In order to empirically test whether these patterns of genome-wide metabolism and energy metabolism are biologically relevant, the next steps will be to take different experimental approaches for a better understanding of the intersection of genotype, phenotype and diet in primates.
What does the anthropological evidence suggest to test questions surrounding the genetic impact of dietary shifts? One possibility would be to look for genetic and genomic signatures of adaptations related to digestion of meats, fats, and marrows, possibly even scavenged meats with attached immune challenges (rotting or parasite infested, for instance). This will be critical for distinguishing how during human evolution adaptations in gut, brain, muscle and fat and reproductive adaptations arose even though all are related to diet. A parallel investigation could be undertaken to see whether there is genetic evidence for more ancient adaptations to the adoption of cooking habits [104
]. For instance, Blekhman et al
] hypothesized that signatures of selection in gene expression in the liver reflected the beginning of cooking meat during human evolution. Since it is challenging to detect specific dietary influences on musculoskeletal anatomy during human evolution, we contend that combining morphological approaches with genomic approaches is a next step in addressing these questions by looking at the evidence for natural selection at the molecular and tissue levels.
Experimentally, this could include exploring changes in pathways between species using other molecular approaches, such as in vitro cell culture assays. For example, one could treat a relevant cell type with varying levels of metabolites or oxygen, and then measure subsequent changes in gene expression or other metabolite concentrations between species. This would allow for a dissection of the genome-wide influence of a single factor between species, possibly helping to elucidate networks of genes that have changed.
Alternatively, detailed investigations of changes over large networks or pathways of genes would be informative. Like many complex traits, if changes in diet have been important in human evolution, we might expect many small changes at multiple loci. Likewise, genomic sequence and expression from other populations will increase our power to understand these adaptations. The recently published Neanderthal genome [105
] will also be valuable in understanding the timing of certain specific mutations.
By comparing gene expression across tissues as well as between species, we may start to understand the genetic underpinnings of phenotypic changes related to dietary changes. For instance, paralogues within a gene family could be differentially ‘tuned’ to function in specific tissues. Phylogenetic histories of gene duplication, and gene family expansion, would help to illuminate this type of pattern, as seen in the olfactory receptors in humans [106
]. Alternatively, if there are tissue changes (e.g. a reduced gut or enlarged brain) between species, analyses looking for shifting patterns of gene expression, protein function or methylation state in these tissues would be valuable. A similar effect might be expected at the level of natural selection on DNA sequence, showing an enrichment of selection on tissue-specific genes in tissues that have changed dramatically in size or energy consumption between species, whereas ubiquitously expressed genes may not show those enrichments.
The pattern we describe would also predict that other studies should see similar shifts in phenotypes (and the underlying genotypic shifts) in other organisms where diet has changed dramatically within a clade. With genome sequencing technologies rapidly advancing as costs decrease, it is now possible to create resources for new ‘model’ organisms to address specific questions. For example, measurements of brain and gut volume in addition to gene expression studies in Onychomys
, a small (approx. 30 g), highly carnivorous cricetid rodent [107
], would be an interesting natural experiment in the morphological and genetic patterns that occur when a carnivore evolves from a seed-eating ancestor. Another system to investigate is the elephant-nose fish Gnathonemus petersii. Gnathonemus petersii
has an extremely large brain (particularly the cerebellum) that is exceptionally expensive for an ectotherm, with 60 per cent of total oxygen consumption being used by the brain compared with 2–8% in most vertebrates and 20 per cent in humans [108
]. The enlarged cerebellum of G. petersii
may be due to an energetic trade-off with the digestive tract [109
], and the size of the brain varies widely within closely related species [110
]. Experimental taxa such as these would be a powerful source of detailed information on the interplay between the genetic, physiological and morphological changes involved in energetic re-allocations.
A difficult gap between genotype and phenotype remains, and so next steps need to look at physiological, developmental and morphological differences—challenging in human and non-human primate species and populations. A combination of the experimental data reviewed here may assist in gaining a comprehensive understanding of how dietary changes have moulded the modern human phenotype.