[ { "study": "Howell 1996", "source": "howell-1996", "region": "crAdjacent", "length": 1194, "window": "howell1996", "kind": "Detected", "counted": "New germline mutations, both heteroplasmic (HVR-II nt 152 and 195), plus one somatic", "trans": "88", "peds": "1 LHON pedigree, 45 members", "notes": "Opened the pedigree-rate literature: the “ten times faster” claim began with two events in one disease pedigree. The primary sequenced nt 16024–16569 and 1–648 (about 1,194 bp), the control region plus 72 adjoining coding bases. Howell 2003 restates 2/88; Sigurðardóttir 2000 says 2/81.", "block": "pedigree", "mu": 0.022727272727272728, "count": "2 / 88", "index": 0, "annualPerSite": 7.613826709304097e-7, "sapiensYears": 16993.19572429045, "combinedBaselineYears": 29492.658730158728, "anchor": { "sapiensPerSite": 0.012938324748203483, "combinedPerSite": 0.02245519927680732, "sapiensDepth": 15.448359749354958, "combinedDepth": 26.811507936507937, "positions": 1194, "usable": 1171, "profileScale": 1.136527828971618, "panelRootDepth": 13.592592592592593, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.036773373038029654, "d19Differences": 43.907407407407405 }, "d19PairYears": [ 117649.07407407407, 132649.07407407407 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Bendall 1996", "source": "howell-2003", "via": "as tabulated by Howell 2003", "region": "hvr1", "length": 360, "window": "hvr1", "kind": "Detected", "counted": "Newly arising substitutions, heteroplasmic or homoplasmic, as Howell pooled them", "trans": "360", "peds": "Not given in Howell’s table", "notes": "Howell 2003 Table 2: 4/360, divergence rate 0.99 (99.5% interval 0.14–3.35) per site per Myr, computed over Howell’s 1,122-bp convention at 20-year generations. HVR-1 only. The exact window was not checked; the age uses the 360-bp HVR-I window.", "block": "pedigree", "mu": 0.011111111111111112, "count": "4 / 360", "index": 1, "annualPerSite": 0.000001234567901234568, "sapiensYears": 17710.89200147438, "combinedBaselineYears": 32772.32142857143, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 121020.83333333333, 136020.83333333334 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Mumm 1997", "source": "howell-2003", "via": "as tabulated by Howell 2003", "region": "hvr1", "length": 360, "window": "hvr1", "kind": "Detected", "counted": "Newly arising substitutions, heteroplasmic or homoplasmic, as Howell pooled them", "trans": "59", "peds": "Not given in Howell’s table", "notes": "Howell 2003 Table 2: 1/59, divergence rate 1.51 (99.5% interval 0.00–11.71) per site per Myr, computed over Howell’s 1,122-bp convention at 20-year generations. HVR-1 only; one event. The exact window was not checked; the age uses the 360-bp HVR-I window.", "block": "pedigree", "mu": 0.01694915254237288, "count": "1 / 59", "index": 2, "annualPerSite": 0.0000018832391713747646, "sapiensYears": 11610.473645410982, "combinedBaselineYears": 21484.07738095238, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 111541.43518518518, 126541.43518518518 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Parsons 1997", "source": "parsons-1997", "region": "hvr12", "length": 610, "approx": true, "kind": "Detected", "counted": "Substitutions between close relatives; heteroplasmic and homoplasmic both counted, per Howell 2003", "trans": "327", "peds": "134 maternal lineages of close relatives", "notes": "The load-bearing young-earth citation. Ten differences across about 610 bp of HVR-I and HVR-II, not the whole molecule. The ~610 bp and the 20-year generation are reverse-engineered from the published 2.5/site/Myr; exact endpoints are unverified, so the age uses a broad HVR-I+II profile. The abstract gives the count. Howell’s Table 2 books this laboratory’s data as Parsons and Holland 1998 (10/306) plus the Forensic Science Service set (1/32): 11/338 together, rows below.", "block": "pedigree", "mu": 0.03058103975535168, "count": "10 / 327", "index": 3, "annualPerSite": 0.000002005314082318143, "sapiensYears": 10216.052321498286, "combinedBaselineYears": 14402.419695688926, "anchor": { "sapiensPerSite": 0.02048639358599947, "combinedPerSite": 0.02888137503522119, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 676, "usable": 653, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04862480824019286, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 105623.98812458909, 120623.98812458909 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Parsons 1997: Forensic Science Service set", "source": "howell-2003", "via": "as tabulated by Howell 2003", "region": "hvr12", "length": 676, "window": "hvr12", "kind": "Detected", "counted": "Newly arising substitutions, heteroplasmic or homoplasmic, as Howell pooled them", "trans": "32", "peds": "Not given in Howell’s table", "notes": "Howell 2003 Table 2: 1/32, divergence rate 2.76 (99.5% interval 0.01–20.43) per site per Myr, computed over Howell’s 1,122-bp convention at 20-year generations. HVR-1 and HVR-2. Howell’s footnote: “the analyses at the U.K. Forensic Science Service that were reported in Parsons et al. (1997).” One event. The age uses the 676-bp HVR-I+II window.", "block": "pedigree", "mu": 0.03125, "count": "1 / 32", "index": 4, "annualPerSite": 0.000001849112426035503, "sapiensYears": 11079.041651308513, "combinedBaselineYears": 15619.04761904762, "anchor": { "sapiensPerSite": 0.02048639358599947, "combinedPerSite": 0.02888137503522119, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 676, "usable": 653, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04862480824019286, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 106648.14814814815, 121648.14814814815 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Soodyall 1997", "source": "howell-2003", "via": "as tabulated by Howell 2003", "region": "hvr12", "length": 676, "window": "hvr12", "zeroN": 108, "kind": "Detected", "counted": "Newly arising substitutions, heteroplasmic or homoplasmic, as Howell pooled them", "trans": "108", "peds": "Not given in Howell’s table", "notes": "Howell 2003 Table 2: 0/108, divergence rate 0.00 (99.5% interval 0.00–4.79) per site per Myr, computed over Howell’s 1,122-bp convention at 20-year generations. HVR-1 and HVR-2. The Tristan da Cunha study, founded by a handful of women in the nineteenth century; Gibbons 1998 reports the same zero in 108. A zero count does not establish a zero rate. The age uses the 676-bp HVR-I+II window.", "block": "pedigree", "mu": 0, "count": "0 / 108", "index": 5, "annualPerSite": 0.0000016413172658086737, "sapiensYears": 12481.677986800356, "combinedBaselineYears": 17596.46086522547, "anchor": { "sapiensPerSite": 0.02048639358599947, "combinedPerSite": 0.02888137503522119, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 676, "usable": 653, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04862480824019286, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 108312.73890585545, 123312.73890585545 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": 0.027738261792166582 }, { "study": "Parsons and Holland 1998", "source": "howell-2003", "via": "as tabulated by Howell 2003", "region": "hvr12", "length": 676, "window": "hvr12", "kind": "Detected", "counted": "Newly arising substitutions, heteroplasmic or homoplasmic, as Howell pooled them", "trans": "306", "peds": "Not given in Howell’s table", "notes": "Howell 2003 Table 2: 10/306, divergence rate 2.91 (99.5% interval 0.99–6.44) per site per Myr, computed over Howell’s 1,122-bp convention at 20-year generations. HVR-1 and HVR-2; the same laboratory as Parsons 1997. The exact window was not checked; the age uses the 676-bp HVR-I+II window.", "block": "pedigree", "mu": 0.032679738562091505, "count": "10 / 306", "index": 6, "annualPerSite": 0.00000193371234095216, "sapiensYears": 10594.333579063765, "combinedBaselineYears": 14935.714285714286, "anchor": { "sapiensPerSite": 0.02048639358599947, "combinedPerSite": 0.02888137503522119, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 676, "usable": 653, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04862480824019286, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 106072.91666666667, 121072.91666666667 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Cavelier 2000: CR", "source": "cavelier-2000", "region": "control", "length": 1122, "zeroN": 292, "kind": "Homoplasmic", "counted": "Homoplasmic substitutions only", "trans": "292", "peds": "33 maternal lineages, 194 people", "notes": "No homoplasmic substitutions detected; a zero count does not establish a zero mutation rate. Only length heteroplasmy, at three poly-C sites (65, 309, 16189). The zero result routinely left out of compilations on both sides. The limit assumes independent detectable events. Howell 2003 books the study as HVR-1 and HVR-2, 0/292.", "block": "pedigree", "mu": 0, "count": "0 / 292", "index": 7, "annualPerSite": 3.6575248132664164e-7, "sapiensYears": 37541.987217306305, "combinedBaselineYears": 64115.87898962703, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 145733.25636713702, 160733.25636713702 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": 0.010259357101212297 }, { "study": "Cavelier 2000: coding sample", "source": "cavelier-2000", "region": "coding", "length": 500, "window": "cavelier", "zeroN": 292, "kind": "Homoplasmic", "counted": "Homoplasmic substitutions only", "trans": "Same 292", "peds": "Same", "notes": "5550–6050 is 501 inclusive positions; the paper calls it 500 bp. The zero-count limit uses that window.", "block": "pedigree", "mu": 0, "count": "0 / 292 · positions 5,550–6,050", "index": 8, "annualPerSite": 8.207485680969837e-7, "sapiensYears": 1228.4279708552178, "combinedBaselineYears": 6794.158630900454, "anchor": { "sapiensPerSite": 0.0010082304980897033, "combinedPerSite": 0.005576295967735311, "sapiensDepth": 0.5051234795429413, "combinedDepth": 2.793724279835391, "positions": 501, "usable": 501, "profileScale": 1.136527828971618, "panelRootDepth": 0.4444444444444444, "basalPair": "human-neanderthal", "d19PerSite": 0.008723294152435869, "d19Differences": 4.37037037037037 }, "d19PairYears": [ 98814.23050341837, 113814.23050341837 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": 0.010259357101212297 }, { "study": "Sigurðardóttir 2000", "source": "sigurdardottir-2000", "region": "hvr12", "length": 673, "window": "sigurdardottir", "kind": "Homoplasmic", "counted": "Base substitutions between relatives: the three homoplasmic changes, per Howell 2003", "trans": "705", "peds": "26 large Icelandic pedigrees, 272 people", "notes": "Largest pre-genomic study, about 8 times slower than Parsons. The published HVR mask is 673 bp; the fully sequenced amplicon is nt 16012–394 (~952 bp), and inclusive endpoint arithmetic does not reproduce 673. Madrigal’s Table 3 pairs Howell’s count with Sigurðardóttir’s rate.", "block": "pedigree", "mu": 0.00425531914893617, "count": "3 / 705", "index": 9, "annualPerSite": 2.52916442730233e-7, "sapiensYears": 81120.64038716194, "combinedBaselineYears": 114362.52204585538, "anchor": { "sapiensPerSite": 0.02051674379871947, "combinedPerSite": 0.028924162257495594, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 675, "usable": 652, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.048696844993141294, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 189770.61899862828, 204770.61899862828 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Sigurðardóttir 2000: rescored", "source": "sigurdardottir-2000", "region": "hvr12", "length": 673, "window": "sigurdardottir", "kind": "Detected; rescored", "counted": "Homoplasmic and heteroplasmic changes, Howell’s rescoring", "trans": "Same 705", "peds": "Same", "notes": "Howell’s five-event rescoring of the same data, using the study’s published 673-bp HVR mask; not an independent study.", "block": "pedigree", "mu": 0.0070921985815602835, "count": "5 / 705", "index": 10, "annualPerSite": 4.2152740455038835e-7, "sapiensYears": 48672.38423229716, "combinedBaselineYears": 68617.51322751323, "anchor": { "sapiensPerSite": 0.02051674379871947, "combinedPerSite": 0.028924162257495594, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 675, "usable": 652, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.048696844993141294, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 151262.37139917695, 166262.37139917695 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Heyer 2001", "source": "heyer-2001", "region": "hvr12", "length": 673, "window": "heyer", "kind": "Pedigree differences", "counted": "Substitutions between relatives; pooled with earlier studies, 18 / 1,729 = 0.0104", "trans": "508", "peds": "Deep-rooting French-Canadian pedigrees (Quebec)", "notes": "HVR-I 16024–16383 and HVR-II 58–370. Only 12 of the pooled 18 mutations sat at independent sites; three positions mutated twice. Fitted model: 40 fast sites (CI 27–54) at 274 per site per million generations. The pooled count overlaps other studies.", "block": "pedigree", "mu": 0.007874015748031496, "count": "4 / 508", "index": 11, "annualPerSite": 4.679949924535807e-7, "sapiensYears": 43969.94655363067, "combinedBaselineYears": 61988.09523809525, "anchor": { "sapiensPerSite": 0.02057771480555073, "combinedPerSite": 0.029010118163164227, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 673, "usable": 650, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04884156072863354, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 145681.71296296298, 160681.71296296298 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Forster 2002: low radiation", "source": "forster-2002", "region": "control", "length": 579, "window": "forster", "kind": "Detected heteroplasmy", "counted": "New heteroplasmies only; none homoplasmic at either dose", "trans": "200", "peds": "248 Kerala families, 988 people, across 2 to 4 generations (795 transmissions in both groups)", "notes": "16093–16390 and 35–315: parts of both HVRs plus adjoining bases. Kerala natural radioactivity, low-dose group.", "block": "pedigree", "mu": 0.005, "count": "1 / 200", "index": 12, "annualPerSite": 3.454231433506045e-7, "sapiensYears": 68191.66973829709, "combinedBaselineYears": 86488.09523809522, "anchor": { "sapiensPerSite": 0.023554980911328873, "combinedPerSite": 0.029874989719549303, "sapiensDepth": 13.638333947659417, "combinedDepth": 17.297619047619047, "positions": 579, "usable": 556, "profileScale": 1.136527828971618, "panelRootDepth": 12, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.05133371713682594, "d19Differences": 29.72222222222222 }, "d19PairYears": [ 167805.55555555556, 182805.55555555556 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Forster 2002: high radiation", "source": "forster-2002", "region": "control", "length": 579, "window": "forster", "kind": "Detected heteroplasmy", "counted": "New heteroplasmies only; none homoplasmic", "trans": "595", "peds": "Same families", "notes": "A 7.4-fold rise in heteroplasmies appearing, and zero fixations. The radiation-hit positions “mutate, on average, 12 times faster during evolution.” The exposure comparison is not a universal clock.", "block": "pedigree", "mu": 0.03697478991596639, "count": "22 / 595", "index": 13, "annualPerSite": 0.0000025543896315002685, "sapiensYears": 9221.37352142881, "combinedBaselineYears": 11695.549242424242, "anchor": { "sapiensPerSite": 0.023554980911328873, "combinedPerSite": 0.029874989719549303, "sapiensDepth": 13.638333947659417, "combinedDepth": 17.297619047619047, "positions": 579, "usable": 556, "profileScale": 1.136527828971618, "panelRootDepth": 12, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.05133371713682594, "d19Differences": 29.72222222222222 }, "d19PairYears": [ 103548.13762626263, 118548.13762626263 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Howell 2003: own pedigrees", "source": "howell-2003", "via": "as tabulated by Howell 2003", "region": "control", "length": 1122, "kind": "Detected", "counted": "Newly arising substitutions, heteroplasmic or homoplasmic, as Howell pooled them", "trans": "185", "peds": "Not given in Howell’s table", "notes": "Howell 2003 Table 2: 1/185, divergence rate 0.48 (99.5% interval 0.00–3.87) per site per Myr, computed over Howell’s 1,122-bp convention at 20-year generations. Control region nt 16024–16569 and 1–576 in five LHON families. One event; included in the pooled row below.", "block": "pedigree", "mu": 0.005405405405405406, "count": "1 / 185", "index": 14, "annualPerSite": 1.9270607505901627e-7, "sapiensYears": 71253.98083302616, "combinedBaselineYears": 121690.7242063492, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 192637.73148148146, 207637.73148148146 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Howell 2003: pooled CR", "source": "howell-2003", "region": "control", "length": 1122, "kind": "Detected; pooled", "counted": "Everything newly arising, heteroplasmic or homoplasmic", "trans": "2,633", "peds": "5 LHON pedigrees (185 transmissions) plus nine earlier data sets", "notes": "The canonical pooled rate, published as a divergence rate of 0.95/site/Myr (twice the mutation rate; 99.5% interval 0.53–1.57) at 20-year generations, treating every study as 1,122 bp. Multiplying it across 16,569 sites is Carter’s error. Regions and assays differ between the pooled studies. Table 2’s ten study rows sum to 2,643 transmissions, not the printed 2,633.", "block": "pedigree", "mu": 0.010634257500949488, "count": "28 / 2,633 · pooled", "index": 15, "annualPerSite": 3.7911791447235255e-7, "sapiensYears": 36218.480990995726, "combinedBaselineYears": 61855.5360685941, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 143891.82374338625, 158891.82374338625 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Howell 2003: coding counts", "source": "howell-2003", "region": "coding", "length": 0, "kind": "Pedigree events", "counted": "Coding-region events in partially sequenced LHON pedigrees", "trans": "462", "peds": "LHON pedigrees and Cavelier’s families", "noAge": true, "notes": "Mixed coverage: earlier LHON fragments, later coding sequences, Cavelier’s 500 bp. The 6,773 bp in Howell 1996 is not the common mask of all 462 transmissions. The raw count has no matched age.", "block": "pedigree", "mu": 0.008658008658008658, "count": "4 / 462", "index": 16, "annualPerSite": null, "sapiensYears": null, "combinedBaselineYears": null, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": null, "d19AllLayerAgesCompatible": null, "idealizedUpperRate": null }, { "study": "Howell 2003: coding approximation", "source": "howell-2003", "region": "coding", "length": 15447, "mu": 0.009268199999999999, "model": true, "count": "0.06/site/Myr divergence, halved, × 15,447 × 20 y", "kind": "Full-region lower estimate", "counted": "The same coding events, converted to a rate", "trans": "Same", "peds": "Same", "notes": "Published 0.06/site/Myr divergence rate (99.5% CI 0.008–0.20), halved, then converted using the study’s 20-year generation. Treating partial coverage as complete coding coverage makes this conservative; it is not a directly observed whole-coding rate.", "block": "pedigree", "index": 17, "annualPerSite": 2.4e-8, "sapiensYears": 112464.48575219644, "combinedBaselineYears": 426748.6457933362, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 509223.57731374586, 524223.57731374586 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Santos 2005: germinal", "source": "santos-2005", "region": "hvr12", "length": 610, "approx": true, "kind": "Detected; germinal class", "counted": "New point substitutions, all heteroplasmic, classified somatic or germinal", "trans": "321", "peds": "Azores families; heteroplasmy in 72% of them", "notes": "Six germinal events; 0.034 = 11/321 counting the five judged somatic. Counts from the abstract; exact windows are unverified, so the regional age is approximate.", "block": "pedigree", "mu": 0.018691588785046728, "count": "6 / 321", "index": 18, "annualPerSite": 0.0000012256779531178182, "sapiensYears": 16714.336366977317, "combinedBaselineYears": 23563.59185686109, "anchor": { "sapiensPerSite": 0.02048639358599947, "combinedPerSite": 0.02888137503522119, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 676, "usable": 653, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04862480824019286, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 113335.88271148367, 128335.88271148367 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Santos 2005: corrected", "source": "santos-2005", "region": "hvr12", "length": 610, "approx": true, "mu": 0.0037, "model": true, "count": "model, corrected to fixation", "kind": "Transmission model", "counted": "The germinal events, corrected for loss before fixation", "trans": "Same 321", "peds": "Same", "notes": "First pedigree study to apply the arising-to-fixing correction; its corrected 0.2415/site/Myr lands “in the upper end” of phylogenetic values. A model-corrected rate for the measured region, not a direct homoplasmic count; it must not be assigned to 16,569 bases.", "block": "pedigree", "index": 19, "annualPerSite": 2.4262295081967213e-7, "sapiensYears": 84437.16275310592, "combinedBaselineYears": 119038.09980733058, "anchor": { "sapiensPerSite": 0.02048639358599947, "combinedPerSite": 0.02888137503522119, "sapiensDepth": 13.848802064135642, "combinedDepth": 19.523809523809526, "positions": 676, "usable": 653, "profileScale": 1.136527828971618, "panelRootDepth": 12.185185185185185, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.04862480824019286, "d19Differences": 32.870370370370374 }, "d19PairYears": [ 193706.53049499204, 208706.53049499204 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Madrigal 2012: maximum", "source": "madrigal-2012", "region": "hvr1", "length": 360, "kind": "Pedigree differences", "counted": "Substitutions between relatives; heteroplasmy status not stated", "trans": "273", "peds": "19 deep-rooting Costa Rican pedigrees of at least 7 generations; 53 people typed", "notes": "HVR-I, 360 bp. Generation time measured, 28.3 years over 289 meioses: at that interval multiply these ages by 1.132. The text reports 7 events over 299 meioses; its printed 71.1 × 10^-6 per site per generation equals 7/273. Three of the mutated sites are known hot spots. The abstract’s 1.24 × 10^-6 per site per year appears nowhere in the results.", "block": "pedigree", "mu": 0.02564102564102564, "count": "7 / 273", "index": 20, "annualPerSite": 0.000002849002849002849, "sapiensYears": 7674.7198673055655, "combinedBaselineYears": 14201.339285714286, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 105425.69444444444, 120425.69444444444 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Madrigal 2012: minimum", "source": "madrigal-2012", "region": "hvr1", "length": 360, "kind": "Pedigree differences", "counted": "Substitutions between relatives; heteroplasmy status not stated", "trans": "220", "peds": "Same", "notes": "Excluding a pedigree and hot-spot sites as the paper does leaves 2/220. Different branch and hot-spot exclusions define the two counts.", "block": "pedigree", "mu": 0.00909090909090909, "count": "2 / 220", "index": 21, "annualPerSite": 0.00000101010101010101, "sapiensYears": 21646.645779579798, "combinedBaselineYears": 40055.05952380953, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 127136.57407407407, 142136.57407407407 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Guo 2013", "source": "guo-2013", "region": "whole", "length": 16569, "zeroN": 26, "kind": "Homoplasmic", "counted": "Homoplasmic changes; heteroplasmies followed down to 0.1%", "trans": "26", "peds": "18 families, 44 people; mother–child pairs plus 9 sibling pairs", "notes": "No discordant homoplasmic SNPs; 12 heteroplasmies shared by mother and child. A zero count does not exclude rare events, and 26 transmissions give only a weak bound. The mothers were childhood-cancer survivors with uterine irradiation, which biases the count upward. Implies a bottleneck near 200, the high outlier.", "block": "pedigree", "mu": 0, "count": "0 / 26 · 3,981× depth", "index": 22, "annualPerSite": 2.7815914553628797e-7, "sapiensYears": 12389.291368807322, "combinedBaselineYears": 39145.67886463705, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 131591.22467934532, 146591.22467934532 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": 0.11522047205976887 }, { "study": "Rebolledo-Jaramillo 2014: arising", "source": "rebolledo-jaramillo-2014b", "region": "whole", "length": 16569, "mu": 0.143, "model": true, "count": "α = μ0/(2 ln 99); μ0 = 51/(39 × 16,569) observed", "kind": "Arising-rate model", "counted": "Germline point heteroplasmies at ≥ 1% in both blood and buccal tissue, fed into a transmission model", "trans": "39", "peds": "39 mother–child pairs, two tissues each", "notes": "Fitted arising parameter α. The paper estimates μ0 as 51/(39 × 16,569 bp): the 51 are heteroplasmies observed above its 1% threshold, which include inherited variation; they are not 51 new mutations. 39% of heteroplasmies were tissue-specific, so somatic.", "block": "pedigree", "index": 23, "annualPerSite": 3.4522300681996497e-7, "sapiensYears": 9982.517482517482, "combinedBaselineYears": 31541.144041144045, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 124191.5306915307, 139191.5306915307 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Rebolledo-Jaramillo 2014: retained", "source": "rebolledo-jaramillo-2014b", "region": "whole", "length": 16569, "mu": 0.0045, "model": true, "count": "2.7 × 10^-7 per site per generation × 16,569 ≈ 0.0045; bottleneck 32.3", "kind": "Transmission model", "counted": "The same heteroplasmies, divided by the measured bottleneck", "trans": "Same 39", "peds": "Same", "notes": "The paper that writes μ = α/N. Fitted μ after frequency and bottleneck modelling (IQR 8.3 × 10^-8 to 8.2 × 10^-7 per site per generation), not a direct count of homoplasmic changes. The authors call their estimate a lower bound. The best usable clock parameter from this study.", "block": "pedigree", "index": 24, "annualPerSite": 1.086366105377512e-8, "sapiensYears": 317222.22222222225, "combinedBaselineYears": 1002307.4661963552, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 1068808.6419753088, 1083808.6419753088 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Rebolledo-Jaramillo 2014: D-loop retained", "source": "rebolledo-jaramillo-2014b", "region": "control", "length": 1122, "mu": 0.001683, "model": true, "count": "1.5 × 10^-6 per site per generation × 1,122", "kind": "Transmission model", "counted": "D-loop heteroplasmies, modelled separately", "trans": "Same 39", "peds": "Same", "notes": "The paper’s separately modelled D-loop rate; its interquartile range, 4.8 × 10^-7 to 4.7 × 10^-6, spans tenfold.", "block": "pedigree", "index": 25, "annualPerSite": 6.000000000000001e-8, "sapiensYears": 228851.2496443807, "combinedBaselineYears": 390842.36388157954, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 411907.38540084945, 426907.38540084945 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Ding 2015: heteroplasmy gains", "source": "ding-2015", "region": "whole", "length": 16569, "kind": "Detected discordance", "counted": "Heteroplasmic discordance between mother and child, lymphocytes only", "trans": "333", "peds": "333 Sardinian parent–child trios", "notes": "Child variants absent from the mother’s called class. Discordance between tissues sampled from mother and child is not automatically a new germline mutation; threshold, somatic origin and calling errors prevent identifying a retained rate.", "block": "pedigree", "mu": 0.42342342342342343, "count": "141 / 333 · ≥ 4% MAF · ~180×", "index": 26, "annualPerSite": 0.0000010222063454002618, "sapiensYears": 3371.329787234042, "combinedBaselineYears": 10652.182539682539, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 103865.24822695035, 118865.24822695035 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Ding 2015: homoplasmy discordance", "source": "ding-2015", "region": "whole", "length": 16569, "kind": "Discordant calls", "counted": "Homoplasmic discordance between mother and child, either direction", "trans": "Same 333", "peds": "Same", "noAge": true, "notes": "The dataset behind Jeanson’s rate: 28 of his 63 discordances are variants the mother had and the child lost. The authors read the 35 child-not-mother calls as noise, and they were never re-examined at the read level. Gains and losses cannot both simply be counted as new inherited substitutions. Not a validated mutation rate.", "block": "pedigree", "mu": 0.1891891891891892, "count": "63 / 333 · 35 gains (0.105) + 28 losses", "index": 27, "annualPerSite": 4.567304947533085e-7, "sapiensYears": null, "combinedBaselineYears": null, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": null, "d19AllLayerAgesCompatible": null, "idealizedUpperRate": null }, { "study": "Jeanson 2015 synthesis, for comparison", "source": "jeanson-2015", "region": "whole", "length": 16569, "kind": "Proposed mutation clock", "counted": "Homoplasmic discordances in Ding 2015, pooled with Guo and Rebolledo-Jaramillo (both zero), treated as homoplasmic changes", "trans": "398", "peds": "Three studies pooled", "notes": "Mostly Ding’s unvalidated discordances. Predicts 4.1 homoplasmic changes in Guo’s 26 transmissions (0 seen), 54.6 in Norfolk’s 345 (2 seen) and 242 near-homoplasmic events in Wei’s 1,526 (3 seen). Shown to test the proposal, not as a measured rate.", "block": "pedigree", "mu": 0.15829145728643215, "count": "63 / 398", "index": 28, "annualPerSite": 3.821388310373158e-7, "sapiensYears": 9018.174603174602, "combinedBaselineYears": 28494.169396153527, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 121226.63139329807, 136226.63139329807 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Wei 2019: detected", "source": "wei-2019", "region": "whole", "length": 16569, "kind": "Detected de novo", "counted": "New heteroplasmies above 1% in the child’s blood", "trans": "1,526", "peds": "1,526 mother–offspring pairs, whole blood", "notes": "614 maternal heteroplasmies lost against 477 gained. Offspring blood variants undetected in the mother; not all germline or destined to persist. Low-level against near-homoplasmic is a factor of 159 in one generation: a snapshot, not the eventual fate of the 477.", "block": "pedigree", "mu": 0.31258191349934467, "count": "477 / 1,526 · > 1% VAF · ~1,900×", "index": 29, "annualPerSite": 7.546186577327411e-7, "sapiensYears": 4566.802935010482, "combinedBaselineYears": 14429.445220902246, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 107540.76403447473, 122540.76403447473 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Wei 2019: control", "source": "wei-2019", "region": "control", "length": 1122, "kind": "Detected de novo", "counted": "The same events in the D-loop", "trans": "Same", "peds": "Same", "notes": "131 D-loop events; the supplementary Table S2’s printed 13 is inconsistent with its rate and totals. Regional clock illustration only.", "block": "pedigree", "mu": 0.08584534731323722, "count": "131 / 1,526", "index": 30, "annualPerSite": 0.0000030604401894202215, "sapiensYears": 4486.633990146397, "combinedBaselineYears": 7662.473494486855, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 99742.38408255584, 114742.38408255584 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Wei 2019: coding", "source": "wei-2019", "region": "coding", "length": 15447, "kind": "Detected de novo", "counted": "The same events outside the D-loop (genes, rRNA, tRNA)", "trans": "Same", "peds": "Same", "notes": "346 outside-D-loop events. Same tissue and threshold limitations.", "block": "pedigree", "mu": 0.22673656618610746, "count": "346 / 1,526", "index": 31, "annualPerSite": 5.871342427296109e-7, "sapiensYears": 4597.155917025496, "combinedBaselineYears": 17443.996199957182, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 110493.3298544209, 125493.3298544209 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Wei 2019: frequency weighted", "source": "wei-2019", "region": "whole", "length": 16569, "mu": 0.01938007863695937, "model": true, "count": "477 × 0.062 / 1,526", "kind": "Neutral illustration", "counted": "The 477, each weighted by its heteroplasmic fraction", "trans": "Same", "peds": "Same", "notes": "Σ-frequency approximation. Blood is not the germline; selection and undetected variants remain unmodelled.", "block": "pedigree", "index": 32, "annualPerSite": 4.6786356779429945e-8, "sapiensYears": 73658.11185500778, "combinedBaselineYears": 232732.9874339072, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 319963.93603991496, 334963.93603991496 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Wei 2019: above 80%", "source": "wei-2019", "region": "whole", "length": 16569, "kind": "Near-homoplasmic", "counted": "De novo variants above 80% heteroplasmic fraction", "trans": "Same", "peds": "Same", "notes": "Two of the three events have ascertainment concerns. Above 80% is not complete homoplasmy, and no population-wide fixation estimate follows.", "block": "pedigree", "mu": 0.001965923984272608, "count": "3 / 1,526", "index": 33, "annualPerSite": 4.74602929391661e-9, "sapiensYears": 726121.6666666666, "combinedBaselineYears": 2294281.790123457, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 2325981.481481482, 2340981.481481482 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Zaidi 2019", "source": "zaidi-2019", "region": "whole", "length": 16569, "mu": 0.007820568, "model": true, "count": "4.72 × 10^-7 per site per generation × 16,569 · ~11,400×", "kind": "Transmission model", "counted": "Germline heteroplasmies (in both blood and buccal) converted to a fixation rate through a bottleneck of 10.3", "trans": "249", "peds": "96 families, 345 people, 2 to 4 generations, at least 2 siblings per mother", "notes": "Independent of Rebolledo-Jaramillo, with a bottleneck three times smaller; per transmission it is 1.7 times Rebolledo-Jaramillo’s retained rate. Nonsynonymous-to-synonymous occurrence 0.43. A model-inferred germline rate, not a count of observed homoplasmic transitions.", "block": "pedigree", "index": 34, "annualPerSite": 1.888e-8, "sapiensYears": 182531.4989908661, "combinedBaselineYears": 576733.5055310046, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 654698.2261248657, 669698.2261248657 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Connell 2022: all", "source": "connell-2022", "region": "whole", "length": 16569, "kind": "Detected; mixed class", "counted": "Homoplasmic changes plus heteroplasmies above 20% MAF", "trans": "345", "peds": "45 maternal lineages, 225 people, from the last four generations of an 11-generation island pedigree", "notes": "Norfolk Island. Seven heteroplasmies and two homoplasmic changes; retaining or excluding heteroplasmy changes the estimand. Its control-region rate, 0.469/site/Myr, matches Howell 2003’s pooled 0.475. Population-specific pedigree.", "block": "pedigree", "mu": 0.02608695652173913, "count": "9 / 345 · Sanger", "index": 35, "annualPerSite": 6.297774523927607e-8, "sapiensYears": 54720.83333333333, "combinedBaselineYears": 172898.03791887124, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 261740.74074074073, 276740.74074074073 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Connell 2022: homoplasmic", "source": "connell-2022", "region": "whole", "length": 16569, "kind": "Homoplasmic", "counted": "The two homoplasmic transitions only", "trans": "Same 345", "peds": "Same", "notes": "The best direct retained-change count here, but only two events, so its interval is broad. No bottleneck model anywhere in the derivation; its published 1.30 × 10^-8 per site per year is 0.78 times the phylogenetic rate. At the paper’s 26.9-year interval, multiply ages by 1.076. Detection and family structure still require modelling.", "block": "pedigree", "mu": 0.005797101449275362, "count": "2 / 345", "index": 36, "annualPerSite": 1.3995054497616904e-8, "sapiensYears": 246243.74999999997, "combinedBaselineYears": 778041.1706349207, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 850583.3333333334, 865583.3333333334 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Connell 2022: control, all", "source": "connell-2022", "region": "control", "length": 1122, "kind": "Detected; mixed class", "window": "control", "counted": "The nine events, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. The count-derived CR rate differs slightly from the printed Table 2 estimate. ", "block": "pedigree", "mu": 0.014492753623188406, "count": "5 / 345", "index": 37, "annualPerSite": 5.166757084915652e-7, "sapiensYears": 26575.809067453003, "combinedBaselineYears": 45387.3511904762, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 130475.69444444445, 145475.69444444444 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Connell 2022: control, homoplasmic", "source": "connell-2022", "region": "control", "length": 1122, "kind": "Homoplasmic", "window": "control", "counted": "The two homoplasmic transitions, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. The count-derived CR rate differs slightly from the printed Table 2 estimate. ", "block": "pedigree", "mu": 0.002898550724637681, "count": "1 / 345", "index": 38, "annualPerSite": 1.0333514169831306e-7, "sapiensYears": 132879.045337265, "combinedBaselineYears": 226936.75595238095, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 278378.47222222225, 293378.47222222225 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Connell 2022: HVR-I, all", "source": "connell-2022", "region": "hvr1", "length": 360, "kind": "Detected; mixed class", "window": "hvr1", "counted": "The nine events, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0.011594202898550725, "count": "4 / 345", "index": 39, "annualPerSite": 0.0000012882447665056363, "sapiensYears": 16972.938168079614, "combinedBaselineYears": 31406.80803571428, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 119874.13194444444, 134874.13194444444 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Connell 2022: HVR-I, homoplasmic", "source": "connell-2022", "region": "hvr1", "length": 360, "kind": "Homoplasmic", "window": "hvr1", "counted": "The two homoplasmic transitions, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0.002898550724637681, "count": "1 / 345", "index": 40, "annualPerSite": 3.220611916264091e-7, "sapiensYears": 67891.75267231846, "combinedBaselineYears": 125627.23214285712, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 198996.52777777775, 213996.52777777775 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Connell 2022: HVR-II, all", "source": "connell-2022", "region": "hvr2", "length": 315, "kind": "Detected; mixed class", "window": "connell_hvr2", "counted": "The nine events, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0.002898550724637681, "count": "1 / 345", "index": 41, "annualPerSite": 3.680699332873246e-7, "sapiensYears": 51554.165130851456, "combinedBaselineYears": 42765.62499999999, "anchor": { "sapiensPerSite": 0.01897553812039621, "combinedPerSite": 0.01574074074074074, "sapiensDepth": 5.977294507924807, "combinedDepth": 4.958333333333333, "positions": 315, "usable": 302, "profileScale": 1.136527828971618, "panelRootDepth": 5.2592592592592595, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.026690182245737798, "d19Differences": 8.407407407407407 }, "d19PairYears": [ 129756.94444444444, 144756.94444444444 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Connell 2022: HVR-II, homoplasmic", "source": "connell-2022", "region": "hvr2", "length": 315, "kind": "Homoplasmic", "window": "connell_hvr2", "zeroN": 345, "counted": "The two homoplasmic transitions, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0, "count": "0 / 345", "index": 42, "annualPerSite": 0.0000011026389780737026, "sapiensYears": 17209.203100679657, "combinedBaselineYears": 14275.516332861394, "anchor": { "sapiensPerSite": 0.01897553812039621, "combinedPerSite": 0.01574074074074074, "sapiensDepth": 5.977294507924807, "combinedDepth": 4.958333333333333, "positions": 315, "usable": 302, "profileScale": 1.136527828971618, "panelRootDepth": 5.2592592592592595, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.026690182245737798, "d19Differences": 8.407407407407407 }, "d19PairYears": [ 105602.86538771068, 120602.86538771068 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": 0.008683281952330408 }, { "study": "Connell 2022: rest of CR, all", "source": "connell-2022", "region": "rest", "length": 447, "kind": "Detected; mixed class", "window": "connell_rest", "zeroN": 345, "counted": "The nine events, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0, "count": "0 / 345", "index": 43, "annualPerSite": 7.770274677700589e-7, "sapiensYears": 4484.0881318672355, "combinedBaselineYears": 19542.433523296855, "anchor": { "sapiensPerSite": 0.0034842596463625715, "combinedPerSite": 0.015185007634672065, "sapiensDepth": 1.5574640619240694, "combinedDepth": 6.787698412698413, "positions": 447, "usable": 447, "profileScale": 1.136527828971618, "panelRootDepth": 1.3703703703703705, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.02237136465324385, "d19Differences": 10 }, "d19PairYears": [ 107895.47865498628, 122895.47865498628 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": 0.008683281952330408 }, { "study": "Connell 2022: coding, all", "source": "connell-2022", "region": "coding", "length": 15447, "kind": "Detected; mixed class", "window": "coding", "counted": "The nine events, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0.011594202898550725, "count": "4 / 345", "index": 44, "annualPerSite": 3.0023183527029775e-8, "sapiensYears": 89902.11366568375, "combinedBaselineYears": 341135.2926587302, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 425822.0486111112, 440822.0486111112 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Connell 2022: coding, homoplasmic", "source": "connell-2022", "region": "coding", "length": 15447, "kind": "Homoplasmic", "window": "coding", "counted": "The two homoplasmic transitions, by position", "trans": "Same 345", "peds": "Same", "notes": "The same nine-event study, partitioned by the positions in its Table 1. HVR-II ends at 371 here. One or zero events give weak constraints. ", "block": "pedigree", "mu": 0.002898550724637681, "count": "1 / 345", "index": 45, "annualPerSite": 7.505795881757444e-9, "sapiensYears": 359608.454662735, "combinedBaselineYears": 1364541.1706349207, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 1422788.1944444447, 1437788.1944444447 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Árnadóttir 2024: all", "source": "arnadottir-2024", "region": "whole", "length": 16569, "kind": "Detected; branch inferred", "counted": "Every mutation reaching 5% of reads, with one carrier at 10% or more", "trans": "116,663", "peds": "64,806 living Icelanders in 2,548 matrilines (deCODE genealogy)", "notes": "Seventy-five times larger than anything before it. Hypermutable positions dominate the count; the control region runs 8.3 times the coding rate per site. At deCODE’s 29.3-year interval, multiply ages by 1.172. A tight bottleneck is not a universal divisor converting this count into retained substitutions.", "block": "pedigree", "mu": 0.07027935163676573, "count": "8,199 / 116,663", "index": 46, "annualPerSite": 1.696646789468664e-7, "sapiensYears": 20311.79808513233, "combinedBaselineYears": 64177.93409926749, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 155949.19434619398, 170949.19434619398 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Árnadóttir 2024: control", "source": "arnadottir-2024", "region": "control", "length": 1092, "mu": 0.025989599999999998, "model": true, "count": "2.38 × 10^-5 per site × 1,092 callable", "kind": "Detected; regional", "counted": "The same events in the control region", "trans": "Same", "peds": "Same", "notes": "Callable CR denominator: 1,092 bp after exclusions. Published per-site parameter; the age uses the broader CR profile. Threshold and hypermutable sites limit its use as a clock.", "block": "pedigree", "index": 47, "annualPerSite": 9.52e-7, "sapiensYears": 14423.398086830719, "combinedBaselineYears": 24632.922093376867, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 113567.6923571964, 128567.6923571964 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Árnadóttir 2024: coding", "source": "arnadottir-2024", "region": "coding", "length": 15443, "mu": 0.04432141, "model": true, "count": "2.87 × 10^-6 per site × 15,443 callable", "kind": "Detected; regional", "counted": "The same events in the coding region", "trans": "Same", "peds": "Same", "notes": "16,535 attempted sites minus 1,092 CR sites gives 15,443. The age uses the broader coding profile; selection and detection thresholds affect the connection to a long-run clock.", "block": "pedigree", "index": 48, "annualPerSite": 1.148e-7, "sapiensYears": 23511.739181643858, "combinedBaselineYears": 89215.7447651574, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 180410.85240008624, 195410.85240008624 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Arbeithuber 2025: total", "source": "arbeithuber-2025", "region": "whole", "length": 16569, "kind": "Detected in oocytes", "counted": "De novo mutations at 1% or more of a single oocyte’s mtDNA copies, counted before any transmission", "trans": "70", "peds": "80 single oocytes from 22 women aged 20–42, with blood and saliva from each donor", "notes": "The fastest human rate measured and the purest arising rate: counted in the germ cell itself, before bottleneck, drift or transmission. No rise with maternal age in oocytes (P = 0.688) against a rise in blood (P = 0.0027). Mature oocytes have already experienced selection; this is not a retained-lineage rate.", "block": "pedigree", "mu": 0.7428571428571429, "count": "52 / 70 · ≥ 1% VAF · duplex sequencing, error < 10^-7", "index": 49, "annualPerSite": 0.0000017933662691946236, "sapiensYears": 1921.6346153846148, "combinedBaselineYears": 6071.670227920227, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 99408.11965811966, 114408.11965811966 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Arbeithuber 2025: D-loop", "source": "arbeithuber-2025", "region": "control", "length": 1122, "mu": 0.44319000000000003, "model": true, "count": "3.95 × 10^-4 per site per generation × 1,122", "kind": "Detected in oocytes", "counted": "The same mutations in the D-loop", "trans": "Same", "peds": "Same", "notes": "The authors’ own regional split. Surviving egg variants are not equivalent to homoplasmic descendant sequences.", "block": "pedigree", "index": 50, "annualPerSite": 0.0000158, "sapiensYears": 869.0553783963825, "combinedBaselineYears": 1484.2115084110617, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 94709.14196987664, 109709.14196987664 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Arbeithuber 2025: coding genes", "source": "arbeithuber-2025", "region": "coding", "length": 15359, "mu": 0.2995005, "model": true, "count": "1.95 × 10^-5 per site per generation × 15,359", "kind": "Detected in oocytes", "counted": "The same mutations in genes, rRNA and tRNA", "trans": "Same", "peds": "Same", "notes": "Protein, rRNA and tRNA genes total 15,359 bp; the 88 bp of other non-coding sequence are reported separately and are not in this denominator. The age uses a coding-region approximation.", "block": "pedigree", "index": 51, "annualPerSite": 7.799999999999999e-7, "sapiensYears": 3460.4457154521983, "combinedBaselineYears": 13130.727562871883, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 106291.4946865768, 121291.4946865768 ], "d19AllLayerAgesCompatible": false, "idealizedUpperRate": null }, { "study": "Horai 1995: control", "source": "horai-1995", "region": "control", "length": 1143, "annual": 7e-8, "compared": "3 human and 4 ape complete genomes", "calibration": "Orangutan–African ape split at 13 Myr; the human–chimp 4.87 Myr is an output", "published": "143 ka ± 18 (synonymous and D-loop); 450 ka ± 70 (nonsynonymous and RNA sites, same paper)", "notes": "The 7.00 × 10^-8 D-loop rate is itself derived from the 3.89 × 10^-8 synonymous rate. 1,143-bp control-region convention; the regional distance is approximate. Other site classes give different dates.", "block": "calibration", "mu": 0.00200025, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 52, "annualPerSite": 7e-8, "sapiensYears": 196158.21398089777, "combinedBaselineYears": 335007.74046992534, "anchor": { "sapiensPerSite": 0.013731074978662845, "combinedPerSite": 0.023450541832894776, "sapiensDepth": 15.40626612605971, "combinedDepth": 26.311507936507937, "positions": 1122, "usable": 1099, "profileScale": 1.136527828971618, "panelRootDepth": 13.555555555555555, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.03820888624810194, "d19Differences": 42.870370370370374 }, "d19PairYears": [ 366420.61605787097, 381420.61605787097 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Ingman 2000", "source": "ingman-2000c", "region": "coding", "length": 15426, "annual": 1.7e-8, "compared": "53 human genomes and 1 chimpanzee; D-loop excluded", "calibration": "Human–chimp split at 5 Myr", "published": "171.5 ka ± 50", "notes": "Uses the coding distance, not the 57.1 whole depth.", "block": "calibration", "mu": 0.00655605, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 53, "annualPerSite": 1.7e-8, "sapiensYears": 158773.39165015967, "combinedBaselineYears": 602468.6764141218, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 680403.8738547, 695403.8738547 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Mishmar 2003", "source": "mishmar-2003", "region": "coding", "length": 15447, "annual": 1.26e-8, "compared": "104 human genomes, coding region", "calibration": "Human–chimp split at 6.5 Myr", "published": "198 ka ± 19", "notes": "Selection and calibration uncertainty remain relevant; the paper argues for climatic selection while dating with a strict clock.", "block": "calibration", "mu": 0.004865805000000001, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 54, "annualPerSite": 1.26e-8, "sapiensYears": 214218.06809942177, "combinedBaselineYears": 812854.5634158783, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": [ 885354.4329785634, 900354.4329785634 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Kivisild 2006: synonymous", "source": "kivisild-2006", "region": "coding", "length": 0, "annual": 3.5e-8, "noAge": true, "missingMu": true, "compared": "277 genomes, synonymous transitions only", "calibration": "6 Myr species split; 6.5 Myr mtDNA coalescence", "published": "160 ka (SD 22)", "notes": "The rate is per synonymous site. No matching synonymous-site count and root profile was established here, so neither a per-transmission figure nor an implied age is calculated.", "block": "calibration", "mu": 0, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 55, "annualPerSite": 3.5e-8, "sapiensYears": null, "combinedBaselineYears": null, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": null, "d19AllLayerAgesCompatible": null, "idealizedUpperRate": null }, { "study": "Endicott & Ho 2008: external", "source": "endicott-2008", "region": "coding", "length": 7198, "annual": 3.82e-9, "noAge": true, "compared": "177 human and 2 chimpanzee genomes; 1st and 2nd codon positions (7,198 bp) analysed alone", "calibration": "Human–chimp split, lognormal, 95% within 5–7.5 Myr", "published": "162 ka (122–213) from the concatenated 11,940 bp at 6.81 × 10^-8; 310 ka (158–508) from these positions alone", "notes": "Table 3’s separately analysed PC1+2 rate (95% HPD 2.44–5.06 × 10^-9). Matching root counts for these positions were not established, so no age is calculated here.", "block": "calibration", "mu": 0.0006874089999999999, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 56, "annualPerSite": 3.82e-9, "sapiensYears": null, "combinedBaselineYears": null, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": null, "d19AllLayerAgesCompatible": null, "idealizedUpperRate": null }, { "study": "Endicott & Ho 2008: internal", "source": "endicott-2008", "region": "coding", "length": 7198, "annual": 1.3e-8, "noAge": true, "compared": "The same 177 genomes and software, calibration swapped", "calibration": "Haplogroup P in Sahul at 40–55 ka, plus H1 and H3 at about 18 ka. No ape", "published": "108 ka (82–134) from the concatenated 11,940 bp at 9.66 × 10^-8; 79 ka (60–106) from these positions alone", "notes": "Table 3’s separately analysed PC1+2 rate (1.01–1.58 × 10^-8), 3.4 times the external one. Not a direct pedigree measurement.", "block": "calibration", "mu": 0.00233935, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 57, "annualPerSite": 1.3e-8, "sapiensYears": null, "combinedBaselineYears": null, "anchor": { "sapiensPerSite": 0.0026991476580527146, "combinedPerSite": 0.010241967499040069, "sapiensDepth": 41.69373387394028, "combinedDepth": 158.20767195767195, "positions": 15447, "usable": 15438, "profileScale": 1.136527828971618, "panelRootDepth": 36.68518518518518, "basalPair": "human-denisovan", "d19PerSite": 0.0199547317110598, "d19Differences": 308.24074074074076 }, "d19PairYears": null, "d19AllLayerAgesCompatible": null, "idealizedUpperRate": null }, { "study": "Soares 2009", "source": "soares-2009", "region": "whole", "length": 16569, "annual": 1.665e-8, "compared": "Tree of 2,196 complete genomes, corrected for purifying selection", "calibration": "Human–chimp split at 6.5 Myr plus 0.5 Myr lineage coalescence", "published": "192.4 ka (Figure 6)", "notes": "The benchmark every pedigree rate is compared against; a model output, not a count. The table uses its summary whole-molecule rate (one mutation every 3,624 years), not the full age-dependent function. The coding-region cross-check gives a very similar 1.708 × 10^-8.", "block": "calibration", "mu": 0.006896846250000001, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 58, "annualPerSite": 1.665e-8, "sapiensYears": 206978.66071757072, "combinedBaselineYears": 653977.6927582803, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 729861.7122665144, 744861.7122665144 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Soares 2009: HVS-I", "source": "soares-2009", "region": "hvr1", "length": 350, "window": "hvr1", "annual": 1.7132235157059766e-7, "compared": "The same tree, HVS-I 16051–16400 (350 bp)", "calibration": "Scaled against the synonymous clock", "published": "Same tree", "notes": "The paper’s average of 1.62 × 10^-7 and 1.784 × 10^-7: “1 mutation every 16,677 years” in the segment. Its window differs from HVR-I 16024–16383; the age uses the HVR-I profile.", "block": "calibration", "mu": 0.0014990705762427297, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 59, "annualPerSite": 1.7132235157059766e-7, "sapiensYears": 127626.65563951344, "combinedBaselineYears": 236160.9895833333, "anchor": { "sapiensPerSite": 0.021865298767252322, "combinedPerSite": 0.040459656084656084, "sapiensDepth": 7.871507556210836, "combinedDepth": 14.56547619047619, "positions": 360, "usable": 350, "profileScale": 1.136527828971618, "panelRootDepth": 6.925925925925926, "basalPair": "neanderthal-denisovan", "d19PerSite": 0.06795267489711934, "d19Differences": 24.462962962962962 }, "d19PairYears": [ 291818.18287037034, 306818.18287037034 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Fu 2013", "source": "fu-2013f", "region": "whole", "length": 16569, "annual": 2.67e-8, "compared": "10 dated ancient and 311 modern genomes", "calibration": "Radiocarbon-dated tips; Bayesian relaxed clock", "published": "157 ka (120–197)", "notes": "Dates, site corrections and shared ancestry matter.", "block": "calibration", "mu": 0.0110598075, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 60, "annualPerSite": 2.67e-8, "sapiensYears": 129070.96258230534, "combinedBaselineYears": 407817.54997847823, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 490332.303716759, 505332.303716759 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Brotherton 2013", "source": "brotherton-2013", "region": "whole", "length": 16569, "annual": 2.4e-8, "compared": "39 Neolithic and Bronze Age genomes", "calibration": "Holocene-only tip calibration", "published": "—", "notes": "A published genome-rate summary rather than a raw homoplasmic count.", "block": "calibration", "mu": 0.0099414, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 61, "annualPerSite": 2.4e-8, "sapiensYears": 143591.4458728147, "combinedBaselineYears": 453697.024351057, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 534975.9378848944, 549975.9378848944 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Rieux 2014", "source": "rieux-2014d", "region": "whole", "length": 16569, "annual": 2.143e-8, "compared": "26 retained ancient and 320 modern genomes; damage screening", "calibration": "Tip, node and root calibration compared", "published": "143 ka (112–180)", "notes": "Its fitted mtEve age and the standardized depth division here are different calculations.", "block": "calibration", "mu": 0.00887684175, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 62, "annualPerSite": 2.143e-8, "sapiensYears": 160811.6985976459, "combinedBaselineYears": 508106.7934869513, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 587920.0890918089, 602920.0890918089 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Fu 2014", "source": "fu-2014", "region": "whole", "length": 16569, "annual": 2.53e-8, "compared": "The Ust’-Ishim femur and 311 modern genomes", "calibration": "A single dated tip", "published": "—", "notes": "The specimen date is part of the inference.", "block": "calibration", "mu": 0.0104798925, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 63, "annualPerSite": 2.53e-8, "sapiensYears": 136213.22928646448, "combinedBaselineYears": 430384.5290286706, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 512291.40352717246, 527291.4035271725 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Posth 2016", "source": "posth-2016", "region": "whole", "length": 16569, "annual": 2.74e-8, "compared": "66 dated ancient and 311 modern genomes", "calibration": "Dated tips; Bayesian skyline, strict rate", "published": "—", "notes": "Shares some comparison data with earlier work.", "block": "calibration", "mu": 0.011349765000000001, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 64, "annualPerSite": 2.74e-8, "sapiensYears": 125773.52923166247, "combinedBaselineYears": 397398.8534461812, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 480194.2521619512, 495194.2521619512 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Cabrera 2021: youngest bin", "source": "cabrera-2021", "region": "whole", "length": 16569, "annual": 4.33e-8, "compared": "423 dated and 784 modern genomes", "calibration": "Direct mutation counts by age bin, no tree", "published": "—", "notes": "The same data, binned by age, give a rate that falls 2.3-fold from the youngest bin to the oldest. A bin-specific rate is not automatically a rate for the complete tree.", "block": "calibration", "mu": 0.0179359425, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 65, "annualPerSite": 4.33e-8, "sapiensYears": 79588.79216968943, "combinedBaselineYears": 251471.79178811476, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 338197.979428117, 353197.979428117 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Cabrera 2021: oldest bin", "source": "cabrera-2021", "region": "whole", "length": 16569, "annual": 1.91e-8, "compared": "423 dated and 784 modern genomes", "calibration": "Direct mutation counts by age bin, no tree", "published": "—", "notes": "The same data, binned by age, give a rate that falls 2.3-fold from the youngest bin to the oldest. A bin-specific rate is not automatically a rate for the complete tree.", "block": "calibration", "mu": 0.0079116975, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 66, "annualPerSite": 1.91e-8, "sapiensYears": 180429.04193442682, "combinedBaselineYears": 570090.5018023753, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 648234.1627873018, 663234.1627873018 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Översti & Palo 2022: U4", "source": "oversti-2022d", "region": "whole", "length": 16569, "annual": 8.8e-8, "compared": "42 Holocene U4 genomes, no moderns", "calibration": "Root-to-tip regression on dated tips", "published": "—", "notes": "The fastest defensible number in the mainstream literature, and the best single figure available to the young-earth side. It is also 42 sequences from one twig of the tree with R² = 0.37, and its own x-intercept still puts that twig’s root at 12,723 years. Not an established universal mtDNA rate.", "block": "calibration", "mu": 0.0364518, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 67, "annualPerSite": 8.8e-8, "sapiensYears": 39161.303419858545, "combinedBaselineYears": 123735.55209574281, "anchor": { "sapiensPerSite": 0.0034461947009475523, "combinedPerSite": 0.010888728584425368, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16569, "usable": 16537, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.02119084501847493, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 213902.5285140621, 228902.5285140621 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null }, { "study": "Project: U-subclade regression", "source": "note-clock-comparison", "region": "whole", "length": 16519, "annual": 2.5915241131792968e-8, "window": "regression50", "compared": "229 dated ancient genomes", "calibration": "Root-to-tip, per-subclade intercepts", "published": "—", "notes": "An in-house descriptive calculation. Independent-error intervals omit phylogenetic covariance and date uncertainty.", "block": "calibration", "mu": 0.010702346706402202, "count": "", "model": true, "kind": "Calibrated substitutions", "counted": "", "trans": "", "peds": "", "index": 68, "annualPerSite": 2.5915241131792968e-8, "sapiensYears": 133381.96184076727, "combinedBaselineYears": 421438.7481191823, "anchor": { "sapiensPerSite": 0.0034566257037350924, "combinedPerSite": 0.010921686779789571, "sapiensDepth": 57.099999999999994, "combinedDepth": 180.41534391534393, "positions": 16519, "usable": 16519, "profileScale": 1.136527828971618, "panelRootDepth": 50.24074074074074, "basalPair": "human-denisovan", "d19PerSite": 0.021254985841219872, "d19Differences": 351.1111111111111 }, "d19PairYears": [ 503586.59215491783, 518586.59215491783 ], "d19AllLayerAgesCompatible": true, "idealizedUpperRate": null } ]