Ashkenazi Population Structure Reassessed: Reference-Panel Sensitivity and the Europe-Levant Cline

This record contains Version 2 of the preprint "Ashkenazi Population Structure Reassessed: Coordinate and Genotype-Level Reference-Panel Sensitivity in the Central Mediterranean."

Version 2 supersedes Version 1 and substantially expands the empirical and reproducibility basis of the study. The manuscript re-examines Ashkenazi Jewish population structure by testing whether the familiar Europe-Levant genetic-intermediacy framing remains stable when Italian Jewish, Southern Italian, Sicilian, Maltese, Aegean, and broader central Mediterranean comparators are included directly rather than omitted or replaced by northern European or northern Italian proxies.

The Version 2 manuscript integrates two complementary but distinct evidence streams. The first is a linked suite of Global25 coordinate-space reference-panel experiments, including full modern competition panels, matched source-omission tests, reciprocal Italian Jewish comparator tests, regional Ashkenazi targets, ancient Levant positive controls, and vector-geometry diagnostics. The second is an AADR-derived individual-level genotype workflow covering source-data preparation, manifests, QC, matched SNP sets, PCA, FST, ADMIXTURE, and integrated rank synthesis. These data streams are not merged at the input level; they are compared at the interpretive level to evaluate whether central Mediterranean comparators remain necessary before Ashkenazi placement is summarized as a simple Europe-Levant cline.

Version 2 adds an AADR strict-pass PCA figure to the main manuscript, updates the data availability and reproducibility language, and provides a public GitHub reproducibility branch containing the manuscript, Global25 Experiments 1-15, AADR Stages 01-08, descriptive FST materials, claim-traceability tables, runbook, manifests, SHA256 checksums, and verification scripts.

The accompanying reproducibility repository is available here:
https://github.com/StevenParker-collab/ashkenazi-population-structure-v1-reproducibility/tree/peer-review-central-mediterranean-reproducibility/Ashkenazi_Population_Structure_Reassessed_Peer_Review_repository

This Zenodo record preserves the exact Version 2 manuscript and reproducibility package for peer review and provides a permanent, citable archive of the updated preprint.