Reconstruction of nine thousand years of agriculture-based diet and impact on human genetic diversity in Asia

Abstract

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 place across 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. Results:The dietary models were constructed to capture different aspects of long-term nutritional information. They incorporate the following unique features: 1) an estimation of a preagricultural diet base, which we term a 'hunter-gatherer diet'; 2) proportionate variation of different dietary components; 3) variation in the length of exposure to dietary components; 4) inclusion of different food processing techniques to obtain nutritional estimates; 5) the use of glycemic index and carbohydrate content to measure nutrition, as both highlight the impact of increased carbohydrate consumption through time and may play a role in diabetes risk [1][2][3]. The first dietary model we constructed examines relative differences in the change of nutrient levels in each of the three ADMIXTURE-defined groups ( Figure S1). In the second model, unlike the first, we incorporate information on pre-domestication diet by including a baseline dietary model for our populations. We assume that the con...

Metabolic Signatures from Genebank Collections: An Underexploited Resource for Human Health?

“…This relationship has resulted in genetic alterations in both human and domesticated crop genomes. The human genome shows genetic footprints in genes related to specific diets (Raj et al 2019), and the domestication of crop plants and their continuous adaptation to our needs resulted in the loss of genetic diversity. Modern elite varieties, which are the result of cross-breeding, show yet lower genetic diversity when compared to their landrace progenitors (Raj et al 2019).…”

Lower Dietary Intake of Plant Protein Is Associated with Genetic Risk of Diabetes-Related Traits in Urban Asian Indian Adults

“…Several large longitudinal studies showed that the intake of animal protein was significantly associated with the risk of T2D [ 13 , 14 , 15 , 16 , 17 ]. In the context of rapid urbanisation and nutrition transition, interactions between Westernised diet, lifestyle and genetic factors have further escalated T2D prevalence in Asia [ 18 , 19 ]. In South Asians, several single nucleotide polymorphisms (SNPs) have been associated with adiposity [ 20 , 21 , 22 , 23 ], insulin resistance [ 24 ], pancreatic β-cell function [ 20 , 25 , 26 ] and T2D [ 20 , 22 , 23 , 26 , 27 ].…”