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  #1  
Old 27th October 2011, 10:29 AM
Mudgeeclarke Mudgeeclarke is offline
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TMRCA Calculators

I've seen TMRCA calculators by Dr McDonald, Bruce Walsh, Moses Walker, and others.

McDONALD: http://dna-project.clan-donald-usa.org/tmrca.htm

WALSH: http://nitro.biosci.arizona.edu/ftDNA/TMRCA.html

WALKER: http://www.moseswalker.com/mrca/calculator.asp

and the comprehensive Gene McGee utility:

http://www.mymcgee.com/tools/yutility.html

The Walsh table tops out at 37 markers.

I notice that mutation rates vary in the calculators (constant, FTDNA, McDonald) which impacts on results, and the years per generations are variable, somewhat.

What do other Forum users think about the various Calculators? And have I missed seeing an even better and/or easier calculator elsewhere?
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  #2  
Old 27th October 2011, 11:25 AM
Zaru Zaru is offline
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By logical thinking, the rhetorical phrase, "mutations happen" to me, leaves the door open for chaos in mutation rates. My brother and I are a GD of 1 @25 markers. Perhaps we will be off more at 67, it IS a possibility. It is also possible that some mutations occurred in our generation, which may account for some of our off modal values and differential between others who are in the family. I also know that mutations can and do occur with an INDIVIDUAL as opposed to a GENERATION of Y chromosomes within a particular line. Thus rendering a wide variety of scenarios.

To this point I have been attributing our genetic distance within our project to a NPE because I assumed that the TMRCA is the grail of genetic algorithms. But if one really considers the possibilities in correlation with probabilities, we might see that sometimes mutations really do happen and does NOT affect kinship.
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  #3  
Old 27th October 2011, 12:32 PM
Mudgeeclarke Mudgeeclarke is offline
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Quote:
Originally Posted by Zaru View Post
By logical thinking, the rhetorical phrase, "mutations happen" to me, leaves the door open for chaos in mutation rates. My brother and I are a GD of 1 @25 markers. Perhaps we will be off more at 67, it IS a possibility. It is also possible that some mutations occurred in our generation, which may account for some of our off modal values and differential between others who are in the family. I also know that mutations can and do occur with an INDIVIDUAL as opposed to a GENERATION of Y chromosomes within a particular line. Thus rendering a wide variety of scenarios.

To this point I have been attributing our genetic distance within our project to a NPE because I assumed that the TMRCA is the grail of genetic algorithms. But if one really considers the possibilities in correlation with probabilities, we might see that sometimes mutations really do happen and does NOT affect kinship.

Quote:
Originally Posted by Mudgeeclarke
What do other Forum users think about the various Calculators? And have I missed seeing an even better and/or easier calculator elsewhere?
Hello Zaru: I'm not quite sure what point you are making about the various calculators and ease of use ... perhaps your comment was for another thread?
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  #4  
Old 27th October 2011, 12:49 PM
Zaru Zaru is offline
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Quote:
Originally Posted by Mudgeeclarke View Post
Hello Zaru: I'm not quite sure what point you are making about the various calculators and ease of use ... perhaps your comment was for another thread?
Boy are you correct. The header and subject matter is quite similar to the thread that I recently put up!

Last edited by Zaru; 27th October 2011 at 12:51 PM.
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  #5  
Old 27th October 2011, 01:51 PM
Mudgeeclarke Mudgeeclarke is offline
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Originally Posted by Zaru View Post
Boy are you correct. The header and subject matter is quite similar to the thread that I recently put up!


Oops!
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  #6  
Old 27th October 2011, 03:02 PM
nathanm nathanm is offline
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Quote:
Originally Posted by Mudgeeclarke View Post
I've seen TMRCA calculators by Dr McDonald, Bruce Walsh, Moses Walker, and others.

McDONALD: http://dna-project.clan-donald-usa.org/tmrca.htm

WALSH: http://nitro.biosci.arizona.edu/ftDNA/TMRCA.html

WALKER: http://www.moseswalker.com/mrca/calculator.asp

and the comprehensive Gene McGee utility:

http://www.mymcgee.com/tools/yutility.html

The Walsh table tops out at 37 markers.

I notice that mutation rates vary in the calculators (constant, FTDNA, McDonald) which impacts on results, and the years per generations are variable, somewhat.

What do other Forum users think about the various Calculators? And have I missed seeing an even better and/or easier calculator elsewhere?
The Walsh link isn't a calculator per se, but does have some of the calculations listed. The good part about his page is the explanation behind the calculations. The 2001 paper he wrote is the basis for almost all of the other calculators out there. I'd recommend everyone read the difference between the infinite alleles model, which all the calculators are using, and the stepwise mutational model, which is closer to reality, but much harder to calculate in practice.

I haven't used one at the Walker link much. It has a default mutation rate, but you can easily change that. I'm just not a fan of how the results are presented; it only allows for GD of 0-5.

Y-Utility is far more than just a MRCA calculator, including its best feature: to output haplotypes in the format required to generate cladograms using PHYLIP and TreeView, or Fluxus Engineering's Network software (.ych files). However, because it tries to do everything, the interface isn't the friendliest.

FTDNATiP does have advantages over the others. It has access to all of FTDNA's data, and it calculates based on the individual mutation rates for each marker. However, if you don't have any close matches, like me, it really doesn't do you any good.

I prefer Dr McDonald's TMRCA calculator. It's a completely self-contained JavaScript app, so you can download the HTML file and use it anywhere. He released it to the public domain, so anyone could use it as the basis for their own calculator. The only thing I don't like is how it uses "transmission events" rather than generations. If you know that, it's not a problem, but I think it confuses people using it for the first time.

Regarding years per generation, that's not part of the calculations, so you can use whatever length you want. Most of the calculators don't say anything about it.
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  #7  
Old 27th October 2011, 10:31 PM
Zaru Zaru is offline
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How were these developed?

What are their algorithms based upon?

How is it possible to understand mutations over the course of thousands of years when we have neither readable samples from that long ago and only been dealing with it en masse for really only the past 5-10 years?

Each individual is its own machine and I would assume with its own mutation rate. How large was the pool sample that the science is based upon? How old were the specimens that they originally tested and based the algorithms on? Where would I find this information?
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  #8  
Old 28th October 2011, 04:32 PM
nathanm nathanm is offline
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Quote:
Originally Posted by Zaru View Post
What are their algorithms based upon?

How is it possible to understand mutations over the course of thousands of years when we have neither readable samples from that long ago and only been dealing with it en masse for really only the past 5-10 years?

Each individual is its own machine and I would assume with its own mutation rate. How large was the pool sample that the science is based upon? How old were the specimens that they originally tested and based the algorithms on? Where would I find this information?
The mathematical model the calculators are based on was described by Bruce Walsh, in his 2001 paper, "Estimating the time to the most recent common ancestor for the Y chromosome or mitochondrial DNA for a pair of individuals." If you just want the gist of the paper without reading lots of technical jargon, he has a shorter explanation on his website, which Colin linked to above.

There are two ways to measure mutation rates, through longitudinal or cross-sectional studies. Good longitudinal studies of Y-DNA aren't possible, because no more than 3 or 4 generations in one line are usually alive at the same time to test, and it wouldn't go back nearly as long as you're asking. For genealogical purposes, we're not actually too interested in mutation rates over 1000s of years, only more recent generations. Lots of cross-sectional studies have been done with father-son pairs. Some of them involved more than 100,000 pairs, so it's a rather large pool of data. However, different studies have found different rates, so it's a good idea to compare them to find any outliers, which may have methodological problems. For at least 16 markers, YHRD compiled various rates from different studies. There's also been plenty of research among results from FTDNA by capable project administrators. For example, see this web page by Charles Kerchner.

For more background on the methodology as it relates to genealogy, see two articles in the Journal of Genetic Genealogy (JoGG): For more general information, there's good discussion related to a few papers by Lev Zhivotovsky, et al. on Dienekes' blog, and an editorial in JoGG by Whit Athey, "[URL="http://www.jogg.info/32/editorial.htm"]Mutation Rates

Last edited by nathanm; 28th October 2011 at 04:46 PM.
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  #9  
Old 28th October 2011, 04:54 PM
nathanm nathanm is offline
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(Last post was cut-off because of a special character in a paper's title. )

For more general information, there's good discussion related to a few papers by Lev Zhivotovsky, et al. on Dienekes' blog, and an editorial in JoGG by Whit Athey, "Mutation Rates - Who's Got the Right Values?" (2007). Only Zhivotovsky's 2004 paper is freely available: "The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time."

More recently, a paper by George Busby, et al. effectively declared STRs useless for estimating long-term MRCAs (he's talking archaeological time frames; STRs are still very much relevant for genealogy). It's not freely accessible, but Dienekes has two, very informative blog posts on the topic:

Last edited by nathanm; 28th October 2011 at 04:55 PM. Reason: special character, again
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  #10  
Old 28th October 2011, 05:15 PM
nathanm nathanm is offline
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I almost forgot this paper, which does a statistical analysis of the various mutation rates found: "Mutation rate estimates for 110 Y-chromosome STRs combining population and father-son pair data;" the supplementary data is especially informative.
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