Is Protocinctus_mansillaensis range in the intervals .tsv correct?

dwbapst / PaleoSoc_phylo_short_course_2019

Materials for the Revbayes-based short course in tip-dating for GSA 2019, presented by The Paleontological Society

https://dwbapst.github.io/PaleoSoc_phylo_short_course_2019/

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Is Protocinctus_mansillaensis range in the intervals .tsv correct? #2

Open dwbapst opened 5 years ago

dwbapst commented 5 years ago

Its unclear to me...

@daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

daveyfwright commented 5 years ago

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst notifications@github.com wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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PeterJWagner3 commented 5 years ago

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright notifications@github.com wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst notifications@github.com wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/issues/2?email_source=notifications&email_token=AK4VIUJ7HWKCJZ7AMIPJV5TQKA3GNA5CNFSM4IXJODZ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HLXLBOA, or mute the thread https://github.com/notifications/unsubscribe-auth/AK4VIUIVJPXNWB3N5RQWQXDQKA3GNANCNFSM4IXJODZQ .

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daveyfwright commented 5 years ago

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner notifications@github.com wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright notifications@github.com wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst notifications@github.com wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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PeterJWagner3 commented 5 years ago

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright notifications@github.com wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner notifications@github.com wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright notifications@github.com wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst notifications@github.com wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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daveyfwright commented 5 years ago

Hi Peter,

Okay, so that would make the youngest taxon age (i.e., at t=0) approximately equal to 499.3Ma in absolute units. In the current version of my script, I'm placing a prior on the root age of the tree to be uniform from 10.8-15.12, which is approximately 510.1 Ma to 514.24 Ma, which makes sense because that assumes they likely originated at some unknown time during Cambrian Series 2 (Stage 4). I feel like it's important to tell the participants where these numbers are coming from because paleontologists in particular are used to dealing with the actual geologic ages, not relative time units!

Cheers,

-Davey

On Tue, Sep 17, 2019 at 9:52 AM Peter Wagner notifications@github.com wrote:

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright notifications@github.com wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner notifications@github.com wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright notifications@github.com wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst < notifications@github.com> wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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daveyfwright commented 5 years ago

Oops! Sorry--I made a mistake. Ignore the previous email.

T=0 should be ~498.2, which would make setting the root age dnUnif(10.8,15.12) approximately 509.0 Ma to 513.3 Ma.

-Davey

On Tue, Sep 17, 2019 at 10:08 AM David Wright davey.f.wright@gmail.com wrote:

Hi Peter,

Okay, so that would make the youngest taxon age (i.e., at t=0) approximately equal to 499.3Ma in absolute units. In the current version of my script, I'm placing a prior on the root age of the tree to be uniform from 10.8-15.12, which is approximately 510.1 Ma to 514.24 Ma, which makes sense because that assumes they likely originated at some unknown time during Cambrian Series 2 (Stage 4). I feel like it's important to tell the participants where these numbers are coming from because paleontologists in particular are used to dealing with the actual geologic ages, not relative time units!

Cheers,

-Davey

On Tue, Sep 17, 2019 at 9:52 AM Peter Wagner notifications@github.com wrote:

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright notifications@github.com wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner <notifications@github.com

wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright <notifications@github.com

wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst < notifications@github.com> wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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PeterJWagner3 commented 5 years ago

Hey Davey,

I was taking the midpoint between the minimum & maximum FA, so the lates is 498.8 Ma for U. acrofera.

Thinking,

Peter

Peter J. Wagner pjwagner3@gmail.org

‎"I hope we shall take warning from the example [in England] and crush in its birth the aristocracy of our monied corporations which dare already to challenge our government to a trial of strength and bid defiance to the laws our country." -- Thomas Jefferson

On Sep 17, 2019, at 9:13 AM, daveyfwright notifications@github.com wrote:

Oops! Sorry--I made a mistake. Ignore the previous email.

T=0 should be ~498.2, which would make setting the root age dnUnif(10.8,15.12) approximately 509.0 Ma to 513.3 Ma.

-Davey

On Tue, Sep 17, 2019 at 10:08 AM David Wright davey.f.wright@gmail.com wrote:

Hi Peter,

Okay, so that would make the youngest taxon age (i.e., at t=0) approximately equal to 499.3Ma in absolute units. In the current version of my script, I'm placing a prior on the root age of the tree to be uniform from 10.8-15.12, which is approximately 510.1 Ma to 514.24 Ma, which makes sense because that assumes they likely originated at some unknown time during Cambrian Series 2 (Stage 4). I feel like it's important to tell the participants where these numbers are coming from because paleontologists in particular are used to dealing with the actual geologic ages, not relative time units!

Cheers,

-Davey

On Tue, Sep 17, 2019 at 9:52 AM Peter Wagner notifications@github.com wrote:

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright notifications@github.com wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner <notifications@github.com

wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright <notifications@github.com

wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst < notifications@github.com> wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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PeterJWagner3 commented 5 years ago

Also, the figure is taking a little longer than I wished: I’m modiying my code to allow plotting of zones as well as stage names & ranges.

Harmoniously in a good way,

Peter Wagner pjwagner3@gmail.com

"These capitalists generally act harmoniously and in concert, to fleece the people."

Abe Lincoln without the benefit of a time machine….

On Sep 17, 2019, at 9:13 AM, daveyfwright notifications@github.com wrote:

Oops! Sorry--I made a mistake. Ignore the previous email.

T=0 should be ~498.2, which would make setting the root age dnUnif(10.8,15.12) approximately 509.0 Ma to 513.3 Ma.

-Davey

On Tue, Sep 17, 2019 at 10:08 AM David Wright davey.f.wright@gmail.com wrote:

Hi Peter,

Okay, so that would make the youngest taxon age (i.e., at t=0) approximately equal to 499.3Ma in absolute units. In the current version of my script, I'm placing a prior on the root age of the tree to be uniform from 10.8-15.12, which is approximately 510.1 Ma to 514.24 Ma, which makes sense because that assumes they likely originated at some unknown time during Cambrian Series 2 (Stage 4). I feel like it's important to tell the participants where these numbers are coming from because paleontologists in particular are used to dealing with the actual geologic ages, not relative time units!

Cheers,

-Davey

On Tue, Sep 17, 2019 at 9:52 AM Peter Wagner notifications@github.com wrote:

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright notifications@github.com wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner <notifications@github.com

wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright <notifications@github.com

wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst < notifications@github.com> wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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daveyfwright commented 5 years ago

Okay, so if t=0 at 498.8 then dnUniform(10.8, 15.12) corresponds to 509.6 Ma to 513.9 Ma, which is close to the start and end of Cambrian Series 2 (Stage4).

-Davey

On Tue, Sep 17, 2019 at 11:16 AM Peter Wagner notifications@github.com wrote:

Hey Davey,

I was taking the midpoint between the minimum & maximum FA, so the lates is 498.8 Ma for U. acrofera.

Thinking,

Peter

Peter J. Wagner pjwagner3@gmail.org

‎"I hope we shall take warning from the example [in England] and crush in its birth the aristocracy of our monied corporations which dare already to challenge our government to a trial of strength and bid defiance to the laws our country." -- Thomas Jefferson

On Sep 17, 2019, at 9:13 AM, daveyfwright notifications@github.com wrote:

Oops! Sorry--I made a mistake. Ignore the previous email.

T=0 should be ~498.2, which would make setting the root age dnUnif(10.8,15.12) approximately 509.0 Ma to 513.3 Ma.

-Davey

On Tue, Sep 17, 2019 at 10:08 AM David Wright davey.f.wright@gmail.com wrote:

Hi Peter,

Okay, so that would make the youngest taxon age (i.e., at t=0) approximately equal to 499.3Ma in absolute units. In the current version of my script, I'm placing a prior on the root age of the tree to be uniform from 10.8-15.12, which is approximately 510.1 Ma to 514.24 Ma, which makes sense because that assumes they likely originated at some unknown time during Cambrian Series 2 (Stage 4). I feel like it's important to tell the participants where these numbers are coming from because paleontologists in particular are used to dealing with the actual geologic ages, not relative time units!

Cheers,

-Davey

On Tue, Sep 17, 2019 at 9:52 AM Peter Wagner <notifications@github.com

wrote:

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright <notifications@github.com

wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner < notifications@github.com

wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6

505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright < notifications@github.com

wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst < notifications@github.com> wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

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daveyfwright commented 5 years ago

Sorry for the spam...but that would mean to get the correct time intervals the values of dnUniform should be 10.2 and 15.2, respectively.

-Davey

On Tue, Sep 17, 2019 at 11:26 AM David Wright davey.f.wright@gmail.com wrote:

Okay, so if t=0 at 498.8 then dnUniform(10.8, 15.12) corresponds to 509.6 Ma to 513.9 Ma, which is close to the start and end of Cambrian Series 2 (Stage4).

-Davey

On Tue, Sep 17, 2019 at 11:16 AM Peter Wagner notifications@github.com wrote:

Hey Davey,

I was taking the midpoint between the minimum & maximum FA, so the lates is 498.8 Ma for U. acrofera.

Thinking,

Peter

Peter J. Wagner pjwagner3@gmail.org

‎"I hope we shall take warning from the example [in England] and crush in its birth the aristocracy of our monied corporations which dare already to challenge our government to a trial of strength and bid defiance to the laws our country." -- Thomas Jefferson

On Sep 17, 2019, at 9:13 AM, daveyfwright notifications@github.com wrote:

Oops! Sorry--I made a mistake. Ignore the previous email.

T=0 should be ~498.2, which would make setting the root age dnUnif(10.8,15.12) approximately 509.0 Ma to 513.3 Ma.

-Davey

On Tue, Sep 17, 2019 at 10:08 AM David Wright <davey.f.wright@gmail.com

wrote:

Hi Peter,

Okay, so that would make the youngest taxon age (i.e., at t=0) approximately equal to 499.3Ma in absolute units. In the current version of my script, I'm placing a prior on the root age of the tree to be uniform from 10.8-15.12, which is approximately 510.1 Ma to 514.24 Ma, which makes sense because that assumes they likely originated at some unknown time during Cambrian Series 2 (Stage 4). I feel like it's important to tell the participants where these numbers are coming from because paleontologists in particular are used to dealing with the actual geologic ages, not relative time units!

Cheers,

-Davey

On Tue, Sep 17, 2019 at 9:52 AM Peter Wagner < notifications@github.com> wrote:

Hey David et al.,

It’s already on GitHub, but here it is again. The detailed fossil information gives the more specific information underlying it.

Also, 0 is the latest first appearance for one of the cinctans. That is important for rho: RevBayes uses that for sampling of the final time slice, on the tacit assumption that it is now. You cannot use rho = 0: they opted for one of the equations that uses N*ln(rho) instead of rho^N, it seems. (If cinctans are still alive & hanging out with Elvis, then their rho is 0.) So, the recommended compromise is to make the final interval = 0.

The rho in my scripts is based on sampling data for all Gu2 echinoderms. It is almost certainly too high, as it uses collections rather than rock-units and thus has some “binge-sampling” effects that elevate the proportion of taxa with 2+ finds.

I didn’t quite finish the figure last night: some family stuff got in the way!

––––––––––––––––––––––––

Peter

Peter J. Wagner pjwagner3@gmail.org

"There is nothing divine about morality; it is a purely human affair." -- Albert Einstein

On Sep 17, 2019, at 8:29 AM, daveyfwright < notifications@github.com> wrote:

Hi Peter,

In that case, can you re-send the .tsv file with ages? We need to all be on the same page with these data! In that case, what is the presumably new age (i.e., absolute age in the Cambrian) associated with t=0 in the .tsv file? I need to know in order to write a section for setting the tree age prior of the clock model.

Cheers,

-Davey

On Mon, Sep 16, 2019 at 11:00 PM Peter Wagner < notifications@github.com

wrote:

Hey all,

P. mansilaenus’ range got updated a while ago. P. mansilaenus appears at the top of the Eccaparadoxides asturianus zone. However, the original dating gave it the entire E. asturianus zone. Because that is an unusually long zone (~507.8 - 505.4 Ma), people informally use an “upper" Eccaparadoxides asturianus zone. (It probably will get divided into subzones at some point: but today is not that day.) So, I have an upper E. asturianus zone for just the upper half of that zone, i.e., 507.6 - 505.4 Ma. (This does not have a big effect on analyses.)

Also: do not use separate FAD & LAD!!!! There is a bug in RevBayes so that it sometimes the last appearance as the first appearance when calculating possible divergence times. This has two effects. One, it will sometimes generate trees in which species diverge from their closest relatives after they first appear in the fossil record. Two, as a side-effect, it can also generate positive log-priors. This almost certainly comes from the program using the difference between a divergence time after a taxon’s first appearance and the correct first appearance, i.e., negative time! That was why I circulated the cintcan_intervals_FA.tsv file.

Pete

“I only work for private amusement, since I find my duties privately amusing.” --- J. R. R. Tolkien

On Sep 16, 2019, at 9:46 PM, daveyfwright < notifications@github.com

wrote:

As far as I can tell at the moment, the 8.4 in your link is (I think) correct. Honestly, I have so many files with the word "cinctan" and various numbers in them I'm...bewildered. Also, I think the LAD for any taxon the whole analyses (i.e, t = 0) is ~497 Ma.

-Davey

On Mon, Sep 16, 2019 at 10:03 PM David Bapst < notifications@github.com> wrote:

Its unclear to me...

@daveyfwright https://github.com/daveyfwright can you take a look at the LAD for Protocinctus_mansillaensis?

https://github.com/dwbapst/PaleoSoc_phylo_short_course_2019/blob/master/data/cincta_fossil_intervals.tsv

I don't know how it got updated, or why, but it had a different value in my repo vs April's... see history

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