https://pubmed.ncbi.nlm.nih.gov/37695319/

The pdf of this article labels it as a point of view article. It is an
open access article where the authors claim that the greater depth of
the estimated phylogenetic node than an estimate based on the existing
fossil record is due to an artifact of the Baysian inference of clade
origin. It is common knowledge that molecular clock estimates of
lineage separation is usually older than the first fossils of a new
branching lineage.

It sounds like it should be true if you have priors that include the
oldest known fossils, but I really do not know if the people looking at
the Cambrian diversification of bilateral animals do that. I haven't
looked into it for decades, but they used to calibrate the clock using
related lineages that had a better fossil record that was dated more
accurately. You didn't use the nodes that you were trying to estimate,
but Baysian methods do, do a reiteration from some original estimate.

Ron Okimoto

On 12/13/2023 7:58 PM, RonO wrote:
> https://pubmed.ncbi.nlm.nih.gov/37695319/
>
> The pdf of this article labels it as a point of view article.  It is an
> open access article where the authors claim that the greater depth of
> the estimated phylogenetic node than an estimate based on the existing
> fossil record is due to an artifact of the Baysian inference of clade
> origin.  It is common knowledge that molecular clock estimates of
> lineage separation is usually older than the first fossils of a new
> branching lineage.
>
> It sounds like it should be true if you have priors that include the
> oldest known fossils, but I really do not know if the people looking at
> the Cambrian diversification of bilateral animals do that.  I haven't
> looked into it for decades, but they used to calibrate the clock using
> related lineages that had a better fossil record that was dated more
> accurately.  You didn't use the nodes that you were trying to estimate,
> but Baysian methods do, do a reiteration from some original estimate.
>
> Ron Okimoto
>

It might be noted that the human-chimp divergence was estimated to be
4.5 to 8 million years ago, back in the 1980's and the subsequent
estimates keep falling within that range. In this case the additional
fossil evidence that has accumlated has pushed the estimate further into
the past rather than closer to the 4.5 million year estimate. The
bipedal fossils are pushing the estimate over 6 million, and I recall
seeing an 8 million year estimate.

Ron Okimoto

On Wednesday, December 13, 2023 at 6:02:08 PM UTC-8, RonO wrote:
> https://pubmed.ncbi.nlm.nih.gov/37695319/
>
> The pdf of this article labels it as a point of view article. It is an
> open access article where the authors claim that the greater depth of
> the estimated phylogenetic node than an estimate based on the existing
> fossil record is due to an artifact of the Baysian inference of clade
> origin. It is common knowledge that molecular clock estimates of
> lineage separation is usually older than the first fossils of a new
> branching lineage.
>
> It sounds like it should be true if you have priors that include the
> oldest known fossils, but I really do not know if the people looking at
> the Cambrian diversification of bilateral animals do that. I haven't
> looked into it for decades, but they used to calibrate the clock using
> related lineages that had a better fossil record that was dated more
> accurately. You didn't use the nodes that you were trying to estimate,
> but Baysian methods do, do a reiteration from some original estimate.
>
> Ron Okimoto
Bilaterian divergence took place deep in the Ediacaran, but the record is
pretty sparse. As you say, the best molecular clock estimates should be
older unless you happened to find a fossil immediately after the divergence..

On Wednesday, December 13, 2023 at 7:22:08 PM UTC-8, erik simpson wrote:
> On Wednesday, December 13, 2023 at 6:02:08 PM UTC-8, RonO wrote:
> > https://pubmed.ncbi.nlm.nih.gov/37695319/
> >
> > The pdf of this article labels it as a point of view article. It is an
> > open access article where the authors claim that the greater depth of
> > the estimated phylogenetic node than an estimate based on the existing
> > fossil record is due to an artifact of the Baysian inference of clade
> > origin. It is common knowledge that molecular clock estimates of
> > lineage separation is usually older than the first fossils of a new
> > branching lineage.
> >
> > It sounds like it should be true if you have priors that include the
> > oldest known fossils, but I really do not know if the people looking at
> > the Cambrian diversification of bilateral animals do that. I haven't
> > looked into it for decades, but they used to calibrate the clock using
> > related lineages that had a better fossil record that was dated more
> > accurately. You didn't use the nodes that you were trying to estimate,
> > but Baysian methods do, do a reiteration from some original estimate.
> >
> > Ron Okimoto
> Bilaterian divergence took place deep in the Ediacaran, but the record is

> pretty sparse. As you say, the best molecular clock estimates should be
> older unless you happened to find a fossil immediately after the divergence.
After looking some detail at Budd & Mann's paper, I notice that the putative
discovery of Ediacaran tunicates (https://doi.org/10.1007/s12542-021-00596-1)
isn't mentioned. If it is indeed a tunicate, it would indicate the presence of chordates
~> 557 Mya.

On 12/13/2023 9:33 PM, erik simpson wrote:
> On Wednesday, December 13, 2023 at 7:22:08 PM UTC-8, erik simpson wrote:
>> On Wednesday, December 13, 2023 at 6:02:08 PM UTC-8, RonO wrote:
>>> https://pubmed.ncbi.nlm.nih.gov/37695319/
>>>
>>> The pdf of this article labels it as a point of view article. It is an
>>> open access article where the authors claim that the greater depth of
>>> the estimated phylogenetic node than an estimate based on the existing
>>> fossil record is due to an artifact of the Baysian inference of clade
>>> origin. It is common knowledge that molecular clock estimates of
>>> lineage separation is usually older than the first fossils of a new
>>> branching lineage.
>>>
>>> It sounds like it should be true if you have priors that include the
>>> oldest known fossils, but I really do not know if the people looking at
>>> the Cambrian diversification of bilateral animals do that. I haven't
>>> looked into it for decades, but they used to calibrate the clock using
>>> related lineages that had a better fossil record that was dated more
>>> accurately. You didn't use the nodes that you were trying to estimate,
>>> but Baysian methods do, do a reiteration from some original estimate.
>>>
>>> Ron Okimoto
>> Bilaterian divergence took place deep in the Ediacaran, but the record is
>
>> pretty sparse. As you say, the best molecular clock estimates should be
>> older unless you happened to find a fossil immediately after the divergence.
> After looking some detail at Budd & Mann's paper, I notice that the putative
> discovery of Ediacaran tunicates (https://doi.org/10.1007/s12542-021-00596-1)
> isn't mentioned. If it is indeed a tunicate, it would indicate the presence of chordates
> ~> 557 Mya.
>

It is what happened with the Human estimate. We knew that we didn't
have the fossils closer to the divergence between chimps and humans.
When we obtained more fossils the divergence started to creep towards
the older boundary. Now, it is pushing the 8 million year estimate.
The first clock with a reasonable amount of molecular data indicated 4.5
to 8 million years for the divergence between chimps and humans, and the
data favored somewhere around 5 million years, but with additional
fossils and the desire to claim them as part of our lineage there has
been a creep to older estimates. The molecular estimate is still within
the 4.5 to 8 million year range, but it looks like the fossils are
indicating that it is in the older part of the range. If we used those
fossils and their dates, you would probably be right in that the age
would extend further into the past.

Ron Okimoto

On Thu, 14 Dec 2023 05:31:59 -0600, the following appeared
in talk.origins, posted by RonO <rokimoto@cox.net>:

>On 12/13/2023 9:33 PM, erik simpson wrote:
>> On Wednesday, December 13, 2023 at 7:22:08?PM UTC-8, erik simpson wrote:
>>> On Wednesday, December 13, 2023 at 6:02:08?PM UTC-8, RonO wrote:
>>>> https://pubmed.ncbi.nlm.nih.gov/37695319/
>>>>
>>>> The pdf of this article labels it as a point of view article. It is an
>>>> open access article where the authors claim that the greater depth of
>>>> the estimated phylogenetic node than an estimate based on the existing
>>>> fossil record is due to an artifact of the Baysian inference of clade
>>>> origin. It is common knowledge that molecular clock estimates of
>>>> lineage separation is usually older than the first fossils of a new
>>>> branching lineage.
>>>>
>>>> It sounds like it should be true if you have priors that include the
>>>> oldest known fossils, but I really do not know if the people looking at
>>>> the Cambrian diversification of bilateral animals do that. I haven't
>>>> looked into it for decades, but they used to calibrate the clock using
>>>> related lineages that had a better fossil record that was dated more
>>>> accurately. You didn't use the nodes that you were trying to estimate,
>>>> but Baysian methods do, do a reiteration from some original estimate.
>>>>
>>>> Ron Okimoto
>>> Bilaterian divergence took place deep in the Ediacaran, but the record is
>>
>>> pretty sparse. As you say, the best molecular clock estimates should be
>>> older unless you happened to find a fossil immediately after the divergence.
>> After looking some detail at Budd & Mann's paper, I notice that the putative
>> discovery of Ediacaran tunicates (https://doi.org/10.1007/s12542-021-00596-1)
>> isn't mentioned. If it is indeed a tunicate, it would indicate the presence of chordates
>> ~> 557 Mya.
>>
>
>It is what happened with the Human estimate. We knew that we didn't
>have the fossils closer to the divergence between chimps and humans.
>When we obtained more fossils the divergence started to creep towards
>the older boundary. Now, it is pushing the 8 million year estimate.
>The first clock with a reasonable amount of molecular data indicated 4.5
>to 8 million years for the divergence between chimps and humans, and the
>data favored somewhere around 5 million years, but with additional
>fossils and the desire to claim them as part of our lineage there has
>been a creep to older estimates. The molecular estimate is still within
>the 4.5 to 8 million year range, but it looks like the fossils are
>indicating that it is in the older part of the range. If we used those
>fossils and their dates, you would probably be right in that the age
>would extend further into the past.
>
Good info; thanks to you both.
>
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

On 14/12/2023 01:58, RonO wrote:
> https://pubmed.ncbi.nlm.nih.gov/37695319/
>
> The pdf of this article labels it as a point of view article.  It is an
> open access article where the authors claim that the greater depth of
> the estimated phylogenetic node than an estimate based on the existing
> fossil record is due to an artifact of the Baysian inference of clade
> origin.  It is common knowledge that molecular clock estimates of
> lineage separation is usually older than the first fossils of a new
> branching lineage.
>
> It sounds like it should be true if you have priors that include the
> oldest known fossils, but I really do not know if the people looking at
> the Cambrian diversification of bilateral animals do that.  I haven't
> looked into it for decades, but they used to calibrate the clock using
> related lineages that had a better fossil record that was dated more
> accurately.  You didn't use the nodes that you were trying to estimate,
> but Baysian methods do, do a reiteration from some original estimate.
>
> Ron Okimoto
>

I had wondered how Bayesian analysis avoided concluding the assumptions.
From the above, it seems that the answer is that sometimes it doesn't.

--
alias Ernest Major