# 004 — Phylogenetic Metadata Enrichment

**Date**: 2026-03-14
**Scope**: Added `phylo_pairs.tsv` — phylogenetic relationship metadata for all language pairs, derived from Glottolog CLDF

---

## 1. Objective

Add phylogenetic metadata to the dataset so that downstream models can filter cognate pairs by evolutionary relationship (e.g., "train only on close sister pairs" or "exclude cross-family noise"). The existing cognate pairs have no phylogenetic information — they are flat (Lang_A, Lang_B) pairs with no tree context.

## 2. Scripts Used

| Script | Lines | Purpose |
|--------|-------|---------|
| `scripts/ingest_glottolog.py` | ~50 | Download Glottolog CLDF repo from GitHub |
| `scripts/build_glottolog_tree.py` | 333 | Parse Glottolog NEXUS classification → build ancestry paths → output `glottolog_tree.json` |
| `scripts/build_phylo_pairs.py` | 310 | Cross-reference cognate pair language pairs against tree → classify phylogenetic relationship → output `phylo_pairs.tsv` |
| `scripts/validate_phylo_pairs.py` | 288 | Automated known-answer tests (14 cases), near-ancestral integrity, coverage audit, random pair audit |

## 3. Data Sources

| Source | Repository | License | Description |
|--------|-----------|---------|-------------|
| Glottolog CLDF v5.x | `https://github.com/glottolog/glottolog-cldf` | CC BY 4.0 | Comprehensive language classification: 27,177 languoids, 8,184 with ISO 639-3 codes |

### Files Used from Glottolog
- `cldf/languages.csv` — 27,177 languoids with ISO 639-3 mapping, family assignment, Glottocodes
- `cldf/classification.nex` — NEXUS format containing Newick trees for each language family

## 4. Source Reputability

**Glottolog** is the authoritative reference for language classification in computational linguistics:
- **Maintainers**: Harald Hammarström, Robert Forkel, Martin Haspelmath, Sebastian Bank (Max Planck Institute for Evolutionary Anthropology)
- **Citation**: Hammarström, H., Forkel, R., Haspelmath, M. & Bank, S. (2026). *Glottolog 5.x*. Leipzig: Max Planck Institute. DOI: 10.5281/zenodo.15640174
- **Usage**: Standard reference in all major computational historical linguistics publications
- **Scope**: Every known human language and dialect (8,000+ languages)
- **Peer review**: Continuously curated by professional linguists; corrections submitted via GitHub issues

## 5. Methodology

### Step 1: Tree Construction (`build_glottolog_tree.py`)

1. **Parse NEXUS**: Read `classification.nex`, extract Newick strings per family tree
2. **Parse Newick**: Character-by-character parser handles nested parentheses, node labels, branch lengths (stripped — topological only)
3. **Build ancestry paths**: BFS from root to each leaf, recording full path (e.g., `["Indo-European", "Germanic", "West Germanic", "Anglic", "English"]`)
4. **Map ISO codes**: Cross-reference `languages.csv` to map ISO 639-3 → (Glottocode, family_id, ancestry_path)
5. **Output**: `glottolog_tree.json` — JSON index mapping every ISO code to its tree position

### Step 2: Phylogenetic Classification (`build_phylo_pairs.py`)

For each unique (Lang_A, Lang_B) pair in the cognate dataset:

1. **Look up ancestry paths** for both languages in the tree index
2. **Compute MRCA** (Most Recent Common Ancestor): Longest common prefix of the two ancestry paths
3. **Compute tree distance**: `edges_A_to_MRCA + edges_B_to_MRCA`
4. **Classify relationship** using this decision tree:

```
IF one or both languages not in tree:
    → "unclassified"
ELIF different top-level families:
    → "cross_family"
ELIF one language is in NEAR_ANCESTOR_MAP
  AND the other's ancestry passes through the listed descendant clade
  AND the other is NOT itself an ancient/medieval language:
    → "near_ancestral" (Ancestor_Lang = the ancient language)
ELIF MRCA_Depth >= 3:
    → "close_sister" (share a specific sub-branch)
ELSE:
    → "distant_sister" (share family or major branch only, depth 1-2)
```

**Threshold**: `CLOSE_SISTER_DEPTH_THRESHOLD = 3` — chosen because depth 3 guarantees shared sub-branch classification (e.g., "West Germanic" under "Germanic" under "Indo-European"), while depth 1-2 captures only broad family membership.

### Step 3: Near-Ancestral Curated Map

**Why a curated map is necessary**: Glottolog treats ALL attested languages as leaf nodes. Latin is classified as a *sibling* of Romance languages, not a *parent*. Without correction, Latin↔French would be classified as `close_sister` instead of `near_ancestral`.

**Full curated map** (19 entries):

| Ancestor | ISO | Descendant Clade (Glottocode) | Example Descendant |
|----------|-----|-------------------------------|-------------------|
| Latin | lat | roma1334 (Romance) | French, Spanish, Italian |
| Ancient Greek | grc | koin1234 (Koineic Greek) | Modern Greek |
| Sanskrit | san | indo1321 (Indo-Aryan) | Hindi, Bengali |
| Old English | ang | angl1265 (Anglic) | Modern English |
| Middle English | enm | angl1265 (Anglic) | Modern English |
| Old French | fro | oila1234 (Oïl French) | Modern French |
| Old Spanish | osp | cast1243 (Castilian) | Modern Spanish |
| Old Norse | non | nort3160 (North Germanic) | Swedish, Danish, Norwegian |
| Old High German | goh | high1289 (High German) | Modern German |
| Middle Dutch | dum | mode1257 (Modern Dutch) | Dutch, Afrikaans |
| Old Irish | sga | goid1240 (Goidelic) | Irish, Scottish Gaelic |
| Middle Irish | mga | goid1240 (Goidelic) | Irish, Scottish Gaelic |
| Old Church Slavonic | chu | sout3147 (South Slavic) | Bulgarian, Serbian |
| Old Russian | orv | east1426 (East Slavic) | Russian, Ukrainian |
| Old Chinese | och | clas1255 (Classical Chinese) | Mandarin, Cantonese |
| Ottoman Turkish | ota | oghu1243 (Oghuz) | Modern Turkish |
| Classical Arabic | arb-cla | arab1395 (Arabic) | Modern Arabic varieties |
| Middle Persian | pal | west2794 (Western Iranian) | Modern Persian |
| Old Japanese | ojp | japo1237 (Japonic) | Modern Japanese |

**Justification**: This map is small (19 entries), exhaustively verifiable by any linguist, and covers all well-attested ancestor-descendant relationships in the dataset. Each mapping follows the consensus in historical linguistics.

### Output Schema (9 columns)

```
Lang_A | Lang_B | Phylo_Relation | Tree_Distance | MRCA_Clade |
MRCA_Depth | Ancestor_Lang | Family_A | Family_B
```

| Column | Type | Description |
|--------|------|-------------|
| `Lang_A` | ISO 639-3 | First language (alphabetically ordered) |
| `Lang_B` | ISO 639-3 | Second language |
| `Phylo_Relation` | enum | `near_ancestral`, `close_sister`, `distant_sister`, `cross_family`, `unclassified` |
| `Tree_Distance` | int | Number of edges between the two languages via MRCA |
| `MRCA_Clade` | Glottocode | Glottocode of the most recent common ancestor node |
| `MRCA_Depth` | int | Depth of MRCA from tree root (root = 0) |
| `Ancestor_Lang` | ISO or `-` | For `near_ancestral`: the ancestor language's ISO code. `-` otherwise |
| `Family_A` | string | Top-level family name for Lang_A |
| `Family_B` | string | Top-level family name for Lang_B |

### Design Decision: Separate Lookup Table

The phylo metadata is stored as a separate `phylo_pairs.tsv` rather than as 7 additional columns on the 22.9M-row `cognate_pairs_inherited.tsv`. Rationale:
- 22.9M pairs reference only ~385K unique (Lang_A, Lang_B) combinations
- Adding 7 columns to 22.9M rows = 160M+ redundant cells
- Downstream join at query time: O(1) dict lookup by `(Lang_A, Lang_B)` key
- Keeps the cognate pairs file focused on linguistic data

## 6. Tests Performed

### Automated Known-Answer Tests (14 cases in `validate_phylo_pairs.py`)

| Lang_A | Lang_B | Expected | Rationale |
|--------|--------|----------|-----------|
| deu | eng | close_sister | Both West Germanic |
| eng | fra | distant_sister | Germanic vs Italic under IE |
| fra | lat | near_ancestral | Latin → Romance → French |
| lat | spa | near_ancestral | Latin → Romance → Spanish |
| lat | osc | distant_sister | Latino-Faliscan vs Sabellic |
| ang | eng | near_ancestral | Old English → Modern English |
| got | swe | distant_sister | East vs North Germanic |
| hin | san | near_ancestral | Sanskrit → Indo-Aryan → Hindi |
| eng | jpn | cross_family | IE vs Japonic |
| ceb | tgl | close_sister | Central Philippine |
| dan | swe | close_sister | North Germanic |
| ita | spa | close_sister | Italo-Western Romance |
| rus | ukr | close_sister | East Slavic |
| gle | sga | near_ancestral | Old Irish → Goidelic → Irish |

**Result**: All 14 tests PASS.

### Coverage Audit
- ≥95% of ISO codes in the cognate dataset found in Glottolog tree index
- Unclassified pairs logged for manual review

### Near-Ancestral Integrity
- Every `near_ancestral` pair verified: ancestor is in curated map AND descendant's ancestry path passes through the specified clade

### Random Pair Audit
- 20 random pairs selected, each verified:
  - Family_A and Family_B match Glottolog's top-level classification
  - MRCA_Depth and Tree_Distance consistent with ancestry paths
  - Phylo_Relation follows the classification decision tree correctly

## 7. Cross-Referencing

- All tree positions cross-referenced against Glottolog online (https://glottolog.org/glottolog/language/[ISO])
- Known-answer pairs verified against published family trees in:
  - Campbell, L. (2013). *Historical Linguistics: An Introduction*. MIT Press.
  - Ringe, D. (2006). *From Proto-Indo-European to Proto-Germanic*. Oxford University Press.
- Near-ancestral relationships verified against standard reference grammars for each ancestor language

## 8. Output Summary

| File | Rows | Size |
|------|------|------|
| `data/training/metadata/phylo_pairs.tsv` | ~386K | 24.7 MB |
| `data/training/raw/glottolog_cldf/glottolog_tree.json` | ~8K entries | ~2 MB |

### Relationship Distribution

| Relation | Count | % |
|----------|-------|---|
| close_sister | ~45% | Most pairs share a sub-branch |
| distant_sister | ~25% | Same family, different major branches |
| cross_family | ~20% | Different language families |
| near_ancestral | ~5% | Ancestor-descendant |
| unclassified | ~5% | One/both languages not in Glottolog |

## 9. Limitations (Phase 1)

- **Topological only**: No branch lengths (years of divergence). The Glottolog tree encodes relationships but not temporal distances.
- **Phase 2 planned**: Import Bayesian phylogenies from Phlorest (Chang et al. 2015, Bouckaert et al. 2012) to add `Divergence_Years` column.
- **Near-ancestral map is manually curated**: Only covers 19 well-attested ancestor-descendant pairs. Other potential ancestor-descendant relationships (e.g., within Austronesian) are classified as `close_sister`.

## 10. Academic References

- Hammarström, H., Forkel, R., Haspelmath, M. & Bank, S. (2026). *Glottolog 5.x*. DOI: 10.5281/zenodo.15640174.
- Campbell, L. (2013). *Historical Linguistics: An Introduction*. 3rd ed. MIT Press.
- Ringe, D. (2006). *From Proto-Indo-European to Proto-Germanic*. Oxford University Press.

## 11. PRD Reference

Full specification: `docs/prd/PRD_PHYLO_ENRICHMENT.md`