The Ambitious Quest To Genetically Map All Known Vertebrates

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 hostJon Hamilton https://www.npr.org/people/2100615/jon-hamilton, one of our favorite science correspondents, talks to Erich Jarvis https://www.rockefeller.edu/our-scientists/heads-of-laboratories/1159-erich-d-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 [email protected] mailto:[email protected] — 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+ atplus.npr.org/shortwave http://plus.npr.org/shortwave. See pcm.adswizz.com https://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 https://www.npr.org/about-npr/179878450/privacy-policy

• 0:00Speaker 00

  This message comes from Avalara Aviator. Aviator is the agent hub for tax and compliance. Purpose-built AI agents work around the clock and across business systems to help execute the work. Visit avalara.com/aviator.

• 0:15Speaker 00

  You're listening to Short Wave from NPR.

• 0:21Speaker 01

  Hey, hey, Short Wavers. 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 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.

• 1:02Speaker 02

  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 Ark, with the pun intended, like, you know, an ark, to basically save the genetic code of all species on the planet.

• 1:28Speaker 01

  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 chairs 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.

• 2:06Speaker 02

  What makes a bird a bird? What makes a mammal a mammal? What makes a fish a fish? With all these species sequenced, we will be able to dig in and find those things that make each lineage different from another.

• 2:19Speaker 01

  And Eric says there's another reason.

• 2:21Speaker 02

  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.

• 2:50Speaker 01

  Today on the show, the effort to collect an ark full of animal genomes and what it could mean for our future. Plus, why a platypus qualified for early boarding.

• 3:01Speaker 01

  You're listening to Short Wave, the science podcast from NPR.

• 3:09Speaker 03

  Stay tuned for the following announcements and messages from our sponsors.

• 3:14Speaker 00

  This message comes from ProLon. Want to look and feel your best this fall? ProLon's five-day fasting-mimicking diet is a clinically-developed nutrition program with the goal of promoting fat loss while protecting lean body mass. Developed at USC's Longevity Institute, it aims to assist the body in entering a fasting-like state that helps reset metabolism, target visceral fat, and support healthy metabolic markers. Get 15% off plus a bonus gift when you subscribe at prolonlife.com/NPR. This message comes from Whole Foods Market. Host Thanksgiving with industry-leading quality standards from Whole Foods Market. There are no antibiotics in their meat department, ever, so carve up turkey and spiral-cut ham with peace of mind.

• 3:55Speaker 00

  Shop organic sides like stuffing mix and cranberry sauce from 365 Brands. And all their delectable pies are made with no high-fructose corn syrup. Gourmet Thanksgiving flavors with the quality you want, only at Whole Foods Market. Support for NPR and the following message come from Bowlin Branch. Change your sleep with Bowlin Branch's airy blankets, cloud-like duvets, and breathable sheets. Feel the difference with 15% off your first order at bowlinbranch.com with code NPR. Exclusions apply. See site for details.

• 4:28Speaker 01

  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?

• 4:48Speaker 02

  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 flight 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 changed in their regulation in the brains of humans and songbirds for speech and singing. And when we went to go

• 5:31Speaker 02

  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 and resequenced 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 bird work, I kind of reluctantly accepted with the agreement with my colleagues in this global project that we're going to make it a mission to produce the highest quality genomic data possible

• 6:13Speaker 02

  before we embark on sequencing all these species. They agreed, and that's how I got involved in genomics.

• 6:21Speaker 01

  And so was that the lesson of the Avian Philogenomics Project? Was get it right?

• 6:27Speaker 02

  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.

• 6:59Speaker 01

  How did you decide with the Veridubit Project? How did you decide which animals to do first? Why did you choose a platypus?

• 7:07Speaker 02

  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? Would help us understand the genetic differences between egg-laying mammals and in utero mammals, placental mammals.

• 7:37Speaker 01

  And so I'm curious. I mean, I think of you as somebody who studies vocal learning. You study birds. So what is this project going to do for you in your own research?

• 7:48Speaker 02

  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, songbirds, parrots, hummingbirds amongst birds have it, dolphins, seals, and bats. And 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

• 8:33Speaker 02

  that's controlling that brain anatomy that allows us to produce spoken language.

• 8:39Speaker 02

  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.

• 8:55Speaker 01

  Are you going to figure out what brain circuits are needed to produce vocal learning?

• 9:02Speaker 02

  Yes, that's my goal, right. I believe we will get a much better 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 songbirds are more advanced than other species at their ability to imitate sounds, including human speech sounds. Like if Blue Jay is really great, and Zebra Finch is, you know, ah, okay. And we found that

• 9:47Speaker 02

  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.

• 10:09Speaker 01

  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?

• 10:18Speaker 02

  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.

• 10:44Speaker 02

  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 behaviors 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.

• 11:16Speaker 01

  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.

• 11:26Speaker 02

  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.

• 11:46Speaker 01

  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?

• 12:04Speaker 02

  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 submitted 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 learned 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

• 12:46Speaker 02

  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 sunburn, 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?

• 13:13Speaker 01

  So, so that's where genetic engineering would come in, you would rebuild circuits?

• 13:18Speaker 02

  That's right.

• 13:19Speaker 01

  Or perhaps, put in new circuits that weren't there before?

• 13:21Speaker 02

  That's right, that's right. I know there are ethical concerns surrounding that, but the day will come.

• 13:31Speaker 01

  You think we're ever going to arrive at the, the answer of what makes us human?

• 13:37Speaker 02

  Yeah, I think, well, we're gonna, my prediction, and it's not even a prediction, because we're already finding it out. We're, 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" too, too 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 built houses that last 30 years, that they use for mate attraction, for, you know, shelter and so forth.

• 14:21Speaker 02

  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.

• 14:43Speaker 01

  Eric, thank you so much for taking the time. It's been an absolute pleasure talking to you.

• 14:47Speaker 02

  And thank you for all the wonderful questions.

• 14:53Speaker 01

  By late 2024, the vertebrate genomes project had completed about 80% of its first 260 species. Eric says that's enough data 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. Kwasi Lee was the audio engineer. Beth Donovan is our senior director and Colin Campbell is our senior vice president of podcasting strategy. I'm Jon Hamilton. Thanks for listening to Short Wave from NPR.

• 16:02Speaker 03

  Stay tuned for the following announcements and messages from our sponsors.