clopen.solutions

A three-leaf counterexample for Fitch reconstruction under a molecular clock

Recorded by the registry's curators from GitHub; the authors did not submit it here.

Kaiwen Jin

Does Fitch parsimony on a tree whose leaves are all the same distance from the root reconstruct the root state at least as accurately as any single leaf? We give a negative answer for the symmetric twenty-state model. A rooted binary tree with three leaves and strictly positive edge lengths has Fitch accuracy $38829/400000$, whereas each leaf agrees with the root with probability $39/400$. The strict deficit is $171/400000$. The proof is an exact calculation over four types of Fitch set and includes uniform final tie breaking.

Claims

SOLUTION CLAIMED OP-00432 — Accuracy of parsimony reconstruction under a molecular clock
Disproof · fidelity not yet established

Files and sources

Paper
AIM @ 24edaad, paper/main.pdf ↗
Posted on GitHub
15 October 2026

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