2025_Lazaridis_Yamnaya

[TCLamnidis]

Adds/Updates 2025_Lazaridis_Yamnaya

Linked to poseidon-framework/minotaur-recipes#65

If this PR adds a new package to the archive, please note:
New packages added to the minotaur archive are always published in version 1.0.0.
This means that any and all changes made to the package during the review process, should only bump the Minor or Patch version of the package.

PR checklist:

• The package description has been updated to the title of the paper.
• This package contains a BibTex file.
• The month field in the BibTex file is formatted as a three letter code.
• If this package already exists in the community archive:
  • The information from the community archive was used to fill-in empty janno fields (if applicable).
  • The commands used for the fill-in and any tool versions are kept track of in the README file.
  • The BibTex key used for the citation is identical to that in the corresponding package in the community archive.
  • The DOI in the BibTex file is identical to the one used in the corresponding package in the community archive.
• If the janno information was collected manually:
  • Add any additional contributors to POSEIDON.yml
• Any scripts/commands used to prepare the pacakge are kept track of in the README file.
• Country information is also present in the Country_ISO column.
• Any columns in the janno that are entirely missing or n/a should be removed from the janno.
• If Y_Haplogroups were provided in the ISOGG format, the column should be renamed to Y_Haplogroups_ISOGG
• Poseidon_IDs in the Relation_To column contain the _MNT suffix.

Once the Pull Request has passed the review process, ensure the package version is bumped once more before publishing with:

trident rectify -d <package_dir> --logText 'Bump version for release' --packageVersion Major --checksumAll

[stschiff]

Thanks, I can review this.

[stschiff]

Great, thanks for contributing the package. Here is my review:

1. ID labels have _IE. Why is this necessary? I can see that some individuals have been resequenced, but others are actually new. The labels used in Supplementary Table 1 in any case do not all have suffixes.

2. The "Collection ID" is inconsistent. The Supplementary Table has a column named "Skeletal Code", which seems more appropriate (e.g. "Mos54 (Deriivka-1, burial 9)") than what is there currently, which looks more like a group name.

3. Relationship columns are impressively filled, lots of work, thanks!

4. C14-dates all entered, great! But calibration is missing!

[TCLamnidis]

1. The _IE suffix comes from the sample_name provided by the authors to the ENA, so I will keep the suffix in this case, even though they do not appear in the paper.

2. Will fix that! Thanks!

3. Thank you!

4. Good point! I think I'll make a quick script to calibrate C14 dates using janno::quickcalibrate() in R.

[TCLamnidis]

Additional note: multiple individuals have no nuclear data.
I reached out to Iosif, and it seems some data was uploaded to the ENA, but was never flagged as public by the ENA.
They are looking into the matter, but in the meantime I have been provided an alternative download for the data in question.
As a result, this package will need reprocessing before it is finalised.