Genetic study The Geographical Distribution of Lactose Tolerance-Associated Alleles 13910*T and 13915*G Is Strongly Linked to Male Founder Events in Eurasia

[Tautalus]

This paper presents some ideas, already known for years, about how genetic variants associated with adult lactose tolerance are distributed across Europe, the Near East, and North Africa, and how these distributions relate to Y-chromosome haplogroups and ancient ancestry components. The study focuses mainly on two mutations: 13910*T, the dominant European lactose persistence allele, and 13915*G, which is characteristic of Arabia.

The author argues that lactose tolerance represents one of the strongest and fastest examples of recent human evolution. Normally, mammals lose the ability to digest lactose after weaning because production of the enzyme lactose declines. Some human populations, however, evolved mutations that maintain lactose production into adulthood. These mutations occur not directly in the LCT gene, but in regulatory regions of the neighbouring MCM6 gene.

The paper reviews previous debates about the origins of lactose tolerance in Europe. Earlier assumptions connected lactose tolerance to the spread of early Neolithic farmers and dairying, but ancient DNA evidence shows that early Anatolian and European farmers practised dairying without carrying the 13910*T mutation. Ancient European farmers also tended to be relatively short, which the author interprets as indirect evidence that milk contributed little nutritionally at the time. The first confirmed European carriers of 13910*T appear much later, during the Eneolithic and Bronze Age in southeastern Europe.

The study strongly supports the hypothesis that the 13910*T allele originated among populations related to the Yamnaya culture of the Pontic-Caspian steppe. Although early Yamnaya individuals themselves carried the mutation at very low frequencies, they already exhibited evidence of dairy-oriented pastoralism and tall stature, implying strong dairy consumption before widespread lactose persistence evolved genetically. The author proposes that the later spread of the allele across Europe was amplified through male founder effects involving expanding patrilineal groups.

The Arabian 13915*G mutation appears to have evolved independently. It is associated with adaptation to camel milk consumption and likely spread during increasing aridity in the Arabian Peninsula around 4,000 years ago. Unlike 13910*T, which spread broadly across Europe, 13915*G remained geographically concentrated in Arabia and nearby regions.

To investigate these patterns, the author compiled genetic data from 60 countries, including frequencies of lactose-tolerance alleles, Y-chromosome haplogroups, autosomal ancestry components, and average male height. Statistical analyses examined correlations between these variables. The results show very strong geographic structure.
The 13910*T allele reaches its highest frequencies in Ireland and Iceland, exceeding 85%, and remains extremely common across Scandinavia and the British Isles. Frequencies decline progressively toward southern and eastern Europe and become very low in the Near East. Moderate frequencies appear in Northwestern Africa, likely reflecting historical gene flow from Europe.
The 13915*G allele displays a sharply different distribution. It peaks in Saudi Arabia and Yemen, where frequencies exceed 50%, but declines rapidly outside the Arabian Peninsula, reaching only low single-digit percentages in places like Egypt and Syria.

One of the paper’s central arguments is that lactose-tolerance alleles correlate strongly with specific Y-chromosome lineages. In Europe, 13910*T is most strongly associated with haplogroup I1, which today peaks in Scandinavia and is linked to Germanic populations. Other positively associated lineages include I2a-M223, R1b-U106, and R1b-S116, all connected with Germanic or Bell Beaker-derived ancestry. The strongest statistical models combined several of these lineages together and explained most of the geographic variation in 13910*T frequencies. In contrast, several lineages associated with southeastern Europe and the Near East correlate negatively with 13910*T, these include E1b-M78, J2, and R1b-M269*.

Outside Europe, the paper identifies more complex patterns. In the Caucasus, the presence of 13910*T correlates positively with Caucasus-associated haplogroups such as G2a and J2, suggesting secondary spread through interactions involving steppe ancestry. In North Africa, the European allele correlates with Berber-associated haplogroup E1b-M81, indicating local founder effects after introduction from Europe.

For the Arabian allele 13915*G, the strongest association is with Y haplogroup J1, a lineage strongly concentrated in Arabia and especially Yemen. Additional positive relationships involve haplogroups E1b-M123 and T, which together form a cluster of “Arabic” paternal lineages. The data suggest that 13915*G spread mainly within populations carrying these Arabian-associated male lineages.

The ancestry analyses reinforce these conclusions. The European allele 13910*T correlates most strongly with Yamnaya ancestry across Europe. Hunter-gatherer ancestry components also show positive relationships, although the author argues these were secondary effects rather than the primary source of lactose tolerance. Near Eastern ancestry components, especially Anatolian Neolithic and Caucasus-related ancestries, generally correlate negatively with 13910*T inside Europe.

Meanwhile, the Arabian 13915*G allele shows an extremely strong relationship with Natufian ancestry, an ancient Levantine ancestry component now concentrated in Yemen and Arabia. The correlation between Natufian ancestry and the Arabic Y-haplogroup cluster is nearly perfect, supporting the idea that the Arabian lactose-tolerance mutation spread within a relatively coherent ancestral population.

The paper also explores the relationship between lactose tolerance and body height. In Europe, lactose-tolerance frequencies correlate positively with average male height, even after controlling for environmental variables like nutrition and child mortality. The author interprets this as another reflection of Yamnaya ancestry, which is itself strongly associated with taller stature. By contrast, the Arabian 13915*G allele correlates negatively with height because it is linked to Natufian ancestry and Arabian-associated haplogroups, which the study associates statistically with shorter average stature.

The author concludes that the spread of lactose tolerance in Eurasia cannot be explained solely by dairying practices. Instead, the evidence points toward demographic expansion and founder effects involving specific male lineages. The European and Arabian lactose-tolerance mutations arose independently, spread through different historical processes, and became associated with distinct ancestral and social structures. The paper ultimately presents lactose tolerance as not only a dietary adaptation but also a marker of ancient migrations, population expansions, and long-term demographic history across Eurasia and North Africa.
​

ABSTRACT
Lactose tolerance (lactase persistence) represents a very progressive human adaptation, the origins of which remain incompletely understood. This study aims to examine the geographical distribution of the two alleles associated with lactose tolerance in Eurasia (13910*T and 13915*G) in relation to the main Y haplogroups and autosomal ancestry components. Data on the frequency of the 13910*T allele were collected from 52 countries across Europe, the Near East, and North Africa. The 13915*G allele was available for 30 countries, but was studied in only 16 Near Eastern and North African countries, as it is absent in Europe. The findings indicate very robust, linear relationships between allele frequencies and the genetic factors examined. The strong correlation between the occurrence of the 13910*T allele and Yamnaya ancestry supports the hypothesis that 13910*T originated from the steppe Yamnaya culture. However, its subsequent dissemination can be attributed to a series of regional male founder events and the spread of specific Y haplogroups, particularly Y haplogroup I1. Conversely, the current occurrence of the 13915*G allele appears to have a less complex origin, associated with the geographically constrained expansion of pastoral populations with Natufian ancestry and Y haplogroup J1 in the Arabian Peninsula.

https://onlinelibrary.wiley.com/doi/full/10.1002/ajhb.70253?campaign=woletoc

Frequencies of lactose tolerance-associated alleles 13910*T (A) and 13915*G (B).

Factor analyses of the lactose tolerance-associated alleles and genetic factors.
How the European lactose-tolerance allele 13910*T relates to ancestry components, Y-haplogroups, and male height. 13910*T clusters strongly with Yamnaya ancestry and with northern/western European male lineages. The main cluster around 13910*T includes Yamnaya ancestry, I1, R1b-U106, R1b-S116, I2a-M223, taller male stature.

 

[Tautalus]

It goes without saying that the Y chromosome contains very few genes, and none are responsible for lactose tolerance. Y haplogroups serve as signatures of male founder events. The Y haplogroup is a demographic marker of the expansion, not the mechanism producing lactose tolerance. Y haplogroups are historical tags for founder expansions, autosomal ancestry carried the lactase persistence alleles, and strong male biased demographic processes preserved the correlation between the two.​

 

[Riverman]

We could also say Germanics, Arabs and Niloto-Hamitic people (the latter not covered here).

 

[—BoNe—]

“Year 2300, 200 years after World War III.

95% of historical data was lost, and the new world order distorted what happened in order to legitimize its sovereignty. Revolutionary scientists try to estimate which country invented the iPhone in order to understand the technological leap that 100 years later led to the nuclear war that wiped out 99% of the population, and they conclude that since 90% of Japanese vs 60% of Anglo-Americans were carriers of an iPhone, it was the Japanese who invented it.”

That is the absurdity of assigning the origin of an autosomal SNP through current Y-haplogroup frequencies and a sampling bias at the level of Malta (60 samples) vs the United Kingdom (170,000 samples).

Relative to total population size, the UK is 20–25 times more represented than Malta.

Northern countries have higher lactose tolerance because in cold climates milk keeps better without needing to be quickly processed into another product; remember that refrigerators have only existed for about 100 years.

I once met a Norwegian woman who told me that in her house they drank milk while eating lunch and dinner. At first I thought it was a joke—I’m not sure if it’s a general thing, but it would explain a lot.

Having the CC homozygous genotype does not make you strictly intolerant. People who get sick from a single sip of milk, in addition to being CC, often carry other mutations that increase intolerance, such as intestinal disorders or allergies to milk proteins.

In Southern countries, even if TT/CT rates are 60–70%, 99% of people take coffee with milk, and the 30% CC individuals have absolutely no issues with 200 ml. Only about 1% actually get sick from a single sip of milk, and that is related to thousands of polymorphisms and epigenetics.

A person with the CC genotype who consumes 200 ml of milk daily may, through dietary adaptation, develop a colonic microbiota more capable of fermenting lactose than someone who does not consume it. However, they do not digest lactose in the small intestine as TT or CT individuals do, where lactase activity enables hydrolysis and absorption.

People reading these articles automatically think Southern Europeans explode if they drink a glass of milk.

If the study were balanced in sample size, perhaps some conclusion could be drawn. But the next step would be to perform phylogenetic analysis of the mutation and classify new SNPs of LCT-13910*T in order to generate distinctive haplotypes and understand how they actually diverged.

But why map the phylogeny of a lactase mutation in detail, right?

It’s more fun to exploit sampling biases to assign a trait to a specific population through Y-haplogroup frequencies—and then be wrong.

The author again absurdly tries to link the origin of a mutation to the Yamnaya, when they did not even have it (<1%).

In other studies he forgets to mention, they take a sample of 20 Late Bronze Age individuals near Germany and only 7% turn out to be tolerant.

Specific autosomal mutations are difficult—almost impossible—to trace in the human phylogenetic tree when you add the mtDNA component from females. So even with 10× more samples you are not guaranteed anything.

Let’s continue the fun thought experiment in an alternate reality where Y-chromosome SNP refinement never happened: the Basques become aware that they are 90% R1-M173, therefore Mr. Romeo, father of all R haplogroups and one of the greatest reproducers in human history, with figures potentially exceeding 600 million male descendants in just 20,000 years… was Basque.

To certify it, they take 100 random Basques and 50,000 samples from Northern European countries. The average TMRCA of Basques is dated to 3000 BC in peer-reviewed papers, while the average TMRCA of Northern populations according to FTDNA and peer-reviewed studies is 2400 BC. Basques obtain the title of the most ancient empirical R1 group.

Basques win elections with a supremacist and pro-terrorist political party, trigger a regional war → then it escalates to civil → European → global war…

And 200 years later… the Japanese invented the iPhone around 2000–2030.

Things like this have been done with other mutations such as blue eyes, and it always ends up as a bad joke once phylogeny is refined or more ancient samples appear.

To estimate the origin of an autosomal SNP you don’t need thousands of samples—you need millions.

The “anthropologist” cites FTDNA population estimates (Northern Europe 4× more sampled than Southern Europe) but then uses a 2016 ISSOG tree…

If they are going to advertise it, they should at least use their own tree for proper refinement.

They mention G25 to extrapolate conclusions…

The academic world has serious problems.


“However, paleogenetic research has shown that the initial expansion of the Corded Ware culture in Central Europe was accompanied by the Y haplogroup R1b-L151, precursor of the R1b-S116 and R1b-U106 mutations (Papac et al. 2021).”

The word “accompanied” is what later gets translated on social media by many as “we are the origin of everything.”

One learns a lot every day—I didn’t know that around 200 million current males carrying the L151 > P312* mutation (TMRCA ~3000 BC) could descend from five L151* individuals from 2800 BC (L151 > U106* branches now extinct or barely detected in modern populations).

Something tells me that Pavel Grasgruber, the author of the article, will soon receive a Nobel Prize.

The intrusion of anthropologists into archaeogenetics is amusing.

But even more amusing is when anthropologists simultaneously intrude into archaeogenetics, archaeology, population biology, and history, while extrapolating data they do not seem to fully understand.

And even more so when a science-illiterate journalist outside the field takes selectively chosen parts, based on the fact that it is a “peer-reviewed scientific paper,” and turns it into sensationalist content that only serves to further misinform the general public.


I think we still haven’t seen anything yet. When “Yamnaya-ists” try to trace the evolution of DAT1 and its relationship to dopamine regulation and intelligence, they will also claim it was invented by the Yamnaya.

And the headline will be:

“The gene of audacity: How the dopamine of steppe horse riders forged the innovative mindset of the West.”