On 8/28/21 3:20 AM, Pandora wrote:
> 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.

True. So it's puzzling that they don't explain it.

>> 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?

I missed that. But one wonders if there was adequate mixing in order to
make that a valid measure.

>> And the analysis assumes that all loci have a common
>> phylogeny, which may not be true.
>
> How can we know?

Assaying single-locus phylogenies would help. As would jackknifing.

> 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

One should still try to attain it, right?

On 8/25/2021 6:20 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.
>
> 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
>

Perhaps this can help elucidate a potential answer:
https://peerj.com/articles/9665/

It's a paper describing the discovery of a thousand year old elephant
seal fossil in Illinois. It swam to there via the Mississippi River.
It's not out of the realm of possibility that something similar happened
with the progenitors of the Baikal seal.

On 8/28/2021 12:25 PM, Oxyaena wrote:
> On 8/25/2021 6:20 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.
>>
>> 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
>>
>
> Perhaps this can help elucidate a potential answer:
> https://peerj.com/articles/9665/
>
> It's a paper describing the discovery of a thousand year old elephant
> seal fossil in Illinois. It swam to there via the Mississippi River.
> It's not out of the realm of possibility that something similar happened
> with the progenitors of the Baikal seal.

No response? For shame, Peter.