Vision begins in the neural retina, a three layered film in the back of the eye composed of five major classes of neurons: photoreceptors, horizontal cells, bipolar cells, amacrine cells, and retinal ganglion cells (RGCs). Each major neuronal class can be further divided into multiple different neuronal cell types based off morphological, physiological, and molecular properties. While the basic plan of the retina is conserved across vertebrates, species differ profoundly in their visual needs. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. We collected and analyzed single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. In this thesis, I present insights into the evolution of retinal cell types gained from these studies.First, we systematically classified retinal ganglion cells in adult and larval zebrafish using single-cell transcriptomics, identifying marker genes for >30 mature types and several developmental intermediates. These analyses guided collaborators to develop transgenic driver lines, enabling specific experimental access to a subset of RGC types. They found that expression of one or few transcription factors predicted dendrite morphologies and axonal projections to specific tectal layers and extratectal targets, and in vivo calcium imaging revealed that molecularly defined RGCs exhibit specific functional tuning.
Second, we studied a specialized downstream circuit used for vision in low-light conditions called the primary rod pathway. We demonstrate that the mammalian primary rod pathway is conserved in zebrafish, which diverged from extant mammals ∼400 million years ago. Using single-cell RNA sequencing, we identified two bipolar cell types in zebrafish that are related to mammalian rod bipolar cell (RBC), the only bipolar type that directly carries rod signals from the outer to the inner retina in the primary rod pathway. Guided by this prediction, coauthors combined electrophysiology, histology and ultrastructural reconstruction experiments of zebrafish RBCs to show that one of the two RBC types is homologous to the mammalian RBC. This suggests that the cell types and circuit design of the primary rod pathway emerged before the divergence of teleost fish and mammals.
Third, we compared the visual systems of two closely related murid species that occupy different visual environments: Rhabdomys pumilio are diurnal and have substantially thicker inner retina than nocturnal Mus musculus. Comparative analysis of single cell transcriptomic atlases between the two species revealed an increase in the relative abundance of bipolar and ganglion cell types supporting OFF and ON-OFF responses in Rhabdomys. Collaborators found that this shift towards OFF and transient responses extends into the dorsal lateral geniculate nucleus (dLGN) using high-density electrophysiological recordings. These measurements further revealed that Rhabdomys attains higher spatiotemporal acuity both by denser coverage of the visual scene and a selective expansion of elements of the visual code characterised by non-linear spatiotemporal summation, illustrating how sensory systems can adapt to different ecologies by adjusting the proportion of cell types comprising a neural circuit.
Finally, we performed an integrative analysis of all 17 species. Collaborators were able to collect the sequencing datasets and found that the structure of the retina as well as all major retinal classes are conserved across all species using histology. We identify conserved molecular signatures of these cell classes, and find that transcriptomic variation across species is related to evolutionary distance. We built retinal atlases for each of these species and find that the degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output.
To identify conserved cell types, we performed an integrative analysis to identify groups of related cell types that we name orthotypes, which we believe represent a cell type blueprint that derived from an early ancestral vertebrate. We identify 14 bipolar orthotypes, including an orthotype corresponding to the rod bipolar cell and a non-canonical OFF bipolar cell described in mice that has yet to be identified in other species, revealing that numerous cell types are shared across species based on conserved gene expression programs. RGC types across species were clustered into 21 orthotypes, including an orthotype containing orthologs of an evolutionarily ancient set of RGC types called intrinsically photosensitive RGCs. Importantly, we identified rodent orthologs of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates. We further argue this correspondence using molecular, functional, and morphological evidence and propose a correlation between the expansion of this cell type in primates and an increased role of the cortex in visual processing.