Population Genomics

Of Stone & Blood: The demography of the Megalithic expansions (work in progress)

February 1, 2019February 3, 2019 populationgenomics18 Comments

One subject that has often been overlooked, is the genetic influence of the first megalith builders of Northern France. This location is meeting point between Danubian and Cardial Neolithic groups. Not only that, but also mixture with Mesolithic hunters of the region. This mixture can be seen quite clearly in the mtDNA (Rivollat et al, 2015; LeRoy et al, 2016). The one thing that is also questioned is just how much genetic impact did Megalithism have on the genetic make-up of Northern European farmers of the Middle and Late Neolithic. Is this a movement of people, or “monumental” ideas?

Since early times, the movement of farmers to Britain was seen as a movement from France, from Michelsberg, or related groups (Childe, 1931). To test this idea, I used datasets from Lipson et al, 2017; Olalde et al, 2018; and Mathieson et al, 2018) to look for a relationship using qpGraph.

Not only are the samples from Southern France and England alike, they are basically identical! Both are probably rooted in the Paris Basin, showing Danubian, Cardial, and Mesolithic roots. As the link is shown below, in Le Roy et al (2016). Also, note the shift towards France, by later Central Farmers of the Middle to Late Neolithic.

Below, is the first graph, showing the genetic ties between England, and Southern France. Both are likely from the Paris Basin group.

D-stats showing France_MN and England_N as a clade

Out	Test	X	Y	D	Z-score	SNPs
Chimp	Ust_Ishim	France_MN	England_N	-0.000325	-1.052	890030
Chimp	WHG	France_MN	England_N	0.000041	0.116	888629
Chimp	Iberia_EN	France_MN	England_N	-0.000248	-0.923	860108
Chimp	LBKAustria	France_MN	England_N	-0.000119	-0.469	887340
Chimp	GermanMN	France_MN	England_N	0.000152	0.514	853634
Chimp	Gokhem2	France_MN	England_N	-0.00022	-0.437	209487
Chimp	MN_Iberia	France_MN	England_N	-0.000539	-1.933	830076
Chimp	GAC_Poland	France_MN	England_N	0.000002	0.007	694973
Chimp	Czech_MN	France_MN	England_N	-0.000167	-0.558	818848

Graph with England_N alone

German Middle Neolithic Funnelbeaker

This same set-up is the one I used to then find the relationship to later Megalith building cultures. The first one I chose to look at was the Funnelbeaker samples from Germany. The surprising thing from this graph is that the German Middle Neolithic samples (minus the Roessen sample) were almost exactly like the England and French Neolithic samples, with a slight bit more Danubian admixture.

Attempt to create TRB-Germany without admixture from French-related groups

The first graph, is just Germany_MN, uplaced, with the worst-Z being one that asks for Germany_MN and England_N to be closer.

The second graph forces Germany_MN to be attached to LBK

The worst-Z from this graph asks for WHG to be closer to Germany_MN. The following graph includes an edge from WHG to Germany_MN.

As a result of this graph, the worst-Z now asks for Germany_MN and Iberia_EN to be closer. Due to this, a migration edge from Iberia_EN is added to the next graph.

This last graph has many issues. Not only the zero drift edges, but a migration edge of 0% from Iberia to Germany and a worst-Z still not resolved. It seems that deviating from the desire to connect Germany_MN and England_N caused the poor outcome.

Iberian Middle Neolithic at La Mina

The second group that I looked at was the Middle Neolithic group from La Mina, in Northern Spain. Once again, the Middle Neolithic population was almost identical to the group with roots in France. Specifically, those that moved to Southern France.

Swedish Funnelbeaker

While Gokhem2 does not have as much coverage as I would like, I thought that they would also be good to check, to make sure they are also rooted in the same group. As suspected, she was also almost exactly like the English and French samples.

Globular Amphora in Poland

Since Globular Amphora is supposed to come out of the TRB group in Northern Germany, I thought that I would also take a look at them and see if they are also closely related to the farmers from France. They also turned out to have a great deal of their ancestry from this group.

So, the picture that is emerging is that at one time, groups from Iberia, to Britain, up to Scandinavia, and all the way to the steppes of Ukraine were rooted in the French Middle Neolithic.

D-stats suggestive of Cardial gene-flow

Out	Test	X	Y	D	Z-score	SNPs
Chimp	England_N	Iberia_EN	LBKAustria	-0.00065	-3.053	922319
Chimp	France_MN	Iberia_EN	LBKAustria	-0.00089	-3.519	877516
Chimp	GermanMN	Iberia_EN	LBKAustria	0.000082	0.311	927867
Chimp	Gokhem2	Iberia_EN	LBKAustria	0.000096	0.253	232081
Chimp	MN_Iberia	Iberia_EN	LBKAustria	-0.001163	-4.727	888929
Chimp	GAC	Iberia_EN	LBKAustria	0.000024	0.103	923159

African Asymmetry

Now, Chimp does have its shortfalls, such as the branch-shortening effect, and ancient attraction, but it is basically symmetrical in relationship to each of these samples. However, the same can not be said for Africans. That is the reason that I have not included them in these graphs. Now, with them, the graphs really don’t change, but you can have the need for edges from farmers to Africans. Farmers, specifically those from Europe, are much closer to basically all Africans, when put against ENA, hunter-gatherers, and more basal sources, such as Natufians.

This is reflected in graphs, and also D-stats. Now, how this is so is the big question. We may see farmer movement taking R1b-V88 and Iberian ancestry as far as South_Africa_2000BP, or something such as ascertainment bias. The fact that Malawi_Hora_Holocene_8100BP is also showing this is quite puzzling and leaning me more towards some kind of bias. The likelihood of a migration of something like a Dzudzuana to SE Africa that early could be possible, but without the actual sample, that is hard to test.

Out	Test	X	Y	D	Z-Score	SNPs
Chimp	Mbuti_DG	Iberia_EN	LBK	-0.000074	-0.522	982851
Chimp	Mbuti_DG	Iberia_EN	Natufian	-0.000816	-2.636	474711
Chimp	Mbuti_DG	Iberia_EN	GanjDareh	-0.000459	-1.691	787482
Chimp	Mbuti_DG	Iberia_EN	IBM	0.000146	0.595	964435
Chimp	Mbuti_DG	Iberia_EN	Van2900BP	-0.000726	-2.156	432540
Chimp	Mbuti_DG	Iberia_EN	Iron_Gates	-0.000646	-3.658	983550
Chimp	Mbuti_DG	Iberia_EN	EHG	-0.00045	-1.947	943281
Chimp	Mbuti_DG	Iberia_EN	SteppeEBA	-0.000218	-1.259	981530
Chimp	Mota	Iberia_EN	LBK	-0.00013	-0.672	982461
Chimp	Mota	Iberia_EN	Natufian	-0.001552	-3.748	474581
Chimp	Mota	Iberia_EN	GanjDareh	-0.000572	-1.566	787235
Chimp	Mota	Iberia_EN	IBM	-0.000134	-0.4	964105
Chimp	Mota	Iberia_EN	Van2900BP	-0.000879	-1.906	432413
Chimp	Mota	Iberia_EN	Iron_Gates	-0.000761	-3.119	983154
Chimp	Mota	Iberia_EN	EHG	-0.0009	-2.745	942951
Chimp	Mota	Iberia_EN	SteppeEBA	-0.00039	-1.64	981147
Chimp	S_A2000BP	Iberia_EN	LBK	-0.000432	-2.587	931815
Chimp	S_A2000BP	Iberia_EN	Natufian	-0.000884	-2.562	455408
Chimp	S_A2000BP	Iberia_EN	GanjDareh	-0.000862	-2.975	750479
Chimp	S_A2000BP	Iberia_EN	IBM	-0.000536	-1.999	914899
Chimp	S_A2000BP	Iberia_EN	Van2900BP	-0.000479	-1.33	414977
Chimp	S_A2000BP	Iberia_EN	Iron_Gates	-0.00093	-4.843	932493
Chimp	S_A2000BP	Iberia_EN	EHG	-0.000834	-3.332	894713
Chimp	S_A2000BP	Iberia_EN	Steppe_EBA	-0.000556	-2.95	930610
Chimp	Malawi_HH	Iberia_EN	LBK	-0.000165	-0.79	575904
Chimp	Malawi_HH	Iberia_EN	Natufian	-0.000828	-1.801	320660
Chimp	Malawi_HH	Iberia_EN	GanjDareh	-0.000506	-1.312	505066
Chimp	Malawi_HH	Iberia_EN	IBM	-0.000526	-1.589	571516
Chimp	Malawi_HH	Iberia_EN	Van2900BP	-0.000141	-0.311	310516
Chimp	Malawi_HH	Iberia_EN	Iron_Gates	-0.000669	-2.642	576018
Chimp	Malawi_HH	Iberia_EN	EHG	-0.000607	-1.87	563496
Chimp	Malawi_HH	Iberia_EN	SteppeEBA	-0.000593	-2.408	575632
Chimp	Yoruba	Iberia_EN	LBK	-0.000133	-0.871	897516
Chimp	Yoruba	Iberia_EN	Natufian	-0.000948	-2.915	432020
Chimp	Yoruba	Iberia_EN	GanjDareh	-0.00057	-1.919	718598
Chimp	Yoruba	Iberia_EN	IBM	0.001219	4.714	881191
Chimp	Yoruba	Iberia_EN	Van2900BP	-0.000978	-2.637	394707
Chimp	Yoruba	Iberia_EN	Iron_Gates	-0.000762	-4.026	898020
Chimp	Yoruba	Iberia_EN	EHG	-0.000876	-3.353	862918
Chimp	Yoruba	Iberia_EN	SteppeEBA	-0.000375	-1.995	896410

Testing with qpGraph also always resulted in gene-flow from a source like Iberia_EN, and sometimes also from Iberomaurusians (IBM). Mbuti is not bad, in that it is nearly perfectly aligned with Danubian and Cardial sources, the problem lies in the HG stats, where Mbuti does want to be closer to farmers than hunters, and the flow is always to Africa. Testing with flow both to and from Iberian farmers illustrates the same with all Africans in a tree. Here is a tree with South_Africa_2000BP as an example:

This asymmetry makes me wary of including them in analysis that includes both hunters and various types of farmers. I also feel adding too many more admixture edges will be distracting and admixture from Eurasians to Africans does need more ancient samples to resolve whether these are all legit or not.

Trying to create a graph without Chimp does lose a more neutral source for sorting out this farmer and hunter ancestry in Northern Europe, although it does seem minimal, judging by this basic tree involving England_N and France_MN. It seems the most affected is the actual Cardial ancestry in the samples. They become less Cardial than Danubian, in the tree not involving TRB samples, but actually are now closer to what they were with the other farmers involved in the tree.

However, moving onto Germany_MN, we see that Chimp would make the fit better, decreasing the worst Z that seems to want more Cardial influence to England_N.

Including Mbuti into the Analyses

As expected, adding an African to a graph, when they are not symmetrically related, created a graph that becomes overly complicated and does not match other statistical methods. This includes haplotype analysis of an Irish farmer that shared more ancestry with Cardial than Danubian farmers.

With this output, it seems safest to avoid using Africans in analysis that is Eurasian specific and stick to using Chimp as a more neutral outgroup. No African can be a purely symmetrical outgroup and can drastically affect the quality of the graph and qpAdm output.

With all of these results, it appears that not only is Funnelbeaker and Globular Amphora share a good amount of ideas regarding pottery and burial, but actual developed as a mix of Atlantic farmers, mixing with local farmer and hunter groups, adopting some of their culture and genes as well.

Discussion

With the results from the graphs, D-stats, and also parental markers, it seems that it is quite probably that farmers from France are responsible for the spread of Megalithism. Not only do graphs prefer a closeness of farmers from France, England, and Germany, but there are new markers of “Western” origin in Germany Middle Neolithic farmers. This includes many shared Y-DNA markers, including I2a1b, and shared mtDNA that are not in Danubian farmers, such as U3, H3, H4, and others. Also notable, is the f3(England_N LBK_Austria Germany_MN -0.000433 -0.382 353272), suggesting gene-flow from France to Germany does work.

While more sampling across France will help, it does seem that there is a shared ancestry between England, France, and Germany that has more to it than shared Danubian ancestry.

Sources

Gordon Childe, V. (1931). The Continental Affinities of British Neolithic Pottery. Archaeological Journal, 88(1), 37–66. doi:10.1080/00665983.1931.10853568

Melie Le Roy et al (2016)Distinct ancestries for similar funerary practices? A GIS analysiscomparing funerary, osteological and aDNA data from the Middle Neolithic necropolis Gurgy “Les Noisats” (Yonne, France) http://dx.doi.org/10.1016/j.jas.2016.07.003

Mark Lipson et al (2017) Parallel paleogenomic transects reveal complex genetic history of early European farmers. Nature volume 551, 368–372 (16 November 2017) https://www.nature.com/articles/nature24476#supplementary-information

Inigo Olalde et al (2018) The Beaker phenomenon and the genomic transformation of Northwest Europe. Nature volume 555, 190–196 (08 March 2018) https://www.nature.com/articles/nature25738

Maïté Rivollat et al., When the Waves of European Neolithization Met: First Paleogenetic Evidence from Early Farmers in the Southern Paris Basin. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0125521]

Nicole Sheridan (2013) Early Neolithic habitation structures in Britain and Ireland: A matter of circumstance and context. https://www.researchgate.net/publication/302214298_Early_Neolithic_Habitation_Structures_in_Britain_and_Ireland_a_Matter_of_Circumstance_and_Context

The Karasuk Culture: Potentially the Ancestors of Iranian and later Scytho-Sarmatian nomads

September 14, 2018September 14, 2018 populationgenomics9 Comments

With the advances of aDNA, we have now begun to tackle questions, such as the origin of the “Scythian peoples”. This was first seen with Unterlander et al (2017), and more were included into Damgaard et al (2018). With the help of Allentoft et al (2015), Mathieson et al. (2018), Narasimhan et al. (2018), along the two previously mentioned papers, I will check the question of origin for the early Iranian nomads.

Bagley (n.d.), attempted to summarize the work on the early Zhou period and their interaction with Siberian Bronze Age center. This was based on work by Loeuwe & Shaugnessy (1999). This highlights interesting aspects of the trade between these two groups, with artifacts related to the Karasuk culture spreading to not only China, but also towards Europe (Bagley, n.d.). While their early dating of a movement (Chernyk, 2008), does not really match the genetic view to this point, there are later samples which hint in this direction.

Since the time of Herodotus, many have had their own ideas on the origins of the Scythians. Mallory (1989) noted that some thought that the origin lie in the west, in the region north of the Black Sea. Others, saw the Scythians, and Iranians in general, as originating in Central Asia, and even Siberia. Some have even thought that a multi-regional origin was more likely, with changes being cultural, rather than demographic.

Davis-Kimball (2005), was one that saw the Scythians as a group that was multi-ethnic, rather than group with a single origin, or denoting a single group of people. Sometimes, anything west of Inner Mongolia and China was referred to as Scythian, but Scythian would also sometimes be restricted to those in the Western and Central Steppes (Di Cosimo, 1999).

The first way to go at this, I feel, is to look at Karasuk. A culture that Mallory (1997), described as very mobile, compared to Andronovo, that is known more by their kurgan burials than their settlements. Karasuk is also seen as being highly influential and starting the animal art so common among the “Scythian” people (Keyser et al, 2009). Mallory (1997) even mentions the potential of the Karasuk to have a specific “proto-Iranian” identity. The influence of the Yenesei, and Slab Grave people cannot be underplayed (Mallory, 1997). Okunevo is thought to be a mix of Afanasievo and local Yeneseian groups (Great Soviet Encyclopedia, 1979), in an area later within the Andronovo sphere, and this mixing may likely be the formation of the Karasuk culture within the Minusinsk Basin. Okunevo is thought to be the group that introduced realistic animal art to these later steppe pastoralists as well.

First of all, I wanted to take a look at the Karasuk cluster that is closer to the Andronovo samples in PCA. To understand the make-up of Karasuk, I first used qpAdm to find a valid model of their origin. With qpAdm, the set of right populations, or outgroups chosen included Mbuti_DG, Ust_Ishim, Kostenki14, EHG, Villabruna, Ganj_Dareh_N, Anatolia_N, Steppe_EMBA, Karitiana, and the Ami.

The most successful model of the Karasuk culture needed excess Han-related ancestry, in addition to the ENA found in the Okunevo samples. Best exemplified with the Shamanka_BA run.

Karasuk

Chi-square	Tail-prob	Andronovo	Okunevo	Han
17.866	0.0222543	0.721	0.279	NA
	std error	0.02	0.02	NA

Chi-square	Tail-prob	Andronovo	Okunevo	Han
9.613	0.211584	0.766	0.178	0.056
	std error	0.026	0.04	0.019

Chi-square	Tail-prob	Andronovo	Shamanka_BA
5.1	0.746845	0.814	0.186
	std error	0.016	0.016

Looking at the Deeper Ancestry of the Karasuk Culture, I tried to make them a mix of Sintashta, Afanasievo, and an ENA group from the Baikal area, Shamanka_EN. This made sense as to making a mixture of a Siberian hunter, Bronze Age steppe pastoralists, and also Middle to Late Bronze Age groups in Central Asia. While the standard errors are a little high, it is clear that the dominant ancestry in Karasuk is Sintashta-related.

Chi-square	Tail-prob	Sintashta	Shamanka_EN	Afanasievo
6.196	0.625314	0.686	0.189	0.125
	std error	0.069	0.014	0.07

After adding Steppe_MLBA, Germany_MN, and West_Siberia_N to the pright outgroups:

Chi-square	Tail-prob	Sintashta	Shamanka_BA	Afanasievo
7.951	0.633621	0.541	0.178	0.281
	std error	0.081	0.017	0.081

Interstingly, the Karasuk is also seen to have expanded, if not influenced all the way towards the Black Sea, and at least the Aral Sea (((((((((Trying to relocate citation!!!!!!))))))))

Other samples, dating to about the same time, North of the Aral sea are seen in Mezhovskaya. Even more interesting, is that samples are near genetic dittos to the Karasuk samples. Could Mezhovskaya be part of the western Karasuk group that creates the great cultural uniformity among earlier Iranian nomads through the Scythian period? Potentially, yes.

Mezhovskaya

Chi-square	Tail-prob	Andronovo	Okunevo	Han
12.248	0.140492	0.741	0.259	NA
	std error	0.028	0.028	NA

Chi-square	Tail-prob	Andronovo	Okunevo	Han
6.036	0.535555	0.784	0.151	0.064
	std error	0.032	0.051	0.025

Chi-square	Tail-prob	Andronovo	Shamanka_BA
5.318	0.723087	0.846	0.154
	std error	..022	0.022

With Chechushkov et al (2018), we see that horse-riding in battle may have begun in Central Asia between 1500-1200 BCE. Which is, of course, during the highly mobile Karasuk period and within the range of these groups.

Mezhovskaya can essentially be modeled as 100% Karasuk with qpAdm, as any additional ancestry is within the standard error of that component.

The next question then is, is Karasuk, and possibly by extension Mezhovskaya, the homeland and ancestors of the Scythians? Are they also ancestral to the western Scythians, as far as Hungary?

The first Scythian group I looked at was the Tagar Culture, which followed the Karasuk in the Minusinsk Basin. The Karasuk is indeed very important here for the Tagar. Even the Karasuk+Karasuk outlier combo works here. What’s even more interesting about the Tagar culture, is the great similarity between their art and that of the European Scythians (Keyser et al, 2009; Encyclopaedia Britannica, n.d.).

Tagar

Chi-square	Tail-prob	Karsuk	Okunevo
5.291	0.726104	0.933	0.067
	std error	0.037	0.037

Chi-square	Tail-prob	Karasuk	Shamanka_BA
7.201	0.515133	0.967	0.033
	std error	0.021	0.021

Pazyryk

The Pazyryk Culture is another well-known group of Scythians, that include the famous tattooed mummy. Their culture is seen as having been very warlike (Citation)))))))))))))

They also require a lot of Karasuk ancestry and also groups that are from nearby, or closely related groups to these samples.

Chi-square	Tail-prob	Karsuk	Okunevo	Han
16.037	0.0247822	0.313	0.34	0.347
	std error	0.036	0.05	0.023

Chi-square	Tail-prob	Karasuk	ShamankaBA	Han
1.761	0.971876	0.43	0.43	0.14
	std error	0.028	0.08	0.061

Zevakino_Chilikta

Chi-square	Tail-prob	Karasuk	Okunevo
116.899	1.45E-21	0.41	0.59
	std error	0.089	0.089

Chi-square	Tail-prob	Karasuk	BMAC	Han
6.075	0.531047	0.568	0.099	0.333
	std error	0.045	0.042	0.019

Tian-Shan Saka

Chi-square	Tail-prob	Karasuk	Okunevo	BMAC	Han
10.628	0.10059	0.574	0.134	0.21	0.082
	std error	0.06	0.047	0.023	0.018

Chi-square	Tail-prob	Karasuk	ShamankaBA	BMAC
10.703	0.152108	0.618	0.173	0.209
	std error	0.04	0.017	0.033

The Tian-Shan Saka graph here did get a little over-complicated for my taste, but with such a complex mixture it might be bound to happen.

Central_Saka

Chi-square	Tail-prob	Karasuk	Okunevo	Han	BMAC
6.786	.341095	0.429	0.284	0.180	0.107
	std error	0.06	0.051	0.02	0.034

Chi-square	Tail-prob	Karasuk	Shamanka_BA	BMAC
2.488	.927977	0.526	0.372	0.102
	std error	0.044	0.019	0.036

Scythian_Samara (Steppe_IA)

Chi-square	Tail-prob	Karasuk	Armenia_EBA
20.194	0.00962638	0.923	0.077
	std error	0.048	0.048

Chi-square	Tail-prob	Karasuk	BMAC
15.104	0.0571488	0.863	0.137
	std error	0.042	0.042

Chi-square	Tail-prob	Karasuk	BMAC	West_Siberia
9.936	0.192223	0.769	0.166	0.065
	std error	0.067	0.045	0.037

Chi-square	Tail-prob	Karasuk	BMAC	Botai
8.261	0.310125	0.674	0.236	0.089
	std error	0.108	0.068	0.056

Chi-square	Tail-prob	Mezhovskaya	BMAC
12.765	0.120182	0.913	0.087
	std error	0.05	0.05

Chi-square	Tail-prob	Tagar	BMAC
17.493	0.0253636	0.841	0.159
	std error	0.042	0.042

Hungarian Scythian

Chi-square	Tail-prob	Karasuk	Hungary_BA
13.624	0.0921081	0.355	0.645
	std error	0.035	0.035

Chi-square	Tail-prob	Karasuk	Balkan_BA
13.99	0.0820368	0.247	0.753
	std error	0.037	0.037

Chi-square	Tail-prob	Scythian_Samara	Hungary_BA
18.514	0.0176836	0.314	0.686
	std error	0.029	0.029

Chi-square	Tail-prob	Mezhovskaya	Hungary_BA
16.258	0.0388319	0.339	0.661
	std error	0.043	0.043

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Bagley, R. Shang Archaeology; The Northern Zone. (1999) http://s155239215.onlinehome.us/turkic/btn_Archeology/Zhou/CambridgeZhouChouArcheologyNorthEn.htm

“Central Asian arts: Neolithic and Metal Age cultures”. Encyclopædia Britannica Online. Encyclopædia Britannica

Chechushkov et al., Early horse bridle with cheekpieces as a marker of social change: An experimental and statistical study, Journal of Archaeological Science, Volume 97, September 2018, Pages 125-136, https://doi.org/10.1016/j.jas.2018.07.012

Chernykh, The Formation of the Eurasian “Steppe Belt” of Stockbreeding Cultures. http://www.academia.edu/22557016/FORMATION_OF_THE_EURASIAN_STEPPE_BELT_OF_STOCKBREEDING_CULTURES.BY_E.N._Chernykh

Di Cosimo, Nicola, “The Northern Frontier in Pre-Imperial China (1,500 – 221 BC)”, in: M. Loeuwe, E.L. Shaughnessy, eds, The Cambridge History of Ancient China: From the Origins of Civilization to 221BC, 1999, Cambridge University Press 1999, ISBN 9780521470308

Keyser, Christine; Bouakaze, Caroline; Crubézy, Eric; Nikolaev, Valery G.; Montagnon, Daniel; Reis, Tatiana; Ludes, Bertrand (May 16, 2009). “Ancient DNA provides new insights into the history of south Siberian Kurgan people”. Human Genetics. Springer-Verlag.

Mallory, J. P. (1997). Encyclopedia of Indo-European Culture. Taylor & Francis. ISBN 1884964982.

Mathieson et al., (2018) The genomic history of southeastern Europe. Nature 555, 197-203. (Paper / doi:10.1038/nature25778)

Narasimhan et al, The Genomic Formation of South and Central Asia, Posted March 31, 2018, doi: https://doi.org/10.1101/292581

“Okunev Culture”. The Great Soviet Encyclopedia. 1979

Unterländer et al., Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe, Nature Communications 8, Article number: 14615 (2017), doi:10.1038/ncomms14615

Another look at South Asian aDNA

August 8, 2018August 22, 2018 populationgenomics25 Comments

With Narasimhan et al (2018), we got our first look at Central, South Central, and South Asian aDNA. Not only did we get to see new steppe samples throughout the Bronze Age, but even from the Chalcolithic, through the Bronze Age in the Turan region, including BMAC. While there certainly looks to be steppe ancestry in South Asia, it has likely been highly inflated with previously available aDNA, and those that did not account for ANE that was already present in the region. The anticipation of the soon to be released Harappan sample(s), the models will only improve further.

This post will be constantly evolving as I add new outputs from qpAdm and qpGraph, so keep checking back in.

What I have noticed using qpAdm is that South Asian Dravidians do wonders as stand-ins for Harappan ancestry. So, we may see that some group greatly resembles them. I have seen that using the Palliyar and Paniya does work well, but the Irula does seem to work best. I don’t know whether that really means anything or the fact that they have more coverage.

The first thing I did was to look for populations to occupy the right pops, or populations which create the most significant D-stats between my left populations, or those set as the populations used in the mixture. Aside from using an African, Mbuti_DG, I found that using Ust-Ishim, Onge, Ami, EHG, Iron_Gates, Anatolia_N, Ganj_Dareh_N, and Karitiana. Kostenki14 is a hit and miss, as it doesn’t always have significant stats involved comparing two populations. This could be due to the age of the sample and not really developing any significant drift that can help differentiate populations in the test. This can lead higher chi-squares and lower tail-probabilities.

For the following, Brahmin_SGDP and Brahmin_Tiwari did have good marker counts, ranging from 170-200K, but the Brahmin_TN and Brahmin_UP sit around 50K, so they should be taken with a grain of salt.

SIS1= Shahr_I_Sokhta_BA1

Arm_EBA= Armenia_EBA

SGDP	chisq	tail prob	SIS1	Irula	Sintashta	Dali_EBA	Arm_EBA
w Kostenki	2.872	0.82475	0.208	0.623	0.1	0.069	NA
		std error	0.038	0.035	0.036	0.035	NA
w/o Kostenki	2.031	0.844866	0.212	0.62	0.103	0.065	NA
		std error	0.037	0.034	0.036	0.035	NA
w Kostenki	1.868	0.760109	0.167	0.609	0.065	0.097	0.063
		std error	*0.071*	0.034	*0.063*	*0.051*	*0.08*
w/o Kostenki	2.599	0.761475	0.178	0.61	0.057	0.097	0.058
		std error	*0.063*	0.035	*0.065*	*0.046*	*0.081*

Tiwari	chisq	tail prob	SIS1	Irula	Sintashta	Dali_EBA	Arm_EBA
w Kostenki	8.292	0.217452	0.138	0.583	0.208	0.071	NA
		std error	0.025	0.021	0.023	0.02	NA
w/o Kostenki	7.332	0.19711	0.139	0.577	0.211	0.073	NA
		std error	0.025	0.02	0.023	0.02	NA
w Kostenki	5.855	0.320606	0.089	0.579	0.154	0.099	0.08
		std error	0.04	0.021	0.039	0.026	*0.049*
w/o Kostenki	5.351	0.253112	0.096	0.574	0.162	0.097	0.071
		std error	0.039	0.02	0.039	0.026	*0.049*

TN	chisq	tail prob	SIS1	Irula	Sintashta	Dali_EBA	Arm_EBA
w Kostenki	0.925	0.988309	0.156	0.656	0.113	0.074	NA
		std error	0.043	0.039	0.04	0.04	NA
w/o Kostenki	0.557	0.989882	0.168	0.643	0.117	0.072	NA
		std error	0.042	0.037	0.038	0.039	NA
w Kostenki	0.861	0.973004	0.145	0.653	0.097	0.086	0.019
		std error	0.079	0.039	0.073	0.049	0.095
w/o Kostenki	0.0624	0.960366	0.191	0.638	0.13	0.068	-0.027
		std error	0.079	0.038	0.072	0.049	0.093

UP	chisq	tail prob	SIS1	Irula	Sintashta	Dali_EBA	Arm_EBA
w Kostenki	7.561	0.272087	0.147	0.598	0.181	0.075	NA
		std error	0.032	0.028	0.031	0.031	NA
w/o Kostenki	5.636	0.343262	0.151	0.59	0.188	0.071	NA
		std error	0.031	0.027	0.029	0.029	NA
w Kostenki	7.338	0.196693	0.11	0.599	0.144	0.094	0.054
		std error	0.066	0.028	0.059	0.039	0.081
w/o Kostenki	5.866	0.209375	0.136	0.59	0.171	0.08	0.022
		std error	0.061	0.027	0.054	0.037	0.073

NEW-8-9-18

Dzh1 = Dzharkutan1_BA, Late BMAC

Steppe_E = Steppe_MLBA_East

SGDP	chisq	tail prob	Irula	Dzh1	Sintashta	Steppe_E	Dali_EBA
w Kostenki	6.954	0.433685	0.681	0.203	0.116	NA	NA
		*std error*	0.023	0.034	0.028	NA	NA
	6.294	0.505837	0.678	0.198	NA	0.124	NA
		*std error*	0.023	0.034	NA	0.028	NA
	3.787	0.705485	0.629	0.225	NA	0.075	0.07
		*std error*	0.029	0.036	NA	0.037	0.033

The above is interesting in that there are whole graves spread around from India to West Asia that are completely late BMAC in character. There seems no possible way for there to not be detectable BMAC ancestry in South Asia, considering the amount of cemeteries and remains. I think the Harappan sample(s) will show that BMAC ancestry is indeed important in South Asia.

Looking at the Swat Valley samples, it gets even more interesting…

Aligrama	chisq	tail prob	Irula	Dzh1	Steppe_E	Dali_EBA
	12.238	0.0568697	0.49	0.355	0.091	0.063
		*std error*	0.03	0.036	0.034	0.03

Butkara_IA	chisq	tail prob	Irula	Dzh1	Steppe_E	Dali_EBA
	5.148	0.524941	0.404	0.489	0.03	0.077
		*std error*	0.029	0.034	0.034	0.031

Pak_IA_Ali	chisq	tail prob	Irula	Dzh1	Steppe_E	Dali_EBA
	8.014	0.237064	0.431	0.419	0.087	0.063
		*std error*	0.042	0.053	0.05	0.043

S_Sharif_IA	chisq	tail prob	Irula	Dzh1	Steppe_E	Dali_EBA
	8.433	0.208056	0.437	0.364	0.141	0.059
		*std error*	0.018	0.023	0.022	0.018

SPGT	chisq	tail prob	Irula	Dzh1	Steppe_E	Dali_EBA
	11.378	0.0773638	0.316	0.503	0.113	0.069
		*std error*	0.014	0.018	0.018	0.015

Interestingly, there seems to be no need for Andronovo admixture in Butkara, Pakistan_IA_Aligrama, and also the first Aligrama can do okay with just Dali, plus late BMAC. Of course, this all depends on the underlying population being similar to the Irula. Either way though, the Steppe ancestry should really not move. Next, I’ll see how including all BMAC samples affects the output.

Aligrama	chisq	tail prob	Irula	BMAC	Steppe_East	WSiberia_N
	15.054	0.0198432	0.5	0.359	0.083	0.058
		*std error*	0.027	0.036	0.034	0.022

Butkara_IA	chisq	tail prob	Irula	BMAC	Steppe_East	WSiberia_N
	8.929	0.177591	0.411	0.477	0.052	0.06
		*std error*	0.025	0.033	0.034	0.022

Pak_IA_Ali	chisq	tail prob	Irula	BMAC	Steppe_East	WSiberia_N
	6.755	0.344126	0.438	0.402	0.104	0.055
		*std error*	0.037	0.053	0.05	0.032

S_Sharif_IA	chisq	tail prob	Irula	BMAC	Steppe_East	WSiberia_N
	10.458	0.106644	0.442	0.368	0.144	0.046
		*std error*	0.015	0.022	0.022	0.013

SPGT	chisq	tail prob	Irula	BMAC	Steppe_East	WSiberia_N
	8.626	0.195754	0.313	0.509	0.102	0.076
		*std error*	0.011	0.016	0.015	0.009

Update 8-22-18– Looking at Shahr_I_Sokhta 1,2, and 3.

SIS1	chisquare	Tail-prob	Ganj_Dareh	W_Siberia
	46.394	7.33E-08	0.953	0.047
		std error	0.02	0.02

SIS1	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia
	2.715	0.84368	0.775	0.148	0.076
		std error	0.03	0.021	0.019

SIS1	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia	Onge
	5.606	0.346473	0.716	0.172	0.095	0.017
		std error	0.051	0.027	0.022	*0.031*

SIS1	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia	Irula
	2.275	0.80994	0.738	0.155	0.073	0.034
		std error	0.051	0.022	0.02	*0.041*

SIS2	chisquare	Tail-prob	Ganj_Dareh	*W_Siberia*
	31.452	5.13E-05	0.837	0.163
		std error	0.021	0.021

SIS2	chisquare	Tail-prob	Ganj_Dareh	Anatolia	*W_Siberia*
	31.336	2.19E-05	0.842	-0.005	0.163
		std error	0.036	*0.023*	0.022

SIS2	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia	Onge
	7.09	0.214035	0.663	0.042	0.15	0.145
		std error	0.057	*0.031*	0.024	0.034

SIS2	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia	Irula
	9.597	0.0874816	0.61	0.031	0.128	0.231
		std error	0.058	*0.023*	0.021	0.049

SIS2	chisquare	Tail-prob	Ganj_Dareh	W_Siberia	Irula
	11.044	0.0870409	0.662	0.124	0.214
		std error	0.043	0.022	0.047

SIS2	chisquare	Tail-prob	SIS1	Irula
	20.805	0.00407046	0.661	0.339
		std error	0.046	0.046

SIS2	chisquare	Tail-prob	SIS1	W_Siberia	Irula
	12.337	0.0548625	0.636	0.074	0.29
		std error	0.045	0.025	0.049

SIS2	chisquare	Tail-prob	Sarazm_EN	*Irula*
	7.525	0.376375	0.707	0.293
		std error	0.043	0.043

SIS3	chisquare	Tail-prob	Ganj_Dareh	*W_Siberia*
	270.628	0	0.835	0.165
		std error	0.023	0.023

SIS3	chisquare	Tail-prob	Ganj_Dareh	W_Siberia	Onge
	14.444	0.0250507	0.494	0.089	0.417
		std error	0.031	0.024	0.03

SIS3	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia	Onge
	10.019	0.074706	0.401	0.063	0.097	0.439
		std error	0.052	0.028	0.023	0.032

SIS3	chisquare	Tail-prob	Ganj_Dareh	Anatolia	W_Siberia	Irula
	6.653	0.247741	0.229	0.004	0.039	0.727
		std error	0.058	*0.024*	0.02	0.048

SIS3	chisquare	Tail-prob	Ganj_Dareh	W_Siberia	Irula
	6.47	0.372669	0.231	0.035	0.734
		std error	0.042	*0.02*	0.047

SIS3	chisquare	Tail-prob	SIS1	Irula
	5.423	0.608532	0.23	0.77
		std error	0.041	0.041

SIS3	chisquare	Tail-prob	Geoksiur	Irula
	5.274	0.626561	0.213	0.787
		std error	0.038	0.038

Narasimhan et al, The Genomic Formation of South and Central Asia, Posted March 31, 2018, doi: https://doi.org/10.1101/292581

European Farmers Part I; Mediterranean vs Danubian

June 17, 2018June 19, 2018 populationgenomics7 Comments

The farmers of Europe appear to be a very closely related group, that derives from a potentially singular source. We’ve seen several papers over the last couple years devoted to farmers. Last year brought us Lipson et al. (2017), and Mathieson et al. (2017). These papers brought us many new samples from the Mediterranean, Central Europe, and the Balkans. The datasets from these two papers will be the source that I am working with here.

Firstly, I wanted to look at a simple tree to find a decent fit. That led to the following:

Farmer simple

This one was not a bad fit. It just had one zero drift edge towards Iron Gates, which would probably be taken care of if more hunters were included that lacked as much ANE as Iron Gates. While the Peloponnese samples are an outgroup to the other farmers, the Koros samples, from the First Temperate Neolithic, appear to be very close to the ancestral population for both the Balkan and Mediterranean groups. For the purpose of starting here, it seems fine. Next, I wanted to add Iberia EN as an offshoot of the Cardial EN samples from Croatia, just to see if the two of Mediterranean origin really are closely related.

simple Farmer2

This graph left what looks to be a needed admixture event from a hunter branch related to Iron Gates, to Iberia EN.

simple Farmer3

This graph actually turned out very nice. Iberia EN was able to branch from the same population as the Croatian Cardial and only needed a little extra HG ancestry. This also removed the zero edge from Iron Gates. For the next run, I am going to place LBK Austria coming off the branch to Starcevo.

The first thing I will try after seeing this worst Z-score is to try an admixture edge from the branch related to Iron_Gates into LBK Austria.

simple Farmer5

Surprisingly, the admixture from a European hunter did not take care of that worst Z-score. So, I scrapped that and decided to go with the admixture from Croatian Cardial into LBK Austria.

simple Farmer6

This graph resulted in LBK being a mix of 59% Starcevo and 41% Cardial. Still, we have a worst Z that wants Starcevo to also be closer to Cardial. In this case, I will first try a shared branch opposite of Koros, and if needed, after the HG-related admixture at B3.

simple Farmer7

While this is not a bad result, we do have a couple zero edges here that I would like to resolve. The admixture from the Cardial branch to LBK has also reduced to 5% in this graph. The worst Z involves the Peloponnese Neolithic and Starcevo, and also Iron Gates and LBK. I first want to try an edge from around Iron Gates to LBK to see how that does.

For this last graph, the A2 node for HG was eliminated since there was a 0 drift edge. All HG admixture now comes off of A1. The extra HG into LBK Austria has now put the worst Z-score around 3, which isn’t too bad. The edges all look good. The surprising part is that LBK comes out nearly 50% Cardial-related. This is interesting because, LBK was seen as just a subset of late Starcevo and potentially some Vinca influence. Since this is unexpected, I am going to see if there is more shared drift between the two before splitting, after the extra HG admixture coming after splitting with a group related to Koros EN.

Still, we have LBK Austria coming out as nearly half Cardial-related. While these results are interesting, they are not matching with D-stats, f3-ratio, or qpAdm results. There may be something else here that will take more complex graphs to figure out.

Here is another way of looking at it.

This graph makes a little more sense, with the separation of Mediterranean and Danubian groups a little more. The next step will be to separate the two before Koros EN. I will continue working from here for the rest of the post. If you have any more ideas, let me know. I will post updates as I have more.

Here are stats that have me thinking there is nothing here as far as admixture from Croatian Cardial.

D-stats

Out	Test	Pop1	Pop2	D-stat	Z-score	SNPs
Mbuti_DG	Cardial_EN	LBK_Austria	Starcevo	-0.000114	-0.537	899799
Mbuti_DG	Cardial_EN	LBK_EN	Starcevo	0.000076	0.398	903127
Mbuti_DG	Cardial_EN	LBK_Austria	Koros_EN	-0.000287	-0.959	892981
Mbuti_DG	Cardial_EN	LBK_EN	Koros_EN	-0.000035	-0.119	895930

Source	Source	Target	f_3	std. Err	Z	SNPs
Koros_EN	LaBrana	Iberia_EN	-0.002397	0.001668	-1.437	403414
Koros_EN	Iron_Gates	Iberia_EN	-0.000355	0.001208	-0.294	598713
Koros_EN	French_HG	Iberia_EN	-0.001492	0.001914	-0.779	127825
Cardial_EN	LaBrana	Iberia_EN	-0.001178	0.001525	-0.773	410098
Cardial_EN	Iron_Gates	Iberia_EN	0.001799	0.001092	1.648	585125
Cardial_EN	French_HG	Iberia_EN	-0.000595	0.001713	-0.348	131631
Koros_EN	LaBrana	LBK_EN	-0.005487	0.00118	-4.65	580503
Koros_EN	Iron_Gates	LBK_EN	-0.005153	0.000779	-6.615	755300
Koros_EN	French_HG	LBK_EN	-0.003943	0.001382	-2.854	175316
Cardial_EN	LaBrana	LBK_EN	-0.002165	0.001022	-2.118	555955
Cardial_EN	Iron_Gates	LBK_EN	-0.001198	0.000649	-1.847	711734
Cardial_EN	French_HG	LBK_EN	-0.001455	0.001165	-1.249	171888
Starcevo	LaBrana	LBK_EN	-0.00003	0.000841	-0.035	600458
Starcevo	Iron_Gates	LBK_EN	0.000585	0.000568	1.031	770549
Starcevo	French_HG	LBK_EN	-0.000667	0.001019	-0.654	180239
Koros_EN	Iron_Gates	LBK_Austria	-0.005504	0.000912	-6.033	715204
Koros_EN	Iron_Gates	Cardial_EN	0.002384	0.001571	1.517	553269
Koros_EN	Iron_Gates	Iberia_EN	-0.000355	0.001208	-0.294	598713
Starcevo	Iberia_EN	LBK_Austria	0.000357	0.000672	0.53	615071
Starcevo	Iberia_EN	LBK_EN	-0.000208	0.000516	-0.403	665936
Starcevo	Cardial_EN	LBK_Austria	0.00095	0.00067	1.419	581722
Starcevo	Cardial_EN	LBK_EN	0.001295	0.000578	2.24	626360
Starcevo	Iron_Gates	LBK_Austria	0.000502	0.000715	0.702	729333
Starcevo	Iron_Gates	LBK_EN	0.000585	0.000568	1.031	770549
Koros_EN	Iberia_EN	LBK_EN	-0.000175	0.000696	-0.251	647053
Koros_EN	Iberia_EN	Starcevo	0.000738	0.001072	0.689	496318
Koros_EN	Cardial_EN	LBK_EN	0.000021	0.000789	0.026	609865
Koros_EN	Cardial_EN	Starcevo	-0.000584	0.001115	-0.524	470485

Resources

Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368–372 (2017)

Mathieson, I. et al. The genomic history of Southeastern Europe. Nature 555, 197-208 (2018)

The first farmers, with a focus on Anatolia

June 4, 2018June 12, 2018 populationgenomics17 Comments

Background on the Sites and Samples

We first learned about the demographics of the first farmers across the Levant and Zagros from Lazaridis et al. (2016). From that work, we saw that there were at least two independent developments towards agriculture, with two distinct populations (Lazaridis et al., 2016). One was located in the Levant (Natufians), while the other was at Ganj Dareh, in Iran (Lazaridis et al., 2016). We learned from the paper that Natufians and Ganj Dareh were both nearly equal in Basal Eurasian, yet Ganj Dareh had a lot of ancestry from a lineage related to ANE, and Natufians had little to none of this ancestry (Lazaridis et al., 2016). The Levant Neolithic samples from PPNB to PPNC were a mix of something related to Natufians, and another lineage related to Anatolian farmers from Barcin and Mentese (Mathieson et al., 2015; Lazaridis et al., 2016).

Also in 2016, we caught our first glimpse of the Early Neolithic in Central Anatolia (Kilinc et al., 2016), on the Konya Plain. The Boncuklu group was actually a very early Neolithic group that did have small-scale agriculture (Baird et al., 2012), but was not “aceramic” as many believe. There were very early styles of pottery production and limited use of ceramics at this site; some of the earliest in West Asia (Fletcher et al., 2017). The Boncuklu farmers were a group with long runs of homozygosity, comparable to Western Hunter Gatherers (WHG) (Kilinc et al., 2016). Despite this, the Boncuklu samples are actually quite similar to the later farmers at Barcin, Mentese, and early European farmers (Kilinc et al., 2016), pointing to Anatolia as a potentially third place of independent farming production, along with the Levant and Zagros.

Broushaki et al. (2016) also brought us more samples from the Zagros, that clustered with those samples from Ganj Dareh. These samples were from Tepe Abdul Hosein and Wezmeh Cave (Broushaki et al., 2016).

When it came to actually looking at the ancestral breakdown of Anatolians, Lazaridis et al. (2016) came up with a very solid model where Anatolians were a mix of lineages related to Ganj Dareh, Levant Neolithic, and WHG, with mixture proportions of 0.387, 0.339, and 0.274, respectively.

For the purpose of this post, I am going to focus on Boncuklu and their role in the formation of the Anatolian Neolithic. Since Boncuklu capture method involved shotgun data, I am also using shotgun sequenced genomes from Broushaki et al. (2016) to use as my Iranian farmers (Tepe Abdul Hosein), and the Barcin farmers (Bar8, Bar31). Also, Kostenki14 and MA1 are being used as hunters, as these two form two poles of variation, and are important in the formation of WHG and EHG. Lineages related to both are also important to the formation of these farmers.

In the analysis of the Boncuklu and Barcin farmers, Kilinc et al. (2016) stated that diversity from mixing with other similar groups and/or admixture from more southern groups is possible in the transition from Boncuklu to the later Neolithic of Anatolia. Taking a look at various methods of analysis, it does seem quite possible that a more southern source did admix into the Anatolian farmers of Barcin Hoyuk.

D-stats

First, looking at D-stats, there isn’t anything that is very significant, in determining if Barcin or Boncuklu share more with any particular population. There are near significant results for Natufians and less for the Levant Neolithic samples.

Outgroup	Test	Pop1	Pop2	f4	Z-score	SNPs
Mbuti_DG	Ust_Ishim	Boncuklu	Anatolia_N1	-0.000282	-0.628	1081252
Chimp	Ust_Ishim	Boncuklu	Anatolia_N1	-0.000416	-0.876	1036168
Mbuti_DG	Natufian	Boncuklu	Anatolia_N1	0.00148	2.878	494327
Chimp	Natufian	Boncuklu	Anatolia_N1	0.001535	2.843	472808
Mbuti_DG	Levant_N	Boncuklu	Anatolia_N1	0.000891	2.171	804093
Chimp	Levant_N	Boncuklu	Anatolia_N1	0.000694	1.556	769663
Mbuti_DG	Tepe_Abdul	Boncuklu	Anatolia_N1	-0.000556	-1.448	1003898
Chimp	Tepe_Abdul	Boncuklu	Anatolia_N1	-0.000645	-1.559	962310
Mbuti_DG	Wezmeh	Boncuklu	Anatolia_N1	-0.00025	-0.562	1082448
Chimp	Wezmeh	Boncuklu	Anatolia_N1	-0.000415	-0.882	1037321
Mbuti_DG	CHG	Boncuklu	Anatolia_N1	-0.000361	-0.867	1083101
Chimp	CHG	Boncuklu	Anatolia_N1	-0.000445	-1.031	1037961
Mbuti_DG	Iron_Gates	Boncuklu	Anatolia_N1	-0.000623	-1.69	1076193
Chimp	Iron_Gates	Boncuklu	Anatolia_N1	-0.000712	-1.803	1031346
Mbuti_DG	EHG	Boncuklu	Anatolia_N1	-0.000393	-0.989	995924
Chimp	EHG	Boncuklu	Anatolia_N1	-0.000544	-1.281	954789
Mbuti_DG	W_Siberia	Boncuklu	Anatolia_N1	0.000176	0.404	818559
Chimp	W_Siberia	Boncuklu	Anatolia_N1	0.000181	0.397	783377
Mbuti_DG	Ami	Boncuklu	Anatolia_N1	-0.001048	-1.936	734487
Chimp	Ami	Boncuklu	Anatolia_N1	-0.001122	-1.945	702374

f3-ratio

Also, looking at f3, there isn’t a lot to really support much in the way of admixture from Levant or Natufians into the Barcin Hoyuk samples.

Pop1	Pop2	Target	f3	std error	Z-score	SNPs
Boncuklu	Tepe_Abdul	Anatolia_N1	0.004	0.002013	1.987	494742
Boncuklu	Wezmeh	Anatolia_N1	0.002506	0.002218	1.13	486870
Boncuklu	Levant_N	Anatolia_N1	-0.000089	0.001916	-0.047	382114
Boncuklu	Tepecik	Anatolia_N1	0.004217	0.00194	2.174	361064
Boncuklu	Natufian	Anatolia_N1	-0.001456	0.00235	-0.619	222845

qpAdm Models

Switching over to qpAdm, the first thing to check is what Boncuklu is best modeled as. For the right populations the simplest and seemingly best for using Kostenki, Natufians, and Tepe_Abdul_Hosein_N as the left pops turned out to be Mbuti_DG, Ust_Ishim, GoyetQ116-1, Vestonice16, MA1, Ami, Onge, and Karitiana.

probability	Natufian	Tepe_Abdul	Kostenki14	std error	std error	std error
0.236	0.232	0.449	0.32	0.142	0.107	0.074

While the probability and standard errors are a little high, it is hard to keep them any lower. While adding something like Ganj_Dareh_N or Levant_N will reduce the standard error, the probability also dips significantly.

Moving onto Anatolia_N1 (Bar31, Bar8), the right pops, or outgroups became Mbuti_DG, Ust_Ishim, Kostenki14, MA1, Natufian, Tepe_Abdul_Hosein_N, Ami, Onge, Karitiana.

probability	Boncuklu	Levant_N	std error	std error
0.815	0.687	0.313	0.064	0.064

Also, swapping Natufian and Levant_N between left and right populations:

probability	Boncuklu	Natufian	std error	std error
0.302	0.771	0.229	0.071	0.071

qpGraph Models

After seeing some decent fits in qpAdm, I tried to use qpGraph and see how easily they could be replicated. To being with, I started with a simple tree that contained just the Natufians and Tepe_Abdul_Hosein_N. The Interestingly, CHG comes out as a mix of Natufian, Tepe_Abdul_Hosein, and MA1. first tree should what would be expected, with Natufians and Tepe_Abdul_Hosein_N having similar amounts of Basal Eurasian, and with Iranian farmers having ancestry from a lineage related to MA1.

6/4/18 New Update: Simple qpGraphs

The purpose of these simple graphs is to avoid a lot of admixture edges and to show the steps in finding the ancestry of Boncuklu, Levant, and Barcin samples. Samples that are not absolutely needed, such as Ust_Ishim, MA1, CHG, and any ENA population will be left out. This also shows the work process in how I find where to look at for admixture events.

The first graph here shows that by branching Boncuklu off of Natufian, there is a significant Z-score with Iranian farmers. The next step will be to branch from Iranians to Boncuklu.

The next output had a worst Z-score that involved Kostenki, meaning that an admixture line from the Kostenki branch will be the next admixture source into Boncuklu.

simpleBoncuklu2

After adding the admixture edge from near Kostenki, Boncuklu comes out mostly Kostenki-related, with the rest being a near even mix of Tepe Abdul Hosein and Natufian.

simpleBoncuklu3

This created a pretty solid fit, so, the next step would be to see how the graph works with Adding Levant_N. Since the Levant samples harbor a lot of Natufian-related ancestry, that is where they will first be branched off of.

This output shows that an admixture edge is needed from a node on the Boncuklu line to Levant_N in order to drop the Z-score. A shared drift edge with Boncuklu was needed to move the worst Z-score closer to 2.

simpleBoncuklu5

For the next run, I added the two shotgun samples from Barcin (Bar8, Bar31) to the tree.This left a worst Z > 3, so, the next step will be an edge from a node related to Natufians into Anatolia_N1.

For the last graph, the edge from a Natufian-related node admixes into the Barcin Hoyuk samples. There remains a worst Z > 2.5, that appears to be asking for Iranian admixture into the Levant_N population. While it isn’t necessary, I did look at adding an admixture edge from the Iranian farmers and it only added 2% admixture. This graph should be sufficient enough for a simple tree that incorporates all of the first farmers.

Below are more complex graphs, with an Eastern non-African source (Onge), Ust-Ishim and also MA-1.

BoncukluTree1

For the next step, I also added CHG to the tree, just to see where it was placed and to add another admixture source in West Asia. As other stats show, CHG was less basal than Iranian farmers, but also shifted towards Natufians, potentially sharing a formation story with Boncuklu.

Boncuklu2wCHG

After achieving a good fit with CHG, I then went on to see just how Boncuklu fit into the picture. As expected, Boncuklu is best fit as a mix of Natufian, Iranian, and a lineage related to Kostenki14, with admixture also from CHG. Trying to do just Iranian or just CHG led to significantly higher Z-scores. Both were needed. It appears there is additional ANE in Boncuklu that is not accounted for in Iranians.

After applying a good fit for Boncuklu, I next wanted to see just how the farmers at Barcin Hoyuk fit into tree. For this, I first created a new simplified tree to use and also co-fit the Levant_N samples to see if the best fit includes additional southern ancestry into the later Northwest Anatolian Neolithic.

I also tried a run with just transversion sites, just to see how that would turn out.

BoncukluWAnatoliaTransversion

Just as a precaution, I ran another test, with Levant_N receiving admixture from a separate branch related to Boncuklu, that is ancestral to Anatolia_N1, to see if that reduced or eliminates the need for admixture from Levant_N. As it turns out, Anatolia then asked first for admixture from Natufians, rather than Levant_N. So, the question then becomes, was there another population that was related to Levant_N which lacked or had less Iranian farmer ancestry and mixed into the ancestors of the Barcin and European farmers? More samples, specifically from southern and especially southeast Anatolia, and PPNA will provide the answers which are needed.For argument sake, I tried both the Natufian and Levant_N admixture edges to see how they turned out. Having more a higher f4 and f3 with Natufians, rather than Levant, leads me to believe this is possible.

BoncukluWAnatolia2

Conclusions

The end result here has the Barcin samples as a mix of Boncuklu and Levant_N (or a more Natufian-like group), in agreement with qpAdm. However, this output is only about two-thirds as much Levantine flow into later Anatolian farmers as qpAdm showed. Transversion sites placed more ancestry related to Iranian farmers into both Boncuklu and Levant_N. Boncuklu became significantly more Iranian than the previous run. The amount of flow from Levant_N into Barcin held pretty steady. While more samples across time and space, with similar capture methods, will help this to be resolved. There aren’t much in the way of D-stats or f3_ratio to suggest there is a lot of gene flow there. qpAdm and qpGraph do provide a strong case of gene-flow into Northwest Anatolia.

In upcoming posts I will look at the formation of European farmers, hunter admixture into the Middle Neolithic, and also at the roots of Epipaleolithic and Mesolithic European hunters.

References

Baird D. The Late Epipaleolithic, Neolithic, and Chalcolithic of the Anatolian Plateau, 13,000–4000 BC. In: Potts D., editor. A Companion to the Archaeology of the Ancient Near East. Wiley-Blackwell; 2012. pp. 431–466.

Broushaki F., Thomas M.G., …, Berger J. Early Neolithic genomes from the eastern Fertile Crescent. Science. 2016; 353: pp. 499-503.

Fletcher A., Baird D., Spataro M. & Fairbairn A. Early ceramics in Anatolia: Implications for the production and use of the earliest pottery. The evidence from Boncuklu Hoyuk. Cambridge Archaeological Journal. 2017; 27 (2): pp. 351-369.

Kilinc G.M., Omrak A., …, Gotherstrom A. The demographic development of the first farmers in Anatolia. Current Biology. 2016; 26(19): pp. 2659–2666.

Lazaridis I., Nadel D., …, Reich D. Genomic insights into the origin on farming in the ancient Near East. Nature. 2016;536: pp. 419-424.

Mathieson I., Lazaridis I., Rohland N., Mallick S., Patterson N., Roodenberg S.A., Harney E., Stewardson K., Fernandes D., Novak M. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 2015;528:499–503. [PubMed]

Here we go!

March 31, 2018June 4, 2018 populationgenomics6 Comments

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