STR Wars, GDs, TMRCA estimates, Variance, Mutation Rates & SNP counting

[MitchellSince1893]

I'm sure this has been posted before (from 2014 International Genetic Genealogy Conference) but I hadn't seen it and found it very informative

Dr Bill Howard's talk on Using correlation techniques on Y chromosome haplotypes to date events

https://m.youtube.com/watch?v=zmuYUI...ature=youtu.be

[JMcB]

Originally Posted by MJost View Post

The “Variance Method” (Slatkin, 1995; Stumpf, 2001) assumes that the variance (average-squared-distance from ancestral value) of each STR marker in a large population, is proportional to the TMRCA of that population.

Ken Nordtvedt has implemented variance into his Generations spreadsheet calculations. Please note that Ken explains Variance Sigma (Standard Deviation) Concepts on his website.

http://knordtvedt.home.bresnan.net/S...0Variance.pptx

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For those who are interested the above link for Ken Nordtvedt is now dead but much of his work can still be found here:

https://onedrive.live.com/?id=8B35AD...35ADFFC37790D0

[MitchellSince1893]

I'm sure this has been posted before (from 2014 International Genetic Genealogy Conference) but I hadn't seen it and found it very informative

Dr Bill Howard's talk on Using correlation techniques on Y chromosome haplotypes to date events

https://m.youtube.com/watch?v=zmuYUI...ature=youtu.be

Found this paper (part 1 and 2 links) from Dr Howard that is quite similar to the video
http://www.jogg.info/52/files/Howard1.pdf
http://www.jogg.info/52/files/Howard2.pdf

And here is a educational video on his method.
https://www.youtube.com/watch?v=wmylJXlHZZs

And lots more info here https://dl.dropboxusercontent.com/u/...TreesIndex.pdf

[MitchellSince1893]

Interesting article on a study of 111 markers, genetic distance and actual relationship distance.

http://linealarboretum.blogspot.com/...er-at.html?m=1

Except that caught my eye

We have seen close relatives (5th cousins and closer) having genetic distances up to 5, while 13th cousins, once removed have a GD=0.

[Joe B]

Klyosov, A. and Kilin, V. (2016) Kilin-Klyosov TMRCA Calculator for Time Spans up to Millions of Years.
Advances in Anthropology, 6, 51-71. doi: 10.4236/aa.2016.63007 Pub. Date: August 24, 2016

This paper was posted by Mis on a R1b-Z2103 thread.

a little theory about Z2103
http://file.scirp.org/pdf/AA_2016082414320572.pdf

This paper covers much more than Z2103 and is appropriate this "STR Wars" thread.

I have to believe that the authors are looking for a good discusion based on the last sentence in Discussion and Conclusions. Page 19 of the PDF.

The authors express hope that a long debate over which mutation rates to employ, how to count mutations,
and how to calculate the TMRCA in various cases, including complicated ones, is eventually over.

Advances in Anthropology, 2016, 6, 51-71
Published Online August 2016 in SciRes.
http://www.scirp.org/journal/aa
http://dx.doi.org/10.4236/aa.2016.63007

[Huntergatherer1066]

Just so you know, Advances in Anthropology is not considered a legitimate journal in anthropology, and Klyosov is not an anthropologist. We were always warned to steer clear of journals like "Advances in Anthropology" in graduate school. It's not unlike the veterinarian who created her own "scholarly" journal to publish her Bigfoot research.

https://scholarlyoa.com/2014/10/02/a...ccess-journal/

Here is another good article from UCL that discusses the problems with illegitimate researchers like Klyosov: https://www.ucl.ac.uk/mace-lab/debunking/theories

[Joe B]

Just so you know, Advances in Anthropology is not considered a legitimate journal in anthropology, and Klyosov is not an anthropologist. We were always warned to steer clear of journals like "Advances in Anthropology" in graduate school. It's not unlike the veterinarian who created her own "scholarly" journal to publish her Bigfoot research.

https://scholarlyoa.com/2014/10/02/a...ccess-journal/

Here is another good article from UCL that discusses the problems with illegitimate researchers like Klyosov: https://www.ucl.ac.uk/mace-lab/debunking/theories

There is a long history of debating Anatole Klyosov on this thread since May of 2013. No affirmation of his work is intended.

[Dave-V]

I'm sure this has been posted before (from 2014 International Genetic Genealogy Conference) but I hadn't seen it and found it very informative

Dr Bill Howard's talk on Using correlation techniques on Y chromosome haplotypes to date events

https://m.youtube.com/watch?v=zmuYUI...ature=youtu.be

FYI we heard on one of the forums recently that Bill Howard has passed away. He was very helpful to me in my surname group analyses and his RCC Correlation technique is worth remembering.

A full list of his papers and applications of his method is at https://dl.dropboxusercontent.com/u/...TreesIndex.pdf. And I posted a more complete analysis of his technique here awhile ago: http://www.anthrogenica.com/showthre...CC-Correlation.

RIP Bill. We can't afford to lose the pioneers.

[razyn]

his RCC Correlation technique is worth remembering.

Amen to that. I was present for Bill Howard's slide presentation of it at the I4GG Conference in Maryland, two years ago. And subsequently we discussed it by phone a bit, a very few months before he died. His method is actually different, and shouldn't be filed away in the archives because he's no longer here to defend it, use it, or improve it. However, I don't have the math chops to do so. Bill was an astrophysicist, I believe. And he was well past 80; so he knew the math the way guys had to know it who did their calculations with slide rules, before computers made some aspects of it much easier.

[razyn]

Incidentally, there has also been just a hint or two here about another method of estimating the age of a mutation, based on pairwise mismatches. I don't pretend to know how it's done. Dr. Hans van Vliet, a geneticist in Amsterdam, discussed this technique just a bit on the old WorldFamilies group for R1b moderated by rms2; and MikeWww and I have alluded to it here, though not very recently. http://www.anthrogenica.com/showthre...ll=1#post15433