## Thursday, May 23, 2013

### 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.