Ecological trait differences are associated with gene expression in the primary visual cortex of primates

Background : Primate species differ drastically from most other mammals in how they visually perceive their environments, which is important for foraging, predator avoidance, and detection of social cues. Although it is well established that primates display diversity in color vision and various ecological specializations, it is not understood how visual system characteristics and ecological adaptations may be associated with gene expression levels within the primary visual cortex (V1). Results : We performed RNA-Seq on V1 tissue samples from 28 individuals, representing 13 species of anthropoid primates, including hominoids, cercopithecoids, and platyrrhines. We explored trait-dependent differential expression (DE) by contrasting species with different visual system phenotypes and ecological traits. Between 4-25% of genes were determined to be differentially expressed in primates that varied in type of color vision (trichromatic or polymorphic di/trichromatic), habitat use (arboreal or terrestrial), group size (large or small), and primary diet (frugivorous, folivorous, or omnivorous). DE analyses revealed that humans and chimpanzees showed the most marked differences between any two species, despite the fact that they are only separated by 6-8 million years of independent evolution. Pathway enrichment analyses of DE genes demonstrated that changes in cellular metabolic pathways (e.g. glycolysis) contribute to altered gene expression in primate V1 more than neuron-specific processes (e.g. synaptic signaling). The exception to this trend is between human and chimpanzee, which exhibited DE for a number of processes related to cholinergic and GABAergic synaptic signaling. Conclusions : Our data significantly expand the number of primate species for which V1 expression data exists. These results show a combination of species-specific and trait-dependent differences in the evolution of gene expression in primate V1. We also show that human-specific changes in brain gene expression extend to the primary visual cortex in a manner similar to that reported of other brain regions.