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figure-2-heterogeneity-population

Figure 2: heterogeneity and population history

Metadata

Statusdone
Assignedagent-698
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-05-05T04:51:42.869346211+00:00
Started2026-05-05T05:28:19.330219443+00:00
Completed2026-05-05T05:48:16.870708184+00:00
Tagspaper-prep,figure, eval-scheduled
Eval score0.76
└ blocking impact0.85
└ completeness0.85
└ constraint fidelity0.85
└ coordination overhead0.70
└ correctness0.75
└ downstream usability0.80
└ efficiency0.80
└ intent fidelity0.85
└ style adherence0.65

Description

Description

Produce Main Fig 2 (4 panels) of the manuscript per paper_prep/synthesis/MANUSCRIPT_SKELETON.md. Implement directly — do not decompose further.

File scope

  • paper_prep/figures/fig2/figure_fig2.{pdf,png}
  • paper_prep/figures/fig2/figure_fig2.{R,py}
  • paper_prep/figures/fig2/caption.md
  • paper_prep/figures/fig2/sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md §Figure 2)

Figure 2 — Within-community heterogeneity, the two-domain model, and population history

Caption. Inter-chromosomal exchange leaves a quantitative population signature. (a) Allele-vs-paralog Wilcoxon paired test across 9 multi-arm communities; allele closer in 8/9 (overall p < 1e-300, 5,946 pairs); C7 reversed (70.5 % paralog closer, p = 2.0e-7). (b) Per-arm Spearman gradient and piecewise breakpoint for the two-domain model (39/48 and 39/41 arms); chr4p, chr4q, chr22q highlighted as the original FISH-era anchors. (c) Cross-arm superpopulation enrichment heatmap (10/19 Fisher BH-significant pairs); AFR vs non-AFR Fst 0.10–0.15. (d) Out-of-Africa population tree from cross-arm-affinity frequencies (9 arms × 5 superpopulations).

PanelContentStatusSource
2aAllele-vs-paralog Wilcoxon panelGENERATEallele_vs_paralog_distance.tsv — SURVEY_04 §1.1
2bTwo-domain gradient + breakpoint composite (priority gap)GENERATEtwo_domain_test.tsv + two_domain_changepoint.tsv + two_domain_binned_means.tsv + its_breakpoint_coloc.tsv — SURVEY_04 §1.3, §6 F9
2cSuperpop composition heatmap + Fst matrixREADY/compositewithin_arm_heterogeneity_04_superpop_composition.pdf + fst_superpop_matrix.tsv — SURVEY_04 §2.1
2dOut-of-Africa dendrogram from cross-arm FstGENERATEcross_arm_superpop_enrichment.tsv + fst_superpop_matrix.tsv — SURVEY_10/11/12 §6 T-4

Validation

  • All 4 panels addressed; each row in sources.tsv with status READY/GENERATE
  • Caption ≤ 200 words; ≥ 2 metrics cited with TSV paths
  • PDF + PNG produced
  • Panel 2b is the priority — no rendered figure for the two-domain analysis exists per SURVEY_04 §5 #1

Inputs

  • paper_prep/synthesis/MANUSCRIPT_SKELETON.md
  • paper_prep/surveys/SURVEY_04_heterogeneity.md, SURVEY_10_11_12_limits_summary_lit.md

Depends on

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