Short Wave - The Ambitious Quest To Genetically Map All Known Vertebrates

Episode Date: December 4, 2024

The Vertebrate Genomes Project: It's an ambitious effort by an international group of scientists to create a "Genome Ark" by sequencing the genomes of about 70,000 animal species. The hope is that through all of this gene sequencing, scientists will be able to answer some basic but important questions like: What makes a bird, well, a bird? What makes a mammal a mammal? Plus, with so many species on the verge of extinction, can scientists record their genetic information before they go extinct – or better yet, maybe help save the population from going extinct? Guest host Jon Hamilton, one of our favorite science correspondents, talks to Erich Jarvis, the chair of this project, to learn what this ark of animal genomes could mean for our future – and why a platypus qualified for early boarding. Want to hear more animal stories? Let us know at [e-mail] — we read every email.Listen to every episode of Short Wave sponsor-free and support our work at NPR by signing up for Short Wave+ at plus.npr.org/shortwave.See pcm.adswizz.com for information about our collection and use of personal data for sponsorship and to manage your podcast sponsorship preferences.NPR Privacy Policy

You're listening to Shortwave from NPR. Hey, hey, shortwavers. John Hamilton here, filling in for Regina Barber, who is caravanning somewhere in the Southern Hemisphere. So here's a question. What makes a human distinctly human? Back in 2003, there was this idea that scientists might be about to answer that question because they had, more or less, completed a map of the human genome. That meant they could read all the genetic instructions you need to build and maintain a member of our genome. species. But that was really just the beginning, because a genome is the genetic blueprint for just one species. To understand how humans are different from other animals and how animals are different from one another, scientists will need lots of genomes. Fortunately, they're working on it.

So we're trying to take one or two individuals per species and sequence the genetic code, the entire code of that animal that represents that species, and do that for everybody. And we're putting it into a database that we're calling genome arc, with the pun intended, like, you know, an arc, to basically save the genetic code of all species on the planet. That's Eric Jarvis, a dancer and neuroscientist from Rockefeller University who says these days he is heavily into genomics. He's also an expert on the brain circuits that allow species,

including people and some birds, to learn new vocalizations. Eric shares the vertebrate genomes, project. It's an international group of scientists who plan to sequence the genomes of about 70,000 species. The first phase is focusing on about 260, including bats, a hummingbird, and even a tortoise. Eric says having those genomes will help answer some basic questions about evolution and biology. What makes a bird a bird? What makes a mammal a mammal? What makes a fish a fish? With all these species sequence, we will be able to dig in and find those things that make each lineage different from another.

And Eric says there's another reason. There's so many species that are on the verge of extinction that there isn't time to do much. We can capture their genetic data before they go extinct or even capture them to help save the population from going extinct. And so this is a moral reason for me to work on such a project and to be a chair of it. Today on the show, the effort to collect an arc full of animal genomes

and what it could mean for our future, plus why a platypus qualified for early boarding. You're listening to Shortwave, the science podcast from NPR. So, Eric, stepping back here for a second, let's talk about your own quest. I know that dance led you to brain science because you wanted to understand how the brain controls the body, then brain science led you to study the circuits that allow some birds

to learn really complex vocalizations. So how did you get to genetics and genomics? So I was always interested in genetics in general and the genetics of complex behaviors. And when I started requiring genetic data from multiple species, I was depending on other scientists who are genome experts to produce that data

and collaborate with me and will use it to find the underlying genetics of vocal learning or flights or something interesting, right? We did a bunch of bird genomes back in 2014 that made a lot of splash on revising the family tree of birds. We were able to find convergent genetic differences or genes that change in their regulation in the brains of humans and songbirds for speech and singing. And when we went to go study the function of those genes in vocal learning of brain circuits, my students and postdocs were finding all these errors that we had to fix. resequence those genes over again across multiple species, spending not just months, sometimes years, and many thousands of dollars to do some of that work over again because of the poor quality genomes.

And when I was asked to lead the vertebrate genomes project because of our success with the birdwork, I kind of reluctantly accepted with the agreement with my colleagues in this global project that we're going to make an admission to produce the highest quality genomes. genomic data possible before we embark on sequencing all these species. They agreed, and that's how I got involved in genomics. And so was that the lesson of the avian phylogenomics project, was get it right? Yeah, we learned the lessons then, you know, in those first few years that it can't just be about quantity. Otherwise, the science is going to suffer. And so that delayed us by a number of years. So I said, if we're going to put all this effort into trying to figure out how to produce high-quality genomes of humans, of primates, of turtles, of birds, of fish, and they each have different kind of requirements, let's just do them all.

How did you decide with the vertebrate project? How did you decide which animals to do first? Why did you choose a platypus? Yeah, so platypus, they represent. They're not the placental mammals. They actually lay eggs, right? So they're at the branches at the base of the mammalian family tree, and there are only a few species left in that lineage.

And so having a platypus would help us understand the origin of mammals, right? It would help us understand the genetic differences between egg-laying mammals and in utero mammals, placental mammals. And so I'm curious, I mean, I think of you as somebody who's, studies vocal learning, you study birds. So what is this project going to do for you in your own research? Yeah, so my own research on vocal learning and language, so the ability to imitate sounds, like what we're doing now, producing imitated sounds that we've learned throughout adulthood and childhood, that's pretty rare. And we have it, sawn birds, parrots, hummingbirds,

amongst birds have it, dolphins, seals, and bats, amongst mammals, cetaceans. Those are whales and dolphins, actually, and elephants. So it's a pretty rare trait. But all of us that have this ability converged on a similar solution in the brain anatomy that we so far have been able to examine. And we've been looking to find if there's a similar genetic solution that's controlling that brain anatomy that allows us to produce. spoken language. And so in order to answer that question, in order to understand how it evolved,

in order to understand is it working similarly or differently in all these different species, we need the genomes of all those different species. And that's how it impacts me personally. Are you going to figure out what brain circuits are needed to produce vocal learning? Yes, that's my goal. Right. I believe we will get a much better, or handle at figuring out the underlying genes and what we call the gene network of how those genes interact with each other from having these 260 species. At the next level, which represents all families, that's going to be over 1,200 species. We've done a study to show that just on behavior alone, that some species of sawnbirds are more advanced than other species at their

ability to imitate sounds, including human speech sounds. Like if Blue J is really great, a zebra finches, yeah, okay. And we found that there's a nice linear correlation between more advanced vocal learning abilities and problem solving skills. So in phase two, we hope to be able to interrogate the genomes of species that are more advanced or less advanced at particular behaviors and get at the underlying genetics of even more detailed vocal learning skills. I take it it's not an accident that the species you mentioned that can do vocal learning are species we think of as having pretty advanced brain capacities. Absolutely. So many people don't even realize this. If you ask people to say,

what are the smartest animals out there, right? Without realizing they'll name a dolphin, they'll say an elephant, they'll say a crow, which is a songbird or a parrot. So there's a high overlap in our natural perceptions of intelligent animals and vocal learners. And so I call this the vocal learning cognitive complex where the ability to imitate sounds and communicate with learned vocalizations

is associated with a set of complex behavior that seem to co-evolve together, one of them being problem-solving, and another being unsuspecting, dancing, synchronizing body movements to sound in a very rhythmic way that other species can't seem to do as well as vocal learners. You know, when you talk about the similarities in function,

it sounds like we may find that we humans have more in common with some birds than we do with, you know, marmosets. That's right. I think it also means for all these species that we're getting the genetic data for, we're going to have to create a trait database for as well. We can say what the commonalities are and how those commonalities evolved either convergently or inherited from a common ancestor. If we really understand the details of the genetics behind speech production or any of these things,

Does that suggest that there are going to be ways to use, say, genetic engineering to make those circuits or transfer those circuits? Yes, actually. That idea is what we're pursuing in my group here to try to genetically engineer or enhance vocal communication circuits, actually in mice. And, you know, we just submit a pre-print on this and we'll see how it gets reviewed. But it's one of my favorite experiments because it takes discoveries that we learn through comparative genetics, comparative neuroscience for a complex trait, and try to recapitulate the evolution of that ability. You know, I think it'll take us a lot of years to really understand how these brain circuits work even more. But, you know, the little steps, you can take a little step and, you know, try to,

engineer these brain circuits. Now, if you're able to do that, let's say, in a mouse, or repair a brain circuit in the Sombard, why not be able to enhance vocal communication circuits in humans or repair them, you know, if there's a disruption in certain connectivity due to stroke or a certain genetic disorder? So that's where genetic engineering would come and you would rebuild circuits or perhaps put in new circuits that weren't there before. That's right. That's right. That's right. I know there are ethical concerns surrounding that, but the day will come. You think we're ever going to arrive at the answer of what makes us human? Yeah, I think, well, we're going to, my prediction, and it's not even a prediction because we're

already finding it out, we're finding out that we have to be careful about making assumptions about what makes us humans or, you know, using the word unique to liberally. When we talk about ourselves. Yes, we can look out there in the rest of the world and find that, you know, we've been the only species that have built these giant tall buildings and airplanes and so forth, but there are other species that are out there building households of natural made products, Bowerbirds, right, that they build houses that last 30 years that they use for made attraction, for, you know, shelter and so forth. And so we have to also kind of reclassify

as to what we think is advanced, complex, intelligent behavior. And I think we're going to learn a lot more than what makes us unique. We're going to learn a lot more about what makes us the same. Eric, thank you so much for taking the time. It's been an absolute pleasure talking to you. And thank you for all the wonderful questions. My late 2024, the vertebrate genomes project

had completed about 80% of its first 260 species. Eric says that's an update to start answering questions about what makes a bird a bird and what makes a fish a fish. He says it will take many more genomes to understand what makes a human, uniquely human. This episode was produced by Jessica Young. It was edited by our showrunner, Rebecca Ramirez, Tyler Jones checked the facts,

Kwayze Lee was the audio engineer. Beth Donovan is our senior director and Colin Campbell is our senior vice president of podcasting strategy. I'm John Hamilton. Thanks for listening to Shortwave from NPR.