How the Green Anole Was Selected To Be The First Reptile Genome Sequenced

As the publication of the anole genome approaches, one might ask: “Just how was Anolis carolinensis selected to be the first non-avian reptile to have its genome sequenced?” Turns out that it’s a long and convoluted story, and this is one man’s first-hand account.

To set the stage, we have to go back to the early days of genome sequencing, all the way back to 2005. This was a time when to sequence a genome was a really big, time-consuming, extremely expensive affair (the human genome had cost ca. $2 billion; by 2005, the price had dropped to ca. $20 million per genome). Such a big deal, in fact, that there was an NIH committee that decided which species would be sequenced, and assigned them to one of the three genome sequencing centers (Baylor University, Washington University in Saint Louis and the Broad Institute in Cambridge) that had been created as part of the human genome sequencing initiative. The first few species selected were chosen exclusively with regard to their potential relevance to human health. They were the laboratory model systems, the workhorses of biomedical research, such as the mouse, chimp, Xenopus, chicken, Drosophila and C. elegans.

By 2005, a couple of mammals had been sequenced and representatives of all classes of vertebrates except one: reptiles. The NIH committee was not particularly evolutionary in its thinking, but by that time, it recognized that there was a hole in their coverage and that a reptile should be sequenced to fill that phylogenetic lacuna. But, which reptile? There were no reptilian biomedical models. Moreover, the committee did not decide on its own which species to sequence. Rather, it worked by evaluating proposals—usually in the form of “white papers”—submitted from the broader scientific community. In particular, it looked to the “scientific community” (whatever that is) to come to consensus on which species should be a priority for sequencing.

At this point, a scientist at the Washington University Genome Sequencing Center got the idea of convening a group of experts—“the herpetological community”— to decide which reptile to propose to NIH. This idea was driven primarily by a love of reptiles, but also for strategic reasons: the genome sequencing pie was shrinking and the genome centers were fighting for the ever smaller slices. By hosting this group and being involved in the resulting white paper, the Wash. U. workers hoped to get the work assigned their way.

And so it was that in April, 2005, an eclectic group of herpetologists, genomicists, and bioinformaticians gathered in Saint Louis to debate, discuss, and ultimately pick a reptile to propose for sequencing. Now, not to be critical, but I suspect that most herpetologists would guffaw at the suggestion that this group was representative of the “herpetological community.”

A WU colleague and I, chosen because we were local, went to the meeting prepared to push for an anole. This was, we felt, a reasonable choice—more research of all sorts (behavior, morphology, ecology, parasitology, etc.) has been done on anoles than any other group of reptiles, and in the 50’s and 60’s, A. carolinensis was “the lizard” in broad scale comparative studies of physiology. Nonetheless, we felt that we were distinct underdogs. A number of others at the meeting were involved in genomics projects (e.g., development of BAC libraries, etc.) on the American alligator. Given that no substantial genomic work had been done on anoles, or any other reptile for that matter, this seemed to give the alligator a leg up, as good a reason as any to choose that species to move forward, especially since 3-4 people of the dozen or so at the meeting were involved in the effort.

Our approach was simple. When our turn for a 10-minute presentation came around, we pointed out that reptile phylogeny was split into two main groups, the lepidosaurs, represented today by lizards, snakes, and the tuatara; and archosaurs, represented by crocodilians and birds (not counting turtles, whose phylogenetic placement is uncertain and whose bizarre morphology made them, we suggested, a less desirable choice for the first reptile to sequence). We then pointed out that members of the archosaur line had already been sequenced (the chicken, with another bird in the works), whereas the diapsid line had been woefully ignored. Rectify that omission, we argued; sequence the anole!

To our amazement, Team Alligator capitulated, agreeing that our rationale was correct. We had won! It was clear that the committee was going to vote to move forward with an anole genome proposal. At that point, we were at the stage of a meeting that you all probably have experienced at some time. We’re sitting around the table, the conversation winding down, everyone knowing where we’re headed, and it’s just a matter of time before someone takes the initiative and declares, “Then, it’s the anole!” and everyone agrees and we all go home. I felt that I shouldn’t be the one to say this, given my vested interest in the outcome. Rather, wait for one of the non-partisans (some committee members had come to the meeting with no preordained position) to call the meeting to a close. So I kept my mouth shut.

And then someone said, “NIH likes to choose species with clear biomedical relevance. Does Anolis have any?” An electric bolt to the brain, warning flags coursed through my body like goosebumps on a cold day. Trouble! I had no good reply (I’ve since learned that anole research does have some direct biomedical relevance, the subject of a post for another day, but the short answer is the anole split brain and the fact that female anoles alternate ovaries in producing eggs, just like one other group of vertebrates—guess which one; read the case for biomedical relevance we made in the White Paper).

So, in the blink of an eye, everything changed. Suddenly, the group, snapped out of its lethargy, was focused on human welfare, one speaker after the next exhorting to think strategically about what would appeal to our NIH overlords. And then someone said, “What about snake venom? There’s enormous biomedical potential in that, and genomic approaches are being taken to understand the pharmacological properties of venom.” True enough. “We should propose a venomous snake.” A murmur of agreement, followed by the inevitable, “but which one?”

And then someone blurted out, “the king cobra!” Of course! Arguably the world’s most deadly snake. Yes, yes, the king cobra, that’s the one, almost everyone seemed to agree. And then a small voice (not mine; I was biting my lip and not saying anything, hoping this would pass) said, “I’m not sure the king cobra would make a good lab animal.” General assent–at a length of 18 feet and highly toxic, perhaps it was not the animal to try to develop as a model system. Brief pause. “Diamondback rattlesnake!” Only six feet long. Much better! Excitement again, then reality—still not a good lab species.

Then someone said something I didn’t know. The common garter snake is ever-so-slightly venomous. Now there’s an idea. Like Anolis, Thamnophis has been the subject of a considerable body of scientific research of many different types, and just as A. carolinensis was “the lizard,” T. sirtalis was “the snake.” A garter snake would be a very reasonable choice as the first reptile to sequence.

The group now had two good choices, anole and garter snake—how to decide? Then someone had a great idea. NIH really wanted these decisions to be made by “the community.” Why not let the broader herpetological community weigh in? Create a website and invite everyone to not only vote, but provide comments. This would not only ensure that we chose the species the community really wanted, but would give us lots of ammunition to bolster our case and convince NIH that this truly was the herpetological community’s wishes.

And so that’s what we did. A website was created explaining what this was all about, how we had gotten to this point, why we had chosen the two candidate species, and so on, asking for people to vote and, if so desired, to provide comments. We were all charged to go out and spread the word, and announcements were sent to e-bulletin boards and other communication outlets.

Now, there was one wrinkle in all of this. The committee, as I have mentioned, was a somewhat haphazardly assembled group of people with a hodgepodge of expertise and interests, some herpetological, some genomic, some technological. As it happened, there were lizard people who worked on anoles, alligator people, and a turtle guy. But, for whatever reason, no one who worked primarily on snakes. Did this matter? You be the judge.

I can’t speak for the other committee members, but I took the charge to heart and contacted as many people as possible. We had all agreed that it was important that we get a lot of votes (votes, by the way, were not anonymous, so multiple voting was not possible). So I contacted a large number of people whom I thought might be interested. I told them how important it was that we get a large response, and implored them to vote. And I played it straight. I didn’t ask them to vote for the anole. Rather, I explained our process of winnowing it down to the two species and why both would make good choices. I was fair and balanced.

But, you know, in retrospect I realize that there was one catch. Just like in True Blood, where the werewolves hang out with other werewolves, and the werepanthers with other werepanthers, I hang with lizard folks. My email address book is chockful of saurologists, with barely an entry for a snake person. And somehow I forgot to look up the addresses of serpentine types. And perhaps even those few snakers in my address book were somehow overlooked—you know, it was a busy time, and a lot was on my mind! So I sent out a lot of emails to the lizard crowd. And wouldn’t you know it, a lot of them did vote, and most of them (not all—traitors!) voted for the anole. And it was truly a landslide, with Anolis capturing 2/3 of the 104 cast votes.

And so the decision was made, and the green anole was put forward in the white paper duly submitted to the NIH committee. And, I think it was the right decision—truly, there has been more research done on all aspects of anole biology than on any other type of reptile and, lacking any compelling biomedical rationale for any species, certainly anoles were as good—and I’d argue better—than any other reptile.

Are there any important take-home messages from this? In the day of the 10,000 Genomes Project, with the price of genome sequencing ever-plummeting and the $1000 genome in sight, it’s hard to remember the time, oh-so-long ago, when this wasn’t true, when genomes were precious and cost tens of millions of dollars, where the decision of which species to choose really was consequential because someone down the street couldn’t take care of sequencing the species not selected. And I think there’s an interesting story about how important—or at least expensive—scientific decisions are made. Naively, I would have thought that an eight-figure decision would have been made as the result of a very careful and controlled process in which all factors were carefully weighed and the outcome the result of deliberate and informed discussion by an appropriate group. I wonder how often the reality is much more like what happened here: well-meaning people, gathered through happenstance and contingency, doing their best. I’m told that the decision-making to choose which mammals were to be sequenced was even more capricious.

One last question: why the green anole, A. carolinensis, and not some other anole species? Indeed, one could make an equally strong case for the brown anole, A. sagrei, itself the subject of a vast body of research, and probably more of a workhorse in recent years. Ultimately, it came down to two considerations: The vast store of physiological work—at least suggestive of biomedical import—done on A. carolinensis decades earlier and patriotism (the American anole!).

 

Alföldi, J., Di Palma, F., Grabherr, M., Williams, C., Kong, L., Mauceli, E., Russell, P., Lowe, C., Glor, R., Jaffe, J., Ray, D., Boissinot, S., Shedlock, A., Botka, C., Castoe, T., Colbourne, J., Fujita, M., Moreno, R., ten Hallers, B., Haussler, D., Heger, A., Heiman, D., Janes, D., Johnson, J., de Jong, P., Koriabine, M., Lara, M., Novick, P., Organ, C., Peach, S., Poe, S., Pollock, D., de Queiroz, K., Sanger, T., Searle, S., Smith, J., Smith, Z., Swofford, R., Turner-Maier, J., Wade, J., Young, S., Zadissa, A., Edwards, S., Glenn, T., Schneider, C., Losos, J., Lander, E., Breen, M., Ponting, C., & Lindblad-Toh, K. (2011). The genome of the green anole lizard and a comparative analysis with birds and mammals Nature, 477 (7366), 587-591 DOI: 10.1038/nature10390

About Jonathan Losos

Professor and Curator of Herpetology at the Museum of Comparative Zoology at Harvard University. I've spent my entire professional career studying anoles and have discovered that the more I learn about anoles, the more I realize I don't know.

6 thoughts on “How the Green Anole Was Selected To Be The First Reptile Genome Sequenced

  1. reptile phylogeny was split into two main groups, the diapsids, represented today by lizards, snakes, and the tuatara; and archosaurs, represented by crocodilians and birds

    Not to put too fine a point on it, but archosaurs are, of course, also diapsids. The split–within diapsids–is between archosaurs and lepidosaurs.

    Trachemys and Thamnophis next!!

  2. The turtle genome is on its way. I’m pretty sure the sequencing is finished at this point. It was all done using next generation sequencing.

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