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View Full Version : Improved models of coalescence ages of Y-DNA haplogroups (Iain McDonald)



deadly77
06-02-2021, 04:11 PM
Iain McDonald has announced an update on his TMRCA calculations - his article on the subject has just been accepted for a special issue in the journal Genes, following peer review. He has placed a pre-print on his personal website for the time being:http://www.jb.man.ac.uk/~mcdonald/genetics/TMRCA.pdf

Nqp15hhu
06-02-2021, 04:39 PM
So where are these new timings posted?

JMcB
06-03-2021, 03:24 AM
Iain McDonald has announced an update on his TMRCA calculations - his article on the subject has just been accepted for a special issue in the journal Genes, following peer review. He has placed a pre-print on his personal website for the time being:http://www.jb.man.ac.uk/~mcdonald/genetics/TMRCA.pdf

Well, as I suspected many months ago when we last spoke about this, most of it went right over my head. ;) Have you had a chance to read it yet?

deadly77
06-03-2021, 08:51 AM
Well, as I suspected many months ago when we last spoke about this, most of it went right over my head. ;) Have you had a chance to read it yet?

Brief skim, but not a full read - hopefully have a closer read over the weekend. Ultimately, I think you may not need to understand the majority of the manuscript in order to apply the age estimate, and a lot of it is explanation and justification of the "how" and "why" this is put together, similar to the Adamov et al 2015 paper "Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data" that you can read but don't fully need to calculate the YFull age estimate (although McDonald's manuscript is a bit more comprehensive. There's a link to some example code in the manuscript on page 21 - Data availability: The code used to generate the examples in this paper is available at https://github.com/iainmcdonald/TMRCA which I'd interpret that computer savvy folks could use to input data for a group of related men and have the code do the calculation for you. Or it may be included and applied as part of Big Tree analysis in the future (assumption on my part - I don't have any inside info).

MacUalraig
06-03-2021, 10:39 AM
Brief skim, but not a full read - hopefully have a closer read over the weekend. Ultimately, I think you may not need to understand the majority of the manuscript in order to apply the age estimate, and a lot of it is explanation and justification of the "how" and "why" this is put together, similar to the Adamov et al 2015 paper "Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data" that you can read but don't fully need to calculate the YFull age estimate (although McDonald's manuscript is a bit more comprehensive. There's a link to some example code in the manuscript on page 21 - Data availability: The code used to generate the examples in this paper is available at https://github.com/iainmcdonald/TMRCA which I'd interpret that computer savvy folks could use to input data for a group of related men and have the code do the calculation for you. Or it may be included and applied as part of Big Tree analysis in the future (assumption on my part - I don't have any inside info).

You mistyped the github link it has a hyphen in it:

https://github.com/iain-mcdonald/TMRCA

JMcB
06-03-2021, 02:02 PM
Brief skim, but not a full read - hopefully have a closer read over the weekend. Ultimately, I think you may not need to understand the majority of the manuscript in order to apply the age estimate, and a lot of it is explanation and justification of the "how" and "why" this is put together, similar to the Adamov et al 2015 paper "Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data" that you can read but don't fully need to calculate the YFull age estimate (although McDonald's manuscript is a bit more comprehensive. There's a link to some example code in the manuscript on page 21 - Data availability: The code used to generate the examples in this paper is available at https://github.com/iainmcdonald/TMRCA which I'd interpret that computer savvy folks could use to input data for a group of related men and have the code do the calculation for you. Or it may be included and applied as part of Big Tree analysis in the future (assumption on my part - I don't have any inside info).

Fortunately, he has spoken about some of this on the U106 forum at a level that laymen can understand. I suspect I’m not going to see anything close to it - and their formulas aren’t exactly the same - until FT finally releases their age estimates. Whenever that may be.

MitchellSince1893
06-03-2021, 02:36 PM
All 3 members of my terminal branch have done 111- marker test and BigY 700 so hopefully it will improve the future TMRCA estimate from FTDNA for this branch. It will be interesting to see how it compares to my own estimate using STR and SNP tests of 1175 AD +/- 75 years.

deadly77
06-03-2021, 02:53 PM
Fortunately, he has spoken about some of this on the U106 forum at a level that laymen can understand. I suspect I’m not going to see anything close to it - and their formulas aren’t exactly the same - until FT finally releases their age estimates. Whenever that may be.

He did say in his update "To pre-empt the question, this code is not directly related to the implementation that Family Tree DNA will be using. I don't know all the details of what they'll be doing, and it would be improper of me to divulge what I do know anyway. However, I would expect various features of this method to show up in their final implementation." and in the manuscript under Conflicts of interest: The author declares prior, unfunded consultancy work with the commercial DNA testing company Gene by Gene Ltd. Neither this company nor its staff had a role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

deadly77
06-03-2021, 02:55 PM
You mistyped the github link it has a hyphen in it:

https://github.com/iain-mcdonald/TMRCA

I went for a copy and paste from the manuscript (which does have the hyphen) - not sure where I lost said hyphen but you are correct.