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Srilakshmi M Raj, Allison Pei, View ORCID ProfileMatthieu Foll, Florencia Schlamp, Laurent Excoffier, Dorian Q Fuller, Toomas Kivisild, Andrew G. Clark
This article is a preprint and has not been peer-reviewed
Domestication of crops and animals during the Holocene epoch played a critical role in shaping human culture, diet and genetic variation. This domestication process took placeacross a span of time and space, especially in Asia. We hypothesize that domestication of plants and animals around the world must have influenced the human genome differentially among human populations to a far greater degree than has been appreciated previously. The range of domesticated foods that were available in different regions can be expected to have created regionally distinct nutrient intake profiles and deficiencies. To capture this complexity, we used archaeobotanical evidence to construct two models of dietary nutrient composition over a 9000 year time span in Asia: one based on Larson et al. (2014) and measured through composition of 8 nutrients, and another taking into account a wider range of crops, cooking and lifestyle variation, and the dietary variables glycemic index and carbohydrate content. We hypothesize that the subtle dietary shifts through time and space have also influenced current human genetic variation among Asians. We used statistical methods BayeScEnv, BayeScan and Baypass, to examine the impact of our reconstructed long-term dietary habits on genome-wide genetic variation in 29 current-day Asian populations (Figure S1, Figure 1, Figure 2). Our results show that genetic variation in diet-related pathways is correlated with dietary differences among Asian populations. SNPs in five genes, GHR, LAMA1, SEMA3A, CAST and TCF7L2, involved in the gene ontologies ‘salivary gland morphogenesis’ and ‘negative regulation of type B pancreatic cell apoptotic process’ suggest that metabolism may have been primary targets of selection driven by dietary shifts. These shifts may have influenced biological pathways in ways that have a lasting impact on health. We present a case that archaeobotanical evidence can provide valuable insight for understanding how historical human niche construction might have influenced modern human genetic variation.
From the full paper:
Our primary dietary model (see Methods) infers that the Southwest Asian populations (mostly sampled from present-day Pakistan) had a greater increase in carbohydrates, lipids and protein content due to domestication events from 9000 years ago. In contrast, South Asian populations showed the latest and at least these three major dietary changes in their diets, as domestication started later here. The greatest nutrient increases in all populations due to diet changes were carbohydrates, followed by protein, then lipids. Separated into segments of 3000 years, consumption of all three components from the domesticated diet increased over time, following known increased adoption of domestication practices throughout Asia (Figure 2a, Tables S1-8).
The Fertile Crescent in the Middle East was the site of much early innovation in agriculture a long time ago, such as growing wheat. Farming rapidly spread outward from there in multiple directions, such as eastward to the Indus River valley in modern Pakistan. But then, apparently, there was a long pause before Middle Eastern wheat could be raised further east in the Indian subcontinent. The problem was that in the Middle East, it mostly rains in the winter, but in South Asia the monsoon dumps rain in the summer, so it took a long time for grain-breeders to flip the seasons.
This is why civilization has less ancient roots in India than in the middle east (treating the Indus as the eastern boundary of the Middle East; interestingly, that’s where Alexander the Great wept because he had no more worlds to conquer, despite the vast South Asian peninsula still in front of him).
Or maybe I’ve got this all wrong …
As for the rest of the paper, I don’t pretend to understand it, but it might be relevant to questions of what kind of diet is best for you individually. For example, in the later 20th Century, federally-funded nutrition experts were much impressed by the fact that the Japanese in Japan lived a long time eating a diet that was relatively low in fat, low in animal protein, high in soy, and high in carbohydrates (like rice), and thus strongly recommended it to white Americans, who just kept getting fatter and then dying younger.
But the Japanese evolved over a long time to eat that kind of diet. Did your ancestors?
Our study complements a growing body of literature showing that the more predictable and static external environmental factors such as elevation, climate and disease affect human evolution, by showing that dietary factors also drove genetic adaptations [28–31]. We have provided data that suggests regional adaptations to Neolithic diets which varied in nutrient profiles. Humans have shaped their own food environment over millennia, through a broadening range of food processing techniques and through domestication and the construction of agricultural systems [32–34]. These changes have left signatures on the genomes of different populations, and may have powerful implications for disparities in disease etiology as well as aging and life expectancy among historical and contemporary human populations.