K12b Analyzing the Mediterranean Cluster C6 from Antonio M et al. 2019

[Leopoldo Leone]

Not only is it citing a forum poster (me), it is even misrepresenting me, because the content is monstrously inaccurate. Antonio et al. 2019 was a paper about Rome, not southern Italy. Also, that bit about C6 in South Africa, is just a visual-cacophony of nonsense.

I get the impression that such programs work like google browser, that is they give as an output what they most often encounter about a topic in the web, thus, given that we already know the fetishist obsession about southern Italians, papers that are NOT about southern Italy and southern Italians get described as about them because so they are treated on the internet.

 

[Jovialis]

I get the impression that such programs work like google browser, that is they give as an output what they most often encounter about a topic in the web, thus, given that we already know the fetishist obsession about southern Italians, papers that are NOT about southern Italy and southern Italians get described as about them because so they are treated on the internet.

I feel like asking for a software program that strictly cites academic sources shouldn't be such a tall order. I am rather disappointed with all this hype behind these programs. Its all hype.

 

[Francesco]

Just a quick note on the C6 cluster throghout the iron age to the imperial age: note how imperial samples outside Rome, from Picenum, are somewhat pretty similar to the Iron Age C6 samples from Latium (expecially the one from Praeneste).
One of the most important center of Picenum was (and still is) the city of Ancona, wich was infact a greek colony founded by Syracuse. Of course it is just few samples analyzed with g25, so take it for what is worth (not much), but one could interpret it as a signal of some kind of continuity between the Iron age and the Imperial Era.

 

[Jovialis]

I can model it again down the line, after I finished processing my own DNA. But R437, the C6 sample from the Iron Age, using a slightly modified version of the Sarno et. al 2022 Calabrian paper (because the Reich Lab data set they used is no longer available) comes out almost similar to modern South Italians, except R437 is about 10% higher in Anatolian_N, and 10% lower in CHG/Iran_N:

 

[Francesco]

I can model it again down the line, after I finished processing my own DNA. But R437, the C6 sample from the Iron Age, using a slightly modified version of the Sarno et. al 2022 Calabrian paper (because the Reich Lab data set they used is no longer available) comes out almost similar to modern South Italians, except R437 is about 10% higher in Anatolian_N, and 10% lower in CHG/Iran_N:

Yes, exactly so. BTW from what I've seen (but this could have been a wrong impression of mine), G25 tends to underestimate the CHG component, so the CHG admixture in the Praenestini sample could actually be higher, and much closer to contemporary Southern Italy.

 

[Jovialis]

Yes, exactly so. BTW from what I've seen (but this could have been a wrong impression of mine), G25 tends to underestimate the CHG component, so the CHG admixture in the Praenestini sample could actually be higher, and much closer to contemporary Southern Italy.

It is impossible to tell how G25 works, because there aren't any white papers. Moreover, it is illegitimate compared to modeling used by professional academic tools.

 

[Hioloi]

It is impossible to tell how G25 works, because there aren't any white papers. Moreover, it is illegitimate compared to modeling used by professional academic tools.

What would you recommend instead of G25?

I have it as well and I was told it's the best.

 

[Jovialis]

What would you recommend instead of G25?

I have it as well and I was told it's the best.

Admixtools, eupator has a good guide for it here:

Admixtools - admixtools2 TUTORIAL for WINDOWS.

Download and install R-Studio for Windows. https://www.rstudio.com/products/rstudio/ Download and install R-tools 4.2 for Windows. https://cran.r-project.org/bin/windows/Rtools/ After you complete the installation, run it (R-Studio) and install admixtools2 and dependencies by following the...

www.eupedia.com

As for your own DNA, I would recommend checking out my thread here:

Utilizing AI for WGS30x FASTQ-Plink conversion & AADR Merge for Downstream Analysis in Admixtools2

> results$weights # A tibble: 3 × 5 target left weight se z 1 Italian_South_ITS7 Steppe_EMBA 0.241 0.0471 5.11 2 Italian_South_ITS7 C_Italian_N 0.551 0.0361 15.3 3 Italian_South_ITS7 CHG_Iran_N 0.209 0.0609 3.43 > results$popdrop # A...

www.eupedia.com

I'm currently in the QC phase of my sorted BAM file.

Ultimately, I want to lead people away from amateur tools, to free and sophisticated academic tools.

 

[Hioloi]

Admixtools, eupator has a good guide for it here:

Admixtools - admixtools2 TUTORIAL for WINDOWS.

Download and install R-Studio for Windows. https://www.rstudio.com/products/rstudio/ Download and install R-tools 4.2 for Windows. https://cran.r-project.org/bin/windows/Rtools/ After you complete the installation, run it (R-Studio) and install admixtools2 and dependencies by following the...

www.eupedia.com

As for your own DNA, I would recommend checking out my thread here:

Utilizing AI for WGS30x FASTQ-Plink conversion & AADR Merge for Downstream Analysis in Admixtools2

> results$weights # A tibble: 3 × 5 target left weight se z 1 Italian_South_ITS7 Steppe_EMBA 0.241 0.0471 5.11 2 Italian_South_ITS7 C_Italian_N 0.551 0.0361 15.3 3 Italian_South_ITS7 CHG_Iran_N 0.209 0.0609 3.43 > results$popdrop # A...

www.eupedia.com

I'm currently in the QC phase of my sorted BAM file.

Ultimately, I want to lead people away from amateur tools, to free and sophisticated academic tools.

Damn I don't have a PC and my laptop recently broke.

 

[Jovialis]

I wouldn't try it unless you have decent computational power in your PC or laptop.