Adding 2024_Ravasini_Picene

[stschiff]

PR Checklist for a new package submission

• The package does not exist already in the community archive, also not with a different name.
• The package title in the POSEIDON.yml conforms to the general title structure suggested here: <Year>_<Last name of first author>_<Region, time period or special feature of the paper>, e.g. 2021_Zegarac_SoutheasternEurope, 2021_SeguinOrlando_BellBeaker or 2021_Kivisild_MedievalEstonia.
• The package is stored in a directory that is named like the package title.

---

• The package is complete and features the following elements:
  • Genotype data in binary PLINK format (not EIGENSTRAT format).
  • A POSEIDON.yml file with not just the file-referencing fields, but also the following meta-information fields present and filled: poseidonVersion, title, description, contributor, packageVersion, lastModified (see here for their definition)
  • A reasonably filled .janno file (for a list of available fields look here and here for more detailed documentation about them).
  • A .bib file with the necessary literature references for each sample in the .janno file.
• Every file in the submission is correctly referenced in the POSEIDON.yml file and there are no additional, supplementary files in the submission that are not documented there.
• Genotype data, .janno and .bib file are all named after the package title and only differ in the file extension.
• The package version in the POSEIDON.yml file is 1.0.0.
• The poseidonVersion of the package in the POSEIDON.yml file is set to the latest version of the Poseidon schema.
• The POSEIDON.yml file contains the corresponding checksums for the fields genoFile, snpFile, indFile, jannoFile and bibFile.
• There is either no CHANGELOG file or one with a single entry for version 1.0.0.

---

• The Publication column in the .janno file is filled and the respective .bib file has complete entries for the listed mentioned keys.
• The .janno file does not include any empty columns or columns only filled with n/a.
• The order of columns in the .janno file adheres to the standard order as defined in the Poseidon schema here.
• The .janno and the .ssf files are not fully quoted, so they only use single- or double quotes ("...", '...') to enclose text fields where it is strictly necessary (i.e. their entry includes a TAB).

---

• The package passes a validation with trident validate --fullGeno.

---

• Large genotype data files are properly tracked with Git LFS and not directly pushed to the repository. For an instruction on how to set up Git LFS please look here. If you accidentally pushed the files the wrong way you can fix it with git lfs migrate import --no-rewrite path/to/file.bed (see here).

[stschiff]

OK, this is now ready for review!

[nevrome]

@TCLamnidis This is a rather minimal package with the bare necessities for analysis. Maybe you could have quick look if it's structurally fine. Thank you 🙏

[nevrome]

@stschiff Angela and I identified an issue with the dating of the samples EV19 and EV7A. They are duplicated samples or monozygotic twins. And they are from the same burial chamber that is contextually (and with two other radiocarbon dates) dated to VII-VI cc. BCE. Curiously EV7A has a radiocarbon date that points to a younger age: 2310±30 BP (413-229 calBCE). The authors seem to have ignored this dating, but they do not explain or justify this decision in the paper or the supplement.

Angela and I think that we should ideally contact the authors about this. Alternatively we could follow their lead and use the age range they adopted for the paper. Then the radiocarbon age for EV7A should be removed from this Poseidon package.

[stschiff]

Thanks! OK, I removed the C14 date from EV7A and adapted its contextual range to that of EV19. I think that's sufficient for now.

[nevrome]

OK - I'll merge this.