Giorgio Gilestro
ab3dc10587
- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
(imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
where they feed none; configs keep their `experiment:` value so parquet
hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
SI Methods/tables updated; make clean no longer deletes tracked manifests;
reproduce.sh hashes the s{seed}/ layouts too
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
28 lines
1.6 KiB
YAML
28 lines
1.6 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/fig5_speciation_bdm
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