# 🧬 AGENTS.md — 2015_CryptoJews

## Purpose

This folder contains materials for **Commentary: Portuguese crypto-Jews: the genetic heritage of a complex history** (2015), a commentary in *Frontiers in Genetics* critiquing population genetic methodology in the study of Iberian Jewish communities.

Research area: **Genetics / Population Genetics**.

## Agents Working With This Paper

### 🔍 Research Agent

- **Role**: Extract and analyze the critique of uniparental marker methodology for Jewish ancestry inference
- **Input**: The PDF (`2015_CryptoJews.pdf`)
- **Output**: Structured summary of methodological critiques, alternative approaches proposed, and implications for population genetics
- **Focus Areas**: Y-chromosome haplotype analysis, mtDNA markers, haplotype polyphyly, admixture modeling, crypto-Jewish demographics

### 📖 Citation Agent

- **Role**: Manage citation metadata and track references to Nogueiro et al. (2015) and related population genetics literature
- **DOI**: [10.3389/fgene.2015.00261](https://doi.org/10.3389/fgene.2015.00261)
- **Output**: BibTeX entries, citation graphs, cross-reference links to Tofanelli et al. (2014) and other key references

### 🔗 Synthesis Agent

- **Role**: Connect this commentary to the broader genetics research program and population genomics discourse
- **Input**: Paper content + context from related papers
- **Related Works**: 2015_EhrlichialInfection, 2015_HoneyBeeEvolution, 2016_NuclearStructure
- **Output**: Thematic links between population genetics methodology and other Friedman genetics publications

## Extraction Log

| Date | Agent | Action |
|------|-------|--------|
| 2026-03-08 15:05 | Indexer | Manual comprehensive extraction from PDF |
| 2026-03-08 15:05 | Research | Extracted full abstract, methodological critiques, and population genetics arguments |

## File Inventory

| File | Description | Status |
|------|-------------|--------|
| README.md | Paper landing page with abstract, citation, and DOI | ✅ |
| AGENTS.md | This file — agent roles and instructions | ✅ |
| SKILL.md | Skills and competencies (Claude Code compatible) | ✅ |
| 2015_CryptoJews.pdf | Paper PDF | ✅ |

## Related

- [Bibliography](../../pages/BIBLIOGRAPHY.md)
- [Software](../../pages/SOFTWARE.md)
- [Repository Root](../../README.md)

### Related Papers in This Repository

- [2015_EhrlichialInfection](../2015_EhrlichialInfection/) — biomedical genetics
- [2015_HoneyBeeEvolution](../2015_HoneyBeeEvolution/) — evolutionary genomics
- [2016_NuclearStructure](../2016_NuclearStructure/) — radiation biology and chromatin
- [2019_DennettExplained](../2019_DennettExplained/) — philosophical commentary tradition