Anole genome published!

by Greg Mayer

As some WEIT readers know, I am a specialist on lizards of the genus Anolis, and the genome sequence of the green anole, Anolis carolinensis, is in press in Nature in a paper by Jennifer Alfoldi, Federica Di Palma, and a cast of thousands (well, dozens). An advance copy has been posted online, along with a brief news item. The publication of the anole genome is a landmark event in comparative genomics, because it is the first reptile to be completely sequenced, as well as a landmark in anole studies

Anolis carolinensis: "You want to do what to my genome?"

Anole ecomorphs, showing characteristic size, station, and morphology. Each of these has evolved two or more times independently in the Greater Antilles. From Losos, 2009, based on E.E. Williams.

Anoles are a group of nearly 400 species found the southeastern U.S., throughout the West Indies, Mexico, Central and South America. Besides being species rich, they are diverse in ecology, behavior, morphology and physiology. Although the modal anole is an arboreal insectivore, some are terrestrial, some are aquatic, some eat fruit and small vertebrates, some live in deserts, and some live in rainforests. They also achieve high local species richness– up to a dozen or more species living in a small area– and very high abundance: James “Skip” Lazell, an eminent anolologist, likes to say that the anoles aren’t really common unless you can catch ten without moving your feet. Perhaps the most striking evolutionary phenomenon in anoles is community- wide convergence: on the islands of the Greater Antilles, whole suites of sympatric lizards have evolved independently, but each suite contains species of characteristic morphology and behavior associated with particular stations in the habitat (each characteristic type being called an ecomorph).

Anole Annals, your source for the latest information on Anolis lizards, is providing a lot of coverage of the event, with a guide to many of the genome-related posts by Jon Losos here, the  announcement of the advance posting by Rich Glor here (see also here), several posts on early genome results here, here, here, here, and here, and my own contribution, on the history of the study of anoles, here.

One of the first results of most interest to me has been the development of primers that allow sequencing of many genes for comparative phylogenetic studies. The tree below from Alfoldi et al., based on these new sequences, confirms a number of things we already knew, but also resolves a number of difficulties in anole phylogeny and biogeography.

Relationships of anoles, from Alfoldi, et al. 2011.The green anole itself, Anolis carolinensis, is the most widespread, and perhaps only native, species of anole in the United States. It is a member of an originally Cuban species group that has dispersed widely to surrounding islands as well as the main. Rich Glor has a review of carolinensis‘s origins at Anole Annals.  The story of how carolinensis was chosen to be the first reptile sequenced, mentioned in my post, is detailed by Jon Losos.

Dispersal of the Anolis carolinensis group, from Glor, Losos & Larson, 2005.

______________________________________________________________

Alfoldi, Jessica, Federica Di Palma, Manfred Grabherr, Christina Williams, Lesheng Kong, Evan Mauceli, Pamela Russell, Craig B. Lowe, Richard Glor, Jacob D. Jaffe, David A. Ray, Stephane Boissinot, Andrew M. Shedlock, Christopher Botka, Todd A. Castoe, John K. Colbourne, Matthew K. Fujita, Ricardo Godinez Moreno, Boudewijn F. ten Hallers, David Haussler, Andreas Heger David Heiman, Daniel E. Janes, Jeremy Johnson, Pieter J. de Jong, Maxim Y. Koriabine, Peter Novick, Marcia Lara, Chris L. Organ, Sally E. Peach, Steven Poe, David D. Pollock, Kevin de Queiroz, Thomas Sanger, Steve Searle, Jeremy D. Smith, Zachary Smith, Ross Swofford, Jason Turner-Maier, Juli Wade, Sarah Young, Amonida Zadissa, Scott V. Edwards, Travis C. Glenn, Christopher J. Schneider, Jonathan B. Losos, Eric S. Lander, Matthew Breen, Chris P. Ponting & Kerstin Lindblad-Toh.2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature in press. (advance post)

Glor, R.E., J.B. Losos, and A. Larson. 2005. Out of Cuba: overwater dispersal and speciation among lizards in the Anolis carolinensis subgroup.Molecular Ecology 14:2419-2432. (pdf)

Losos, J.B. 2009. Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles, University of California Press, Berkeley. (publisher)

32 Comments

  1. Posted September 1, 2011 at 10:58 am | Permalink

    I’m surprised nobody’s sequenced any reptile genomes until now. What other gaping holes might there be?

    We don’t have any Anoles ’round these here parts, but we’ve got comparable numbers of blue-bellied fence lizards. I’d offer to send Baihu into the yard to catch a specimen for you, but I’m afraid he’d nom it all rather than surrender it….

    Cheers,

    b&

    • whyevolutionistrue
      Posted September 1, 2011 at 11:25 am | Permalink

      Among tetrapods, the gaping holes are the tuatara, a turtle, a crocodilian, and a salamander.

      GCM

      • Posted September 1, 2011 at 12:59 pm | Permalink

        Those’re some big holes. But some quick Googling suggests it’s still in the $30K range to sequence a genome, so I suppose it’s not as surprising as I though at first.

        We need to get that cost down at least an order of magnitude, preferably two. At $300 / ea, you can easily imagine the bigger zoos sequencing one of every species on display.

        b&

        • Posted September 1, 2011 at 5:28 pm | Permalink

          > $30K range

          Well, it beats $2 billion.

          • Posted September 1, 2011 at 6:10 pm | Permalink

            Wikipedia, which of course is always suspect, claims:

            Knome[79] provides full genome (98% genome) sequencing services for US$39,500 for whole genome sequencing and interpretation for consumers. It’s US$29,500 for whole genome sequencing and analysis for researchers depending on their requirements.

            Cheers,

            b&

            • whyevolutionistrue
              Posted September 1, 2011 at 6:28 pm | Permalink

              That’s got to be a human-only price, not for a previously unsequenced species.

              GCM

              • Posted September 1, 2011 at 6:30 pm | Permalink

                Ah.

                …do I even want to know how much a new species sequencing costs, then…?

                b&

              • Anna Haynes
                Posted September 1, 2011 at 7:06 pm | Permalink

                p.s. hi Greg!

              • whyevolutionistrue
                Posted September 2, 2011 at 9:42 am | Permalink

                Anna– I thought that might be you–hi!

                GCM

              • Anna Haynes
                Posted September 3, 2011 at 3:55 pm | Permalink

                Hey, email me please – ncvoices.us at gmail
                (don’t forget the .us)

  2. SeanK
    Posted September 1, 2011 at 12:24 pm | Permalink

    Anoles were my first pet as a child (we don’t have many lizards in Canada). I was fascinated with one anole that had a taste for fruit juice.

    I had a couple baby iguanas at the time and I would keep them in the same terrarium as the anoles until they got too big and presented a danger for the anoles. While the iguanas were there, any time I placed their food in the terrarium, this one anole would always jump down and lick up the droplets of juice that collected on the side of the dish. Out of the five or six anoles I had, this was the only one to display this behavior. I’m not sure if it’s common or not, but I’ve always wondered.

    • whyevolutionistrue
      Posted September 1, 2011 at 1:25 pm | Permalink

      Anoles generally drink by licking droplets, rather than from standing water (e.g. a bowl), and many also eat fruit, so fruity droplets would appeal to many anoles.

      GCM

  3. Posted September 1, 2011 at 1:26 pm | Permalink

    Have no fear. A crocodilian genome is on the way. In fact, we’re doing three of them. Preliminary drafts for two are being played with now and we hope to have final drafts ready by early next year. If anyone is interested in joining our group (the International Crocodilian Genomes Working Group) and helping analyze the data, contact me.

    • whyevolutionistrue
      Posted September 1, 2011 at 1:31 pm | Permalink

      The American alligator was one of the top contenders for the first reptile genome (see Jon Losos on how the green anole was picked, and the anole genome white paper), so I expected and am glad to hear that a crocodilian is next up.

      GCM

      • Posted September 1, 2011 at 6:34 pm | Permalink

        Yes, I was in on that meeting. I was rooting for the gator because of my background but was happy to be involved in the Anolis project. I was a signatory on the white paper, in fact.

        I hadn’t read Jon’s summary. A good perspective.

  4. Dr. I. Needtob Athe
    Posted September 1, 2011 at 1:26 pm | Permalink

    There are hundreds of green anoles in the bushes outside of my home in South Florida. I guess I’ll never look at them quite the same again.

    • ChasCPeterson
      Posted September 1, 2011 at 3:15 pm | Permalink

      In many parts of FLorida, the native green anoles are being driven out by Anolis sagrei, the brown anole, a much more recent invader from Cuba. Last time I was in Tampa that’s all that could be seen. And lots of em.

      • Diane G.
        Posted September 2, 2011 at 12:51 am | Permalink

        Was that a “natural” invasion, or have they been brought in, say, for the pet trade, and then irresponsibly released?

        (Having kept both, it surprises me that the browns drive out the greens; the browns seemed much more…phlegmatic, the greens much more aggressive to me…)

        • Dominic
          Posted September 2, 2011 at 1:16 am | Permalink

          I was going to ask the same thing!

          • Dominic
            Posted September 2, 2011 at 1:26 am | Permalink

            I am guessing from the present spread along the gulf coast as far as N.Carolina and the name carolinensis, named by the German botanist Friedrich Siegmund Voigt in 1832, that it was a natural ‘invasion’ – Greg? The key question would be is it still spreading, and if so at what rate? Presumably there is an isotherm barrier as it were, beyond which it cannot pass. Do they remain active all year in their northernmost areas? Sorry, too many questions…

            • Dominic
              Posted September 2, 2011 at 3:39 am | Permalink

              Sorry, now I see – the answers are in the lastt link!

              • whyevolutionistrue
                Posted September 2, 2011 at 9:56 am | Permalink

                Anolis carolinensis, the green anole, is native to the SE USA (see map above). The brown anole, Anolis sagrei, like carolinensis is a member of a Cuban-centered species group that has naturally dispersed widely (Bahamas, Caymans, Swan, Yucatan), but also been spread widely by human introduction. It was at one time thought that sagrei was native in the far southern Florida Keys, but even if it were native there, its spread over much of the SE USA is clearly human-aided.

                Although many early reports of sagrei‘s spread reported it as pushing out the native green anole, this seems not to be the case. Rather, the green anole, which is a member of the trunk-crown ecomorph (up in the trees) in Cuba, has returned to its ancestral station higher in the vegetation, while the brown anole, a member of the trunk-ground ecomorph (lower on the trees) has taken up the ecological station it has in Cuba. Because this station puts it in sparser vegetation and at eye-level and below, it is much more visible, while the green anole has not disappeared, but moved higher in the vegetation, where it is more rarely seen.

                The pre-brown anole situation involved an ecological release by the green anole, allowing it to extend its habitat range in the absence of the competing brown anole. With the brown anole now introduced, the two species have re-established the ancestral ecological relations that they had in Cuba, with the green anole retreating vertically in the vegetation to its Cuban station. The same thing has occurred in the Bahamas, except that both are naturally dispersed there: the ecomorphs of the Bahamas were not evolved there; rather, the Cuban ecomorphs dispersed to the Bahamas, to recreate the Cuban ecological situation.

                GCM

              • Posted September 2, 2011 at 10:10 am | Permalink

                I can’t help but wonder: why, then, would there not have been brown anoles in the Southeast before? Had they not made it that far yet, or did something wipe them out, or…?

                b&

              • ChasCPeterson
                Posted September 2, 2011 at 11:31 am | Permalink

                That’s very interesting about sagrei and carolinensis (re-)partitioning the vertical habitat. Is anybody looking for morphological correlates? Character displacement and all that? It shouldn;t be difficult to compare a recent collection of carolinensis to museum specimens from back before the relatively recent sagrei invasion. And/or with current sagrei-free populations further north.

              • whyevolutionistrue
                Posted September 2, 2011 at 12:11 pm | Permalink

                People realize these studies need to be done, and some good ones have been (see, e.g. Yoel Stuart’s work here), but more is needed. See Jon Losos’s exhortation at Anole Annals here.

                GCM

              • Diane G.
                Posted September 3, 2011 at 10:14 pm | Permalink

                @ GMC post, 9:56 am

                Thank you very much for the detailed answer to my question about the spread of the browns and the interactions of the two species. Very interesting about the niche (do we still say niche?) expansion and then retraction of A. carolinensis. The opportunity to observe this process sounds like a scientist’s delight!

  5. Diane G.
    Posted September 2, 2011 at 12:53 am | Permalink

    To provide probably one of the dumber comments, I can’t tell you how glad I was to read “Among anolologists, anole is almost invariably pronounced “uh-nole” or “an-ole”, but the etymologically correct pronunciation is probably “a-no-lee”. ”

    Phew. I can stop trying train myself not to say uh-nole. I’m in good company!

    • Posted September 2, 2011 at 1:01 am | Permalink

      Is there an avocado-eating species? The guacanole?

      /@

      • Dominic
        Posted September 2, 2011 at 1:17 am | Permalink

        🙂

      • Diane G.
        Posted September 3, 2011 at 10:06 pm | Permalink

        Good one. 😀

  6. IW
    Posted September 2, 2011 at 5:19 am | Permalink

    Who cares about anole genome? Now if it were a new genome…

  7. Veritas
    Posted September 2, 2011 at 7:21 am | Permalink

    So, what’s the verdict? 400 independent lizard-fairy creation events, or are they all the same “kind”?

    Seriously though, I love looking at that phylogenetic tree and trying to tease out the historical migrations. I just wish I knew which region the basal anole came from.


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