James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 13:48:41

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Diana (diana.spurite@uni-jena.de)
2023-10-19 13:48:52

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Marcel Keller (marcel.keller@ut.ee)
2023-10-19 13:48:52

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Maria Lopopolo (maria.lopopolo1989@gmail.com)
2023-10-19 13:48:52

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James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 13:49:29

Hey all, you've so far expressed interested in a possible C14 date extension to AncientMetagenomeDir

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 13:50:17

This has potential for another paper, that

  1. Describes the dataset
  2. Makes quantitative statement on the quality of C14 reporting in ancient metagenomics (to get people to do better!)
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 13:50:44

@Diana has already started gathering all this inforamtion, but we will need help

  1. Completeing getting all the data
  2. Reviewing all the data
  3. Inteprerting the reporting qualtiy
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 13:50:48

Would you guys still be interested?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 13:51:13

The main thing is I'm on leave and I'm basically at capacity with projects atm...

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 13:52:39

I would be interested, as I’ve dealt with the issue already to some degree in my recent preprint: https://www.biorxiv.org/content/10.1101/2023.07.18.549544v1

👍 James Fellows Yates
Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:04:20

the problem is that radiocarbon dates are sometimes also reported in other papers. In the preprint we also report raw data for samples where previously only calibrated or modelled dates were reported.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:04:57

You can see we have the reference_citation_depth

👍 Marcel Keller
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:04:58

column

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:05:01

to record how bad this is

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:05:40

And there are also samples where the (historical) dating is questionable. I guess that would go under “notes and comments”

👀 Diana
Diana (diana.spurite@uni-jena.de)
2023-10-19 14:06:43

Would definitely like to carry on with this. The data I have gathered should be reviewed before getting forward, I think. If there’s something to improve in the way it’s gathered it should be figured out sooner better than latter.

👍 James Fellows Yates
Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:08:21

I will be quite busy before December, but then I should have a bit more time and could check the data

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:08:31

Awesome 😄 I'm back end of January

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:08:45

We will likely go through the same github procedure as before I suspect

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:09:01

IIRC I got most of the way there but hit an unresolved bug with AMDirT

Diana (diana.spurite@uni-jena.de)
2023-10-19 14:09:30

I’d be happy to have session with anyone to go through the table which we have started, if there is anything unclear, though James had nicely annotated each column

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:10:23

It looks great on the first glance, amazing job! I know now how tricky it is to collect all that data.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:10:34

Yes, @Diana has done a great job so far

🤓 Diana
Diana (diana.spurite@uni-jena.de)
2023-10-19 14:10:34

And very much the same - can’t do much this semester. Should be free-er in February.

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:11:34

I would maybe add more data, e.g. C/N isotope data, as some labs provide it along with rc dates, and it can be used to check for reservoir effects

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:11:55

but this will be available only for the minority of the samples

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:12:24

Yeah I explored that but it was not included so many times it wasn't worth the effort recording it

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:12:32

That's why the resevoir effect columns are so few

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-19 14:12:46

It was taking @Diana a long time to get the information we already have there for each study 😕

Diana (diana.spurite@uni-jena.de)
2023-10-19 14:19:20

reservoir effect reporting is very much unclear. Often “reservoir effect” is mentioned, but it’s unclear if it’s calculated in the reported date. If it’s calculated very often there are no other details. Therefore we had decided to have those three columns with yes or no questions basically, as otherwise due to ambiguity we’d have to say no it’s not reported at all. Do you think the isotope data would help with that or make it more complex? or somewhere in-between?

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:26:56

If, then I would include it independently. E.g., in the preprint we report the isotope data, but don’t use it for calculating reservoir offsets (since we don’t have enough data for proper calculations)

Marcel Keller (marcel.keller@ut.ee)
2023-10-19 14:27:09

I think the current format is fine, but could be extended

Bjorn Bartholdy (bpbartholdy@pm.me)
2023-10-19 21:56:46

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Florencia Alvarez Gallego (florencia.alihuen.lab@gmail.com)
2024-01-04 14:22:17

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