Datasets:

Nacryos
/

ancient-scripts-datasets

The cognate pair dataset (23.4M pairs) currently has NO metadata about the phylogenetic relationship between language pairs — no distinction between mother-daughter (Latin→Spanish), close sisters (Spanish~~Italian), or distant sisters (Spanish~~Hindi). Every pair should indicate its degree of cognacy.

Solution

A post-processing enrichment pipeline that cross-references cognate pairs against an authoritative phylogenetic tree (Glottolog CLDF v5.x) to classify each unique language pair.

Data Source

Primary: Glottolog CLDF v5.x (Hammarström, Forkel, Haspelmath & Bank)

Repository: https://github.com/glottolog/glottolog-cldf
Archive: Zenodo DOI: 10.5281/zenodo.15640174
License: CC BY 4.0
Key files: cldf/languages.csv (27,177 languoids with ISO mapping), cldf/classification.nex (NEXUS with Newick trees per family)
8,184 languoids have ISO 639-3 codes
Trees are topological (no branch lengths)

Download method: scripts/ingest_glottolog.py — downloads the CLDF CSV and NEXUS files from GitHub raw content into data/training/raw/glottolog_cldf/. Follows the same pattern as ingest_acd.py.

Supplementary (Phase 2, not in scope): Phlorest Bayesian phylogenies for calibrated branch lengths (years of divergence).

Output

File: data/training/metadata/phylo_pairs.tsv

A lookup table keyed on canonically-ordered (Lang_A, Lang_B) pairs. NOT inline columns in the 23M-row cognate pair files — that would add massive redundancy since the same language pair always has the same phylo classification.

Schema (9 columns)

Column	Type	Description
`Lang_A`	str	ISO 639-3 code (alphabetically first)
`Lang_B`	str	ISO 639-3 code (alphabetically second)
`Phylo_Relation`	enum	`near_ancestral`, `close_sister`, `distant_sister`, `cross_family`, `unclassified`
`Tree_Distance`	int	Edge count through MRCA (0 = same leaf group, 99 = unclassified/cross-family)
`MRCA_Clade`	str	Glottocode or name of MRCA node (e.g., `roma1334`, `germ1287`)
`MRCA_Depth`	int	Depth of MRCA in tree (0 = root, higher = more specific)
`Ancestor_Lang`	str	For `near_ancestral`: ISO of the ancestor. `-` otherwise
`Family_A`	str	Top-level Glottolog family of Lang_A
`Family_B`	str	Top-level Glottolog family of Lang_B

Classification Taxonomy

Relation	Definition	Example
`near_ancestral`	One language is an attested ancestor of the other's clade (from curated NEAR_ANCESTOR_MAP)	Latin↔Spanish, Old English↔English, Sanskrit↔Hindi
`close_sister`	MRCA depth ≥ 3 (share a specific sub-branch)	Spanish↔Italian (both under Romance), Swedish↔Danish (both under North Germanic)
`distant_sister`	MRCA depth = 1 or 2 (share family or major branch only)	English↔Hindi (both IE, but Germanic vs Indo-Iranian)
`cross_family`	Different top-level families	English↔Japanese
`unclassified`	One or both languages not in Glottolog tree	Undeciphered/isolate languages without Glottocode

Depth thresholds: The boundary between close and distant is at MRCA depth 3+. This means:

Depth 0: root (should not occur for same-family pairs)
Depth 1: top-level family (e.g., indo1319 = Indo-European) → distant_sister
Depth 2: major branch (e.g., germ1287 = Germanic) → distant_sister
Depth 3+: sub-branch (e.g., west2793 = West Germanic) → close_sister

Near-Ancestral Detection

A curated NEAR_ANCESTOR_MAP lists ~25 attested ancient/medieval languages and the Glottolog clades they are historically ancestral to:

NEAR_ANCESTOR_MAP = {
    "lat": ["roma1334"],           # Latin → Romance
    "grc": ["mode1248", "medi1251"],  # Ancient Greek → Modern Greek clades
    "san": ["indo1321"],           # Sanskrit → Indic
    "ang": ["angl1265"],           # Old English → Anglian/English
    "enm": ["angl1265"],           # Middle English → English
    "fro": ["oilf1242"],           # Old French → Oïl French
    "osp": ["cast1243"],           # Old Spanish → Castilian
    "non": ["nort3160"],           # Old Norse → North Germanic modern
    "goh": ["high1289"],           # Old High German → High German
    "dum": ["mode1258"],           # Middle Dutch → Modern Dutch
    "sga": ["goid1240"],           # Old Irish → Goidelic modern
    "mga": ["goid1240"],           # Middle Irish → Goidelic modern
    "wlm": ["bryt1239"],           # Middle Welsh → Brythonic modern
    "chu": ["sout3147"],           # Old Church Slavonic → South Slavic
    "orv": ["east1426"],           # Old East Slavic → East Slavic modern
    "och": ["sini1245"],           # Old Chinese → Sinitic modern
    "ota": ["oghu1243"],           # Ottoman Turkish → Oghuz modern
    "okm": ["kore1284"],           # Middle Korean → Korean modern
}

Logic:

If either language is in NEAR_ANCESTOR_MAP
AND the other language's ancestry path in Glottolog passes through one of the listed descendant clades
AND the other language is NOT itself an ancient/medieval language (to avoid classifying Latin↔Oscan as near_ancestral)
THEN classify as near_ancestral with Ancestor_Lang = the ancient language's ISO

Gothic (got) edge case: Gothic is ancient but has NO modern descendants (East Germanic is extinct). Gothic↔Swedish should be distant_sister, not near_ancestral. The map correctly handles this by only listing clades with living descendants.

Scripts

Script 1: `scripts/ingest_glottolog.py`

Downloads Glottolog CLDF data from GitHub.

Script 2: `scripts/build_glottolog_tree.py`

Parses the Glottolog NEXUS file into a usable Python tree structure.

Script 3: `scripts/build_phylo_pairs.py`

The main enrichment script that generates the lookup table.

Script 4: `scripts/validate_phylo_pairs.py`

Validation script with known-answer checks.

Execution Order

Write PRD → push to docs/prd/PRD_PHYLO_ENRICHMENT.md
Write scripts/ingest_glottolog.py → download Glottolog CLDF
Write scripts/build_glottolog_tree.py → parse NEXUS, build tree index
Adversarial audit: Verify tree covers ≥95% of ISO codes in cognate pairs
Write scripts/build_phylo_pairs.py → generate lookup table
Adversarial audit: Verify 20 random pairs trace back to Glottolog tree
Write scripts/validate_phylo_pairs.py → automated known-answer tests
Update docs/DATABASE_REFERENCE.md with phylo_pairs documentation
Commit + push to GitHub + HuggingFace

Critical Design Decisions

Why a separate lookup table (not inline columns)?

The 22.9M inherited pairs reference ~385K unique language pairs. Adding 7 columns to 22.9M rows = 160M+ redundant cells.
Downstream consumers join at query time: pair_key = (min(a,b), max(a,b)); lookup is O(1) with a dict.
The phylo classification is orthogonal to the cognate data — it can be updated independently when Glottolog releases new versions.

Why Glottolog (not the existing phylo_tree.json)?

phylo_tree.json has 755 Austronesian languages in ONE flat list — zero sub-classification for 90% of the dataset
Glottolog has deep sub-classification for ALL families including Austronesian
Glottolog is the authoritative academic reference (Hammarström et al.)

Why curated near-ancestor map (not purely algorithmic)?

Glottolog classifies ALL attested languages as leaf nodes (siblings), never as parent nodes
Even Latin is a sibling of Romance under "Imperial Latin" in Glottolog — not a parent
Algorithmic detection from tree topology alone would classify ALL pairs as sister-sister
The curated map (~25 entries) is linguistically defensible and small enough to verify exhaustively

Why not branch-length / time-calibrated distances?

Phase 1 focuses on topological classification
Branch-length data requires Phlorest Bayesian phylogenies (separate download per family, inconsistent coverage)
Branch lengths can be added in Phase 2 as a Divergence_Years column

Honest Limitations

"Near-ancestral" is approximate: Latin is not literally the ancestor of French — Vulgar Latin (unattested) is. We use "near-ancestral" to mean "the attested language is historically ancestral to the clade containing the other language."
Topological distance ≠ temporal distance: Two languages with tree_distance=4 in Austronesian may have diverged 1,000 years ago, while two with tree_distance=4 in Indo-European may have diverged 5,000 years ago.
Glottolog is a single hypothesis: Disputed affiliations are not represented. The tree reflects Glottolog's conservative consensus classification.
The similarity file (465K pairs) may contain cross-family pairs that are correctly labeled cross_family — these are algorithmic similarity matches, not genetic relationships.
Proto-language codes (ine-pro, gem-pro, etc.) are NOT in Glottolog — any cognate pairs involving proto-languages will be unclassified. (Currently zero such pairs exist in the dataset.)

Verification

python scripts/validate_phylo_pairs.py — all known-answer checks PASS
Coverage: ≥95% of ISO codes in cognate pairs have a Glottolog classification
Distribution: close_sister should be majority (most pairs are intra-family from ABVD/ACD)
Adversarial audit: 20 random pairs traced back to Glottolog NEXUS tree
No unclassified for any language that has a Glottocode in languages.tsv

PRD: Phylogenetic Relationship Metadata for Cognate Pairs

Problem