The Strange, Scrambled Genomes Of Squids And Octopuses

JOHN DANKOSKY: This is Science Friday. I’m John Dankosky. Today is a very special day for us all at Science Friday. Why? Well, because Cephalopod Week starts today! Yes, if you love the big brains, complex behavior, scintillating colors, and ineffable strangeness of octopus, squids, and their cousins, then you’re already a cephalopod convert.

And you may already be attending one of our cephalopod movie night events next week. But even if you’re on the fence about our tentacled friends you can’t deny that there’s something kind of special about them. In fact, new research into the genomes of several cephalopods is finding even more amazing things about them. For example, they carry genes that we’ve never seen in any other animal. They can actually edit how their genetic code is expressed, and some of the strangest genetic findings are connected to, you guessed it, their big donut-shaped brains!

Here with me to “cephalo-brate” is Dr. Carrie Albertin, a cephalopod researcher and Hibbitt Early Career Fellow at the University of Chicago’s Marine Biological Laboratory in Woods Hole, Massachusetts. Welcome, Carrie.

CARRIE ALBERTIN: Thank you so much, John. It’s a pleasure to be here.

JOHN DANKOSKY: It’s great to have you, and Dr. Yan Wang is an incoming assistant professor at the University of Washington in Seattle. And she studies cephalopod at death. Yan, welcome to the show!

YAN WANG: Thank you so much, John. Great to be here with you and Carrie. I

JOHN DANKOSKY: Just mentioned these big donut-shaped brains and tentacles, but pretend that you, Carrie, were describing cephalopods to someone who’d never seen one or encountered them in all the media that’s out there. I mean, what would you tell them about these animals?

CARRIE ALBERTIN: I mean, the first thing honestly that they make me think of are the Yip Yip Muppets from Sesame Street. They have this ring of flexible, sucker-lined arms that surround a beaked mouth and then their esophagus passes from their beak on up through the middle of their brain that sits right in between these two massive camera-type eyes on up to their muscular mantle that contains three hearts, two gills, and an ink sac. So they just look utterly bizarre.

JOHN DANKOSKY: They look utterly bizarre to us, and I’m sure we’ll get to some of that. I’m sure to them, they’re just perfect, right? But I don’t know, Yan, how about you?

YAN WANG: I would say that they’re very fancy water balloons. I think Carrie highlighted they have these massive eyes, and I think that’s really something that we as humans gravitate to. And behind those eyes there’s that squishy mantle, as Kerry mentioned, with all of their inner organs that to me kind of just looks like a water balloon. And then their arms are– well the arms of an octopus that are just constantly moving, sensing the world. And so yeah, they’re really, really, special.

JOHN DANKOSKY: So we’re going to get into a little bit more about how special they are and why they’re so special. Carrie, as I teased at the front, you’ve been doing cephalopod genomic research for years, and new research is getting a bit closer to understanding just how they do what they do. So I don’t know– what’s the story there?

CARRIE ALBERTIN: Yeah, Yan and I both actually worked on the first cephalopod genome for octopus bimaculoides macrolides, or the California two-spot octopus, which came out a couple of years ago. Since then we’ve been trying to dive in and really understand the genomes of not only octopus, but different kinds of squid, to try and harness and understand some of the really unusual properties that we see in these animals because of course a genome is essentially the toolkit for building an animal and contains all of the instructions, all of the proteins that are important in their development and their biology.

And so when we sequenced the first octopus genome we found out a lot of things about these animals. We found out that they have really large genomes. So our genome contains about 3.2 billion letters. So if you think about all of the letters in, for example, War and Peace and then multiply it by like 2000, that’s how many letters are in our genome. Squid genomes are half again as large, so they’re 4.5 and 5.5 billion letters, and that’s kind of a mind blowing number.

And so when we went in and tried to figure out what all of those letters code for, we saw a couple of really surprising things. The first thing that we saw is that they’re really very rearranged relative to other animals. So we know that there are groups of genes that tend to be near each other and on the same chromosome in very distantly related animals, so for example in a scallop and a cnidarian. We see that in cephalopods that order has been completely mixed up, so it’s like they’ve been put into a blender and then just let the pieces fall where they do.

And this is really exciting because where a gene is in the genome can affect how it’s turned on and turned off, and this happened at a genome-wide scale. So essentially cephalopods have all of this new gene orders to begin to play with and change how genes are turned on and turned off. We also see that they have lots of genes that are important for neuronal function and in particular a family of genes that are thought to act as molecular bar codes that are important for helping neurons wire up correctly. And this is a family of genes that have only been studied in mammals and other vertebrates.

The octopus genome had 168 of these genes, and the squid genomes that we’ve just finished sequencing have nearly 300. But the first thing that we did to try and figure out what these kinds of genes were doing is to look at where these genes were expressed, or turned on, in these different squid and octopus. And we see that, for example, these genes that we think are important in making mammalian brains are also expressed in the brains of both squid and octopus, so this seems to be kind of a molecular smoking gun underlying these very different, very large, very complex nervous systems.

JOHN DANKOSKY: So Yan, as I said at the top, you look at octopus death, which is a fascinating thing to study, and this phenomenon where most octopus moms will actually die in the process of tending their eggs. Now I had no idea they don’t only just starve to death, but they actually kind of self-destruct. I mean, what can you tell us about this behavior, and what are you learning about this death process?

YAN WANG: Yeah, so this is a completely normal process in a mother octopus’s life. So most octopuses are completely solitary, so they come together perhaps only once in their adult lives which is to mate and reproduce. And after this point the female will find a nice safe spot to lay her eggs. As she lays her eggs, that really marks the beginning of the end for her.

So from that point on, her primary behavior is to guard the eggs, protect them, blow water on them to keep them clean, and just watch over them essentially as they develop. Now, in the beginning of this maternal period, the female is still eating, and then as you mentioned she stops eating. And then as the eggs are approaching the time when they would hatch the female undergoes a period that we call decline.

And this is a process that is whole body death, and so she begins to lose color and muscle tone and oftentimes engages in self-cannibalistic behaviors. So for example she will eat the tips of her arms. Often, she’ll create lesions using her suckers on her arms or on her mantle and behaves in really erratic ways until finally she dies. And so it is this whole process that is called– it was originally called the self-destruct system by Jerome Wodinsky in 1977 because he found that when you remove a part of the nervous system called the optic glands, this entire sequence disappears.

So if you remove the optic glands, this entire post-maternal sequence of behaviors stops, and the female is able to eat again. She can meet again, and she can live for four to six months longer. So unlike other death processes that we’re kind of familiar with thinking about it is a very, very active process.

JOHN DANKOSKY: Why would it be evolutionarily smart for octopuses to have this feature this self-destruct mechanism?

YAN WANG: Well, there’s a couple of different theories, and I think the most compelling reason is that the purpose of sexual reproduction is to create genetic diversity and for the next generation of baby octopuses to be able to grow up strong and healthy. And the one thing that you should know about octopuses is that they are very, very cannibalistic. As I mentioned, they are primarily solitary, and I can’t guarantee that a mother wouldn’t necessarily eat her own eggs, but a mother might eat another octopus’s clutch of eggs.

So if the previous generation the mother did not die, it’s very possible that the eggs really wouldn’t stand a chance. And so this entire process, if we looked at it on a larger scale, is a really foolproof way of ensuring that the next generation of young octopuses have a chance at survival.

JOHN DANKOSKY: Do other cephalopods do the same kinds of things? Do they have the same sort of death processes?

YAN WANG: So that’s a really exciting area of research. So other species of soft-bodied cephalopods, so that’s cuttlefish and squid in addition to octopuses, do have an optic gland, but they don’t seem to go through this exact sequence of behaviors as octopuses do.

JOHN DANKOSKY: I know that when I look at an octopus or a squid, one of my biggest questions is always how did this happen? Like as you were describing it, Carrie at the start, how you would describe this creature to someone else, it does seem remarkable that this thing lives, that this is on the Earth with us. So, I don’t know, do we know how they evolved to be the way they are?

CARRIE ALBERTIN: That’s a fantastic question, and really the driving question for me is trying to understand how this forms over both the course of evolution and development. We know that their close relatives are kind of equally bizarre, so snails and clams also put together their bodies in really very strange ways. And to me the genome is the first tool we need to start exploring how they use all of their different genes to put together these incredibly bizarre bodies.

And we’re really at a place where we can start to try and understand this because a couple of years ago in collaboration with Karen Crawford and Josh Rosenthal, we’ve been able to create CRISPR-Cas guided genome manipulations. So we can start to study the role of these different genes in patterning these extraordinary animals.

JOHN DANKOSKY: Are genes, though, the best way to understand why cephalopods are cephalopods? I mean, is there something about just watching their behavior that we can learn about them? I guess I’m wondering what are the various ways you look at these creatures that you study and think about the ways in which we can take something away from them? We can learn something really fundamental about them.

CARRIE ALBERTIN: Mhm. Yeah, well I think that genes, genomes, and genetic tools are really the exciting cutting edge of what’s available in cephalopod research. So I think that cephalopods have long captured human fascinations, not just from a scientific point of view but from just a curiosity or a cultural point of view. We see them accompanying human art and literature all throughout human civilization. I think behavior is one of the most immediate ways that we can connect with cephalopods, our large eyes looking at their large eyes.

That is really wonderful and I think a really strong foundation for behavioral neurobiology and neuroethology. But as modern science has kind of progressed, the technologies that are available in other model animals that help us ask new questions and find new answers to the questions that we ask, they’ve kind of eclipsed the study of cephalopods. And so I do think that genes, genomes, and genetic resources are really what is exciting about cephalopod research right now because in addition to behavior it allows us to study these amazing creatures in a totally new way.

JOHN DANKOSKY: I’m John Dankosky, and this is Science Friday from WNYC Studios. Talking to cephalopod researchers Carrie Albertin and Yan Wang about the mysteries of octopus, squid, and other tentacled creatures. This idea that these are such strange creatures is one of the reasons we’re drawn to them. It’s why we do Cephalopod Week.

But do you think that they’re strange based on what we know about other life forms we can study here on Earth, or now that you understand so much about their genes and about the way they’re built some people have said that they’re like aliens. Are they like aliens, or are they actually really ingeniously put together?

CARRIE ALBERTIN: They are fantastically, wonderfully bizarre animals. They very clearly are related to other mollusks and other animals just like us. So if we look in their genomes, animal genomes typically have on the order of 18,000 to 25,000 different genes. Tens of thousands of these genes are shared between all these different animal groups with genomes that we’ve sequenced, including octopuses.

And so this is sort of a little bit disappointing because you want to discover the new thing that makes cephalopods just the way they are. But it’s also a fantastic opportunity to be able to understand how these shared genes make such a weird animal, right? I’ve been digging into the developmental biology of these very highly conserved ancient genes, and in so many ways we see over and over and over again that cephalopods are animals that are just using the same typical animal genes in their own particular way.

JOHN DANKOSKY: OK, lightning round last question. Yan, what’s your favorite cephalopod?

YAN WANG: [GASPS] That’s an unfair question I feel especially during Cephalopod Week, wow! Dang, I think my– if I had to pick one exact favorite cephalopod it would be the deep sea octopus mom who was found brooding her eggs or taking care of her eggs for 53 months without feeding. She is my number one.

JOHN DANKOSKY: That’s a pretty good one. That’s good. Carrie, how about you?

CARRIE ALBERTIN: Oh, I agree this is just such an impossible question because there are so many fantastic adaptations that we see in these animals. I do have a very soft spot in my heart for metasepia pfefferi, which is the flamboyant cuttlefish. They can just put on these fantastic coloration displays. They are very appropriately named, and they also walk around on the floor with these projections out of the back of their mantle. And they look like little quadrupedal cephalopods. It’s really impossible to not have them be completely endearing, but it’s really hard to choose a favorite.

JOHN DANKOSKY: Yeah, every cephalopod researcher we’ve ever talked to has the same reaction, but thank you for trying for us. I appreciate it. That’s all the time we have. Dr. Carrie Albertin is a Hibbitt Early Career Fellow at the University of Chicago’s Marine Biological Lab in Woods Hole, Massachusetts. Dr. Yan Wang is assistant professor at the University of Washington in Seattle. Thank you both so much for kicking off Cephalopod Week with us this time on Science Friday.

CARRIE ALBERTIN: Thank you so much, John.

YAN WANG: Thank you.

JOHN DANKOSKY: But we’re not done with cephalopods. No, we’re not. Follow us on Twitter, Facebook, and Instagram to fill your week with squid, cuttlefish, and nautilus joy, share your questions for our cephalopod experts, and vote for this year’s smartest, sneakiest, and most sparkly cephalopods. Or you can visit www.sciencefriday.com/squid to subscribe to our Cephalopod of the Day newsletter. You’ll get a squishy new ceph story from the Science Friday team every single day of Cephalopod Week. Again, that’s sciencefriday.com/squid.

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