The big picture for West Asia, and specifically Anatolia, after Pinarbasi

Thanks to Feldman et al (2019), we got our first look at the ancient Anatolians from the Pleistocene. Due to the strong cultural links with later peoples, such as Boncuklu, I kind of figured that the hunter-gatherers would be pretty similar to the first farmers. The piece by Baird et al (2013), “Juniper Smoke, Skulls, and Wolves’ Tails“, was very insightful and does hint at continuity in the region.

To take a look at the formation of the first farmers of West Asia, I used the samples from Feldman et al (2019), Lazaridis et al (2016), and van de Loosdrecht et al (2018) to see what kind of picture emerges.

This first graph, is a simple tree that involves the formation of Boncuklu_N and Anatolia_N (Barcin), while using farmers from Iran and the Levant as additional sources, besides Anatolia_HG (Pinarbasi).

 

qpGraph Models for the Anatolian Farmers

The first graph is a simple set up of the base populations that are the most likely contributors to the formation of Boncuklu and Barcin. While there may be a better source in Eastern Anatolia or Syria, these will do for now.

The addition of Boncuklu to the graph led to a worst-Z score approaching five, asking for admixture between Ganj_Dareh_N and Boncuklu_N.

The inclusion of admixture from Ganj_Dareh_N to Boncuklu brought the Z-score down below three and formed a good base for Barcin, and is in general agreement with the findings of Feldman et al (2019).

While Anatolia_N is significantly closer to Boncuklu than any of the other populations, there is still a significant relationship with Levant_N shared only with the Barcin farmers.

This next graph shows more agreement with Feldman et al (2019), with significant Levant_N ancestry being found in the Barcin farmers. However, there is still a significant relationship between Ganj_Dareh and Barcin that is not resolved.

This last graph did bring the worst Z-score to a more acceptable level, around three. This does differ a bit from qpAdm, where you can create a successful model without any Iranian admixture on top of what is found in Boncuklu. The Iranian admixture is essentially at the level of the standard error, making it unnecessary.

 

qpGraph Models for the Mixing Between Populations in North Africa and West Asia from 15,000-10,000 Years Ago

To begin this simple graph, I started with the older samples from each region, with Natufians being a mix between Iberomaurusians and ancient Anatolians, which does fit fine and first demonstrated by Lazaridis et al (2018)(pre-print). Since I do not have the Dzudzuana genomes, I used Anatolia_HG (Pinarbasi) as the stand-in for that admixture into the Iberomaurusians (IBM).

For the next graph, I started by adding Levant_N to a branch related to Natufians. I didn’t think starting with Levant_N before Boncuklu_N is a big deal as several of the samples are contemporary and one need not come from the other. The most significant score left from this graph asks for a stronger relationship between Ganj_Dareh and the Levantine farmers.

After adding an admixture event between Natufians and Ganj_Dareh to create Levant_N, there is still a need for a stronger relationship between Anatolia_HG and Levant_N.

This next graph only required minimal admixture from Anatolia_HG (five percent), to bring down the Z-score below 2.

For the last tree, I added in Boncuklu and also needed the admixture from Ganj_Dareh to Boncuklu to bring the Z-score down. In this last graph, Anatolia_HG ancestry does overtake Ganj_Dareh ancestry in the Levant_N samples. Anatolia_HG-related ancestry also is the most widespread component in Anatolia, the Levant, and North Africa.

 

Full qpGraph of Ancient Farmers 15,000-10000 Years Ago

For the last set of graphs, I included GoyetQ116-1 and MA1 to cover ancient European to Siberian ancestry.  Ust_Ishim was added to try and figure out the amount of Basal Eurasian that would be needed for each sample. I also included the Onge for any additional East Eurasian ancestry that might be needed.

As a base, I started with just Anatolia_HG, IBM (Iberomaurusians), and Natufians.

For the next graph, I included Ganj_Dareh_N as a mix of MA1 and Basal Eurasian. This left a very significant Z-score between the Onge and Ganj_Dareh_N, suggesting additional East Eurasian ancestry is needed for Ganj_Dareh_N.

For this graph, an additional 29 percent admixture from Onge to Ganj_Dareh_N helped bring down the worst Z-score significantly.

This next graph includes Boncuklu_N, coming from a branch related to Anatolia_HG. The worst Z-score is also suggestive of gene-flow from a population related to Ganj_Dareh_N into the Boncuklu_N farmers.

With admixture from Ganj_Dareh_N to Boncuklu, the worst Z-score has dropped to near 3. The next addition to the graph will be Levant_N, from a branch related to Natufians.

With the inclusion of Levant_N, admixture is again needed from Ganj_Dareh, to Levant_N, just as with the simpler graphs.

With the addition of Ganj_Dareh admixture, the Levantine farmers next needed some extra ancestry from a group related to Anatolia_HG.

This last graph shows what is an effective model for the deeper ancestry and mixture between ancient North African and West Asian populations.

 

Discussion

From what I have been able to put together, there is an agreement with the findings of Feldman et al (2019) when it comes to the formation of Anatolian farmers and the importance of the Pleistocene hunters, or a related group, to the formation of not only Anatolian farmers but also Levant_N. The only difference with qpGraph is that it does want additional ancestry from Ganj_Dareh_N into the Barcin farmers. To re-iterate Feldman et al (2019), there is the appearance of great continuity through the development of agriculture in Anatolia, but this could change with more samples, particularly Eastern Anatolia and Syria.

 

Sources

Baird et al. (2013) Juniper smoke, skull sand wolves’ tails. The Epipaleolithic of the Anatolian plateau in its South-west Asian context; insights from Pinarbasi. https://www.academia.edu/13587260/Juniper_smoke_skulls_and_wolves_tails._The_Epipalaeolithic_of_the_Anatolian_plateau_in_its_South-west_Asian_context_insights_from_P%C4%B1narba%C5%9F%C4%B1

Feldman et al. (2019) Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. https://www.nature.com/articles/s41467-019-09209-7#Sec20

Lazaridis et al. (2016) Genomic insights into the origin of farming in the ancient Near East. https://www.nature.com/articles/nature19310

Lazaridis et al. (2018) (pre-print) Paleolithic DNA from the Caucasus reveals the core of West Eurasian ancestry. https://www.biorxiv.org/content/10.1101/423079v1

van de Loosdrecht et al (2018) Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations.