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How many genes does it take to make a squid eye?

This is an article about cephalopods and eye evolution, but I have to confess at the beginning that the paper it describes isn’t all that interesting. I don’t want you to have excessive expectations! I wanted to say a few words about it, though, because it addresses a basic question I get all the time, and while I was at it, I thought I’d mention a few results that set the stage for future studies.

I’m often asked to resolve some confusion: the scientific literature claims that eyes evolved multiple times, but I keep saying that eyes show evidence of common origin. Who is right? Why are you lying to me, Myers? And the answer is that we’re both right.

Eyes evolved independently multiple times: the cephalopod eye evolved about 480 million years ago, and the vertebrate eye is even older (490 to 600 million years), but both evolved long after the last common ancestor of molluscs and chordates, which lived about 750 million years ago. The LCA probably did not have an image-forming eye at all.

And that’s the key point: a true eye is a structure that has an image forming element, a retina, and some kind of morphological organization that allows a distant object to form a pattern of light on that retina. That organization can be something as simple as a cup-shaped depression or pinhole lens, or as elaborate as our camera eye, or an insect’s compound eye, or the mirror eyes of a scallop. An eye is photoreceptors + structure. Eyes have evolved multiple times; they’ve even evolved multiple times within the phylum Mollusca, and different lineages have adopted different strategies for forming images.


(Click for larger image)

Phylogenetic view of molluscan eye diversification. Camera eyes were independently acquired in the coleoid cephalopod (squids and octopuses) and vertebrate lineages.

The LCA probably didn’t have an eye, but it did have photoreceptors, and the light sensitive cells were localized to patches on the side of the head. It even had two different classes of photoreceptors, ciliary and rhabdomeric. That’s how I can say that eyes demonstrate a pattern of common descent: animals share the same building block for an eye, these photoreceptor cells, but different lineages have assembled those building blocks into different kinds of eyes.

Photoreceptors are fundamental and relatively easy to understand; we’ve worked out the full pathways in photoreceptors that take an incoming photon of light and convert it into a change in the cell’s membrane properties, producing an electrical signal. Making an eye, though, is a whole different matter, involving many kinds of cells organized in very specific ways. The big question is how you evolve an eye from a photoreceptor patch, and that’s going to involve a whole lot of genes. How many?

This is where I turn to the paper by Yoshida and Ogura, which I’ve accused of being a bit boring. It’s an exercise in accounting, trying to identify the number and isolate genes that are associated with building a camera eye in cephalopods. The approach is to take advantage of molluscan phylogeny.

As shown in the diagram above, molluscs are diverse: it’s just the coleoid cephalopods, squid and octopus, that have evolved a camera eye, while other molluscs have mirror, pinhole, or compound eyes. So one immediate way to narrow the range of relevant genes is a homology search: what genes are found in molluscs with camera eyes that are not present in molluscs without such eyes. That narrows the field, stripping out housekeeping genes and generic genes involved in basic cellular processes, even photoreception. Unfortunately, it doesn’t narrow the field very much: they identified 5,707 candidate genes that might be evolved in camera eye evolution.

To filter it further, the authors then looked at just those genes among the 5,707 that were expressed in embryos. Eye formation is a developmental process, after all, so the interesting genes will be expressed in embryos, not adults (a sentiment with which I always concur). Unfortunately, development is a damnably complicated and interesting process, so this doesn’t narrow the field much, either: we’re down to 3,075 candidate genes.

Their final filter does have a dramatic effect, though. They looked at the ratio of non-synonymous to synonymous nucleotide changes in the candidate genes, a common technique for identifying genes that have been the target of selection, and found a grand total of 156 genes that showed a strong signal for selection. That’s 156 total genes that are different between coleoids and other molluscs, are expressed in the embryonic eye, and that show signs of adaptive evolution. That’s manageable and interesting.

They also looked for homologs between cephalopod camera eyes and vertebrate camera eyes, and found 1,571 of them; this analysis would have been more useful if it were also cross-checked against other non-camera-eye molluscs. As it is, that number just tells us some genes are shared, but they could have been genes involved in photoreceptor signalling (among others), which we already expect to be similar. I’d like to know if certain genes have been convergently adopted in both lineages to build a camera eye, and it’s not possible to tell from this preliminary examination.

And that’s where the paper more or less stops (I told you not to get your hopes up too high!) We have a small number of genes identified in cephalopods that are probably important in the evolution of their vision, but we have no idea what they do, precisely, yet. The authors have done some preliminary investigations of a few of the genes, and one important (and with hindsight, rather obvious) observation is that some of the genes are expressed not just in the retina, but in the brain and optic lobes. Building an eye involved not just constructing an image-forming sensor, but expanding central tissues involved in processing visual information.


Fernald RD (2006) Casting a genetic light on the evolution of eyes. Science 313(5795):1914-8.

Yoshida MA, Ogura A (2011) Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies.. BMC Evol Biol 11:180.

(Also on Sb)

Comments

  1. says

    And when will this achieve the sophistication of ID research into the design of the eye?

    What’s always funny is how even their objections have to use evolutionary biology to get some sciency-sounding bleat out there. Oh, they’ll be demanding that we explain every step of the evolutionary process, meanwhile only the evolutionary processes yield insight into the production of the eye.

    Limits, morons, it’s limits that tell us something. Every time you point out the difficulties in explanation caused by those limits speaks to the actual value of the limited mechanisms of evolution. You acknowledge the power of evolution every time you stupidly whine that we don’t know everything–you know nothing without evolution and physics.

    Glen Davidson

  2. says

    I’m curious, do these squids all have Pax-6 as a toolkit gene for eye development ? And what are all these other hundrets of genes meant to be doing ?

  3. Nerd of Redhead, Dances OM Trolls says

    The authors have done some preliminary investigations of a few of the genes, and one important (and with hindsight, rather obvious) observation is that some of the genes are expressed not just in the retina, but in the brain and optic lobes. Building an eye involved not just constructing an image-forming sensor, but expanding central tissues involved in processing visual information.

    Having working receptors does nothing if the animal can’t make use of the information. Not surprising that more genes than just the eyes per se where found, especially for areas that transmit the information, and then interpret it.

  4. says

    … the scientific literature claims that eyes evolved multiple times, ~.

    Huh? Isn’t an organism continuously evolving? I get that changes will show up at a specific point as those mutations are realized, but is that what they’re counting as “an evolution”?

    Does it make sense to describe my trip to the supermarket as:
    1. I took a trip from my home to Main street.
    2. I took a trip from Main street to First street.
    3. I took a trop from First street to the supermarket parking lot.
    4. I walked from my car to the supermarket

    So, I took several trips, four in fact!

    WTF.

  5. Realee says

    I get that changes will show up at a specific point as those mutations are realized, but is that what they’re counting as “an evolution”?

    They’re referring to the eye structure evolving independently more than once. For example birds and bats evolved wings separately, they do not have a common ancestor with wings (perhaps similar limbs but not wings). This is what is meant by more than one separate evolutions of the eye structure. Like you and someone else you lived with took two different routes to the market. Two trips were accomplished.

    Do a search for convergent evolution and you’ll easily see it put in better words than I have.

  6. Katharine says

    Attempting to wring bits of the cephalopod nuclear genome out of papers is a maddening exercise, considering that the only genes listed on GenBank are the mitochondrial ones.

  7. Katharine says

    That’s it, I’m going to make sequencing Loligo pealei, Octopus vulgaris, or Sepia officinalis’s nuclear genome something that I’m going to have to do during my career. IT WILL NOT BE UNDONE.

  8. crissakentavr says

    Of course, it probably takes all of the chromosomes to make an eye, and yet only one gene removed may leave the eye untouched, or bodge it completely out. Or any place inbetween.

    Nature is such a messy programmer.

  9. crissakentavr says

    I’m more interested to know how the cephalopod camera eye diverges from a vertebrate camera eyes… Does it have the retina-blank spot? Does it use cone-cells? What are the effective absorption rates of its sensory cells? Does it see compound colors or distinct layers? I’m not even sure how to test the latter…

  10. aggressivePerfector says

    PZ, thanks for the explanation. Nice to think that my question a few days ago was the right kind of constructive ignorance to contribute to inspiring a nice post like this … or maybe you just slapped your head and thought “uh, not this question again!”

    One thing has tickled my ignorance again, though. They wanted to find the genes responsible for building a certain kind of eye, so they excluded all genes that are also expressed in eyes of related organisms but without that kind of eye. How did they know that some of the genes used to make camera eyes (differently from other eyes) are not also present in these other mollusks, just with different associated information processing technology (the cis part of the genome) governing where and when they are used?

    Apologies if my question is profoundly stupid – this is not my area, but I find it fascinating nonetheless.

  11. Amphiox, OM says

    Does it have the retina-blank spot?

    The vertebrate blind spot is a consequence of having the nerves in front of the photoreceptors. There’s a place where all those axons have to converge and dive through the retina to form the optic nerve and get to the brain, and that spot can’t, for simple space reasons, have any photoreceptors in it, and hence the blind spot.

    Since cephalopods are wired the other way, they presumably shouldn’t have a blind spot.

    Does it use cone-cells?

    I believe that cone-cells are a vertebrate adaption for color vision. So cephalopods, in the strictest sense, shouldn’t have any. Whether they have cone cell equivalents would depend on whether or not they have color vision. IIRC, all known current examples that have been studied apparently do not (which makes their ability to control their skin coloration even more mind-boggling), but I could be wrong.

  12. crissakentavr says

    Well, they have some sort of cell that absorbs light; I wonder if they use a similar structure and number of types of cells. I know /why/ we have the blind spot, I’m just curious if the same or similar error is there as well. I wouldn’t assume one way or another…

  13. Hercules Grytpype-Thynne says

    @Usernames:

    Eyes evolved independently multiple times

    Meaning that eyes were innovations in separate lineages, instead of, say, having arisen only once in the ancestors of all creatures that now have eyes.

  14. Amphiox, OM says

    I know /why/ we have the blind spot, I’m just curious if the same or similar error is there as well.

    Because the photoreceptors in vertebrate eyes are ciliary and derive embryologically from brain (more or less), they end up underneath the neurons whose axons form the optic nerve. This means that the convergence point where all those axons come together occurs in front of the photoreceptor cell layer, and then pierce through that layer to get to the brain behind it, producing the blind spot.

    Because the photoreceptors in the cephalopod eye are rhabdomeric and derive embryologically from skin (more or less), they end up on top of the neurons whose axons end up forming the optic nerve. This means that the convergence point where those axons come together occurs behind the photoreceptor cell layer, meaning there is no need to pierce the photoreceptor layer to get to the brain behind it. The photoreceptor layer can remain a continuous sheet on top of the neural wiring, and thus there is no blind spot.

    So no, the same or similar “error” does not occur.

  15. A. R says

    I wonder how closely the developmental process of the cephlapod eye mirrors that of the human eye.

  16. says

    The fact that genes for eye development do have an effect on how the brain develops is actually a very good insight. I’ve never thought of that, although it makes perfect sense. This actually is a pretty cool fact to point out to someone (some Christian, of course) who says that specific brain connections and behavior are not influenced by genetics. When seen this way, that the brain develops along with the organs that send it information, that the brain structures necessary to use that information appear during embryologic development, it is pretty obvious that this is a ridiculous claim.

  17. Ichthyic says

    I’m more interested to know how the cephalopod camera eye diverges from a vertebrate camera eyes… Does it have the retina-blank spot? Does it use cone-cells? What are the effective absorption rates of its sensory cells? Does it see compound colors or distinct layers? I’m not even sure how to test the latter…

    assuming Amphiox answered most of this for you for squid eyes…

    you really should check out Stomatopod eyes:

    http://www.mbari.org/seminars/2001/spring2001/apr18_caldwell.html

    Roy was on my PhD committee so I got endlessly exposed to mantis shrimp as a grad student.

    here’s a nice pdf detailing their structure:

    http://scubageek.com/articles/mantis_eye.pdf

  18. Ichthyic says

    I believe that cone-cells are a vertebrate adaption for color vision. So cephalopods, in the strictest sense, shouldn’t have any. Whether they have cone cell equivalents would depend on whether or not they have color vision. IIRC, all known current examples that have been studied apparently do not (which makes their ability to control their skin coloration even more mind-boggling), but I could be wrong.

    some additions to that:

    while cephs don’t have cone cells, it’s not why they don’t see in color, it’s rather because they only have one visual pigment. That said, there actually IS one ceph studied that indeed does have 3 visual pigments, the firefly squid (Watasenia scintillans).

    Interestingly, that squid is also bio-luminescent.

    What’s more, it appears that most, or all, cephs have the ability to detect light polarization, and even change their color patterns to reflect polarized light.

    which, btw, the Stomatopods I just mentioned also can process polarized light. What’s more, they see in color. In fact, their color discrimination is FAR beyond what we can accomplish.

    FWIW, here’s a diagram of a ceph retina vs a human one:

    http://www.bio.davidson.edu/people/midorcas/animalphysiology/websites/2003/Muller/thecephalopodeye2.htm

  19. says

    Science types, can anyone clarify this for me please ? So in the 35 or however many instances of independent eye development that we know of, are we talking 35 different master genes, or are they all based on PAX-6 ?

  20. says

    From Fernald:

    Of around 33 animal phyla, about one-third have no specialized organ for detecting light, one-third have light sensitive organs, and the rest are animals with what we would consider eyes. Image-forming eyes appeared in 6 of the 33 extant metazoan phyla (Cnidaria, Mollusca, Annelida, Onychophora, Arthropoda, and Chordata), and these six contribute about 96% of the known species alive today.

    All the ones I know of use Pax-6 as the master control gene for eye formation. It’s considered likely that the bilaterian LCA used Pax-6 to specify the location of a photoreceptor patch.

  21. says

    “That’s how I can say that eyes demonstrate a pattern of common descent: animals share the same building block for an eye…”

    WOW! AMAZING DISCOVERY! I can’t believe I didn’t see it before.

    “Making an eye, though, is a whole different matter, involving many kinds of cells organized in very specific ways.”

    Hmmm, if only we had a director for our play, then we could make some beautiful meaningless dancing to look at.

    “And that’s where the paper more or less stops (I told you not to get your hopes up too high!) We have a small number of genes identified in cephalopods that are probably important in the evolution of their vision, but we have no idea what they do, precisely, yet.”

    Really? Still no collection of ‘builder genes that invented the eye’? 156 is small? relatively I guess. But again, assuming these little bastards (no pun intended) DID dance their dance in random synchronicity to the synchronous-ness of the dancing nervous system bastards in timing such as to bring about the amazing revelation of sight, would would have been the driver for the squid to know that there was light that needed to be seen?

  22. Nerd of Redhead, Dances OM Trolls says

    Yawn, some me has a wacky-backy/hallucinogen overload, making no sense.

  23. says

    Sorry if I was unclear, we all know the driver for the troll police to apprehend and cut down any intruders to their exact shoe size, tread pattern and recent whereabouts. Or do we?

    What was the purpose for the squid to want to see when it’s ancestors couldn’t?

    Sometimes science doesn’t make sense and must be questioned, but if I just agree and concede could it make some dollars? (Sorry, that was my attempt at shallowness, fail).

  24. KG says

    What was the purpose for the squid to want to see when it’s ancestors couldn’t? – Just Me

    You’re an ignorant idiot. There are many organisms, including single-celled ones, without anything like a fully developed eye, but nonetheless able to detect light, so the squid’s ancestors would have evolved their eyes step by step from simple light-sensitive spots. You also demonstrate your ignorant idiocy by making it clear you think evolution is a matter of organisms wanting some feature they do not have. It isn’t, you blithering moron. If you were really interested in the larger picture of what we do and don’t know about the evolution of vision (you’re not, of course), I would recommend the relevant chapter in Nick Lane’s Life Ascending: The Ten Great Inventions of Evolution.

  25. Nerd of Redhead, Dances OM Trolls says

    What was the purpose for the squid to want to see when it’s ancestors couldn’t?

    Since evolution isn’t driven by want, but rather random mutation and natural selection, your idiocy is apparent. You should avoid scientific posts.

    Even just being able to barely sense if a prey and/or preditor is between you and the sun can be an evolutionary advantage. Even more of an advantage if you can see well enough to determine which is which.

  26. says

    Evolution as an inventor, must have a purpose, no?

    So in the story of evolution who is predator and who is prey?

    As advantages on evolutionary scorecard how many developmental +1’s ya got in your trophy room?

    Or are you just thinking with limits?

  27. says

    Evolution as an inventor, must have a purpose, no?

    No, dumbshit, you don’t know the first thing about evolution.

    So in the story of evolution who is predator and who is prey?

    Predators are predators, and prey are prey, although predators in one case can be prey in another. How stupid are you, troll?

    Or are you just thinking with limits?

    Unlike shithead creaitonists, we do think with limits. You don’t think at all.

    Glen Davidson

  28. Nerd of Redhead, Dances OM Trolls says

    Evolution as an inventor,

    Nothing “invented” on purpose. What part of RM/NS don’t you understand?

    So in the story of evolution who is predator and who is prey?

    Varies by animal, ecosystem, and vegetation. No true defined roles. I’ve heard of rabbits eating a duck. Another stupid question from an idjit.

    Or are you just thinking with limits?

    The only one with limited thinking is you. You can’t see beyond your delusions of an imaginary deity. If you could think, you would understand the idiocy of the deity/creator/designer bullshit for ignoramouses.

    As advantages on evolutionary scorecard how many developmental +1′s ya got in your trophy room?

    We know you have about 175 mutations compared to your parents. Most are neutral, some are postitive, and some are negative. But that isn’t known until you pass your stupid genes to the next generation of stupid.

  29. Kevin says

    So, for the creationist’s benefit, the simplest question is always the best.

    Why?

    Why would an all-powerful god that could build one type of eye or a billion use such a cludgy, unintuitive, complex process to build different types of eyes?

    A truly omnipotent god could build an eye with one gene — or none. One gene for each type of eye. Or none. If the eye were irreducibly complex, why would it need building blocks at all? Why not just an eye?

    For that matter, why would a god bother with all the different types of eyes, all based on the same underlying basic genetic backbone? Why shouldn’t all creatures have the best possible eye? Why would a god want to give some creatures a superior eye?

    And why should humans have a deficient eye? Why should our eyes be best of all possible eyes? Aren’t we god’s special creatures? And yet it’s scientifically true that our eyes are not as acute as an eagle’s, or an owl’s, or a cat’s, or an octopus’.

    A god that uses materials at hand (ie, DNA) to build different types of eyes is certainly not omnipotent. And a god that requires thousands of variants of the same basic plan, one idea built quietly on top of another, is no god at all.

    It’s nature. Evolution.

  30. says

    Ah, palatable food for digestion.

    All these questions are easily put in perspective when you factor in the whole equation (Supernatural good and evil).

    At an astounding 8-10% grey matter use, do you really think we are even able to ponder the right question to decode the universe?

    With all that nonsense DNA information we disregard as nothing, what could we have been capable of if not perverted, as the story goes.

    For the benefit of the non-assumptive scientific mind, consider me not a creationist, but a mutant. I’ve seen and heard it all, but need to consider things from the ‘cage’ up. (caged by the limits of societal labels).

    Thanks in advance for your humoring of an ignorant idiot, I’ll be here through the weekend ‘trolling’ as some would have it. Then I’ll leave you to your vacuum.

  31. says

    Just Me #32

    All these questions are easily put in perspective when you factor in the whole equation (Supernatural good and evil).

    Since there is no evidence for good, evil or the supernatural, none of them are part of the equation at all.

    At an astounding 8-10% grey matter use, do you really think we are even able to ponder the right question to decode the universe?

    I’m sorry to see you are leaving the vast majority of your brain unused. Unsurprised, but sorry.

    With all that nonsense DNA information we disregard as nothing, what could we have been capable of if not perverted, as the story goes.

    Could you please restate this in some language that is not gibberish? Thanks.

  32. says

    On top of all of his creationist idiocy, did Just Me really just repeat the myth that we only use 10% of our brain?

    Man. The stupid, it burns.

  33. Ichthyic says

    cool, I get to say this as both an expression AND a direct reference:

    Is it Just Me, or does this:

    dance their dance in random synchronicity to the synchronous-ness of the dancing nervous system bastards

    make zero sense?

  34. Ichthyic says

    Evolution as an inventor, must have a purpose, no?

    nope.

    So in the story of evolution who is predator and who is prey?

    sense making this isn’t.

    No, I really tried. Really.

    “Just Me” must be on drugs. It produces no coherent thought.

  35. Ichthyic says

    we all know the driver for the troll police to apprehend and cut down any intruders to their exact shoe size

    this is a post-bot, right?

    I mean, this isn’t even a case of English not being first, second, or third language.

    this is at the level of GOATS ON FIRE.

  36. Nerd of Redhead, Dances OM Trolls says

    “Just Me” must be on drugs. It produces no coherent thought.

    I believe it thinks (har) that it is funny (har). Pitiful is more like it.

  37. Ing says

    With all that nonsense DNA information we disregard as nothing, what could we have been capable of if not perverted, as the story goes.

    Could you please restate this in some language that is not gibberish? Thanks

    He’s claiming that the fall corrupted formerly coding DNA into noncoding DNA and Retroviral DNA.

  38. Ing says

    At an astounding 8-10% grey matter use, do you really think we are even able to ponder the right question to decode the universe?

    I fully believe that you only use 8% of your mind.

    Incidentally do you know what we say when we see someone using 100% of their brain? “Call 911! They’re having a seizure!!!!”

  39. says

    No 10% rule, dang it. Who pushed that propaganda? Does that mean the top minds really do not have any further potential?

    I am sure you understand what a bastard is. Also was assuming you know the DNA/RNA ‘dance of the building blocks’.

  40. says

    Ing

    He’s claiming that the fall corrupted formerly coding DNA into noncoding DNA and Retroviral DNA.

    Ooh, do you offer a gibberish to English translation service? What are your rates?

  41. Ing says

    No 10% rule, dang it. Who pushed that propaganda? Does that mean the top minds really do not have any further potential?

    No it does not mean that

    *DING* post 2/3

  42. Ing says

    Ooh, do you offer a gibberish to English translation service? What are your rates?</blockquote

    —————————————————————

    Sorry if I was unclear, we all know the driver for the troll police to apprehend and cut down any intruders to their exact shoe size, tread pattern and recent whereabouts. Or do we?

    Sorry if I was unclear…we all know that you’re an echo chamber and cut down disenters to size. You’re all conformist nazi cheer leaders

    What was the purpose for the squid to want to see when it’s ancestors couldn’t?

    I am a moron who thinks evolution is Lamarkian. Why would a squid need to see when it’s ancestors couldn’t?

    Sometimes science doesn’t make sense and must be questioned, but if I just agree and concede could it make some dollars? (Sorry, that was my attempt at shallowness, fail).

    Evolution is a scam

    Ah, palatable food for digestion.

    I present food for thought

    All these questions are easily put in perspective when you factor in the whole equation (Supernatural good and evil).

    All the questions are easily seen when you look at the big picture, presuming a supernatural good and a supernatural evil

    At an astounding 8-10% grey matter use, do you really think we are even able to ponder the right question to decode the universe?

    We’re too dumb to know what questions to ask. Possibly a Hitchhikers reference

    With all that nonsense DNA information we disregard as nothing, what could we have been capable of if not perverted, as the story goes.

    See above

    For the benefit of the non-assumptive scientific mind, consider me not a creationist, but a mutant. I’ve seen and heard it all, but need to consider things from the ‘cage’ up. (caged by the limits of societal labels).

    You all practice scientism. I am not a creationism, I am above the debate. I do not accept your primitive dogmatic ‘science’. All hail John Fort.

    Thanks in advance for your humoring of an ignorant idiot, I’ll be here through the weekend ‘trolling’ as some would have it. Then I’ll leave you to your vacuum.

    Thanks to everyone who answered me. You are all an echo chamber hive mind, fuck you all. Your mothers suck the turds out of bulls.

    No 10% rule, dang it. Who pushed that propaganda? Does that mean the top minds really do not have any further potential?

    I was misinformed, damnations and curses! I put blame on people who repeated that debunked meme. Does this mean the smartest have already reached their full potential?

    I am sure you understand what a bastard is. Also was assuming you know the DNA/RNA ‘dance of the building blocks’.

    ??????????????????

  43. Ichthyic says

    He’s claiming that the fall corrupted formerly coding DNA into noncoding DNA and Retroviral DNA.

    ORLY?

    your skills are impressive, but are you a Jedi yet?

  44. Ichthyic says

    I just want to know one thing, Ing, now that you are working gibberish translation:

    Who drives the squid, man?