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lit-review-topic-03

Lit review topic 03: pseudohomologous regions concept

Metadata

Statusdone
Assignedagent-915
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Modelclaude:sonnet
Created2026-05-06T01:43:32.777448096+00:00
Started2026-05-06T13:22:04.431655903+00:00
Completed2026-05-06T13:37:01.340048200+00:00
Tagslit-review, eval-scheduled
Tokens2453042 in / 15403 out
Eval score0.91
└ blocking impact0.94
└ completeness0.88
└ constraint fidelity0.55
└ coordination overhead0.96
└ correctness0.92
└ downstream usability0.92
└ efficiency0.78
└ intent fidelity0.82
└ style adherence0.95

Description

SHARED CONTEXT — Lit review fanout for the canonical Nature-format abstract (paper_prep/synthesis/ABSTRACT_nature.md, written by upstream task; falls back to ABSTRACT_BoG.md if Nature version not yet committed in your worktree). The deck/talk substrate is slides/v2/SLIDES_v2_PLAN.md + paper_prep/synthesis/CROSSWALK.md + end-to-end-report/. The author needs a chronologically structured, claim-anchored review per topic that pulls the field together so he can speak confidently in talk, Q&A, and during manuscript writing. OUTPUT FILES: paper_prep/lit_review/topic_NN_.md (1500-3000 words, chronological narrative tying each era`s key findings to claims C1-C8 of the abstract — be honest about which claims a reference supports vs only tangentially relates to) AND paper_prep/lit_review/topic_NN_.bib (BibTeX entries for new references this review introduces; do NOT duplicate entries already in paper_prep/synthesis/REFERENCES.bib — check first). USE WebSearch / WebFetch tools to find recent papers; combine with seed references provided per topic. SCOPE 10-30 references per topic (more for foundational topics, fewer for narrow ones). DO NOT write the manuscript itself; do NOT modify any other lit_review file; single commit per task: "docs: lit review topic NN — ".

THIS TOPIC (03): The pseudohomologous region (PHR) concept — Mefford & Trask 2002 Nat Rev Genetics is the foundational paper; predecessors include Flint 1997 (subtelomere allelic diversity) and Linardopoulou 2005 (subtelomeric "hot-spots"); inheritors include Stong 2014 (assembly-based), Ambrosini 2007 (gene-content blocks 1-12). The naming, characterization, and evolution of the PHR concept.

TIME RANGE: 1997-present.

SEED REFERENCES: Mefford&Trask 2002; Flint 1997; Linardopoulou 2005; Stong 2014; Ambrosini 2007. Find ~15-25 more — especially anyone challenging or refining the PHR concept.

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RE-DISPATCH NOTE (claude:sonnet, 2026-05-06)

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This task has been redispatched from codex:gpt-5.5 (which had ~14-50%

engagement on these tasks — see ~/.claude/projects/-moosefs-erikg-phrs/memory/

feedback_codex_gpt55_lazy_execution.md for the full incident report).

When you start, you may see:

- paper_prep/lit_review/topic_03_*.md and .bib (committed, ~14kB each) —

QUALITY BENCHMARK. Format / depth / structure to match or exceed.

- paper_prep/lit_review/topic_11_*.md and .bib (committed, ~14kB each) —

same — also a benchmark.

- SYNTHESIS.md, CHRONOLOGY.md, GAPS.md from a partial earlier synthesis run

(built from incomplete substrate; will be regenerated by the synth task).

- prior wg log entries showing codex agents bailing in 30-60s — that is

the failure mode you must NOT repeat.

You are claude:sonnet. The task is a literature review with web search +

1500-3000 words of prose + 10-30 BibTeX entries. Take the time to do the

work properly. The mandatory step-ordered preamble above this note still

applies (if the original preamble is present). If your topic does not have

the strict-step preamble (topic-03 and topic-11-2 retained their original

prompts), follow the same shape as those benchmark files.

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Required by

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