Giorgio Gilestro
db9452c9d4
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>
28 lines
1.5 KiB
YAML
28 lines
1.5 KiB
YAML
experiment: E12
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kind: speciation
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seed: 12
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n_replicates: 15
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# E12 — MODEL SPECIATION / reproductive isolation (the merge-compatibility limit of the sexual society).
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# The Bateson-Dobzhansky-Muller construction: an ancestor; two lineages each substitute a DISJOINT set
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# of loci (each parent adaptive, neither carrying an incompatibility); a fraction `rho` of cross-lineage
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# locus pairs are incompatibilities (penalty `s`) that only bite when a recombinant inherits BOTH derived
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# alleles. Sweeping the divergence d (total substitutions) gives the predicted signature
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# COMPATIBLE -> OUTBREEDING DEPRESSION -> HYBRID INVIABILITY, arriving earlier the denser the epistasis
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# (rho), with the Orr-Turelli snowball (# incompatibilities ~ (d/2)^2, so fitness falls super-linearly).
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# A merged model is a single recombinant (F2-like: hybrid breakdown / recombination load), so this maps
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# to postzygotic isolation, not F1 vigour. Falsifier: no outbreeding-depression/isolation progression as
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# d and rho grow. Pure seeded NumPy on the E7-E11 genotype machinery (bitwise-reproducible).
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speciation:
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landscape: bdm
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L: 20
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rho: [0.1, 0.25, 0.5] # epistasis DENSITY: fraction of cross-lineage locus pairs that are BDMIs
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divergences: [0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20]
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s: 1.0 # incompatibility penalty per realised BDMI
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beta: 1.0 # additive benefit per derived (adaptive) allele — makes parents fit
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recomb_rate: 0.5 # free recombination (each locus ~ independent parent)
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n_offspring: 500
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output:
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dir: results/E12
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