R1a tree

Today, I want to update the STR111 tree of R1a1a that I have presented earlier here and here and here. For the first time I tried to implement some SNP information into the tree as well, which made the R1a1a branching much clearer but it is still not perfect. Assuming an initial branching of R1a 8000BP I also calculated the age of each node of the tree (see table below). Last but not least, I increased the number of individuals in this tree (N=547).

Rectangular tree of R1a (as pdf):

Polar tree of R1a (as pdf):

SNP	Age in years based on tree	Age in years based on STR111 variability
M420	8000	8000
SRY10831.2	7798	7907
L664	4965	4375
Z645/Z647	6117	7294
Z283	5938	6751
M458	4625	3931
L260	3598	2411
CTS11962	4013	3069
L1029	4341	3078
Z280	5614	6050
Z92	4597	3996
CTS1211	5322	5381
P278	3719	2473
CTS3402	5046	4937
L366	3079	1038
L365	4095	2041
L1280	3281	2169
Z284	5063	4688
L448	4069	2857
CTS4179	3740	2212
L176	2956	1128
Z287/Z288	4908	4499
Z93	5989	6979
Z94	5795	6900
Z2121/Z2124	5322	5319
Z2122	4124	2457
Z2123	4781	3998
L657	4729	4131
Y7	3885	2197

Due to the size of the tree I split the tree into pieces.

 

Edit May 25th 2013:

I did not use a molecular clock, I just defined the total age of the whole tree at 8000 years BP.

Example Z94:
1. First I calculated the standard deviation (STDEV) for each STR within Z94+ individuals (Note: For STDEV I only used individuals with STR111 data).
2. I calculated the sum of all STR111 standard deviations (STDEV DYS393 + STDEV DYS390 + STDEV DYS19+ STDEV DYS391 + STDEV DYS385a + STDEV DYS385b + STDEV DYS426 + STDEV DYS388 + STDEV DYS439 + STDEV DYS389i + STDEV DYS392 + STDEV DYS389ii + etc.). For Z94+ individuals sum of all STR111 standard deviations is 51.307. The sum of all STR111 standard deviations within R1a (all individuals of tree N=547) is 53.823.
3. I figured out a correlation between the sum of all STR111 standard deviations within Z94+ individuals and the relative age of the SNP (see formula below).
4. Arbitrarily, I defined the total age of the whole tree at 8000 years BP. It might be better to see the age estimates as relative age estimates, not as absolute age estimates.

Age of SNP Z94=8000/(2.8863*e^(0.0588*(sum of all STR111 standard deviations within all 547 R1a individuals)))*(2.8863*e^(0.0588*(sum of all STR111 standard deviations within Z94+ individuals)))

Age of SNP Z94=8000*(2.8863*e^(0.0588*51.307))/(2.8863*e^(0.0588*53.823))
=8000*(2.8863*2.71828^(0.0588*51.307))/(2.8863*2.71828^(0.0588*53.823))
=8000*59.0/68.4
=6900

Update 06/18/2013:

I generated a Z282+* STR67 tree.

Radial tree:

Rectangular tree: