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MJost
12-29-2012, 04:59 PM
Just released my TMRCA Estimator V2.2-U106 Load

Download directly at

https://docs.google.com/file/d/0By9Y3jb2fORNNF9ma2JfZEtKUlk/edit
(Close all other spreadsheets for speed.)

Interclade work requires using the CladeA tab's button CopyA to B.

Also opinions of the sheet are welcome.

MJost

Ezana
12-29-2012, 07:02 PM
Can you reveal your algorithm? I haven't dabbled much in TMRCA calculation techniques, but I know there's a lot of controversy on which mutation rates are most accurate. How did you determine what numbers to use?

MJost
12-30-2012, 05:55 AM
Can you reveal your algorithm? I haven't dabbled much in TMRCA calculation techniques, but I know there's a lot of controversy on which mutation rates are most accurate. How did you determine what numbers to use?

The Mutation rates used in the spreadsheet are from Marko Heinila's 111 marker Mutation Rates he published in May 2012. Ken Nordtvedt used these new rates in his Gen111t Age estimator. I then took his idea and expanded it into a major spreadsheet.

Marko Heinila's results are based on about 4,000 111 level samples. He used an estimation process that each haplotype pair was considered an independent random draw from a model distribution. Model distribution suggests what is the ratio of mismatches and matches in a given marker if pairs with a given number of matching markers in general are considered. The pair data was then used to solve the mutation rates. He said that this is the same idea as in Chandler's paper on mutation rate estimation.

Also Marko's reponse to a question I had months ago.

>MJost wrote: ... would you say you are very confident in using these rates going forward? (in reference to 111 marker summed mutation rates) Looks like Ken and others are confident.

"The about 0.3 number feels very reasonable. It is based on matching the expected number of mutations with the observed by scaling relative rate estimates with common factor. Very different methods for relative rates seem to lead to about same as long as the scaling principle is the same."

MJost

MJost
02-19-2013, 02:46 PM
I have ran the U106 67 marker TMRCA Estimates showing IntraClade Coalescence (n-1) age and Founder Modal ages for U106 and ran only IntraClade Coalescence (n-1) ages for subclades with variances and by regions. Data sets I used were included in my latest TRMCA spreadsheet.

The sheer subclade haplotypes have improved lately. I have now broke out regions where I could.

I have the belief that Coalescence (n-1 sampled), the point where Hts converge back to a single founder would be a better indication for expansion ages. Modal is the True TMRCA but the time line from Modal age forward towards the Coalescence expansion point may have been bottlenecked for many many generations and not represent the correct movements. Coalescence variance seems to be a much better reference geographically.

Depending on how bushy the subclade is, the modal may not be much difference than the Coalescence expansion point. My previous use of Z156 England stats appear now to be saturated by the subclade R1b-U106>Z381>Z156>Z305>L1's

YrsPerGen Count
30 N=1586

IntraCladeCoalescence (n-1)Age Generations StdDevInGen YBP +OR-YBP CI-SD-GenCoal(n-1) CI+OR-YBP
U106 ALL 107.7 33.7 3,232.3 1,011.9 17.28 518.5

IntracladeFounder'sModal Age ModalGenAge StdDevInGen YBP +OR-YBP CI-SD-GenModal CI+OR-YBP
U106 ALL 119.0 35.5 3,571.3 1,195.9 20.07 602.2
Confidence (CI) Level = 95.45

= Filtered Var / Coal. Ybp Age (n-1)
R1b-U106>L217.1+ n=6 6.63 / 2,101.31

R1b-U106>Z18 * n=137 9.28 / 2,941.04

R1b-U106>Z18>Z14 n=80 8.14 / 2,578.20

R1b-U106>Z18>Z14>Z372 *- n=6 6.97 / 2,206.90

R1b-U106>Z18>Z14>Z372 n=63 6.58 / 2,084.45

R1b-U106>Z18>Z14>Z372>L257+ n=55 5.72 / 1,813.00
England n=8 4.98 / 1,578.24
Ireland n=4 6.67 / 2,111.87
Scotland n=26 3.50 / 1,109.22

R1b-U106>Z381>Z301 n=652 9.92 / 3,142.60
R1b-U106>Z381>Z301 *- n=4 5.92 / 1,874.28
R1b-U106>Z381>Z301>L48>L200+ n=5 6.40 / 2,027.39
R1b-U106>Z381>Z301>L48>L47>L44 *- n=5 9.70 / 3,072.76
R1b-U106>Z381>Z301>L48>L47>L44>L46>L164 *- n=5 4.20 / 1,330.48

R1b-U106>Z381>Z156 n=124 8.49 / 2,687.97
R1b-U106>Z381>Z156 *- n=4 8.33 / 2,639.83
R1b-U106>Z381>Z156>Z305 *- n=10 11.27 / 3,569.05
R1b-U106>Z381>Z156>Z305>L1 *- n=7 5.81 / 1,840.34
R1b-U106>Z381>Z156>Z305>P89.2+ n=6 1.17 / 369.58

R1b-U106>Z381>Z301 ALL 9.57 / 3,031.47
R1b-U106>Z381>Z301 *- n=4 5.92 / 1,874.28

R1b-U106>Z381>Z301>L48>L47 ALL 9.27 / 2,936.54
Poland n=9 9.28 / 2,939.01
Ireland n=7 8.19 / 2,594.58
Germany n=5 12.20 / 3,864.71
Scotland n=8 11.14 / 3,529.83

R1b-U106>Z381>Z301>L48>L47>L44 *- n=5 9.70 / 3,072.76

R1b-U106>Z381>Z301>L48>L47>L44>L46>L164 n=13 5.95 / 1,884.43

R1b-U106>Z381>Z301>L48>L47>Z159+ n=32 7.66 / 2,426.35
Poland n=4 7.25 / 2,296.65
England n=4 5.33 / 1,689.49
Lithuania n=4 1.58 / 501.57

R1b-U106>Z381>Z301>L48>Z9>Z2 *- n=9 11.72 / 3,713.36

R1b-U106>Z381>Z301>L48>Z9>Z2>Z7 n=134 9.11 / 2,885.66
IS Eng South West n=8 9.41 / 2,981.12
Ireland n=10 9.39 / 2,974.21
England n=43 8.87 / 2,810.32
Italy/Switzerland n=5 8.80 / 2,787.66
IS Eng South East n=7 7.48 / 2,368.31
Scotland n=14 6.75 / 2,137.39
Poland n=6 6.37 / 2,016.83
IS Eng East n=4 5.08 / 1,610.30
Germany n=15 10.32 / 3,270.37

Here the latest Z156 All by region sorted by variance High to Low the IntraClade Coalescence (n-1) Ages.
R1b-U106>Z381>Z156 ALL Scotland n=13 10.59 / 3,355.29 <<<<<< What is the historical timeline of these surnames as most have no identified subregion other than just Scotland?
R1b-U106>Z381>Z156 ALL Germany n=18 9.41 / 2,980.50
R1b-U106>Z381>Z156 ALL Ireland n=16 8.72 / 2,761.74
R1b-U106>Z381>Z156 n=124 8.49 / 2,687.97
R1b-U106>Z381>Z156 *- n=4 8.33 / 2,639.83
R1b-U106>Z381>Z156 ALL England n=33 7.41 / 2,347.98
R1b-U106>Z381>Z156 ALLScotland n=13 10.59 / 3,355.29

R1b-U106>Z381>Z156 ALLScotland contains these subclades (not just one or two):
R1b-U106>Z381>Z156
R1b-U106>Z381>Z156
R1b-U106>Z381>Z156 *
R1b-U106>Z381>Z156 *-
R1b-U106>Z381>Z156>L782+
R1b-U106>Z381>Z156>Z305
R1b-U106>Z381>Z156>Z305 *-
R1b-U106>Z381>Z156>Z305>L1
R1b-U106>Z381>Z156>Z305>L1
R1b-U106>Z381>Z156>Z305>L1
R1b-U106>Z381>Z156>Z305>L1
R1b-U106>Z381>Z156>Z305>L1>L132.2+
R1b-U106>Z381>Z156>Z305>L128+

MJost

MJost
10-26-2013, 04:57 PM
TMRCA Estimator - Coalescence & Modal Ages MJost

I have uploaded my latested TMRCA Estimator spreadsheet loaded with MWalsh's most current U106 haplotypes both 67 and 111 markers. Excel 2007 or newer Required.

TMRCA Estimator allows use of flexable study down to a SubClade for Intra & InterClade Coalescence & Modal Ages

This file is a compressed 'Zipped' File which will have to be downloaded to your computer and then opened and extracted. Click 'File' and then 'Download'.

This is a Macro Enable Spreadsheet which is required for many calculations. Re-Calculation button is require when any Filtering is selected. Read the Notes listed near the end of the Results-TMRCA Tab prior to its use.

I have posted info in my Google Documents. Corrected Link, click here:
https://drive.google.com/file/d/0By9Y3jb2fORNdkhxYVlzMVVHUmM/edit?usp=sharing

MJost

MJost
10-27-2013, 02:29 AM
Ok, sorry folks. Dang Google changed some things. I have reset the Public view of my TMRCA spreadsheet. This should work now.

https://drive.google.com/file/d/0By9Y3jb2fORNdkhxYVlzMVVHUmM/edit?usp=sharing

MJost