New lactase persistence study rejects "calcium absorption" hypothesis

The "calcium absorption" hypothesis has been proposed as hypothetical mechanism to explain the apparent genetic sweep of lactose persistence alleles in Europe. According to this hypothesis, the possible role of milk in improved calcium absorption would counter the poor vitamin D synthesis in Northern Europe, preventing rickets.

However this hypothesis seems very weak, as I explained recently, notably because bone formation is only one of the various roles of vitamin D and it is probably much more crucial in correct brain development in childhood. Also there is another clear adaptation that actually solves the problem very well: whiter skin able to much more efficiently produce vitamin D in our bodies surfaces by mere exposition to sunlight, a trait that seems to have been increasingly favored after the Neolithic drop in fish consumption (the only actual nutritional source of vitamin D at relevant doses).

This new paper confirms my skepticism.

Oddný Ósk Sverrisdóttir et al., Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe. MBE 2014. Pay per view → LINK  

[doi:10.1093/molbev/msu049]

Abstract

Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose – the main carbohydrate in milk – and its production is down-regulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans LP is strongly associated with, and probably caused by, a single C to T mutation 13,910bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remains poorly understood. In this study we examine one of the most widely cited hypotheses for selection on LP – that fresh milk consumption supplements the poor vitamin D and calcium status of northern Europe's early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB-light levels. None of the 8 samples successfully typed in the study had the derived T-allele. In addition, we reanalyse published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of lactase persistence in Europe.

The study finds most likely that, most likely, there is population continuity between Neolithic farmers and modern local peoples in Northern Iberia and SE France. Technically they could only not reject this population continuity for all population parameters, but, considering that the same tests strongly reject it for Central Europe and Scandinavia, the most parsimonious conclusion is that some important population continuity does exist in SW Europe since Neolithic. In the words of the researchers:

It thus seems likely that population turnover since or shortly after the Neolithic transition has been less severe in southwestern Europe than in central or northern Europe.

However these ancient populations were lactose intolerant (rs4988235(C)) while modern ones in Northern Iberia are massively able to digest lactose (rs4988235(T)). This supports the theory of adaptive sweep for this allele. 

They suspect that the real reason behind the lactose persistence sweep is caused by basic nutritional reasons (calories and proteins) because milk may have been less subject to fluctuations in crops (traditionally cattle ate grass and not cereals, as happens in modern industrial production, while goats have even more varied natural food sources). In such circumstances episodic famines would have strongly favored lactose tolerant phenotypes, more so if lactose intolerant people would have drank milk or ate high-lactose dairies in desperation, causing them potentially deadly diarrhea.

This is not the same but fits well with my class structure hypothesis, outlined recently. The main reason why I favor this hypothesis is that this generalizing pattern should have affected farmers since very early in the Neolithic, even when they were still living in Asia or Greece, so it is very strange that the genetic sweep only appears since or after the Chalcolithic period, when a hierarchical class society is formed everywhere.


Correction: I wrongly reported the main European lactase persistence SNP as rs13910*T, when it is in fact rs4988235(T) (already corrected in the text above) This was caused by the nomenclature used in the Sverrisdóttir paper, where it refers to it as -13910*T, which must be some other sort of naming convention. Thanks to Can for noticing.

See also:

• Actual lactase persistence more common than genes predict
• Childhood and death in Neolithic and Bronze Age Iberia
• Medieval Germans, Hungarians and the spread of lactose tolerance
• Caught in the act: lactose intolerant and lactose tolerant populations together but mostly unmixed in Chalcolithic Upper Ebro
• And in general category: lactose intolerance