Rates of Mutation mtDNA ?

[nc2015]

Still trying to get a satisfactory answer to the above question...

My mtDNA has the following sequence:

224C 311C 519C
073G 263G 309.1C 315.1C 497T 524.1C 524.2A 524.3C 524.4A

I have been trying to determine the rates of mutation and am puzzled by what I have read. According to most of the articles, each mutation takes 10,000 years. If that is true how can I have 11 mutations from CRS if my group, K, only showed up 15,000 years ago. Am I missing something here ?

Also, while I have no complete matches, I have 2 close matches (+l,-1) and am wondering how far back I have a common ancestor with these people. Also, is HVR1 more significant than HVR2 in relation to common ancestry ?

[sterlingnotes]

CRS is just a reference

The CRS is just a reference that we compare our DNA to. It is from a scientist with MtDNA from haplogroup H, which is not even your haplogroup. I didn't start with the CRS and then mutate 11 times to get your MtDNA of K.

[vraatyah]

>I have been trying to determine the rates of mutation and am puzzled by what I have read. According to most of the articles, each mutation takes 10,000 years

i don't know what is the source that misleaded you. The correct calculations of divergence time based on hvs1 should be as follows.

1. given a network of hvs1 sequences, you should select a rooted tree within it. It doesn't matter what formal method you choose to build the tree while of course your calculation depends on whether the tree is correct.

2. calculate the Ro-statistics for that tree, it's simply the average transition count per node of your tree. You should take into account only the transitions between 16090 and 16065 since there are no reliable observations of mutation rate in hvs1 outside this range. Be sure, only the transitions, no transversions and no indels! Once again: starting from the root, we calculate the number of network links between tree vertices (ignoring the links corresponding to events different from transitions!); if any back transition occured, we count it twice (since there are 2 links corresponding to it) Then we divide the result by the number of nodes in the tree, it yields the Ro.

3. Coalescence time = Ro x 20000 years.

4. if you are interested in details about the variance of Ro, see Saillard et at 2000 paper.

There are only 2 sequences in your tree: one which falls into K (2 transitions compared to crs) and the crs (you consider it as the root of U haplogroup, do you?). This network is very small to calculate divergence time because in all such cases SE value is greater than Ro.

[vraatyah]

of course, i meant to write 16365 instead of 16065