{ "report_id": "coalescent-native-vs-astral-v578-calibration-v1", "title": "Quartet Multispecies Coalescent & Incomplete Lineage Sorting Calibration: Native Rust Quartet MSC Engine vs. ASTRAL v5.7.8 Across 1,064 Gene Trees (28.64 Million Quartets)", "default_policy": "CoalescentMode::Native (4-Stage Quartet MSC + LPP + ABBA-BABA) is the default across all bio-suite multi-locus workflows; external ASTRAL v5.7.8 is invoked only when --coalescent astral is explicitly passed.", "astral_version": "ASTRAL v5.7.8 (Mirarab et al. 2014 / Zhang et al. 2018; OpenJDK 21.0.12.1 64-Bit Server VM)", "upstream_native_stack": "AlignerMode::Native (Gotoh Affine-Gap) -> ModelTestMode::Native (Felsenstein Pruning) -> TreeBuilderMode::Native (4-Stage ML BIONJ+NNI)", "total_duration_ms": 2933, "total_cohorts_evaluated": 4, "total_gene_trees_analyzed": 1064, "total_quartets_evaluated": 28656824, "mean_topological_concordance_pct": 100.0, "mean_q1_pearson_r": 1.0, "mean_branch_cu_pearson_r": 0.9873, "mean_native_speedup_factor": 23.7899, "cohorts": [ { "cohort_id": "COHORT-01-CARNIVORA-16TAXA-NATIVE-CHAIN", "title": "16-Taxon Carnivora Sub-Locus Window Coalescent Panel (16 ML Trees Built via 100% Native Upstream Stack)", "taxonomic_scope": "Order Carnivora (Feliformia vs. Caniformia: Felidae, Canidae, Ursidae, Mustelidae, Phocidae)", "upstream_pipeline_provenance": "100% Native Upstream Stack: Native Gotoh Aligner v2 -> Native Felsenstein ModelTest (best model HKY+I) -> 16 Window ML Gene Trees via Native BIONJ+NNI (239.5 ms total upstream)", "taxa_count": 16, "internal_branches_count": 13, "gene_tree_count": 16, "total_quartets_evaluated": 29120, "native_result": { "engine_name": "bio-suite Native Quartet MSC v1 (Exact Tripartition DP + Quartet NNI + LPP)", "engine_mode": "CoalescentMode::Native", "taxa_count": 16, "gene_tree_count": 16, "total_quartets_evaluated": 29120, "satisfied_quartet_score": 27482, "normalized_quartet_score": 0.9438, "mean_local_posterior_pp1": 0.9899, "mean_branch_length_cu": 1.9632, "wall_clock_ms": 5.1817, "species_tree_newick": "(Ursus_americanus_NC_003426,(Ursus_americanus_JX196366,(Ursus_thibetanus_NC_009971,(((Ursus_maritimus_NC_003428,Ursus_maritimus_GU573490)1.0000:2.4567,(Ursus_arctos_AP012578,Ursus_arctos_NC_003427)1.0000:2.3671)1.0000:2.4567,((Meles_anakuma_NC_009677,Mustela_putorius_NC_020638)0.9940:0.7577,((Vulpes_vulpes_NC_008434,(Canis_lupus_NC_008092,Canis_lupus_familiaris_NC_002008)1.0000:2.4567)1.0000:2.6184,(Felis_catus_NC_001700,(Panthera_pardus_NC_010641,(Panthera_tigris_NC_010642,Panthera_tigris_EF551003)1.0000:2.4567)0.9999:1.2685)1.0000:2.4567)0.9989:0.9808)1.0000:2.4567)0.8764:0.4212)1.0000:2.3671):0.0000);", "focal_branches": [ { "branch_id": "BR-01", "clade_label": "Ursus_maritimus_NC_003428 + Ursus_maritimus_GU573490", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4567, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-02", "clade_label": "Ursus_arctos_AP012578 + Ursus_arctos_NC_003427", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.9375, "q2_alt1_freq": 0.0625, "q3_alt2_freq": 0.0, "f1_quartet_weight": 15.0, "f2_quartet_weight": 1.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 93.75, "local_posterior_pp1": 1.0, "branch_length_cu": 2.3671, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-03", "clade_label": "Ursus_maritimus_NC_003428 + Ursus_maritimus_GU573490 + Ursus_arctos_AP012578 + Ursus_arctos_NC_003427", "subset_size": 4, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4567, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-04", "clade_label": "Meles_anakuma_NC_009677 + Mustela_putorius_NC_020638", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.6875, "q2_alt1_freq": 0.1875, "q3_alt2_freq": 0.125, "f1_quartet_weight": 11.0, "f2_quartet_weight": 3.0, "f3_quartet_weight": 2.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 68.75, "local_posterior_pp1": 0.994, "branch_length_cu": 0.7577, "discordance_asymmetry_chisq": 0.2, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-05", "clade_label": "Canis_lupus_NC_008092 + Canis_lupus_familiaris_NC_002008", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4567, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-06", "clade_label": "Vulpes_vulpes_NC_008434 + Canis_lupus_NC_008092 + Canis_lupus_familiaris_NC_002008", "subset_size": 3, "total_taxa": 16, "q1_main_freq": 0.9514, "q2_alt1_freq": 0.0486, "q3_alt2_freq": 0.0, "f1_quartet_weight": 15.2222, "f2_quartet_weight": 0.7778, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 93.75, "local_posterior_pp1": 1.0, "branch_length_cu": 2.6184, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-07", "clade_label": "Panthera_tigris_NC_010642 + Panthera_tigris_EF551003", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4567, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-08", "clade_label": "Panthera_pardus_NC_010641 + Panthera_tigris_NC_010642 + Panthera_tigris_EF551003", "subset_size": 3, "total_taxa": 16, "q1_main_freq": 0.8125, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.1875, "f1_quartet_weight": 13.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 3.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 81.25, "local_posterior_pp1": 0.9999, "branch_length_cu": 1.2685, "discordance_asymmetry_chisq": 3.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-09", "clade_label": "Felis_catus_NC_001700 + Panthera_pardus_NC_010641 + Panthera_tigris_NC_010642 + Panthera_tigris_EF551003", "subset_size": 4, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4567, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-10", "clade_label": "Vulpes_vulpes_NC_008434 + Canis_lupus_NC_008092 (+5 taxa)", "subset_size": 7, "total_taxa": 16, "q1_main_freq": 0.75, "q2_alt1_freq": 0.0938, "q3_alt2_freq": 0.1563, "f1_quartet_weight": 12.0, "f2_quartet_weight": 1.5, "f3_quartet_weight": 2.5, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 68.75, "local_posterior_pp1": 0.9989, "branch_length_cu": 0.9808, "discordance_asymmetry_chisq": 0.25, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-11", "clade_label": "Meles_anakuma_NC_009677 + Mustela_putorius_NC_020638 (+7 taxa)", "subset_size": 9, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4567, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-12", "clade_label": "Meles_anakuma_NC_009677 + Mustela_putorius_NC_020638 (+11 taxa)", "subset_size": 13, "total_taxa": 16, "q1_main_freq": 0.5625, "q2_alt1_freq": 0.0625, "q3_alt2_freq": 0.375, "f1_quartet_weight": 9.0, "f2_quartet_weight": 1.0, "f3_quartet_weight": 6.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 56.25, "local_posterior_pp1": 0.8764, "branch_length_cu": 0.4212, "discordance_asymmetry_chisq": 3.5714, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-13", "clade_label": "Ursus_thibetanus_NC_009971 + Meles_anakuma_NC_009677 (+12 taxa)", "subset_size": 14, "total_taxa": 16, "q1_main_freq": 0.9375, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0625, "f1_quartet_weight": 15.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 1.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 93.75, "local_posterior_pp1": 1.0, "branch_length_cu": 2.3671, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" } ] }, "astral_result": { "engine_name": "ASTRAL v5.7.8 (Mirarab et al. — Exact Quartet DP + Polytree Weighting)", "engine_mode": "CoalescentMode::Astral", "taxa_count": 16, "gene_tree_count": 16, "total_quartets_evaluated": 29120, "satisfied_quartet_score": 27482, "normalized_quartet_score": 0.9438, "mean_local_posterior_pp1": 0.9892, "mean_branch_length_cu": 1.7486, "wall_clock_ms": 195.4886, "species_tree_newick": 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"focal_branches": [ { "branch_id": "ASTRAL-BR-01", "clade_label": "Internal Branch 1", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4277, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-02", "clade_label": "Internal Branch 2", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.9375, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0625, "f1_quartet_weight": 15.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 1.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 93.75, "local_posterior_pp1": 1.0, "branch_length_cu": 1.7346, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-03", "clade_label": 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"q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0486, "f1_quartet_weight": 15.2222, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.7778, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 95.1389, "local_posterior_pp1": 1.0, "branch_length_cu": 1.8524, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-06", "clade_label": "Internal Branch 6", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4277, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-07", "clade_label": "Internal Branch 7", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.8125, "q2_alt1_freq": 0.1875, "q3_alt2_freq": 0.0, "f1_quartet_weight": 13.0, "f2_quartet_weight": 3.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 81.25, "local_posterior_pp1": 0.9998, "branch_length_cu": 1.0415, "discordance_asymmetry_chisq": 3.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-08", "clade_label": "Internal Branch 8", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4277, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-09", "clade_label": "Internal Branch 9", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.75, "q2_alt1_freq": 0.1563, "q3_alt2_freq": 0.0938, "f1_quartet_weight": 12.0, "f2_quartet_weight": 2.5, "f3_quartet_weight": 1.5, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 75.0, "local_posterior_pp1": 0.9987, "branch_length_cu": 0.8183, "discordance_asymmetry_chisq": 0.25, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-10", "clade_label": "Internal Branch 10", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.6875, "q2_alt1_freq": 0.125, "q3_alt2_freq": 0.1875, "f1_quartet_weight": 11.0, "f2_quartet_weight": 2.0, "f3_quartet_weight": 3.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 68.75, "local_posterior_pp1": 0.9929, "branch_length_cu": 0.636, "discordance_asymmetry_chisq": 0.2, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-11", "clade_label": "Internal Branch 11", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 1.0, "q2_alt1_freq": 0.0, "q3_alt2_freq": 0.0, "f1_quartet_weight": 16.0, "f2_quartet_weight": 0.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 100.0, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4277, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-12", "clade_label": "Internal Branch 12", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.5625, "q2_alt1_freq": 0.375, "q3_alt2_freq": 0.0625, "f1_quartet_weight": 9.0, "f2_quartet_weight": 6.0, "f3_quartet_weight": 1.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 56.25, "local_posterior_pp1": 0.8685, "branch_length_cu": 0.3483, "discordance_asymmetry_chisq": 3.5714, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-13", "clade_label": "Internal Branch 13", "subset_size": 2, "total_taxa": 16, "q1_main_freq": 0.9375, "q2_alt1_freq": 0.0625, "q3_alt2_freq": 0.0, "f1_quartet_weight": 15.0, "f2_quartet_weight": 1.0, "f3_quartet_weight": 0.0, "effective_loci_en": 16.0, "gene_concordance_gcf_pct": 93.75, "local_posterior_pp1": 1.0, "branch_length_cu": 1.7346, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" } ] }, "robinson_foulds_distance": 0, "max_robinson_foulds": 26, "topological_concordance_pct": 100.0, "quartet_score_ratio": 1.0, "normalized_quartet_delta": 0.0, "q1_pearson_r": 1.0, "branch_cu_pearson_r": 0.9525, "lpp_concordance_pct": 100.0, "native_speedup_factor": 37.7267, "abba_baba_tests": [ { "quartet_id": "ABBA-01-URSIDAE", "p1_taxon": "Ursus americanus (NC_003426)", "p2_taxon": "Ursus arctos (NC_003427)", "p3_donor_taxon": "Ursus maritimus (NC_003428)", "outgroup_taxon": "Ursus thibetanus (NC_009971)", "bbaa_concordant_sites": 4, "abba_shared_p2_p3_sites": 70, "baba_shared_p1_p3_sites": 2, "patterson_d_stat": 0.9444, "z_score": 8.0139, "biological_interpretation": "Strong derived site sharing between Ursus arctos and Ursus maritimus relative to Ursus americanus (Ursus thibetanus outgroup), consistent with close sister-clade affinity and Pleistocene mitochondrial introgression across Holarctic bears." }, { "quartet_id": "ABBA-02-FELIDAE", "p1_taxon": "Panthera tigris (NC_010642)", "p2_taxon": "Panthera pardus (NC_010641)", "p3_donor_taxon": "Felis catus (NC_001700)", "outgroup_taxon": "Meles anakuma (NC_009677)", "bbaa_concordant_sites": 36, "abba_shared_p2_p3_sites": 27, "baba_shared_p1_p3_sites": 24, "patterson_d_stat": 0.0588, "z_score": 0.4201, "biological_interpretation": "High BBAA concordance between Panthera tigris and Panthera pardus relative to Felis catus, with moderate ABBA/BABA site sharing reflecting rapid Plio-Pleistocene felid radiation and incomplete lineage sorting." }, { "quartet_id": "ABBA-03-CANIDAE", "p1_taxon": "Canis lupus (NC_008092)", "p2_taxon": "Canis lupus familiaris (NC_002008)", "p3_donor_taxon": "Vulpes vulpes (NC_008434)", "outgroup_taxon": "Ursus arctos (NC_003427)", "bbaa_concordant_sites": 88, "abba_shared_p2_p3_sites": 0, "baba_shared_p1_p3_sites": 0, "patterson_d_stat": 0.0, "z_score": 0.0, "biological_interpretation": "High BBAA concordance and balanced ABBA/BABA counts confirm symmetric neutral sorting between Gray wolf (Canis lupus) and Domestic dog (Canis lupus familiaris) relative to Red fox (Vulpes vulpes)." } ], "ascii_cohort_comparison_table": "====================================================================================================================\nCOHORT: COHORT-01-CARNIVORA-16TAXA-NATIVE-CHAIN — 16-Taxon Carnivora Sub-Locus Window Coalescent Panel (16 ML Trees Built via 100% Native Upstream Stack)\nTaxa: 16 | Internal Splits: 13 | Input Gene Trees: 16 | Total Quartets Evaluated: 29120\nUpstream Provenance: 100% Native Upstream Stack: Native Gotoh Aligner v2 -> Native Felsenstein ModelTest (best model HKY+I) -> 16 Window ML Gene Trees via Native BIONJ+NNI (239.5 ms total upstream)\n--------------------------------------------------------------------------------------------------------------------\nMetric Native Quartet MSC (Rust) ASTRAL v5.7.8 (Java) Concordance\n--------------------------------------------------------------------------------------------------------------------\nSatisfied Quartet Score Q(T) 27482 27482 Ratio = 1.000000\nNormalized Quartet Score 0.943800 0.943800 Delta = +0.000000\nRobinson-Foulds Split Distance 0 0 100.00% Match (RF=0/26)\nMean Local Posterior Prob (LPP) 0.9899 0.9892 r(q1) = 1.0000\nMean Coalescent Branch Length (CU) 1.9632 1.7486 r(CU) = 0.9525\nWall-Clock Execution Time (ms) 5.18 195.49 37.73x Speedup\n====================================================================================================================" }, { "cohort_id": "COHORT-02-SONG-PRIMATES-14TAXA-424LOCI", "title": "14-Taxon Primate & Euarchontoglires 424-Nuclear-Gene Phylogenomic Benchmark (Song et al. 2012 PNAS)", "taxonomic_scope": "Euarchontoglires & Outgroups (Hominidae, Cercopithecidae, Platyrrhini, Strepsirrhini, Scandentia, Glires)", "upstream_pipeline_provenance": "Empirical 424 Mammalian Nuclear Ortholog ML Gene Trees (Song et al. 2012 PNAS; 424,424 Quartets)", "taxa_count": 14, "internal_branches_count": 11, "gene_tree_count": 424, "total_quartets_evaluated": 424424, "native_result": { "engine_name": "bio-suite Native Quartet MSC v1 (Exact Tripartition DP + Quartet NNI + LPP)", "engine_mode": "CoalescentMode::Native", "taxa_count": 14, "gene_tree_count": 424, "total_quartets_evaluated": 424424, "satisfied_quartet_score": 389734, "normalized_quartet_score": 0.9183, "mean_local_posterior_pp1": 0.9933, "mean_branch_length_cu": 1.963, "wall_clock_ms": 20.2736, "species_tree_newick": "(Marmoset,((Macaque,(Orangutan,(Gorilla,(Human,Chimpanzee)1.0000:0.6452)1.0000:2.3596)1.0000:2.6357)1.0000:2.7522,(Tarsier,((Galago,Mouse_Lemur)1.0000:2.4392,((Horse,Sloth)1.0000:2.6522,(Tree_Shrew,(Rat,Rabbit)1.0000:0.8080)0.9259:0.0869)1.0000:2.0089)1.0000:0.6597)1.0000:4.5457):0.0000);", "focal_branches": [ { "branch_id": "BR-01", "clade_label": "Human + Chimpanzee", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.6503, "q2_alt1_freq": 0.1844, "q3_alt2_freq": 0.1653, "f1_quartet_weight": 275.7273, "f2_quartet_weight": 78.1818, "f3_quartet_weight": 70.0909, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 63.6792, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6452, "discordance_asymmetry_chisq": 0.4415, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-02", "clade_label": "Human + Chimpanzee + Gorilla", "subset_size": 3, "total_taxa": 14, "q1_main_freq": 0.937, "q2_alt1_freq": 0.0235, "q3_alt2_freq": 0.0395, "f1_quartet_weight": 397.3, "f2_quartet_weight": 9.95, "f3_quartet_weight": 16.75, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 91.2736, "local_posterior_pp1": 1.0, "branch_length_cu": 2.3596, "discordance_asymmetry_chisq": 1.7318, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-03", "clade_label": "Orangutan + Human + Chimpanzee + Gorilla", "subset_size": 4, "total_taxa": 14, "q1_main_freq": 0.9522, "q2_alt1_freq": 0.0253, "q3_alt2_freq": 0.0224, "f1_quartet_weight": 403.7407, "f2_quartet_weight": 10.7407, "f3_quartet_weight": 9.5185, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 93.6321, "local_posterior_pp1": 1.0, "branch_length_cu": 2.6357, "discordance_asymmetry_chisq": 0.0737, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-04", "clade_label": "Orangutan + Human (+3 taxa)", "subset_size": 5, "total_taxa": 14, "q1_main_freq": 0.9575, "q2_alt1_freq": 0.0274, "q3_alt2_freq": 0.0151, "f1_quartet_weight": 405.9688, "f2_quartet_weight": 11.625, "f3_quartet_weight": 6.4063, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.0472, "local_posterior_pp1": 1.0, "branch_length_cu": 2.7522, "discordance_asymmetry_chisq": 1.5105, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-05", "clade_label": "Galago + Mouse_Lemur", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.9418, "q2_alt1_freq": 0.0352, "q3_alt2_freq": 0.0229, "f1_quartet_weight": 399.3429, "f2_quartet_weight": 14.9429, "f3_quartet_weight": 9.7143, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 92.4528, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4392, "discordance_asymmetry_chisq": 1.1087, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-06", "clade_label": "Horse + Sloth", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.953, "q2_alt1_freq": 0.0275, "q3_alt2_freq": 0.0195, "f1_quartet_weight": 404.0741, "f2_quartet_weight": 11.6667, "f3_quartet_weight": 8.2593, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 91.2736, "local_posterior_pp1": 1.0, "branch_length_cu": 2.6522, "discordance_asymmetry_chisq": 0.5827, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-07", "clade_label": "Rat + Rabbit", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.7028, "q2_alt1_freq": 0.1389, "q3_alt2_freq": 0.1582, "f1_quartet_weight": 298.0, "f2_quartet_weight": 58.9091, "f3_quartet_weight": 67.0909, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 63.9151, "local_posterior_pp1": 1.0, "branch_length_cu": 0.808, "discordance_asymmetry_chisq": 0.5313, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-08", "clade_label": "Tree_Shrew + Rat + Rabbit", "subset_size": 3, "total_taxa": 14, "q1_main_freq": 0.3888, "q2_alt1_freq": 0.2556, "q3_alt2_freq": 0.3555, "f1_quartet_weight": 164.8611, "f2_quartet_weight": 108.3889, "f3_quartet_weight": 150.75, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 32.0755, "local_posterior_pp1": 0.9259, "branch_length_cu": 0.0869, "discordance_asymmetry_chisq": 6.9247, "coalescent_regime": "Asymmetric Discordance (Candidate Introgression)" }, { "branch_id": "BR-09", "clade_label": "Tree_Shrew + Rat (+3 taxa)", "subset_size": 5, "total_taxa": 14, "q1_main_freq": 0.9106, "q2_alt1_freq": 0.038, "q3_alt2_freq": 0.0514, "f1_quartet_weight": 386.0833, "f2_quartet_weight": 16.119, "f3_quartet_weight": 21.7976, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 78.7736, "local_posterior_pp1": 1.0, "branch_length_cu": 2.0089, "discordance_asymmetry_chisq": 0.8504, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-10", "clade_label": "Galago + Mouse_Lemur (+5 taxa)", "subset_size": 7, "total_taxa": 14, "q1_main_freq": 0.6553, "q2_alt1_freq": 0.1703, "q3_alt2_freq": 0.1744, "f1_quartet_weight": 277.8667, "f2_quartet_weight": 72.2, "f3_quartet_weight": 73.9333, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 62.5, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6597, "discordance_asymmetry_chisq": 0.0206, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-11", "clade_label": "Galago + Mouse_Lemur (+6 taxa)", "subset_size": 8, "total_taxa": 14, "q1_main_freq": 0.9929, "q2_alt1_freq": 0.0027, "q3_alt2_freq": 0.0044, "f1_quartet_weight": 421.0, "f2_quartet_weight": 1.1429, "f3_quartet_weight": 1.8571, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 98.5849, "local_posterior_pp1": 1.0, "branch_length_cu": 4.5457, "discordance_asymmetry_chisq": 0.1701, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" } ] }, "astral_result": { "engine_name": "ASTRAL v5.7.8 (Mirarab et al. — Exact Quartet DP + Polytree Weighting)", "engine_mode": "CoalescentMode::Astral", "taxa_count": 14, "gene_tree_count": 424, "total_quartets_evaluated": 424424, "satisfied_quartet_score": 389734, "normalized_quartet_score": 0.9183, "mean_local_posterior_pp1": 0.9932, "mean_branch_length_cu": 1.9138, "wall_clock_ms": 482.8271, "species_tree_newick": 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"focal_branches": [ { "branch_id": "ASTRAL-BR-01", "clade_label": "Internal Branch 1", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.9418, "q2_alt1_freq": 0.0229, "q3_alt2_freq": 0.0352, "f1_quartet_weight": 399.3429, "f2_quartet_weight": 9.7143, "f3_quartet_weight": 14.9429, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 94.1846, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4018, "discordance_asymmetry_chisq": 1.1087, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-02", "clade_label": "Internal Branch 2", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.953, "q2_alt1_freq": 0.0195, "q3_alt2_freq": 0.0275, "f1_quartet_weight": 404.0741, "f2_quartet_weight": 8.2593, "f3_quartet_weight": 11.6667, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.3005, "local_posterior_pp1": 1.0, "branch_length_cu": 2.6056, "discordance_asymmetry_chisq": 0.5827, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-03", "clade_label": "Internal Branch 3", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.7028, "q2_alt1_freq": 0.1582, "q3_alt2_freq": 0.1389, "f1_quartet_weight": 298.0, "f2_quartet_weight": 67.0909, "f3_quartet_weight": 58.9091, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 70.283, "local_posterior_pp1": 1.0, "branch_length_cu": 0.8024, "discordance_asymmetry_chisq": 0.5313, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-04", "clade_label": "Internal Branch 4", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.3888, "q2_alt1_freq": 0.3555, "q3_alt2_freq": 0.2556, "f1_quartet_weight": 164.8611, "f2_quartet_weight": 150.75, "f3_quartet_weight": 108.3889, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 38.8823, "local_posterior_pp1": 0.9247, "branch_length_cu": 0.0854, "discordance_asymmetry_chisq": 6.9247, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-05", "clade_label": "Internal Branch 5", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.9106, "q2_alt1_freq": 0.0514, "q3_alt2_freq": 0.038, "f1_quartet_weight": 386.0833, "f2_quartet_weight": 21.7976, "f3_quartet_weight": 16.119, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 91.0574, "local_posterior_pp1": 1.0, "branch_length_cu": 1.9852, "discordance_asymmetry_chisq": 0.8504, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-06", "clade_label": "Internal Branch 6", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.6553, "q2_alt1_freq": 0.1744, "q3_alt2_freq": 0.1703, "f1_quartet_weight": 277.8667, "f2_quartet_weight": 73.9333, "f3_quartet_weight": 72.2, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 65.5346, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6553, "discordance_asymmetry_chisq": 0.0206, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-07", "clade_label": "Internal Branch 7", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.9929, "q2_alt1_freq": 0.0044, "q3_alt2_freq": 0.0027, "f1_quartet_weight": 421.0, "f2_quartet_weight": 1.8571, "f3_quartet_weight": 1.1429, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 99.2925, "local_posterior_pp1": 1.0, "branch_length_cu": 4.2603, "discordance_asymmetry_chisq": 0.1701, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-08", "clade_label": "Internal Branch 8", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.6503, "q2_alt1_freq": 0.1653, "q3_alt2_freq": 0.1844, "f1_quartet_weight": 275.7273, "f2_quartet_weight": 70.0909, "f3_quartet_weight": 78.1818, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 65.03, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6408, "discordance_asymmetry_chisq": 0.4415, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-09", "clade_label": "Internal Branch 9", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.937, "q2_alt1_freq": 0.0235, "q3_alt2_freq": 0.0395, "f1_quartet_weight": 397.3, "f2_quartet_weight": 9.95, "f3_quartet_weight": 16.75, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 93.7028, "local_posterior_pp1": 1.0, "branch_length_cu": 2.3252, "discordance_asymmetry_chisq": 1.7318, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-10", "clade_label": "Internal Branch 10", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.9522, "q2_alt1_freq": 0.0224, "q3_alt2_freq": 0.0253, "f1_quartet_weight": 403.7407, "f2_quartet_weight": 9.5185, "f3_quartet_weight": 10.7407, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.2219, "local_posterior_pp1": 1.0, "branch_length_cu": 2.5898, "discordance_asymmetry_chisq": 0.0737, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-11", "clade_label": "Internal Branch 11", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.9575, "q2_alt1_freq": 0.0151, "q3_alt2_freq": 0.0274, "f1_quartet_weight": 405.9688, "f2_quartet_weight": 6.4063, "f3_quartet_weight": 11.625, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.7473, "local_posterior_pp1": 1.0, "branch_length_cu": 2.7005, "discordance_asymmetry_chisq": 1.5105, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" } ] }, "robinson_foulds_distance": 0, "max_robinson_foulds": 22, "topological_concordance_pct": 100.0, "quartet_score_ratio": 1.0, "normalized_quartet_delta": 0.0, "q1_pearson_r": 1.0, "branch_cu_pearson_r": 0.9993, "lpp_concordance_pct": 100.0, "native_speedup_factor": 23.8156, "abba_baba_tests": [], "ascii_cohort_comparison_table": "====================================================================================================================\nCOHORT: COHORT-02-SONG-PRIMATES-14TAXA-424LOCI — 14-Taxon Primate & Euarchontoglires 424-Nuclear-Gene Phylogenomic Benchmark (Song et al. 2012 PNAS)\nTaxa: 14 | Internal Splits: 11 | Input Gene Trees: 424 | Total Quartets Evaluated: 424424\nUpstream Provenance: Empirical 424 Mammalian Nuclear Ortholog ML Gene Trees (Song et al. 2012 PNAS; 424,424 Quartets)\n--------------------------------------------------------------------------------------------------------------------\nMetric Native Quartet MSC (Rust) ASTRAL v5.7.8 (Java) Concordance\n--------------------------------------------------------------------------------------------------------------------\nSatisfied Quartet Score Q(T) 389734 389734 Ratio = 1.000000\nNormalized Quartet Score 0.918300 0.918300 Delta = +0.000000\nRobinson-Foulds Split Distance 0 0 100.00% Match (RF=0/22)\nMean Local Posterior Prob (LPP) 0.9933 0.9932 r(q1) = 1.0000\nMean Coalescent Branch Length (CU) 1.9630 1.9138 r(CU) = 0.9993\nWall-Clock Execution Time (ms) 20.27 482.83 23.82x Speedup\n====================================================================================================================" }, { "cohort_id": "COHORT-03-SONG-MAMMALS-37TAXA-424LOCI", "title": "37-Taxon Amniote & Placental Mammal Radiation 424-Nuclear-Gene Benchmark (28,003,080 Quartets)", "taxonomic_scope": "Class Mammalia & Outgroups (Atlantogenata, Laurasiatheria, Scrotifera, Chiroptera, Euarchontoglires, Marsupialia, Monotremata)", "upstream_pipeline_provenance": "Empirical 424 Nuclear Coding Ortholog ML Gene Trees Across 37 Vertebrate Genomes (28,003,080 Quartets)", "taxa_count": 37, "internal_branches_count": 34, "gene_tree_count": 424, "total_quartets_evaluated": 28003080, "native_result": { "engine_name": "bio-suite Native Quartet MSC v1 (Exact Tripartition DP + Quartet NNI + LPP)", "engine_mode": "CoalescentMode::Native", "taxa_count": 37, "gene_tree_count": 424, "total_quartets_evaluated": 28003080, "satisfied_quartet_score": 25526915, "normalized_quartet_score": 0.9116, "mean_local_posterior_pp1": 0.9944, "mean_branch_length_cu": 2.0103, "wall_clock_ms": 333.5833, "species_tree_newick": "(Chicken,(Platypus,((Opossum,Wallaby)1.0000:5.6443,(((Sloth,Armadillos)1.0000:4.6441,(Lesser_Hedgehog_Tenrec,(Hyrax,Elephant)1.0000:1.5209)1.0000:3.1061)0.9978:0.1191,(((Shrew,Hedgehog)1.0000:1.0202,((Microbat,Megabat)1.0000:1.5674,((Horse,(Dog,Cat)1.0000:2.9701)0.9065:0.0655,(Alpaca,(Pig,(Dolphin,Cow)1.0000:1.3664)1.0000:0.6436)1.0000:3.7047)0.9973:0.1168)1.0000:0.4339)1.0000:1.9947,((Tree_Shrew,((Rabbit,Pika)1.0000:3.5648,(Squirrel,(Guinea_Pig,(Kangaroo_Rat,(Mouse,Rat)1.0000:5.8384)1.0000:0.6196)0.9999:0.1509)1.0000:1.6747)1.0000:0.8491)0.9096:0.0876,((Galagos,Mouse_Lemur)1.0000:2.4554,(Tarsier,(Marmoset,(Macaque,(Orangutan,(Gorilla,(Human,Chimpanzee)1.0000:0.6479)1.0000:2.3711)1.0000:2.6264)1.0000:2.7388)1.0000:4.6634)1.0000:0.6556)1.0000:2.1492)1.0000:2.3712)1.0000:1.5778)1.0000:3.4586)1.0000:0.9328):0.0000);", "focal_branches": [ { "branch_id": "BR-01", "clade_label": "Opossum + Wallaby", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9976, "q2_alt1_freq": 0.0024, "q3_alt2_freq": 0.0, "f1_quartet_weight": 423.0, "f2_quartet_weight": 1.0, "f3_quartet_weight": 0.0, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 99.7642, "local_posterior_pp1": 1.0, "branch_length_cu": 5.6443, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-02", "clade_label": "Sloth + Armadillos", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9936, "q2_alt1_freq": 0.0023, "q3_alt2_freq": 0.0041, "f1_quartet_weight": 421.2813, "f2_quartet_weight": 0.9688, "f3_quartet_weight": 1.75, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 98.5849, "local_posterior_pp1": 1.0, "branch_length_cu": 4.6441, "discordance_asymmetry_chisq": 0.2245, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-03", "clade_label": "Hyrax + Elephant", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.8543, "q2_alt1_freq": 0.0893, "q3_alt2_freq": 0.0563, "f1_quartet_weight": 362.2353, "f2_quartet_weight": 37.8824, "f3_quartet_weight": 23.8824, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 85.3774, "local_posterior_pp1": 1.0, "branch_length_cu": 1.5209, "discordance_asymmetry_chisq": 3.1733, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-04", "clade_label": "Lesser_Hedgehog_Tenrec + Hyrax + Elephant", "subset_size": 3, "total_taxa": 37, "q1_main_freq": 0.9702, "q2_alt1_freq": 0.0051, "q3_alt2_freq": 0.0248, "f1_quartet_weight": 411.3438, "f2_quartet_weight": 2.1563, "f3_quartet_weight": 10.5, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 93.8679, "local_posterior_pp1": 1.0, "branch_length_cu": 3.1061, "discordance_asymmetry_chisq": 5.5007, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-05", "clade_label": "Lesser_Hedgehog_Tenrec + Hyrax (+3 taxa)", "subset_size": 5, "total_taxa": 37, "q1_main_freq": 0.4082, "q2_alt1_freq": 0.3107, "q3_alt2_freq": 0.2811, "f1_quartet_weight": 173.0833, "f2_quartet_weight": 131.7351, "f3_quartet_weight": 119.1815, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 37.5, "local_posterior_pp1": 0.9978, "branch_length_cu": 0.1191, "discordance_asymmetry_chisq": 0.6281, "coalescent_regime": "Severe ILS / Rapid Radiation Zone (< 0.20 CU)" }, { "branch_id": "BR-06", "clade_label": "Shrew + Hedgehog", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.7597, "q2_alt1_freq": 0.1258, "q3_alt2_freq": 0.1146, "f1_quartet_weight": 322.094, "f2_quartet_weight": 53.3248, "f3_quartet_weight": 48.5812, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 69.1038, "local_posterior_pp1": 1.0, "branch_length_cu": 1.0202, "discordance_asymmetry_chisq": 0.2208, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-07", "clade_label": "Microbat + Megabat", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.8609, "q2_alt1_freq": 0.0814, "q3_alt2_freq": 0.0577, "f1_quartet_weight": 365.0408, "f2_quartet_weight": 34.4949, "f3_quartet_weight": 24.4643, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 78.7736, "local_posterior_pp1": 1.0, "branch_length_cu": 1.5674, "discordance_asymmetry_chisq": 1.7065, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-08", "clade_label": "Dog + Cat", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9658, "q2_alt1_freq": 0.0177, "q3_alt2_freq": 0.0165, "f1_quartet_weight": 409.5, "f2_quartet_weight": 7.5, "f3_quartet_weight": 7.0, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.0472, "local_posterior_pp1": 1.0, "branch_length_cu": 2.9701, "discordance_asymmetry_chisq": 0.0172, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-09", "clade_label": "Horse + Dog + Cat", "subset_size": 3, "total_taxa": 37, "q1_main_freq": 0.3756, "q2_alt1_freq": 0.3072, "q3_alt2_freq": 0.3172, "f1_quartet_weight": 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"f1_quartet_weight": 385.5432, "f2_quartet_weight": 18.0247, "f3_quartet_weight": 20.4321, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 90.93, "local_posterior_pp1": 1.0, "branch_length_cu": 1.9714, "discordance_asymmetry_chisq": 0.1507, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-16", "clade_label": "Internal Branch 16", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9811, "q2_alt1_freq": 0.0164, "q3_alt2_freq": 0.0025, "f1_quartet_weight": 416.0, "f2_quartet_weight": 6.9333, "f3_quartet_weight": 1.0667, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 98.1132, "local_posterior_pp1": 1.0, "branch_length_cu": 3.4494, "discordance_asymmetry_chisq": 4.3022, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-17", "clade_label": "Internal Branch 17", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9981, "q2_alt1_freq": 0.0019, "q3_alt2_freq": 0.0001, "f1_quartet_weight": 423.1765, "f2_quartet_weight": 0.7941, "f3_quartet_weight": 0.0294, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 99.8058, "local_posterior_pp1": 1.0, "branch_length_cu": 5.0459, "discordance_asymmetry_chisq": 0.0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-18", "clade_label": "Internal Branch 18", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.6412, "q2_alt1_freq": 0.211, "q3_alt2_freq": 0.1478, "f1_quartet_weight": 271.8788, "f2_quartet_weight": 89.4697, "f3_quartet_weight": 62.6515, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 64.1224, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6154, "discordance_asymmetry_chisq": 4.7279, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-19", "clade_label": "Internal Branch 19", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.4267, "q2_alt1_freq": 0.2792, "q3_alt2_freq": 0.2941, "f1_quartet_weight": 180.9271, "f2_quartet_weight": 118.3646, "f3_quartet_weight": 124.7083, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 42.6715, "local_posterior_pp1": 0.9999, "branch_length_cu": 0.1492, "discordance_asymmetry_chisq": 0.1656, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-20", "clade_label": "Internal Branch 20", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.8751, "q2_alt1_freq": 0.0781, "q3_alt2_freq": 0.0468, "f1_quartet_weight": 371.0375, "f2_quartet_weight": 33.1292, "f3_quartet_weight": 19.8333, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 87.5088, "local_posterior_pp1": 1.0, "branch_length_cu": 1.6583, "discordance_asymmetry_chisq": 3.3378, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-21", "clade_label": "Internal Branch 21", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.7148, "q2_alt1_freq": 0.1233, "q3_alt2_freq": 0.1619, "f1_quartet_weight": 303.0793, "f2_quartet_weight": 52.2724, "f3_quartet_weight": 68.6483, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 71.481, "local_posterior_pp1": 1.0, "branch_length_cu": 0.8433, "discordance_asymmetry_chisq": 2.2177, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-22", "clade_label": "Internal Branch 22", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.3893, "q2_alt1_freq": 0.2503, "q3_alt2_freq": 0.3604, "f1_quartet_weight": 165.0421, "f2_quartet_weight": 106.1476, "f3_quartet_weight": 152.8103, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 38.925, "local_posterior_pp1": 0.9084, "branch_length_cu": 0.0861, "discordance_asymmetry_chisq": 8.4083, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-23", "clade_label": "Internal Branch 23", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9428, "q2_alt1_freq": 0.0329, "q3_alt2_freq": 0.0243, "f1_quartet_weight": 399.7398, "f2_quartet_weight": 13.9439, "f3_quartet_weight": 10.3163, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 94.2783, "local_posterior_pp1": 1.0, "branch_length_cu": 2.4174, "discordance_asymmetry_chisq": 0.5424, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-24", "clade_label": "Internal Branch 24", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.6512, "q2_alt1_freq": 0.1647, "q3_alt2_freq": 0.1841, "f1_quartet_weight": 276.1176, "f2_quartet_weight": 69.8235, "f3_quartet_weight": 78.0588, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 65.1221, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6435, "discordance_asymmetry_chisq": 0.4586, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-25", "clade_label": "Internal Branch 25", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9378, "q2_alt1_freq": 0.0396, "q3_alt2_freq": 0.0227, "f1_quartet_weight": 397.6061, "f2_quartet_weight": 16.7879, "f3_quartet_weight": 9.6061, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 93.775, "local_posterior_pp1": 1.0, "branch_length_cu": 2.3363, "discordance_asymmetry_chisq": 1.9542, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-26", "clade_label": "Internal Branch 26", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9518, "q2_alt1_freq": 0.0227, "q3_alt2_freq": 0.0256, "f1_quartet_weight": 403.5521, "f2_quartet_weight": 9.6042, "f3_quartet_weight": 10.8438, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.1774, "local_posterior_pp1": 1.0, "branch_length_cu": 2.581, "discordance_asymmetry_chisq": 0.0751, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-27", "clade_label": "Internal Branch 27", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9569, "q2_alt1_freq": 0.0274, "q3_alt2_freq": 0.0157, "f1_quartet_weight": 405.7258, "f2_quartet_weight": 11.5968, "f3_quartet_weight": 6.6774, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 95.69, "local_posterior_pp1": 1.0, "branch_length_cu": 2.6879, "discordance_asymmetry_chisq": 1.3243, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-28", "clade_label": "Internal Branch 28", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9937, "q2_alt1_freq": 0.0023, "q3_alt2_freq": 0.004, "f1_quartet_weight": 421.3333, "f2_quartet_weight": 0.9667, "f3_quartet_weight": 1.7, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 99.3711, "local_posterior_pp1": 1.0, "branch_length_cu": 4.3473, "discordance_asymmetry_chisq": 0.2017, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-29", "clade_label": "Internal Branch 29", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.6539, "q2_alt1_freq": 0.1755, "q3_alt2_freq": 0.1706, "f1_quartet_weight": 277.2619, "f2_quartet_weight": 74.4107, "f3_quartet_weight": 72.3274, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 65.392, "local_posterior_pp1": 1.0, "branch_length_cu": 0.6512, "discordance_asymmetry_chisq": 0.0296, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-30", "clade_label": "Internal Branch 30", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9223, "q2_alt1_freq": 0.0349, "q3_alt2_freq": 0.0429, "f1_quartet_weight": 391.0478, "f2_quartet_weight": 14.7777, "f3_quartet_weight": 18.1746, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 92.2282, "local_posterior_pp1": 1.0, "branch_length_cu": 2.1217, "discordance_asymmetry_chisq": 0.3502, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-31", "clade_label": "Internal Branch 31", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.9378, "q2_alt1_freq": 0.0292, "q3_alt2_freq": 0.0331, "f1_quartet_weight": 397.608, "f2_quartet_weight": 12.3605, "f3_quartet_weight": 14.0314, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 93.7755, "local_posterior_pp1": 1.0, "branch_length_cu": 2.3364, "discordance_asymmetry_chisq": 0.1058, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-32", "clade_label": "Internal Branch 32", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.8624, "q2_alt1_freq": 0.0563, "q3_alt2_freq": 0.0813, "f1_quartet_weight": 365.6484, "f2_quartet_weight": 23.8864, "f3_quartet_weight": 34.4652, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 86.2378, "local_posterior_pp1": 1.0, "branch_length_cu": 1.5631, "discordance_asymmetry_chisq": 1.9179, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-33", "clade_label": "Internal Branch 33", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.979, "q2_alt1_freq": 0.0066, "q3_alt2_freq": 0.0144, "f1_quartet_weight": 415.1036, "f2_quartet_weight": 2.7929, "f3_quartet_weight": 6.1036, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 97.9018, "local_posterior_pp1": 1.0, "branch_length_cu": 3.3545, "discordance_asymmetry_chisq": 1.232, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-34", "clade_label": "Internal Branch 34", "subset_size": 2, "total_taxa": 37, "q1_main_freq": 0.7377, "q2_alt1_freq": 0.1395, "q3_alt2_freq": 0.1228, "f1_quartet_weight": 312.7879, "f2_quartet_weight": 59.1515, "f3_quartet_weight": 52.0606, "effective_loci_en": 424.0, "gene_concordance_gcf_pct": 73.7707, "local_posterior_pp1": 1.0, "branch_length_cu": 0.9262, "discordance_asymmetry_chisq": 0.4521, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" } ] }, "robinson_foulds_distance": 0, "max_robinson_foulds": 68, "topological_concordance_pct": 100.0, "quartet_score_ratio": 1.0, "normalized_quartet_delta": 0.0, "q1_pearson_r": 1.0, "branch_cu_pearson_r": 0.9974, "lpp_concordance_pct": 100.0, "native_speedup_factor": 3.4928, "abba_baba_tests": [], "ascii_cohort_comparison_table": "====================================================================================================================\nCOHORT: COHORT-03-SONG-MAMMALS-37TAXA-424LOCI — 37-Taxon Amniote & Placental Mammal Radiation 424-Nuclear-Gene Benchmark (28,003,080 Quartets)\nTaxa: 37 | Internal Splits: 34 | Input Gene Trees: 424 | Total Quartets Evaluated: 28003080\nUpstream Provenance: Empirical 424 Nuclear Coding Ortholog ML Gene Trees Across 37 Vertebrate Genomes (28,003,080 Quartets)\n--------------------------------------------------------------------------------------------------------------------\nMetric Native Quartet MSC (Rust) ASTRAL v5.7.8 (Java) Concordance\n--------------------------------------------------------------------------------------------------------------------\nSatisfied Quartet Score Q(T) 25526915 25526915 Ratio = 1.000000\nNormalized Quartet Score 0.911600 0.911600 Delta = +0.000000\nRobinson-Foulds Split Distance 0 0 100.00% Match (RF=0/68)\nMean Local Posterior Prob (LPP) 0.9944 0.9943 r(q1) = 1.0000\nMean Coalescent Branch Length (CU) 2.0103 1.9229 r(CU) = 0.9974\nWall-Clock Execution Time (ms) 333.58 1165.15 3.49x Speedup\n====================================================================================================================" }, { "cohort_id": "COHORT-04-ANOMALY-ZONE-14TAXA-200LOCI", "title": "14-Taxon Deep Coalescent Anomaly-Zone & 5x Short-Internode ILS Benchmark (200 Gene Trees)", "taxonomic_scope": "Controlled Multispecies Coalescent 5x ILS Short-Internode Anomaly Zone (14 Taxa, 200 Gene Trees)", "upstream_pipeline_provenance": "200 Multispecies Coalescent Gene Trees Under Extreme 5x Incomplete Lineage Sorting (200,200 Quartets)", "taxa_count": 14, "internal_branches_count": 11, "gene_tree_count": 200, "total_quartets_evaluated": 200200, "native_result": { "engine_name": "bio-suite Native Quartet MSC v1 (Exact Tripartition DP + Quartet NNI + LPP)", "engine_mode": "CoalescentMode::Native", "taxa_count": 14, "gene_tree_count": 200, "total_quartets_evaluated": 200200, "satisfied_quartet_score": 118477, "normalized_quartet_score": 0.5918, "mean_local_posterior_pp1": 0.9209, "mean_branch_length_cu": 0.3054, "wall_clock_ms": 15.4524, "species_tree_newick": "(Sloth,(Horse,((Rabbit,Tree_Shrew)1.0000:0.3228,(Rat,((Galago,Mouse_Lemur)0.7670:0.0705,(Tarsier,((Marmoset,Macaque)0.9778:0.1328,(Orangutan,(Gorilla,(Human,Chimpanzee)0.9999:0.2389)1.0000:0.4042)1.0000:0.9460)0.9996:0.2262)0.7335:0.1127)1.0000:0.2848)0.6518:0.0608)1.0000:0.5601):0.0000);", "focal_branches": [ { "branch_id": "BR-01", "clade_label": "Rabbit + Tree_Shrew", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.5173, "q2_alt1_freq": 0.1888, "q3_alt2_freq": 0.294, "f1_quartet_weight": 103.45, "f2_quartet_weight": 37.75, "f3_quartet_weight": 58.8, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 16.5, "local_posterior_pp1": 1.0, "branch_length_cu": 0.3228, "discordance_asymmetry_chisq": 4.5894, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-02", "clade_label": "Galago + Mouse_Lemur", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.3787, "q2_alt1_freq": 0.2899, "q3_alt2_freq": 0.3314, "f1_quartet_weight": 75.7429, "f2_quartet_weight": 57.9714, "f3_quartet_weight": 66.2857, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 29.0, "local_posterior_pp1": 0.767, "branch_length_cu": 0.0705, "discordance_asymmetry_chisq": 0.5563, "coalescent_regime": "Severe ILS / Rapid Radiation Zone (< 0.20 CU)" }, { "branch_id": "BR-03", "clade_label": "Marmoset + Macaque", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.4163, "q2_alt1_freq": 0.303, "q3_alt2_freq": 0.2808, "f1_quartet_weight": 83.25, "f2_quartet_weight": 60.5938, "f3_quartet_weight": 56.1563, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 19.5, "local_posterior_pp1": 0.9778, "branch_length_cu": 0.1328, "discordance_asymmetry_chisq": 0.1687, "coalescent_regime": "Severe ILS / Rapid Radiation Zone (< 0.20 CU)" }, { "branch_id": "BR-04", "clade_label": "Human + Chimpanzee", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.475, "q2_alt1_freq": 0.2473, "q3_alt2_freq": 0.2777, "f1_quartet_weight": 95.0, "f2_quartet_weight": 49.4545, "f3_quartet_weight": 55.5455, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 46.5, "local_posterior_pp1": 0.9999, "branch_length_cu": 0.2389, "discordance_asymmetry_chisq": 0.3533, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-05", "clade_label": "Gorilla + Human + Chimpanzee", "subset_size": 3, "total_taxa": 14, "q1_main_freq": 0.555, "q2_alt1_freq": 0.329, "q3_alt2_freq": 0.116, "f1_quartet_weight": 111.0, "f2_quartet_weight": 65.8, "f3_quartet_weight": 23.2, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 50.0, "local_posterior_pp1": 1.0, "branch_length_cu": 0.4042, "discordance_asymmetry_chisq": 20.3906, "coalescent_regime": "Asymmetric Discordance (Candidate Introgression)" }, { "branch_id": "BR-06", "clade_label": "Orangutan + Gorilla + Human + Chimpanzee", "subset_size": 4, "total_taxa": 14, "q1_main_freq": 0.7411, "q2_alt1_freq": 0.1596, "q3_alt2_freq": 0.0993, "f1_quartet_weight": 148.2292, "f2_quartet_weight": 31.9167, "f3_quartet_weight": 19.8542, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 46.5, "local_posterior_pp1": 1.0, "branch_length_cu": 0.946, "discordance_asymmetry_chisq": 2.8105, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-07", "clade_label": "Marmoset + Orangutan (+4 taxa)", "subset_size": 6, "total_taxa": 14, "q1_main_freq": 0.4683, "q2_alt1_freq": 0.177, "q3_alt2_freq": 0.3547, "f1_quartet_weight": 93.6607, "f2_quartet_weight": 35.3929, "f3_quartet_weight": 70.9464, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 16.5, "local_posterior_pp1": 0.9996, "branch_length_cu": 0.2262, "discordance_asymmetry_chisq": 11.887, "coalescent_regime": "Asymmetric Discordance (Candidate Introgression)" }, { "branch_id": "BR-08", "clade_label": "Marmoset + Orangutan (+5 taxa)", "subset_size": 7, "total_taxa": 14, "q1_main_freq": 0.4044, "q2_alt1_freq": 0.2096, "q3_alt2_freq": 0.386, "f1_quartet_weight": 80.8833, "f2_quartet_weight": 41.9167, "f3_quartet_weight": 77.2, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 10.0, "local_posterior_pp1": 0.7335, "branch_length_cu": 0.1127, "discordance_asymmetry_chisq": 10.4512, "coalescent_regime": "Asymmetric Discordance (Candidate Introgression)" }, { "branch_id": "BR-09", "clade_label": "Marmoset + Galago (+7 taxa)", "subset_size": 9, "total_taxa": 14, "q1_main_freq": 0.4986, "q2_alt1_freq": 0.2987, "q3_alt2_freq": 0.2028, "f1_quartet_weight": 99.7143, "f2_quartet_weight": 59.7321, "f3_quartet_weight": 40.5536, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 5.0, "local_posterior_pp1": 1.0, "branch_length_cu": 0.2848, "discordance_asymmetry_chisq": 3.6677, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-10", "clade_label": "Marmoset + Galago (+8 taxa)", "subset_size": 10, "total_taxa": 14, "q1_main_freq": 0.3726, "q2_alt1_freq": 0.3486, "q3_alt2_freq": 0.2788, "f1_quartet_weight": 74.5278, "f2_quartet_weight": 69.7222, "f3_quartet_weight": 55.75, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 16.5, "local_posterior_pp1": 0.6518, "branch_length_cu": 0.0608, "discordance_asymmetry_chisq": 1.5559, "coalescent_regime": "Severe ILS / Rapid Radiation Zone (< 0.20 CU)" }, { "branch_id": "BR-11", "clade_label": "Marmoset + Galago (+10 taxa)", "subset_size": 12, "total_taxa": 14, "q1_main_freq": 0.6193, "q2_alt1_freq": 0.1123, "q3_alt2_freq": 0.2685, "f1_quartet_weight": 123.85, "f2_quartet_weight": 22.45, "f3_quartet_weight": 53.7, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 38.0, "local_posterior_pp1": 1.0, "branch_length_cu": 0.5601, "discordance_asymmetry_chisq": 12.8242, "coalescent_regime": "Asymmetric Discordance (Candidate Introgression)" } ] }, "astral_result": { "engine_name": "ASTRAL v5.7.8 (Mirarab et al. — Exact Quartet DP + Polytree Weighting)", "engine_mode": "CoalescentMode::Astral", "taxa_count": 14, "gene_tree_count": 200, "total_quartets_evaluated": 200200, "satisfied_quartet_score": 118477, "normalized_quartet_score": 0.5918, "mean_local_posterior_pp1": 0.9202, "mean_branch_length_cu": 0.3, "wall_clock_ms": 465.4921, "species_tree_newick": "(Sloth,(Horse,((Rabbit,Tree_Shrew)'[q1=0.5172499999999999;q2=0.2940000000000003;q3=0.1887500000000001;f1=103.44999999999997;f2=58.80000000000006;f3=37.75000000000002;pp1=0.9999998042641985;pp2=1.4348597793089057E-7;pp3=5.22498233785466E-8;QC=20;EN=200.0]':0.31747473288179084,(Rat,((Galago,Mouse_Lemur)'[q1=0.37871428571428595;q2=0.33142857142857146;q3=0.2898571428571427;f1=75.74285714285719;f2=66.28571428571429;f3=57.97142857142854;pp1=0.764210714982115;pp2=0.16057223620359998;pp3=0.07521704881428493;QC=35;EN=200.0]':0.06747103281247409,(Tarsier,((Marmoset,Macaque)'[q1=0.41625;q2=0.28078125;q3=0.30296875;f1=83.25;f2=56.15625;f3=60.59375;pp1=0.9770305045636168;pp2=0.009644074993352165;pp3=0.013325420443029952;QC=32;EN=200.0]':0.1292760670543843,((Gorilla,(Human,Chimpanzee)'[q1=0.47500000000000014;q2=0.27772727272727277;q3=0.24727272727272723;f1=95.00000000000003;f2=55.545454545454554;f3=49.454545454545446;pp1=0.9999394579443107;pp2=3.526742598528362E-5;pp3=2.5274629704043648E-5;QC=11;EN=200.0]':0.23440070583884456)'[q1=0.555;q2=0.11600000000000002;q3=0.32900000000000007;f1=111.0;f2=23.200000000000003;f3=65.80000000000001;pp1=0.9999999994457438;pp2=6.390838813839593E-11;pp3=4.903478418912494E-10;QC=20;EN=200.0]':0.3980301296206464,Orangutan)'[q1=0.7411458333333334;q2=0.1595833333333333;q3=0.09927083333333332;f1=148.22916666666669;f2=31.916666666666657;f3=19.854166666666664;pp1=1.0;pp2=5.459301568252935E-32;pp3=4.1298708819546285E-32;QC=48;EN=200.0]':0.9318811608571277)'[q1=0.46830357142857154;q2=0.35473214285714283;q3=0.17696428571428569;f1=93.6607142857143;f2=70.94642857142857;f3=35.39285714285714;pp1=0.9996021251682204;pp2=3.654466751705035E-4;pp3=3.2428156609103746E-5;QC=56;EN=200.0]':0.2218450876468987)'[q1=0.40441666666666626;q2=0.38599999999999995;q3=0.2095833333333334;f1=80.88333333333325;f2=77.19999999999999;f3=41.91666666666668;pp1=0.7318328458665919;pp2=0.2600920373671225;pp3=0.008075116766285572;QC=60;EN=200.0]':0.1093763072485703)'[q1=0.4985714285714286;q2=0.20276785714285717;q3=0.2986607142857142;f1=99.71428571428572;f2=40.55357142857143;f3=59.73214285714285;pp1=0.9999968321043236;pp2=8.594745491462529E-7;pp3=2.308421127465349E-6;QC=56;EN=200.0]':0.2798944224740972)'[q1=0.3726388888888892;q2=0.27874999999999966;q3=0.348611111111111;f1=74.52777777777784;f2=55.74999999999993;f3=69.7222222222222;pp1=0.6494412459059083;pp2=0.07161969905689493;pp3=0.2789390550371762;QC=36;EN=200.0]':0.05781710307223991)'[q1=0.6192500000000004;q2=0.2684999999999998;q3=0.11225000000000004;f1=123.85000000000008;f2=53.69999999999996;f3=22.45000000000001;pp1=0.9999999999999997;pp2=2.7603441291231316E-16;pp3=9.3850432497539E-17;QC=20;EN=200.0]':0.5520882211417425):0.0);", "focal_branches": [ { "branch_id": "ASTRAL-BR-01", "clade_label": "Internal Branch 1", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.5172, "q2_alt1_freq": 0.294, "q3_alt2_freq": 0.1888, "f1_quartet_weight": 103.45, "f2_quartet_weight": 58.8, "f3_quartet_weight": 37.75, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 51.725, "local_posterior_pp1": 1.0, "branch_length_cu": 0.3175, "discordance_asymmetry_chisq": 4.5894, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-02", "clade_label": "Internal Branch 2", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.3787, "q2_alt1_freq": 0.3314, "q3_alt2_freq": 0.2899, "f1_quartet_weight": 75.7429, "f2_quartet_weight": 66.2857, "f3_quartet_weight": 57.9714, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 37.8714, "local_posterior_pp1": 0.7642, "branch_length_cu": 0.0675, "discordance_asymmetry_chisq": 0.5563, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-03", "clade_label": "Internal Branch 3", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.4163, "q2_alt1_freq": 0.2808, "q3_alt2_freq": 0.303, "f1_quartet_weight": 83.25, "f2_quartet_weight": 56.1563, "f3_quartet_weight": 60.5938, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 41.625, "local_posterior_pp1": 0.977, "branch_length_cu": 0.1293, "discordance_asymmetry_chisq": 0.1687, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-04", "clade_label": "Internal Branch 4", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.475, "q2_alt1_freq": 0.2777, "q3_alt2_freq": 0.2473, "f1_quartet_weight": 95.0, "f2_quartet_weight": 55.5455, "f3_quartet_weight": 49.4545, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 47.5, "local_posterior_pp1": 0.9999, "branch_length_cu": 0.2344, "discordance_asymmetry_chisq": 0.3533, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-05", "clade_label": "Internal Branch 5", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.555, "q2_alt1_freq": 0.116, "q3_alt2_freq": 0.329, "f1_quartet_weight": 111.0, "f2_quartet_weight": 23.2, "f3_quartet_weight": 65.8, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 55.5, "local_posterior_pp1": 1.0, "branch_length_cu": 0.398, "discordance_asymmetry_chisq": 20.3906, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-06", "clade_label": "Internal Branch 6", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.7411, "q2_alt1_freq": 0.1596, "q3_alt2_freq": 0.0993, "f1_quartet_weight": 148.2292, "f2_quartet_weight": 31.9167, "f3_quartet_weight": 19.8542, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 74.1146, "local_posterior_pp1": 1.0, "branch_length_cu": 0.9319, "discordance_asymmetry_chisq": 2.8105, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-07", "clade_label": "Internal Branch 7", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.4683, "q2_alt1_freq": 0.3547, "q3_alt2_freq": 0.177, "f1_quartet_weight": 93.6607, "f2_quartet_weight": 70.9464, "f3_quartet_weight": 35.3929, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 46.8304, "local_posterior_pp1": 0.9996, "branch_length_cu": 0.2218, "discordance_asymmetry_chisq": 11.887, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-08", "clade_label": "Internal Branch 8", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.4044, "q2_alt1_freq": 0.386, "q3_alt2_freq": 0.2096, "f1_quartet_weight": 80.8833, "f2_quartet_weight": 77.2, "f3_quartet_weight": 41.9167, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 40.4417, "local_posterior_pp1": 0.7318, "branch_length_cu": 0.1094, "discordance_asymmetry_chisq": 10.4512, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-09", "clade_label": "Internal Branch 9", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.4986, "q2_alt1_freq": 0.2028, "q3_alt2_freq": 0.2987, "f1_quartet_weight": 99.7143, "f2_quartet_weight": 40.5536, "f3_quartet_weight": 59.7321, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 49.8571, "local_posterior_pp1": 1.0, "branch_length_cu": 0.2799, "discordance_asymmetry_chisq": 3.6677, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-10", "clade_label": "Internal Branch 10", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.3726, "q2_alt1_freq": 0.2787, "q3_alt2_freq": 0.3486, "f1_quartet_weight": 74.5278, "f2_quartet_weight": 55.75, "f3_quartet_weight": 69.7222, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 37.2639, "local_posterior_pp1": 0.6494, "branch_length_cu": 0.0578, "discordance_asymmetry_chisq": 1.5559, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-11", "clade_label": "Internal Branch 11", "subset_size": 2, "total_taxa": 14, "q1_main_freq": 0.6193, "q2_alt1_freq": 0.2685, "q3_alt2_freq": 0.1123, "f1_quartet_weight": 123.85, "f2_quartet_weight": 53.7, "f3_quartet_weight": 22.45, "effective_loci_en": 200.0, "gene_concordance_gcf_pct": 61.925, "local_posterior_pp1": 1.0, "branch_length_cu": 0.5521, "discordance_asymmetry_chisq": 12.8242, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" } ] }, "robinson_foulds_distance": 0, "max_robinson_foulds": 22, "topological_concordance_pct": 100.0, "quartet_score_ratio": 1.0, "normalized_quartet_delta": 0.0, "q1_pearson_r": 1.0, "branch_cu_pearson_r": 1.0, "lpp_concordance_pct": 100.0, "native_speedup_factor": 30.1243, "abba_baba_tests": [], "ascii_cohort_comparison_table": "====================================================================================================================\nCOHORT: COHORT-04-ANOMALY-ZONE-14TAXA-200LOCI — 14-Taxon Deep Coalescent Anomaly-Zone & 5x Short-Internode ILS Benchmark (200 Gene Trees)\nTaxa: 14 | Internal Splits: 11 | Input Gene Trees: 200 | Total Quartets Evaluated: 200200\nUpstream Provenance: 200 Multispecies Coalescent Gene Trees Under Extreme 5x Incomplete Lineage Sorting (200,200 Quartets)\n--------------------------------------------------------------------------------------------------------------------\nMetric Native Quartet MSC (Rust) ASTRAL v5.7.8 (Java) Concordance\n--------------------------------------------------------------------------------------------------------------------\nSatisfied Quartet Score Q(T) 118477 118477 Ratio = 1.000000\nNormalized Quartet Score 0.591800 0.591800 Delta = +0.000000\nRobinson-Foulds Split Distance 0 0 100.00% Match (RF=0/22)\nMean Local Posterior Prob (LPP) 0.9209 0.9202 r(q1) = 1.0000\nMean Coalescent Branch Length (CU) 0.3054 0.3000 r(CU) = 1.0000\nWall-Clock Execution Time (ms) 15.45 465.49 30.12x Speedup\n====================================================================================================================" } ], "ascii_master_summary_table": "==========================================================================================================================================\nTOOL PAIR 4 CALIBRATION SUMMARY: Native Quartet Multispecies Coalescent (Rust) vs. ASTRAL v5.7.8 (Java)\n==========================================================================================================================================\nCohort ID Taxa Loci Total Quartets Native Q-Score ASTRAL Q-Score Split Match r(q1) r(CU) Speedup\n------------------------------------------------------------------------------------------------------------------------------------------\nCOHORT-01-CARNIVORA-16TAXA-NATIVE-CHAIN 16 16 29120 27482 27482 100.00% 1.0000 0.9525 37.73x\nCOHORT-02-SONG-PRIMATES-14TAXA-424LOCI 14 424 424424 389734 389734 100.00% 1.0000 0.9993 23.82x\nCOHORT-03-SONG-MAMMALS-37TAXA-424LOCI 37 424 28003080 25526915 25526915 100.00% 1.0000 0.9974 3.49x\nCOHORT-04-ANOMALY-ZONE-14TAXA-200LOCI 14 200 200200 118477 118477 100.00% 1.0000 1.0000 30.12x\n------------------------------------------------------------------------------------------------------------------------------------------\nOVERALL / CUMULATIVE (4 Cohorts) 1064 28656824 100.00% 1.0000 0.9873 23.79x\n==========================================================================================================================================", "ascii_mammalian_species_cladogram": "Amniota Root (Gallus gallus Outgroup | 424 Nuclear Loci | 28,003,080 Quartets | Q_norm = 0.9116)\n ├───Gallus_gallus (Red Junglefowl — Sauropsida Outgroup)\n └───Class Mammalia (q1 = 0.9976, LPP = 1.00, tau = 4.9535 CU)\n ├───Prototheria: Ornithorhynchus_anatinus (Platypus)\n └───Theria (q1 = 0.9976, LPP = 1.00, tau = 4.9535 CU)\n ├───Metatheria / Marsupialia (q1 = 0.9976, LPP = 1.00, tau = 4.9535 CU)\n │ ├───Monodelphis_domestica (Opossum)\n │ └───Macropus_eugenii (Wallaby)\n └───Eutheria / Placentalia\n ├───Atlantogenata [ILS Zone #1: q1 = 0.4082, q2 = 0.2811, q3 = 0.3107 | LPP = 0.9977 | tau = 0.1175 CU]\n │ ├───Xenarthra (q1 = 0.9936, LPP = 1.00, tau = 4.3332 CU): Choloepus (Sloth) + Dasypus (Armadillo)\n │ └───Afrotheria (q1 = 0.9702, LPP = 1.00, tau = 3.0324 CU): Echinops (Tenrec) + [Procavia (Hyrax) + Loxodonta (Elephant) | q1 = 0.8543, tau = 1.5072 CU]\n └───Boreoeutheria (q1 = 0.9093, LPP = 1.00, tau = 1.9714 CU)\n ├───Laurasiatheria (q1 = 0.5680, q2 = 0.2312, q3 = 0.2007 | LPP = 1.00 | tau = 0.4308 CU)\n │ ├───Eulipotyphla (q1 = 0.7597, LPP = 1.00, tau = 1.0128 CU): Sorex (Shrew) + Erinaceus (Hedgehog)\n │ └───Scrotifera [ILS Zone #2: q1 = 0.4068, q2 = 0.3131, q3 = 0.2800 | LPP = 0.9972 | tau = 0.1152 CU]\n │ ├───Chiroptera (q1 = 0.8609, LPP = 1.00, tau = 1.5530 CU): Myotis (Microbat) + Pteropus (Megabat)\n │ └───Fereuungulata [ILS Zone #3: q1 = 0.3756, q2 = 0.3172, q3 = 0.3072 | LPP = 0.9044 | tau = 0.0641 CU]\n │ ├───Zooamata (Perissodactyla + Ferae): Equus (Horse) + [Canis (Dog) + Felis (Cat) | q1 = 0.9658, tau = 2.9058 CU]\n │ └───Cetartiodactyla (q1 = 0.9836, LPP = 1.00, tau = 3.5728 CU): Vicugna (Alpaca) + [Sus (Pig) + (Tursiops + Bos | q1 = 0.8300, tau = 1.3550 CU) | q1 = 0.6497, tau = 0.6392 CU]\n └───Euarchontoglires (q1 = 0.6553, q2 = 0.1744, q3 = 0.1703 | LPP = 1.00 | tau = 0.6553 CU)\n ├───Gliriformes + Scandentia [ILS Zone #4: q1 = 0.3888, q2 = 0.3555, q3 = 0.2556 | LPP = 0.9247 | tau = 0.0854 CU]\n │ ├───Scandentia: Tupaia_belangeri (Tree Shrew)\n │ └───Glires (q1 = 0.7028, LPP = 1.00, tau = 0.8024 CU)\n │ ├───Lagomorpha (q1 = 0.9811, tau = 3.4494 CU): Oryctolagus (Rabbit) + Ochotona (Pika)\n │ └───Rodentia (q1 = 0.9560, tau = 2.6680 CU): Spermophilus (Squirrel) + [Cavia (Guinea Pig) + (Dipodomys + (Mus + Rattus | q1 = 0.9981))]\n └───Order Primates (q1 = 0.9106, LPP = 1.00, tau = 1.9852 CU)\n ├───Strepsirrhini (q1 = 0.9418, tau = 2.4018 CU): Otolemur (Galago) + Microcebus (Mouse Lemur)\n └───Haplorhini (q1 = 0.6553, tau = 0.6553 CU)\n ├───Tarsiiformes: Tarsius_syrichta (Tarsier)\n └───Simiiformes / Anthropoidea (q1 = 0.9929, tau = 4.2603 CU)\n ├───Platyrrhini: Callithrix_jacchus (Marmoset)\n └───Catarrhini (q1 = 0.9575, tau = 2.7005 CU)\n ├───Cercopithecidae: Macaca_mulatta (Rhesus Macaque)\n └───Hominidae / Great Apes (q1 = 0.9522, tau = 2.5898 CU)\n ├───Ponginae: Pongo_abelii (Orangutan)\n └───Homininae [ILS Zone #5: q1 = 0.9370, tau = 2.3252 CU]\n ├───Gorilla_gorilla (Gorilla)\n └───Hominini [35% ILS: q1 = 0.6503, q2 = 0.1653, q3 = 0.1844 | LPP = 1.00 | tau = 0.6408 CU]\n ├───Homo_sapiens (Human)\n └───Pan_troglodytes (Chimpanzee)" }