Vitamin D scarcity and natural selection

 

In humans who are dark-skinned or who live above the Arctic Circle, natural selection has favored those who use vitamin D more efficiently or have workarounds of one sort or another for vitamin D scarcity. Yakut family, Wikicommons (Uyban)

 

 

Vitamin D is less easily obtained by some people than by others. It is less available to those who are dark-skinned or who live above the Arctic Circle. Because less UV light enters the skin for biosynthesis, natural selection has favored individuals who use this vitamin more efficiently or have workarounds of one sort or another (Frost 2009; Frost 2012; Frost 2018).

 

Vitamin D levels are thus naturally lower in Arctic and dark-skinned humans. Some variation exists even among Europeans, with levels being lower in darker-skinned southern Europeans than in lighter-skinned northern Europeans (Snellman et al. 2009; van der Wielen et al. 1995).

 

Unfortunately, vitamin D deficiency is diagnosed on the basis of norms developed for light-skinned people from temperate latitudes. Inuit and African Americans are thus diagnosed as “deficient” and offered vitamin supplementation, which has the effect of bathing their body tissues in concentrations of vitamin D that they and their ancestors have not experienced for tens of thousands of years, if not longer.

 

If  Arctic and darker-skinned humans naturally have lower levels of vitamin D, their optimal range of levels will likewise be lower, and toxic effects may occur at levels that lie within the optimal range of Europeans. You may have been told that this cannot happen because toxicity occurs only if you ingest huge amounts of this vitamin. Actually, toxicity begins at relatively low levels. In light-skinned humans from the temperate zone, the optimal range seems to extend only from 40 nmol/L to 100 nmol/L:

 

·         The total mortality rate is about 50% greater in men whose vitamin D levels are either below 46 nmol/L or above 98 nmol/L (Michaelsson et al. 2010).

·         The risk of prostate cancer is significantly greater below 40 nmol/L and above 60 nmol/L (Tuohimaa 2008; Tuohimaa et al. 2009).

·         Mortality for 7 types of cancer (endometrial, esophageal, gastric, kidney, non-Hodgkin's lymphoma, pancreatic, ovarian) is significantly greater below 45 nmol/L and above 124 nmol/L (Helzlsouer et al. 2010).

·         The risk of pancreatic cancer is significantly greater above 100 nmol/L (Stolzenberg-Solomon et al. 2010).

·         The risk of cardiovascular disease is significantly greater below 50 nmol/L and above 62.5 nmol/L, and mortality from all causes is significantly greater above 122.5 nmol/L (Davis 2009).

 

Perhaps most worrisome, studies on mice indicate a U-shaped response curve for the aging process, with premature aging associated with both too little and too much vitamin D (Tuohimaa 2009; Tuohimaa et al. 2009).

 

Vitamin D metabolism and gene-culture coevolution among the Inuit

 

To what extent has the safe range of vitamin D been shifted downward in Arctic and dark-skinned humans? To answer that question, we need to understand gene-culture coevolution. When humans enter a new environment, they adapt by pushing the bounds of phenotypic plasticity—they do the most with what they have already. There is then natural selection for genetic variants that can stabilize this new pattern of adaptation and make it more innate. A new phenotype thus ends up becoming a new genotype.

 

Traditionally, Inuit coped with vitamin D scarcity through a high-meat/low-cereal diet and through extended breastfeeding of children for two years or longer. This diet not only provided vitamin D but also helped the body use this vitamin more efficiently, specifically by means of β-casein in breast milk, unknown substances in meat, and absence of phytic acid (Frost 2018). 

 

Those cultural adaptations were followed by physiological adaptations: receptors that bind more tightly to the vitamin D molecule; a lower set-point for calcium-regulated release of parathyroid hormone; and conversion of vitamin D at a higher rate from its common form to its most active form. Inuit breast milk might also be richer in β-casein (Frost 2018).

 

That gene-culture coevolution has been notably demonstrated by a genome study of the Greenland Inuit, whose marine diet has apparently selected for genetic variants that help their bodies digest and use polyunsaturated fatty acids (Fumagalli et al. 2015).

 

Research on indigenous northern Eurasian peoples

 

Before 2020, the Inuit were the only non-European population for whom we had research on cultural and physiological adaptations to vitamin D scarcity (Frost 2012; Frost 2018). Two studies have since been published on this subject with regard to indigenous peoples in northern Eurasia.

 

Research by Khrunin et al. (2020)

 

This research team looked for signals of natural selection in the genomes of eight northern populations: Russians from the Archangelsk and Vologda regions; Izhemski Komi; Priluzski Komi; Veps; Khanty; Mansi; and Nenets. The strongest signal came from two genes: SLC37A2 and PKNOX2. The first gene is expressed when vitamin D₃ is present in peripheral blood cells. The authors go on to note:

 

Deficit of vitamin D is often observed in northern populations, where exposure to sunlight is limited for many months. Hypothetically, mutations in the VDR-controlled SLC37A2 gene may help northern populations adjust to vitamin D levels. At the same time, the same mutations could have effects on alcohol tolerance in these populations through the PKNOX2 gene, located on the opposite strand of DNA in the same locus. 

 

The second gene, PKNOX2, is associated with alcohol addiction in mice and humans. The authors add that this finding “is of special interest in the context of the well-known alcohol addiction that occurs widely in indigenous populations of Northern Eurasia.”

 

Could vulnerability to alcoholism be a side-effect of adaptation to vitamin D scarcity? The hypothesis is interesting, although I lean more toward another explanation. Some populations, like those around the Mediterranean, have had a long history of drinking fermented beverages instead of water, which might be contaminated with bacteria that cause dysentery and other diseases. Consequently, natural selection has favored individuals who have higher levels of alcohol dehydrogenase and other physiological adaptations that make alcohol less toxic. Conversely, other populations, like northern Eurasians, have consumed fermented beverages for a shorter time, and their bodies are less adapted to alcohol (Nabhan 2004, pp. 27-30; Ridley 2000).

 

Research by Malyarchuk (2020)

 

This is a study of a single polymorphic gene, GC, in several indigenous peoples of northeastern Siberia (Eskimos, Chukchi, Koryaks), central Siberia (Evens, Evenks, Yakuts), southern Siberia (Tuvinians, Shorts, Altaians, Buryats), and western Siberia (Kets, Khanty, Mansi, Selkups, Nenets, Nganasans). The GC gene produces a protein that is the main carrier of vitamin D in the body.

 

One GC variant, specifically the T variant at rs4588, is much less frequent in northeast and central Siberians (5.4%, 3.1%) than in southern and western Siberians (28.6%, 27.5%). Conversely, the G variant is much more frequent in the northeast and center (32.1%, 46.9%) than in the south and west (16.1%, 12.5%). I initially thought the reason was a higher level of European admixture in southern and western Siberia. But there is little European admixture in East Asians, and they resemble southern and western Siberians in having the same high frequency of the T variant (26.1%).

 

The G variant may have become more frequent in northeast and central Siberians as an adaptation to vitamin D scarcity. As one goes farther north, the skin produces less vitamin D because less UV light enters the skin. More research is needed, however, on two other factors: (1) amount of vitamin D from dietary sources; and (2) skin pigmentation. It may be that southern Siberians are somewhat darker-skinned than northern Siberians, although that isn’t my impression. These points are made by Malyarchuk (2020) in the Results and Discussion section. Researchers should study:

 

… the gene-environment interactions by taking into account the vitamin D status of the indigenous population, ethnicity, influence of environmental conditions (the level of natural ambient light and seasonal patterns), and specifics of nutrition. The influence of such factors on the distribution of GC polymorphism variants is evidenced by the data obtained in this work on the high prevalence of haplotypes encoding the Gc1F isoform in northeast Asia under condition of low intensity of solar radiation. In addition, an important factor contributing to vitamin D deficiency may be a relatively high level of melanin in the skin of representatives of the Arctic peoples, which prevents the penetration of ultraviolet rays into the skin and thereby hinders the synthesis of vitamin D₃

 

References

 

Davis, C.D. (2009). Vitamin D and health: can too much be harmful? American Journal of Lifestyle Medicine 3(5): 407-408. https://doi.org/10.1177/1559827609338154

 

Frost, P. (2009). Black-White differences in cancer risk and the vitamin-D hypothesis. Journal of the National Medical Association 101: 1310-1313.

https://doi.org/10.1016/s0027-9684(15)31151-2

 

Frost, P. (2012). Vitamin D deficiency among northern Native Peoples: a real or apparent problem? International Journal of Circumpolar Health 71(S2): 18001

https://doi.org/10.3402/IJCH.v71i0.18001

 

Frost, P. (2018). To supplement or not to supplement: are Inuit getting enough vitamin D? Études Inuit Studies 40(2): 271-291.

https://doi.org/10.7202/1055442ar

 

Frost, P. (2020). Ethnic differences in vitamin-D metabolism. E Scholarly Community Encyclopedia.

https://encyclopedia.pub/3033

 

Fumagalli, M., I. Moltke, N. Grarup, F. Racimo, P. Bjerregaard, M.E. Jørgensen et al. (2015). Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349(6254): 1343-1347. https://doi.org/10.1126/science.aab2319

 

Helzlsouer, K.J. and Steering Committee of Vitamin D Pooling Project of Rarer Cancers (2010).  Abstract PL04-05: Vitamin D: panacea or a Pandora’s box for prevention? Cancer Prevention Research 3(1 Suppl 1): PL04-05. https://doi.org/10.1158/1940-6207.PREV-09-PL04-05

 

Khrunin, A.V., G.V. Khvorykh, A.N. Fedorov, and S.A. Limborska (2020). Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia. PLoS ONE 15(2): e0228778. https://doi.org/10.1371/journal.pone.0228778

 

Malyarchuk, B.A. (2020). Polymorphism of GC gene, encoding vitamin D binding protein, in aboriginal populations of Siberia. Ecological Genetics 18(2): 243-250.

https://doi.org/10.17816/ecogen18634

 

Michaëlsson, K., J.A. Baron, G. Snellman, R. Gedeborg, L. Byberg, J. Sundström et al. (2010). Plasma vitamin D and mortality in older men: a community-based prospective cohort study. American Journal of Clinical Nutrition 92(4): 841-848. https://doi.org/10.3945/ajcn.2010.29749 

 

Nabhan, G.P. (2004). Why Some Like It Hot. Food, Genes, and Cultural Diversity. Washington: Island Press/Shearwater Books.

 

Ridley, M. (2000).Genome: The Autobiography of a Species in 23 Chapters. New York: HarperCollins.

 

Snellman, G., H. Melhus, R. Gedeborg, et al. (2009). Seasonal genetic influence on serum 25-hydroxyvitamin D levels: a twin study. PLoS ONE 4(11): e7747. https://doi.org/10.1371/journal.pone.0007747

 

Stolzenberg-Solomon, R.Z., E.J. Jacobs, A.A. Arslan, D. Qi, A.V. Patel, K.J. Helzlsouer et al.

(2010). Circulating 25-hydroxyvitamin D and risk of pancreatic cancer, Cohort Consortium Vitamin D Pooling Project of Rarer Cancers. American Journal of Epidemiology 172(1): 81-93.

https://doi.org/10.1093/aje/kwq120

 

Tuohimaa, P. (2009). Vitamin D and aging. The Journal of Steroid Biochemistry and Molecular Biology 114(1-2): 78-84. https://doi.org/10.1016/j.jsbmb.2008.12.020 

 

Tuohimaa, P., T. Keisala, A. Minasyan, J. Cachat, and A Kalueff (2009). Vitamin D, nervous system and aging. Psychoneuroendocrinology 34S: S278-286. https://doi.org/10.1016/j.psyneuen.2009.07.003

 

van der Wielen R.P., M.R. Lowik, H. van den Berg, L.C. de Groot, J. Haller J, et al. (1995). Serum vitamin D concentrations among elderly people in Europe. Lancet 346: 207–210. https://doi.org/10.1016/S0140-6736(95)91266-5

Selection for fair skin in Europeans and North Asians

 

Selection for fair skin in different human populations (Huang et al. 2021)

Selection for fair skin was about four times stronger among ancestral Europeans than it was among ancestral North Asians or the earlier shared ancestors of both groups. So says a recent genome study.

 

Huang et al. (2021) examined genes that influence skin pigmentation to calculate the strength of selection for lighter skin among the ancestors of today’s Europeans and North Asians. They concluded that selection for lighter skin was strongest among the unique ancestors of present-day Europeans, with a selection pressure of 25.9. It was about four times weaker among the unique ancestors of North Asians (5.61) and the earlier shared ancestors of both groups (6.5). East Asians actually became darker after they split from North Asians, with a negative selection pressure of -5.53.

 

Our estimate shows that the modern European lineage had the largest selective pressure (s4=0.0259/generation) on light pigmentation than the other branches, suggesting that recent natural selection favoured light pigmentation in Europeans. Recent studies using ancient DNA could support our observation of recent directional selection in Europeans (Huang et al. 2021, p. 3)

 

This finding supports earlier findings. Modern humans remained dark-skinned in Europe long after they had spread north into northern latitudes some 45,000 years ago. It was not until 20,000 years ago that alleles for white skin made their appearance (Beleza et al. 2013; Canfield et al. 2014; Norton and Hammer 2007). As a Science correspondent concluded: "The implication is that our European ancestors were brown-skinned for tens of thousands of years" (Gibbons 2007).

 

Those ancestors were initially proto-Eurasians, and it was only later that they differentiated to become respectively Europeans and North Asians. Only then, and only in the European lineage, did skin color begin to lighten at a fast rate. This rapid evolution seems to have been confined to a relatively small area that stretched from the Baltic to central Siberia. Elsewhere, in western and southern Europe, people remained dark-skinned until almost the dawn of history, as shown by DNA dated to 11,000 years ago from England, 8,000 years ago from Luxembourg, and 7,000 years ago from Spain (Brace et al. 2019; Lazaridis et al. 2014; Olalde et al. 2014).

 

The fair skin phenotype, together with a variety of hair and eye colors, would later spread throughout all of Europe, while going extinct east of the Urals. In the latter region it would persist into historic times. At sites in south-central Siberia, dating from the third millennium BC to the fourth century AD, genetic analysis has shown that most of the buried individuals had blue or green eyes, light hair (blond, red, light brown), and light skin (Bouakaze et al. 2009). South Siberian peoples were, in fact, described as having "green eyes" and "red hair" in old Chinese records (Keane 1886, p. 703).

 

It seems that Europeans acquired their current appearance very fast, perhaps ten to twenty thousand years ago during the last ice age. Initially confined to northeastern Europe and parts of Siberia, the new phenotype would in time spread to the rest of the continent ... on the eve of recorded history. Only then did all Europeans come to look “European” (Frost 2014; Frost 2020).

 

References

 

Beleza, S., A.M. Santos, B. McEvoy, I. Alves, C. Martinho, E. Cameron, et al. (2013). The timing of pigmentation lightening in Europeans. Molecular Biology and Evolution 30(1): 24-35. https://doi.org/10.1093/molbev/mss207

 

Bouakaze, C., C. Keyser, E. Crubézy, D. Montagnon, and B. Ludes. (2009). Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis. International Journal of Legal Medicine 123(4): 315-325.

https://doi.org/10.1007/s00414-009-0348-5

 

Brace, S., Y. Diekmann, T.J. Booth, Z. Faltyskova, N. Rohland, S. Mallick, et al. (2019). Ancient genomes indicate population replacement in Early Neolithic Britain. Nature Ecology & Evolution 3(5): 765-771. https://doi.org/10.1038/s41559-019-0871-9

 

Canfield, V.A., A. Berg, S. Peckins, S.M. Wentzel, K.C. Ang, S. Oppenheimer, and K.C. Cheng. (2014). Molecular phylogeography of a human autosomal skin color locus under natural selection. G3, 3(11): 2059-2067. https://doi.org/10.1534/g3.113.007484

 

Frost, P. (2014). The puzzle of European hair, eye, and skin color. Advances in Anthropology 4(2): 78-88. http://www.scirp.org/journal/PaperInformation.aspx?PaperID=46104

 

Frost, P. (2020). White Skin Privilege: Modern Myth, Forgotten Past. Evolutionary Studies in Imaginative Culture 4(2): 63-82. https://doi.org/10.26613/esic/4.2.190

https://www.jstor.org/stable/10.26613/esic.4.2.190

 

Gibbons, A. (2007). American Association of Physical Anthropologists Meeting: European skin turned pale only recently, gene suggests. Science 20 April 2007, 316(5823): 364.

https://doi.org/10.1126/science.316.5823.364a

 

Huang, X., S. Wang, L. Jin, and Y. He. (2021). Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation. Biology Open 15 February 2021; 10(2): bio056523. https://doi.org/10.1242/bio.056523

 

Keane, A.H. (1886). Asia with Ethnological Appendix. London: Edward Stanford.

 

Lazaridis, I., N. Patterson, A. Mittnik, G. Renaud, S. Mallick, K. Kirsanow, et al. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513(7518): 409-413. https://doi.org/10.1038/nature13673

 

Norton, H.L., and M.F. Hammer. (2007). Sequence variation in the pigmentation candidate gene SLC24A5 and evidence for independent evolution of light skin in European and East Asian populations. Program of the 77th Annual Meeting of the American Association of Physical Anthropologists, p. 179.

 

Olalde, I., M.E. Allentoft, F. Sanchez-Quinto, G. Santpere, C.W.K. Chiang, M. DeGiorgio, et al. (2014). Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507 (7491): 225-228. https://doi.org/10.1038/nature12960