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G25 Improved IllustrativeDNA-like HG & Farmer ancestry (For Europeans)

T

thunorr

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Ethnic group
Scots-Irish Appalachian
Y-DNA haplogroup
R-CTS8277
mtDNA haplogroup
N1a1a1a2
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I'm thinking that Illustrative probably miscalculated my CHG percentage. Don't really know.


It does kind of mess up when we get a sample with Asiatic admixture (like Finns), but the calculator should remain fairly accurate to IllustrativeDNA.
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Attachments

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My results with simulated G25 for those who do not have actual G25.
 
52.0Anatolian_Neolithic_Farmer
40.0European_Hunter-Gatherer
8.0Caucasus_Hunter-Gatherer
 
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The Turkey_N sample in your list appears to have a good amount of Natufian admix
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The distances are a bit high.
 
Vallicanus said:
The distances are a bit high.
Click to expand...
I asked Chatgpt about that. according to it the fit numbers are fine for such ancient samples:

"When modeling mesolithic and neolithic populations in g25 with myself and modern populations, are fit numbers ranging from 0.04-0.10 acceptable?"

ChatGPT said:​

In the context of using the Global25 (G25) coordinates to model ancient populations (such as Mesolithic and Neolithic) alongside yourself and modern populations, fit numbers in the range of 0.04–0.10 are generally considered very good. Here’s a quick breakdown of what those numbers indicate:

  1. Fit Value Interpretation:
    • A lower fit number indicates a better fit, meaning the model is accurately capturing the relationships and proportions between your sample and the reference populations.
    • For G25 models, a fit below 1.0 is typically acceptable, and a fit below 0.5 is considered very good for most purposes. Getting fit values as low as 0.04–0.10 suggests an exceptionally close fit, especially when modeling ancient populations, which can be challenging due to the genetic drift and admixture in modern populations.
  2. Mesolithic and Neolithic Populations:
    • These ancient populations are often challenging to model because they represent genetic profiles that are quite distinct from most modern populations.
    • A fit as low as 0.04–0.10 in this context implies that your genetic profile has components that match very well with those ancient samples, or that the model is capturing those ancient signals accurately when combined with modern populations.
  3. Modern Populations in the Model:
    • Adding modern populations can sometimes increase fit values slightly due to admixture and genetic shifts over time.
    • However, your low fit values suggest that your genetic profile aligns well with both the selected ancient populations and modern populations in the model.
In summary, a fit range of 0.04–0.10 is indeed excellent and suggests that the model is capturing your genetic relationships with the Mesolithic, Neolithic, and modern populations very accurately. This kind of fit quality can lend confidence to the proportional contributions that the model provides, giving you more reliable insights into your ancient ancestry.

"For G25 models, a fit below 1.0 is typically acceptable"

I don't quite agree with this statement it made. The rest seems reasonable
 
thunorr said:
It should be the same Turkey_N sample used in Illustrative.
Click to expand...
The reason I keep bringing it up in various posts is because I held a misconception that Neolithic Anatolians and Natufians were disconnected groups. And I think it's important to share this information.




This comes from ChatGPT:

it is generally agreed among geneticists and archaeologists that Neolithic Anatolian farmers had some Natufian-related ancestry. The Natufians, who lived in the Levant around 15,000 to 11,500 years ago, are considered one of the earliest known groups with a sedentary lifestyle and are associated with the transition from foraging to farming.

When ancient DNA from early Anatolian farmers was analyzed, it showed that their genetic profile was not purely European hunter-gatherer or indigenous Anatolian. Instead, it included a significant component similar to the Natufians, along with European hunter-gatherer ancestry, suggesting a blend of these ancestries. This admixture is thought to have happened before or during the migration of these early farmers from the Near East into Anatolia and eventually into Europe, where they played a key role in spreading agriculture.

This Natufian-related ancestry in Anatolian Neolithic farmers is viewed as part of the broader Near Eastern genetic influence, which helped shape the genetic landscape of early agricultural communities across Anatolia and Europe.




Are there any peer reviewed papers that support this?

ChatGPT said:​

Yes, several peer-reviewed studies have explored the genetic relationship between Neolithic Anatolian farmers and Natufians, confirming that Anatolian farmers carried Natufian-related ancestry. Here are a few prominent papers:

  1. Lazaridis et al. (2016) - "Genomic insights into the origin of farming in the ancient Near East"
    This study analyzed ancient DNA from Neolithic populations in the Near East, including Anatolia, the Levant, and Iran. It demonstrated that early Anatolian farmers had a genetic component related to Natufians, alongside other ancestry from the broader Near East. The paper highlights that Neolithic Anatolian farmers were genetically distinct but shared a common ancestry with the Natufians and early Levantine populations.

    Reference:
    Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., ... & Reich, D. (2016). Genomic insights into the origin of farming in the ancient Near East. Nature, 536(7617), 419-424.
    DOI: 10.1038/nature19310
  2. Lazaridis et al. (2014) - "Ancient human genomes suggest three ancestral populations for present-day Europeans"
    This earlier study introduced the concept of “Basal Eurasian” ancestry, which Natufians carried in higher proportions than other contemporary populations. Later studies confirmed that early Anatolian farmers, like the Natufians, had Basal Eurasian ancestry, linking them to Near Eastern and Levantine populations. While this paper does not analyze Anatolian farmers directly, it established a framework that later studies used to trace Natufian-related ancestry in Neolithic farmers.

    Reference:
    Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., ... & Reich, D. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, 513(7518), 409-413.
    DOI: 10.1038/nature13673
  3. Kılınç et al. (2016) - "The Demographic Development of the First Farmers in Anatolia"
    This study focused on the genetic diversity of early farming populations in Anatolia. The researchers found that Anatolian Neolithic farmers had a distinct Near Eastern ancestry component, consistent with shared ancestry with the Natufians. This paper provides evidence that early Anatolian farmers had contributions from populations in the Levant, reflecting Natufian-like ancestry in their genetic makeup.

    Reference:
    Kılınç, G. M., Omrak, A., Özer, F., Günther, T., Büyükkarakaya, A. M., Bıçakçı, E., ... & Götherström, A. (2016). The Demographic Development of the First Farmers in Anatolia. Current Biology, 26(19), 2659-2666.
    DOI: 10.1016/j.cub.2016.07.057
  4. Lazaridis et al. (2022) - "The genetic history of the Southern Arc: A bridge between West Asia and Europe"
    This recent study provides an extensive overview of the genetic history of Anatolia and its connections to Europe and West Asia. It confirms that Anatolian farmers, who played a significant role in the spread of agriculture into Europe, carried ancestry associated with Natufian-like populations. This paper further supports the idea of genetic continuity and admixture between Natufian-related populations and early Anatolian farmers.

    Reference:
    Lazaridis, I., Alpaslan-Roodenberg, S., Acar, A., Açıkkol, A., Baykal, A., Begeny, F., ... & Reich, D. (2022). The genetic history of the Southern Arc: A bridge between West Asia and Europe. Science, 377(6609), 615-624.
    DOI: 10.1126/science.abm4247
These studies collectively provide a clear picture of how Neolithic Anatolian farmers carried Natufian-related ancestry, confirming the connection between these early farming populations and the Natufians of the Levant.
 
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