The Natufian puzzle

One of the biggest surprises in the new Lazaridis et al. preprint is that the Natufians don't show any Sub-Saharan African admixture when poked and prodded directly with formal statistics. However, TreeMix, which runs on formal statistics, doesn't have much trouble finding Sub-Saharan or related ancestry in both the Natufians and Neolithic farmers from the Levant. So what's going on?

Also worth noting in the fourth graph is the heavy migration edge from near the base of the East Eurasian Dai/Han branch to the early Neolithic farmers from Iran. My bet is that this is a signal of admixture from a Central Asian forager population, perhaps representing a parallel clade to that of the East Asians? Or is it just Ancient North Eurasian (ANE) admixture? I'll try and investigate that soon.

German Bell Beakers in the context of the prehistoric Near East

Fascinating stuff, and basically in line with the generally accepted archaeological model of Bell Beaker origins in Iberia.

Of course, these TreeMix results don't necessarily mean that German Beakers are a straight two-way mixture between Yamnaya pastoralists and Chalcolithic Iberians; they simply suggest that the ancestors of German Beakers experienced a significant pulse of admixture from a Chalcolithic Iberian-like population.

All of the samples used in this analysis are freely available for download at the Reich Lab website here.

Update 30/06/2016: Below is the same graph but with German Corded Ware added to the line up. The German Beakers still receive a significant admixture edge from the base of the Iberia Chalcolithic branch. However, the percentage of this edge as a proportion of their ancestry has fallen to 33%.

D-stats/nMonte open thread #3

For the latest datasheets with D-stats of the form D(Chimp,Columns)(Mbuti.DG,Rows), featuring samples from Lazaridis et al. 2016, see here, here and here.

Datasheets with D-stats of the form D(Chimp,Rows)(Mbuti.DG,Columns) are available here, here and here. D-stats 1 and 1b include Iran_Chalcolithic in both the rows and columns, while D-stats 3 and 3b have Eastern_HG in both the rows and columns.

The interesting question is, which of these sheets is the best for estimating admixture proportions, primarily in populations from West Eurasia?

A moment of clarity

A lot of things now make so much more sense thanks to all of the recently published ancient DNA. For instance, in the Principal Component Analysis (PCA) below, South Central Asians (SC_Asia) finally look like a three-way mixture of Bronze Age steppe pastoralists, early farmers from Iran and surrounds, and indigenous South Asians, which is exactly what they are.

By the way, I also ran a global analysis but didn't get the chance to make a decent plot. However, the datasheet is available for download here. The samples are from a variety of recent DNA papers and freely available at the Reich Lab site here.

Yamnaya =/= Eastern Hunter-Gatherers + Iran Chalcolithic

The public version of the Lazaridis et al. 2016 dataset is now available for download at the Reich Lab website here. Many thanks to the authors for releasing their data before formal publication, and in fact apparently even before the end of the peer review.

As usual from this team, it's high quality stuff with hundreds of thousands of SNPs genotyped in most of the 45 ancient samples from the Near East. And to think that only a couple of years ago the idea of getting genome-wide data from even a single ancient individual from hot places like the Near East was just that, an idea.

I'm planning to do a lot with this data, but the first issue I want to tackle is the genetic structure of the Yamnaya pastoralists from the Early Bronze Age (EBA) European steppes.

Lazaridis et al. show that Early to Middle Bronze Age steppe groups, including Yamnaya, tagged by them as Steppe EMBA, are best modeled with formal statistics as a mixture of Eastern European Hunter-Gatherers (EHG) and Chalcolithic farmers from western Iran. The mixture ratios are 56.8/43.2, respectively.

However, they add that a model of Steppe EMBA as a three-way mixture between EHG, the Chalcolithic farmers and Caucasus Hunter-Gatherers (CHG) is also a good fit and plausible.

I've looked at the topic before and concluded that Yamnaya had to be in large part of CHG origin, with only minor admixture from early farmers, probably from Eastern Europe (see here and here). After having a chance to study the data from Lazaridis et al. 2016, I stand by my earlier results.

Below are a couple of TreeMix graphs featuring Yamnaya alongside a variety of modern and ancient groups, including several potentially relevant to its ancestry, such as Armenia_Chalcolithic and Iran_Chalcolithic from Lazaridis et al. 2016. The full output is available for download here.

Now, it is true that TreeMix is a temperamental algorithm. It can react in extreme ways to the types of samples chosen by the user, often showing results that might appear wrong, or at the very least counter-intuitive. On the other hand, my experience shows that it's also exceptionally effective at picking up and characterizing significant and relatively sudden pulses of admixture. Moreover, unlike modeling with formal stats, it's an unsupervised test.

Clearly, the graphs below are very much at odds with the claim that Yamnaya might be in large part of Iranian Chalcolithic or similar ancestry. As per my earlier tests, it appears to be overwhelmingly a mixture between EHG and CHG.

It's also important to note that the uniparental marker data in Lazaridis et al. firmly back up my TreeMix output, with the Steppe EMBA groups showing starkly different Y-chromosome and mitochondrial (mtDNA) haplogroups from the ancient samples from Iran.

Indeed, mtDNA haplogroup U7 is an excellent diagnostic marker for ancestry from the southern Caspian region, and, sure enough, it appears in the Iranian Chalcolithic set. Conversely, it's conspicuous by its absence from all Bronze Age steppe remains tested to date.

Admittedly, it's still extremely difficult to be precise about the source of the southern admixture in Yamnaya without lots of high quality samples from all over the steppe and surrounds. But already Iran looks a highly unlikely proposition.

See also...

Modeling Steppe_EMBA

The story of mtDNA haplogroup U7

Another look at the genetic structure of Yamnaya

Genetics of an early Neolithic pastoralist from western Iran (Gallego Llorente et al. preprint)

Just in at bioRxiv:

Abstract: The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding,ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in the region. Runs of homozygosity are of a similar length to those from Neolithic Anatolians, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity of early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.

Gallego Llorente et al., The genetics of an early Neolithic pastoralist from the Zagros, Iran, bioRxiv prerprint, posted June 18, 2016, doi: http://dx.doi.org/10.1101/059568

The same individual, tagged as GD13a by Gallego Llorente et al., is also featured in the new Lazaridis et al. prerprint as I1290 (see here). Not sure if there's much point in two different papers on the same sample, but at least the sequences are different.

In any case, here's a very interesting part from the paper dealing with the population history of South Asia:

It is possible that farmers related to GD13a contributed to the eastern diffusion of agriculture from the Near East that reached Turkmenistan (34) by the 6th millennium BP, and continued further east to the Indus Valley (35). However, detecting such a contribution is complicated by a later influx from Steppe populations with Caucasus Hunter-Gatherer ancestry during the Bronze Age. We tested whether the Western Eurasian component found in Indian populations can be better attributed to either of these two sources, GD13a and Kotias (a Caucasus Hunter-Gatherer), using D-statistics to detect gene flow into an ancestral Indian component (represented by the Onge). For all tests where a difference could be detected, Kotias acted a better proxy than GD13a (Fig. S9 and Table S6). This result implies that the majority of the West Eurasian component seen in India derives from the Bronze age migrations; this interpretation is supported by dating of last contact based on patterns of Linkage Disequilibrium (36).

Dating admixture events with Linkage Disequilibrium patterns is somewhat controversial, but what they're saying is more or less in agreement with what I've been bleating about on this blog for the last few years (for instance, see here). So I'm very happy to finally see others noticing the same thing.

However, I have to say that the Principal Component Analysis (PCA) in this paper is off the wall. Many of the ancient samples don't appear to cluster where they should. For instance, most of the European Hunter-Gatherers (HGs) are way too close to present-day samples, and in fact in some cases they're overlapping with them, which is just wrong. Note also the unusual elongated cluster formed by the Neolithic Anatolians, stretching all the way from where they should all cluster (south of the Sardinians), to where they really shouldn't (right next to the North Caucasians).

My bet is that the results are affected by missing markers, with the ancient samples with high rates of missing markers being pulled into the middle of the plot (towards 0.00 in both dimensions).

Below is a similar PCA that I ran using my dataset minus GD13a, which I don't yet have access to. Note the relatively tight clusters formed by all of the ancient populations. The European Hunter-Gatherers are distinct from present-day Europeans, while none of the Neolithic Anatolians (Anatolia_N) fall near the North Caucasians in dimension 2. This is of course in line with a wide range of formal stats.

See also...

Early Neolithic genomes from the eastern Fertile Crescent (Broushaki et al. 2016)

The genetic structure of the world's first farmers (Lazaridis et al. 2016 preprint)

Huge one from the Laz at bioRxiv:

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Lazaridis et al., The genetic structure of the world's first farmers, bioRxiv preprint, posted June 16, 2016, doi: http://dx.doi.org/10.1101/059311

And here's a list of the Y-chromosome haplogroups for the new samples in this paper:

Armenia_ChL (Chalcolithic Armenia)

I1407: L1a
I1632: L1a
I1634: L1a

Armenia_EBA

I1635: R1b1-M415(xM269)

Iran_Mesolithic (Hotu Cave)

I1293: J(xJ2a1b3, J2b2a1a1)

Iran_N

I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)

My guess here is that this is R2, and hopefully we shall see when the bam files are released.

I1949: CT

Iran_LN

I1671: G2a1(xG2a1a)

Iran_ChL (Chalcolithic Iran)

I1662: J(xJ1a, J2a1, J2b)
I1674: G1a(xG1a1)

Natufians

I0861: E1b1b1b2(x E1b1b1b2a, E1b1b1b2b)
I1069: E1b1(xE1b1a1, E1b1b1b1)
I1072: E1b1b1b2(xE1b1b1b2a, E1b1b1b2b)
I1685: CT
I1690: CT

Levant_N

I0867: H2 (PPNB)
I1414: E(xE2, E1a, E1b1a1a1c2c3b1, E1b1b1b1a1, E1b1b1b2b) (PPNB)
I1415: E1b1b1 (PPNB)
I1416: CT (PPNB)
I1707: T(xT1a1, T1a2a) (PPNB)
I1710: E1b1b1(x E1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c) (PPNB)
I1727: CT(xE, G, J, LT, R, Q1a, Q1b) (PPNB)
I1700: CT (PPNC)

Levant_BA

I1705: J1(xJ1a)
I1730: J(xJ1, J2a, J2b2a)

Update 25/07/2016: The peer-reviewed paper was published at Nature today under the title Genomic insights into the origin of farming in the ancient Near East. See here.

See also...

A homeland, but not the homeland

A moment of clarity

Early Neolithic genomes from the eastern Fertile Crescent (Broushaki et al. 2016)