E12: model speciation — the merge-compatibility limit of the sexual society

New analytic result for the evolution-of-sex paper: how far can two lineages
diverge before recombination (model merging) stops working? Frames merge failure
as biological reproductive isolation via Bateson-Dobzhansky-Muller
incompatibilities. src/knowledge/speciation.py, kind: speciation, on the E7-E11
genotype machinery (pure seeded NumPy, bitwise-reproducible; no external
simulator whose separate RNG would break that).

- BDM construction (E12.yaml): ancestor + two lineages substituting disjoint loci
  (each parent adaptive, incompatibility-free), a fraction rho of cross-lineage
  pairs are BDMIs. Sweeping divergence d reproduces the predicted
  compatible -> outbreeding depression -> hybrid inviability curve; the isolation
  cliff moves to lower d as epistasis density rises (iso at d=20: 0.00/0.03/0.50
  for rho 0.1/0.25/0.5); incompatibilities snowball ~ (d/2)^2 (Orr-Turelli).
- NK variant (E12_nk.yaml): parents = hill-climbed local optima; the epistasis
  wedge — recombination gain flips 0 -> -0.13 and OD rate 0 -> 0.90 as ruggedness
  K rises. At matched divergence, mergeability is governed by epistasis, the axis
  no divergence-only ML merge predictor captures.

plot_E12.py (3-panel), +7 tests (138 green), README with honest positioning
(concedes the empirical phenomenon to Pari 2024 / Zhou 2026 + permutation
artefacts to Git Re-Basin; claims the predictive theory + the epistasis wedge).
Wired into make layer1.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

configs/layer1/E12.yaml

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+experiment: E12
+kind: speciation
+seed: 12
+n_replicates: 15
+
+# E12 — MODEL SPECIATION / reproductive isolation (the merge-compatibility limit of the sexual society).
+# The Bateson-Dobzhansky-Muller construction: an ancestor; two lineages each substitute a DISJOINT set
+# of loci (each parent adaptive, neither carrying an incompatibility); a fraction `rho` of cross-lineage
+# locus pairs are incompatibilities (penalty `s`) that only bite when a recombinant inherits BOTH derived
+# alleles. Sweeping the divergence d (total substitutions) gives the predicted signature
+# COMPATIBLE -> OUTBREEDING DEPRESSION -> HYBRID INVIABILITY, arriving earlier the denser the epistasis
+# (rho), with the Orr-Turelli snowball (# incompatibilities ~ (d/2)^2, so fitness falls super-linearly).
+# A merged model is a single recombinant (F2-like: hybrid breakdown / recombination load), so this maps
+# to postzygotic isolation, not F1 vigour. Falsifier: no outbreeding-depression/isolation progression as
+# d and rho grow. Pure seeded NumPy on the E7-E11 genotype machinery (bitwise-reproducible).
+
+speciation:
+  landscape: bdm
+  L: 20
+  rho: [0.1, 0.25, 0.5]       # epistasis DENSITY: fraction of cross-lineage locus pairs that are BDMIs
+  divergences: [0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20]
+  s: 1.0                      # incompatibility penalty per realised BDMI
+  beta: 1.0                   # additive benefit per derived (adaptive) allele — makes parents fit
+  recomb_rate: 0.5            # free recombination (each locus ~ independent parent)
+  n_offspring: 500
+
+output:
+  dir: results/E12