I'll have to read it carefully
when I have more time.

One has to pay special heed to which representatives of the
various orders are used, especially since Primates has had
worldwide (save maybe Antarctica) distribution, but not everywhere
at once until the 19th century. So first I will read the supplements to the following
article carefully:

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

Hey, I remember this one! We discussed it in detail when it first came out in 2013.

Thanks for taking the time to find it!

But the meat is in the supplemental information, if you want to get that far.

I have to, for reasons given above, if I want to see how reliable the conclusions
of the Mills et. al. paper are.

And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution
and KPg extinction on mammal diversification. Science 334, 521 (2011).

Haven't looked for it so far.

You've done very well on such short notice. I may not have time
to look at it this week.

There is a kind of amateur biologist who always treats the latest molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Thanks for finding it. Published in May, so it wasn't a sneak preview after all.

Yes, though it's not the amateur biologists but the science journalists
and university flacks that are the main representatives of that viewpoint.

Good point.


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

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best
guide is probably the recorded Bremer and bootstrap support for the
relevant nodes, which tend to be correlated with branch length.

Towards the end, where I actually give the data on the 2022 molecular tree, it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it
seems more human-based propaganda. Not only are we wise, we're also the aristocrats of the animal kingdom.

Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five,
the only difference is that the morphological tree puts Dermoptera as sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An
interesting question, but not a big thing.

The big thing is that the 2022 morphological resolution is much closer to the 2017 molecular than the latter is to the 2022 molecular. Isn't morphological supposed to be so much less reliable than molecular that the latter always takes precedence
when available?

No. Depends on the quality of the data. Of course quantity has a quality
all its own too.

Also, I wonder where the 2022 morphological tree comes from. For many decades,
Scandentia was believed to be closer to Primates than either is to Dermoptera.
In fact, in _Evolution of the Vertebrates_ (1955), E.H. Colbert put them in Primates,
and even in the suborder Lemuroidea.

Also from O'Leary.

[Not] so the molecular tree in the 2022 article. Its "very new news" is that
Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of
all sorts. It bears further investigation.

So I guess you misread what I wrote earlier.

Apparently. I thought we were talking about the relationships among
Primates, Scandentia, and Dermoptera. Adding Glires of course makes it a tetratomy.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

Mills, the author of the popularization, is one of the co-authors.

It's a fascinating comparison of molecular and morphological
trees in the light of biogeography. I'll have to read it carefully
when I have more time.

One has to pay special heed to which representatives of the
various orders are used, especially since Primates has had
worldwide (save maybe Antarctica) distribution, but not everywhere
at once until the 19th century. So first I will read the supplements to the following
article carefully:

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg
radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

Hey, I remember this one! We discussed it in detail when it first came out in 2013.

Thanks for taking the time to find it!

But the meat is in the supplemental information, if you want to get that far.

I have to, for reasons given above, if I want to see how reliable the conclusions
of the Mills et. al. paper are.

And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution
and KPg extinction on mammal diversification. Science 334, 521 (2011).

Haven't looked for it so far.

You've done very well on such short notice. I may not have time
to look at it this week.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Thanks for finding it. Published in May, so it wasn't a sneak preview after all.

Yes, though it's not the amateur biologists but the science journalists
and university flacks that are the main representatives of that viewpoint.

Good point.

I would suggest looking for other publications on mammal phylogeny,
hopefully with better information on the nature of the data than O'Leary
et al. Some of that may be the fault of the restrictions of publishing
in Science, but there are other potential ideological problems.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 8/16/22 8:51 AM, John Harshman wrote:

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies
talked about below,
but they differ completely in who the closest relatives of primates
are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures
that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews
(Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's
"very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly
at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short
branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best
guide is probably the recorded Bremer and bootstrap support for the
relevant nodes, which tend to be correlated with branch length.

Towards the end, where I actually give the data on the 2022 molecular
tree,
it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still
curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu"
means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it
seems more human-based propaganda. Not only are we wise, we're also the aristocrats of the animal kingdom.

(good) (rule) (existence)

https://en.wiktionary.org/wiki/%CE%B5%E1%BD%90-#Ancient_Greek

https://en.wiktionary.org/wiki/eudemonia

https://en.wiktionary.org/wiki/%E1%BC%84%CF%81%CF%87%CF%89

https://en.wiktionary.org/wiki/archon

https://en.wiktionary.org/wiki/%E1%BD%A4%CE%BD

https://en.wiktionary.org/wiki/ontology

Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires
as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that
Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on
these five,
the only difference is that the morphological tree puts Dermoptera
as sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An
interesting question, but not a big thing.

The big thing is that the 2022 morphological resolution is much closer
to the
2017 molecular than the latter is to the 2022 molecular.  Isn't
morphological
supposed to be so much less reliable than molecular that the latter
always takes precedence
when available?

No. Depends on the quality of the data. Of course quantity has a quality
all its own too.

Also, I wonder where the 2022 morphological tree comes from.  For many
decades,
Scandentia was believed to be closer to Primates than either is to
Dermoptera.
In fact, in _Evolution of the Vertebrates_ (1955), E.H. Colbert put
them in Primates,
and even in the suborder Lemuroidea.

Also from O'Leary.

[Not] so the molecular tree in the 2022 article. Its "very new news"
is that
Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of
all sorts. It bears further investigation.

So I guess you misread what I wrote earlier.

Apparently. I thought we were talking about the relationships among
Primates, Scandentia, and Dermoptera. Adding Glires of course makes it a tetratomy.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

Mills, the author of the popularization, is one of the co-authors.

It's a fascinating comparison of molecular and morphological
trees in the light of biogeography. I'll have to read it carefully
when I have more time.

One has to pay special heed to which representatives of the
various orders are used, especially since Primates has had
worldwide (save maybe Antarctica) distribution, but not everywhere
at once until the 19th century. So first I will read the supplements
to the following
article carefully:

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg >>> radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

Hey, I remember this one! We discussed it in detail when it first came
out in 2013.

Thanks for taking the time to find it!

But the meat is in the supplemental information, if you want to get
that far.

I have to, for reasons given above, if I want to see how reliable the
conclusions
of the Mills et. al. paper are.

And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution >>> and KPg extinction on mammal diversification. Science 334, 521 (2011).

Haven't looked for it so far.

You've done very well on such short notice. I may not have time
to look at it this week.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Thanks for finding it. Published in May, so it wasn't a sneak preview
after all.

Yes, though it's not the amateur biologists but the science journalists
and university flacks that are the main representatives of that
viewpoint.

Good point.

I would suggest looking for other publications on mammal phylogeny,
hopefully with better information on the nature of the data than O'Leary
et al. Some of that may be the fault of the restrictions of publishing
in Science, but there are other potential ideological problems.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On Tuesday, August 16, 2022 at 11:51:21 AM UTC-4, John Harshman wrote:

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best guide is probably the recorded Bremer and bootstrap support for the
relevant nodes, which tend to be correlated with branch length.

Is that somewhere in the supplemental info?

Towards the end, where I actually give the data on the 2022 molecular tree,
it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it
seems more human-based propaganda. Not only are we wise, we're also the aristocrats of the animal kingdom.

Whereas a case could be made for Rodentia to be the most successful.
We can't "rule them all" as "Archonta" suggests.

Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five,
the only difference is that the morphological tree puts Dermoptera as sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An
interesting question, but not a big thing.

The big thing is that the 2022 morphological resolution is much closer to the
2017 molecular than the latter is to the 2022 molecular. Isn't morphological
supposed to be so much less reliable than molecular that the latter always takes precedence
when available?

No. Depends on the quality of the data. Of course quantity has a quality
all its own too.

Good to know.

Also, I wonder where the 2022 morphological tree comes from. For many decades,
Scandentia was believed to be closer to Primates than either is to Dermoptera.
In fact, in _Evolution of the Vertebrates_ (1955), E.H. Colbert put them in Primates,
and even in the suborder Lemuroidea.

Also from O'Leary.

What do you mean? the main tree not only puts Scandentia outside Primates,
it also teams it up with Dermoptera as the sister clade of Primates.

The phenomic data-only tree (fig. S2A) supports the clade Sundatheria [Scandentia (treeshrews) + Dermoptera (flying lemurs)] as the sister taxon of Primates,
a topology that prevails in the combined analysis, in contrast to molecules-only trees t
that favored Dermoptera in this role (7, 22), https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

[Not] so the molecular tree in the 2022 article. Its "very new news" is that
Primates is all by its lonesome while the other four orders are in a
separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of >> all sorts. It bears further investigation.

So I guess you misread what I wrote earlier.

Apparently. I thought we were talking about the relationships among Primates, Scandentia, and Dermoptera. Adding Glires of course makes it a tetratomy.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

Mills, the author of the popularization, is one of the co-authors.

It's a fascinating comparison of molecular and morphological
trees in the light of biogeography. I'll have to read it carefully
when I have more time.

One has to pay special heed to which representatives of the
various orders are used, especially since Primates has had
worldwide (save maybe Antarctica) distribution, but not everywhere
at once until the 19th century. So first I will read the supplements to the following
article carefully:

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg >> radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree
is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

Hey, I remember this one! We discussed it in detail when it first came out in 2013.

Thanks for taking the time to find it!

But the meat is in the supplemental information, if you want to get that far.

I have to, for reasons given above, if I want to see how reliable the conclusions
of the Mills et. al. paper are.

And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution >> and KPg extinction on mammal diversification. Science 334, 521 (2011).

Haven't looked for it so far.

You've done very well on such short notice. I may not have time
to look at it this week.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Thanks for finding it. Published in May, so it wasn't a sneak preview after all.

Yes, though it's not the amateur biologists but the science journalists >> and university flacks that are the main representatives of that viewpoint.

Good point.

I would suggest looking for other publications on mammal phylogeny, hopefully with better information on the nature of the data than O'Leary
et al. Some of that may be the fault of the restrictions of publishing
in Science, but there are other potential ideological problems.

I get the impression that the study that Pandora linked is still the gold standard:

https://academic.oup.com/gbe/article/9/9/2308/4095375
[repeated from far above]


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

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On Friday, August 19, 2022 at 3:02:32 PM UTC-7, peter2...@gmail.com wrote:

On Tuesday, August 16, 2022 at 11:51:21 AM UTC-4, John Harshman wrote:

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=

0&referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best guide is probably the recorded Bremer and bootstrap support for the relevant nodes, which tend to be correlated with branch length.

Is that somewhere in the supplemental info?

Towards the end, where I actually give the data on the 2022 molecular tree,
it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it
seems more human-based propaganda. Not only are we wise, we're also the aristocrats of the animal kingdom.

Whereas a case could be made for Rodentia to be the most successful.

Forgive me for interrupting, but I couldn't resist. John's "aristocrats" sound like Darwin's 'civilized' race. Rats and mice are much more civilized than "we" humans, in my opinion and meaning of the word. And "wise"??

We can't "rule them all" as "Archonta" suggests.

Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five,
the only difference is that the morphological tree puts Dermoptera as sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An
interesting question, but not a big thing.

The big thing is that the 2022 morphological resolution is much closer to the
2017 molecular than the latter is to the 2022 molecular. Isn't morphological
supposed to be so much less reliable than molecular that the latter always takes precedence
when available?

No. Depends on the quality of the data. Of course quantity has a quality all its own too.

Good to know.

Also, I wonder where the 2022 morphological tree comes from. For many decades,
Scandentia was believed to be closer to Primates than either is to Dermoptera.
In fact, in _Evolution of the Vertebrates_ (1955), E.H. Colbert put them in Primates,
and even in the suborder Lemuroidea.

Also from O'Leary.

What do you mean? the main tree not only puts Scandentia outside Primates, it also teams it up with Dermoptera as the sister clade of Primates.

The phenomic data-only tree (fig. S2A) supports the clade Sundatheria [Scandentia (treeshrews) + Dermoptera (flying lemurs)] as the sister taxon of Primates,
a topology that prevails in the combined analysis, in contrast to molecules-only trees t
that favored Dermoptera in this role (7, 22), https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

[Not] so the molecular tree in the 2022 article. Its "very new news" is that
Primates is all by its lonesome while the other four orders are in a >>> separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of >> all sorts. It bears further investigation.

So I guess you misread what I wrote earlier.

Apparently. I thought we were talking about the relationships among Primates, Scandentia, and Dermoptera. Adding Glires of course makes it a tetratomy.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

Mills, the author of the popularization, is one of the co-authors.

It's a fascinating comparison of molecular and morphological
trees in the light of biogeography. I'll have to read it carefully
when I have more time.

One has to pay special heed to which representatives of the
various orders are used, especially since Primates has had
worldwide (save maybe Antarctica) distribution, but not everywhere
at once until the 19th century. So first I will read the supplements to the following
article carefully:

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg
radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree >> is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

Hey, I remember this one! We discussed it in detail when it first came out in 2013.

Thanks for taking the time to find it!

But the meat is in the supplemental information, if you want to get that far.

I have to, for reasons given above, if I want to see how reliable the conclusions
of the Mills et. al. paper are.

And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution
and KPg extinction on mammal diversification. Science 334, 521 (2011). >>
Haven't looked for it so far.

You've done very well on such short notice. I may not have time
to look at it this week.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Thanks for finding it. Published in May, so it wasn't a sneak preview after all.

Yes, though it's not the amateur biologists but the science journalists >> and university flacks that are the main representatives of that viewpoint.

Good point.

I would suggest looking for other publications on mammal phylogeny, hopefully with better information on the nature of the data than O'Leary et al. Some of that may be the fault of the restrictions of publishing
in Science, but there are other potential ideological problems.

I get the impression that the study that Pandora linked is still the gold standard:

https://academic.oup.com/gbe/article/9/9/2308/4095375
[repeated from far above]
Peter Nyikos
Professor, Dept. of Mathematics
Univ. of South Carolina -- standard disclaimer-- http://people.math.sc.edu/nyikos

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 8/19/22 3:02 PM, Peter Nyikos wrote:

On Tuesday, August 16, 2022 at 11:51:21 AM UTC-4, John Harshman wrote:

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote:

On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman
<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&csi=0&

referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best
guide is probably the recorded Bremer and bootstrap support for the
relevant nodes, which tend to be correlated with branch length.

Is that somewhere in the supplemental info?

Yes, on the various trees, and specifically the molecular trees.

Towards the end, where I actually give the data on the 2022 molecular tree, >>> it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it
seems more human-based propaganda. Not only are we wise, we're also the
aristocrats of the animal kingdom.

Whereas a case could be made for Rodentia to be the most successful.
We can't "rule them all" as "Archonta" suggests.

Bats: even better case.

Primates + Dermoptera = Primatomorpha:
https://academic.oup.com/gbe/article/9/9/2308/4095375

Also, it shows Primatomorpha + Scandentia = Euarchonta, with Glires as its sister group.

Surprise! the *morphological* tree in the June 2022 articles that Daud and I linked
*also* recognizes Euarchonta as a clade!

In fact, if we ignore all other mammalian orders and focus just on these five,
the only difference is that the morphological tree puts Dermoptera as sister
to Scandentia rather than to Primates.

Again, the resolution of one trichotomy with very short branches. An
interesting question, but not a big thing.

The big thing is that the 2022 morphological resolution is much closer to the
2017 molecular than the latter is to the 2022 molecular. Isn't morphological
supposed to be so much less reliable than molecular that the latter always takes precedence
when available?

No. Depends on the quality of the data. Of course quantity has a quality
all its own too.

Good to know.

Also, I wonder where the 2022 morphological tree comes from. For many decades,
Scandentia was believed to be closer to Primates than either is to Dermoptera.
In fact, in _Evolution of the Vertebrates_ (1955), E.H. Colbert put them in Primates,
and even in the suborder Lemuroidea.

Also from O'Leary.

What do you mean? the main tree not only puts Scandentia outside Primates,
it also teams it up with Dermoptera as the sister clade of Primates.

I mean that the answer to your question about where the 2022
morphological tree comes from is that it's from O'Leary et al. It may be
only in the supplemental data, though.

The phenomic data-only tree (fig. S2A) supports the clade Sundatheria [Scandentia (treeshrews) + Dermoptera (flying lemurs)] as the sister taxon of Primates,
a topology that prevails in the combined analysis, in contrast to molecules-only trees t
that favored Dermoptera in this role (7, 22), https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

[Not] so the molecular tree in the 2022 article. Its "very new news" is that
Primates is all by its lonesome while the other four orders are in a >>>>> separate clade, where Scandentia and Dermoptera form one subclade
while Glires (of course) forms the other.

Now that's a bit bigger deal that goes against a great many analyses of >>>> all sorts. It bears further investigation.

So I guess you misread what I wrote earlier.

Apparently. I thought we were talking about the relationships among
Primates, Scandentia, and Dermoptera. Adding Glires of course makes it a
tetratomy.

This is the real paper:

https://www.nature.com/articles/s42003-022-03482-x

Mills, the author of the popularization, is one of the co-authors.

It's a fascinating comparison of molecular and morphological
trees in the light of biogeography. I'll have to read it carefully
when I have more time.

One has to pay special heed to which representatives of the
various orders are used, especially since Primates has had
worldwide (save maybe Antarctica) distribution, but not everywhere
at once until the 19th century. So first I will read the supplements to the following
article carefully:

But that's not the data paper. The tree is taken from here:

O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg >>>> radiation of placentals. Science 339, 662–667 (2013).

Sadly, that one is paywalled, and I don't know what the molecular tree >>>> is based on.

But wait, here it is:

https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals

Hey, I remember this one! We discussed it in detail when it first came out in 2013.

Thanks for taking the time to find it!

But the meat is in the supplemental information, if you want to get that far.

I have to, for reasons given above, if I want to see how reliable the conclusions
of the Mills et. al. paper are.

And even more, this seems to be the source of most of the molecular
data:

Meredith R. W., et al., Impacts of the Cretaceous Terrestrial Revolution >>>> and KPg extinction on mammal diversification. Science 334, 521 (2011). >>>>
Haven't looked for it so far.

You've done very well on such short notice. I may not have time
to look at it this week.

There is a kind of amateur biologist who always treats the latest
molecular evidence as though it had definitively overthrown the
earlier ones. But I think that in this case, we need to await the
serious research article of which the June 2022 articles are
a sneak-preview popularization before deciding how correct
the "very new news" is.

Thanks for finding it. Published in May, so it wasn't a sneak preview after all.

Yes, though it's not the amateur biologists but the science journalists >>>> and university flacks that are the main representatives of that viewpoint. >>>

Good point.

I would suggest looking for other publications on mammal phylogeny,
hopefully with better information on the nature of the data than O'Leary
et al. Some of that may be the fault of the restrictions of publishing
in Science, but there are other potential ideological problems.

I get the impression that the study that Pandora linked is still the gold standard:

https://academic.oup.com/gbe/article/9/9/2308/4095375
[repeated from far above]

I'm not sure what a gold standard would be, but that paper has much to recommend it. Lots of data, certainly. But note that the branches in
question (Fig. 1) are very, very short and have some of the lower
bootstrap values on the tree. It's possible that there is a hard
polytomy (by which I mean that there is no fully bifurcating tree in
that region, and that speciation was effectively simultaneous in
multiple lineages). Note that Fig. 2A shows a different resolution with
low support.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On Friday, August 19, 2022 at 7:23:53 PM UTC-4, Glenn wrote:

On Friday, August 19, 2022 at 3:02:32 PM UTC-7, peter2...@gmail.com wrote:

On Tuesday, August 16, 2022 at 11:51:21 AM UTC-4, John Harshman wrote:

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote: >>>> On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman

<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&

csi=0&referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the
resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best guide is probably the recorded Bremer and bootstrap support for the relevant nodes, which tend to be correlated with branch length.

Is that somewhere in the supplemental info?

Towards the end, where I actually give the data on the 2022 molecular tree,
it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological.
In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it seems more human-based propaganda. Not only are we wise, we're also the aristocrats of the animal kingdom.

Whereas a case could be made for Rodentia to be the most successful.

Forgive me for interrupting, but I couldn't resist. John's "aristocrats" sound like Darwin's 'civilized' race. Rats and mice are much more civilized than "we" humans, in my opinion and meaning of the word.

That may depend on your definition of "civilized." Do you think rats and mice are "social animals"
to the extent we are? I don't. Of course, there is the exception of mole rats, which are not only
more social than we, they fit some definitions of "eusocial." So do wolves, by the way.

And "wise"??

Harshman, of course, was referring to Linneaus's designation "Homo sapiens" for us humans without endorsing it.


To end this on a light note, Wikipedia has this to say about that designation:

"Linnaeus's remains constitute the type specimen for the species Homo sapiens following the International Code of Zoological Nomenclature, since the sole specimen that he is known to have examined was himself.[note 2]"
.

Peter Nyikos

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On Friday, August 19, 2022 at 5:41:49 PM UTC-7, peter2...@gmail.com wrote:

On Friday, August 19, 2022 at 7:23:53 PM UTC-4, Glenn wrote:

On Friday, August 19, 2022 at 3:02:32 PM UTC-7, peter2...@gmail.com wrote:

On Tuesday, August 16, 2022 at 11:51:21 AM UTC-4, John Harshman wrote:

On 8/16/22 7:29 AM, Peter Nyikos wrote:

On Monday, August 15, 2022 at 11:33:44 PM UTC-4, John Harshman wrote:

On 8/15/22 6:27 PM, Peter Nyikos wrote:

This is a reply to a post by Pandora on the thread,
Re: Man closer kin to naked mole rats than bats

The thread title is reflected in the two molecular phylogenies talked about below,
but they differ completely in who the closest relatives of primates are, as I will detail.

On Wednesday, June 29, 2022 at 10:02:40 AM UTC-4, Pandora wrote: >>>> On Wed, 29 Jun 2022 06:47:02 -0700, John Harshman

<jhar...@pacbell.net> wrote:

On 6/28/22 5:51 PM, Daud Deden wrote:

https://www-sciencealert-com.cdn.ampproject.org/v/s/www.sciencealert.com/new-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree/amp?amp_gsa=1&amp_js_v=a9&usqp=mq331AQIKAGwASCAAgM%3D#amp_tf=From%20%251%24s&aoh=16564338853839&

csi=0&referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fwww.sciencealert.com%2Fnew-dna-technology-is-shaking-up-the-branches-of-the-evolutionary-tree

The original article on which the above is based has a few pictures that this one does not,
as well as having a less cumbersome url:
https://theconversation.com/evolutionary-tree-of-life-modern-science-is-showing-how-we-got-so-much-wrong-185077

Very old news. Euarchontoglires.

This refers to the following group: primates, tree shrews (Scandentia), "flying lemurs" (Dermoptera),
and Glires [rodents + Lagomorpha (rabbits, hares, pikas)]. It's "very old news" where these 5 orders
about the placement of the orders within the clade. It is strongly at odds with the 2017 article that Pandora links next.

Strongly? I think that overstates the case. The difference is the >> resolution of one trichotomy and a very short branch.

I don't follow you. Which trichotomy? Where do you get the "very short branch" information?

It's hard to get from O'Leary, even in the supplemental info. Your best
guide is probably the recorded Bremer and bootstrap support for the relevant nodes, which tend to be correlated with branch length.

Is that somewhere in the supplemental info?

Towards the end, where I actually give the data on the 2022 molecular tree,
it appears that you misinterpreted my last sentence and thought
I was comparing the 2017 molecular with the the 2022 morphological. In that case, the trichotomy in question is obvious, but I'm still curious about "very short branch."

These are expected to be difficult.

Yet, man is closer kin to skinny wings than to naked mole rats.

"skinny wings" is a literal translation of "Dermoptera,"
once one realizes that "skinny" is a bit of a pun.

By the way, John, how would you parse "Euarchonta"? Of course, "eu" means "true,"
but does "archonta" have any etymological explanation?

"arch" of course means "ruling"; not sure about the "nta". Still, it seems more human-based propaganda. Not only are we wise, we're also the
aristocrats of the animal kingdom.

Whereas a case could be made for Rodentia to be the most successful.

Forgive me for interrupting, but I couldn't resist. John's "aristocrats" sound like Darwin's 'civilized' race. Rats and mice are much more civilized than "we" humans, in my opinion and meaning of the word.

That may depend on your definition of "civilized." Do you think rats and mice are "social animals"
to the extent we are? I don't. Of course, there is the exception of mole rats, which are not only
more social than we, they fit some definitions of "eusocial." So do wolves, by the way.

The subject may be more complex than it appears, but yes, I think rats and mice are much more social than humans. Any lack of organization does not reduce their behavior, nor does auntie needed to care for her families young to be seen as social animals.
But the comparison is focused on human behavior. We are a moments notice away from complete annihilation, and have always been, whether individually, regionally or globally, by our own kind.

And "wise"??

Harshman, of course, was referring to Linneaus's designation "Homo sapiens" for us humans without endorsing it.

To end this on a light note, Wikipedia has this to say about that designation:

"Linnaeus's remains constitute the type specimen for the species Homo sapiens following the International Code of Zoological Nomenclature, since the sole specimen that he is known to have examined was himself.[note 2]"
.

That's funny. He and they could have used any specimen for that. But what does Linnaeus "examining" himself mean?

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)