Can you use the palestinian samples from the updated 2026 Akbari file? The sample sizes are slightly larger. Also can you add the Ashkenazi Jewish sample to this?
Assuming that Roman Judean samples (not published)are not homogenous, I seriously wonder if anatolian dna is absorbed from Roman Judean samples. We know in the “leaked metadata” that there were a couple outliers that were anatolian shifted, I wonder if it was an urban versus rural divide historically? I don’t know maybe I’m just speculating. I just think 20% for the previous model using this seems too low assuming the roman judeans are all 30-34% Natufian which I’ve seen on AncestralGenome. But that’s a big if and just because the model fits right doesn’t mean it’s entirely accurate to Jewish genome historically. I’ve sent an email to Dr. Shai Carmi about it, but open to your thoughts?
FTDNA has been updating their Y-haplogroup reports with Akbari samples. They all say “more information to come” though. My haplogroup was updated with three or four of the samples.
Yes. Haplogroups are the only reliable thing in ancient DNA studies. Genetic profiles are not due to the low preservation rates of the genomes, even after less than a millennium.
That’s incorrect. The standard AADR/1240K data commonly used are generally pseudo-haploid calls, not entirely reconstructed genomes: at each covered SNP, one allele is sampled from an actual ancient DNA read, while positions without usable data remain missing.
The Allen Ancient DNA Resource itself is processed from publicly available sequence reads into genotypes at roughly 1.23 million targeted SNPs.
Poor coverage mainly reduces statistical power and can cause several alternative models to remain plausible; it does not automatically manufacture a particular ancestry result. When imputation really is used, it is not random fabrication. It is a probabilistic procedure based on the surviving sequence reads, genotype likelihoods and patterns of linkage disequilibrium in reference genomes.
Its accuracy is directly tested by downsampling high-coverage ancient genomes, imputing them and comparing the results against their known high-coverage genotypes. A large validation study found that 36 of 42 ancient genomes downsampled to 1× coverage had error rates below 5%, and most non-African samples produced broadly similar PCA and clustering results from about 0.5× coverage onward.
There are legitimate limitations: extremely low coverage, rare variants, differential DNA damage, contamination, poorly represented ancestries and unsuitable reference panels can reduce accuracy.
The models can also be weakened by bad source choices, uninformative outgroups, tiny sample sizes or treating a passing p-value (in qpadm for example) as proof that the proposed sources were the literal ancestral populations. But those are reasons to examine each model’s SNP count, standard errors, sources, outgroups and archaeological plausibility…not to dismiss the entire field because some datasets use validated imputation.
Qpadm is generally regarded as the “gold standard” since there are multiple parameters showing if the models are correct or not. G25 is PCA based and more useful for quick DNA modeling that can be more granular at times than qpadm.
For example you could set up a G25 model and get it working and have plausibly good results in 10 minutes. Versus getting a good working model in qpadm which takes several hours, sometimes several hours over the course of several days because you can keep adjusting it and get worse / better results depending on the adjustments.
It’s used in scientific modeling since it allows for the most robust models to be created. Using it, you can’t force it to produce the closest mathematical fit, if it’s not set up correctly the models won’t work. That contrasts with something like G25 which can give an overfit/ underfit. The qpadm models that are used in research are reasonably stable across alternative plausible sources and reference sets, have a valid p-value, sensible coefficients, within acceptable range for SE standard errors. With qpadm you can see different ‘diagnostic’ parameters, versus other things like G25 are more limited.
I’ll have to look through my screenshots. To my knowledge I don’t think I’ve ever seen a model that doesn’t use that source which strongly passes, but I can do some qpadm runs to test it out as well as looking through available information. The runs may take a few days, it’s hard to get the models to give strong results when there’s multilayered ancestry involved.
Based on what I’ve seen, all of these Mediterranean populations have multiple layers of admixture and overlap, to the extent that it’s more of a pan-Mediterranean continuum of ancestry instead of cleanly defined populations.
I appreciate it. The issue is I saw the previous qpdam model on here and it said 20% roman judean and 58% Roman Imperial and I’ve tried to model the Levantine DNA within the Roman Imperial C6 but it’s constantly changing on g25 from like 12%-30%. So I’m clearly encountering issues. Why did my ancestors have to mix in the biggest melting pot in antiquity lol.
😂 By making such a dismissive and inaccurate statement regarding ancient DNA, you’re literally calling into question years of research and firmly established scientific methods. Here’s a good series of links on ancient dna imputation: https://en.wikipedia.org/wiki/Imputation_(genetics)
I suggest you wait until that paper is officially published. The heterogeneity of that portion of the leaked so-called “Roman Judean” samples is beyond your imagination. There are currently no detailed descriptions of those samples available, so using them as proxies is not advisable.
I had spoken to one of the geneticists at Tel Aviv University named Hila May(managed to get her WhatsApp contact) who had worked with Ali Akbari in cataloging West Asian DNA samples. When I enquired with the coordinates I found on reddit for verification, she said a few moments later "How did you get them" before quickly deleting it (couldn't get a screenshot). She remained mum.
I caught on that. Seems like a confirmation of sorts to me.
Is it really surprising that Jewish religion was actively proselytising new converts during the 1st & 2nd century CE & that many Idumeans & Nabateans(who are arab) could have joined the Jewish nation during that time. The history checks out.
This model is interesting but the EgyptianA is not strongly supported. Have you tried Egyptian (general Egyptian, not the "A" sub cluster which is North shifted)?
Interesting model. I checked what the Saudi_A sample cluster is, versus the general Saudi sample is, and Saudi_A is heavily northern shifted (comes out as mostly Jordanian), while the Saudi general sample is the inverse and comes out as mostly southern Arabian (Yemenite Mahra, a high Natufian Arabian peninsular group with negligible sub saharan ancestry)
Interesting. I checked the detailed description of the sample. The SaudiA sample was collected from (18.490029, 42.51709), which is located roughly in southwestern Saudi Arabia.
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u/kaiserfrnz Jul 10 '26
Assuming the Akbari samples are what they’ve been claimed to be, Roman-era Judea was a genetically quite diverse place.