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Tuesday, November 28, 2017

The ancient genomics revolution (Skoglund & Mathieson 2017 preprint)

Two former Harvard scientists Pontus Skoglund and Iain Mathieson are working on a new review paper on the wide range of scientific breakthroughs provided by ancient genomics over the past decade. The preprint is available at Dropbox here. There's also a thread about the preprint at Mathieson's Twitter account here.

I've read through it a couple of times, especially the parts about Europe, and haven't been able to spot any major problems; the authors obviously chose their words very carefully, and their geography is beyond reproach. [Edit: first problem spotted, see here]

Now, you might think that geography is easy, but apparently not when it comes to the location of the Pontic-Caspian steppe. Recent media articles have claimed that it's located in West Asia, and, I kid you not, even that it's hilly (for instance, see here), while scientists from Max Planck and other supposedly high brow places seem to think that it's in Central Eurasia (see here). Nope, as Skoglund and Mathieson correctly point out, it's actually located in (far) Eastern Europe, while Central Eurasia is generally posited to be further to the east. From the preprint (emphasis is mine):

Anatomically modern humans were widely distributed in Europe by at least 42,000-45,000 BP (3; 41). The oldest genomic data from a modern human in Europe is the Oase 1 individual from present-day Romania dated to 37,600-41,600 BP. This individual, which had a direct Neanderthal ancestor in the past four to six generations, did not contribute detectable ancestry to later Upper Paleolithic populations (24). During the Upper Palaeolithic, a major transformation ~30,000-35,000 years ago was likely associated with the replacement of the Aurignacian with the Gravettian culture in western Europe(28). As the Last Glacial Maximum (LGM) came to an end and the ice sheets receded, Europe was repopulated, possibly from southern European and central Eurasian refugia (28). Another transformation may have taken place during an interstadial warm period ~14.5 kya, replacing the original recolonizers with a population that would come to form the Mesolithic populations of Europe (28; 93). These Mesolithic populations were outside the genetic diversity of present-day Europe (114; 131) and themselves display a clinal structure, with an east-to-west cline (32; 37; 38; 47; 57; 62; 72; 78; 112; 130). The origin of this cline is not clear, although it plausibly reflects two or more major sources of ancestry in the post-LGM or post-14.5kya expansions.

Starting from the southwest around 8,500 BP, the Mesolithic ancestry of Europe was largely replaced (29; 38; 42; 130; 131) as a new type of ancestry related to that found in Neolithic northwest Anatolia (73; 87) and, ultimately, to early farming populations of the Levant and Northern Iran (11; 56) expanded throughout Europe. This ancestry rapidly reached the extreme edges of Europe, with direct evidence of its presence in Iberia at 7300 BP (86), in Ireland at 5100 BP (14) and in Scandinavia at 4900 BP (131). This “Anatolian Neolithic” ancestry was highly diverged relative to the “hunter-gatherer” ancestry of the populations that previously inhabited Europe (F ST ~ 0.1, similar to the divergence between present-day European and East Asian populations) (73; 132). Across Europe, its appearance was closely linked in time and space to the adoption of an agricultural lifestyle, and it now seems established that this change in lifestyle was driven, at least in part, by the migration. However, the Anatolian Neolithic migrants did not replace the hunter-gatherer populations. Over the next 4000 years, the two populations merged, and by 4500 BP, almost all European populations were admixed between these two ancestries, typically with 10-25% hunter-gatherer ancestry (29; 38; 42; 50; 62; 71; 73; 130; 131). Across Europe, this “resurgence” of hunter-gatherer ancestry (10) was independent–driven by local hunter-gatherer populations who lived in close proximity to farming groups (7; 62; 72; 130).

The next substantial change is closely related to ancestry that by around 5000 BP extended over a region of more than 2000 miles of the Eurasian steppe, including in individuals associated with the Yamnaya Cultural Complex in far-eastern Europe (1; 38) and with the Afanasievo culture in the central Asian Altai mountains (1). This “steppe” ancestry is itself a mixture between ancestry that is related to Mesolithic hunter-gatherers of eastern Europe and ancestry that is related to both present-day populations (38) and Mesolithic hunter-gatherers (46) from the Caucasus mountains, and also to the populations of Neolithic (11), and Copper Age (56) Iran. Steppe ancestry appeared in southeastern Europe by 6000 BP (72), northeastern Europe around 5000 BP (47) and central Europe at the time of the Corded Ware Complex around 4600 BP (1; 38). These dates are reasonably tight constraints, because in each case there is no evidence of steppe ancestry in individuals immediately preceding these dates (47; 72). Gene flow on the steppe was extensive and bidirectional, as shown by the eastward flow of Anatolian Neolithic ancestry–reaching well into central Eurasia by the time of the Andronovo culture ~3500 BP (1)–and the westward flow of East Asian ancestry–found in individuals associated with the Iron Age Scythian culture close to the Black Sea ~2500 BP (143).

Copper and Bronze Age population movements (14; 78 Martiniano, 2017 #8761; 85; 112), as well as later movements in the Iron Age and Historical period (70; 119) further distributed steppe ancestry around Europe. Present-day western European populations can be modeled as mixtures of these three ancestry components (Mesolithic hunter-gatherer, Anatolian Neolithic and Steppe) (38; 57). In eastern Europe, further shifts in ancestry are the result of additional or distinct gene flow from Anatolia throughout the Neolithic and Bronze Age in the Aegean (42; 51; 55; 72; 87), and gene flow from Siberian-related populations in Finland and the Baltic region (38).

And I really like this part; sounds ominous for the Out-of-India (OIT) crowd, doesn't it? Hopefully we won't have to wait too long for the relevant paper from Harvard, which, I can assure you, is coming sooner or later.

There are no published ancient DNA studies from South- or Southeast Asia. However, data from neighboring regions provides clues to the population history of this region. In particular, present-day South Asian populations share ancestry with Neolithic Iranian (11) and Steppe (56) populations. This strongly suggests Neolithic or Bronze Age contact between South Asia and west/central Eurasia, although only direct ancient DNA evidence from the region will resolve the timing and structure of this contact.


Pontus Skoglund and Iain Mathieson, Ancient genomics: a new view into human prehistory and evolution, preprint 2017

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Who's your (proto) daddy Western Europeans?

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts


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Carlos Aramayo said...

@ Rob,

you mention a chronology for Pit-Grave (Yamnaya) culture by Frinculeasa and Heyd (2015), but this is "only" for Lower Danube (Hungarian plain), a region of later movement, not the core region.

Here is the Pit-Grave (Yamnaya) Culture´s chronology in the "original" zone of Volga-Ural interfluve:

- Early (Repino) Stage (4000-3300 BC)

- Advanced (Classical) Stage (3300-2600 BC)

- Substage A (3300-2900 BC)

- Substage B (2900-2600 BC)

- Late (Poltavkinsky) Stage (2600-2300 BC)


Morgunova & Khokhlova, 2013. "Chronology and Periodization of The Pit-Grave Culture in The Region Between the Volga and Ural Rivers Based on Radiocarbon Dating and Paleopedological Research", in Proceedings of the 21st International Radiocarbon Conference, edited by A.J.T. Juli & C. Hatté, Radiocarbon, Vol. 55, No. 2-3, p. 1286-1296.

Matt said...

@ Shahanshah of Persia: While I concede the point that the Indo-Europeans did establish ruling castes in Southern Europe and the Middle East, one cannot deny the influence the natives of these regions had on their rulers, both culturally, and to a lesser extent, genetically as well.

As I understand it, the sequence for Western Iranian peoples in Iran was one of entering the country around 1000BC, establishing some sort of fairly wide presence, being somewhat of a subordinate people to the Neo-Assyrian Empire, then expanding to a greater presence after the fall of the Neo-Assyrian Empire at around 600BC.

I guess dna will show if any of these peoples were ethnically separate for any length of time after entering the Iranian plateau, or if they were well intermixed during that 400 odd years.

Aram said...


This connection of Shulaveri and Yamna mtdna are remarkable offcourse. But mtdna can be sometimes misleading. For example H5 was found in Carpathian Neolithic, CT. Then in Sintashta. One may think that G2-s migrated to South Ural, but nope it was R1a warriors. So you see that mitogenomes can change their "husbands".
Anyway I assure You that Y dna of Shulaveri will be published in coming year(s). No hiding.

Btw I agree with You that Areni is not Shulaveri.

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