Guest post: we owe many of our genetic traits to ancient steppe pastoralists, but...

This is a guest post courtesy of Samuel Andrews, a regular commentator for several years at this blog. I did edit parts of the original text submitted to me, but these were just cosmetic changes. If you spot any issues with this article, feel free to complain to Samuel in the comments below.

Massive migrations of pastoralists from the Pontic-Caspian steppe in the 3rd millennium BC abruptly ended generations of genetic stability in Europe. These large-scale population movements spread Yamnaya and Yamnaya-related ancestry throughout most of the continent, and indeed also much of Eurasia. Moreover, they also carried a specific type of European farmer ancestry, which was picked up by the migrating herders just west of the steppe.

By the end of the 3rd millennium BC, people across long distances within Europe shared very recent ancestry from the Pontic-Caspian steppe and surrounds. As a result, far away locations in Europe were more connected than they were ever before.

Ancient genome-wide data suggest that these migrations also spread unique genetic traits, such as lactase persistence and fair hair (blonde & red), that were once mostly restricted to a fairly limited region within Europe. However, some of these traits were originally derived from the farmers, or rather agropastoralists, who lived just west of the steppe, such as the Globular Amphora and Funnel Beaker peoples, rather than the steppe herders, and indeed this appears to be the case for both lactase persistence and fair hair.

In the 3rd millennium BC, both of these traits went from relative obscurity to widespread prominence across and beyond Europe. The Bell Beaker people, who dominated the western half of Europe during the Early Bronze Age (EBA), and the Sintashta people, who, soon after, lived just east of Europe's present-day border in the Trans-Ural steppe of what is now Russia, demonstrate this well.

The pre-Sintashta and pre-Beaker populations of present-day Russia and Britain, respectively, showed low frequencies of alleles associated with fair hair. Thus, the Beaker and Sintashta peoples took high frequencies of these alleles, which they both probably inherited from Eastern European farmers, to the opposite ends of Europe, and then, via the expansions of Sintashta-related Andronovo populations, also deep into Asia.

rs4988235 > lactase persistence
rs16891982 > light skin & blonde hair
rs12913832 > blue eyes & blonde hair
rs1805008 > red hair

When the Andronovo groups mixed with the indigenous inhabitants of Asia, the frequencies of most of these European-specific alleles among them were reduced, until they almost disappeared in the new populations that formed as a result of this mixture process. Nevertheless, they continued to exist wherever there was significant Andronovo ancestry, including in the Iron Age peoples of the Swat Valley in what is now Pakistan:

Swat Valley, Udegram_IA, S8195.E1.L1; allele T at rs1805008 (aka R160W), the most popular red hair variant among present-day Europeans.

Swat Valley; 17% derived allele frequency at rs16891982; 11% at rs12913832; twice as much as what Neolithic, Chalcolithic, and Bronze Age South Central Asians could boast.

Swat Valley, Barikot_IA, I6547; allele A at rs4988235 (aka I3910-T), the main lactase persistence mutation in both present-day Europe and South Asia.

Hence, I3910-T is a direct link between the populations of the Iron Age Swat Valley and ancient Europe. Indeed, Ukraine_Eneolithic I6561, from a burial associated with the Sredny Stog II archaeological culture in the North Pontic steppe, present-day Ukraine, is the oldest, UDG-treated sample in the ancient DNA record to date to show I3910-T. And he's also the oldest individual to belong to Y-chromosome haplogroup R1a-M417, which is today one of the most common Y-chromosome haplogroups in both Eastern Europe and South Asia, especially among the speakers of Indo-European languages.

After its expansion from Eastern Europe, I3910-T was heavily selected for both across most of Europe and in large parts of South Asia. Today, its frequencies vary significantly by region and ethnic group in India. By and large, much like R1a-M417, it’s more common in Indo-European-speaking North Indians than Dravidian-speaking South Indians. But it clearly peaks in Indian pastoralist populations that consume a lot of dairy products. They carry I3910-T at frequencies equal to those seen in many European groups.

The red hair variant R160W, seen in Swat Valley sample S8195.E1.L1, is another direct link between ancient South Asia and Europe. Just like I3910-T, R160W has been shown to have been present in Europe at least 2,000 years before the Andronovo Culture. Balkans_ChL I2423, a sample from what is now Bulgaria, carries R160W. This individual dates to 4400 BC, so he's of a similar age to Ukraine_Eneolithic I6561, the above mentioned early I3910-T carrier from the North Pontic steppe.

Other than that, as things stand, R160W is absent from pre-Kurgan Europe. In the aftermath of the Steppe migrations, around 2400-1800 BC, R160W pops up in many places in Europe just like I3910-T does. Four Andronovo/Sintashta samples out of about 100 carry R160W. Thus, a few, perhaps 1%, of the Andronovo and Sintashta people almost certainly had red hair.

Though very rare, R160W and other red hair variants do exist in South and Central Asia today. Several South Asians from the 1000 Genomes dataset carry R160W (see here). A Pathan or Pashtun from the HGDP dataset is predicted to have red hair by HIrisPlex-S. There is little doubt that this is associated with their Andronovo ancestry.

Main data sources...

Lazaridis et al. 2016

Lipson et al. 2017

Mathieson et al. 2018

Narasimhan et al. 2018

Olalde et al. 2018

See also...

Yamnaya isn't from Iran just like R1a isn't from India