Opsin evolution: key critters
Imaging eyes developed in deuterostomes quite late relative to protostomes, after divergence of echinoderms, acornworms, amphioxus, and tunicates but before divergence of lamprey. Consequently visual systems in these species that bracket the origin of eyes are vital to understand.
Unfortunately we don't have fossil dna nearly this far back and so are forced to work with a limited to non-existent fossil record of soft body parts or genomes of living species 400-500 million years removed from the ancestral chain of events. Thus anatomical transcript-labelling studies of photoreceptor systems or whole-genome recover of opsin genes in modern amphioxus only speak to the current situation. That may be seriously different from the ancestor both in terms of innovations and losses.
It's worth addressing this perpetual source of confusion by emphasizing again that contemporary tunicates, lancelets, and lamprey are not ancient, ancestral, antiquated, archaic, character-retaining, dead-end, failed experiments, frozen in time, genetically stationary, living fossil, primitive, primordial, relic, or retro species. They're full modern -- the tree of life is right-justified. Indeed their genes, regulatory signalling systems, and enzymes may be more finely honed than human because of more rapid evolution attributable to larger effective population sizes, reproductive mode, generation time, and marine selective predatory pressures.
However we hope that ancestral character traits will still be reflected to some extent in these earlier diverging species and that with enough complete opsin repertoires from taxonomically appropriate species, the ancestral genes and even visual systems can be reconstructed at key nodes on the phylogenetic tree. The story describing the evolution of the human eye then amounts to describing the status at these successive nodes and perhaps interpolating between them. There are definitely limits to knowledge here as metazoans provide only 35 nodes between sponge and human -- gaps between nodes average 30 million years but can seriously exceed that.
The plan below is to summarize several most excellent experimental papers on visual systems in echinoderms, amphioxus, tunicates, lamprey, and chondrichtyhes and supplement that with genomewide recoverable opsin sequences, about half of which are new here and never considered experimentally. That genomic data -- which by itself would have limited interpretability -- can also be processed to determine times of gene origin, gene family relationships, and ancestral sequence which yields, by standard theory, ancestral adsorption specta.
In recent years, our whole framing of vision has undergone immense refinement. Many animal species possess multiple photoreception systems that are not conventional high resolution imaging eyes (eg lack cornea, lens, retina) by human standards. In fact some 83% of animal phyla have flourished over geological time scales without such eyes, in seeming contradiction of popular nonsense (In the Blink of an Eye). The supposed deuterostome advantage in the Cambrian needs to contend with the fact that hemichordates, echinoderms, cephalochordates, and urochordates completely lack imaging eyes even today. Moreover, their genomes totally lack any hint of having developed the requisite ciliary opsin family members.
First it's worth reviewing the recent experimental literature. Note abstracts are readily available at PubMed but access to free full text is unpredictable and so links are collected below. It suffice to note just recent substantial articles because they cite the earlier literature and their citation in turn by more recent is collected by Google Scholar. Most opsin sequences have a source at PubMed as part of their fasta header database and those can simply be compiled to an active link that opens all of them.
under development ...
Vertebrate-type opsin in invertebrate brain
What good are cone opsin gene duplications without brain rewiring:
"The nervous systems of vertebrates are not "hard-wired" at birth (or hatch or the end of metamorphosis...). Decisions about which nerve cells should be connected to which other nerve cells are made during a long space of time prior to adulthood, and in some animals (though usually to a much more limited extent) even during adulthood. Genetics seem to specify (in unknown ways) some of the gross features of connectivity--for example in mammals the axons of ganglion cells in the eye mostly grow through the optic nerve to a particular group of cells in the thalamus. However, the fine distinctions about, for instance, which ganglion cells connect to which cells in the thalamus are made initially by the formation of a lot of random connections. Many of these connections are then pruned back so that each ganglion cell stimulates only a small subset of the cells it initially connected with. The "rules" governing the pruning back are largely based on correlations in the activity of different cells--if two cells in the retina are generally active at the same time, then they will probably end up being connected to the same cells in the thalamus."
"This activity-dependent pruning of connections appears to be the way that "maps" are created in higher brain areas. The best indicator of whether or not two cells in the retina will be simultaneously active, is how close they are to each other in space. Cells in the thalamus thus form a map of cells in the retina according to their activity, and hence their connectivity. Now it's easy to imagine that another determinant of whether or not two cells will be active at the same time is whether or not they are connected to cells which express the same pigment (within the retina, the same rules are followed in the creation of connections, so ganglion cells will preferentially be connected to cells which express the same pigment). So in the thalamus and other brain regions, there will be maps of the different receptor types within the maps of retinal location."
