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Thread: A TMRCA Estimator Excel spreadsheet

  1. #31
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    Added a macro in V8.5 to import MikeW's P312xL21 haplotypes. I ended up removing all the suspects to be able to combine the 67 lists and had plenty of rows for the 111 but again I only keep those HTs with Positive P312 or better Results. I ended up with a little over 1,900 111 marker HTs and 5,535 with the 67 length. I also removed Ysearch HTs. I left out the L21 duplicate HTs but did not check P312's list as it didnt seem to affect the the entire picture much.


    http://tinyurl.com/TMRCA-Estimator



    MJost
    Last edited by MJost; 08-09-2013 at 02:36 AM.
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  2. #32
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    Quote Originally Posted by MJost View Post
    Lets look at calculating a TRMCA using the Scots Sc clade which is a very bushy group. The new Daddy L1335 is a small Wales based clade to the L1065 Scots. Reviewing that set of 111 marker Haplotypes, if one counts the mutations between the two at 111 markers there are 27 , which are based on the current Today's haplotypes, but this is all between their two associated modals which in essence will need to be divided by two to get to the MRCA. Recall, that increasing the number of markers used brings more confidence.

    For a more detailed examination, using my TMRCA spreadsheet, I look at several criteria where I look and see if there are any possible bi-modal STRs or outlier haplotypes that show a wider than +- two allele range from the Modal. This more critical on smaller sets of HTs than the larger groups and in smaller panels vs larger and larger. You can treat the outliers by excluding them. Example was where I had a one haplotype out of 20 with an odd DYS456 value of 18 (all others had a 23) throwing my calculation off by a large amount at 25 markers at more than 10 plus generations. I use my Filter Clade(x) for STR GD's with plus or minus two from Modal in the displayed Dashboard report for those odd allele values first and try to determine how it will affect the TMRCA results via different panel size etc.

    Next in order is to choose which size panel represents the best overall closest to the modal variance between the haplotypes using a Bruce Walsh designed tool called the k/n ratio which he states:

    Http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461668/

    "We assume that n markers are scored nonrecombining chromosome of interest (either the Y or mtDNA) and that we observe matches in allelic state at k of these. We start by assuming the infinite alleles model, where each mutation is assumed to be unique. We then modify our results by assuming a (symmetric single-step) stepwise mutational model, which is a more descriptor for microsatellite markers. As we show, when k/n is close to one and n moderate to large, the two different mutational models give essentially the distribution for t (time)."

    My method is that when k/n is closest to one it gives essentially the best distribution for time. As you can notice the 37 marker panel is shows the worst k/n and should not be used for TMRCAs. This is what I might consider as the parallel to see how every HT including the outliers in the group fit.

    Match k/n scored markers - Filtered (goal is closest to 1) for the CladeA: Scots 1335-Sc and CladeB: L1335 All
    Ratio 111 (k/n) 67 (k/n) 37 (k/n) 25 (k/n)
    CladeA 0.90319 0.90294 0.85399 0.89988
    CladeB 0.89890 0.89739 0.84751 0.89409


    I next look at the Confidence Index numbers to help decided which is the best set of markers to use in the above best determined panel size (This tool is also used to set a specific CI for standardization when running multiple clade aging). I usually just set the Confidence Level to 1 sigma (68.27%), for an assumed normal distribution, the probability that a measurement falls within 1 standard deviation of the mean. When performing TMRCA's on different size and/or clade data sets, using the same CI results helps confer standardization for simplicity when comparing of multiple different subclades.

    Combining ancestral subclades sometime requires mixing with its subclade(s) for an IntraClade Coalescence, Founders Modal, and Interclade for the both. In the case of the Wales guys, their TMRCA is much younger by itself due to very small number of HTs that have about a 475 ybp modal which as we would have to assume, are missing lineages that possibly daughtered out or have yet to be found and tested. But when combined with its Subclades, the HTs creates a wider modal foot print where the number of generations appears to separate nicely. If the TMRCA is significanty outside the average of the others, then it probably should not be considered such as the IAM-MCM TMRCA ages as shown below. Combined, there are zero GD between them.

    HTML Code:
    111 Markers	Bird's 48			94 NMCM			IAM-MCM			111 ALL	
    IntraClade Coalescence (n-1) Age
    YBP	CI-SD-Gen-Coal(n-1)		YBP	CI-SD-Gen-Coal(n-1)		YBP	CI-SD-Gen-Coal(n-1)		YBP	CI-SD-Gen-Coal(n-1)
    Clade A: 1335-Sc's
    1,373.5	10.06		1,326.9	10.86		1,278.7	11.57		1,397.7	13.23
    Clade B: 1335 All
    1,461.9	10.82		1,419.5	11.77		1,355.9	12.38		1,477.4	14.08
    
    Diff =	88.4	0.76	92.7	0.91		77.2	0.81		79.7	0.86
    
    Intraclade Founder's Modal Age
    YBP	CI-SD-GenModal		YBP	CI-SD-GenModal		YBP	CI-SD-GenModal		YBP	CI-SD-GenModal
    Clade A: 1335-Sc's
    1,512.6	11.59		1,444.1	12.29		1,152.1	9.87		1,525.9	15.04
    
    Clade B: 1335 All
    1,601.7	12.37		1,538.6	13.25		1,226.2	10.62		1,607.7	15.94
    The CI concept is to chose the most stable type of markers with in the best overall panel as shown by the CI results. In this calculation the Interclade Founders modal is the same as the Intraclade Founders age, which should be and is the high end of the Clade A's TMRCA.

    And the result shows that L1335* appears to be only about three generations older than the L1065's at a TMRCA of 1,601.7 vs 1,512.6 ybp, three generations. Only more L1335 haplotypes will confirm or not the truth. There was a quick SNP mutation between Wale and the Scots Guys. Need to look for a 1335 Sc variety that did not get the L1065 to prove that the SNP L1065 was farther apart in generations from L1335 than about three.


    Soon I will show how these same methods produced a very close number of generations compared to a known Paper trail. The known ages information remained hidden until after TMRCA result were produced and then was compared to the actual known data in a TRMCA Methods Study which should be due out shortly.

    MJost
    Full Info PDF
    https://docs.google.com/file/d/0By9Y...it?usp=sharing

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  3. #33
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    Quote Originally Posted by MJost View Post
    Soon I will show how these same methods produced a very close number of generations compared to a known Paper trail. The known ages information remained hidden until after TMRCA result were produced and then was compared to the actual known data in a TRMCA Methods Study which should be due out shortly.

    MJost
    Here is my Second Look results on the Marleen Van Horn TRMCA challange on Rootsweb which used her known paper trail haplotypes. The original submission requested 37, 67 and 111 marker TMRCA's for four parts of the tree and my Second review was submitted before Marleen released the specific birth ages and other notes. Several changes by Marleen were distributed at several stages during the study. After the reveal of the true ages, I made some revisions, one removing a haploytpe in Ancestor 8 who was actually a dupicate of Ancestor 2 and the other main change was that Haplotype Number Three had an odd DYS447 value of 18 (all others had a 23). I treated number three's allele value as IAM changing it to a 22 and reran the numbers. Here are my Revised Second Look TMRCA's.

    https://docs.google.com/file/d/0By9Y...it?usp=sharing

    The formal Study Results are here:
    http://tinyurl.com/ChallengeSummary


    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  4. #34
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    TMRCA_Estimator Loaded with the latest MIkeW's L21 with subclades 67 and 111 Markers Ver8.7b MJost 09/17/2013


    http://tinyurl.com/TMRCA-Estimator



    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  5. #35
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    I have combined MikeW's recently updated R1b subclades spreadsheets, R1b including U106, P312 xL21 and L21 creating my TMRCA Estimator V8.7b spreadsheet loaded with 67 markers.

    TMRCA EstimatorV8.7b-R1bALL-67M

    https://docs.google.com/file/d/0By9Y...it?usp=sharing

    Bird's Stable STRs

    HTML Code:
    Count	IntraCladeCoalescence(n-1)Age	MeanGenerations	StdDevInGen	YBP	 +OR-YBP	Max-YBP
    N=5712	Clade A: R1b-P312 All	120.2	35.6	3,606.3	1,068.8	4,675.1
    N=268	Clade B: R1b xP312-xU106	162.2	41.4	4,867.4	1,241.7	6,109.2
    	Diff =	42.0		1,261.2		1,434.1
    Count	IntracladeFounder'sModalAge	ModalGenAge	StdDevInGen	YBP	 +OR-YBP	Max-YBP
    N=5712	Clade A: R1b-P312 All	130.8	37.2	3,924.9	1,115.0	5,040.0
    N=268	Clade B: R1b xP312-xU106	192.7	45.1	5,780.0	1,353.1	7,133.2
    	Diff =	61.8		1,855.1		2,093.2
    
    TRUEMRCA	InterCladeGAB 	Generations	StdDevInGen	YBP	 +OR-YBP	Max-YBP
    Pooled SD Clades          A & B	InterCladeCoalescence(n-1)Age: R1b-All for R1b-P312 All  &  R1b xP312-xU106	124.6	36.3	3,737.4	1,088.1	4,825.5
    Pooled SD Clades          A & B	IntercladeModalFounder's: R1b-All for R1b-P312 All & R1b xP312-xU106	178.3	32.8	5,348.2	983.3	6,331.5
    HTML Code:
    Count	IntraCladeCoalescence(n-1)Age	MeanGenerations	StdDevInGen	YBP	 +OR-YBP	Max-YBP
    N=1800	Clade A: R1b-U106 All	108.6	33.9	3,257.9	1,015.9	4,273.8
    N=268	Clade B: R1b xP312-xU106	162.2	41.4	4,867.4	1,241.7	6,109.2
    	Diff =	53.7		1,609.5		1,835.4
    
    Count	IntracladeFounder'sModalAge	ModalGenAge	StdDevInGen	YBP	 +OR-YBP	Max-YBP
    N=1800	Clade A: R1b-U106 All	119.7	35.6	3,592.0	1,066.7	4,658.7
    N=268	Clade B: R1b xP312-xU106	192.7	45.1	5,780.0	1,353.1	7,133.2
    	Diff =	72.9		2,188.0		2,474.5
    
    TRUEMRCA	InterCladeGAB 	Generations	StdDevInGen	YBP	 +OR-YBP	Max-YBP
    PooledSDClades          A & B	InterCladeCoalescence(n-1)Age: R1b-All for R1b-U106 All  &  R1b xP312-xU106	124.4	36.2	3,730.8	1,087.1	4,817.9
    PooledSDClades          A & B	IntercladeModalFounder's: R1b-All for R1b-U106 All  &  R1b xP312-xU106	177.7	32.5	5,330.4	975.7	6,306.1
    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  6. #36
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    TMRCA Estimator Loaded with the latest 10/28 HTs from MikeW's L21 spreadsheet pulling down all available 67 and 111 Markers. I also imported MikeW's 67Markers from R1b-Early and the P312** only haplotypes. Ver 8.8 MJost 10/30/2013

    http://tinyurl.com/TMRCA-Estimator

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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     George Chandler (10-30-2013)

  8. #37
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    TMRCA Estimator V10.1 loaded with the latest 12/18/13 HTs from MikeW's L21 spreadsheet pulling down all available 67 and 111 Markers. MJost 12/19/2013
    http://tinyurl.com/TMRCA-Estimator

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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     Silesian (12-19-2013)

  10. #38
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    Updated the TMRCA Estimator V10.3 loaded with the latest 01/14/14 HTs from MikeW's L21 spreadsheet pulling 67 and 111 Markers. The number of 67 markers were over the max 9990 haplotypes limit. I removed Ysearch HTs to bring it down under the max. MJost 01/18/14

    http://tinyurl.com/TMRCA-Estimator

    MJost
    Last edited by MJost; 01-18-2014 at 08:13 PM.
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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  12. #39
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    Quote Originally Posted by MJost View Post
    Updated the TMRCA Estimator V10.3 loaded with the latest 01/14/14 HTs from MikeW's L21 spreadsheet pulling 67 and 111 Markers. The number of 67 markers were over the max 9990 haplotypes limit. I removed Ysearch HTs to bring it down under the max. MJost 01/18/14

    http://tinyurl.com/TMRCA-Estimator

    MJost
    Newbie here.
    I have downloaded the TMRCA Estimator and am currently exploring it - it will take me a while to digest it all.
    Kudos for the impressive design and programming and to all the contributors.

    I am keen to develop TMRCA trees for my project, to graphically show the relatedness of the member tests.
    See here to get an idea of what I am trying to achieve, and to note the spread of our project haplotypes and how they are currently divided into groups.
    The method I used (which I gleaned from here) uses the yutility111 to generate the TMRCA data (hybrid mutation model, 95% probability, 25 years per generation, FTDNA mutation rates).
    The resulting PHYLIP data text was then fed into the Kitsch program (using commands l, j, 9, 1000), and the resulting tree file was then massaged and labelled and the graph images created from that.
    I don't know what the Kitsch program is doing exactly, but I do understand that it is juggling and ordering the branch nodes.
    The output looks pretty good to me, but may well be inaccurate due to the yutility111 and Kitsch parameters used.

    Anyway, I hope I will get more accurate results by using the TMRCA Estimator, or some cutdown version of the toolset used in it.
    Any ideas about how I might generate graphical tree output from it?
    Or else (working backwards), how I might generate PHYLIP style data from it?

    Thanks,
    Rod
    Last edited by Rod Bruce; 03-28-2014 at 03:43 AM. Reason: clarity
    L21+ DF21+ S190+ (L144- L159.2- L193- L226- L96- M222- M37- P314.2- P66-)
    Little Scottish Cluster - Littleton Airlie, Forfarshire, Scotland circa 1750
    Co-Admin of the Hidden Content

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    Last edited by Rod Bruce; 03-28-2014 at 03:30 AM. Reason: clarity

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