docs/changelog/004_phylo_enrichment.md

004 — Phylogenetic Metadata Enrichment

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

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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