{ "release_id": "RELEASE-2026-RHINOLOPHIDAE-ASIA-RADIATION-ASTRAL-SKYLINE", "slug": "rhinolophidae-asia-radiation-astral-skyline", "preprint_slug": "rhinolophidae-asia-radiation-preprint", "title": "Asian Horseshoe Bat (Rhinolophidae) Radiation, Acoustic & Sarbecovirus Co-Evolution, and Quartet Coalescent Species-Tree Inference Across 212 NCBI Records", "validation_set_id": "VAL-SET-060-RHINOLOPHIDAE-ASIA-RADIATION-212RECS", "beaker_signal_rating": "5🧪", "published_at": "2026-11-08", "dataset_summary": { "total_records_on_disk": 212, "total_raw_bp_on_disk": 1292186, "core_mitogenome_species": 64, "functional_nuclear_cds_records": 40, "conspecific_popset_isolates": 108, "supermatrix_aligned_columns_bp": 48513, "mitogenome_aligned_columns_bp": 33996, "nuclear_aligned_columns_bp": 14517, "parsimony_informative_sites_ry3": 11505, "distinct_alignment_patterns_ry3": 12109 }, "solved_newick_topology": 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"molecular_clock_lsd2": { "substitution_rate_per_site_per_ma": 0.00315381, "rate_ci95_lower": 0.00283022, "rate_ci95_upper": 0.00362527, "root_tmrca_ma": 62.8, "calibrated_nodes": [ { "node": "Node I", "clade": "Chiroptera Crown (Yangochiroptera / Yinpterochiroptera Split)", "age_ma": 62.8, "hpd95_ma": [ 58.6, 66.4 ], "quartet_q1": 0.9412, "lpp": 1 }, { "node": "Node II", "clade": "Yinpterochiroptera Crown (Pteropodidae / Rhinolophoidea Split)", "age_ma": 58.2, "hpd95_ma": [ 53.4, 62.1 ], "quartet_q1": 0.9108, "lpp": 1 }, { "node": "Node III", "clade": "Rhinolophidae + Hipposideridae Sister Split", "age_ma": 41.6, "hpd95_ma": [ 37.5, 45.8 ], "quartet_q1": 0.9612, "lpp": 1 }, { "node": "Node IV", "clade": "Crown Family Rhinolophidae Radiation (34 Asian Species)", "age_ma": 33.4, "hpd95_ma": [ 29.6, 37.2 ], "quartet_q1": 0.9824, "lpp": 1 }, { "node": "Node V", "clade": "Core Asian Karst Rhinolophus Clade (Sectors E + F + G)", "age_ma": 21.8, "hpd95_ma": [ 18.9, 24.9 ], "quartet_q1": 0.8915, "lpp": 1 }, { "node": "Node VI", "clade": "High-CF pusillus Group + Sarbecovirus Reservoir Clade Split", "age_ma": 17.4, "hpd95_ma": [ 14.8, 20.1 ], "quartet_q1": 0.924, "lpp": 1 }, { "node": "Node VII", "clade": "Asian Sarbecovirus Reservoir Crown (R. sinicus / R. affinis / R. ferrumequinum)", "age_ma": 9.8, "hpd95_ma": [ 7.9, 11.9 ], "quartet_q1": 0.9518, "lpp": 1 } ] }, "paml_codeml_selection": { "SLC26A5_Prestin": { "label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & High-Duty-Cycle CF-FM Echolocation", "nSeqs": 6, "codons": 180, "bp": 540, "accessions": [ "KJ645609.1", "EU914924.1", "GU219835.1", "GU219834.1", "EU914937.1", "EU914936.1" ], "lnL": -1231.379164, "kappa": 3.20185, "omega": 0.15061, "treeLenDN": 0.0852, "treeLenDS": 0.566, "cpuSec": 0.613 }, "ACE2_Sarbeco": { "label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Interface", "nSeqs": 6, "codons": 180, "bp": 540, "accessions": [ "LC921174.1", "LC921170.1", "XM_019667409.1", "PZ112778.1", "XM_081081848.1", "PX315811.1" ], "lnL": -2412.528558, "kappa": 1.82837, "omega": 0.84313, "treeLenDN": 19.2813, "treeLenDS": 22.8686, "cpuSec": 2.718 }, "STING_IRF3_ISG15": { "label": "STING1 (TMEM173) / IRF3 / NLRP3 Dampened Antiviral & Inflammasome Tolerance Complex", "nSeqs": 6, "codons": 160, "bp": 480, "accessions": [ "XM_019741528.3", "XM_019667829.1", "XM_081035220.1", "XM_081106923.1", "XM_039836264.1", "XM_074313609.2" ], "lnL": -3906.93246, "kappa": 9.35619, "omega": 1.05632, "treeLenDN": 53.6475, "treeLenDS": 50.787, "cpuSec": 1.98 }, "FOXP2_KCNQ4": { "label": "FOXP2 Vocal-Laryngeal Sensorimotor Transcription Factor & KCNQ4 Cochlear Channel", "nSeqs": 6, "codons": 180, "bp": 540, "accessions": [ "XM_088793262.1", "XM_087820841.1", "XM_081147833.1", "XM_036232571.1", "XM_023752818.1", "KJ645625.1" ], "lnL": -3734.426538, "kappa": 1.56008, "omega": 0.05912, "treeLenDN": 12.3976, "treeLenDS": 209.6951, "cpuSec": 2.052 }, "EPAS1_UCP1_Karst": { "label": "EPAS1 / HIF1A Subterranean Karst Hypoxia & UCP1 Cave Torpor Thermogenesis", "nSeqs": 4, "codons": 160, "bp": 480, "accessions": [ "XM_090281243.1", "XM_019730721.3", "XM_016213682.2", "XM_084897918.1" ], "lnL": -2600.274656, "kappa": 0.1478, "omega": 0.12833, "treeLenDN": 11.7432, "treeLenDS": 91.5043, "cpuSec": 0.842 } }, "astral_vs_native_ry3_coalescent": { "cohort_id": "COHORT-RHINOLOPHIDAE-64TAXA-18LOCI-RY3-MSC-VS-ASTRAL", "title": "64-Species Asian Horseshoe Bat & Rhinolophoidea 18-Locus RY3-Cleaned Quartet Multispecies Coalescent (Native Rust vs. *ASTRAL v5.7.8)", "taxonomic_scope": "Chiroptera: Yinpterochiroptera (Rhinolophidae 34 spp., Hipposideridae 14 spp., Megadermatidae/Rhinopomatidae/Pteropodidae 8 spp.) + Yangochiroptera Outgroups (8 spp.)", "upstream_pipeline_provenance": "super-blast-adaptive -> *MAFFT v7.526 / gotoh-msa (L=48,513 bp across 18 loci: 13 mtDNA PCG/rRNA + 5 nuclear CDS) -> popgen-blind-dualpass (RY3) -> 18 *IQ-TREE v2.4.0 Gene Trees -> runie-quartet-coalescent vs. 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"discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-48", "clade_label": "Internal Branch 48", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.6483, "q2_alt1_freq": 0.0991, "q3_alt2_freq": 0.2526, "f1_quartet_weight": 11.67, "f2_quartet_weight": 1.7829, "f3_quartet_weight": 4.547, "effective_loci_en": 18, "gene_concordance_gcf_pct": 64.8335, "local_posterior_pp1": 0.9879, "branch_length_cu": 0.547, "discordance_asymmetry_chisq": 1.207, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-49", "clade_label": "Internal Branch 49", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.7925, "q2_alt1_freq": 0.0895, "q3_alt2_freq": 0.1179, "f1_quartet_weight": 14.2658, "f2_quartet_weight": 1.6117, "f3_quartet_weight": 2.1225, "effective_loci_en": 18, "gene_concordance_gcf_pct": 79.2546, "local_posterior_pp1": 0.9999, "branch_length_cu": 0.9842, "discordance_asymmetry_chisq": 0.0699, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-50", "clade_label": "Internal Branch 50", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.5974, "q2_alt1_freq": 0.2414, "q3_alt2_freq": 0.1612, "f1_quartet_weight": 10.7532, "f2_quartet_weight": 4.345, "f3_quartet_weight": 2.9018, "effective_loci_en": 18, "gene_concordance_gcf_pct": 59.7398, "local_posterior_pp1": 0.9637, "branch_length_cu": 0.4291, "discordance_asymmetry_chisq": 0.2874, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-51", "clade_label": "Internal Branch 51", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.9606, "q2_alt1_freq": 0.0086, "q3_alt2_freq": 0.0308, "f1_quartet_weight": 17.2914, "f2_quartet_weight": 0.1547, "f3_quartet_weight": 0.5539, "effective_loci_en": 18, "gene_concordance_gcf_pct": 96.0633, "local_posterior_pp1": 1, "branch_length_cu": 2.0033, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-52", "clade_label": "Internal Branch 52", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4618, "q2_alt1_freq": 0.4753, "q3_alt2_freq": 0.063, "f1_quartet_weight": 8.3117, "f2_quartet_weight": 8.5549, "f3_quartet_weight": 1.1333, "effective_loci_en": 18, "gene_concordance_gcf_pct": 46.1762, "local_posterior_pp1": 0.4415, "branch_length_cu": 0.1698, "discordance_asymmetry_chisq": 5.6853, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-53", "clade_label": "Internal Branch 53", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.5803, "q2_alt1_freq": 0.3483, "q3_alt2_freq": 0.0714, "f1_quartet_weight": 10.4457, "f2_quartet_weight": 6.2686, "f3_quartet_weight": 1.2857, "effective_loci_en": 18, "gene_concordance_gcf_pct": 58.0314, "local_posterior_pp1": 0.9303, "branch_length_cu": 0.3925, "discordance_asymmetry_chisq": 3.2868, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-54", "clade_label": "Internal Branch 54", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.3682, "q2_alt1_freq": 0.3448, "q3_alt2_freq": 0.287, "f1_quartet_weight": 6.6277, "f2_quartet_weight": 6.2061, "f3_quartet_weight": 5.1662, "effective_loci_en": 18, "gene_concordance_gcf_pct": 36.8204, "local_posterior_pp1": 0.416, "branch_length_cu": 0.0235, "discordance_asymmetry_chisq": 0.0951, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-55", "clade_label": "Internal Branch 55", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.7074, "q2_alt1_freq": 0.1724, "q3_alt2_freq": 0.1202, "f1_quartet_weight": 12.7325, "f2_quartet_weight": 3.1033, "f3_quartet_weight": 2.1642, "effective_loci_en": 18, "gene_concordance_gcf_pct": 70.7362, "local_posterior_pp1": 0.9977, "branch_length_cu": 0.7036, "discordance_asymmetry_chisq": 0.1674, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-56", "clade_label": "Internal Branch 56", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.9359, "q2_alt1_freq": 0.062, "q3_alt2_freq": 0.0021, "f1_quartet_weight": 16.8454, "f2_quartet_weight": 1.1161, "f3_quartet_weight": 0.0385, "effective_loci_en": 18, "gene_concordance_gcf_pct": 93.5856, "local_posterior_pp1": 1, "branch_length_cu": 1.7714, "discordance_asymmetry_chisq": 1.0059, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-57", "clade_label": "Internal Branch 57", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 1, "q2_alt1_freq": 0, "q3_alt2_freq": 0, "f1_quartet_weight": 18, "f2_quartet_weight": 0, "f3_quartet_weight": 0, "effective_loci_en": 18, "gene_concordance_gcf_pct": 100, "local_posterior_pp1": 1, "branch_length_cu": 2.539, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-58", "clade_label": "Internal Branch 58", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4861, "q2_alt1_freq": 0.3472, "q3_alt2_freq": 0.1667, "f1_quartet_weight": 8.75, "f2_quartet_weight": 6.25, "f3_quartet_weight": 3, "effective_loci_en": 18, "gene_concordance_gcf_pct": 48.6111, "local_posterior_pp1": 0.7425, "branch_length_cu": 0.2117, "discordance_asymmetry_chisq": 1.1419, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-59", "clade_label": "Internal Branch 59", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4496, "q2_alt1_freq": 0.3489, "q3_alt2_freq": 0.2015, "f1_quartet_weight": 7.6431, "f2_quartet_weight": 5.9314, "f3_quartet_weight": 3.4255, "effective_loci_en": 17, "gene_concordance_gcf_pct": 44.9593, "local_posterior_pp1": 0.6293, "branch_length_cu": 0.1473, "discordance_asymmetry_chisq": 0.6711, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-60", "clade_label": "Internal Branch 60", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4646, "q2_alt1_freq": 0.3549, "q3_alt2_freq": 0.1805, "f1_quartet_weight": 7.8989, "f2_quartet_weight": 6.0325, "f3_quartet_weight": 3.0687, "effective_loci_en": 17, "gene_concordance_gcf_pct": 46.4638, "local_posterior_pp1": 0.6658, "branch_length_cu": 0.1723, "discordance_asymmetry_chisq": 0.9652, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-61", "clade_label": "Internal Branch 61", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 1, "q2_alt1_freq": 0, "q3_alt2_freq": 0, "f1_quartet_weight": 17, "f2_quartet_weight": 0, "f3_quartet_weight": 0, "effective_loci_en": 17, "gene_concordance_gcf_pct": 100, "local_posterior_pp1": 1, "branch_length_cu": 2.4849, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" } ] }, "robinson_foulds_distance": 2, "max_robinson_foulds": 122, "topological_concordance_pct": 98.3607, "quartet_score_ratio": 1, "normalized_quartet_delta": 0, "q1_pearson_r": 0.9996, "branch_cu_pearson_r": 0.8828, "lpp_concordance_pct": 100, "native_speedup_factor": 15.1778, "abba_baba_tests": [ { "quartet_id": "ABBA-01-SINICUS-AFFINIS-FERRUMEQUINUM", "p1_taxon": "T058 (Rhinolophus sinicus)", "p2_taxon": "T060 (Rhinolophus affinis)", "p3_donor_taxon": "T061 (Rhinolophus ferrumequinum tragatus)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 187, "abba_shared_p2_p3_sites": 342, "baba_shared_p1_p3_sites": 139, "patterson_d_stat": 0.422, "z_score": 9.256, "biological_interpretation": "Historical karst cave-roost introgression & mitochondrial-nuclear discordance between R. affinis and R. ferrumequinum sarbecovirus reservoirs" }, { "quartet_id": "ABBA-02-THOMASI-SINICUS-PEARSONII", "p1_taxon": "T057 (Rhinolophus thomasi)", "p2_taxon": "T058 (Rhinolophus sinicus)", "p3_donor_taxon": "T043 (Rhinolophus pearsonii)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 147, "abba_shared_p2_p3_sites": 172, "baba_shared_p1_p3_sites": 376, "patterson_d_stat": -0.3723, "z_score": 8.7144, "biological_interpretation": "Subtropical Yunnan-Guizhou-Indochina karst corridor gene flow between R. sinicus and R. pearsonii lineages" }, { "quartet_id": "ABBA-03-PUSILLUS-MONOCEROS-AFFINIS", "p1_taxon": "T053 (Rhinolophus pusillus)", "p2_taxon": "T055 (Rhinolophus monoceros)", "p3_donor_taxon": "T060 (Rhinolophus affinis)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 594, "abba_shared_p2_p3_sites": 47, "baba_shared_p1_p3_sites": 54, "patterson_d_stat": -0.0693, "z_score": 0.6965, "biological_interpretation": "Pleistocene Sundaland-Mainland Southeast Asia syntopic cave roosting and ILS across small-bodied pusillus-group and affinis clades" }, { "quartet_id": "ABBA-04-LUCTUS-TRIFOLIATUS-MACROTIS", "p1_taxon": "T031 (Rhinolophus trifoliatus)", "p2_taxon": "T032 (Rhinolophus luctus)", "p3_donor_taxon": "T040 (Rhinolophus macrotis)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 422, "abba_shared_p2_p3_sites": 113, "baba_shared_p1_p3_sites": 94, "patterson_d_stat": 0.0918, "z_score": 1.3206, "biological_interpretation": "Deep Miocene divergence between basal wooly/trifoliatus Sundaic lineages and continental Asian macrotis acoustic-specialist clades" } ], "ascii_cohort_comparison_table": "====================================================================================================================\nCOHORT: COHORT-RHINOLOPHIDAE-64TAXA-18LOCI-RY3-MSC-VS-ASTRAL — 64-Species Asian Horseshoe Bat & Rhinolophoidea 18-Locus RY3-Cleaned Quartet Multispecies Coalescent (Native Rust vs. *ASTRAL v5.7.8)\nTaxa: 64 | Internal Splits: 61 | Input Gene Trees: 18 | Total Quartets Evaluated: 10858000\nUpstream Provenance: super-blast-adaptive -> *MAFFT v7.526 / gotoh-msa (L=48,513 bp across 18 loci: 13 mtDNA PCG/rRNA + 5 nuclear CDS) -> popgen-blind-dualpass (RY3) -> 18 *IQ-TREE v2.4.0 Gene Trees -> runie-quartet-coalescent vs. *ASTRAL v5.7.8\n--------------------------------------------------------------------------------------------------------------------\nMetric Native Quartet MSC (Rust) ASTRAL v5.7.8 (Java) Concordance\n--------------------------------------------------------------------------------------------------------------------\nSatisfied Quartet Score Q(T) 9934509 9934509 Ratio = 1.000000\nNormalized Quartet Score 0.914900 0.914900 Delta = +0.000000\nRobinson-Foulds Split Distance 0 2 98.36% Match (RF=2/122)\nMean Local Posterior Prob (LPP) 0.9047 0.9001 r(q1) = 0.9996\nMean Coalescent Branch Length (CU) 1.7177 1.2873 r(CU) = 0.8828\nWall-Clock Execution Time (ms) 37.31 566.31 15.18x Speedup\n====================================================================================================================" }, "astral_vs_native_unrec_coalescent": { "cohort_id": "COHORT-RHINOLOPHIDAE-64TAXA-18LOCI-UNREC-MSC-VS-ASTRAL", "title": "64-Species Asian Horseshoe Bat & Rhinolophoidea 18-Locus Unrecoded Quartet Multispecies Coalescent (Native Rust vs. *ASTRAL v5.7.8)", "taxonomic_scope": "Chiroptera: Yinpterochiroptera (Rhinolophidae 34 spp., Hipposideridae 14 spp., Basal Rhinolophoidea/Pteropodidae 8 spp.) + Yangochiroptera (8 spp.)", "upstream_pipeline_provenance": "*MAFFT v7.526 (L=48,513 bp across 18 loci, 4-state unrecoded) -> 18 *IQ-TREE v2.4.0 Gene Trees -> runie-quartet-coalescent vs. *ASTRAL v5.7.8", "taxa_count": 64, "internal_branches_count": 61, "gene_tree_count": 18, "total_quartets_evaluated": 10858000, "native_result": { "engine_name": "bio-suite Native Quartet MSC v1 (Exact Tripartition DP + Quartet NNI + LPP)", "engine_mode": "CoalescentMode::Native", "taxa_count": 64, "gene_tree_count": 18, "total_quartets_evaluated": 10858000, "satisfied_quartet_score": 10108414, "normalized_quartet_score": 0.931, "mean_local_posterior_pp1": 0.9146, "mean_branch_length_cu": 1.7264, "wall_clock_ms": 34.7674, "species_tree_newick": "(T001,(T002,(T003,(T006,(T007,((T004,T005)1.0000:2.5326,(T008,((T058,T016)1.0000:2.1945,(((T010,T011)0.9994:0.9706,(T009,T012)0.3952:0.0454)1.0000:2.5161,((T014,T015)1.0000:2.5279,(T013,(((T018,T019)1.0000:2.5494,(T017,((T030,(T029,(T027,T028)0.4564:0.0762)0.5764:0.1372)0.9402:0.4396,((T025,(T022,T023)1.0000:2.5523)0.9940:0.7051,(T024,(T026,(T020,T021)1.0000:2.5523)0.9986:0.8783)1.0000:2.5514)1.0000:2.5503)1.0000:2.5282)0.9286:0.4140)0.9998:1.1322,((T034,((T035,T048)0.7157:0.2776,(T031,(T032,T033)1.0000:2.1924)1.0000:5.4582)0.9989:0.9961)1.0000:5.1311,((T049,(T050,(T052,(T051,(T061,(T063,(T062,T064)0.9998:1.1098)1.0000:2.5520)1.0000:1.8208)1.0000:2.5516)1.0000:1.8127)1.0000:2.1912)0.7715:0.2530,((T045,(T046,T047)1.0000:2.5523)1.0000:2.5477,((T060,(T057,T059)1.0000:2.2780)0.9537:0.4750,((T056,(T055,(T053,T054)1.0000:1.8199)1.0000:1.5580)1.0000:6.4003,(T036,((T037,(T038,T039)1.0000:2.5523)0.6502:0.2108,(T040,(T043,(T041,(T042,T044)1.0000:2.4712)0.7401:0.2849)0.9994:0.9748)0.9871:0.6352)1.0000:1.4650)0.7252:0.2213)1.0000:2.8421)0.9999:1.2779)1.0000:1.4674)0.7974:0.2979)1.0000:4.1396)1.0000:2.0279)0.4253:0.0796)0.9704:0.5360)0.6072:0.2473)0.9701:0.5884)1.0000:5.7818)0.5883:0.2333)0.9253:0.4217)0.6758:0.2205)1.0000:2.5016):0.0000);", "focal_branches": [ { "branch_id": "BR-01", "clade_label": "T004 + T005", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 1, "q2_alt1_freq": 0, "q3_alt2_freq": 0, "f1_quartet_weight": 17.3789, "f2_quartet_weight": 0, "f3_quartet_weight": 0, "effective_loci_en": 17.3789, "gene_concordance_gcf_pct": 100, "local_posterior_pp1": 1, "branch_length_cu": 2.5326, "discordance_asymmetry_chisq": 0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-02", "clade_label": "T058 + T016", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 1, "q2_alt1_freq": 0, "q3_alt2_freq": 0, "f1_quartet_weight": 11.963, "f2_quartet_weight": 0, "f3_quartet_weight": 0, "effective_loci_en": 11.963, "gene_concordance_gcf_pct": 66.6667, "local_posterior_pp1": 1, "branch_length_cu": 2.1945, "discordance_asymmetry_chisq": 0, "coalescent_regime": "High-Concordance Coalescent Split (> 1.00 CU)" }, { "branch_id": "BR-03", "clade_label": "T010 + T011", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.7474, "q2_alt1_freq": 0.0845, "q3_alt2_freq": 0.1681, "f1_quartet_weight": 13.2667, "f2_quartet_weight": 1.5, "f3_quartet_weight": 2.9833, "effective_loci_en": 17.75, "gene_concordance_gcf_pct": 72.2222, "local_posterior_pp1": 0.9994, "branch_length_cu": 0.9706, "discordance_asymmetry_chisq": 0.4908, "coalescent_regime": "Moderate Incomplete Lineage Sorting (0.20–1.00 CU)" }, { "branch_id": "BR-04", "clade_label": "T009 + T012", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.3629, "q2_alt1_freq": 0.2775, "q3_alt2_freq": 0.3596, "f1_quartet_weight": 6.4417, "f2_quartet_weight": 4.925, "f3_quartet_weight": 6.3833, "effective_loci_en": 17.75, "gene_concordance_gcf_pct": 27.7778, "local_posterior_pp1": 0.3952, "branch_length_cu": 0.0454, "discordance_asymmetry_chisq": 0.1881, "coalescent_regime": "Severe ILS / Rapid Radiation Zone (< 0.20 CU)" }, { "branch_id": "BR-05", "clade_label": "T009 + T010 + T011 + T012", "subset_size": 4, "total_taxa": 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"branch_id": "ASTRAL-BR-46", "clade_label": "Internal Branch 46", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4642, "q2_alt1_freq": 0.2639, "q3_alt2_freq": 0.2719, "f1_quartet_weight": 8.355, "f2_quartet_weight": 4.75, "f3_quartet_weight": 4.895, "effective_loci_en": 18, "gene_concordance_gcf_pct": 46.4167, "local_posterior_pp1": 0.7154, "branch_length_cu": 0.1739, "discordance_asymmetry_chisq": 0.0022, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-47", "clade_label": "Internal Branch 47", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.9618, "q2_alt1_freq": 0, "q3_alt2_freq": 0.0382, "f1_quartet_weight": 17.3121, "f2_quartet_weight": 0, "f3_quartet_weight": 0.6879, "effective_loci_en": 18, "gene_concordance_gcf_pct": 96.1781, "local_posterior_pp1": 1, "branch_length_cu": 2.0155, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-48", "clade_label": "Internal Branch 48", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.8136, "q2_alt1_freq": 0.0926, "q3_alt2_freq": 0.0939, "f1_quartet_weight": 14.6439, "f2_quartet_weight": 1.6667, "f3_quartet_weight": 1.6894, "effective_loci_en": 18, "gene_concordance_gcf_pct": 81.3552, "local_posterior_pp1": 0.9999, "branch_length_cu": 1.0674, "discordance_asymmetry_chisq": 0.0002, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-49", "clade_label": "Internal Branch 49", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.8457, "q2_alt1_freq": 0.0893, "q3_alt2_freq": 0.0649, "f1_quartet_weight": 15.2235, "f2_quartet_weight": 1.6081, "f3_quartet_weight": 1.1684, "effective_loci_en": 18, "gene_concordance_gcf_pct": 84.5749, "local_posterior_pp1": 1, "branch_length_cu": 1.2102, "discordance_asymmetry_chisq": 0.0696, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-50", "clade_label": "Internal Branch 50", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.5031, "q2_alt1_freq": 0.3287, "q3_alt2_freq": 0.1683, "f1_quartet_weight": 9.0551, "f2_quartet_weight": 5.9157, "f3_quartet_weight": 3.0292, "effective_loci_en": 18, "gene_concordance_gcf_pct": 50.306, "local_posterior_pp1": 0.7987, "branch_length_cu": 0.2419, "discordance_asymmetry_chisq": 0.9315, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-51", "clade_label": "Internal Branch 51", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.9901, "q2_alt1_freq": 0.0065, "q3_alt2_freq": 0.0033, "f1_quartet_weight": 17.8222, "f2_quartet_weight": 0.1176, "f3_quartet_weight": 0.0602, "effective_loci_en": 18, "gene_concordance_gcf_pct": 99.012, "local_posterior_pp1": 1, "branch_length_cu": 2.3753, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-52", "clade_label": "Internal Branch 52", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.9068, "q2_alt1_freq": 0.0647, "q3_alt2_freq": 0.0284, "f1_quartet_weight": 16.3233, "f2_quartet_weight": 1.1648, "f3_quartet_weight": 0.5119, "effective_loci_en": 18, "gene_concordance_gcf_pct": 90.6848, "local_posterior_pp1": 1, "branch_length_cu": 1.5544, "discordance_asymmetry_chisq": 0.2543, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-53", "clade_label": "Internal Branch 53", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.3778, "q2_alt1_freq": 0.3873, "q3_alt2_freq": 0.2349, "f1_quartet_weight": 6.8001, "f2_quartet_weight": 6.9718, "f3_quartet_weight": 4.2281, "effective_loci_en": 18, "gene_concordance_gcf_pct": 37.7782, "local_posterior_pp1": 0.403, "branch_length_cu": 0.0375, "discordance_asymmetry_chisq": 0.6721, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-54", "clade_label": "Internal Branch 54", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.616, "q2_alt1_freq": 0.1441, "q3_alt2_freq": 0.2399, "f1_quartet_weight": 11.0879, "f2_quartet_weight": 2.5946, "f3_quartet_weight": 4.3175, "effective_loci_en": 18, "gene_concordance_gcf_pct": 61.5994, "local_posterior_pp1": 0.9754, "branch_length_cu": 0.4706, "discordance_asymmetry_chisq": 0.4294, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-55", "clade_label": "Internal Branch 55", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4013, "q2_alt1_freq": 0.4885, "q3_alt2_freq": 0.1102, "f1_quartet_weight": 7.2236, "f2_quartet_weight": 8.7925, "f3_quartet_weight": 1.9839, "effective_loci_en": 18, "gene_concordance_gcf_pct": 40.1311, "local_posterior_pp1": 0.2631, "branch_length_cu": 0.0729, "discordance_asymmetry_chisq": 4.3018, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-56", "clade_label": "Internal Branch 56", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.6604, "q2_alt1_freq": 0.1174, "q3_alt2_freq": 0.2222, "f1_quartet_weight": 11.8868, "f2_quartet_weight": 2.1132, "f3_quartet_weight": 4, "effective_loci_en": 18, "gene_concordance_gcf_pct": 66.0377, "local_posterior_pp1": 0.9915, "branch_length_cu": 0.577, "discordance_asymmetry_chisq": 0.5823, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-57", "clade_label": "Internal Branch 57", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.998, "q2_alt1_freq": 0.0016, "q3_alt2_freq": 0.0004, "f1_quartet_weight": 17.9643, "f2_quartet_weight": 0.0286, "f3_quartet_weight": 0.0071, "effective_loci_en": 18, "gene_concordance_gcf_pct": 99.8016, "local_posterior_pp1": 1, "branch_length_cu": 2.5039, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-58", "clade_label": "Internal Branch 58", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4598, "q2_alt1_freq": 0.4425, "q3_alt2_freq": 0.0977, "f1_quartet_weight": 8.2763, "f2_quartet_weight": 7.9649, "f3_quartet_weight": 1.7588, "effective_loci_en": 18, "gene_concordance_gcf_pct": 45.9795, "local_posterior_pp1": 0.5196, "branch_length_cu": 0.1665, "discordance_asymmetry_chisq": 3.9611, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-59", "clade_label": "Internal Branch 59", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.5626, "q2_alt1_freq": 0.2379, "q3_alt2_freq": 0.1995, "f1_quartet_weight": 9.5646, "f2_quartet_weight": 4.0444, "f3_quartet_weight": 3.391, "effective_loci_en": 17, "gene_concordance_gcf_pct": 56.2622, "local_posterior_pp1": 0.9207, "branch_length_cu": 0.3525, "discordance_asymmetry_chisq": 0.0574, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-60", "clade_label": "Internal Branch 60", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 0.4637, "q2_alt1_freq": 0.3539, "q3_alt2_freq": 0.1825, "f1_quartet_weight": 7.8825, "f2_quartet_weight": 6.0158, "f3_quartet_weight": 3.1017, "effective_loci_en": 17, "gene_concordance_gcf_pct": 46.3674, "local_posterior_pp1": 0.664, "branch_length_cu": 0.1706, "discordance_asymmetry_chisq": 0.9314, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" }, { "branch_id": "ASTRAL-BR-61", "clade_label": "Internal Branch 61", "subset_size": 2, "total_taxa": 64, "q1_main_freq": 1, "q2_alt1_freq": 0, "q3_alt2_freq": 0, "f1_quartet_weight": 17, "f2_quartet_weight": 0, "f3_quartet_weight": 0, "effective_loci_en": 17, "gene_concordance_gcf_pct": 100, "local_posterior_pp1": 1, "branch_length_cu": 2.4849, "discordance_asymmetry_chisq": 0, "coalescent_regime": "ASTRAL v5.7.8 Exact Quartet Branch" } ] }, "robinson_foulds_distance": 0, "max_robinson_foulds": 122, "topological_concordance_pct": 100, "quartet_score_ratio": 1, "normalized_quartet_delta": 0, "q1_pearson_r": 0.9995, "branch_cu_pearson_r": 0.8692, "lpp_concordance_pct": 100, "native_speedup_factor": 16.3944, "abba_baba_tests": [ { "quartet_id": "ABBA-01-SINICUS-AFFINIS-FERRUMEQUINUM", "p1_taxon": "T058 (Rhinolophus sinicus)", "p2_taxon": "T060 (Rhinolophus affinis)", "p3_donor_taxon": "T061 (Rhinolophus ferrumequinum tragatus)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 187, "abba_shared_p2_p3_sites": 342, "baba_shared_p1_p3_sites": 139, "patterson_d_stat": 0.422, "z_score": 9.256, "biological_interpretation": "Historical karst cave-roost introgression & mitochondrial-nuclear discordance between R. affinis and R. ferrumequinum sarbecovirus reservoirs" }, { "quartet_id": "ABBA-02-THOMASI-SINICUS-PEARSONII", "p1_taxon": "T057 (Rhinolophus thomasi)", "p2_taxon": "T058 (Rhinolophus sinicus)", "p3_donor_taxon": "T043 (Rhinolophus pearsonii)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 147, "abba_shared_p2_p3_sites": 172, "baba_shared_p1_p3_sites": 376, "patterson_d_stat": -0.3723, "z_score": 8.7144, "biological_interpretation": "Subtropical Yunnan-Guizhou-Indochina karst corridor gene flow between R. sinicus and R. pearsonii lineages" }, { "quartet_id": "ABBA-03-PUSILLUS-MONOCEROS-AFFINIS", "p1_taxon": "T053 (Rhinolophus pusillus)", "p2_taxon": "T055 (Rhinolophus monoceros)", "p3_donor_taxon": "T060 (Rhinolophus affinis)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 594, "abba_shared_p2_p3_sites": 47, "baba_shared_p1_p3_sites": 54, "patterson_d_stat": -0.0693, "z_score": 0.6965, "biological_interpretation": "Pleistocene Sundaland-Mainland Southeast Asia syntopic cave roosting and ILS across small-bodied pusillus-group and affinis clades" }, { "quartet_id": "ABBA-04-LUCTUS-TRIFOLIATUS-MACROTIS", "p1_taxon": "T031 (Rhinolophus trifoliatus)", "p2_taxon": "T032 (Rhinolophus luctus)", "p3_donor_taxon": "T040 (Rhinolophus macrotis)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 422, "abba_shared_p2_p3_sites": 113, "baba_shared_p1_p3_sites": 94, "patterson_d_stat": 0.0918, "z_score": 1.3206, "biological_interpretation": "Deep Miocene divergence between basal wooly/trifoliatus Sundaic lineages and continental Asian macrotis acoustic-specialist clades" } ], "ascii_cohort_comparison_table": "====================================================================================================================\nCOHORT: COHORT-RHINOLOPHIDAE-64TAXA-18LOCI-UNREC-MSC-VS-ASTRAL — 64-Species Asian Horseshoe Bat & Rhinolophoidea 18-Locus Unrecoded Quartet Multispecies Coalescent (Native Rust vs. *ASTRAL v5.7.8)\nTaxa: 64 | Internal Splits: 61 | Input Gene Trees: 18 | Total Quartets Evaluated: 10858000\nUpstream Provenance: *MAFFT v7.526 (L=48,513 bp across 18 loci, 4-state unrecoded) -> 18 *IQ-TREE v2.4.0 Gene Trees -> runie-quartet-coalescent vs. *ASTRAL v5.7.8\n--------------------------------------------------------------------------------------------------------------------\nMetric Native Quartet MSC (Rust) ASTRAL v5.7.8 (Java) Concordance\n--------------------------------------------------------------------------------------------------------------------\nSatisfied Quartet Score Q(T) 10108414 10108414 Ratio = 1.000000\nNormalized Quartet Score 0.931000 0.931000 Delta = +0.000000\nRobinson-Foulds Split Distance 0 0 100.00% Match (RF=0/122)\nMean Local Posterior Prob (LPP) 0.9146 0.9041 r(q1) = 0.9995\nMean Coalescent Branch Length (CU) 1.7264 1.3439 r(CU) = 0.8692\nWall-Clock Execution Time (ms) 34.77 569.99 16.39x Speedup\n====================================================================================================================" }, "abba_baba_introgression_tests": [ { "quartet_id": "ABBA-01-SINICUS-AFFINIS-FERRUMEQUINUM", "p1_taxon": "T058 (Rhinolophus sinicus)", "p2_taxon": "T060 (Rhinolophus affinis)", "p3_donor_taxon": "T061 (Rhinolophus ferrumequinum tragatus)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 187, "abba_shared_p2_p3_sites": 342, "baba_shared_p1_p3_sites": 139, "patterson_d_stat": 0.422, "z_score": 9.256, "biological_interpretation": "Historical karst cave-roost introgression & mitochondrial-nuclear discordance between R. affinis and R. ferrumequinum sarbecovirus reservoirs" }, { "quartet_id": "ABBA-02-THOMASI-SINICUS-PEARSONII", "p1_taxon": "T057 (Rhinolophus thomasi)", "p2_taxon": "T058 (Rhinolophus sinicus)", "p3_donor_taxon": "T043 (Rhinolophus pearsonii)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 147, "abba_shared_p2_p3_sites": 172, "baba_shared_p1_p3_sites": 376, "patterson_d_stat": -0.3723, "z_score": 8.7144, "biological_interpretation": "Subtropical Yunnan-Guizhou-Indochina karst corridor gene flow between R. sinicus and R. pearsonii lineages" }, { "quartet_id": "ABBA-03-PUSILLUS-MONOCEROS-AFFINIS", "p1_taxon": "T053 (Rhinolophus pusillus)", "p2_taxon": "T055 (Rhinolophus monoceros)", "p3_donor_taxon": "T060 (Rhinolophus affinis)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 594, "abba_shared_p2_p3_sites": 47, "baba_shared_p1_p3_sites": 54, "patterson_d_stat": -0.0693, "z_score": 0.6965, "biological_interpretation": "Pleistocene Sundaland-Mainland Southeast Asia syntopic cave roosting and ILS across small-bodied pusillus-group and affinis clades" }, { "quartet_id": "ABBA-04-LUCTUS-TRIFOLIATUS-MACROTIS", "p1_taxon": "T031 (Rhinolophus trifoliatus)", "p2_taxon": "T032 (Rhinolophus luctus)", "p3_donor_taxon": "T040 (Rhinolophus macrotis)", "outgroup_taxon": "T022 (Hipposideros armiger Outgroup)", "bbaa_concordant_sites": 422, "abba_shared_p2_p3_sites": 113, "baba_shared_p1_p3_sites": 94, "patterson_d_stat": 0.0918, "z_score": 1.3206, "biological_interpretation": "Deep Miocene divergence between basal wooly/trifoliatus Sundaic lineages and continental Asian macrotis acoustic-specialist clades" } ], "combinatorial_sweep_32chains": [ { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 8, "global_rank": 1, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+R4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+R4", "k_free_params": 125, "marginal_ln_l": -339762.41, "delta_ln_l_vs_best": 0, "aic": 679802.82, "bic": 681024.5726, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 511625, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 573022 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 7, "global_rank": 2, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+I+G4", "k_free_params": 127, "marginal_ln_l": -340825.9406, "delta_ln_l_vs_best": -1063.5306, "aic": 681921.8813, "bic": 683108.4755, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 54141, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 115538 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 6, "global_rank": 3, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (GTR+F+G4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "GTR+F+G4", "k_free_params": 129, "marginal_ln_l": -341126.0518, "delta_ln_l_vs_best": -1363.6418, "aic": 682520.1035, "bic": 683697.9082, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 28625, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 90022 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 5, "global_rank": 4, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "TIM2+F+I+G4", "k_free_params": 131, "marginal_ln_l": -341543.7983, "delta_ln_l_vs_best": -1781.3883, "aic": 683353.5966, "bic": 684522.6116, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 49828, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 111225 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 4, "global_rank": 5, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "TN+F+I+G4", "k_free_params": 133, "marginal_ln_l": -341745.1176, "delta_ln_l_vs_best": -1982.7076, "aic": 683754.2351, "bic": 684914.4606, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 40188, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 101585 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 3, "global_rank": 6, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "HKY+F+I+G4", "k_free_params": 135, "marginal_ln_l": -341750.4526, "delta_ln_l_vs_best": -1988.0426, "aic": 683762.9051, "bic": 684914.341, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 43594, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 104991 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 1, "global_rank": 7, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (GTR+F+R4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "GTR+F+R4", "k_free_params": 137, "marginal_ln_l": -344289.2692, "delta_ln_l_vs_best": -4526.8592, "aic": 688852.5384, "bic": 690056.7118, "rcfv": 0.0084, "bootstrap_support_pct": 99.7, "posterior_prob": 0.9999, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 2, "global_rank": 8, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (GTR+F+I+G4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "GTR+F+I+G4", "k_free_params": 135, "marginal_ln_l": -345554.5364, "delta_ln_l_vs_best": -5792.1264, "aic": 691379.0728, "bic": 692565.6671, "rcfv": 0.0084, "bootstrap_support_pct": 99.7, "posterior_prob": 0.9999, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 4, "global_rank": 9, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (TIM2+F+I+G4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "TIM2+F+I+G4", "k_free_params": 133, "marginal_ln_l": -345925.8668, "delta_ln_l_vs_best": -6163.4568, "aic": 692117.7335, "bic": 693286.7486, "rcfv": 0.0084, "bootstrap_support_pct": 96.9, "posterior_prob": 0.954, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 6, "global_rank": 10, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (HKY+F+I+G4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "HKY+F+I+G4", "k_free_params": 131, "marginal_ln_l": -346214.1988, "delta_ln_l_vs_best": -6451.7888, "aic": 692690.3976, "bic": 693841.8336, "rcfv": 0.0084, "bootstrap_support_pct": 96.9, "posterior_prob": 0.954, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 5, "global_rank": 11, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (TN+F+I+G4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "TN+F+I+G4", "k_free_params": 132, "marginal_ln_l": -346262.5516, "delta_ln_l_vs_best": -6500.1416, "aic": 692789.1032, "bic": 693949.3287, "rcfv": 0.0084, "bootstrap_support_pct": 96.9, "posterior_prob": 0.954, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 3, "global_rank": 12, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (GTR+F+G4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "GTR+F+G4", "k_free_params": 134, "marginal_ln_l": -349315.2798, "delta_ln_l_vs_best": -9552.8698, "aic": 698898.5596, "bic": 700076.3643, "rcfv": 0.0084, "bootstrap_support_pct": 96.9, "posterior_prob": 0.954, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 2, "global_rank": 13, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (K80+G4) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "K80+G4", "k_free_params": 137, "marginal_ln_l": -352807.0425, "delta_ln_l_vs_best": -13044.6325, "aic": 705868.0849, "bic": 706984.3625, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 10984, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 72381 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 7, "global_rank": 14, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (K80+G4) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "K80+G4", "k_free_params": 127, "marginal_ln_l": -360384.5502, "delta_ln_l_vs_best": -20622.1402, "aic": 721023.1004, "bic": 722139.378, "rcfv": 0.0084, "bootstrap_support_pct": 96.9, "posterior_prob": 0.954, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 3: Unconstrained Hybrid RuNIE (super-blast -> *MAFFT v7.526 -> popgen-blind-dualpass [RY3] -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 / runie-quartet-coalescent -> *LSD2 -> runie-mcmc-skyline -> *PAML v4.10.10)", "chain_rank_in_regime": 1, "global_rank": 15, "tool_chain_summary": "super-blast-adaptive -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest -> *IQ-TREE v2.4.0 (JC) -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10", "model_name": "JC", "k_free_params": 139, "marginal_ln_l": -397250.6261, "delta_ln_l_vs_best": -57488.2161, "aic": 794751.2522, "bic": 795849.9506, "rcfv": 0.0084, "bootstrap_support_pct": 100, "posterior_prob": 1, "msa_time_ms": 58320, "modeltest_time_ms": 1797, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 63194 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 8, "global_rank": 16, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (GTR+F+R4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "GTR+F+R4", "k_free_params": 125, "marginal_ln_l": -402202.1156, "delta_ln_l_vs_best": -62439.7056, "aic": 804682.2313, "bic": 805903.9839, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 87938, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 150638 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 8, "global_rank": 17, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+R4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "GTR+F+R4", "k_free_params": 125, "marginal_ln_l": -402235.1676, "delta_ln_l_vs_best": -62472.7576, "aic": 804748.3351, "bic": 805970.0877, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 1132281, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 1195547 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 7, "global_rank": 18, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "GTR+F+I+G4", "k_free_params": 127, "marginal_ln_l": -403422.4507, "delta_ln_l_vs_best": -63660.0407, "aic": 807114.9015, "bic": 808301.4957, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 66719, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 129419 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 7, "global_rank": 19, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+I+G4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "GTR+F+I+G4", "k_free_params": 127, "marginal_ln_l": -403422.7961, "delta_ln_l_vs_best": -63660.3861, "aic": 807115.5923, "bic": 808302.1865, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 72250, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 135516 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 6, "global_rank": 20, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (GTR+F+G4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "GTR+F+G4", "k_free_params": 129, "marginal_ln_l": -403560.6708, "delta_ln_l_vs_best": -63798.2608, "aic": 807389.3417, "bic": 808567.1464, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 46266, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 108966 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 6, "global_rank": 21, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (GTR+F+G4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "GTR+F+G4", "k_free_params": 129, "marginal_ln_l": -403560.7728, "delta_ln_l_vs_best": -63798.3628, "aic": 807389.5457, "bic": 808567.3503, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 52875, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 116141 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 5, "global_rank": 22, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "TIM2+F+I+G4", "k_free_params": 131, "marginal_ln_l": -403569.2672, "delta_ln_l_vs_best": -63806.8572, "aic": 807404.5344, "bic": 808573.5495, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 61922, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 125188 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 5, "global_rank": 23, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (TIM2+F+I+G4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "TIM2+F+I+G4", "k_free_params": 131, "marginal_ln_l": -403569.2972, "delta_ln_l_vs_best": -63806.8872, "aic": 807404.5943, "bic": 808573.6094, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 61750, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 124450 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 4, "global_rank": 24, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "TN+F+I+G4", "k_free_params": 133, "marginal_ln_l": -403762.3664, "delta_ln_l_vs_best": -63999.9564, "aic": 807788.7327, "bic": 808948.9582, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 51172, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 114438 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 4, "global_rank": 25, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (TN+F+I+G4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "TN+F+I+G4", "k_free_params": 133, "marginal_ln_l": -403762.3664, "delta_ln_l_vs_best": -63999.9564, "aic": 807788.7327, "bic": 808948.9582, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 56375, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 119075 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 3, "global_rank": 26, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "HKY+F+I+G4", "k_free_params": 135, "marginal_ln_l": -403911.6881, "delta_ln_l_vs_best": -64149.2781, "aic": 808085.3762, "bic": 809236.8121, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 54516, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 117216 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 3, "global_rank": 27, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (HKY+F+I+G4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "HKY+F+I+G4", "k_free_params": 135, "marginal_ln_l": -403911.735, "delta_ln_l_vs_best": -64149.325, "aic": 808085.47, "bic": 809236.9059, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 62359, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 125625 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 2, "global_rank": 28, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (K80+G4) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "K80+G4", "k_free_params": 137, "marginal_ln_l": -407612.508, "delta_ln_l_vs_best": -67850.098, "aic": 815479.0159, "bic": 816595.2935, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 35781, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 99047 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 2, "global_rank": 29, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (K80+G4) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "K80+G4", "k_free_params": 137, "marginal_ln_l": -407612.508, "delta_ln_l_vs_best": -67850.098, "aic": 815479.016, "bic": 816595.2935, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 34766, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 97466 }, { "regime_id": "Regime 1: 100% Native Rust (super-blast -> gotoh-msa -> popgen-blind-dualpass -> RY3 -> felsenstein-modeltest -> runie-quartet-coalescent -> runie-mcmc-skyline)", "chain_rank_in_regime": 8, "global_rank": 30, "tool_chain_summary": "super-blast-adaptive -> gotoh-msa -> popgen-blind-dualpass (RY3) -> felsenstein-modeltest (JC) -> runie-quartet-coalescent (18 loci, LPP) -> runie-mcmc-skyline (10k gen, 20% burn-in) -> dnds-selection", "model_name": "JC", "k_free_params": 125, "marginal_ln_l": -410994.293, "delta_ln_l_vs_best": -71231.883, "aic": 822238.5859, "bic": 823337.2843, "rcfv": 0.0084, "bootstrap_support_pct": 96.9, "posterior_prob": 0.954, "msa_time_ms": 9820, "modeltest_time_ms": 102, "tree_mcmc_time_ms": 3077, "total_cpu_time_ms": 12999 }, { "regime_id": "Regime 4: 0-Beaker Rejected Uncleaned Negative Control (Unrecoded Saturation + Unfiltered NUMT Pseudogene Chimera)", "chain_rank_in_regime": 1, "global_rank": 31, "tool_chain_summary": "Raw Uncleaned Supermatrix -> No RY3 / No NUMT Chimera Filter -> *IQ-TREE v2.4.0 (JC) -> Uncleaned ASTRAL / Skyline (0-Beaker Rejected)", "model_name": "JC", "k_free_params": 139, "marginal_ln_l": -468510.5684, "delta_ln_l_vs_best": -128748.1584, "aic": 937271.1367, "bic": 938369.8351, "rcfv": 0.0468, "bootstrap_support_pct": 58.6, "posterior_prob": 0.0001, "msa_time_ms": 58320, "modeltest_time_ms": 2250, "tree_mcmc_time_ms": 4380, "total_cpu_time_ms": 64950 }, { "regime_id": "Regime 2: 100% External Reference (*MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10)", "chain_rank_in_regime": 1, "global_rank": 32, "tool_chain_summary": "*MAFFT v7.526 -> *IQ-TREE v2.4.0 (JC) -> *ASTRAL v5.7.8 (18 loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 (10k gen, 20% burn-in) -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10", "model_name": "JC", "k_free_params": 139, "marginal_ln_l": -468602.4522, "delta_ln_l_vs_best": -128840.0422, "aic": 937454.9043, "bic": 938553.6027, "rcfv": 0.0468, "bootstrap_support_pct": 98.4, "posterior_prob": 0.9992, "msa_time_ms": 58320, "modeltest_time_ms": 2266, "tree_mcmc_time_ms": 4946, "total_cpu_time_ms": 65532 } ], "popset_skyline_cohorts": [ { "popset_id": "POPSET-1-RHINOLOPHIDAE-RHINOLOPHUS-PUSILLUS-INDOCHINA-KARST", "family": "Rhinolophidae (Subtropical & Tropical Karst Clade — pusillus Group)", "species": "Rhinolophus pusillus (Least Horseshoe Bat — Thailand Indochinese Karst PopSet PZ496420–PZ496472)", "ecological_hypothesis": "Late Pleistocene Sundaic-Indochinese monsoon forest expansion -> LGM limestone cave refugial stability -> Holocene agricultural edge insect-foraging surge -> Anthropocene cave-tourism & guano-mining disturbance", "num_isolates": 36, "raw_bp": 41040, "aligned_cols_bp": 1140, "distinct_patterns_ry3": 129, "parsimony_informative_ry3": 64, "rcfv_ry3": 0.0031, "rcfv_unrecoded": 0.0133, "rcfv_raw_0star": 0.0139, "tajima_d": -0.6895, "watterson_theta_per_site": 0.0558, "nucleotide_diversity_pi": 0.0457, "runie_marginal_ln_l": -3218.6402, "runie_posterior_mean_ln_l": -3216.7402, "iqtree_ry3_ln_l": -3085.9757, "iqtree_unrec_ln_l": -4441.5793, "beast_mean_ln_l": -4855.05, "ess": 384.9034, "rhat": 1.0227, "runie_cpu_ms": 430, "beast_cpu_ms": 1845, "epochs": [ { "epoch_index": 1, "epoch_label": "Late Pleistocene MIS 5e–5a Asian Monsoon Forest Expansion", "time_start_ka": 180, "time_end_ka": 75, "time_midpoint_ka": 127.5, "eco_driver": "Warm interglacial East & Southeast Asian monsoon expansion connecting Indochinese limestone karst demes", "runie_ne_median": 710698, "runie_ne_hpd95_lower": 533856, "runie_ne_hpd95_upper": 914067, "beast_ne_median": 732872, "raw_0star_ne_median": 676584, "active_lineages": 13, "coalescent_events": 11, "coalescent_exposure": 2853.605, "empirical_pi_ry3": 0.0187, "empirical_pi_unrec": 0.0457 }, { "epoch_index": 2, "epoch_label": "Last Glacial Maximum (LGM) Indochina-Tenasserim Karst Refugia", "time_start_ka": 75, "time_end_ka": 18, "time_midpoint_ka": 46.5, "eco_driver": "Persistence of Rhinolophus pusillus colonies inside thermally buffered Thai-Burmese limestone cave networks", "runie_ne_median": 991082, "runie_ne_hpd95_lower": 733899, "runie_ne_hpd95_upper": 1286843, "beast_ne_median": 1022004, "raw_0star_ne_median": 943510, "active_lineages": 19, "coalescent_events": 6, "coalescent_exposure": 6811.7685, "empirical_pi_ry3": 0.0187, "empirical_pi_unrec": 0.0457 }, { "epoch_index": 3, "epoch_label": "Bølling-Allerød & Early Holocene Tropical Rainforest Recovery", "time_start_ka": 18, "time_end_ka": 4, "time_midpoint_ka": 11, "eco_driver": "Rapid post-glacial demographic expansion across Indochinese river valleys and karst towers", "runie_ne_median": 1108199, "runie_ne_hpd95_lower": 806093, "runie_ne_hpd95_upper": 1455621, "beast_ne_median": 1142775, "raw_0star_ne_median": 1055005, "active_lineages": 22, "coalescent_events": 3, "coalescent_exposure": 2762.464, "empirical_pi_ry3": 0.0187, "empirical_pi_unrec": 0.0457 }, { "epoch_index": 4, "epoch_label": "Mid-to-Late Holocene Rice-Paddy & Agrarian Insect Subsidy", "time_start_ka": 4, "time_end_ka": 0.3, "time_midpoint_ka": 2.15, "eco_driver": "Irrigated paddy ecosystems elevating nocturnal Diptera/Lepidoptera prey density around karst roosts", "runie_ne_median": 1179602, "runie_ne_hpd95_lower": 858031, "runie_ne_hpd95_upper": 1549409, "beast_ne_median": 1216406, "raw_0star_ne_median": 1122981, "active_lineages": 25, "coalescent_events": 3, "coalescent_exposure": 1046.0724, "empirical_pi_ry3": 0.0187, "empirical_pi_unrec": 0.0457 }, { "epoch_index": 5, "epoch_label": "Late-20th-Century Deforestation & Limestone Quarrying Onset", "time_start_ka": 0.3, "time_end_ka": 0.04, "time_midpoint_ka": 0.17, "eco_driver": "Tropical forest clearance and cement limestone quarrying fragmenting peripheral cave colonies", "runie_ne_median": 1199595, "runie_ne_hpd95_lower": 828926, "runie_ne_hpd95_upper": 1625864, "beast_ne_median": 1237022, "raw_0star_ne_median": 1460507, "active_lineages": 25, "coalescent_events": 0, "coalescent_exposure": 78, "empirical_pi_ry3": 0.0187, "empirical_pi_unrec": 0.0457 }, { "epoch_index": 6, "epoch_label": "2000–2025 Anthropocene Cave Disturbance & Sarbecovirus Interface", "time_start_ka": 0.04, "time_end_ka": 0, "time_midpoint_ka": 0.02, "eco_driver": "High-density syntopic cave roosting with R. affinis/R. malayanus & human guano-harvesting exposure", "runie_ne_median": 1230933, 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"coalescent_events": 7, "coalescent_exposure": 3275.1041, "empirical_pi_ry3": 0.0107, "empirical_pi_unrec": 0.0468 }, { "epoch_index": 4, "epoch_label": "Imperial & Early Modern Subtropical Forest Transformation", "time_start_ka": 3.5, "time_end_ka": 0.25, "time_midpoint_ka": 1.875, "eco_driver": "Terraced hillslope cultivation and secondary bamboo-broadleaf mosaic expansion across South China", "runie_ne_median": 1780615, "runie_ne_hpd95_lower": 1230414, "runie_ne_hpd95_upper": 2413346, "beast_ne_median": 1836170, "raw_0star_ne_median": 1695145, "active_lineages": 25, "coalescent_events": 0, "coalescent_exposure": 975, "empirical_pi_ry3": 0.0107, "empirical_pi_unrec": 0.0468 }, { "epoch_index": 5, "epoch_label": "Late-20th-Century Urbanization & Hydroelectric Karst Inundation", "time_start_ka": 0.25, "time_end_ka": 0.04, "time_midpoint_ka": 0.145, "eco_driver": "River valley reservoir inundation and highway tunneling disrupting traditional subterranean hibernacula", "runie_ne_median": 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& Sino-Japanese Reservoir Clade — ferrumequinum Group)", "species": "Rhinolophus ferrumequinum (Greater Horseshoe Bat — East Asian Sino-Japanese PopSet 2170330412 / LC605906–LC605937)", "ecological_hypothesis": "Pleistocene Tsushima/Korean Strait land-bridge colonization -> LGM temperate hibernaculum bottleneck -> Holocene deciduous forest expansion -> Contemporary abandoned-mine roost shift & acoustic divergence", "num_isolates": 36, "raw_bp": 41040, "aligned_cols_bp": 1140, "distinct_patterns_ry3": 24, "parsimony_informative_ry3": 6, "rcfv_ry3": 0.0005, "rcfv_unrecoded": 0.0031, "rcfv_raw_0star": 0.0032, "tajima_d": -2.2821, "watterson_theta_per_site": 0.0216, "nucleotide_diversity_pi": 0.0083, "runie_marginal_ln_l": -1707.1161, "runie_posterior_mean_ln_l": -1705.2161, "iqtree_ry3_ln_l": -1697.26, "iqtree_unrec_ln_l": -2175.556, "beast_mean_ln_l": -2228.68, "ess": 129.1332, "rhat": 1.0442, "runie_cpu_ms": 430, "beast_cpu_ms": 1460, "epochs": [ { "epoch_index": 1, "epoch_label": 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"active_lineages": 9, "coalescent_events": 2, "coalescent_exposure": 2714.2644, "empirical_pi_ry3": 0.0021, "empirical_pi_unrec": 0.0083 }, { "epoch_index": 3, "epoch_label": "Bølling-Allerød & Holocene Temperate Deciduous Forest Surge", "time_start_ka": 20, "time_end_ka": 3, "time_midpoint_ka": 11.5, "eco_driver": "Post-glacial northward expansion of Quercus-Fagus temperate forests & Coleoptera/Lepidoptera prey base", "runie_ne_median": 480865, "runie_ne_hpd95_lower": 332280, "runie_ne_hpd95_upper": 651738, "beast_ne_median": 495868, "raw_0star_ne_median": 457783, "active_lineages": 9, "coalescent_events": 0, "coalescent_exposure": 612, "empirical_pi_ry3": 0.0021, "empirical_pi_unrec": 0.0083 }, { "epoch_index": 4, "epoch_label": "Historical Satoyama Agro-Forestry & Mine-Tunnel Proliferation", "time_start_ka": 3, "time_end_ka": 0.2, "time_midpoint_ka": 1.6, "eco_driver": "Traditional coppice-woodland mosaics and historic copper/silver mine adits expanding artificial winter hibernacula", "runie_ne_median": 499142, "runie_ne_hpd95_lower": 344910, "runie_ne_hpd95_upper": 676509, "beast_ne_median": 514715, "raw_0star_ne_median": 475183, "active_lineages": 9, "coalescent_events": 0, "coalescent_exposure": 100.8, "empirical_pi_ry3": 0.0021, "empirical_pi_unrec": 0.0083 }, { "epoch_index": 5, "epoch_label": "Post-1950 Pesticide Intensification & Cave/Mine Sealing", "time_start_ka": 0.2, "time_end_ka": 0.04, "time_midpoint_ka": 0.12, "eco_driver": "Organochlorine/neonicotinoid agricultural intensification and sealing of abandoned mine shafts reducing colony size", "runie_ne_median": 504260, "runie_ne_hpd95_lower": 348446, "runie_ne_hpd95_upper": 683446, "beast_ne_median": 519993, "raw_0star_ne_median": 613937, "active_lineages": 9, "coalescent_events": 0, "coalescent_exposure": 5.76, "empirical_pi_ry3": 0.0021, "empirical_pi_unrec": 0.0083 }, { "epoch_index": 6, "epoch_label": "2000–2025 Anthropocene Acoustic Micro-Evolution & Roost Protection", "time_start_ka": 0.04, "time_end_ka": 0, "time_midpoint_ka": 0.02, "eco_driver": "Contemporary resting-frequency (CF ~66–71 kHz) geographic character displacement & protected maternity roost stabilization", "runie_ne_median": 526907, "runie_ne_hpd95_lower": 383267, "runie_ne_hpd95_upper": 692093, "beast_ne_median": 543346, "raw_0star_ne_median": 641509, "active_lineages": 12, "coalescent_events": 3, "coalescent_exposure": 2.4633, "empirical_pi_ry3": 0.0021, "empirical_pi_unrec": 0.0083 } ] } ], "core_64_species_manifest": [ { "node_id": "A:T002", "tip_id": "T002", "sector": "A", "species": "Myotis pilosus", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_056111.1", "length_bp": 17098, "gc_pct": 35.47, "sha256_prefix": "633bce47d35bb2bf", "parent_node": "N03 (95%)", "terminal_branch_length": 0.013116, "ecological_and_epidemiological_guild": "Subtropical East Asian piscivorous/insectivorous cave bat (Rickettia pilosa)" }, { "node_id": "A:T008", "tip_id": "T008", "sector": "A", "species": "Miniopterus schreibersii", "family": "Miniopteridae", "suborder": "Yangochiroptera", "accession": "NW_027669850.1", "length_bp": 16632, "gc_pct": 39.9, "sha256_prefix": "e4882707e8a97424", "parent_node": "N02 (98%)", "terminal_branch_length": 0.248575, "ecological_and_epidemiological_guild": "Eurasian colonial cave-roosting long-winged migratory insectivore" }, { "node_id": "A:T004", "tip_id": "T004", "sector": "A", "species": "Pipistrellus pipistrellus", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_088543.1", "length_bp": 16571, "gc_pct": 35.67, "sha256_prefix": "0d03cab1dab9b8ff", "parent_node": "N01 (100%)", "terminal_branch_length": 0.059677, "ecological_and_epidemiological_guild": "Palaearctic & Central Asian synanthropic edge-space FM/QCF insectivore" }, { "node_id": "A:T005", "tip_id": "T005", "sector": "A", "species": "Nyctalus aviator", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_060309.1", "length_bp": 16863, "gc_pct": 38.51, "sha256_prefix": "275b90fdbb14f6c9", "parent_node": "N01 (100%)", "terminal_branch_length": 0.139741, "ecological_and_epidemiological_guild": "East Asian open-air aerial hawking & bird-hunting noctule" }, { "node_id": "A:T001", "tip_id": "T001", "sector": "A", "species": "Myotis petax", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_056773.1", "length_bp": 17299, "gc_pct": 35.39, "sha256_prefix": "0ee3e02080dfaa27", "parent_node": "N04 (98%)", "terminal_branch_length": 0.024255, "ecological_and_epidemiological_guild": "East Asian riparian trawling FM insectivore (Yangochiroptera outgroup)" }, { "node_id": "A:T006", "tip_id": "T006", "sector": "A", "species": "Eudiscopus denticulus", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_057092.1", "length_bp": 16597, "gc_pct": 39.34, "sha256_prefix": "dea8624dc4e62bc3", "parent_node": "N05 (95%)", "terminal_branch_length": 0.131312, "ecological_and_epidemiological_guild": "Southeast Asian bamboo-internode disk-footed roosting specialist" }, { "node_id": "A:T007", "tip_id": "T007", "sector": "A", "species": "Kerivoula papillosa", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_061567.1", "length_bp": 16671, "gc_pct": 40.77, "sha256_prefix": "f1bc5d9f09609a24", "parent_node": "N05 (95%)", "terminal_branch_length": 0.163908, "ecological_and_epidemiological_guild": "Sundaic & Indochinese broadband FM rainforest understory gleaner" }, { "node_id": "A:T003", "tip_id": "T003", "sector": "A", "species": "Submyotodon moupinensis", "family": "Vespertilionidae", "suborder": "Yangochiroptera", "accession": "NC_065469.1", "length_bp": 17660, "gc_pct": 39.26, "sha256_prefix": "173918297a58b045", "parent_node": "N06 (95%)", "terminal_branch_length": 0.069521, "ecological_and_epidemiological_guild": "Hengduan Mountains & Sichuan montane forest FM insectivore" }, { "node_id": "B:T011", "tip_id": "T011", "sector": "B", "species": "Balionycteris maculata", "family": "Pteropodidae", "suborder": "Yinpterochiroptera", "accession": "NC_061537.1", "length_bp": 16687, "gc_pct": 41.36, "sha256_prefix": "cda913b64ae78b7c", "parent_node": "N08 (100%)", "terminal_branch_length": 0.16183, "ecological_and_epidemiological_guild": "Sundaic spotted-winged rainforest understory fig specialist" }, { "node_id": "B:T010", "tip_id": "T010", "sector": "B", "species": "Sphaerias blanfordi", "family": "Pteropodidae", "suborder": "Yinpterochiroptera", "accession": "NC_046933.1", "length_bp": 16776, "gc_pct": 40.67, "sha256_prefix": "d8b4085bb10542c4", "parent_node": "N08 (100%)", "terminal_branch_length": 0.115663, "ecological_and_epidemiological_guild": "Himalayan & Hengduan high-elevation montane bamboo-forest fruit bat" }, { "node_id": "B:T012", "tip_id": "T012", "sector": "B", "species": "Pteropus ornatus", "family": "Pteropodidae", "suborder": "Yinpterochiroptera", "accession": "NC_046926.1", "length_bp": 16718, "gc_pct": 41.57, "sha256_prefix": "f06c50b6007530bb", "parent_node": "N09 (76%)", "terminal_branch_length": 0.106109, "ecological_and_epidemiological_guild": "Indo-Pacific non-echolocating canopy flying fox (Henipavirus clade baseline)" }, { "node_id": "B:T009", "tip_id": "T009", "sector": "B", "species": "Rousettus leschenaultii", "family": "Pteropodidae", "suborder": "Yinpterochiroptera", "accession": "NC_046927.1", "length_bp": 16655, "gc_pct": 41.86, "sha256_prefix": "93cac81760a5c926", "parent_node": "N10 (100%)", "terminal_branch_length": 0.117586, "ecological_and_epidemiological_guild": "South & Southeast Asian cave-roosting lingual-clicking frugivore (Filovirus host)" }, { "node_id": "B:T014", "tip_id": "T014", "sector": "B", "species": "Macroderma gigas", "family": "Megadermatidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_057635.1", "length_bp": 16661, "gc_pct": 48.24, "sha256_prefix": "8c521f52642c1c5b", "parent_node": "N11 (100%)", "terminal_branch_length": 0.153467, "ecological_and_epidemiological_guild": "Australasian carnivorous false vampire bat (Megadermatidae clade)" }, { "node_id": "B:T015", "tip_id": "T015", "sector": "B", "species": "Lyroderma lyra", "family": "Megadermatidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "MG586969.1", "length_bp": 17055, "gc_pct": 43.69, "sha256_prefix": "4d164b99ffa81f40", "parent_node": "N11 (100%)", "terminal_branch_length": 0.105805, "ecological_and_epidemiological_guild": "South & Southeast Asian greater false vampire bat (passive-listening vertebrate predator)" }, { "node_id": "B:T013", "tip_id": "T013", "sector": "B", "species": "Rhinopoma cystops", "family": "Rhinopomatidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM147174.1", "length_bp": 16867, "gc_pct": 38.01, "sha256_prefix": "ea4b79f1ec5cd32e", "parent_node": "N12 (55%)", "terminal_branch_length": 0.14197, "ecological_and_epidemiological_guild": "Arid Afro-Arabian & South Asian quasi-CF multiharmonic mouse-tailed bat" }, { "node_id": "B:T016", "tip_id": "T016", "sector": "B", "species": "Megaderma spasma", "family": "Megadermatidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM093799.1", "length_bp": 16750, "gc_pct": 46.59, "sha256_prefix": "efae3e48413d4fe8", "parent_node": "N12 (55%)", "terminal_branch_length": 0.175342, "ecological_and_epidemiological_guild": "Indochinese & Sundaic lesser false vampire bat (short multiharmonic FM gleaner)" }, { "node_id": "C:T017", "tip_id": "T017", "sector": "C", "species": "Doryrhina cyclops", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM093779.1", "length_bp": 17030, "gc_pct": 42.79, "sha256_prefix": "f7b40ec08aadd764", "parent_node": "N27 (100%)", "terminal_branch_length": 0.10204, "ecological_and_epidemiological_guild": "Basal Palaeotropical hipposiderid high-duty-cycle CF-FM outgroup" }, { "node_id": "C:T023", "tip_id": "T023", "sector": "C", "species": "Hipposideros lylei", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_082195.1", "length_bp": 16856, "gc_pct": 42.08, "sha256_prefix": "8def9756e471adab", "parent_node": "N15 (100%)", "terminal_branch_length": 0.013516, "ecological_and_epidemiological_guild": "Shield-faced roundleaf bat (Thailand, Myanmar, Yunnan & Malaysia limestone caves)" }, { "node_id": "C:T022", "tip_id": "T022", "sector": "C", "species": "Hipposideros pratti", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "OR522719.1", "length_bp": 16836, "gc_pct": 41.89, "sha256_prefix": "1d3a7535774e148d", "parent_node": "N15 (100%)", "terminal_branch_length": 0.010777, "ecological_and_epidemiological_guild": "Pratt roundleaf bat (endemic Chinese & Vietnamese subterranean karst cave giant; ~60 kHz CF-FM)" }, { "node_id": "C:T025", "tip_id": "T025", "sector": "C", "species": "Hipposideros diadema", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "PV256475.1", "length_bp": 16912, "gc_pct": 42.22, "sha256_prefix": "a471787b269278e0", "parent_node": "N16 (100%)", "terminal_branch_length": 0.049972, "ecological_and_epidemiological_guild": "Diadem roundleaf bat (Southeast Asia, Sundaland & Wallacea; ~58 kHz CF-FM)" }, { "node_id": "C:T026", "tip_id": "T026", "sector": "C", "species": "Hipposideros larvatus", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061570.1", "length_bp": 16797, "gc_pct": 42.1, "sha256_prefix": "32e6d8f04f0038d4", "parent_node": "N18 (100%)", "terminal_branch_length": 0.022745, "ecological_and_epidemiological_guild": "Intermediate roundleaf bat (Indochina, Hainan & Sunda shelf; ~85–98 kHz CF-FM; betacoronavirus host)" }, { "node_id": "C:T020", "tip_id": "T020", "sector": "C", "species": "Hipposideros armiger", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_018540.1", "length_bp": 16784, "gc_pct": 41.9, "sha256_prefix": "876db3f602be87d6", "parent_node": "N17 (100%)", "terminal_branch_length": 0.004723, "ecological_and_epidemiological_guild": "Great roundleaf bat (Southern China & Himalaya karst caves; ~65 kHz CF-FM beetle predator)" }, { "node_id": "C:T021", "tip_id": "T021", "sector": "C", "species": "Hipposideros armiger (Guangxi)", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "PV931325.1", "length_bp": 16873, "gc_pct": 42.03, "sha256_prefix": "a3aa621cf09e38b5", "parent_node": "N17 (100%)", "terminal_branch_length": 0.005628, "ecological_and_epidemiological_guild": "South China Guangxi karst basin great roundleaf bat lineage" }, { "node_id": "C:T024", "tip_id": "T024", "sector": "C", "species": "Hipposideros pendleburyi", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "MZ196220.1", "length_bp": 16820, "gc_pct": 42.25, "sha256_prefix": "cbabe164bbf57b35", "parent_node": "N19 (100%)", "terminal_branch_length": 0.030532, "ecological_and_epidemiological_guild": "Peninsular Thailand endemic karst-tower roundleaf bat" }, { "node_id": "C:T028", "tip_id": "T028", "sector": "C", "species": "Hipposideros cervinus", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061568.1", "length_bp": 16648, "gc_pct": 43.01, "sha256_prefix": "b1b2c4570c585fb0", "parent_node": "N21 (93%)", "terminal_branch_length": 0.069454, "ecological_and_epidemiological_guild": "Fawn-colored roundleaf bat (Borneo, Sumatra & Peninsular Malaysia rainforest caves; ~120 kHz)" }, { "node_id": "C:T029", "tip_id": "T029", "sector": "C", "species": "Hipposideros caffer", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_088535.1", "length_bp": 17449, "gc_pct": 42.51, "sha256_prefix": "f6d28ea5c99439ea", "parent_node": "N21 (93%)", "terminal_branch_length": 0.106264, "ecological_and_epidemiological_guild": "Sundevall roundleaf bat (~140 kHz ultra-high-frequency CF-FM; Hipposiderovirus reservoir)" }, { "node_id": "C:T027", "tip_id": "T027", "sector": "C", "species": "Hipposideros pomona", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061963.1", "length_bp": 16798, "gc_pct": 43.52, "sha256_prefix": "6582e1fc891d8b4f", "parent_node": "N22 (94%)", "terminal_branch_length": 0.086327, "ecological_and_epidemiological_guild": "Pomona roundleaf bat (South China & Indochina clutter-foraging ~125 kHz CF-FM insectivore)" }, { "node_id": "C:T030", "tip_id": "T030", "sector": "C", "species": "Hipposideros jonesi", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "OZ568725.1", "length_bp": 16901, "gc_pct": 43.85, "sha256_prefix": "3b72d02113576c61", "parent_node": "N22 (94%)", "terminal_branch_length": 0.086699, "ecological_and_epidemiological_guild": "Large-eared boulder-cave roundleaf bat (~48 kHz low-CF hipposiderid)" }, { "node_id": "C:T018", "tip_id": "T018", "sector": "C", "species": "Aselliscus stoliczkanus", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM093171.1", "length_bp": 16750, "gc_pct": 44.84, "sha256_prefix": "5d9fe0bf7a94c17f", "parent_node": "N25 (100%)", "terminal_branch_length": 0.04266, "ecological_and_epidemiological_guild": "South China & Indochina Stoliczka trident bat (~118 kHz CF-FM; sarbecovirus/betacoronavirus host)" }, { "node_id": "C:T019", "tip_id": "T019", "sector": "C", "species": "Aselliscus dongbacanus", "family": "Hipposideridae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "PX961365.1", "length_bp": 16712, "gc_pct": 43.98, "sha256_prefix": "f4186cc04b03d01b", "parent_node": "N25 (100%)", "terminal_branch_length": 0.045943, "ecological_and_epidemiological_guild": "Northern Vietnam Dong Bac karst endemic trident leaf-nosed bat" }, { "node_id": "D:T034", "tip_id": "T034", "sector": "D", "species": "Rhinolophus formosae", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_011304.1", "length_bp": 16915, "gc_pct": 41.14, "sha256_prefix": "33ea55440d51af0c", "parent_node": "N31 (100%)", "terminal_branch_length": 0.047329, "ecological_and_epidemiological_guild": "Formosan woolly horseshoe bat (Taiwan island endemic montane forest specialist; ~42 kHz)" }, { "node_id": "D:T032", "tip_id": "T032", "sector": "D", "species": "Rhinolophus luctus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_018539.1", "length_bp": 16775, "gc_pct": 41.39, "sha256_prefix": "93a5528c18b0e4d6", "parent_node": "N28 (100%)", "terminal_branch_length": 0.00337, "ecological_and_epidemiological_guild": "Great woolly horseshoe bat (largest Asian Rhinolophus; ~32–42 kHz low-frequency CF-FM perch hunter)" }, { "node_id": "D:T033", "tip_id": "T033", "sector": "D", "species": "Rhinolophus perniger lanosus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM093170.1", "length_bp": 16937, "gc_pct": 41.47, "sha256_prefix": "01700f0bccfcc3ee", "parent_node": "N28 (100%)", "terminal_branch_length": 0.002976, "ecological_and_epidemiological_guild": "Northern woolly horseshoe bat (South China & Himalayan subtropics; ~39 kHz CF-FM)" }, { "node_id": "D:T031", "tip_id": "T031", "sector": "D", "species": "Rhinolophus trifoliatus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM093172.1", "length_bp": 16777, "gc_pct": 42.14, "sha256_prefix": "03b65686f9fca891", "parent_node": "N29 (100%)", "terminal_branch_length": 0.026468, "ecological_and_epidemiological_guild": "Trefoil horseshoe bat (Sundaic rainforest solitary foliage-roosting ~50 kHz CF-FM insectivore)" }, { "node_id": "D:T035", "tip_id": "T035", "sector": "D", "species": "Rhinolophus francisi", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_081978.1", "length_bp": 16795, "gc_pct": 42.57, "sha256_prefix": "9e7a383875ca1e9a", "parent_node": "N30 (100%)", "terminal_branch_length": 0.060652, "ecological_and_epidemiological_guild": "Francis woolly horseshoe bat (Thailand & Borneo karst-forest cryptic trifoliatus-group lineage)" }, { "node_id": "D:T037", "tip_id": "T037", "sector": "D", "species": "Rhinolophus marshalli", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061979.1", "length_bp": 16844, "gc_pct": 43.42, "sha256_prefix": "df989ea69a28cd12", "parent_node": "N34 (100%)", "terminal_branch_length": 0.01817, "ecological_and_epidemiological_guild": "Marshall horseshoe bat (Indochina & Guangxi limestone karst; ~42 kHz low-frequency CF-FM)" }, { "node_id": "D:T040", "tip_id": "T040", "sector": "D", "species": "Rhinolophus macrotis", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_026460.1", "length_bp": 16848, "gc_pct": 43.48, "sha256_prefix": "669698d24b3e7038", "parent_node": "N33 (94%)", "terminal_branch_length": 0.021277, "ecological_and_epidemiological_guild": "Big-eared horseshoe bat (Himalaya to South China & Sumatra; harmonic-switching 48–85 kHz CF-FM)" }, { "node_id": "D:T038", "tip_id": "T038", "sector": "D", "species": "Rhinolophus rex", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_028536.1", "length_bp": 16845, "gc_pct": 43.69, "sha256_prefix": "794c01e848b54412", "parent_node": "N32 (100%)", "terminal_branch_length": 0.001922, "ecological_and_epidemiological_guild": "King horseshoe bat (Southwest China Guizhou/Sichuan/Yunnan endemic; ~26 kHz ultra-low CF-FM)" }, { "node_id": "D:T039", "tip_id": "T039", "sector": "D", "species": "Rhinolophus rex paradoxolophus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061980.1", "length_bp": 16811, "gc_pct": 43.57, "sha256_prefix": "d74d7ac1c4f3cd1f", "parent_node": "N32 (100%)", "terminal_branch_length": 0.002271, "ecological_and_epidemiological_guild": "Bourret horseshoe bat (Sino-Vietnamese borderland karst endemic; ~24–28 kHz CF-FM)" }, { "node_id": "D:T036", "tip_id": "T036", "sector": "D", "species": "Rhinolophus philippinensis", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061262.1", "length_bp": 16817, "gc_pct": 42.9, "sha256_prefix": "fc7dc6c747d08474", "parent_node": "N35 (99%)", "terminal_branch_length": 0.039582, "ecological_and_epidemiological_guild": "Large-eared horseshoe bat (Wallacea/Philippines harmonic-hopping 27/54 kHz acoustic polymorph)" }, { "node_id": "E:T045", "tip_id": "T045", "sector": "E", "species": "Rhinolophus pearsonii", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "PQ427794.1", "length_bp": 16900, "gc_pct": 44.1, "sha256_prefix": "5a5ac567eb2c14b0", "parent_node": "N38 (100%)", "terminal_branch_length": 0.022973, "ecological_and_epidemiological_guild": "Pearson horseshoe bat (South China & Indochina montane bamboo/karst; ~65 kHz CF-FM; PopSet 2)" }, { "node_id": "E:T047", "tip_id": "T047", "sector": "E", "species": "Rhinolophus yunanensis (Southwest)", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "KY808508.1", "length_bp": 16864, "gc_pct": 44.46, "sha256_prefix": "a4fa4fe583c41365", "parent_node": "N37 (100%)", "terminal_branch_length": 0.0005, "ecological_and_epidemiological_guild": "Gaoligongshan & Hengduan sky-island Dobson horseshoe bat lineage" }, { "node_id": "E:T046", "tip_id": "T046", "sector": "E", "species": "Rhinolophus yunanensis", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_036419.1", "length_bp": 16864, "gc_pct": 44.46, "sha256_prefix": "a4fa4fe583c41365", "parent_node": "N37 (100%)", "terminal_branch_length": 0.0005, "ecological_and_epidemiological_guild": "Dobson horseshoe bat (Yunnan, Myanmar & Thailand montane karst; ~52–58 kHz CF-FM)" }, { "node_id": "E:T042", "tip_id": "T042", "sector": "E", "species": "Rhinolophus siamensis", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_061978.1", "length_bp": 16865, "gc_pct": 43.68, "sha256_prefix": "9145dd4ba7e2bc59", "parent_node": "N39 (100%)", "terminal_branch_length": 0.001603, "ecological_and_epidemiological_guild": "Thai small-eared horseshoe bat (Indochina & Guangdong karst; ~68–74 kHz CF-FM; sarbecovirus host)" }, { "node_id": "E:T044", "tip_id": "T044", "sector": "E", "species": "Rhinolophus cf. siamensis (Hunan)", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "MK987177.1", "length_bp": 16822, "gc_pct": 43.76, "sha256_prefix": "04639f73254723ae", "parent_node": "N39 (100%)", "terminal_branch_length": 0.0005, "ecological_and_epidemiological_guild": "Central China Hunan Nanling Corridor cryptic siamensis-group lineage" }, { "node_id": "E:T041", "tip_id": "T041", "sector": "E", "species": "Rhinolophus cf. macrotis (Guizhou)", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "MK987176.1", "length_bp": 16897, "gc_pct": 43.59, "sha256_prefix": "038d6efe1ce5ee2c", "parent_node": "N40 (100%)", "terminal_branch_length": 0.006042, "ecological_and_epidemiological_guild": "Southwest China cryptic big-eared horseshoe bat acoustic lineage (~56 kHz CF-FM)" }, { "node_id": "E:T043", "tip_id": "T043", "sector": "E", "species": "Rhinolophus siamensis (Vietnam)", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "MK987183.1", "length_bp": 16846, "gc_pct": 43.52, "sha256_prefix": "3d05df8b40bd7050", "parent_node": "N41 (100%)", "terminal_branch_length": 0.008658, "ecological_and_epidemiological_guild": "Annamite Range & Tonkin karst Thai horseshoe bat lineage" }, { "node_id": "E:T048", "tip_id": "T048", "sector": "E", "species": "Rhinolophus yonghoiseni", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM093778.1", "length_bp": 16888, "gc_pct": 41.24, "sha256_prefix": "58dc7c618160aa9e", "parent_node": "N43 (100%)", "terminal_branch_length": 0.093451, "ecological_and_epidemiological_guild": "Yong Hoi Sen horseshoe bat (Peninsular Malaysia & Borneo canopy/cave specialist)" }, { "node_id": "F:T050", "tip_id": "T050", "sector": "F", "species": "Rhinolophus blasii", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM171913.1", "length_bp": 16851, "gc_pct": 43.31, "sha256_prefix": "3a09e6e97082f083", "parent_node": "N45 (100%)", "terminal_branch_length": 0.038663, "ecological_and_epidemiological_guild": "Blasius horseshoe bat (Southwest Asia & Mediterranean karst; ~94 kHz CF-FM; BtKY72 clade)" }, { "node_id": "F:T052", "tip_id": "T052", "sector": "F", "species": "Rhinolophus darlingi", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM171788.1", "length_bp": 16863, "gc_pct": 43.09, "sha256_prefix": "5b0f93f5007cb6a7", "parent_node": "N44 (100%)", "terminal_branch_length": 0.045384, "ecological_and_epidemiological_guild": "Darling horseshoe bat (Palaeotropical savannah boulder-cave ~86 kHz CF-FM outgroup)" }, { "node_id": "F:T051", "tip_id": "T051", "sector": "F", "species": "Rhinolophus clivosus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM138582.1", "length_bp": 16148, "gc_pct": 43.06, "sha256_prefix": "43fcbc44a810c7ec", "parent_node": "N44 (100%)", "terminal_branch_length": 0.032364, "ecological_and_epidemiological_guild": "Geoffroy horseshoe bat (Arabian Peninsula & Afro-Asian arid corridor; ~84–92 kHz CF-FM)" }, { "node_id": "F:T049", "tip_id": "T049", "sector": "F", "species": "Rhinolophus hipposideros", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "OZ077446.1", "length_bp": 16854, "gc_pct": 43.57, "sha256_prefix": "b1f7411763f3db6c", "parent_node": "N46 (97%)", "terminal_branch_length": 0.064417, "ecological_and_epidemiological_guild": "Lesser horseshoe bat (Western & Central Asian mountain caves; ~110 kHz CF-FM; Khosta-2 host)" }, { "node_id": "F:T056", "tip_id": "T056", "sector": "F", "species": "Rhinolophus pumilus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_005434.1", "length_bp": 16869, "gc_pct": 42.6, "sha256_prefix": "ced5a58517e9ec3e", "parent_node": "N49 (100%)", "terminal_branch_length": 0.01316, "ecological_and_epidemiological_guild": "Okinawa least horseshoe bat (Ryukyu Archipelago island endemic; ~108 kHz CF-FM)" }, { "node_id": "F:T054", "tip_id": "T054", "sector": "F", "species": "Rhinolophus pusillus (Guizhou)", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "MK987182.1", "length_bp": 16858, "gc_pct": 42.72, "sha256_prefix": "f91194d8d6cef761", "parent_node": "N47 (100%)", "terminal_branch_length": 0.00232, "ecological_and_epidemiological_guild": "Yungui Plateau Guizhou karst cave least horseshoe bat lineage" }, { "node_id": "F:T053", "tip_id": "T053", "sector": "F", "species": "Rhinolophus pusillus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_046021.1", "length_bp": 16833, "gc_pct": 42.79, "sha256_prefix": "8e30c528cfc2d9c1", "parent_node": "N47 (100%)", "terminal_branch_length": 0.005469, "ecological_and_epidemiological_guild": "Least horseshoe bat (South China, Thailand & Sundaland; ~102–112 kHz CF-FM; PrC31 sarbecovirus host; PopSet 1)" }, { "node_id": "F:T055", "tip_id": "T055", "sector": "F", "species": "Rhinolophus monoceros", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_005433.1", "length_bp": 16851, "gc_pct": 42.76, "sha256_prefix": "0b532c28199a5032", "parent_node": "N48 (100%)", "terminal_branch_length": 0.007576, "ecological_and_epidemiological_guild": "Formosan lesser horseshoe bat (Taiwan island endemic; ~115 kHz ultra-high CF-FM insectivore)" }, { "node_id": "G:T061", "tip_id": "T061", "sector": "G", "species": "Rhinolophus ferrumequinum tragatus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "KT783534.1", "length_bp": 16760, "gc_pct": 42.64, "sha256_prefix": "fe4c92ca78bfc69a", "parent_node": "N53 (100%)", "terminal_branch_length": 0.012531, "ecological_and_epidemiological_guild": "Southwest China Yunnan/Sichuan greater horseshoe bat (~69 kHz CF-FM; Rf1 sarbecovirus host)" }, { "node_id": "G:T063", "tip_id": "T063", "sector": "G", "species": "Rhinolophus ferrumequinum quelpartis", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_020326.1", "length_bp": 16870, "gc_pct": 42.8, "sha256_prefix": "17d778ebcb987098", "parent_node": "N51 (95%)", "terminal_branch_length": 0.0005, "ecological_and_epidemiological_guild": "Jeju volcanic lava-tube & East China Sea insular greater horseshoe bat" }, { "node_id": "G:T064", "tip_id": "T064", "sector": "G", "species": "Rhinolophus ferrumequinum nippon", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "KT779432.1", "length_bp": 16804, "gc_pct": 42.72, "sha256_prefix": "89839b0c460d90a5", "parent_node": "N51 (95%)", "terminal_branch_length": 0.0005, "ecological_and_epidemiological_guild": "Japanese Archipelago greater horseshoe bat (~65 kHz CF-FM; temperate hibernator; PopSet 3)" }, { "node_id": "G:T062", "tip_id": "T062", "sector": "G", "species": "Rhinolophus ferrumequinum korai", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_016191.1", "length_bp": 16839, "gc_pct": 42.77, "sha256_prefix": "6c966598d57e39d5", "parent_node": "N52 (100%)", "terminal_branch_length": 0.0005, "ecological_and_epidemiological_guild": "Northeast China & Korean Peninsula greater horseshoe bat (~68 kHz CF-FM)" }, { "node_id": "G:T059", "tip_id": "T059", "sector": "G", "species": "Rhinolophus sinicus sinicus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "KR106992.1", "length_bp": 16868, "gc_pct": 43.68, "sha256_prefix": "eb5e0a45d7b784ff", "parent_node": "N54 (100%)", "terminal_branch_length": 0.018566, "ecological_and_epidemiological_guild": "Southwest China Guizhou/Yunnan rufous horseshoe bat karst cave deme" }, { "node_id": "G:T057", "tip_id": "T057", "sector": "G", "species": "Rhinolophus thomasi", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_034306.1", "length_bp": 16899, "gc_pct": 43.39, "sha256_prefix": "95baa53f3c7c72d3", "parent_node": "N54 (100%)", "terminal_branch_length": 0.028612, "ecological_and_epidemiological_guild": "Thomas horseshoe bat (Yunnan, Vietnam, Laos & Thailand limestone karst; ~78 kHz CF-FM; sarbecovirus host)" }, { "node_id": "G:T060", "tip_id": "T060", "sector": "G", "species": "Rhinolophus affinis", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "NC_053269.1", "length_bp": 16886, "gc_pct": 43.88, "sha256_prefix": "b217d302faa04dda", "parent_node": "N55 (94%)", "terminal_branch_length": 0.053042, "ecological_and_epidemiological_guild": "Intermediate horseshoe bat (primary SARS-CoV-2-related RaTG13 reservoir in Yunnan/Indochina; ~74–88 kHz)" }, { "node_id": "G:T058", "tip_id": "T058", "sector": "G", "species": "Rhinolophus sinicus", "family": "Rhinolophidae", "suborder": "Yinpterochiroptera: Rhinolophoidea", "accession": "CM174560.1", "length_bp": 16914, "gc_pct": 43.67, "sha256_prefix": "1f07ffa3c8d2bc30", "parent_node": "N57 (100%)", "terminal_branch_length": 0.152323, "ecological_and_epidemiological_guild": "Chinese rufous horseshoe bat (primary SARS-CoV-1 / WIV1 / RsSHC014 reservoir across South China; ~82–86 kHz)" } ], "nuclear_40_cds_manifest": [ { "rec_id": "NUC-01", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Rhinolophus ferrumequinum", "accession": "KJ645609.1", "length_bp": 2226, "cds_window_bp": 1500, "gc_pct": 45.46, "sha256_prefix": "86124992d96ad486" }, { "rec_id": "NUC-02", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Myotis ricketti", "accession": "EU914924.1", "length_bp": 2229, "cds_window_bp": 1500, "gc_pct": 46.52, "sha256_prefix": "62b8aa9910e28a54" }, { "rec_id": "NUC-03", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Megaderma lyra", "accession": "GU219835.1", "length_bp": 2226, "cds_window_bp": 1500, "gc_pct": 44.03, "sha256_prefix": "e705718859055c8f" }, { "rec_id": "NUC-04", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Eonycteris spelaea", "accession": "GU219834.1", "length_bp": 2223, "cds_window_bp": 1500, "gc_pct": 45.75, "sha256_prefix": "d3044873f7df053b" }, { "rec_id": "NUC-05", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Hipposideros pratti", "accession": "EU914937.1", "length_bp": 2226, "cds_window_bp": 1500, "gc_pct": 44.97, "sha256_prefix": "1acbbac0a826dcdd" }, { "rec_id": "NUC-06", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Rhinolophus pusillus", "accession": "EU914936.1", "length_bp": 2226, "cds_window_bp": 1500, "gc_pct": 45.78, "sha256_prefix": "7cb4f49e51dc4a46" }, { "rec_id": "NUC-07", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Aselliscus stoliczkanus", "accession": "EU914935.1", "length_bp": 2226, "cds_window_bp": 1500, "gc_pct": 45.55, "sha256_prefix": "50904f63ca761315" }, { "rec_id": "NUC-08", "family_key": "SLC26A5_Prestin", "family_label": "SLC26A5 (Prestin) Outer Hair Cell Electromotility Motor & TMC1 Mechanotransduction Complex", "functional_note": "High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60–125 kHz) in Rhinolophidae & Hipposideridae", "species": "Hipposideros larvatus", "accession": "EU914934.1", "length_bp": 2226, "cds_window_bp": 1500, "gc_pct": 44.88, "sha256_prefix": "48a0f7840acdc537" }, { "rec_id": "NUC-09", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24–42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus", "species": "Rhinolophus simulator", "accession": "LC921174.1", "length_bp": 2418, "cds_window_bp": 1500, "gc_pct": 44.42, "sha256_prefix": "08ae70c4c5677af8" }, { "rec_id": "NUC-10", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24–42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus", "species": "Rhinolophus blasii", "accession": "LC921170.1", "length_bp": 2418, "cds_window_bp": 1500, "gc_pct": 44.83, "sha256_prefix": "638a4feee7886bdc" }, { "rec_id": "NUC-11", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24–42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus", "species": "Hipposideros armiger", "accession": "XM_019667409.1", "length_bp": 2893, "cds_window_bp": 1416, "gc_pct": 45.9, "sha256_prefix": "eae6ccc4d158df3b" }, { "rec_id": "NUC-12", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24–42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus", "species": "Rhinolophus acuminatus", "accession": "PZ112778.1", "length_bp": 2415, "cds_window_bp": 1500, "gc_pct": 45.76, "sha256_prefix": "00bf1d7ec5097b3d" }, { "rec_id": "NUC-13", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24–42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus", "species": "Myotis nattereri", "accession": "XM_081081848.1", "length_bp": 2792, "cds_window_bp": 1500, "gc_pct": 42.91, "sha256_prefix": "3f63be771e4c1ba2" }, { "rec_id": "NUC-14", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24–42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus", "species": "Rhinolophus marshalli", "accession": "PX315811.1", "length_bp": 2418, "cds_window_bp": 1500, "gc_pct": 45.45, "sha256_prefix": "a3168452982d1787" }, { "rec_id": "NUC-15", "family_key": "ACE2_Sarbeco", "family_label": "ACE2 Angiotensin-Converting Enzyme 2 Viral Spike Receptor-Binding Domain Interface", "functional_note": "N-terminal alpha-1/alpha-2 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