Lactose Tolerance Came From Central Asia Approximately 4,000 Years Ago

That recent study published in the journal Nature, that I commented on last week, also documents that Europeans began digesting cow’s milk about 4,000 years ago and that was all thanks to a group of nomadic Russian herders from Great Steppes. This contradicts a long time understanding that the genetic mutation for lactose tolerance was introduced by Anatolian farmers from modern-day Turkey, who started raising cattle around 6,500 B.C.

nature16152-f3
Dots and solid lines show maximum likelihood frequency estimates and a 1.9-log-likelihood support interval for the derived allele frequency in each ancient population. Horizontal dashed lines show allele frequencies in the four modern 1000 Genomes populations. AN, Anatolian Neolithic; HG, hunter-gatherer; CEM, central European Early and Middle Neolithic; INC, Iberian Neolithic and Chalcolithic; CLB, central European Late Neolithic and Bronze Age; STP, steppe; CEU, Utah residents with northern and western European ancestry; IBS, Iberian population in Spain. The hunter-gatherer, early farmer and steppe ancestry classifications correspond approximately to the three populations used in the genome-wide scan with some differences (See Extended Data Table 1 for details).

The study examined DNA from the remains of 230 Eurasians who lived between 6,500 and 300 B.C. The authors discovered that the mutation that lets adult Europeans produce lactase throughout their adult lives was introduced right at the time that the Russian herders arrived in Europe.  Here’s an excerpt from the original paper,

“The strongest signal of selection is at the SNP (rs4988235) responsible for lactase persistence in Europe15, 16. Our data (Fig. 3) strengthens previous reports that an appreciable frequency of lactase persistence in Europe only dates to the last 4,000 years3, 5, 17. The allele’s earliest appearance in the dataset is in a central European Bell Beaker sample (individual I0112) dated to between 2450 and 2140 BC.”

If you pay attention to the figure I’ve included, the graph in the left upper corner documents how the SNP for persistent lactase derived from Steppe populations and not early Anatolian or Central/Iberian populations.

3 thoughts on “Lactose Tolerance Came From Central Asia Approximately 4,000 Years Ago

  1. “This contradicts a long time understanding that the genetic mutation for lactose tolerance was introduced by Anatolian farmer . . . ”

    The understanding which I had understood to be the conventional wisdom at the time that this study was published was that the gene emerged around that time in NW Europe and quickly spread south due to the fitness advantage it provided (the exact mechanism of which is far less obvious than it seems to be at first glance).

    This conventional wisdom is not inconsistent with data showing that: “The allele’s earliest appearance in the dataset is in a central European Bell Beaker sample (individual I0112) dated to between 2450 and 2140 BC.”, because the central European Bell Beaker culture appears to be derived from the earlier Western European Bell Beaker culture in a West to East migration. So, if Bell Beaker people acquired the LT mutation in Western Europe ca. 2900-2500 BCE and then migrated east after having acquired it, this would be consistent with the data. And, since the allele apparently has strong selective fitness benefits, it wouldn’t just spread more or less in lockstep with demic migration patterns the way that selectively neutral, ancestry informative alleles do.

    I can’t honestly recall any recent claims that it was introduced by Anatolian farmers, who appear to have used dairy milk mostly for cheese (which reduces lactose content) and for children and animals.

    One really tricky issue is that LT seems to emerge at about the same time as proportions of Y-DNA R1b and mtDNA H surge in Western Europe, and at about the same time as proportions of Y-DNA R1a and mtDNA H surge in Eastern Europe, presumably although not definitively, as part of the same demographic phenomena. A steppe source for LT would be consistent with all of these trends emerging from the steppe mass migration. But, if steppe people are reshaping European demographics because the 4.2 kiloyear event creates a vacuum in Europe and they pick up the LT gene from their conquered populations fairly early on, and then LT surges in frequency due to its selective fitness benefits within the steppe people (which may be greater for them than for the locals because they have more livestock than the locals did), it would be hard to distinguish the two scenarios after the fact.

    To establish a source on the Steppe (which admittedly, a priori without having any actual genetic evidence in hand, seems perfectly plausible), you really need to establish the presence of the LT gene there (ideally at close to fixation given its strong selective impact), in ancient DNA before steppe descendants reach Europe. In the alternative, you could show the LT gene in populations with steppe origins at the right time that we genetically isolated from Europe, such as ancient Tarim Basin DNA. The nice point there is that the prolonged isolation from Europe would allow you to use less old ancient DNA from the Tarim Basin as a proxy for the harder to recover pre-4kya ancient DNA from the steppe that you would otherwise need. (Also, the Tarim Basin didn’t adopt cremation to nearly the same extent as other populations with lots of autosomal DNA similar to ancient steppe DNA, so there are more remains available to test there and the Tarim Basin preservation conditions are excellent).

    Another plausible possibility is that the LT mutation was present at low frequencies across Europe, but that prior to the 4.2 kiloyear climate event, that this mutation did not confer a selective fitness advantage, but that the intense famines and famine driven plagues (worse than those of Bronze Age collapse) that struck at that time dramatically increased the selective fitness advantage conferred by the LT mutation in some way, causing it to go from a low frequency curiosity spread across Europe and West Eurasia to a predominant trait in every part of Europe and West Eurasia where this trait conferred significant selective fitness.

    One good place to test the hypothesis would be in Hittite ancient autosomal DNA (something we don’t have now, but have a decent chance of having before too long). If the source was Steppe Indo-Europeans, Hittites should have high levels of LT. But, if the source was NW Europe or was diffuse across Europe, Hittite levels should be much lower than in Northern Europe.

    1. Actually “conventional wisdom” had long ago discarded that the (known) European LCT allele was brought by Neolithic farmers, because all early farmers lacked it, just as do all early Indoeuropean migrants at later date. I’m not really sure where does the “conventional wisdom” stems from.

      There are two issues here: one is that there is a lot of people who is effectively (phenotype) lactose tolerant and do not carry any of the known alleles. This happens in Europe too, for example in Italy, most of Germany. See: HERE. So quite probably there are other LCT alleles that have gone so far undetected, a fact that is simply ignored by most of the literature and related discussions. It’s possible that Neolithic farmers or other groups were to some extent lactase tolerant yet did not carry the T-13910 allele, but some other unknown variants.

      The other issue is that the European LCT allele, distributed mostly by the Westernmost parts of the subcontinent (but also found in Africa: Mozabites, Bulala, Fulani, Baggara “Arabs”), is related (via non-LCT nodes) to other LCT alleles important in the Red Sea area and, quite apparently, with an East or NE African “heart of diversity”, rather than a West Asian one. See HERE for details. This suggests that the European LCT allele or its precursor, should have been carried to the subcontinent not by steppe pastoralists (no apparent connection whatsoever) but by a population with African connections of some sort, for example Early European farmers but also possible source are pre-Neolithic populations of Iberia, etc., which had some contacts and genetic exchange with NW Africa, something that would be consistent with the Mozabite and Fulani connection (Fulani are like 1/4 North African like, of the West Saharan subtype).

      One thing is that (maybe) the LCT allele was selected for in agricultural contexts and another very different one is to reject the possibility that it already existed “in the wild” in pre-agricultural contexts with no purpose whatsoever (at least not one affecting milk digestion). In pre-agricultural contexts, unless some other data says otherwise (and AFAIK there’s nothing), the allele was surely neutral or close to neutrality and hence it could exist without causing any trouble nor being selected against. So it’s also possible that it was initially inherited, like blue eyes, from hunter-gatherers, only later going under some sort of positive selection.

      But then the other possibility is that a non-LCT precursor not just of “European” T-13010 but also of East African G-13907 and of East African and Arabian G-13915 was common in the early Neolithic peoples of the Levant, or rather the Mesolithic ones of the Nile that influenced these, causing later an array of founder effects and finally being subject to selection here and there.

      The selection itself I have argued that was caused because milk is rich in fat and proteins, and goats are a very “cheap” agro-pastoralist resource that nearly everybody had access to, becoming a fall-back line of survival in times of scarcity, be it natural or socially caused. Acorn bread and goat milk: the poor man’s diet not so long ago.

  2. As I commented back in the day in my blog, Matthieson does not have any actual evidence for that and is also pruning, cherry-picking the available ancient DNA evidence of pre-IE Western Europe (Basque Country, Sweden) that clearly indicates that the LCT mutation was present and even fixated in some cases already in the Chalcolithic.

    Another bit of evidence is the massive consuption of dairies Neolithic Britain. Britain is pretty much central to the European LCT allele distribution (Britain, Scandinavia, West France and North Iberia are the core areas), so it makes total sense that those early Brits were already LCT+, at least to a great extent.

    Finally the only pseudo-evidence they present is a Bell Beaker individual (among many LCT-) and Bell Beaker is a cultural phenomenon originating in Southwestern Europe, not the steppes.

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