I compared mean pairwise mismatches from DF27xL176,2 and its sub-clades with some MRCA calculations. The third column are mean pairwise mismatches calculated with the Arlequin program; the MRCA based on Nordtvedt’s calculator are in the 4th column.
1 df27 20.7 3.7k
2 z196 18.8 3,5k
3 z209 18 2.7k
4 z220 17.6 4.0k
5 z278 17 2.1k
6 m153 15 2.4k
Plotting the numeric SNP order against the mean pwmm produces a polynomial of the third degree; the time interval of the SNP’s as well as the rise in the effective population will cause a deviation of linearity.
Producing a similar plotting with the MRCA’s gives a polynomial function of the 5th degree. Indicating that inherent assumptions in the MRCA calculations are inconsistent.
The pattern changes If one calculates with Nordtvedt method a SNP together with its downstream SNP’s; but still the polynomial is of the 6th degree!
DF27xL176.2 and sub clades 3.9k
Z196 and sub clades 3.5k
Z209 and sub clades 3.2k
Z220 and sub clades 3.2k
Z278 and sub clades 2.4k
Further I like to present the differences of FST values of the subpopulations of the DF27 metapopulation; FST values represent distances in subpopulations and are well used in population genetics:
FST differences from Df27 with:
It looks as if the mean pairwise mismatches and the FST calculations are more reliable to date subpopulations associated with a defining SNP. The Nordtvedt based MRCA calculates the age of an clade including its sub clades acceptable.
When I plot the mean pairwise mismatch of DF27xL176.2 and sub clades (each time including its sub clades) against the associated MRCA I get a straight line with a linear relationship.The formula is MRCA=1000(0.23xmean pairwise mismatch – 0.65) ybp (R2=0.9718).
The Z220 subpopulation becomes then: 3.4K and not 4.0K. And DF27 subpopulation 4.1K. The L484 subpopulation is aged 1.3K . A small cluster inside a phylogenetic tree including Bob Bjorkman, Nik Okkels and myself have a MRCA of 0.9K.
I have no expertise in field of the Klyosov or Dieneke calculations. May be there is someone who could provide them in regard to the data used here. They came from the spreadsheet of Mike Walsh.
May I end with a quote from a recent article in Plos by Rocco et al:The paucity of haplogroup defining genetic markers has meant that these microsatellite-derived dating calculations have to be conducted without regard to lower level phylogenetic relationships, and therefore erroneously compare populations that may be phylogenetically distant. By identifying the lower level branches of the R1b1a2 phylogenetic tree, more accurate dating of truly related haplogroups will be possible.
PS My Word file looks here slightly distorted.