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Archiver > GENEALOGY-DNA > 2007-03 > 1172847622


From: James Heald <>
Subject: [DNA] J2 distance matrix (was: Challenge to YDNA J Gurus)
Date: Fri, 02 Mar 2007 15:00:22 +0000
References: <001901c75c2a$8ba69340$6400a8c0@Ken1> <45E7892D.70408@ucl.ac.uk>
In-Reply-To: <45E7892D.70408@ucl.ac.uk>


Here's a distance matrix for J2.

Data and classification is from Bonnie Schrack's Y-DNA-J project page,
http://www.familytreedna.com/public/Y-DNA_J/index.aspx?fixed_columns=on

Distance measure is again
= (1/37*100) * Sum{ (Mismatch^2)/ Mutation Rate }
so numbers should roughly represent hundreds of generations.

Mutation rates are Chandler (2006) with the exception of DYS 388 set to
0.00225, rather than 0.00022.


Plotting up principal components for the data, the most notable feature
is the separation between J2b1 and all the J2a clades. They appear very
clearly as two separate blobs of points.

The individual J2a clades are somewhat difficult to distinguish, as can
be seen from their self-ASDs, compared to the ASDs between the central
haplotypes.

For this reason, many J2a haplotypes are left unclassified by the
Y-DNA-J project. This will tend to particularly affect further flung
members of each clade, so the self-ASD numbers are likely to be
systematically undercounted.

The range of distances within the clades from the clade centres (not
shown) is also interesting. While many of the distances are short, some
clade members (confirmed by SNP tests) are *much* further away -- in
probability distribution terms, the distribution has quite a heavy tail.
This is probably typical in other haplogroups too; and may be a
warning, that there may be a significant risk of misclassification, and
of losing the outliers from clusters (which contribute most heavily to
estimates of its date), if we trust STR-based haplotype categorisation
too far. (On the other hand, we don't have a lot of choice!)

Anyhow, here are my estimates of distances and central haplotypes for J2.


J2a* J2a1* J2a1b J2a1b1 J2a1k J2b1 J2b1b
N (1) (9) (18) (8) (10) (12) (1)


Self- NA 3.66 1.65 0.56 1.43 1.36 NA
ASD

J2a* 0 3.13 3.12 3.39 4.09 4.85 13.9
J2a1* 3.13 0 1.25 1.7 2.07 3.98 11.6
J2a1b 3.12 1.25 0 1.58 2.06 3.38 11.77
J2a1b1 3.39 1.7 1.58 0 2.62 4.66 12.86
J2a1k 4.09 2.07 2.06 2.62 0 4.86 11.56
J2b1 4.85 3.98 3.38 4.66 4.86 0 11.21
J2b1b 13.9 11.6 11.77 12.86 11.56 11.21 0

J1-S1 11.36 7.63 7.53 9.48 9.11 10.01 15.48
J1-S2 7.14 7.62 7.23 8.08 6.97 9.67 14.5
J1-S3 6.53 4.64 4.21 6.42 6.46 7.57 14.48
J1-S4 5.65 4.26 2.88 3.78 4.68 5.59 12.62
J1-S5 3.75 3.66 2.38 4.11 3.92 6.21 12.82
J1-S6 8.23 4.82 4.52 5.8 5.92 6.39 13.71
J1-S7 3.55 2.27 2.46 3.45 3.16 6.22 13.21
J1-S8 3.89 3.61 3.56 4.36 4.52 7 13.34
J1-S9 5.43 3.42 3.8 5.19 5.38 7.24 13.96
J1-S9a 5.76 3.7 4.62 4.87 5.01 8.12 16.2


J2a* J2a1* J2a1b J2a1b1 J2a1k J2b1 J2b1b
393 12 12 12 12 12 12 12
390 24 23 23 22 24 24 24
19 15 14 14 14 15 15 15
19b
391 10 10 10 10 9 10 11
385a 13 13 13 14 14 13 16
385b 15 16 17 15 16 17 18
426 11 11 11 11 11 11 11
388 17 15 16 15 16 15 15
439 12 12 11 12 12 12 12
389|1 13 13 13 14 13 12 12
392 11 11 11 11 11 11 11
389|2 16 16 17 17 16 16 15
458 16 16 17 15 14 16 17
459a 9 9 9 9 8 8 8
459b 9 9 9 9 9 9 9
455 11 11 11 11 11 11 11
454 11 11 11 11 11 11 13
447 25 25 26 26 26 28 24
437 16 15 15 15 14 16 14
448 20 20 20 20 21 19 19
449 27 31 29 29 31 29 30
464a 13 12 12 13 12 13 13
464b 13 13 14 14 14 15 15
464c 14 15 15 16 15 15 15
464d 16 16 16 16 16 17 17
464e
464f
464g
460 11 11 10 10 10 11 10
H4 10 10 11 10 11 10 10
YCAIIa 19 20 19 19 19 19 19
YCAIIb 22 22 22 22 22 20 20
456 16 15 15 15 16 13 14
607 14 14 13 12 14 14 14
576 15 18 18 16 17 17 16
570 17 18 17 17 18 17 18
CDYa 34 35 35 34 36 36 34
CDYb 36 37 38 36 38 39 41
442 10 12 12 12 12 11 11
438 10 9 9 9 9 9 9
425 12 12 12 NULL 12 12 NA
461
462
A10
635
1B07
441
444 10 12 12 11 13 12 NA
445
446 14 12 13 13 15 12 NA
452
463
531 11 11 10 10 11 11 NA
578 7 7 7 7 7 8 NA
395S1a 14 14 15 15 14 15 NA
395S1b 14 15 15 15 15 18 NA
590 8 8 8 8 8 8 NA
537 11 11 11 11 11 12 NA
641 10 10 10 10 10 10 NA
472 8 8 8 8 8 8 NA
406S1 11 11 11 11 10 11 NA
511 9 9 9 9 10 9 NA
413a 22 17 17 17 17 23 NA
413b 22 17 17 17 17 23 NA
557 14 14 14 15 16 16 NA
594 11 10 11 10 10 11 NA
436 12 12 12 12 12 12 NA
490 12 12 12 12 12 13 NA
534 16 16 16 15 15 16 NA
450 8 8 8 8 9 8 NA
481 26 23 21 22 22 23 NA
520 20 21 21 21 21 20 NA
617 12 12 12 12 12 12 NA
568 11 11 11 11 11 11 NA
487 14 14 13 13 15 14 NA
572 10 11 10 11 11 10 NA
640 12 12 12 12 12 12 NA
492 12 12 12 12 12 12 NA
565 11 11 11 11 12 11 NA







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