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From: "Tim Janzen" <>
Subject: Re: [DNA] How old is Y-Chromosome Adam?
Date: Wed, 5 Jan 2011 01:10:41 -0800


Dear All,
I decided to compare John Chandler's most recent mutation rates (see
http://freepages.genealogy.rootsweb.ancestry.com/~geneticgenealogy/ratestuff
.htm) with those found in Ballantyne's paper as well as those found in YHRD
(see http://www.yhrd.org/Research/Loci). I created the chart below which I
sorted by John Chandler's estimated mutation rate for each marker. Column
headings are as follows:
1. Marker
2. John Chandler's estimated mutation rate
3. Ballantye's estimated mutation rate
4. Number of mutations for the marker as found in Ballantye's paper
5. Number of meioses for the marker as found in Ballantye's paper
6. My calculated mutation rate for the marker by simply dividing the number
of mutations by the meioses for the markers found in Ballantye's paper
7. Number of mutations for the marker as found in YHRD
8. Number of meioses for the marker as found in YHRD
9. YHRD's estimated mutation rate
ND stands for "no data".

1. 2. 3. 4. 5. 6. 7. 8. 9.
472 0.00001 0.000446 0 1549 0 ND ND ND
578 0.00008 0.000995 1 1686 0.000593 ND ND ND
426 0.00009 0.000398 0 1736 0 ND ND ND
455 0.00016 0.000426 0 1618 0 ND ND ND
454 0.00016 0.000475 0 1458 0 ND ND ND
641 0.00018 0.00039 0 1768 0 ND ND ND
425 0.00018 0.00151 2 1778 0.001125 ND ND ND
436 0.00018 0.000384 0 1798 0 ND ND ND
490 0.00019 0.000395 0 1759 0 ND ND ND
450 0.0002 0.00104 1 1598 0.000626 ND ND ND
388 0.00022 0.000425 0 1635 0 ND ND ND
594 0.00029 0.00103 1 1635 0.000612 ND ND ND
395s1 0.00031 ND ND ND ND ND ND ND
395s1 0.00031 ND ND ND ND ND ND ND
640 0.00034 0.000398 0 1716 0 ND ND ND
531 0.00037 0.001 1 1682 0.000595 ND ND ND
617 0.00042 0.000413 0 1684 0 ND ND ND
492 0.00042 0.000392 0 1770 0 ND ND ND
392 0.00052 0.00097 1 1728 0.000579 6 14,553 0.0004123
5680.00053 0.00108 1 1547 0.000646 ND ND ND
590 0.00054 0.000391 0 1780 0 ND ND ND
438 0.00055 0.000945 1 1751 0.000571 3 9808 0.0003059
537 0.00057 0.00238 3 1539 0.00195 ND ND ND
393 0.00076 0.00211 3 1750 0.00171 14 13,399 0.001045
565 0.00087 0.00209 3 1757 0.00171 ND ND ND
487 0.00097 0.00177 2 1511 0.00132 ND ND ND
437 0.00099 0.00153 2 1760 0.00114 12 9787 0.001226
YCAIIa0.00123 ND ND ND ND ND ND ND
YCAIIb0.00123 ND ND ND ND ND ND ND
511 0.00128 0.00152 2 1760 0.00114 ND ND ND
459a 0.00132 0.00267 4 1741 0.00240 ND ND ND
459b 0.00132 0.00267 4 1741 0.00230 ND ND ND
448 0.00135 0.000394 0 1747 0 10 6364 0.001571
19 0.00151 0.00437 7 1756 0.00399 35 5,225 0.002299
406s1 0.00154 0.00382 6 1744 0.00344 ND ND ND
389i 0.00186 0.00551 9 1751 0.00514 34 13,474 0.002523
413a 0.00202 ND ND ND ND ND ND ND
413b0.00202 ND ND ND ND ND ND ND
H4 0.00208 0.00322 5 1755 0.00285 18 7395 0.002434
572 0.00212 0.00207 3 1770 0.00169 ND ND ND
385a 0.00226 0.00208 3 1762 0.00170 54 25306 0.002134
385b 0.00226 0.00414 6 1615 0.00372 54 25306 0.002134
389ii 0.00242 0.00383 6 1743 0.00344 49 13445 0.003644
520 0.00245 0.00266 4 1760 0.00227 ND ND ND
447 0.00264 0.00212 3 1722 0.00174 ND ND ND
391 0.00265 0.00323 5 1759 0.00284 38 14621 0.002599
390 0.00311 0.00152 2 1758 0.00114 31 14747 0.002102
444 0.00321 0.00545 9 1775 0.00507 ND ND ND
557 0.00321 0.0038 6 1758 0.00341 ND ND ND
442 0.00324 0.00978 14 1497 0.00935 ND ND ND
446 0.00365 0.00267 4 1747 0.00229 ND ND ND
460 0.00402 0.00622 10 1717 0.00582 ND ND ND
607 0.00411 ND ND ND ND ND ND ND
439 0.00477 0.00384 6 1736 0.00346 51 9782 0.005214
481 0.00544 0.00497 8 1744 0.00459 ND ND ND
464a 0.00566 0.00727 12 1745 0.00688 ND ND ND
464b 0.00566 0.00727 12 1745 0.00688 ND ND ND
464c 0.00566 0.00727 12 1745 0.00688 ND ND ND
464d0.00566 0.00727 12 1745 0.00688 ND ND ND
456 0.00735 0.00494 8 1757 0.00455 27 6364 0.004242
570 0.0079 0.0124 17 1426 0.01192 ND ND ND
458 0.00814 0.00836 14 1756 0.00797 41 6363 0.006444
534 0.00832 0.00651 11 1794 0.00613 ND ND ND
449 0.00838 0.0122 19 1617 0.01175 ND ND ND
576 0.01022 0.0143 24 1727 0.01390 ND ND ND
CDYa 0.03531 ND ND ND ND ND ND ND
CDYb 0.03531 ND ND ND ND ND ND ND

The average mutation rate for the 58 markers above that Ballantyne
had data for was .00334. The average mutation rate for those same 58
markers using Chandler's mutation rates is .002456. Thus Ballantyne's
average mutation rate is about 36% higher than Chandler's for these markers.
If you remove the multi-copy markers, the average mutation rate for the
remaining 49 markers above that Ballantyne had data for was .003093 and the
average mutation rate for those same 49 markers using Chandler's mutation
rates is .002295. Thus Ballantyne's average mutation rate is about 35%
higher than Chandler's for these markers. If we look at only the 10 slowest
mutating markers per Chandler's rates (472, 578, 426, 455, 454, 436, 641,
490, 450, 388), then the average mutation rate for those 10 markers using
Chandler's mutation rates is .000147. The average mutation rate for those
10 markers using Ballantye's mutation rates is .000537. Thus Ballantyne's
mutation rates for these markers are approximately 3.66 x higher than
Chandler's rates for these markers. If we take the 2 mutations in the
slowest mutating markers (1 each for 578, 450) and calculate the average
mutation rate for those markers using the sum of their meioses (16,605) then
we get 0.00012 as the average mutation rate for that group of markers. Note
that this is relatively close to the average mutation rate for these markers
based on Chandler's mutation rates. Chandler's average mutation rate is
about 22% higher than the calculation using the two mutations and the sum of
the meioses.
The bottom line for me based on this review is that it is not
reasonable to use Ballantyne's estimated mutation rates for the 10 slowest
mutating markers to calculate a TMRCA estimate for Y Adam. Ballantyne's
estimated mutation rates for the 10 slowest mutating markers are simply too
high on average. Ballantyne's study was did not include enough father-son
pairs to generate accurate mutation rates for these 10 markers. I believe
that the same applies to the next 10 slowest mutating markers as well. I
think that one would need to have at least 20,000 father-son pairs and
possibly as many as 100,000 father-son pairs in order to have enough meioses
to calculate truly accurate mutation rates for the 10 slowest mutating
markers in the FTDNA 67-marker set.
Sincerely,
Tim Janzen

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