Diet, Changes in Gene Expression and Human Evolution


Changes in food availability and diet represent selective pressures that acted on multiple biological processes and anatomical features during human evolution. Anthropological studies have long investigated these dietary transitions; however, many questions are still open and aspects of these events are still strongly debated. More recently, evolutionary geneticists have provided evidence, both genome‐wide and from single‐gene studies, that diet is an important evolutionary force in humans. Changes in regulation of gene expression have played a major role during human evolution in response to a variety of selective pressures including dietary transitions. Furthermore, recent studies have highlighted the role of variation in gene regulation in risk for common diseases. Future studies promise to leverage the information from variation in gene expression to learn about adaptations to dietary shifts and disease predisposition in humans.

Key Concepts:

  • Changes in food availability and diet composition during hominin evolution created strong selective pressures on multiple biological processes and anatomical features.

  • Genes involved in metabolism carry a signature of selection in single‐gene and genome‐wide studies.

  • The two most interpretable examples of genetic adaptations to dietary shifts in humans have implied changes in the expression level of the lactase and amylase genes.

  • Adaptations to dietary changes may have acted on different molecular aspects of regulation of gene expression.

  • By gaining further knowledge on past human diets, it is possible to achieve a better understanding of potential adaptations to and clinical consequences of our current ones.

Keywords: natural selection; evolutionary genetics; dietary shift; transcription factor; eQTL; mRNA

Figure 1.

The distribution of salivary amylase copy number in the population samples analysed by Perry et al. . The bar chart represents the average copy number for each sample (error bars represent two standard errors). Reproduced from Novembre et al. with permission from Nature.



Aiello LC and Wheeler P (1995) The expensive‐tissue hypothesis: the brain and the digestive system in human and primate evolution. Current Anthropology 36: 199–221.

Ambrose S (1998) Chronology of the Later Stone Age and food production in East Africa. Journal of Archaeological Science 25: 377–391.

Bersaglieri T, Sabeti PC, Patterson N et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. American Journal of Human Genetics 74: 1111–1120.

Blekhman R, Marioni JC, Zumbo P, Stephens M and Gilad Y (2010) Sex‐specific and lineage‐specific alternative splicing in primates. Genome Research 20: 180–189.

Blekhman R, Oshlack A, Chabot AE, Smyth GK and Gilad Y (2008) Gene regulation in primates evolves under tissue‐specific selection pressures. PLoS Genetics 4: e1000271.

Blumenschine RJ, Prassack KA, Kreger CD and Pante MC (2007) Carnivore tooth‐marks, microbial bioerosion, and the invalidation of Dominguez‐Rodrigo and Barba's (2006) test of Oldowan hominin scavenging behavior. Journal of Human Evolution 53: 420–426.

Cartmill M (1993) A View to a Death in the Morning: Hunting and Nature Through History. Cambridge: Harvard University Press.

Copeland L, Blazek J, Salman H and Chiming Tang M (2009) Form and functionality of starch. Food Hydrocolloids 23: 1527–1534.

Dominguez‐Rodrigo M and Barba R (2006) New estimates of tooth mark and percussion mark frequencies at the FLK Zinj site: the carnivore–hominid–carnivore hypothesis falsified. Journal of Human Evolution 50: 170–194.

Dominy NJ, Vogel ER, Yeakel JD, Constantino P and Lucas PW (2008) Mechanical properties of plant underground storage organs and implications for dietary models of early hominins. Evolutionary Biology 35: 159–175.

Enattah NS, Jensen TG, Nielsen M et al. (2008) Independent introduction of two lactase‐persistence alleles into human populations reflects different history of adaptation to milk culture. American Journal of Human Genetics 82: 57–72.

Finch CE and Stanford CB (2004) Meat‐adaptive genes and the evolution of slower aging in humans. Quarterly Review of Biology 79: 3–50.

Fish JL and Lockwood CA (2003) Dietary constraints on encephalization in primates. American Journal of Physical Anthropology 120: 171–181.

Gaulin SJ and Kurland JA (1976) Letter: primate predation and bioenergetics. Science 191: 314–317.

Gifford‐Gonzalez D (2005) African Archeology. London: Blackwell.

Goren‐Inbar N, Alperson N, Kislev ME et al. (2004) Evidence of hominin control of fire at Gesher Benot Ya'aqov, Israel. Science 304: 725–727.

Groot PC, Bleeker MJ, Pronk JC et al. (1989) The human alpha‐amylase multigene family consists of haplotypes with variable numbers of genes. Genomics 5: 29–42.

Hancock AM, Witonsky DB, Gordon AS et al. (2008) Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genetics 4: e32.

Haygood R, Fedrigo O, Hanson B, Yokoyama KD and Wray GA (2007) Promoter regions of many neural‐ and nutrition‐related genes have experienced positive selection during human evolution. Nature Genetics 39: 1140–1144.

de Heinzelin J, Clark JD, White T et al. (1999) Environment and behavior of 2.5‐million‐year‐old Bouri hominids. Science 284: 625–629.

Helgason A, Palsson S, Thorleifsson G et al. (2007) Refining the impact of TCF7L2 gene variants on type 2 diabetes and adaptive evolution. Nature Genetics 39: 218–225.

Hernandez Fernandez M and Vrba ES (2006) Plio‐Pleistocene climatic change in the Turkana Basin (East Africa): evidence from large mammal faunas. Journal of Human Evolution 50: 595–626.

Iafrate AJ, Feuk L, Rivera MN et al. (2004) Detection of large‐scale variation in the human genome. Nature Genetics 36: 949–951.

Ingram CJ, Mulcare CA, Itan Y, Thomas MG and Swallow DM (2009) Lactose digestion and the evolutionary genetics of lactase persistence. Human Genetics 124: 579–591.

Khaitovich P, Lockstone HE, Wayland MT et al. (2008) Metabolic changes in schizophrenia and human brain evolution. Genome Biology 9: R124.

Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET and Pritchard JK (2009) Gene expression levels are a target of recent natural selection in the human genome. Molecular Biology and Evolution 26: 649–658.

Leonard WR, Robertson ML, Snodgrass JJ and KuzawaCW (2003) Metabolic correlates of hominid brain evolution. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 136: 5–15.

Louchart A, Wesselman H, Blumenschine RJ et al. (2009) Taphonomic, avian, and small‐vertebrate indicators of Ardipithecus ramidus habitat. Science 326: 66e61–66e64.

Mann N (2000) Dietary lean red meat and human evolution. European Journal of Nutrition 39: 71–79.

Marlowe FW (2006) Hunter‐gatherers and human evolution. Evolutionary Anthropology 14: 54–67.

Neel JV (1962) Diabetes mellitus: a ‘thrifty’ genotype rendered detrimental by ‘progress’? American Journal of Human Genetics 14: 353–362.

Novembre J, Pritchard JK and Coop G (2007) Adaptive drool in the gene pool. Nature Genetics 39: 1188–1190.

Perry GH, Dominy NJ, Claw KG et al. (2007) Diet and the evolution of human amylase gene copy number variation. Nature Genetics 39: 1256–1260.

Reed KE (1997) Early hominid evolution and ecological change through the African Plio‐Pleistocene. Journal of Human Evolution 32: 289–322.

Sabeti PC, Schaffner SF, Fry B et al. (2006) Positive natural selection in the human lineage. Science 312: 1614–1620.

Sabeti PC, Varilly P, Fry B et al. (2007) Genome‐wide detection and characterization of positive selection in human populations. Nature 449: 913–918.

Savic D, Ye H, Aneas I et al. (2011) Alterations in TCF7L2 expression define its role as a key regulator of glucose metabolism. Genome Research 21: 1417–1425.

Shipman P (1986) Scavenging or hunting in early hominids: theoretical framework and tests. American anthropologist 88: 27–43.

Stahl AB (1984) Hominid dietary selection before fire. Current Anthropology 25: 151–168.

Stanford CB (1999) The Hunting Apes: Meat Eating and the Origins of Human Behavior. Princeton: Princeton University Press.

Stanford CB and Bunn HT (2001) Meat‐eating and Human Evolution. Oxford: Oxford University Press.

Strait DS, Weber GW, Neubauer S et al. (2009) The feeding biomechanics and dietary ecology of Australopithecus africanus. Proceedings of the National Academy of Sciences of the USA 106: 2124–2129.

Suwa G, Asfaw B, Kono RT et al. (2009) The Ardipithecus ramidus skull and its implications for hominid origins. Science 326: 68e61–68e67.

Swallow DM (2003) Genetics of lactase persistence and lactose intolerance. Annual Review of Genetics 37: 197–219.

Tishkoff SA, Reed FA, Ranciaro A et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics 39: 31–40.

Voight BF, Kudaravalli S, Wen X and Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biology 4: e72.

Weir BS, Cardon LR, Anderson AD, Nielsen DM and Hill WG (2005) Measures of human population structure show heterogeneity among genomic regions. Genome Research 15: 1468–1476.

White TD, Ambrose SH, Suwa G et al. (2009) Macrovertebrate paleontology and the Pliocene habitat of Ardipithecus ramidus. Science 326: 87–93.

Williamson SH, Hubisz MJ, Clark AG et al. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genetics 3: e90.

WoldeGabriel G, Ambrose SH, Barboni D et al. (2009) The geological, isotopic, botanical, invertebrate, and lower vertebrate surroundings of Ardipithecus ramidus. Science 326: 65e61–65e65.

Wrangham R and Conklin‐Brittain N (2003) Cooking as a biological trait. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 136: 35–46.

Wrangham RW (2009) Catching Fire: How Cooking Made us Human. New York: Basic Books.

Wrangham RW, Jones JH, Laden G, Pilbeam D and Conklin‐Brittain N (1999) The raw and the stolen – cooking and the ecology of human origins. Current Anthropology 40: 567–594.

Further Reading

Novembre J and Di Rienzo A (2009) Spatial patterns of variation due to natural selection in humans. Nature Reviews Genetics 10: 745–755.

Pickrell JK, Marioni JC, Pai AA et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768–772.

Pritchard JK, Pickrell JK and Coop G (2010) The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Current Biology 20: 208–215.

Stranger BE, Nica AC, Forrest MS et al. (2007) Population genomics of human gene expression. Nature Genetics 39: 1217–1224.

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Luca, Francesca(Apr 2012) Diet, Changes in Gene Expression and Human Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0023644]