pirl-unc / mhcgnomes / 33189993016
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Document that the species tree is prefix scope, not phylogeny (#120)

Two people independently filed the same bug against Bubalus bubalis
sitting under Bos sp. -- #109 from here and #115 downstream -- because
nothing in the repo says what a parent link means. It is not descent. A
parent says "this species may be named under the ancestor's umbrella
prefix", which is why _is_taxonomic_prefix decides whether a prefix is
inherited at all.

The clearest evidence was already in the file: Homo sapiens attaches
straight to the root rather than under Primata sp., despite humans being
primates, because human alleles are never written NHP-*.

Water buffalo is the mirror image. Taxonomically Bubalus is a sister
genus of Bos, so the edge looks wrong; as prefix scope it is right.
IPD-MHC files the species in the BoLA group, and the literature assigns
buffalo class II sequences to cattle loci by trans-species polymorphism
-- Bubu-DRB is the orthologue of BoLA-DRB3 (PMC3313522, PMID 12580780).

It is also load-bearing. The entry declares only DQA, DQA1 and DQB, so
these all parse by inheritance and would have stopped:

  Bubu-DRA   Bubu-DRB -> Bubu-DRB3   Bubu-DRB3   Bubu-DQA2   Bubu-DQB1

every one of them named in the published literature. Bubu-DRB
normalizing to Bubu-DRB3 is precisely the orthology the papers describe,
and only works because of the inheritance. I had measured the 55 -> 11
gene drop while proposing the re-parenting and read it as an acceptable
cost; it was the evidence against the change.

No data change. README and docs/curation.md now state the semantics with
both worked examples, and AGENTS.md gains the inverse of the lesson
added last time: do not assume our curation is wrong either -- check
what depends on a structure before changing it.

Claude-Session: https://claude.ai/code/session_012s4siLj2Vm33eNMGjNSazH

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