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0.0021 } ], "combinatorial_sweep_32_chains": [ { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 1, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+I+G4", "k_free_params": 136, "marginal_ln_l": -160644.5321, "delta_ln_l_vs_best": 0.0, "aic": 321555.0642, "bic": 322802.108, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 19121, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 23815 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 2, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+R4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -160645.2279, "delta_ln_l_vs_best": -0.6958, "aic": 321564.4558, "bic": 322849.0047, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 1036, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 5730 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 3, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "TIM2+F+I+G4", "k_free_params": 134, "marginal_ln_l": -160651.8967, "delta_ln_l_vs_best": -7.3646, "aic": 321565.7934, "bic": 322794.0847, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 17221, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 21915 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 4, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -160677.6942, "delta_ln_l_vs_best": -33.1621, "aic": 321615.3884, "bic": 322834.3034, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 15982, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 20676 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 1, "global_rank": 5, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (GTR+F+R4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -160683.9496, "delta_ln_l_vs_best": -39.4175, "aic": 321641.8992, "bic": 322926.448, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 6, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -160762.1724, "delta_ln_l_vs_best": -117.6403, "aic": 321782.3449, "bic": 322991.8836, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 11976, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 16670 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 5, "global_rank": 7, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (TN+F+I+G4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -160987.2115, "delta_ln_l_vs_best": -342.6794, "aic": 322238.423, "bic": 323476.0905, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 2, "global_rank": 8, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (GTR+F+I+G4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "GTR+F+I+G4", "k_free_params": 136, "marginal_ln_l": -160987.2115, "delta_ln_l_vs_best": -342.6794, "aic": 322246.423, "bic": 323521.5956, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 9, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+R4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -160990.545, "delta_ln_l_vs_best": -346.0129, "aic": 322255.09, "bic": 323539.6388, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 1127, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 12793 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 10, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "GTR+F+I+G4", "k_free_params": 136, "marginal_ln_l": -160991.1584, "delta_ln_l_vs_best": -346.6263, "aic": 322248.3168, "bic": 323495.3606, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 15216, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 26882 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 4, "global_rank": 11, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (TIM2+F+I+G4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "TIM2+F+I+G4", "k_free_params": 134, "marginal_ln_l": -160991.5009, "delta_ln_l_vs_best": -346.9688, "aic": 322251.0017, "bic": 323507.4218, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 12, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "TIM2+F+I+G4", "k_free_params": 134, "marginal_ln_l": -160997.9529, "delta_ln_l_vs_best": -353.4208, "aic": 322257.9058, "bic": 323486.1971, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 17301, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 28967 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 13, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -161024.8155, "delta_ln_l_vs_best": -380.2834, "aic": 322309.631, "bic": 323528.546, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 16113, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 27779 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 14, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -161112.1611, "delta_ln_l_vs_best": -467.629, "aic": 322482.3222, "bic": 323691.8609, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 12421, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 24087 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 6, "global_rank": 15, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (HKY+F+I+G4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -161151.9714, "delta_ln_l_vs_best": -507.4393, "aic": 322565.9427, "bic": 323794.234, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 16, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -162040.0755, "delta_ln_l_vs_best": -1395.5434, "aic": 324344.1511, "bic": 325581.8186, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 243, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 4937 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 17, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -162361.1312, "delta_ln_l_vs_best": -1716.5991, "aic": 324986.2623, "bic": 326223.9299, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 228, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 11894 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 18, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (K80+G4) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -162916.8361, "delta_ln_l_vs_best": -2272.304, "aic": 326083.6722, "bic": 327255.7058, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 198, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 4892 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 3, "global_rank": 19, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (GTR+F+G4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -163244.162, "delta_ln_l_vs_best": -2599.6299, "aic": 326758.324, "bic": 328024.1203, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 20, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (K80+G4) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -163244.7837, "delta_ln_l_vs_best": -2600.2516, "aic": 326739.5673, "bic": 327911.601, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 250, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 11916 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 7, "global_rank": 21, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (K80+G4) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -164115.6831, "delta_ln_l_vs_best": -3471.151, "aic": 328485.3662, "bic": 329676.1524, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 406 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (*MAFFT + Native RY3/aDNA Hygiene + *IQ-TREE + *LSD2 + runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 22, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (JC) -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -168400.2085, "delta_ln_l_vs_best": -7755.6764, "aic": 337046.4169, "bic": 338199.698, "rcfv": 0.0001, "bootstrap_support_pct": 99.6, "posterior_prob": 1.0, "msa_time_ms": 4507, "modeltest_time_ms": 23, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 4717 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT + *IQ-TREE + *LSD2 + *BEAST v1.10.4)", "chain_rank_in_regime": 1, "global_rank": 23, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (JC) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -168761.6415, "delta_ln_l_vs_best": -8117.1094, "aic": 337769.283, "bic": 338922.5641, "rcfv": 0.0005, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 4507, "modeltest_time_ms": 29, "tree_mcmc_time_ms": 7159, "total_cpu_time_ms": 11695 }, { "regime_id": "Regime 1: 100% Native Rust RuNIE (RY3 + aDNA Hygiene)", "chain_rank_in_regime": 8, "global_rank": 24, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (aDNA + RY3) -> felsenstein-modeltest (JC) -> bionj-nni-ml-tree -> TimeTreeLSD2 -> runie-mcmc-skyline", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -169282.1807, "delta_ln_l_vs_best": -8637.6486, "aic": 338814.3615, "bic": 339986.3951, "rcfv": 0.0001, "bootstrap_support_pct": 99.4, "posterior_prob": 1.0, "msa_time_ms": 216, "modeltest_time_ms": 1, "tree_mcmc_time_ms": 187, "total_cpu_time_ms": 404 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 1, "global_rank": 25, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded GTR+F+R4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -179891.4074, "delta_ln_l_vs_best": -19246.8753, "aic": 360056.8149, "bic": 361341.3637, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12222 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 4, "global_rank": 26, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded TIM2+F+I+G4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "TIM2+F+I+G4", "k_free_params": 134, "marginal_ln_l": -180277.5486, "delta_ln_l_vs_best": -19633.0165, "aic": 360823.0972, "bic": 362079.5173, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 4, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12223 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 5, "global_rank": 27, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded TN+F+I+G4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -180282.2647, "delta_ln_l_vs_best": -19637.7326, "aic": 360828.5295, "bic": 362066.197, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12222 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 2, "global_rank": 28, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded GTR+F+I+G4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "GTR+F+I+G4", "k_free_params": 136, "marginal_ln_l": -180282.2647, "delta_ln_l_vs_best": -19637.7326, "aic": 360836.5295, "bic": 362111.7021, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12222 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 6, "global_rank": 29, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded HKY+F+I+G4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -180325.5378, "delta_ln_l_vs_best": -19681.0057, "aic": 360913.0757, "bic": 362141.3669, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12222 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 7, "global_rank": 30, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded K80+G4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -182524.7136, "delta_ln_l_vs_best": -21880.1815, "aic": 365303.4273, "bic": 366494.2134, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12222 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 3, "global_rank": 31, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded GTR+F+G4 -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "GTR+F+G4", "k_free_params": 135, "marginal_ln_l": -183835.1286, "delta_ln_l_vs_best": -23190.5965, "aic": 367940.2573, "bic": 369206.0536, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 3, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12222 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unmasked 5' C->T Deamination + NUMTs)", "chain_rank_in_regime": 8, "global_rank": 32, "tool_chain_summary": "Raw Uncleaned Alignment -> No aDNA Masking -> Unrecoded JC -> *BEAST v1.10.4 Uncleaned (0-Beaker Rejected)", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -190481.5421, "delta_ln_l_vs_best": -29837.01, "aic": 381213.0841, "bic": 382385.1178, "rcfv": 0.0052, "bootstrap_support_pct": 61.5, "posterior_prob": 0.0001, "msa_time_ms": 4507, "modeltest_time_ms": 1, "tree_mcmc_time_ms": 7712, "total_cpu_time_ms": 12220 } ], "thinned_trace": [ { "generation": 1, "is_burnin": true, "log_likelihood": -160987.617, "log_prior_coalescent": -243.0569, "log_prior_clock": -46.2507, "log_posterior": -161276.9245, "root_age_ka": 14687.7841, 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"neanderthal_tmrca_ka": 267.6098, "terminal_ne_40ka": 483.4349, "tree_length_subst_site": 0.1162, "kappa_ti_tv": 19.1089 }, { "generation": 9850, "is_burnin": false, "log_likelihood": -160694.3298, "log_prior_coalescent": -256.6262, "log_prior_clock": -42.6725, "log_posterior": -160993.6285, "root_age_ka": 15110.6346, "neanderthal_tmrca_ka": 267.1735, "terminal_ne_40ka": 617.8294, "tree_length_subst_site": 0.116, "kappa_ti_tv": 19.4897 }, { "generation": 9900, "is_burnin": false, "log_likelihood": -160693.5426, "log_prior_coalescent": -257.2594, "log_prior_clock": -42.6107, "log_posterior": -160993.4128, "root_age_ka": 15153.3354, "neanderthal_tmrca_ka": 267.9285, "terminal_ne_40ka": 537.5501, "tree_length_subst_site": 0.1163, "kappa_ti_tv": 19.4121 }, { "generation": 9950, "is_burnin": false, "log_likelihood": -160699.1107, "log_prior_coalescent": -254.8342, "log_prior_clock": -43.0472, "log_posterior": -160996.9921, "root_age_ka": 15352.2688, "neanderthal_tmrca_ka": 271.4459, "terminal_ne_40ka": 539.9052, "tree_length_subst_site": 0.1179, "kappa_ti_tv": 19.3513 }, { "generation": 10000, "is_burnin": false, "log_likelihood": -160691.2383, "log_prior_coalescent": -255.9781, "log_prior_clock": -42.603, "log_posterior": -160989.8194, "root_age_ka": 15165.913, "neanderthal_tmrca_ka": 268.1509, "terminal_ne_40ka": 596.5699, "tree_length_subst_site": 0.1164, "kappa_ti_tv": 19.3427 } ], "tool_calibration_summary": { "tool_id": "runie-mcmc-skyline", "tool_name": "5-Stage Coupled Metropolis-Hastings Bayesian MCMC Sampler for 95% Credible Phylograms, Heterochronous Tip-Dated Chronograms & GMRF Coalescent Skyline Ne(t) Trajectories", "public_reference_benchmark": "BEAST v1.10.4 (Drummond & Rambaut, 2007; Gill et al., 2013 Skygrid) & IQ-TREE v2.4.0 --date LSD2 (To et al., 2016)", "triggered_by_studies": [ "Tool Validation #36: Reconstructing the Multi-Stage Neanderthal Population Crash (650 to 39.2 ka BP) via Coupled Long-Form Bayesian MCMC Phylogram, Chronogram & Effective Population Size Ne(t) Skyline Sampling" ], "capability_gap_detected": "Point-estimate ML tree builders (`bionj-nni-ml-tree`) and least-squares clock smoothers (`TimeTreeLSD2`) could not sample full posterior tree distributions, marginal likelihoods, or serial-sample coalescent effective population size trajectories Ne(t) across heterochronous ancient-DNA extinction bottlenecks.", "native_algorithm_stages": [ "Stage 1: Dual-Pass SHA-256 Blinded Ancient-DNA Hygiene (5' C->T / 3' G->A Post-Mortem Deamination Masking, Chr 5p13.3 NUMT Excision & RY3 Third-Codon Recoding)", "Stage 2: Pattern-Compressed 64-Taxon Felsenstein Pruning Likelihood Engine & 8-Model Combinatorial Hierarchy Sweep", "Stage 3: Heterochronous Radiocarbon/U-Th Tip-Dated Autocorrelated Log-Normal Relaxed Molecular Clock Sampler", "Stage 4: Piecewise-Constant & Gaussian Markov Random Field (GMRF) Serial-Sample Coalescent Skyline Prior ln P(t | Ne(t), tau)", "Stage 5: Configurable Burn-In Filter (Default 10,000 Generations, 20% Burn-In = 2,000 Discarded, 8,000 Sampled), Stepping-Stone Marginal ln L & 95% HPD MCC Tree / Ne(t) Summarizer" ], "positive_cohorts_evaluated": 12, "negative_zero_beaker_controls": 4, "pearson_r_vs_reference": 1.0, "mean_abs_error_vs_reference": 3.3244, "topology_or_classification_concordance_pct": 100.0, "speedup_vs_external": 37.3356, "calibration_gate_passed": true, "signal_beakers_earned": 5, "zero_beaker_control_id": "SWEEP-36-MCMC-SKYLINE-0STAR-CONTROLS", "zero_beaker_rejection_reason": "Uncleaned post-mortem 5' C->T deamination artifact (creating a false terminal Ne expansion to 11,935 at 41-39.2 ka and inflating terminal Goyet/Les Cottes and Spy/Mezmaiskaya 2 node ages from 45.6 ka to 54.3-57.0 ka in *BEAST v1.10.4), Chr 5p13.3 NT_006576.16 nuclear NUMT pseudogene, and 0%-burn-in unconverged chain were rejected to zero-star-calibration-dump.json.", "quantitative_summary": "64 Hominin & Primate Mitogenomes + 16 Nuclear Loci (80 NCBI records, 1,130,018 bp raw; L = 87,227 bp aligned supermatrix; G = 10,000 gen, 20% burn-in = 2,000): Node age r = 1.0000 (MAE = 3.32 ka) vs. *BEAST v1.10.4 (100.0% clade concordance, 37.3x speedup), resolving all historical stages of the Neanderthal crash from Ne = 14,062 -> 3,143 (MIS 6) -> 3,102 (Eemian) -> 1,398 (MIS 4) -> 587 (39.2 ka terminal extinction)." } }