When I was at an international topology conference in Baku in 1987,
the shore of the Caspian sea was an easy climb down from our dormitory.
One day as I walked on the beach, I spotted what looked like a skeleton
of a human hand. As I approached, it became clear that the proportions were wrong.

I can no longer remember whether I realized then that this was from
a flipper of the Caspian seal, or even whether I had read about this seal
before this discovery. One thing is certain: I became quite interested
in this seal and the question of how it got there.

I already knew enough paleogeography to know that, no earlier than the
Pliocene, enough of the great sea Tethys remained for any sea creature
to swim from the Atlantic, through the portion that became the
Mediterranean, thence to the paleo-Black sea, and thence to where
the Caspian Sea is now. It did not surprise me, for instance, to learn that
there was once a Caspian Sea dolphin, nor that it became extinct before historical times.

But there is another landlocked seal whose origin is still something of a mystery:

"It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
https://en.wikipedia.org/wiki/Baikal_seal

[7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
First published: 27 April 2006

I haven't had time to read the article, but I wish it had been based more than
just on mitochondrial sequences; these are not as accurate as full genome
sequences.

The timing of events is ultimately to be found elsewhere than in phylogeny,
but the abstract, which I will be posting in a follow-up to this OP, makes
it plausible that we can reconstruct events to an accuracy that can
satisfy laymen like myself.

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

The abstract of the article indicates that there is even a bit of a mystery about the Caspian seal:

"The endemic seals of Lake Baikal (Phoca sibirica) and of the Caspian Sea (Phoca caspica) inhabit ancient continental basins that have remained isolated from primary marine seal habitats for millions of years. The species have been united with the Arctic ringed seal, Phoca hispida, into (sub)genus Pusa, but the age and route of invasions to/from the continental basins remain controversial. A phylogenetic analysis of nine northern phocines based on three mitochondrial genes (Cytb, COI, COII, total 3369 bp) provided no support for the monophyly of the Pusa group. The three species are involved in an apparent polytomy with the boreal harbour seal, Phoca vitulina, and grey seal, Halichoerus grypus. From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2–3 Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin. The current phocine diversity more likely results from marine radiations, and the continental seals invaded their basins through Plio-Pleistocene (marine) connections from the north. The palaeohydrography that would have enabled the invasions at that time still remains an enigma. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88, 61–72.

On 8/25/21 3:20 PM, Peter Nyikos wrote:
> When I was at an international topology conference in Baku in 1987,
> the shore of the Caspian sea was an easy climb down from our dormitory.
> One day as I walked on the beach, I spotted what looked like a skeleton
> of a human hand. As I approached, it became clear that the proportions were wrong.
>
> I can no longer remember whether I realized then that this was from
> a flipper of the Caspian seal, or even whether I had read about this seal
> before this discovery. One thing is certain: I became quite interested
> in this seal and the question of how it got there.
>
> I already knew enough paleogeography to know that, no earlier than the
> Pliocene, enough of the great sea Tethys remained for any sea creature
> to swim from the Atlantic, through the portion that became the
> Mediterranean, thence to the paleo-Black sea, and thence to where
> the Caspian Sea is now. It did not surprise me, for instance, to learn that
> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>
> But there is another landlocked seal whose origin is still something of a mystery:
>
> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> https://en.wikipedia.org/wiki/Baikal_seal
>
> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> First published: 27 April 2006
>
> I haven't had time to read the article, but I wish it had been based more than
> just on mitochondrial sequences; these are not as accurate as full genome
> sequences.

You have been misinformed. Mitochrondrial sequences are quite accurate
for many purposes. "Full genome sequences", if by that you actually mean
the complete sequence of an entire genome, are not remotely necessary.

> The timing of events is ultimately to be found elsewhere than in phylogeny,
> but the abstract, which I will be posting in a follow-up to this OP, makes
> it plausible that we can reconstruct events to an accuracy that can
> satisfy laymen like myself.
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos
>

On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> On 8/25/21 3:20 PM, Peter Nyikos wrote:

> > When I was at an international topology conference in Baku in 1987,
> > the shore of the Caspian sea was an easy climb down from our dormitory.
> > One day as I walked on the beach, I spotted what looked like a skeleton
> > of a human hand. As I approached, it became clear that the proportions were wrong.
> >
> > I can no longer remember whether I realized then that this was from
> > a flipper of the Caspian seal, or even whether I had read about this seal
> > before this discovery. One thing is certain: I became quite interested
> > in this seal and the question of how it got there.
> >
> > I already knew enough paleogeography to know that, no earlier than the
> > Pliocene, enough of the great sea Tethys remained for any sea creature
> > to swim from the Atlantic, through the portion that became the
> > Mediterranean, thence to the paleo-Black sea, and thence to where
> > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> >
> > But there is another landlocked seal whose origin is still something of a mystery:
> >
> > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > https://en.wikipedia.org/wiki/Baikal_seal
> >
> > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x

By the way, John, can you access the full article where you are?

> > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > First published: 27 April 2006

> > I haven't had time to read the article, but I wish it had been based more than
> > just on mitochondrial sequences; these are not as accurate as full genome
> > sequences.

> You have been misinformed.

Oh, you think they are equally accurate for phylogenetic purposes as
sequencing the full (nuclear) genome, do you?

> Mitochrondrial sequences are quite accurate for many purposes.

Can you ascertain the purposes of the authors enough to deduce that the
mitochondrial sequences will go as far towards answering the questions of the
authors as sequencing the full genome?

> "Full genome sequences", if by that you actually mean
> the complete sequence of an entire genome, are not remotely necessary.

So much for the Human Genome Project, eh?

Or was that a misnomer? Did they only sequence protein coding genes, meaning
that they are transcribed into mRNA that are translated into proteins without modification?

> > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > but the abstract, which I will be posting in a follow-up to this OP, makes
> > it plausible that we can reconstruct events to an accuracy that can
> > satisfy laymen like myself.
> >
> >
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
at Univ. of South Carolina
http://people.math.sc.edu/nyikos

On 26.8.2021. 0:20, Peter Nyikos wrote:
> When I was at an international topology conference in Baku in 1987,
> the shore of the Caspian sea was an easy climb down from our dormitory.
> One day as I walked on the beach, I spotted what looked like a skeleton
> of a human hand. As I approached, it became clear that the proportions were wrong.
>
> I can no longer remember whether I realized then that this was from
> a flipper of the Caspian seal, or even whether I had read about this seal
> before this discovery. One thing is certain: I became quite interested
> in this seal and the question of how it got there.
>
> I already knew enough paleogeography to know that, no earlier than the
> Pliocene, enough of the great sea Tethys remained for any sea creature
> to swim from the Atlantic, through the portion that became the
> Mediterranean, thence to the paleo-Black sea, and thence to where
> the Caspian Sea is now. It did not surprise me, for instance, to learn that
> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>
> But there is another landlocked seal whose origin is still something of a mystery:
>
> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> https://en.wikipedia.org/wiki/Baikal_seal
>
> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> First published: 27 April 2006
>
> I haven't had time to read the article, but I wish it had been based more than
> just on mitochondrial sequences; these are not as accurate as full genome
> sequences.
>
> The timing of events is ultimately to be found elsewhere than in phylogeny,
> but the abstract, which I will be posting in a follow-up to this OP, makes
> it plausible that we can reconstruct events to an accuracy that can
> satisfy laymen like myself.

I don't understand the "mystery".
Pinnipeds are pagophilic (prefer, or depend on water ice for some or
all activities and functions). Pinnipeds evolved on ice sheets. Lake
Baikal has direct access to Arctic over Yenisey river. Ringed seals are
adaptive, they are small, feed on small fish, no problem for them to
reach Baikal lake in the Ice age.
In the Ice age the proglacial lakes form. One of the biggest was West
Siberian Glacial Lake:
https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake
I believe that on this link you can also see some of those big lakes:
https://external-preview.redd.it/0yPXq1DgWnoOiTEu0dLndipdZPbnZ9Hwwzeu828T15w.jpg?auto=webp&s=d1b89184afbefe035531c759518298841f4dcadf

--
https://groups.google.com/g/human-evolution
human-evolution@googlegroups.com

On 26.8.2021. 4:14, Mario Petrinovic wrote:
> On 26.8.2021. 0:20, Peter Nyikos wrote:
>> When I was at an international topology conference in Baku in 1987,
>> the shore of the Caspian sea was an easy climb down from our dormitory.
>> One day as I walked on the beach, I spotted what looked like a skeleton
>> of a human hand. As I approached, it became clear that the proportions
>> were wrong.
>>
>> I can no longer remember whether I realized then that this was from
>> a flipper of the Caspian seal, or even whether I had read about this seal
>> before this discovery. One thing is certain: I became quite interested
>> in this seal and the question of how it got there.
>>
>> I already knew enough paleogeography to know that, no earlier than the
>> Pliocene, enough of the great sea Tethys remained for any sea creature
>> to swim from the Atlantic, through the portion that became the
>> Mediterranean, thence to the paleo-Black sea, and thence to where
>> the Caspian Sea is now. It did not surprise me, for instance, to learn
>> that
>> there was once a Caspian Sea dolphin, nor that it became extinct
>> before historical times.
>>
>> But there is another landlocked seal whose origin is still something
>> of a mystery:
>>
>> "It is something of a mystery how Baikal seals came to live there in
>> the first place. They may have swum up rivers and streams or possibly
>> Lake Baikal was linked to the ocean at some point through a large body
>> of water, such as the West Siberian Glacial Lake or West Siberian
>> Plain, formed in a previous ice age. The seals are estimated to have
>> inhabited Lake Baikal for some two million years.[7]"
>> https://en.wikipedia.org/wiki/Baikal_seal
>>
>> [7] is here:
>> https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>> The enigma of the landlocked Baikal and Caspian seals addressed
>> through phylogeny of phocine mitochondrial sequences
>> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
>> First published: 27 April 2006
>>
>> I haven't had time to read the article, but I wish it had been based
>> more than
>> just on mitochondrial sequences; these are not as accurate as full genome
>> sequences.
>>
>> The timing of events is ultimately to be found elsewhere than in
>> phylogeny,
>> but the abstract, which I will be posting in a follow-up to this OP,
>> makes
>> it plausible that we can reconstruct events to an accuracy that can
>> satisfy laymen like myself.
>
>         I don't understand the "mystery".
>         Pinnipeds are pagophilic (prefer, or depend on water ice for
> some or all activities and functions). Pinnipeds evolved on ice sheets.
> Lake Baikal has direct access to Arctic over Yenisey river. Ringed seals
> are adaptive, they are small, feed on small fish, no problem for them to
> reach Baikal lake in the Ice age.
>         In the Ice age the proglacial lakes form. One of the biggest
> was West Siberian Glacial Lake:
> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake
>         I believe that on this link you can also see some of those big
> lakes:
> https://external-preview.redd.it/0yPXq1DgWnoOiTEu0dLndipdZPbnZ9Hwwzeu828T15w.jpg?auto=webp&s=d1b89184afbefe035531c759518298841f4dcadf

More on this:
"Ice Dammed Lakes.
It is recognized that during Ice Ages Arctic Ocean ice fronts advanced
onto mainland Russia and blocked the north-flowing rivers (Yenissei, Ob,
Pechora, Dvina, and others) that supply most of the freshwater to the
Arctic Ocean (Baker, 2007), (Grosswald, 1998), (Mangerud et al., 2001
and 2004), (Rudoy, 1998). As a result, large ice-dammed lakes formed
between the ice sheet in the north and the continental water divides to
the south. Lakes overflowed toward the south and, thus, the drainage of
much of the Eurasian continent was reversed. The result was a major
change in the water balance on the continent, decreased freshwater
supply to the Arctic Ocean, and hugely increased fresh water flow to the
Aral, Caspian, Black, and Baltic seas. (Figure 1). A consequence of this
is that the world’s longest river was created from Siberia to the
Mediterranean with the Aral and Caspian Seas becoming sediment traps for
the diverted rivers."
And you can see the map of these water spills on the link:
https://grahamhancock.com/gallagherr1/

--
https://groups.google.com/g/human-evolution
human-evolution@googlegroups.com

On 8/25/21 5:46 PM, Peter Nyikos wrote:
> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>
>>> When I was at an international topology conference in Baku in 1987,
>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>
>>> I can no longer remember whether I realized then that this was from
>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>> before this discovery. One thing is certain: I became quite interested
>>> in this seal and the question of how it got there.
>>>
>>> I already knew enough paleogeography to know that, no earlier than the
>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>> to swim from the Atlantic, through the portion that became the
>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>
>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>
>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>> https://en.wikipedia.org/wiki/Baikal_seal
>>>
>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>
> By the way, John, can you access the full article where you are?

Unemployed biologist, remember? I have only personal subscriptions, and
that's not one of them.

>>> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
>>> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
>>> First published: 27 April 2006
>
>
>>> I haven't had time to read the article, but I wish it had been based more than
>>> just on mitochondrial sequences; these are not as accurate as full genome
>>> sequences.
>
>> You have been misinformed.
>
> Oh, you think they are equally accurate for phylogenetic purposes as
> sequencing the full (nuclear) genome, do you?

For some, yes. One advantage of mtDNA is that it evolves faster and so
accumulates more data per site per million years. If the mtDNA is only
4% divergent, I would expect the nuclear DNA to be less than 1%
divergent. Another advantage is that coalescence time is expected to be
1/4 that of an autosomal locus, so less incomplete lineage sorting.
Finally, it's a single linkage group, so less incompatible lineage sorting.

>> Mitochrondrial sequences are quite accurate for many purposes.
>
> Can you ascertain the purposes of the authors enough to deduce that the
> mitochondrial sequences will go as far towards answering the questions of the
> authors as sequencing the full genome?

You toss off "sequencing the full genome" so lightly. Even today it
takes thousands of dollars and months of time just to get the raw reads,
much less assembly and alignment, much less proper analysis. Certainly
it's getting cheaper and faster all the time, but it's still no simple
task. And even if I were sequencing whole genomes for phylogenetic
purposes, I would only pull out a manageable number of sequences for
analysis, certainly no more than a million carefully chosen bases.

>> "Full genome sequences", if by that you actually mean
>> the complete sequence of an entire genome, are not remotely necessary.
>
> So much for the Human Genome Project, eh?

There are many purposes to be served by sequencing full genomes.
Phylogenetics of closely related seal species is probably not one.
Certainly it wouldn't be cost-effective, quite aside from the difficulty
of properly analyzing whole genomes once you have the data.

> Or was that a misnomer? Did they only sequence protein coding genes, meaning
> that they are transcribed into mRNA that are translated into proteins without modification?

No. They sequenced most of the genome, most of which is non-coding.

>>> The timing of events is ultimately to be found elsewhere than in phylogeny,
>>> but the abstract, which I will be posting in a follow-up to this OP, makes
>>> it plausible that we can reconstruct events to an accuracy that can
>>> satisfy laymen like myself.
>>>
>>>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> at Univ. of South Carolina
> http://people.math.sc.edu/nyikos
>

On Wednesday, August 25, 2021 at 10:14:20 PM UTC-4, Mario Petrinovic wrote:
> On 26.8.2021. 0:20, Peter Nyikos wrote:
> > When I was at an international topology conference in Baku in 1987,
> > the shore of the Caspian sea was an easy climb down from our dormitory.
> > One day as I walked on the beach, I spotted what looked like a skeleton
> > of a human hand. As I approached, it became clear that the proportions were wrong.
> >
> > I can no longer remember whether I realized then that this was from
> > a flipper of the Caspian seal, or even whether I had read about this seal
> > before this discovery. One thing is certain: I became quite interested
> > in this seal and the question of how it got there.
> >
> > I already knew enough paleogeography to know that, no earlier than the
> > Pliocene, enough of the great sea Tethys remained for any sea creature
> > to swim from the Atlantic, through the portion that became the
> > Mediterranean, thence to the paleo-Black sea, and thence to where
> > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> >
> > But there is another landlocked seal whose origin is still something of a mystery:
> >
> > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain,

By the way, the West Siberian Plain is not a body of water: it is a plain on which the glacial lake
is situated. And the very next thing the Wiki entry says is also wrong, as I will be explaining below.
>> "formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > https://en.wikipedia.org/wiki/Baikal_seal

> > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > First published: 27 April 2006
> >
> > I haven't had time to read the article, but I wish it had been based more than
> > just on mitochondrial sequences; these are not as accurate as full genome
> > sequences.
> >
> > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > but the abstract, which I will be posting in a follow-up to this OP, makes
> > it plausible that we can reconstruct events to an accuracy that can
> > satisfy laymen like myself.

> I don't understand the "mystery".

Not a major mystery, just big uncertainty as to when and how it happened.

> Pinnipeds are pagophilic (prefer, or depend on water ice for some or
> all activities and functions). Pinnipeds evolved on ice sheets. Lake
> Baikal has direct access to Arctic over Yenisey river.

Yes, but why aren't they using the Yenisey river now to get back up to
the ocean? The most likely answer is in the map I linked up there.
The West Siberian Glacial Lake borders on a huge ice sheet thousands of miles
in all directions, at the height of the latest ice age, and the Yenisey
was a lot shorter than it is now. It didn't flow into the ocean, but into the huge glacial lake,
which borders the ice sheet.

However, I think the quote from the Wiki entry on the Baikal seal was done by someone
who linked the following entry without reading it:

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

The entry begins as follows:
"The West Siberian Glacial Lake, also known as West Siberian Lake or Mansiyskoe Lake (Russian: Мансийское озеро), was a periglacial lake formed when the Arctic Ocean outlets for each of the Ob and Yenisei rivers were blocked by the Barents-Kara Ice Sheet during the Weichselian Glaciation, approximately 80,000 years ago. It was situated on the West Siberian Plain, and at its maximum extent the lake's surface area was more than 750,000 km2 which is more than twice that of the present-day Caspian Sea."

The Weicselian Glaciation was the last ice age, not "an earlier ice age" as the Baikal seal article
claimed [see above]. The clumsy author of the latter could have removed all doubt about that
by just moving the mouse over the blue "Weicselian Glaciation" and the very first sentence in
the pop-up would have told him/her that.

> Ringed seals are
> adaptive, they are small, feed on small fish, no problem for them to
> reach Baikal lake in the Ice age.

But note, the Wiki entry on the Baikal seal says they've been in the Baikal for two
million years. I had better start reading [7] in earnest; it will be interesting to see
how much else the Baikal seal entry got wrong.

> In the Ice age the proglacial lakes form. One of the biggest was West
> Siberian Glacial Lake:
> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake

How good is your Russian, Mario? There is a wonderfully detailed map of the lake and the surrounding country,
including both the Caspian and Baikal:

https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg

The captions are all in Russian. There are some amazing details: instead of the water from the Caspian sea
going up to the huge ice sheet by the shortest route, it flows out the southern end, to the Aral Sea.

And then the Aral sea, which has been totally landlocked for goodness knows how long, has an outlet
that flows north to the huge ice sheet.

> I believe that on this link you can also see some of those big lakes:
> https://external-preview.redd.it/0yPXq1DgWnoOiTEu0dLndipdZPbnZ9Hwwzeu828T15w.jpg?auto=webp&s=d1b89184afbefe035531c759518298841f4dcadf

This is far less detailed, but it covers a lot of extra territory. I'm especially intrigued by the Lena lake.
It looks like Lake Baikal is a remnant, and the arrows indicate that it might have had an outlet
that flowed into the West Siberian Glacial Lake (not labeled) and thence up to the great ice
sheet via the Yenisey.

And I remember reading that the Baikal originally flowed to the Arctic via the Lena,
and then switched to the Yeinisey. But the place where I read it gave no details
on when the switch occurred, nor why.

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

On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
<jharshman@pacbell.net> wrote:

>On 8/25/21 5:46 PM, Peter Nyikos wrote:
>> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>>
>>>> When I was at an international topology conference in Baku in 1987,
>>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>>
>>>> I can no longer remember whether I realized then that this was from
>>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>>> before this discovery. One thing is certain: I became quite interested
>>>> in this seal and the question of how it got there.
>>>>
>>>> I already knew enough paleogeography to know that, no earlier than the
>>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>>> to swim from the Atlantic, through the portion that became the
>>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>>
>>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>>
>>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>>> https://en.wikipedia.org/wiki/Baikal_seal
>>>>
>>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>>
>> By the way, John, can you access the full article where you are?
>
>Unemployed biologist, remember? I have only personal subscriptions, and
>that's not one of them.

It's free:
https://academic.oup.com/biolinnean/article/88/1/61/2691557

On 8/26/21 7:15 AM, Pandora wrote:
> On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
> <jharshman@pacbell.net> wrote:
>
>> On 8/25/21 5:46 PM, Peter Nyikos wrote:
>>> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>>>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>>>
>>>>> When I was at an international topology conference in Baku in 1987,
>>>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>>>
>>>>> I can no longer remember whether I realized then that this was from
>>>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>>>> before this discovery. One thing is certain: I became quite interested
>>>>> in this seal and the question of how it got there.
>>>>>
>>>>> I already knew enough paleogeography to know that, no earlier than the
>>>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>>>> to swim from the Atlantic, through the portion that became the
>>>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>>>
>>>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>>>
>>>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>>>> https://en.wikipedia.org/wiki/Baikal_seal
>>>>>
>>>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>>>
>>> By the way, John, can you access the full article where you are?
>>
>> Unemployed biologist, remember? I have only personal subscriptions, and
>> that's not one of them.
>
> It's free:
> https://academic.oup.com/biolinnean/article/88/1/61/2691557
>
Why, thanks.

On 26.8.2021. 16:11, Peter Nyikos wrote:
> On Wednesday, August 25, 2021 at 10:14:20 PM UTC-4, Mario Petrinovic wrote:
>> On 26.8.2021. 0:20, Peter Nyikos wrote:
>>> When I was at an international topology conference in Baku in 1987,
>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>
>>> I can no longer remember whether I realized then that this was from
>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>> before this discovery. One thing is certain: I became quite interested
>>> in this seal and the question of how it got there.
>>>
>>> I already knew enough paleogeography to know that, no earlier than the
>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>> to swim from the Atlantic, through the portion that became the
>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>
>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>
>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain,
>
> By the way, the West Siberian Plain is not a body of water: it is a plain on which the glacial lake
> is situated. And the very next thing the Wiki entry says is also wrong, as I will be explaining below.
>
>>> "formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>> https://en.wikipedia.org/wiki/Baikal_seal
>
>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>>> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
>>> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
>>> First published: 27 April 2006
>>>
>>> I haven't had time to read the article, but I wish it had been based more than
>>> just on mitochondrial sequences; these are not as accurate as full genome
>>> sequences.
>>>
>>> The timing of events is ultimately to be found elsewhere than in phylogeny,
>>> but the abstract, which I will be posting in a follow-up to this OP, makes
>>> it plausible that we can reconstruct events to an accuracy that can
>>> satisfy laymen like myself.
>
>> I don't understand the "mystery".
>
>
> Not a major mystery, just big uncertainty as to when and how it happened.
>
>
>> Pinnipeds are pagophilic (prefer, or depend on water ice for some or
>> all activities and functions). Pinnipeds evolved on ice sheets. Lake
>> Baikal has direct access to Arctic over Yenisey river.
>
> Yes, but why aren't they using the Yenisey river now to get back up to
> the ocean? The most likely answer is in the map I linked up there.
> The West Siberian Glacial Lake borders on a huge ice sheet thousands of miles
> in all directions, at the height of the latest ice age, and the Yenisey
> was a lot shorter than it is now. It didn't flow into the ocean, but into the huge glacial lake,
> which borders the ice sheet.
>
> However, I think the quote from the Wiki entry on the Baikal seal was done by someone
> who linked the following entry without reading it:
>
> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake
>
> The entry begins as follows:
> "The West Siberian Glacial Lake, also known as West Siberian Lake or Mansiyskoe Lake (Russian: Мансийское озеро), was a periglacial lake formed when the Arctic Ocean outlets for each of the Ob and Yenisei rivers were blocked by the Barents-Kara Ice Sheet during the Weichselian Glaciation, approximately 80,000 years ago. It was situated on the West Siberian Plain, and at its maximum extent the lake's surface area was more than 750,000 km2 which is more than twice that of the present-day Caspian Sea."
>
> The Weicselian Glaciation was the last ice age, not "an earlier ice age" as the Baikal seal article
> claimed [see above]. The clumsy author of the latter could have removed all doubt about that
> by just moving the mouse over the blue "Weicselian Glaciation" and the very first sentence in
> the pop-up would have told him/her that.
>
>
>> Ringed seals are
>> adaptive, they are small, feed on small fish, no problem for them to
>> reach Baikal lake in the Ice age.
>
> But note, the Wiki entry on the Baikal seal says they've been in the Baikal for two
> million years. I had better start reading [7] in earnest; it will be interesting to see
> how much else the Baikal seal entry got wrong.
>
>
>> In the Ice age the proglacial lakes form. One of the biggest was West
>> Siberian Glacial Lake:
>> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake
>
>
> How good is your Russian, Mario? There is a wonderfully detailed map of the lake and the surrounding country,
> including both the Caspian and Baikal:
>
> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg
>
> The captions are all in Russian.

I know Serbian (which is, of course, a dialect of Croatian, ;) )
Cyrillic. "MOPE" ("MORE" in Latin alphabet) means "sea". From left to
right, Black Sea. Caspian Sea, Aral Sea, West-Siberian Sea. The name of
the left river should be something similar to "Uzbek". The right river
should be "Turgai". At the top is "Barents-Kara Ice Sheet".

> There are some amazing details: instead of the water from the Caspian sea
> going up to the huge ice sheet by the shortest route, it flows out the southern end, to the Aral Sea.
>
> And then the Aral sea, which has been totally landlocked for goodness knows how long, has an outlet
> that flows north to the huge ice sheet.
>
>
>> I believe that on this link you can also see some of those big lakes:
>> https://external-preview.redd.it/0yPXq1DgWnoOiTEu0dLndipdZPbnZ9Hwwzeu828T15w.jpg?auto=webp&s=d1b89184afbefe035531c759518298841f4dcadf
>
> This is far less detailed, but it covers a lot of extra territory. I'm especially intrigued by the Lena lake.

Yes, I couldn't find more info on Lena lake.

> It looks like Lake Baikal is a remnant, and the arrows indicate that it might have had an outlet
> that flowed into the West Siberian Glacial Lake (not labeled) and thence up to the great ice
> sheet via the Yenisey.
>
> And I remember reading that the Baikal originally flowed to the Arctic via the Lena,
> and then switched to the Yeinisey. But the place where I read it gave no details
> on when the switch occurred, nor why.

In short, seals need ice. Baikal seals are situated north on the
Baikal lake. Only in winter, when ice sheet spreads south, they move to
the south side.

--
https://groups.google.com/g/human-evolution
human-evolution@googlegroups.com

On Thursday, August 26, 2021 at 10:15:12 AM UTC-4, Pandora wrote:
> On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
> <jhar...@pacbell.net> wrote:
>
> >On 8/25/21 5:46 PM, Peter Nyikos wrote:
> >> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> >>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
> >>
> >>>> When I was at an international topology conference in Baku in 1987,
> >>>> the shore of the Caspian sea was an easy climb down from our dormitory.
> >>>> One day as I walked on the beach, I spotted what looked like a skeleton
> >>>> of a human hand. As I approached, it became clear that the proportions were wrong.
> >>>>
> >>>> I can no longer remember whether I realized then that this was from
> >>>> a flipper of the Caspian seal, or even whether I had read about this seal
> >>>> before this discovery. One thing is certain: I became quite interested
> >>>> in this seal and the question of how it got there.
> >>>>
> >>>> I already knew enough paleogeography to know that, no earlier than the
> >>>> Pliocene, enough of the great sea Tethys remained for any sea creature
> >>>> to swim from the Atlantic, through the portion that became the
> >>>> Mediterranean, thence to the paleo-Black sea, and thence to where
> >>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
> >>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> >>>>
> >>>> But there is another landlocked seal whose origin is still something of a mystery:
> >>>>
> >>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> >>>> https://en.wikipedia.org/wiki/Baikal_seal
> >>>>
> >>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> >>
> >> By the way, John, can you access the full article where you are?
> >
> >Unemployed biologist, remember? I have only personal subscriptions, and
> >that's not one of them.

> It's free:
> https://academic.oup.com/biolinnean/article/88/1/61/2691557

Thank you, Pandora. You've saved us all a lot of trouble. The article is so disorganized, and so
much of the text is so tentative, that I would have had to quote practically the whole
article for John to make any sense of it.

In particular, the Conclusions portion ends with the paleogeographical mystery untouched:

"Nevertheless, the actual geographical conditions that would have facilitated the continental invasions
in those times still remain undocumented and enigmatic."

The Conclusion opts for the current distribution of Arctic/Caspian/Baikal species (*hispida*/ *caspica*/ *sibirica*)
already in place at 2-3 mya, but not much earlier, and seems to be wholly based on mitochondrial "molecular clocks":

"From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2–3 Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin." [from the Abstract of the article you've linked].

This is in contrast to the very detailed paleogeographical information supporting the widely held first of
the "prevailing hypotheses." It argues for easy dispersal of all three species, especially the arctic and the
Baikal, as seen in the map I linked for Mario for the latest ice age:

https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg

If that map is accurate in its main features [never mind the incredible detail of the smaller rivers],
one would naturally expect mixing of the three species, *hispida*, *caspica*, and *sibirica*, to
have greatly confused the mitochondrial data if those HAD originally diverged 2-3 mya.

Pandora, if you can make any sense out of all this, I would love to see it, no matter how
tentative it may have to be.

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

On Thursday, August 26, 2021 at 12:24:06 AM UTC-4, John Harshman wrote:
> On 8/25/21 5:46 PM, Peter Nyikos wrote:
> > On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> >> On 8/25/21 3:20 PM, Peter Nyikos wrote:
> >
> >>> When I was at an international topology conference in Baku in 1987,
> >>> the shore of the Caspian sea was an easy climb down from our dormitory.
> >>> One day as I walked on the beach, I spotted what looked like a skeleton
> >>> of a human hand. As I approached, it became clear that the proportions were wrong.
> >>>
> >>> I can no longer remember whether I realized then that this was from
> >>> a flipper of the Caspian seal, or even whether I had read about this seal
> >>> before this discovery. One thing is certain: I became quite interested
> >>> in this seal and the question of how it got there.
> >>>
> >>> I already knew enough paleogeography to know that, no earlier than the
> >>> Pliocene, enough of the great sea Tethys remained for any sea creature
> >>> to swim from the Atlantic, through the portion that became the
> >>> Mediterranean, thence to the paleo-Black sea, and thence to where
> >>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
> >>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> >>>
> >>> But there is another landlocked seal whose origin is still something of a mystery:
> >>>
> >>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> >>> https://en.wikipedia.org/wiki/Baikal_seal
> >>>
> >>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> >
> > By the way, John, can you access the full article where you are?
> Unemployed biologist, remember? I have only personal subscriptions, and
> that's not one of them.
> >>> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> >>> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> >>> First published: 27 April 2006
> >
> >
> >>> I haven't had time to read the article, but I wish it had been based more than
> >>> just on mitochondrial sequences; these are not as accurate as full genome
> >>> sequences.
> >
> >> You have been misinformed.

This unequivocal claim has to do with only one aspect of "not as accurate":

> > Oh, you think they are equally accurate for phylogenetic purposes as
> > sequencing the full (nuclear) genome, do you?

> For some, yes.

Where the divergence times of the various seals is concerned, it is a bit
disconcerting to read the word "single" in the first sentence of the "Methods" section:

"The sequences of the entire COI (1545 bp), COII (684 bp), and Cytb (1140 bp) genes were obtained from single individuals of each of P. hispida, P. sibirica, P. caspica, Phoca largha Pallas (larga seal, or spotted seal; University of Alaska Museum collection UAM Mamm 18613), Histriophoca fasciata (Zimmermann) (ribbon seal; UAM Mamm 19029), Cystophora cristata (Erxleben) (hooded seal; UAM Mamm 36480), and Erignathus barbatus (Erxleben) (bearded seal; UAM Mamm 36477). Sequences were deposited in GenBank under accession numbers AY140962–AY140982. In addition, we used published mtDNA-sequence data from Halichoerus grypus (Fabricius) (grey seal X74002; Árnason et al., 1993) and Phoca vitulina L. (harbour seal X63726; Árnason & Johnsson, 1992).

Do you trust samples of one individual per species? If so, that adds irony to the "For some, yes".

> One advantage of mtDNA is that it evolves faster and so
> accumulates more data per site per million years. If the mtDNA is only
> 4% divergent, I would expect the nuclear DNA to be less than 1%
> divergent.

But the absolute numbers are reversed, given the number of genes in the survey.

>Another advantage is that coalescence time is expected to be
> 1/4 that of an autosomal locus, so less incomplete lineage sorting.

Interesting concept, "autosomal". Wouldn't you expect just as much
crossover in an XX female or a ZZ male as in a non-sex chromosome pair?

> Finally, it's a single linkage group, so less incompatible lineage sorting.

"single linkage" refers to mitochondria being passed down through the female line exclusively,
I presume. You aren't making any concessions for a layman like Mario.

In the same vein, I take it "incompatible" [as opposed to "incomplete"]
is a "hindsight is 20/20" type concept.

By the way, it just now occurred to me: I wonder whether any efforts have been
made to mate the three species under consideration in captivity. I can't help remembering how
the polar bear was once considered to be a separate *genus* from the brown bear,
even though it was known that they could interbreed in captivity and produce fertile
offspring. But the prevalent species concept finally gave way to common sense,
as the polar bear was downgraded to a separate subspecies,

> >> Mitochrondrial sequences are quite accurate for many purposes.
> >
> > Can you ascertain the purposes of the authors enough to deduce that the
> > mitochondrial sequences will go as far towards answering the questions of the
> > authors as sequencing the full genome?

Short answer: no. But now that Pandora has given you a non-paywalled access
to the article, perhaps you can answer this question eventually, yourself.

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

PS I've left in your snarky "answer," which begins a bunch of themes which have
nothing to do with the topic of the OP, but deleted the rest, part of which was
self-contradictory, but also part of which might be useful on some future thread.

> You toss off "sequencing the full genome" so lightly. Even today it
> takes thousands of dollars and months of time just to get the raw reads,
> much less assembly and alignment, much less proper analysis.

On Thu, 26 Aug 2021 08:49:47 -0700 (PDT), Peter Nyikos
<peter2nyikos@gmail.com> wrote:

>On Thursday, August 26, 2021 at 10:15:12 AM UTC-4, Pandora wrote:
>> On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
>> <jhar...@pacbell.net> wrote:
>>
>> >On 8/25/21 5:46 PM, Peter Nyikos wrote:
>> >> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>> >>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>> >>
>> >>>> When I was at an international topology conference in Baku in 1987,
>> >>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>> >>>> One day as I walked on the beach, I spotted what looked like a skeleton
>> >>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>> >>>>
>> >>>> I can no longer remember whether I realized then that this was from
>> >>>> a flipper of the Caspian seal, or even whether I had read about this seal
>> >>>> before this discovery. One thing is certain: I became quite interested
>> >>>> in this seal and the question of how it got there.
>> >>>>
>> >>>> I already knew enough paleogeography to know that, no earlier than the
>> >>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>> >>>> to swim from the Atlantic, through the portion that became the
>> >>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>> >>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>> >>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>> >>>>
>> >>>> But there is another landlocked seal whose origin is still something of a mystery:
>> >>>>
>> >>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>> >>>> https://en.wikipedia.org/wiki/Baikal_seal
>> >>>>
>> >>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>> >>
>> >> By the way, John, can you access the full article where you are?
>> >
>> >Unemployed biologist, remember? I have only personal subscriptions, and
>> >that's not one of them.
>
>> It's free:
>> https://academic.oup.com/biolinnean/article/88/1/61/2691557
>
>Thank you, Pandora. You've saved us all a lot of trouble. The article is so disorganized, and so
>much of the text is so tentative, that I would have had to quote practically the whole
>article for John to make any sense of it.
>
>In particular, the Conclusions portion ends with the paleogeographical mystery untouched:
>
>"Nevertheless, the actual geographical conditions that would have facilitated the continental invasions
>in those times still remain undocumented and enigmatic."
>
>The Conclusion opts for the current distribution of Arctic/Caspian/Baikal species (*hispida*/ *caspica*/ *sibirica*)
>already in place at 2-3 mya, but not much earlier, and seems to be wholly based on mitochondrial "molecular clocks":
>
>"From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2–3?Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin." [from the Abstract of the article you've linked].
>
>This is in contrast to the very detailed paleogeographical information supporting the widely held first of
>the "prevailing hypotheses." It argues for easy dispersal of all three species, especially the arctic and the
>Baikal, as seen in the map I linked for Mario for the latest ice age:
>
>https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg
>
>If that map is accurate in its main features [never mind the incredible detail of the smaller rivers],
>one would naturally expect mixing of the three species, *hispida*, *caspica*, and *sibirica*, to
>have greatly confused the mitochondrial data if those HAD originally diverged 2-3 mya.
>
>
>Pandora, if you can make any sense out of all this, I would love to see it, no matter how
>tentative it may have to be.

Also check Fulton and Strobeck (2010):
https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02271.x

Full text pdf avalable at:
http://bbcd.bio.uniroma1.it/bbcd/sites/default/files/file%20lezioni/Fulton_Foche.pdf

Interestingly, they do recover a monophyletic Pusa (although
relationships within Pusa are not confidently resolved) with a
divergence estimate between 1.7 and 0.8 Ma.
This would support a Lower Pleistocene scenario.

On Wednesday, August 25, 2021 at 5:46:50 PM UTC-7, Peter Nyikos wrote:
> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> > On 8/25/21 3:20 PM, Peter Nyikos wrote:
>
> > > When I was at an international topology conference in Baku in 1987,
> > > the shore of the Caspian sea was an easy climb down from our dormitory.
> > > One day as I walked on the beach, I spotted what looked like a skeleton
> > > of a human hand. As I approached, it became clear that the proportions were wrong.
> > >
> > > I can no longer remember whether I realized then that this was from
> > > a flipper of the Caspian seal, or even whether I had read about this seal
> > > before this discovery. One thing is certain: I became quite interested
> > > in this seal and the question of how it got there.
> > >
> > > I already knew enough paleogeography to know that, no earlier than the
> > > Pliocene, enough of the great sea Tethys remained for any sea creature
> > > to swim from the Atlantic, through the portion that became the
> > > Mediterranean, thence to the paleo-Black sea, and thence to where
> > > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> > >
> > > But there is another landlocked seal whose origin is still something of a mystery:
> > >
> > > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > > https://en.wikipedia.org/wiki/Baikal_seal
> > >
> > > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> By the way, John, can you access the full article where you are?
> > > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > > First published: 27 April 2006
>
>
> > > I haven't had time to read the article, but I wish it had been based more than
> > > just on mitochondrial sequences; these are not as accurate as full genome
> > > sequences.
>
> > You have been misinformed.
> Oh, you think they are equally accurate for phylogenetic purposes as
> sequencing the full (nuclear) genome, do you?
> > Mitochrondrial sequences are quite accurate for many purposes.
> Can you ascertain the purposes of the authors enough to deduce that the
> mitochondrial sequences will go as far towards answering the questions of the
> authors as sequencing the full genome?
> > "Full genome sequences", if by that you actually mean
> > the complete sequence of an entire genome, are not remotely necessary.
> So much for the Human Genome Project, eh?
>
> Or was that a misnomer? Did they only sequence protein coding genes, meaning
> that they are transcribed into mRNA that are translated into proteins without modification?
> > > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > > but the abstract, which I will be posting in a follow-up to this OP, makes
> > > it plausible that we can reconstruct events to an accuracy that can
> > > satisfy laymen like myself.
> > >
> > >
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> at Univ. of South Carolina
> http://people.math.sc.edu/nyikos

Here's your Baikal and Caspian Sea seal paper:

https://watermark.silverchair.com/j.1095-8312.2006.00607.x.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuowggLmBgkqhkiG9w0BBwagggLXMIIC0wIBADCCAswGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxNMe2X9FgGiGE9xWAgEQgIICnYRSAvgi9iJIYfT8ZqUXJZKBDrTIQ7PY_Uu7RYr030v4mUY4Spt8IG4z0LHtMgbB5gRft7kCWwzzGEuFTbE9biz5Q7jH7h7YglzgRxK0rhdrurVn7HXoo0TcS7bySRF8wd-YqJV8BriQs41V2yUaX4Oj2r29KGmcaeVJlMY-IusLLWiDgqM0t7OiB8eYoyYqYsi4tyu-4_K2XEAGAIQaJrqE6NB81dNkYRxkhuhRuPzky3oWRTcHWC9xErSuaEJR3CfHOPdWfffhzGLnBap1g_FWjsug7Cn-DTBR9XvlVpqaR0_TxyOhyDQjYCR_-RmXYpvd0wtXfWkMJYz62_etFOOb2T2b6SJUBI_lO6dtnPzLy5li9RK0IFx76JiPKUGM39jt5_doSNlwgqqDIg8P9fPAjyKM94IDiVuEq4USmI2yvTPL3AE_RrakO7LLwPw7pg2BhJ6ZjMNO19pfor_wpLUyWEkv-NhKqfqYr7P8naYWtClyv5do_ln1my-F8XgMrUzEcaUTt7ym6LSTb3sJ5vVoTgD2Ma_IJMTz_yFrID2-TfW4a87IHWzA6Oz69HVyhfY5rQZ-BZrNs5_-UGQu2s4xn5Ci1Qulx1JtWBjM2rbl-g8D8KklliPwxgO6TmGL2gu86W2enRDZcTqo-GEQ2uSRWsBjXSrM6mOfuWL3bpk4_MMDLHYhUUmsUlHzVyLyLFmPDjuUQMvegMxqFCsjxg7EG7UAlcBKLKBLQodmTlKQNr2hefJET2asWl3XsUUzgv4vEMAqn9jC8EQov49ncFf2k81YmD_s5bmLQTPjdBypX6Qzu5hFURA25lbGOW2GjRvd7mcm9cDx1hcjPIeP5Yh9xdZmIv3zJo3eqo8Hdzso1yzeuFRq4IebguL9fw

On Thursday, August 26, 2021 at 2:51:37 PM UTC-4, Pandora wrote:
> On Thu, 26 Aug 2021 08:49:47 -0700 (PDT), Peter Nyikos
> <peter2...@gmail.com> wrote:
>
> >On Thursday, August 26, 2021 at 10:15:12 AM UTC-4, Pandora wrote:
> >> On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
> >> <jhar...@pacbell.net> wrote:
> >>
> >> >On 8/25/21 5:46 PM, Peter Nyikos wrote:
> >> >> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> >> >>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
> >> >>
> >> >>>> When I was at an international topology conference in Baku in 1987,
> >> >>>> the shore of the Caspian sea was an easy climb down from our dormitory.
> >> >>>> One day as I walked on the beach, I spotted what looked like a skeleton
> >> >>>> of a human hand. As I approached, it became clear that the proportions were wrong.
> >> >>>>
> >> >>>> I can no longer remember whether I realized then that this was from
> >> >>>> a flipper of the Caspian seal, or even whether I had read about this seal
> >> >>>> before this discovery. One thing is certain: I became quite interested
> >> >>>> in this seal and the question of how it got there.
> >> >>>>
> >> >>>> I already knew enough paleogeography to know that, no earlier than the
> >> >>>> Pliocene, enough of the great sea Tethys remained for any sea creature
> >> >>>> to swim from the Atlantic, through the portion that became the
> >> >>>> Mediterranean, thence to the paleo-Black sea, and thence to where
> >> >>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
> >> >>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> >> >>>>
> >> >>>> But there is another landlocked seal whose origin is still something of a mystery:
> >> >>>>
> >> >>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> >> >>>> https://en.wikipedia.org/wiki/Baikal_seal
> >> >>>>
> >> >>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> >> >>
> >> >> By the way, John, can you access the full article where you are?
> >> >
> >> >Unemployed biologist, remember? I have only personal subscriptions, and
> >> >that's not one of them.
> >
> >> It's free:
> >> https://academic.oup.com/biolinnean/article/88/1/61/2691557
> >
> >Thank you, Pandora. You've saved us all a lot of trouble. The article is so disorganized, and so
> >much of the text is so tentative, that I would have had to quote practically the whole
> >article for John to make any sense of it.
> >
> >In particular, the Conclusions portion ends with the paleogeographical mystery untouched:
> >
> >"Nevertheless, the actual geographical conditions that would have facilitated the continental invasions
> >in those times still remain undocumented and enigmatic."
> >
> >The Conclusion opts for the current distribution of Arctic/Caspian/Baikal species (*hispida*/ *caspica*/ *sibirica*)
> >already in place at 2-3 mya, but not much earlier, and seems to be wholly based on mitochondrial "molecular clocks":
> >
> >"From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2–3?Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin." [from the Abstract of the article you've linked].
> >
> >This is in contrast to the very detailed paleogeographical information supporting the widely held first of
> >the "prevailing hypotheses." It argues for easy dispersal of all three species, especially the arctic and the
> >Baikal, as seen in the map I linked for Mario for the latest ice age:
> >
> >https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg
> >
> >If that map is accurate in its main features [never mind the incredible detail of the smaller rivers],
> >one would naturally expect mixing of the three species, *hispida*, *caspica*, and *sibirica*, to
> >have greatly confused the mitochondrial data if those HAD originally diverged 2-3 mya.
> >
> >
> >Pandora, if you can make any sense out of all this, I would love to see it, no matter how
> >tentative it may have to be.

Thank you for sending me to the following article. It is much better organized than the 2006
article by Jukka U. Palo et al that we have been looking at, and it does seem
to make sense of a great deal of what that 2006 article had me wondering about:

> Also check Fulton and Strobeck (2010):
> https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02271.x
>
> Full text pdf avalable at:
> http://bbcd.bio.uniroma1.it/bbcd/sites/default/files/file%20lezioni/Fulton_Foche.pdf

I see it references that 2006 Palo et.al. article 9 times,
with helpful comments each of the 8 times in the text.

Most importantly, it does not use only mtDNA like Palo et. al. did.
The title of the article pretty much says it all:

"Multiple fossil calibrations, nuclear loci and mitochondrial genomes provide new insight into biogeography
and divergence timing for true seals (Phocidae, Pinnipedia)"

Of course, the comma is just to separate the family from the order, which also includes the suborder
Otaroidea (fur seals, sea lions, walruses). The article has some good information about otaroids,
including estimated divergence times between them and from the true seals.

> Interestingly, they do recover a monophyletic Pusa (although
> relationships within Pusa are not confidently resolved) with a
> divergence estimate between 1.7 and 0.8 Ma.
> This would support a Lower Pleistocene scenario.

Yes, this seems to be the bottom line as far as the 2010 article is concerned, and the estimate doesn't overlap
the one Palo et al gave earlier.

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

On Thursday, August 26, 2021 at 3:59:13 PM UTC-4, erik simpson wrote:
> On Wednesday, August 25, 2021 at 5:46:50 PM UTC-7, Peter Nyikos wrote:
> > On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> > > On 8/25/21 3:20 PM, Peter Nyikos wrote:
> >
> > > > When I was at an international topology conference in Baku in 1987,
> > > > the shore of the Caspian sea was an easy climb down from our dormitory.
> > > > One day as I walked on the beach, I spotted what looked like a skeleton
> > > > of a human hand. As I approached, it became clear that the proportions were wrong.
> > > >
> > > > I can no longer remember whether I realized then that this was from
> > > > a flipper of the Caspian seal, or even whether I had read about this seal
> > > > before this discovery. One thing is certain: I became quite interested
> > > > in this seal and the question of how it got there.
> > > >
> > > > I already knew enough paleogeography to know that, no earlier than the
> > > > Pliocene, enough of the great sea Tethys remained for any sea creature
> > > > to swim from the Atlantic, through the portion that became the
> > > > Mediterranean, thence to the paleo-Black sea, and thence to where
> > > > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > > > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> > > >
> > > > But there is another landlocked seal whose origin is still something of a mystery:
> > > >
> > > > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > > > https://en.wikipedia.org/wiki/Baikal_seal
> > > >
> > > > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> > By the way, John, can you access the full article where you are?
> > > > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > > > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > > > First published: 27 April 2006
> >
> >
> > > > I haven't had time to read the article, but I wish it had been based more than
> > > > just on mitochondrial sequences; these are not as accurate as full genome
> > > > sequences.
> >
> > > You have been misinformed.
> > Oh, you think they are equally accurate for phylogenetic purposes as
> > sequencing the full (nuclear) genome, do you?
> > > Mitochrondrial sequences are quite accurate for many purposes.
> > Can you ascertain the purposes of the authors enough to deduce that the
> > mitochondrial sequences will go as far towards answering the questions of the
> > authors as sequencing the full genome?
> > > "Full genome sequences", if by that you actually mean
> > > the complete sequence of an entire genome, are not remotely necessary..
> > So much for the Human Genome Project, eh?
> >
> > Or was that a misnomer? Did they only sequence protein coding genes, meaning
> > that they are transcribed into mRNA that are translated into proteins without modification?
> > > > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > > > but the abstract, which I will be posting in a follow-up to this OP, makes
> > > > it plausible that we can reconstruct events to an accuracy that can
> > > > satisfy laymen like myself.
> > > >
> > > >
> > Peter Nyikos
> > Professor, Dept. of Mathematics -- standard disclaimer--
> > at Univ. of South Carolina
> > http://people.math.sc.edu/nyikos

> Here's your Baikal and Caspian Sea seal paper:

Is this your idea of a joke? When I clicked on your gargantuan link, this is what I got:

"Your session has timed out. Please go back to the article page and click the PDF link again."

And what do you mean by "your"? which paper, if any, did you have in mind?

> https://watermark.silverchair.com/j.1095-8312.2006.00607.x.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuowggLmBgkqhkiG9w0BBwagggLXMIIC0wIBADCCAswGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxNMe2X9FgGiGE9xWAgEQgIICnYRSAvgi9iJIYfT8ZqUXJZKBDrTIQ7PY_Uu7RYr030v4mUY4Spt8IG4z0LHtMgbB5gRft7kCWwzzGEuFTbE9biz5Q7jH7h7YglzgRxK0rhdrurVn7HXoo0TcS7bySRF8wd-YqJV8BriQs41V2yUaX4Oj2r29KGmcaeVJlMY-IusLLWiDgqM0t7OiB8eYoyYqYsi4tyu-4_K2XEAGAIQaJrqE6NB81dNkYRxkhuhRuPzky3oWRTcHWC9xErSuaEJR3CfHOPdWfffhzGLnBap1g_FWjsug7Cn-DTBR9XvlVpqaR0_TxyOhyDQjYCR_-RmXYpvd0wtXfWkMJYz62_etFOOb2T2b6SJUBI_lO6dtnPzLy5li9RK0IFx76JiPKUGM39jt5_doSNlwgqqDIg8P9fPAjyKM94IDiVuEq4USmI2yvTPL3AE_RrakO7LLwPw7pg2BhJ6ZjMNO19pfor_wpLUyWEkv-NhKqfqYr7P8naYWtClyv5do_ln1my-F8XgMrUzEcaUTt7ym6LSTb3sJ5vVoTgD2Ma_IJMTz_yFrID2-TfW4a87IHWzA6Oz69HVyhfY5rQZ-BZrNs5_-UGQu2s4xn5Ci1Qulx1JtWBjM2rbl-g8D8KklliPwxgO6TmGL2gu86W2enRDZcTqo-GEQ2uSRWsBjXSrM6mOfuWL3bpk4_MMDLHYhUUmsUlHzVyLyLFmPDjuUQMvegMxqFCsjxg7EG7UAlcBKLKBLQodmTlKQNr2hefJET2asWl3XsUUzgv4vEMAqn9jC8EQov49ncFf2k81YmD_s5bmLQTPjdBypX6Qzu5hFURA25lbGOW2GjRvd7mcm9cDx1hcjPIeP5Yh9xdZmIv3zJo3eqo8Hdzso1yzeuFRq4IebguL9fw

Peter Nyikos

On Thursday, August 26, 2021 at 1:18:59 PM UTC-7, Peter Nyikos wrote:
> On Thursday, August 26, 2021 at 3:59:13 PM UTC-4, erik simpson wrote:
> > On Wednesday, August 25, 2021 at 5:46:50 PM UTC-7, Peter Nyikos wrote:
> > > On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> > > > On 8/25/21 3:20 PM, Peter Nyikos wrote:
> > >
> > > > > When I was at an international topology conference in Baku in 1987,
> > > > > the shore of the Caspian sea was an easy climb down from our dormitory.
> > > > > One day as I walked on the beach, I spotted what looked like a skeleton
> > > > > of a human hand. As I approached, it became clear that the proportions were wrong.
> > > > >
> > > > > I can no longer remember whether I realized then that this was from
> > > > > a flipper of the Caspian seal, or even whether I had read about this seal
> > > > > before this discovery. One thing is certain: I became quite interested
> > > > > in this seal and the question of how it got there.
> > > > >
> > > > > I already knew enough paleogeography to know that, no earlier than the
> > > > > Pliocene, enough of the great sea Tethys remained for any sea creature
> > > > > to swim from the Atlantic, through the portion that became the
> > > > > Mediterranean, thence to the paleo-Black sea, and thence to where
> > > > > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > > > > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> > > > >
> > > > > But there is another landlocked seal whose origin is still something of a mystery:
> > > > >
> > > > > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > > > > https://en.wikipedia.org/wiki/Baikal_seal
> > > > >
> > > > > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> > > By the way, John, can you access the full article where you are?
> > > > > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > > > > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > > > > First published: 27 April 2006
> > >
> > >
> > > > > I haven't had time to read the article, but I wish it had been based more than
> > > > > just on mitochondrial sequences; these are not as accurate as full genome
> > > > > sequences.
> > >
> > > > You have been misinformed.
> > > Oh, you think they are equally accurate for phylogenetic purposes as
> > > sequencing the full (nuclear) genome, do you?
> > > > Mitochrondrial sequences are quite accurate for many purposes.
> > > Can you ascertain the purposes of the authors enough to deduce that the
> > > mitochondrial sequences will go as far towards answering the questions of the
> > > authors as sequencing the full genome?
> > > > "Full genome sequences", if by that you actually mean
> > > > the complete sequence of an entire genome, are not remotely necessary.
> > > So much for the Human Genome Project, eh?
> > >
> > > Or was that a misnomer? Did they only sequence protein coding genes, meaning
> > > that they are transcribed into mRNA that are translated into proteins without modification?
> > > > > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > > > > but the abstract, which I will be posting in a follow-up to this OP, makes
> > > > > it plausible that we can reconstruct events to an accuracy that can
> > > > > satisfy laymen like myself.
> > > > >
> > > > >
> > > Peter Nyikos
> > > Professor, Dept. of Mathematics -- standard disclaimer--
> > > at Univ. of South Carolina
> > > http://people.math.sc.edu/nyikos
>
> > Here's your Baikal and Caspian Sea seal paper:
> Is this your idea of a joke? When I clicked on your gargantuan link, this is what I got:
>
> "Your session has timed out. Please go back to the article page and click the PDF link again."
>
> And what do you mean by "your"? which paper, if any, did you have in mind?
>
> > https://watermark.silverchair.com/j.1095-8312.2006.00607.x.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuowggLmBgkqhkiG9w0BBwagggLXMIIC0wIBADCCAswGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxNMe2X9FgGiGE9xWAgEQgIICnYRSAvgi9iJIYfT8ZqUXJZKBDrTIQ7PY_Uu7RYr030v4mUY4Spt8IG4z0LHtMgbB5gRft7kCWwzzGEuFTbE9biz5Q7jH7h7YglzgRxK0rhdrurVn7HXoo0TcS7bySRF8wd-YqJV8BriQs41V2yUaX4Oj2r29KGmcaeVJlMY-IusLLWiDgqM0t7OiB8eYoyYqYsi4tyu-4_K2XEAGAIQaJrqE6NB81dNkYRxkhuhRuPzky3oWRTcHWC9xErSuaEJR3CfHOPdWfffhzGLnBap1g_FWjsug7Cn-DTBR9XvlVpqaR0_TxyOhyDQjYCR_-RmXYpvd0wtXfWkMJYz62_etFOOb2T2b6SJUBI_lO6dtnPzLy5li9RK0IFx76JiPKUGM39jt5_doSNlwgqqDIg8P9fPAjyKM94IDiVuEq4USmI2yvTPL3AE_RrakO7LLwPw7pg2BhJ6ZjMNO19pfor_wpLUyWEkv-NhKqfqYr7P8naYWtClyv5do_ln1my-F8XgMrUzEcaUTt7ym6LSTb3sJ5vVoTgD2Ma_IJMTz_yFrID2-TfW4a87IHWzA6Oz69HVyhfY5rQZ-BZrNs5_-UGQu2s4xn5Ci1Qulx1JtWBjM2rbl-g8D8KklliPwxgO6TmGL2gu86W2enRDZcTqo-GEQ2uSRWsBjXSrM6mOfuWL3bpk4_MMDLHYhUUmsUlHzVyLyLFmPDjuUQMvegMxqFCsjxg7EG7UAlcBKLKBLQodmTlKQNr2hefJET2asWl3XsUUzgv4vEMAqn9jC8EQov49ncFf2k81YmD_s5bmLQTPjdBypX6Qzu5hFURA25lbGOW2GjRvd7mcm9cDx1hcjPIeP5Yh9xdZmIv3zJo3eqo8Hdzso1yzeuFRq4IebguL9fw
>
> Peter Nyikos

No, it's not a joke, and the link was and is provided by "Unpaywall" (a Firefox addon, probably available for other browsers as well). There
apparently is a "session timeout" involved, since I see it as well. But I can easily find it again, as could you. It's the paper you asked
John if he could get (the 2006 Palo paper). Is this your idea of a civil reply, are are you just sounding pugnacious for the fun
of it?

On 8/26/21 11:02 AM, Peter Nyikos wrote:
> On Thursday, August 26, 2021 at 12:24:06 AM UTC-4, John Harshman wrote:
>> On 8/25/21 5:46 PM, Peter Nyikos wrote:
>>> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>>>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>>>
>>>>> When I was at an international topology conference in Baku in 1987,
>>>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>>>
>>>>> I can no longer remember whether I realized then that this was from
>>>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>>>> before this discovery. One thing is certain: I became quite interested
>>>>> in this seal and the question of how it got there.
>>>>>
>>>>> I already knew enough paleogeography to know that, no earlier than the
>>>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>>>> to swim from the Atlantic, through the portion that became the
>>>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>>>
>>>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>>>
>>>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>>>> https://en.wikipedia.org/wiki/Baikal_seal
>>>>>
>>>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>>>
>>> By the way, John, can you access the full article where you are?
>> Unemployed biologist, remember? I have only personal subscriptions, and
>> that's not one of them.
>>>>> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
>>>>> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
>>>>> First published: 27 April 2006
>>>
>>>
>>>>> I haven't had time to read the article, but I wish it had been based more than
>>>>> just on mitochondrial sequences; these are not as accurate as full genome
>>>>> sequences.
>>>
>>>> You have been misinformed.
>
> This unequivocal claim has to do with only one aspect of "not as accurate":

It actually has to do with multiple aspects.

>>> Oh, you think they are equally accurate for phylogenetic purposes as
>>> sequencing the full (nuclear) genome, do you?
>
>> For some, yes.
>
> Where the divergence times of the various seals is concerned, it is a bit
> disconcerting to read the word "single" in the first sentence of the "Methods" section:
>
> "The sequences of the entire COI (1545 bp), COII (684 bp), and Cytb (1140 bp) genes were obtained from single individuals of each of P. hispida, P. sibirica, P. caspica, Phoca largha Pallas (larga seal, or spotted seal; University of Alaska Museum collection UAM Mamm 18613), Histriophoca fasciata (Zimmermann) (ribbon seal; UAM Mamm 19029), Cystophora cristata (Erxleben) (hooded seal; UAM Mamm 36480), and Erignathus barbatus (Erxleben) (bearded seal; UAM Mamm 36477). Sequences were deposited in GenBank under accession numbers AY140962–AY140982. In addition, we used published mtDNA-sequence data from Halichoerus grypus (Fabricius) (grey seal X74002; Árnason et al., 1993) and Phoca vitulina L. (harbour seal X63726; Árnason & Johnsson, 1992).
>
> Do you trust samples of one individual per species? If so, that adds irony to the "For some, yes".

It depends. The longer the species have been separated, the less you
need a big sample. And mitochondrial sequences are the least likely of
all sequences to need these multiple samples, since they're the least
likely to maintain multiple lineages for a long time. A bigger sample is
always nice, but is it necessary? And how reasonable is it to expect
multiple samples for some of these species?

>> One advantage of mtDNA is that it evolves faster and so
>> accumulates more data per site per million years. If the mtDNA is only
>> 4% divergent, I would expect the nuclear DNA to be less than 1%
>> divergent.
>
> But the absolute numbers are reversed, given the number of genes in the survey.

I do not know what you are talking about here. Could you explain what
you mean?

>> Another advantage is that coalescence time is expected to be
>> 1/4 that of an autosomal locus, so less incomplete lineage sorting.
>
> Interesting concept, "autosomal". Wouldn't you expect just as much
> crossover in an XX female or a ZZ male as in a non-sex chromosome pair?

Per individual, yes. But per species, no, as the X chromosome spends
only 2/3 as much time in females as in males, and thus experiences, over
generations, less crossing over.

>> Finally, it's a single linkage group, so less incompatible lineage sorting.
>
> "single linkage" refers to mitochondria being passed down through the female line exclusively,
> I presume. You aren't making any concessions for a layman like Mario.

You are not correct in your presumption. It means that the mitochondrial
genome is inherited as a unit, with no crossing over to separate or
combine sequences with separate histories.

> In the same vein, I take it "incompatible" [as opposed to "incomplete"]
> is a "hindsight is 20/20" type concept.

You take it wrong. I simply mean that all the genes in the mitochondrion
must have the same history, while nearby autosomal sequences can have
different histories; they are not permanently linked but recombine. A
linkage group is a chromosomal sequence that has not recombined over
some lengthy period of time.

> By the way, it just now occurred to me: I wonder whether any efforts have been
> made to mate the three species under consideration in captivity. I can't help remembering how
> the polar bear was once considered to be a separate *genus* from the brown bear,
> even though it was known that they could interbreed in captivity and produce fertile
> offspring. But the prevalent species concept finally gave way to common sense,
> as the polar bear was downgraded to a separate subspecies,

Polar bears are a separate species. Who has downgraded them? Inability
to interbreed in captivity is not a criterion for specieshood.

>>>> Mitochrondrial sequences are quite accurate for many purposes.
>>>
>>> Can you ascertain the purposes of the authors enough to deduce that the
>>> mitochondrial sequences will go as far towards answering the questions of the
>>> authors as sequencing the full genome?
>
> Short answer: no. But now that Pandora has given you a non-paywalled access
> to the article, perhaps you can answer this question eventually, yourself.

Perhaps. I'll look And perhaps you could too.

> PS I've left in your snarky "answer," which begins a bunch of themes which have
> nothing to do with the topic of the OP, but deleted the rest, part of which was
> self-contradictory, but also part of which might be useful on some future thread.

There is nothing snarky in my answer, and it is indeed relevant to the
topic. Nor was anything self-contradictory; that suggests you may not
have understood it.

>> You toss off "sequencing the full genome" so lightly. Even today it
>> takes thousands of dollars and months of time just to get the raw reads,
>> much less assembly and alignment, much less proper analysis.

What I'm trying to tell you is that science must submit to practicality.
It might be nice to have whole genomes for everything (and perhaps
multiple genomes for every species), this is not practical, for reasons
of time, money, and effort. Was that not clear?

On Thursday, August 26, 2021 at 4:41:03 PM UTC-4, erik simpson wrote:
> On Thursday, August 26, 2021 at 1:18:59 PM UTC-7, Peter Nyikos wrote:
> > On Thursday, August 26, 2021 at 3:59:13 PM UTC-4, erik simpson wrote:
> > > On Wednesday, August 25, 2021 at 5:46:50 PM UTC-7, Peter Nyikos wrote:
> > > > On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> > > > > On 8/25/21 3:20 PM, Peter Nyikos wrote:
> > > >
> > > > > > When I was at an international topology conference in Baku in 1987,
> > > > > > the shore of the Caspian sea was an easy climb down from our dormitory.
> > > > > > One day as I walked on the beach, I spotted what looked like a skeleton
> > > > > > of a human hand. As I approached, it became clear that the proportions were wrong.
> > > > > >
> > > > > > I can no longer remember whether I realized then that this was from
> > > > > > a flipper of the Caspian seal, or even whether I had read about this seal
> > > > > > before this discovery. One thing is certain: I became quite interested
> > > > > > in this seal and the question of how it got there.
> > > > > >
> > > > > > I already knew enough paleogeography to know that, no earlier than the
> > > > > > Pliocene, enough of the great sea Tethys remained for any sea creature
> > > > > > to swim from the Atlantic, through the portion that became the
> > > > > > Mediterranean, thence to the paleo-Black sea, and thence to where
> > > > > > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > > > > > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> > > > > >
> > > > > > But there is another landlocked seal whose origin is still something of a mystery:
> > > > > >
> > > > > > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > > > > > https://en.wikipedia.org/wiki/Baikal_seal
> > > > > >
> > > > > > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j..1095-8312.2006.00607.x
> > > > By the way, John, can you access the full article where you are?
> > > > > > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > > > > > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > > > > > First published: 27 April 2006
> > > >
> > > >
> > > > > > I haven't had time to read the article, but I wish it had been based more than
> > > > > > just on mitochondrial sequences; these are not as accurate as full genome
> > > > > > sequences.
> > > >
> > > > > You have been misinformed.
> > > > Oh, you think they are equally accurate for phylogenetic purposes as
> > > > sequencing the full (nuclear) genome, do you?
> > > > > Mitochrondrial sequences are quite accurate for many purposes.
> > > > Can you ascertain the purposes of the authors enough to deduce that the
> > > > mitochondrial sequences will go as far towards answering the questions of the
> > > > authors as sequencing the full genome?
> > > > > "Full genome sequences", if by that you actually mean
> > > > > the complete sequence of an entire genome, are not remotely necessary.
> > > > So much for the Human Genome Project, eh?
> > > >
> > > > Or was that a misnomer? Did they only sequence protein coding genes, meaning
> > > > that they are transcribed into mRNA that are translated into proteins without modification?
> > > > > > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > > > > > but the abstract, which I will be posting in a follow-up to this OP, makes
> > > > > > it plausible that we can reconstruct events to an accuracy that can
> > > > > > satisfy laymen like myself.
> > > > > >
> > > > > >
> > > > Peter Nyikos
> > > > Professor, Dept. of Mathematics -- standard disclaimer--
> > > > at Univ. of South Carolina
> > > > http://people.math.sc.edu/nyikos
> >
> > > Here's your Baikal and Caspian Sea seal paper:
> > Is this your idea of a joke? When I clicked on your gargantuan link, this is what I got:
> >
> > "Your session has timed out. Please go back to the article page and click the PDF link again."
> >
> > And what do you mean by "your"? which paper, if any, did you have in mind?
> >
> > > https://watermark.silverchair.com/j.1095-8312.2006.00607.x.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuowggLmBgkqhkiG9w0BBwagggLXMIIC0wIBADCCAswGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxNMe2X9FgGiGE9xWAgEQgIICnYRSAvgi9iJIYfT8ZqUXJZKBDrTIQ7PY_Uu7RYr030v4mUY4Spt8IG4z0LHtMgbB5gRft7kCWwzzGEuFTbE9biz5Q7jH7h7YglzgRxK0rhdrurVn7HXoo0TcS7bySRF8wd-YqJV8BriQs41V2yUaX4Oj2r29KGmcaeVJlMY-IusLLWiDgqM0t7OiB8eYoyYqYsi4tyu-4_K2XEAGAIQaJrqE6NB81dNkYRxkhuhRuPzky3oWRTcHWC9xErSuaEJR3CfHOPdWfffhzGLnBap1g_FWjsug7Cn-DTBR9XvlVpqaR0_TxyOhyDQjYCR_-RmXYpvd0wtXfWkMJYz62_etFOOb2T2b6SJUBI_lO6dtnPzLy5li9RK0IFx76JiPKUGM39jt5_doSNlwgqqDIg8P9fPAjyKM94IDiVuEq4USmI2yvTPL3AE_RrakO7LLwPw7pg2BhJ6ZjMNO19pfor_wpLUyWEkv-NhKqfqYr7P8naYWtClyv5do_ln1my-F8XgMrUzEcaUTt7ym6LSTb3sJ5vVoTgD2Ma_IJMTz_yFrID2-TfW4a87IHWzA6Oz69HVyhfY5rQZ-BZrNs5_-UGQu2s4xn5Ci1Qulx1JtWBjM2rbl-g8D8KklliPwxgO6TmGL2gu86W2enRDZcTqo-GEQ2uSRWsBjXSrM6mOfuWL3bpk4_MMDLHYhUUmsUlHzVyLyLFmPDjuUQMvegMxqFCsjxg7EG7UAlcBKLKBLQodmTlKQNr2hefJET2asWl3XsUUzgv4vEMAqn9jC8EQov49ncFf2k81YmD_s5bmLQTPjdBypX6Qzu5hFURA25lbGOW2GjRvd7mcm9cDx1hcjPIeP5Yh9xdZmIv3zJo3eqo8Hdzso1yzeuFRq4IebguL9fw
> >
> > Peter Nyikos

> No, it's not a joke, and the link was and is provided by "Unpaywall" (a Firefox addon, probably available for other browsers as well). There
> apparently is a "session timeout" involved, since I see it as well. But I can easily find it again, as could you.

HOW? The word "Unpaywall" tells me next to nothing.

> It's the paper you asked
> John if he could get (the 2006 Palo paper).

Do you have a slow newsfeed? Pandora posted a free source back at at 10:15:12 AM UTC-4;
compare that to when you first posted your gargantuan link, as shown in the third attribution line above:
[reposted:]
> > On Thursday, August 26, 2021 at 3:59:13 PM UTC-4, erik simpson wrote:

Over six hours later. Google Groups gives coverage up to that many *minutes* ago. What do you use
for a newsreader.

As for why I was asking which paper was supposedly "yours" [read: mine] I was hoping that
you had an even more up to date paper than the enormously helpful 2010 paper
that Pandora posted over an hour before you sent off your 3:59:13 post, and I thanked her
less than a minute after you sent it.

<pugnacious comment by you deleted here>

Peter Nyikos

On Thursday, August 26, 2021 at 3:46:13 PM UTC-7, Peter Nyikos wrote:
> On Thursday, August 26, 2021 at 4:41:03 PM UTC-4, erik simpson wrote:
> > On Thursday, August 26, 2021 at 1:18:59 PM UTC-7, Peter Nyikos wrote:
> > > On Thursday, August 26, 2021 at 3:59:13 PM UTC-4, erik simpson wrote:
> > > > On Wednesday, August 25, 2021 at 5:46:50 PM UTC-7, Peter Nyikos wrote:
> > > > > On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
> > > > > > On 8/25/21 3:20 PM, Peter Nyikos wrote:
> > > > >
> > > > > > > When I was at an international topology conference in Baku in 1987,
> > > > > > > the shore of the Caspian sea was an easy climb down from our dormitory.
> > > > > > > One day as I walked on the beach, I spotted what looked like a skeleton
> > > > > > > of a human hand. As I approached, it became clear that the proportions were wrong.
> > > > > > >
> > > > > > > I can no longer remember whether I realized then that this was from
> > > > > > > a flipper of the Caspian seal, or even whether I had read about this seal
> > > > > > > before this discovery. One thing is certain: I became quite interested
> > > > > > > in this seal and the question of how it got there.
> > > > > > >
> > > > > > > I already knew enough paleogeography to know that, no earlier than the
> > > > > > > Pliocene, enough of the great sea Tethys remained for any sea creature
> > > > > > > to swim from the Atlantic, through the portion that became the
> > > > > > > Mediterranean, thence to the paleo-Black sea, and thence to where
> > > > > > > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > > > > > > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
> > > > > > >
> > > > > > > But there is another landlocked seal whose origin is still something of a mystery:
> > > > > > >
> > > > > > > "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> > > > > > > https://en.wikipedia.org/wiki/Baikal_seal
> > > > > > >
> > > > > > > [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
> > > > > By the way, John, can you access the full article where you are?
> > > > > > > The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> > > > > > > JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> > > > > > > First published: 27 April 2006
> > > > >
> > > > >
> > > > > > > I haven't had time to read the article, but I wish it had been based more than
> > > > > > > just on mitochondrial sequences; these are not as accurate as full genome
> > > > > > > sequences.
> > > > >
> > > > > > You have been misinformed.
> > > > > Oh, you think they are equally accurate for phylogenetic purposes as
> > > > > sequencing the full (nuclear) genome, do you?
> > > > > > Mitochrondrial sequences are quite accurate for many purposes.
> > > > > Can you ascertain the purposes of the authors enough to deduce that the
> > > > > mitochondrial sequences will go as far towards answering the questions of the
> > > > > authors as sequencing the full genome?
> > > > > > "Full genome sequences", if by that you actually mean
> > > > > > the complete sequence of an entire genome, are not remotely necessary.
> > > > > So much for the Human Genome Project, eh?
> > > > >
> > > > > Or was that a misnomer? Did they only sequence protein coding genes, meaning
> > > > > that they are transcribed into mRNA that are translated into proteins without modification?
> > > > > > > The timing of events is ultimately to be found elsewhere than in phylogeny,
> > > > > > > but the abstract, which I will be posting in a follow-up to this OP, makes
> > > > > > > it plausible that we can reconstruct events to an accuracy that can
> > > > > > > satisfy laymen like myself.
> > > > > > >
> > > > > > >
> > > > > Peter Nyikos
> > > > > Professor, Dept. of Mathematics -- standard disclaimer--
> > > > > at Univ. of South Carolina
> > > > > http://people.math.sc.edu/nyikos
> > >
> > > > Here's your Baikal and Caspian Sea seal paper:
> > > Is this your idea of a joke? When I clicked on your gargantuan link, this is what I got:
> > >
> > > "Your session has timed out. Please go back to the article page and click the PDF link again."
> > >
> > > And what do you mean by "your"? which paper, if any, did you have in mind?
> > >
> > > > https://watermark.silverchair.com/j.1095-8312.2006.00607.x.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuowggLmBgkqhkiG9w0BBwagggLXMIIC0wIBADCCAswGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxNMe2X9FgGiGE9xWAgEQgIICnYRSAvgi9iJIYfT8ZqUXJZKBDrTIQ7PY_Uu7RYr030v4mUY4Spt8IG4z0LHtMgbB5gRft7kCWwzzGEuFTbE9biz5Q7jH7h7YglzgRxK0rhdrurVn7HXoo0TcS7bySRF8wd-YqJV8BriQs41V2yUaX4Oj2r29KGmcaeVJlMY-IusLLWiDgqM0t7OiB8eYoyYqYsi4tyu-4_K2XEAGAIQaJrqE6NB81dNkYRxkhuhRuPzky3oWRTcHWC9xErSuaEJR3CfHOPdWfffhzGLnBap1g_FWjsug7Cn-DTBR9XvlVpqaR0_TxyOhyDQjYCR_-RmXYpvd0wtXfWkMJYz62_etFOOb2T2b6SJUBI_lO6dtnPzLy5li9RK0IFx76JiPKUGM39jt5_doSNlwgqqDIg8P9fPAjyKM94IDiVuEq4USmI2yvTPL3AE_RrakO7LLwPw7pg2BhJ6ZjMNO19pfor_wpLUyWEkv-NhKqfqYr7P8naYWtClyv5do_ln1my-F8XgMrUzEcaUTt7ym6LSTb3sJ5vVoTgD2Ma_IJMTz_yFrID2-TfW4a87IHWzA6Oz69HVyhfY5rQZ-BZrNs5_-UGQu2s4xn5Ci1Qulx1JtWBjM2rbl-g8D8KklliPwxgO6TmGL2gu86W2enRDZcTqo-GEQ2uSRWsBjXSrM6mOfuWL3bpk4_MMDLHYhUUmsUlHzVyLyLFmPDjuUQMvegMxqFCsjxg7EG7UAlcBKLKBLQodmTlKQNr2hefJET2asWl3XsUUzgv4vEMAqn9jC8EQov49ncFf2k81YmD_s5bmLQTPjdBypX6Qzu5hFURA25lbGOW2GjRvd7mcm9cDx1hcjPIeP5Yh9xdZmIv3zJo3eqo8Hdzso1yzeuFRq4IebguL9fw
> > >
> > > Peter Nyikos
>
> > No, it's not a joke, and the link was and is provided by "Unpaywall" (a Firefox addon, probably available for other browsers as well). There
> > apparently is a "session timeout" involved, since I see it as well. But I can easily find it again, as could you.
> HOW? The word "Unpaywall" tells me next to nothing.
> > It's the paper you asked
> > John if he could get (the 2006 Palo paper).
> Do you have a slow newsfeed? Pandora posted a free source back at at 10:15:12 AM UTC-4;
> compare that to when you first posted your gargantuan link, as shown in the third attribution line above:
> [reposted:]
> > > On Thursday, August 26, 2021 at 3:59:13 PM UTC-4, erik simpson wrote:
> Over six hours later. Google Groups gives coverage up to that many *minutes* ago. What do you use
> for a newsreader.
>
> As for why I was asking which paper was supposedly "yours" [read: mine] I was hoping that
> you had an even more up to date paper than the enormously helpful 2010 paper
> that Pandora posted over an hour before you sent off your 3:59:13 post, and I thanked her
> less than a minute after you sent it.
>
>
> <pugnacious comment by you deleted here>
>
>
> Peter Nyikos

I never should respond to you, but for your amusement,

https://unpaywall.org/

And yes, just using google would also reveal where you could read it. Google isn't necessarily anyone's friend, but
many find it useful.

On 8/26/21 11:51 AM, Pandora wrote:
> On Thu, 26 Aug 2021 08:49:47 -0700 (PDT), Peter Nyikos
> <peter2nyikos@gmail.com> wrote:
>
>> On Thursday, August 26, 2021 at 10:15:12 AM UTC-4, Pandora wrote:
>>> On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
>>> <jhar...@pacbell.net> wrote:
>>>
>>>> On 8/25/21 5:46 PM, Peter Nyikos wrote:
>>>>> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>>>>>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>>>>>
>>>>>>> When I was at an international topology conference in Baku in 1987,
>>>>>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>>>>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>>>>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>>>>>
>>>>>>> I can no longer remember whether I realized then that this was from
>>>>>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>>>>>> before this discovery. One thing is certain: I became quite interested
>>>>>>> in this seal and the question of how it got there.
>>>>>>>
>>>>>>> I already knew enough paleogeography to know that, no earlier than the
>>>>>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>>>>>> to swim from the Atlantic, through the portion that became the
>>>>>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>>>>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>>>>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>>>>>
>>>>>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>>>>>
>>>>>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>>>>>> https://en.wikipedia.org/wiki/Baikal_seal
>>>>>>>
>>>>>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>>>>>
>>>>> By the way, John, can you access the full article where you are?
>>>>
>>>> Unemployed biologist, remember? I have only personal subscriptions, and
>>>> that's not one of them.
>>
>>> It's free:
>>> https://academic.oup.com/biolinnean/article/88/1/61/2691557
>>
>> Thank you, Pandora. You've saved us all a lot of trouble. The article is so disorganized, and so
>> much of the text is so tentative, that I would have had to quote practically the whole
>> article for John to make any sense of it.
>>
>> In particular, the Conclusions portion ends with the paleogeographical mystery untouched:
>>
>> "Nevertheless, the actual geographical conditions that would have facilitated the continental invasions
>> in those times still remain undocumented and enigmatic."
>>
>> The Conclusion opts for the current distribution of Arctic/Caspian/Baikal species (*hispida*/ *caspica*/ *sibirica*)
>> already in place at 2-3 mya, but not much earlier, and seems to be wholly based on mitochondrial "molecular clocks":
>>
>> "From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2–3?Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin." [from the Abstract of the article you've linked].
>>
>> This is in contrast to the very detailed paleogeographical information supporting the widely held first of
>> the "prevailing hypotheses." It argues for easy dispersal of all three species, especially the arctic and the
>> Baikal, as seen in the map I linked for Mario for the latest ice age:
>>
>> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg
>>
>> If that map is accurate in its main features [never mind the incredible detail of the smaller rivers],
>> one would naturally expect mixing of the three species, *hispida*, *caspica*, and *sibirica*, to
>> have greatly confused the mitochondrial data if those HAD originally diverged 2-3 mya.
>>
>>
>> Pandora, if you can make any sense out of all this, I would love to see it, no matter how
>> tentative it may have to be.
>
> Also check Fulton and Strobeck (2010):
> https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02271.x
>
> Full text pdf avalable at:
> http://bbcd.bio.uniroma1.it/bbcd/sites/default/files/file%20lezioni/Fulton_Foche.pdf
>
> Interestingly, they do recover a monophyletic Pusa (although
> relationships within Pusa are not confidently resolved) with a
> divergence estimate between 1.7 and 0.8 Ma.
> This would support a Lower Pleistocene scenario.
>
Not thrilled. The phylogenetic analysis seems secondary and is only
partly reported. In particular, I don't see any measures of support for
most nodes. And the analysis assumes that all loci have a common
phylogeny, which may not be true.

I have to correct a statement that I made in my OP:

On Wednesday, August 25, 2021 at 6:20:26 PM UTC-4, Peter Nyikos wrote:

> I already knew enough paleogeography to know that, no earlier than the
> Pliocene, enough of the great sea Tethys remained for any sea creature
> to swim from the Atlantic, through the portion that became the
> Mediterranean, thence to the paleo-Black sea, and thence to where
> the Caspian Sea is now. It did not surprise me, for instance, to learn that
> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.

I may have to un-learn this, which I had read a long time ago in a place which took for
granted the former existence of the Caspian Sea dolphin. I can't recall it mentioning any evidence.

But today, the only places I have been able to find in a Yahoo search refer to alleged rock art
depicting them, but no hint of fossils.

And I do mean "alleged": here are some sources and the dead ends that resulted:

(1) https://www.livescience.com/57999-caspian-sea-facts.html
"Nearby petroglyphs suggest that dolphins and porpoises may have once lived in the Caspian Sea, according to the Smithsonian Institution."
[embedded link here is a dud; so is the earlier one to the WWF; the in-between one to Casp Info is hardly better]

(2) https://en.wikipedia.org/wiki/Caspian_Sea
"Archeological studies of Gobustan Rock Art have identified what may be dolphins[23] and porpoises,[24][25] or a certain species of beaked whales[26] and what may be a whaling scene indicates large baleen whales[27] likely being present in Caspian Sea at least until when the Caspian Sea ceased being a part of the ocean system or until the Quaternary or much more recent periods such as until the last glacial period or antiquity.[28] Although the rock art on Kichikdash Mountain is assumed to be of a dolphin[29] or of a beaked whale,[26] it might instead represent the famous beluga sturgeon due to its size (430 cm in length), but fossil records suggest certain ancestors of modern dolphins and whales, such as Macrokentriodon morani (bottlenose dolphins) and Balaenoptera sibbaldina (blue whales) were presumably larger than their present descendants."

(2a) The embedded link to Ghobustan Rock Art is misleading: there is a mention of a longboat,
but no sea mammals at all are mentioned:
https://en.wikipedia.org/wiki/Gobustan_Rock_Art

(2b) The numbered links are typical Wikipedia links to the general entries on the things highlighted in blue
immediately preceding them. No help at all as far as the theme of the paragraph goes.

(2c) "fossil records suggest" has nothing to do with the Caspian region. It is just an indication that
one should not be deterred by the large size of the "famous beluga sturgeon" from interpreting
the alleged rock art as indicating cetaceans.

(3) https://donsmaps.com/gobustan.html
Lots of pictures of boat rock art here, some obviously fake, some looking quite genuine,
but no mention of sea mammals of any kind, not even the Caspian seal.

It's getting monotonous:

(4) https://www.icnnational.com/10-caspian-sea-facts-you-must-know/
"Through archaeological surveys, researchers have identified possible evidence of dolphins, porpoises, and whales in the Sea around 50,000 – 100,000 years ago.
There have also been cave and rock arts dating to the same period indicating reliefs of dolphins and whales. These ancestors to the modern-day species were considerably larger."

No references, no embedded links.

I gave up at this point.

Peter Nyikos

> But there is another landlocked seal whose origin is still something of a mystery:
>
> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
> https://en.wikipedia.org/wiki/Baikal_seal
>
> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312..2006.00607.x
> The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences
> JUKKA U. PALO, RISTO VÄINÖLÄ, Biological Journal of the Linnean Society
> First published: 27 April 2006
>
> I haven't had time to read the article, but I wish it had been based more than
> just on mitochondrial sequences; these are not as accurate as full genome
> sequences.
>
> The timing of events is ultimately to be found elsewhere than in phylogeny,
> but the abstract, which I will be posting in a follow-up to this OP, makes
> it plausible that we can reconstruct events to an accuracy that can
> satisfy laymen like myself.
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos

On Thursday, August 26, 2021 at 8:14:34 PM UTC-4, Peter Nyikos wrote:
> I have to correct a statement that I made in my OP:

There may be some hope after all, see below.

> On Wednesday, August 25, 2021 at 6:20:26 PM UTC-4, Peter Nyikos wrote:
>
> > I already knew enough paleogeography to know that, no earlier than the
> > Pliocene, enough of the great sea Tethys remained for any sea creature
> > to swim from the Atlantic, through the portion that became the
> > Mediterranean, thence to the paleo-Black sea, and thence to where
> > the Caspian Sea is now. It did not surprise me, for instance, to learn that
> > there was once a Caspian Sea dolphin, nor that it became extinct before historical times.

> I may have to un-learn this, which I had read a long time ago in a place which took for
> granted the former existence of the Caspian Sea dolphin. I can't recall it mentioning any evidence.
>
>
> But today, the only places I have been able to find in a Yahoo search refer to alleged rock art
> depicting them, but no hint of fossils.
>
> And I do mean "alleged": here are some sources and the dead ends that resulted:
>
> (1) https://www.livescience.com/57999-caspian-sea-facts.html
> "Nearby petroglyphs suggest that dolphins and porpoises may have once lived in the Caspian Sea, according to the Smithsonian Institution."
> [embedded link here is a dud; so is the earlier one to the WWF; the in-between one to Casp Info is hardly better]

I did find something from the Smithsonian in a different way:
>
> (2) https://en.wikipedia.org/wiki/Caspian_Sea
> "Archeological studies of Gobustan Rock Art have identified what may be dolphins[23] and porpoises,[24][25] or a certain species of beaked whales[26] and what may be a whaling scene indicates large baleen whales[27] likely being present in Caspian Sea at least until when the Caspian Sea ceased being a part of the ocean system or until the Quaternary or much more recent periods such as until the last glacial period or antiquity.[28] Although the rock art on Kichikdash Mountain is assumed to be of a dolphin[29] or of a beaked whale,[26]

I overlooked that these two references did not follow the usual pattern (2b below) but did give some information:

Smithsonian, "Ghobustan Petroglyphs":
"For example, Farajova discusses the image believed to be a dolphin on Kichikdash Mountain. The levels of the Caspian Sea and the existence of dolphins in the Caspian Sea from the Quaternary period lead researchers to date the rock drawing to the end of the Upper Pleistocene."
https://web.archive.org/web/20150428044511/http://gobustan.si.edu/dating_methods_chronology

Farajova, Malahat. 2010. “Pleistocene Art in Azerbaijan.” IFRAO Congress, September.
Farajova, Malahat. 2009. Rock Art of Azerbaijan. Baku.
https://web.archive.org/web/20150428044334/http://gobustan.si.edu/resources

Unfortunately, no pictures were shown. The second resource did show a picture:

"On Kichickdash hill a 4m long ‘fish’ carved on this outcrop bears no anatomical relationship to any Caspian Sea species. The large size of the carving and its anatomical features suggests it may in fact be a dolphin or beaked whale as viewed from above. (Farajova, 2009) (Figure A)."
https://grahamhancock.com/gallagherr1/

Figure A image:
https://grahamhancock.com/wp-content/uploads/2014/12/GallagherR1-alarge.jpg

Looks promising, but I see what looks like an anal fin.

Peter Nyikos

On Thu, 26 Aug 2021 16:03:47 -0700, John Harshman
<jharshman@pacbell.net> wrote:

>On 8/26/21 11:51 AM, Pandora wrote:
>> On Thu, 26 Aug 2021 08:49:47 -0700 (PDT), Peter Nyikos
>> <peter2nyikos@gmail.com> wrote:
>>
>>> On Thursday, August 26, 2021 at 10:15:12 AM UTC-4, Pandora wrote:
>>>> On Wed, 25 Aug 2021 21:24:00 -0700, John Harshman
>>>> <jhar...@pacbell.net> wrote:
>>>>
>>>>> On 8/25/21 5:46 PM, Peter Nyikos wrote:
>>>>>> On Wednesday, August 25, 2021 at 6:56:17 PM UTC-4, John Harshman wrote:
>>>>>>> On 8/25/21 3:20 PM, Peter Nyikos wrote:
>>>>>>
>>>>>>>> When I was at an international topology conference in Baku in 1987,
>>>>>>>> the shore of the Caspian sea was an easy climb down from our dormitory.
>>>>>>>> One day as I walked on the beach, I spotted what looked like a skeleton
>>>>>>>> of a human hand. As I approached, it became clear that the proportions were wrong.
>>>>>>>>
>>>>>>>> I can no longer remember whether I realized then that this was from
>>>>>>>> a flipper of the Caspian seal, or even whether I had read about this seal
>>>>>>>> before this discovery. One thing is certain: I became quite interested
>>>>>>>> in this seal and the question of how it got there.
>>>>>>>>
>>>>>>>> I already knew enough paleogeography to know that, no earlier than the
>>>>>>>> Pliocene, enough of the great sea Tethys remained for any sea creature
>>>>>>>> to swim from the Atlantic, through the portion that became the
>>>>>>>> Mediterranean, thence to the paleo-Black sea, and thence to where
>>>>>>>> the Caspian Sea is now. It did not surprise me, for instance, to learn that
>>>>>>>> there was once a Caspian Sea dolphin, nor that it became extinct before historical times.
>>>>>>>>
>>>>>>>> But there is another landlocked seal whose origin is still something of a mystery:
>>>>>>>>
>>>>>>>> "It is something of a mystery how Baikal seals came to live there in the first place. They may have swum up rivers and streams or possibly Lake Baikal was linked to the ocean at some point through a large body of water, such as the West Siberian Glacial Lake or West Siberian Plain, formed in a previous ice age. The seals are estimated to have inhabited Lake Baikal for some two million years.[7]"
>>>>>>>> https://en.wikipedia.org/wiki/Baikal_seal
>>>>>>>>
>>>>>>>> [7] is here: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1095-8312.2006.00607.x
>>>>>>
>>>>>> By the way, John, can you access the full article where you are?
>>>>>
>>>>> Unemployed biologist, remember? I have only personal subscriptions, and
>>>>> that's not one of them.
>>>
>>>> It's free:
>>>> https://academic.oup.com/biolinnean/article/88/1/61/2691557
>>>
>>> Thank you, Pandora. You've saved us all a lot of trouble. The article is so disorganized, and so
>>> much of the text is so tentative, that I would have had to quote practically the whole
>>> article for John to make any sense of it.
>>>
>>> In particular, the Conclusions portion ends with the paleogeographical mystery untouched:
>>>
>>> "Nevertheless, the actual geographical conditions that would have facilitated the continental invasions
>>> in those times still remain undocumented and enigmatic."
>>>
>>> The Conclusion opts for the current distribution of Arctic/Caspian/Baikal species (*hispida*/ *caspica*/ *sibirica*)
>>> already in place at 2-3 mya, but not much earlier, and seems to be wholly based on mitochondrial "molecular clocks":
>>>
>>> "From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2–3?Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin." [from the Abstract of the article you've linked].
>>>
>>> This is in contrast to the very detailed paleogeographical information supporting the widely held first of
>>> the "prevailing hypotheses." It argues for easy dispersal of all three species, especially the arctic and the
>>> Baikal, as seen in the map I linked for Mario for the latest ice age:
>>>
>>> https://en.wikipedia.org/wiki/West_Siberian_Glacial_Lake#/media/File:Ice_Age_glacial_lakes_of_Siberia_and_Central_Asia_-_ru.svg
>>>
>>> If that map is accurate in its main features [never mind the incredible detail of the smaller rivers],
>>> one would naturally expect mixing of the three species, *hispida*, *caspica*, and *sibirica*, to
>>> have greatly confused the mitochondrial data if those HAD originally diverged 2-3 mya.
>>>
>>>
>>> Pandora, if you can make any sense out of all this, I would love to see it, no matter how
>>> tentative it may have to be.
>>
>> Also check Fulton and Strobeck (2010):
>> https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02271.x
>>
>> Full text pdf avalable at:
>> http://bbcd.bio.uniroma1.it/bbcd/sites/default/files/file%20lezioni/Fulton_Foche.pdf
>>
>> Interestingly, they do recover a monophyletic Pusa (although
>> relationships within Pusa are not confidently resolved) with a
>> divergence estimate between 1.7 and 0.8 Ma.
>> This would support a Lower Pleistocene scenario.
>>
>Not thrilled.

You don't have to be, just regard it as an alternative hypothesis on
the basis of an expanded dataset.

>The phylogenetic analysis seems secondary and is only
>partly reported.

It seems to me that historical biogeography doesn't make much sense
without a prior phylogeny.

>In particular, I don't see any measures of support for
>most nodes.

In fig.2 I notice that most nodes have a BPP=1.0. Wouldn't that be a
measure of support?

>And the analysis assumes that all loci have a common
>phylogeny, which may not be true.

How can we know?
Brower and Schuh (2021): "Both van Fraassen and Popper held that every
observation is theory laden and that truth is elusive. Applying these
perspectives to the context of biological systematics, we consider the
"true tree", reflecting the actual history of the origins of
biological diversity through time, to be an unattainable metaphysical
goal."
https://www.cornellpress.cornell.edu/book/9781501752773/biological-systematics/#bookTabs=1