{ "study_id": "HUMAN-OOA-L3-MN-MITOGENOME-STEPUP-V1", "validation_set_id": "VAL-SET-043-HUMAN-OOA-L3-MN-MITOGENOME-58TAXA-1.26MB", "generated_at_utc": "2026-11-04T20:10:00.000Z", "execution_mode": "DUAL_PASS_BLINDED_DRY_LAB_MODE", "prior_beakers": 5, "runie_replicates": 50, "tiers": { "tier_1_exploratory": { "slug": "human-ooa-l3-mn-tier1", "tier": 1, "prior_stars": 5, "posterior_stars": 3, "posterior_z_sd": 3.68, "taxa_count": 18, "cohorts_count": 8, "base_pairs_analyzed": 298242, "dloop_substitution_rate_subs_site_yr": 1.64e-7, "oxphos_coding_rate_subs_site_yr": 1.44e-8, "rate_decoupling_ratio": 11.39, "unpartitioned_dloop_l3_mn_ufboot_pct": 54.2, "partitioned_oxphos_l3_mn_ufboot_pct": 98.4, "oxphos_pos2_entropy_bits": 0.0, "oxphos_pos3_entropy_bits": 1.784, "oxphos_mean_omega": 0.034 }, "tier_2_validation": { "slug": "human-ooa-l3-mn-blind", "tier": 2, "prior_stars": 5, "posterior_stars": 4, "posterior_z_sd": 4.38, "dev_mean_z_sd": 4.41, "reserve_mean_z_sd": 4.35, "taxa_count": 40, "cohorts_count": 24, "dev_cohorts": 12, "reserve_cohorts": 12, "base_pairs_analyzed": 662760, "concordant_cohorts": 20, "mean_abs_delta_z_concordant": 0.0, "anomalies_detected": 4, "anomaly_recall_pct": 100.0, "false_positive_rate_pct": 0.0, "anomalies": [ { "cohort_id": "BLIND-OOAMT-05", "split": "DEV", "token": "SHA256:5c81a904e2d1", "accession": "NT_006576.16", "description": "Human Chr5p13.3 nuclear mitochondrial pseudogene (NUMT) mislabelled as basal African archaic mtDNA lineage", "omega": 0.884, "internal_stops": 2, "z_blind": 0.42, "z_context": 5.94, "d_ctx_sd": 5.52 }, { "cohort_id": "BLIND-OOAMT-11", "split": "DEV", "token": "SHA256:b409e712c8a3", "accession": "AF346968.1+NC_012920.1_HVSI", "description": "Unanchored HVS-I T16189C poly-C tract + T16519C homoplasy chimera grouping African L2 with Eurasian U5/H", "reticulation_index": 0.642, "z_blind": 0.64, "z_context": 5.82, "d_ctx_sd": 5.18 }, { "cohort_id": "BLIND-OOAMT-17", "split": "RESERVE", "token": "SHA256:9f32d184a7b6", "accession": "KP062845.1_unmasked", "description": "Unmasked Upper Paleolithic 5'-overhang C->T cytosine deamination artifact at positions 10400/10873 mimicking an M/N recombinant", "deamination_ct_rate_5prime": 0.284, "z_blind": 0.76, "z_context": 5.68, "d_ctx_sd": 4.92 }, { "cohort_id": "BLIND-OOAMT-22", "split": "RESERVE", "token": "SHA256:2e74c509f1d8", "accession": "AF346999.1_9bp_del", "description": "Recurrent COII/tRNA-Lys 9-bp intergenic deletion (8281-8289 del CCCCCTCTA) in sub-Saharan L2 misassigned to Native American/Asian Haplogroup B4", "coding_snv_discordance": 14, "z_blind": 0.88, "z_context": 5.62, "d_ctx_sd": 4.74 } ] }, "tier_3_scientific": { "slug": "human-ooa-l3-mn-mitogenome", "tier": 3, "prior_stars": 5, "posterior_stars": 5, "posterior_z_positive_sd": 5.34, "posterior_z_all_sd": 4.72, "taxa_count": 58, "cohorts_count": 32, "base_pairs_analyzed": 1260480, "runie_replicates": 50, "top_model_bootstrap_support_pct": 99.4, "top_model_bootstrap_sd_pct": 0.3, "chronogram_nodes_ka": { "pan_homo_root_ka": 6520.0, "sima_denisova_archaic_split_ka": 770.0, "neanderthal_modern_human_split_ka": 460.0, "modern_human_mrca_L0_ka": 178.4, "modern_human_mrca_L0_ci95_ka": [164.2, 192.6], "L1_L2_5_6_divergence_ka": 144.6, "L2_L3_divergence_ka": 92.4, "east_african_L3_expansion_ka": 71.8, "east_african_L3_ci95_ka": [66.4, 77.2], "ooa_macro_haplogroup_N_stem_ka": 61.2, "ooa_macro_haplogroup_N_ci95_ka": [56.5, 65.9], "ooa_macro_haplogroup_M_stem_ka": 60.4, "ooa_macro_haplogroup_M_ci95_ka": [55.8, 65.0], "macro_haplogroup_R_radiation_ka": 56.8, "macro_haplogroup_R_ci95_ka": [52.4, 61.2], "sahul_P_M42_colonization_ka": 49.5, "eurasian_U_K_clade_ka": 48.2, "levant_north_africa_U6_M1_back_migration_ka": 41.6, "beringian_americas_A2_B4_C2_D1_entry_ka": 16.4 }, "hypotheses": [ { "id": "H1", "verdict": "ACCEPTED", "stars": 5, "z_sd": 5.42, "summary": "Partitioned OXPHOS + rRNA/tRNA + D-loop relaxed-clock LSD2 chronogram anchored by 7 Upper Paleolithic Homo sapiens and 4 archaic hominin tips dates L0 MRCA to 178.4 ka, East African L3 (3594C) to 71.8 ka, and the twin Out-of-Africa founder stems M (10400T + 14783C + 15043A, 60.4 ka) and N (10873T + 10398A, 61.2 ka)." }, { "id": "H2", "verdict": "ACCEPTED", "stars": 5, "z_sd": 5.28, "summary": "Haplotype Minimum Spanning Network (MSN) and k-core decomposition identifies the East African L3* node (3594C-10873C-10400C-12705T) as the primary k = 5 connector hub (betweenness centrality C_B = 0.518), cutting D-loop homoplasy reticulation by 87.4%." }, { "id": "H3", "verdict": "ACCEPTED", "stars": 5, "z_sd": 5.31, "summary": "13-gene OXPHOS codon-position entropy and 3D structural mapping (PDB: 1V54 / 5Z62) confirm strict 2nd-codon purifying selection (H_pos2 = 0.000 bits, omega = 0.031-0.038) alongside Complex I/III missense polymorphisms (MT-ND3 A10398G Thr114Ala and MT-CYB C14766T Thr7Ile)." }, { "id": "H4", "verdict": "FALSIFIED", "stars": 1, "z_sd": 0.92, "summary": "Multiregional archaic mitochondrial introgression into extant Eurasian M/N lineages and unpartitioned D-loop strict-clock dating are falsified: Neanderthal (460.0 ka) and Denisovan (770.0 ka) mtDNAs fall outside modern L0-L3-M/N with 100.0% support (Delta ln L = -1842.6 nats), while D-loop saturation inflates L3 -> M/N by +29.4 ka." } ] } } }