Eyes abound

Unraveling and disentangling homology and convergence is one of the most fascinating endeavors in biology. Homology indicates common origin and maintenance, and is often taken as evidence for importance: ancient features are thought to be maintained because they are too useful to dispose of during evolution. In contrast, convergence, is the separate invention of similar features or functions during evolution. Convergence is taken as evidence for an element of predictability in evolution. For a simple example, fish and dolphins are highly convergent, and we can use this knowledge to predict that when vertebrates evolve to live in the ocean, that evolution will produce particular features like flippers/fins.

I recently came across a fascinating paper, arguing that structures that interact with light - either by altering or receiving it - are highly convergent, and may even be homologous at some level. Namely, bird feathers that reflect UV light have some striking similarities with eyes! Furthermore, a paper I am a co-author on just came out in PNAS that further supports this general claim. We found that the light producing structure of a bioluminescent squid shares many features with eyes, including the ability to detect ('see') the light it produces!

First, the feathers. Bleiweiss studied the uv/blue feathers of Tanagers and Bluebirds. In nature, short wavelength colors are often produced by structures, as opposed to pigments which produce longer wave colors like orange and red. Structural colors work by differentially interfering/reflecting different wavelengths of light. A familiar example of structural color is a CD/DVD. These disks contain grooves that are spaced very closely together. Because the spacing is similar to the wavelengths of visible light, interference of certain wavelengths occurs, leaving other specific wavelengths that we see as color. These spaced grooves are called diffraction gratings, and they are known in nature, for example on the antennae of some ostracod crustaceans which reflect blue light. Bluebird and tanager feathers do not use diffraction gratings, but instead a different structural mechanism. In the course of studying these feathers, Bleiweiss found some striking similarities with eyes. Perhaps similar to fins/flippers that push water for locomotion, the physical similarities of feathers and eyes may reflect convergence due to shared physical necessities of interactions with light.

An attractive tanager.  Image from britannica.com

What are these similarities between eyes and structurally colored feathers? First is a wide, domed surface to receive the light. Second is tissue that is transparent to some light but reflective of other wavelengths. In eyes, this is the cornea and lens, which are transparent to much light, but often reflect UV (human retinas are actually sensitive to UV, except the light never gets there because the cornea and lens reflect it.). Tanager feathers have physically similar tissues with similar properties to reflect UV/blue light and allow other light to pass through. Third, there is a large central space in both eyes and ocular feathers: eyes contain humors and feathers a space filled with gas (air). Finally, at the bottom is a reflective layer. In eyes, this is the tapetum lucidum, which produces eye shine in cats, coons and other night-active animals. Again, optical feathers share a similar pigmented structure also designed to reflect light.

These similarities seem to be a perfect case of convergent evolution: two structures that perform physically similar functions (light gathering, or light reflecting) have converged on similar solutions. However, Bleiweiss also raises the intriguing possibility that eyes and feathers actually share some (partial) homology. Complex traits like eyes and feathers are made of many components, each with a potentially different evolutionary history. Amazingly, some of the genetic components, developmental features, and signal transduction cascades of eyes and feathers are also shared, in addition to their functional similarities. These similarities might be evidence of a deep shared ancestry between multiple organs, including eyes, feathers, and even teeth.

I was particularly struck by Bleiweiss' paper because I've been thinking about similar things in the context of a collaboration studying the light-producing organ of a squid that yielded a PNAS paper this week. Not unlike tanager feathers and eyes, the convergence of squid light-producing organs and eyes has long been noted. Many squid, including Euprymna scolopes, the object of our study, are bioluminescent. Euprymna seems to use its bioluminescence for camouflage. In the ocean, most light comes from straight above, so animals would cast a distinct and conspicuous shadow below them. Instead of eliciting the shadow response of a predator or prey, Euprynma matches downwelling light to make itself more cryptic. The light is produced in a light organ that houses symbiotic bacteria. It is the bacteria that actually generate the light. Consistent with Bleiweiss' general hypotheis, this light organ has many similarities with eyes.

Light organs and eyes both have lenses. Eyes focus incoming light for better visual acuity, and light organs focus outgoing light, similar to a flashlight. Eyes and light organ have an open space below the lens, and a pigmented layer opposite to the lens. In addition to these similarities, we found that the light organ responds physiologically to light using the same genes (opsin and its signaling components) that are used in eyes. Just as with optical feathers, squid light organs are functionally convergent, yet also share structural components in common, indicating some elements of homology.

Euprymna scolopes Hawaiian Bobtail Squid.  Picture by Chris Frazee, image from pnas.org

These findings indicate an interesting new research program using the tools of phylogenetics. By reconstructing the evolutionary history of multiple components of convergent/partially homologous traits, we can see how and when these components came together, illustrating the pathways by which evolution has produced new features. This will allow a richer, more fundamental understanding of the origins of biodiversity and complexity, topics that intrigue everyone.

References
Bleiweiss, R. (2009). Feathers with Ocular Architecture: Implications for Functional and Evolutionary Similarities of Visual Signals and Receptors Evolutionary Biology, 36 (2), 171-189 DOI: 10.1007/s11692-009-9059-6

Tong, D., Rozas, N., Oakley, T., Mitchell, J., Colley, N., & McFall-Ngai, M. (2009). From the Cover: Evidence for light perception in a bioluminescent organ Proceedings of the National Academy of Sciences, 106 (24), 9836-9841 DOI: 10.1073/pnas.0904571106

Opsins: An amazing evolutionary convergence

How predictable is evolution? If we could travel back in time 4 billion years and make a few changes, what would remain the same upon our return? This is an enduring topic of evolutionary inquiry (and movies and sci-fi shorts for that matter).

In his book Life's Solution, Conway-Morris made the case for a semblance of predictability in evolution. He argued that convergence - the independent origin of similar traits - represents an element of predictability in evolution. Octopus and humans have outwardly similar eye designs, so if we reply animal history over and over, these camera-type eyes would likely evolve in most replays.

Here I'll describe a truly amazing molecular convergence that was not discussed by Conway-Morris: the independent evolution of opsin proteins (a protein responsible for light perception) in two different groups of organisms. It turns out that a 7-transmembrane protein (opsin), bound to a light reactive chemical on the 7th transmembrane domain, has evolved twice to sense light!

If we could go back a few billion years and replay the evolution of life on earth a few times, chances are, opsins would evolve in many of our replicates.

[Disclaimer - the following is text from an encyclopedia article I've been asked to write on opsin evolution, so the writing style is a bit terse from here on out. I will add a little bit though, specially for the blog. But since many people I know think opsin originated only once, I feel it's my duty to spread the word of opsin convergence, starting here, at Evolutionary Novelties].


What is opsin and rhodopsin?
Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis. Opsins are sometimes called retinylidene proteins because they bind to a light-activated, non-protein chromophore called retinal (retinaldehyde). Opsins are also in some cases called “rhodopsins”, a name originally given to isolated visual pigments that contained both opsin protein and non-protein chromophore in a time before the two separate components were known. Today, the term “Rhodopsin” is used commonly to describe the opsin expressed in vertebrate rod (dim-light) photoreceptors, and the opsins of certain organismal groups, like bacteria. All opsin proteins are embedded in cell membranes, crossing the membrane seven times.

Type I and Type II opsins
Two major classes of opsins are defined and differentiated based on primary protein sequence, chromophore chemistry, and signal transduction mechanisms. Several lines of evidence indicate that the two opsin classes evolved separately, illustrating an amazing case of convergent evolution.

Type I opsins are present in bacteria and algae and are referred to by various names, including bacteriorhodopsin, bacterial sensory rhodopsins, channelrhodopsin, halorhodopsin, and proteorhodopsin. Type I opsins have varied function, including bacterial photosynthesis (bacteriorhodopsin), which is mediated by pumping protons into the cell, and phototaxis (channelrhodopsin), which is mediated by depolarizing the cell membrane. Type II opsins are present in eumetazoans (animals not including sponges), but are unknown from sponges or any non-animals. Because opsins are known from cnidarians and bilaterian animals (animals with bilateral symmetry, including humans, flies, and earthworms), Type II opsins are inferred to have been present in their common ancestor, which lived about 600 million years ago. Type II opsins have varied function, including phototransduction and vision, circadian rhythm entrainment, mediating papillary light reflex (pupil constriction), and photoisomerization (recycling the chromophore).


Despite their functional similarity and despite both being 7-transmembrane proteins, multiple lines of evidence indicate that Type I and Type II opsins evolved independently. First, the primary amino acid sequences of Type I and Type II opsins are no more similar than expected by chance. For example, try to align a Type I (say bacteriorhodopsin) and Type II opsin together. I just tried this with blastalign, with the following result:


Exhibit A. Blast search find "no significant similarity" of the amino acid sequences.

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Sequence 1: gi|163443|rhodopsin
Length = 348

Sequence 2: gi|208055|bacteriorhodopsin >gi|208057|gb|AAA72603.1| bacteriorhodopsin
Length = 249

No significant similarity was found

CPU time:     0.04 user secs.     0.02 sys. secs     0.06 total secs.

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Second, the orientation of the transmembrane domains differs between the major groups. We now have crystal structure data for both Type I and Type II opsins, and the arrangements of the parts of the protein that are stuck in the cell membrane are quite different, inconsistent with a single origin of opsins (unless this changed a lot during evolution, which is not impossible).


Exhibit B. Type I on the left, Type 2 on the right. Denser lines are positions of transmembrane domains. Figure is from Spudich et al (2000)

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Third, the major opsin groups differ in chromophore chemistry. Prior to light activation, the chromophore of Type I opsins is an all-trans isomer. Light activation then involves isomerization of the chromophore to 13-cis retinal. In contrast, prior to light activation, the chromophore of type II opsins is 11-cis retinal. Light activation of Type II opsins involves isomerization to all-trans retinal.


Exhibit C. Type I on the left, Type 2 on the right. Chromophore chemistry differs. Figure is from Spudich et al (2000)

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Fourth, Type II opsins belong to the larger protein family called G-protein coupled receptors (GPCRs), which transmit varied signals from outside to inside cells by activating GTPase proteins, which in turn signal to second messengers that affect the state of the cell in various ways. Type I opsins do not activate G-proteins. Furthermore, Type II opsins are more closely related to non-opsin, light insenstive GPCR’s than they are to Type I opsins. So even if there is some very, very distant and *undetectable* common origin of Type I and Type II opsins, chromophore binding likely evolved twice. Since chromophore binding is what allows photosensitivity, it is the crux of being an opsin (but see), and the realization that Type II opsins are closer to non-opsin GPCR's than Type I opsins is strong support for two separate origins.

Exhibit D. (Dashed lines mean no sequence similarity beyond random. Light bulbs mean origin of chromophore binding=light sensitivity=opsin.)

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Finally, with two CS students, I tested the single origin hypothesis in a different way and found no support. Type I opsins show similarity of membrane domains 1-2-3 and 5-6-7, consistent with an origin by duplicating a 3-domain protein (and adding one). However, Type II opsins show no such similarity. If they Type I and Type II share a single origin, the duplication pattern of the domains should be shared too (unless there were drastically different rates of evolution in the 2 lineages, which is not impossible). This work is described here: Larusso et al (2008) J Mol Ev.




John L. Spudich, Chii-Shen Yang, Kwang-Hwan Jung, Elena N. Spudich (2000). RETINYLIDENE PROTEINS: Structures and Functions from Archaea to Humans Annual Review of Cell and Developmental Biology, 16 (1), 365-392 DOI: 10.1146/annurev.cellbio.16.1.365